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Serialized Form

Package gov.nih.mipav.model.algorithms

Class gov.nih.mipav.model.algorithms.RandomNumberGen extends Random implements Serializable

serialVersionUID: -4394735859119506749L

Package gov.nih.mipav.model.algorithms.itk

Class gov.nih.mipav.model.algorithms.itk.FilterRecordItk extends Object implements Serializable

serialVersionUID: 4244L

Serialized Fields

m_Name

String m_Name
Name directly from the Itk class, InsightToolkit.itkBinaryDilateImageFilterF2F2 becomes BinaryDilateImage

m_Active

boolean m_Active
Is this filter shown in the menu. Default yes, user can turn them off.

m_IOType

ArrayList<E> m_IOType
List of i/o types for the filter. F2F2 is a typical one.

Class gov.nih.mipav.model.algorithms.itk.ItkFilterSelectorDialog extends JDialog implements Serializable

serialVersionUID: 6211274967141606057L

Serialized Fields

m_CheckBoxPanel

JPanel m_CheckBoxPanel
panel for checkboxes, turning on/off the filters.

m_FilterRecordItk

List<E> m_FilterRecordItk
List of filters, which we modify the active state of.

Package gov.nih.mipav.model.dicomcomm

Class gov.nih.mipav.model.dicomcomm.DICOM_Exception extends Exception implements Serializable

serialVersionUID: 4502658752483534014L

Class gov.nih.mipav.model.dicomcomm.DICOM_ObjectList extends Vector implements Serializable

serialVersionUID: 5505943813889560828L

Package gov.nih.mipav.model.file

Class gov.nih.mipav.model.file.FileDicomItem extends ModelSerialCloneable implements Serializable

serialVersionUID: 788152239624831704L

Serialized Fields

dataSet

TreeMap<K,V> dataSet
TreeMap containing key-tag pairs, string is like a FileDicomKey

Class gov.nih.mipav.model.file.FileDicomKey extends ModelSerialCloneable implements Serializable

serialVersionUID: -8327760986088567748L

Serialized Fields

key

String key
The dicom tag identifier in the format 'group,element'. 'x' is allowed in the group number for wildcards in the dicom dictionary. E.g., '0002,0010' or '50xx,00E1'.

Class gov.nih.mipav.model.file.FileDicomSQ extends ModelSerialCloneable implements Serializable

serialVersionUID: -6705966363824982534L

Serialized Fields

sequence

Vector<E> sequence
Sequences are composed of items (DICOM items) and store in a vector object.

Class gov.nih.mipav.model.file.FileDicomTag extends ModelSerialCloneable implements Serializable

serialVersionUID: -5648244595999602634L

Serialized Fields

element

int element
Integer element word (in hexadecimal).

group

int group
Integer group word (in hexadecimal).

length

int length
Length of the tag.

tagInfo

FileDicomTagInfo tagInfo
Pointer to more information about this tag, read in and contained within the dicom dictionary.

value

Object value
Actual value of the tag.

valueRepresentation

String valueRepresentation
Value representation for this tag, if the tags in this dicom file have explicit VRs. If the dicom tags have implicit VRs, then the DicomDictionary VR is used.

Class gov.nih.mipav.model.file.FileDicomTagInfo extends ModelSerialCloneable implements Serializable

serialVersionUID: 3009696612758502873L

Serialized Fields

key

FileDicomKey key
The DICOM tag 'group,element' key indicating what tag this information pertains to.

keyword

String keyword
The tag keyword (no spaces).

name

String name
The real world DICOM tag name.

valueMultiplicity

int valueMultiplicity
Allowed value multiplicity (vm) for this tag.

valueRepresentation

String valueRepresentation
DICOM value representation (vr) for this tag.

version

String version
Version of the tag. Usually '2' or '3', although some tags get strings like 'GEM' or 'TSH' when the tag is from a private manufacturer.

Class gov.nih.mipav.model.file.FileDicomTagTable extends Object implements Serializable

serialVersionUID: -7828203960779215940L

Serialized Fields

childTagTables

FileDicomTagTable[] childTagTables
A list of tag tables which point to this as their reference tag table.

isReferenceTagTable

boolean isReferenceTagTable
Whether this tag table is a reference table (meaning it contains all of the tags for a given fileInfo and does not need to refer anywhere else when retrieving values).

parentFileInfo

FileInfoDicom parentFileInfo
The dicom file info that this tag table belongs to. Used to update file info fields based on tag table changes.

referenceTagTable

FileDicomTagTable referenceTagTable
The reference table to check when a tag is not found in this table. If this table is a reference table, then the value should be this and no checking of the referenceTagTable should take place.

tagTable

Hashtable<K,V> tagTable
Tags unique to this slice, or all of the tags for this slice if this is a reference tag table.

Class gov.nih.mipav.model.file.FileImageXML.Thumbnail extends JComponent implements Serializable

serialVersionUID: 6645327578121170860L

Serialized Fields

brightness

int brightness
DOCUMENT ME!

contrast

float contrast
DOCUMENT ME!

data

int[] data
DOCUMENT ME!

img

Image img
DOCUMENT ME!

imgWidth

int imgWidth
DOCUMENT ME!

imgHeight

int imgHeight
DOCUMENT ME!

memImage

MemoryImageSource memImage
DOCUMENT ME!

Class gov.nih.mipav.model.file.FileInfoAfni extends FileInfoBase implements Serializable

serialVersionUID: 5706392093050163138L

Serialized Fields

acquisitionDuration

float acquisitionDuration
DOCUMENT ME!

AFNIOrigExtents

int[] AFNIOrigExtents
DOCUMENT ME!

AFNIOrigResolutions

float[] AFNIOrigResolutions
DOCUMENT ME!

AFNITypeString

int AFNITypeString
DOCUMENT ME!

AFNIViewType

int AFNIViewType
DOCUMENT ME!

alpha

WildMagic.LibFoundation.Mathematics.Vector3f alpha
DOCUMENT ME!

alphaArray

WildMagic.LibFoundation.Mathematics.Vector3f[] alphaArray
arrays of 12 values used for Talairach conversions.

anotherPt

WildMagic.LibFoundation.Mathematics.Vector3f anotherPt
DOCUMENT ME!

anteriorPt

WildMagic.LibFoundation.Mathematics.Vector3f anteriorPt
markers used for +ACPC to +tlrc transformation.

beta

WildMagic.LibFoundation.Mathematics.Vector3f beta
DOCUMENT ME!

betaArray

WildMagic.LibFoundation.Mathematics.Vector3f[] betaArray
DOCUMENT ME!

botX

int[] botX
DOCUMENT ME!

botY

int[] botY
DOCUMENT ME!

botZ

int[] botZ
DOCUMENT ME!

brickStatAux

float[] brickStatAux
DOCUMENT ME!

datasetName

String datasetName
DOCUMENT ME!

firstPt

WildMagic.LibFoundation.Mathematics.Vector3f firstPt
DOCUMENT ME!

funcType

int funcType
DOCUMENT ME!

gamma

WildMagic.LibFoundation.Mathematics.Vector3f gamma
DOCUMENT ME!

gammaArray

WildMagic.LibFoundation.Mathematics.Vector3f[] gammaArray
DOCUMENT ME!

gapArray

int[] gapArray
If planeGap is not -1, then gapArray contains the values at which zero filling gaps are present.

highXmm

float highXmm
DOCUMENT ME!

highYmm

float highYmm
DOCUMENT ME!

highZmm

float highZmm
DOCUMENT ME!

idcodeDate

String idcodeDate
DOCUMENT ME!

idcodeString

String idcodeString
DOCUMENT ME!

inferiorEdge

WildMagic.LibFoundation.Mathematics.Vector3f inferiorEdge
DOCUMENT ME!

inferiorPt

WildMagic.LibFoundation.Mathematics.Vector3f inferiorPt
DOCUMENT ME!

isDicom

boolean isDicom
DOCUMENT ME!

label1

String label1
DOCUMENT ME!

label2

String label2
DOCUMENT ME!

leftPt

WildMagic.LibFoundation.Mathematics.Vector3f leftPt
DOCUMENT ME!

lowXmm

float lowXmm
DOCUMENT ME!

lowYmm

float lowYmm
DOCUMENT ME!

lowZmm

float lowZmm
DOCUMENT ME!

marksFlag

int marksFlag
DOCUMENT ME!

marksFlags

int marksFlags
DOCUMENT ME!

noteDate001

String noteDate001
DOCUMENT ME!

noteDate002

String noteDate002
DOCUMENT ME!

noteDate003

String noteDate003
DOCUMENT ME!

noteDate004

String noteDate004
DOCUMENT ME!

noteDate005

String noteDate005
DOCUMENT ME!

noteNumber001

String noteNumber001
DOCUMENT ME!

noteNumber002

String noteNumber002
DOCUMENT ME!

noteNumber003

String noteNumber003
DOCUMENT ME!

noteNumber004

String noteNumber004
DOCUMENT ME!

noteNumber005

String noteNumber005
DOCUMENT ME!

origDicom

boolean origDicom
DOCUMENT ME!

OriginalPosteriorMargin

WildMagic.LibFoundation.Mathematics.Vector3f OriginalPosteriorMargin
DOCUMENT ME!

OriginalSuperiorEdge

WildMagic.LibFoundation.Mathematics.Vector3f OriginalSuperiorEdge
DOCUMENT ME!

pcie

WildMagic.LibFoundation.Mathematics.Vector3f pcie
The posterior commisure inferior edge. pcie is the coordinated transformed inferiorEdge

planeGap

int planeGap
Used to show a zero filling gap in functional AFNI images -1 if no gap is present, 0 = x gap, 1 = y gap, 2 = z gap Interpolation is not performed across zero filling gaps.

posteriorMargin

WildMagic.LibFoundation.Mathematics.Vector3f posteriorMargin
DOCUMENT ME!

posteriorPt

WildMagic.LibFoundation.Mathematics.Vector3f posteriorPt
DOCUMENT ME!

rightPt

WildMagic.LibFoundation.Mathematics.Vector3f rightPt
DOCUMENT ME!

rr

WildMagic.LibFoundation.Mathematics.Vector3f rr
rr is the dicom ordered original image Talairach center location.

rrArray

WildMagic.LibFoundation.Mathematics.Vector3f[] rrArray
DOCUMENT ME!

slicesWithTimeOffsets

int slicesWithTimeOffsets
DOCUMENT ME!

statAux

float[] statAux
DOCUMENT ME!

superiorEdge

WildMagic.LibFoundation.Mathematics.Vector3f superiorEdge
markers used for +orig to +ACPC transformation.

superiorPt

WildMagic.LibFoundation.Mathematics.Vector3f superiorPt
DOCUMENT ME!

TalairachCenter

WildMagic.LibFoundation.Mathematics.Vector3f TalairachCenter
DOCUMENT ME!

tAxisOffsets

float[] tAxisOffsets
If TAXIS_NUMS[1] > 0, then this array gives the time offsets of the

timeOrigin

float timeOrigin
DOCUMENT ME!

timeStep

float timeStep
DOCUMENT ME!

topX

int[] topX
DOCUMENT ME!

topY

int[] topY
DOCUMENT ME!

topZ

int[] topZ
DOCUMENT ME!

translation

WildMagic.LibFoundation.Mathematics.Vector3f translation
DOCUMENT ME!

zAxisOffset

float zAxisOffset
DOCUMENT ME!

zAxisStep

float zAxisStep
DOCUMENT ME!

Class gov.nih.mipav.model.file.FileInfoAnalyze extends FileInfoBase implements Serializable

serialVersionUID: 7319414471012796383L

Serialized Fields

aux_file

String aux_file
DOCUMENT ME!

bitpix

short bitpix
Bits per pixel. Valid values include: 1, 8, 16, 32, 64, 24(rgb).

cal_max

float cal_max
Range of calibration values.

cal_min

float cal_min
Values of 0.0 for both fields imply that no calibration min and max values are used !

cal_units

String cal_units
Specifies the name of the calibration unit.

compressed

float compressed
Indicates if compression is used. Default is -1 indicating no compression

data_type

String data_type
Unknown use 10 chars.

datatype

short datatype
Stores the image data type DT_NONE = 0; DT_UNKNOWN = 0; DT_BINARY = 1; DT_UNSIGNED_CHAR = 2; DT_SIGNED_SHORT = 4; DT_UNSIGNED_SHORT = 4; DT_SIGNED_INT = 8; DT_FLOAT = 16; DT_COMPLEX = 32; DT_DOUBLE = 64; DT_RGB = 128; DT_ALL = 255;

db_name

String db_name
Name of file with a length of 18 chars.

descrip

String descrip
String with a max character length of 80 used to describe image.

dim_un0

short dim_un0
Unused.

exp_date

String exp_date
String with a max character length of 10 used to indicate the experiment date.

exp_time

String exp_time
String with a max character length of 10 used to indicate the experiment time.

extents

int extents
Should be 16384.

field_skip

int field_skip
Unknown length.

funused1

float funused1
MIPAV uses this variable to define the X-axis origin.

funused2

float funused2
MIPAV uses this variable to define the Y-axis origin.

funused3

float funused3
MIPAV uses this variable to define the Z-axis origin.

generated

String generated
Unknown use. Length of 10.

glmax

int glmax
Maximum pixel values for the entire dataset.

glmin

int glmin
Minimum pixel values for the entire database.

hist_un0

String hist_un0
Unknown use. Length of 3.

hkey_un0

char hkey_un0
Unknown use. Length of 1.

omax

int omax
Unknown use.

omin

int omin
Unknown use.

orient

byte orient
DOCUMENT ME!

originator

String originator
Unknown use. Length of 10.

patient_id

String patient_id
Patient's ID. Length of 10.

regular

char regular
I think it means data has uniform spacing (resolutions).

scannum

String scannum
Scan ID Length of 10.

session_error

short session_error
Unknown use.

sizeof_hdr

int sizeof_hdr
Always of length 348.

smax

int smax
Unknown use.

smin

int smin
Unknown use.

start_field

int start_field
Unknown use.

unused1

short unused1
MIPAV uses this variable to define the X-axis orientation.

unused2

short unused2
MIPAV uses this variable to define the Y-axis orientation.

unused3

short unused3
MIPAV uses this variable to define the Z-axis orientation.

verified

float verified
Unknown use.

views

int views
Unknown use.

vols_added

int vols_added
Unknown use.

vox_units

String vox_units
specifies the spatial units of measure for a voxel.

Class gov.nih.mipav.model.file.FileInfoAvi extends FileInfoBase implements Serializable

serialVersionUID: -5524135420342875298L

Serialized Fields

numFrames

int numFrames
DOCUMENT ME!

totalFrames

int totalFrames
DOCUMENT ME!

Class gov.nih.mipav.model.file.FileInfoBase extends ModelSerialCloneable implements Serializable

serialVersionUID: 6605143084958470864L

Serialized Fields

axisOrientation

int[] axisOrientation
axis orientation used to support image ordering and display for medical images. We support the right hand rule where the origin is the upper left hand of the image with the positive axis.

x - left to right y - top to botton z - into the screen

fileName

String fileName
The file name which includes the path information.

fileSuffix

String fileSuffix
File suffix (ex. "jpg")

imageOrientation

int imageOrientation
Indicates the image orientation (i.e. Axial, Coronal, ...)

modality

int modality
Indicates the modality (medical image type) of the dataset.

origin

float[] origin
The origin to support image locations (ie. DICOM, MINC ...) it is relative to the image origin. the positive axis are right hand rule.

x - left to right y - top to botton z - into the screen

compressionType

int compressionType
Used to indicate if the raw data was also compression (0 = no, 1 = zip).

dataType

int dataType
The data type of the data (i.e. byte, short, float ...

dimResolutions

float[] dimResolutions
Pixel or voxel resolutions for each dimension - default = 1.0. The z-dim resolution should be the spacing between the centers of adjacent slices; sometimes this will match the slice thickness, but not always.

endianess

boolean endianess
The Endianess of the data. Intel, DEC Alpha ***** LSB first byte LITTLE_ENDIAN (false) Motorola (MAC), SPARC (SUN), SGI IRIX MSB first byte BIG_ENDIAN (true)

extents

int[] extents
Image extents as decribed by the image file format.

fileFormat

int fileFormat
File format as defined in the Filebase.

is2_5D

boolean is2_5D
If the image is 2.5D.

max

double max
Image maximum intensity for single channel image.

maxB

double maxB
Image maximum intensity for the blue channel of an RGB image.

maxG

double maxG
Image maximum intensity for the green channel of an RGB image.

maxR

double maxR
Image maximum intensity for the red channel of an RGB image.

min

double min
Image minimum intensity for single channel image.

minB

double minB
Image minimum intensity for the blue channel of an RGB image.

minG

double minG
Image minimum intensity for the green channel of an RGB image.

minR

double minR
Image minimum intensity for the red channel of an RGB image.

multiFile

boolean multiFile
Flag that indicates whether or not the image is in multiple files (tiff).

offset

int offset
Number of bytes to the start the image data - ie. the header length

photometric

short photometric
Image minimum intensity for single channel image.

pixelPadValue

Short pixelPadValue
Some file formats have a pad value for pixels outside the acquisition domain.

rescaleIntercept

double rescaleIntercept
DICOM images have a rescale y-intercept value that we have also kept in the base.

rescaleSlope

double rescaleSlope
DICOM images have a rescale slope value that we have also kept in the base.

sliceThickness

float sliceThickness
The thickness of individual slices in the image volume. Stored in dicom tag 0018,0050 and various other places in other file formats.

transformID

int transformID
Transform ID associated with the matrix.

unitsOfMeasure

int[] unitsOfMeasure
Describes the units of measure for the dataset.

Class gov.nih.mipav.model.file.FileInfoBFLOAT extends FileInfoBase implements Serializable

Class gov.nih.mipav.model.file.FileInfoBioRad extends FileInfoBase implements Serializable

serialVersionUID: 4850818161207332016L

Serialized Fields

imageDescription

String imageDescription
DOCUMENT ME!

Class gov.nih.mipav.model.file.FileInfoBRUKER extends FileInfoBase implements Serializable

serialVersionUID: 292865443840539139L

Serialized Fields

haveZResol

boolean haveZResol
DOCUMENT ME!

recoSize

int recoSize
DOCUMENT ME!

sliceSeparationMode

String sliceSeparationMode
DOCUMENT ME!

sliceThickness

float sliceThickness
DOCUMENT ME!

Class gov.nih.mipav.model.file.FileInfoCheshire extends FileInfoBase implements Serializable

serialVersionUID: 4776092584175024015L

Class gov.nih.mipav.model.file.FileInfoCOR extends FileInfoBase implements Serializable

serialVersionUID: 8537756143101265528L

Serialized Fields

fov

float fov
DOCUMENT ME!

te

float te
DOCUMENT ME!

ti

float ti
DOCUMENT ME!

tr

float tr
DOCUMENT ME!

Class gov.nih.mipav.model.file.FileInfoDicom extends FileInfoBase implements Serializable

serialVersionUID: -3072660161266896186L

Serialized Fields

bitsAllocated

short bitsAllocated
Bits allocated per pixel.

bytesPerPixel

short bytesPerPixel
Number of bytes per pixel.

containsDICM

boolean containsDICM
True if the DICOM file has the ID DICM at beginning at file pointer 128.

displayType

int displayType
Data type.

instanceNumber

int instanceNumber
DICOM instance number.

isCurrentTagSQ

boolean isCurrentTagSQ
Whether the tag currently being processed and read in is a sequence tag.

multiFrame

boolean multiFrame
True indicates image has multiple image planes in a single file.

olderVersion

boolean olderVersion
True is image format < DICOM 3.0.

orientation

String orientation
Orientation - SAGITTAL, CORONAL, AXIAL.

photometricInterp

String photometricInterp
Type of image - color, monochrome etc.

pixelPaddingValue

Short pixelPaddingValue
Pixel Padding Value (0028, 0120). Value of pixels added to non-rectangular image to pad to rectangular format.

pixelRepresentation

short pixelRepresentation
DICOM tag (0028,103) -1 = undefined 0 = unsigned 1 = signed

planarConfig

short planarConfig
0 = RGB, RGB, 1 = R R R, G G G, B B B.

sliceLocation

float sliceLocation
DICOM slice location.

vr_type

boolean vr_type
VR type can be IMPLICIT or EXPLICIT.

xLocation

float xLocation
DICOM x coordianate of the slice location.

yLocation

float yLocation
DICOM y coordianate of the slice location.

zLocation

float zLocation
DICOM z coordianate of the slice location.

tagTable

FileDicomTagTable tagTable
Stores all the information about the DICOM tags.

Class gov.nih.mipav.model.file.FileInfoDM3 extends FileInfoBase implements Serializable

serialVersionUID: 6502186871127970871L

Class gov.nih.mipav.model.file.FileInfoFits extends FileInfoBase implements Serializable

serialVersionUID: 8285638648507573285L

Serialized Fields

origin

String origin

dateAcquired

String dateAcquired

timeAcquired

String timeAcquired

dateProcessed

String dateProcessed

timeProcessed

String timeProcessed

dateWritten

String dateWritten

timeWritten

String timeWritten

jobName

String jobName

object

String object

observer

String observer

instrument

String instrument

focalRatio

float focalRatio

CTYPE1

String CTYPE1

CTYPE2

String CTYPE2

CTYPE3

String CTYPE3

CTYPE4

String CTYPE4

CTYPE5

String CTYPE5

CUNIT1

String CUNIT1

CUNIT2

String CUNIT2

CUNIT3

String CUNIT3

CUNIT4

String CUNIT4

CUNIT5

String CUNIT5

BUNIT

String BUNIT

author

String author

Class gov.nih.mipav.model.file.FileInfoGESigna4X extends FileInfoBase implements Serializable

serialVersionUID: -6230885244735581982L

Serialized Fields

aCenter

float aCenter
DOCUMENT ME!

actualReceiveFrequency

int actualReceiveFrequency
DOCUMENT ME!

actualTransmitFrequency

int actualTransmitFrequency
DOCUMENT ME!

aNormal

float aNormal
DOCUMENT ME!

apCenter

float apCenter
DOCUMENT ME!

arrythmiaRejectionRatio

short arrythmiaRejectionRatio
DOCUMENT ME!

autoCenterFrequency

String autoCenterFrequency
DOCUMENT ME!

autoManualPrescan

String autoManualPrescan
DOCUMENT ME!

averageSAR

float averageSAR
DOCUMENT ME!

averagesNumber

short averagesNumber
DOCUMENT ME!

bitsPerPixel

short bitsPerPixel
DOCUMENT ME!

cardiacHeartRate

short cardiacHeartRate
DOCUMENT ME!

cardiacPhaseNumber

short cardiacPhaseNumber
DOCUMENT ME!

cardiacRepTime

String cardiacRepTime
DOCUMENT ME!

changedValues

String changedValues
DOCUMENT ME!

coilName

String coilName
DOCUMENT ME!

coilType

String coilType
DOCUMENT ME!

collapseImage

String collapseImage
DOCUMENT ME!

concatenatedSATSelection

String concatenatedSATSelection
DOCUMENT ME!

contiguousSlices

String contiguousSlices
DOCUMENT ME!

contrastAgent

String contrastAgent
DOCUMENT ME!

contrastAmount

float contrastAmount
DOCUMENT ME!

contrastDescription

String contrastDescription
DOCUMENT ME!

contrastUsed

String contrastUsed
DOCUMENT ME!

cPhase

short cPhase
DOCUMENT ME!

defaultLevel

short defaultLevel
DOCUMENT ME!

defaultWindow

short defaultWindow
DOCUMENT ME!

diognostician

String diognostician
DOCUMENT ME!

echoNumber

short echoNumber
DOCUMENT ME!

echoTrainLength

int echoTrainLength
DOCUMENT ME!

endX

float endX
DOCUMENT ME!

endY

float endY
DOCUMENT ME!

endZ

float endZ
DOCUMENT ME!

excitationsNumber

float excitationsNumber
DOCUMENT ME!

extremityCoil

String extremityCoil
DOCUMENT ME!

fieldOfView

float fieldOfView
DOCUMENT ME!

fieldStrength

short fieldStrength
DOCUMENT ME!

fileBlocks

short fileBlocks
DOCUMENT ME!

fileFormat

String fileFormat
DOCUMENT ME!

flipAngle

short flipAngle
DOCUMENT ME!

fractionalEffectiveEcho

String fractionalEffectiveEcho
DOCUMENT ME!

gatingType

String gatingType
DOCUMENT ME!

gatingType2

String gatingType2
DOCUMENT ME!

graphicallyPrescribed

String graphicallyPrescribed
DOCUMENT ME!

histogramPresent

String histogramPresent
DOCUMENT ME!

history

String history
DOCUMENT ME!

horizontalLandmark

float horizontalLandmark
DOCUMENT ME!

hospitalName

String hospitalName
DOCUMENT ME!

imageCreationDate

String imageCreationDate
DOCUMENT ME!

imageCreationTime

String imageCreationTime
DOCUMENT ME!

imageFieldStrength

int imageFieldStrength
DOCUMENT ME!

imageHeaderBlocks

short imageHeaderBlocks
DOCUMENT ME!

imageHeaderCreatorProcess

String imageHeaderCreatorProcess
DOCUMENT ME!

imageHeaderCreatorTask

short imageHeaderCreatorTask
DOCUMENT ME!

imageHeaderDisclaimer

short imageHeaderDisclaimer
DOCUMENT ME!

imageHeaderID

String imageHeaderID
DOCUMENT ME!

imageHeaderRevisionNumber

String imageHeaderRevisionNumber
DOCUMENT ME!

imageLocation

float imageLocation
DOCUMENT ME!

imageMatrix

short imageMatrix
DOCUMENT ME!

imageMode

String imageMode
DOCUMENT ME!

imageNumber

String imageNumber
DOCUMENT ME!

imageOffset

short imageOffset
DOCUMENT ME!

imageRawDataSystemID

String imageRawDataSystemID
DOCUMENT ME!

imagesAllocated

short imagesAllocated
DOCUMENT ME!

imageShape

String imageShape
DOCUMENT ME!

imageSpacing

float imageSpacing
DOCUMENT ME!

imagesPerCardiacCycle

short imagesPerCardiacCycle
DOCUMENT ME!

imageSystemGenerationID

String imageSystemGenerationID
DOCUMENT ME!

imageType

String imageType
DOCUMENT ME!

imgBLHC_A

float imgBLHC_A
DOCUMENT ME!

imgBLHC_R

float imgBLHC_R
DOCUMENT ME!

imgBLHC_S

float imgBLHC_S
DOCUMENT ME!

imgTLHC_A

float imgTLHC_A
DOCUMENT ME!

imgTLHC_R

float imgTLHC_R
DOCUMENT ME!

imgTLHC_S

float imgTLHC_S
DOCUMENT ME!

imgTRHC_A

float imgTRHC_A
DOCUMENT ME!

imgTRHC_R

float imgTRHC_R
DOCUMENT ME!

imgTRHC_S

float imgTRHC_S
DOCUMENT ME!

interImageDelay

float interImageDelay
DOCUMENT ME!

landmarkCounter

int landmarkCounter
DOCUMENT ME!

longitudinalAnatomicalReference

String longitudinalAnatomicalReference
DOCUMENT ME!

minimumDelay

short minimumDelay
DOCUMENT ME!

MRIProcessName

String MRIProcessName
DOCUMENT ME!

numberOfEchos

short numberOfEchos
DOCUMENT ME!

obliquePlane

String obliquePlane
DOCUMENT ME!

operator

String operator
DOCUMENT ME!

orientation

String orientation
DOCUMENT ME!

originalSeriesNumber

String originalSeriesNumber
DOCUMENT ME!

patientAge

String patientAge
DOCUMENT ME!

patientID

String patientID
DOCUMENT ME!

patientName

String patientName
DOCUMENT ME!

patientSex

String patientSex
DOCUMENT ME!

patientStatus

String patientStatus
DOCUMENT ME!

patientWeight

int patientWeight
DOCUMENT ME!

pauseInterval

short pauseInterval
DOCUMENT ME!

pauseTime

float pauseTime
DOCUMENT ME!

PCVelocityEncoding

short PCVelocityEncoding
DOCUMENT ME!

peakSAR

float peakSAR
DOCUMENT ME!

pfSwapped

String pfSwapped
DOCUMENT ME!

phaseContrastFlowAxis

String phaseContrastFlowAxis
DOCUMENT ME!

pImage2

String pImage2
DOCUMENT ME!

pixelSize

float pixelSize
DOCUMENT ME!

planeName

String planeName
DOCUMENT ME!

planeType

String planeType
DOCUMENT ME!

position

String position
DOCUMENT ME!

prescanReceiveAttenuation1

short prescanReceiveAttenuation1
DOCUMENT ME!

prescanReceiveAttenuation2

short prescanReceiveAttenuation2
DOCUMENT ME!

prescribedImageNumbers

String prescribedImageNumbers
DOCUMENT ME!

prescribedSeriesNumbers

String prescribedSeriesNumbers
DOCUMENT ME!

projectionAngle

float projectionAngle
DOCUMENT ME!

psdDay

short psdDay
DOCUMENT ME!

psdFileName

String psdFileName
DOCUMENT ME!

psdHour

short psdHour
DOCUMENT ME!

psdMinute

short psdMinute
DOCUMENT ME!

psdMonth

short psdMonth
DOCUMENT ME!

psdName

String psdName
DOCUMENT ME!

psdSeconds

short psdSeconds
DOCUMENT ME!

psdYear

short psdYear
DOCUMENT ME!

pSeries2

String pSeries2
DOCUMENT ME!

pulseSequence

String pulseSequence
DOCUMENT ME!

pulseSequenceMode

String pulseSequenceMode
DOCUMENT ME!

pulseSequenceSubtype

String pulseSequenceSubtype
DOCUMENT ME!

R1

short R1
DOCUMENT ME!

R2

short R2
DOCUMENT ME!

rawDataStudyNumber

String rawDataStudyNumber
DOCUMENT ME!

rawDataSystemID

String rawDataSystemID
DOCUMENT ME!

rCenter

float rCenter
DOCUMENT ME!

receiveAttenuatorSetting

short receiveAttenuatorSetting
DOCUMENT ME!

recommendedReceiveAttenuation

int recommendedReceiveAttenuation
DOCUMENT ME!

recommendedReceiveFrequency

int recommendedReceiveFrequency
DOCUMENT ME!

recommendedTransmitAttenuation

int recommendedTransmitAttenuation
DOCUMENT ME!

recommendedTransmitFrequency

int recommendedTransmitFrequency
DOCUMENT ME!

referringPhysician

String referringPhysician
DOCUMENT ME!

requestedNumber

String requestedNumber
DOCUMENT ME!

researchMode

String researchMode
DOCUMENT ME!

rlCenter

float rlCenter
DOCUMENT ME!

rNormal

float rNormal
DOCUMENT ME!

round

String round
DOCUMENT ME!

SARMonitored

String SARMonitored
DOCUMENT ME!

satSelections

String satSelections
DOCUMENT ME!

satXLoc1

short satXLoc1
DOCUMENT ME!

satXLoc2

short satXLoc2
DOCUMENT ME!

satXThick

short satXThick
DOCUMENT ME!

satYLoc1

short satYLoc1
DOCUMENT ME!

satYLoc2

short satYLoc2
DOCUMENT ME!

satYThick

short satYThick
DOCUMENT ME!

satZLoc1

short satZLoc1
DOCUMENT ME!

satZLoc2

short satZLoc2
DOCUMENT ME!

satZThick

short satZThick
DOCUMENT ME!

scanAcquisitionNumber

short scanAcquisitionNumber
DOCUMENT ME!

scanARRs

int scanARRs
DOCUMENT ME!

scanMatrixX

short scanMatrixX
DOCUMENT ME!

scanMatrixY

short scanMatrixY
DOCUMENT ME!

scanProtocolName

String scanProtocolName
DOCUMENT ME!

sCenter

float sCenter
DOCUMENT ME!

scIma

String scIma
DOCUMENT ME!

scSer

String scSer
DOCUMENT ME!

series

String series
DOCUMENT ME!

seriesDate

String seriesDate
DOCUMENT ME!

seriesDescription

String seriesDescription
DOCUMENT ME!

seriesHeaderBlocks

short seriesHeaderBlocks
DOCUMENT ME!

seriesHeaderID

String seriesHeaderID
DOCUMENT ME!

seriesHeaderRevisionNumber

String seriesHeaderRevisionNumber
DOCUMENT ME!

seriesNumber

String seriesNumber
DOCUMENT ME!

seriesProcessName

String seriesProcessName
DOCUMENT ME!

seriesPSDName

String seriesPSDName
DOCUMENT ME!

seriesRawDataSystemID

String seriesRawDataSystemID
DOCUMENT ME!

seriesSystemGenerationID

String seriesSystemGenerationID
DOCUMENT ME!

seriesTaskID

short seriesTaskID
DOCUMENT ME!

seriesTime

String seriesTime
DOCUMENT ME!

seriesType

String seriesType
DOCUMENT ME!

siCenter

float siCenter
DOCUMENT ME!

sliceMultiplier

short sliceMultiplier
DOCUMENT ME!

sliceQuantity

short sliceQuantity
DOCUMENT ME!

sliceThicknessDisclaimer

String sliceThicknessDisclaimer
DOCUMENT ME!

sNormal

float sNormal
DOCUMENT ME!

startX

float startX
DOCUMENT ME!

startY

float startY
DOCUMENT ME!

startZ

float startZ
DOCUMENT ME!

studyDate

String studyDate
DOCUMENT ME!

studyDescription

String studyDescription
DOCUMENT ME!

studyHeaderBlocks

short studyHeaderBlocks
DOCUMENT ME!

studyHeaderID

String studyHeaderID
DOCUMENT ME!

studyHeaderRevisionNumber

String studyHeaderRevisionNumber
DOCUMENT ME!

studyNumber

String studyNumber
DOCUMENT ME!

studyTaskID

short studyTaskID
DOCUMENT ME!

studyTime

String studyTime
DOCUMENT ME!

suppressionTechnique

String suppressionTechnique
DOCUMENT ME!

surfaceCoilIntensityCorrection

String surfaceCoilIntensityCorrection
DOCUMENT ME!

surfaceCoilsCorrectionType

String surfaceCoilsCorrectionType
DOCUMENT ME!

surfaceCoilType

String surfaceCoilType
DOCUMENT ME!

swapPF

String swapPF
DOCUMENT ME!

systemConfigHospitalName

String systemConfigHospitalName
DOCUMENT ME!

systemGenerationID

String systemGenerationID
DOCUMENT ME!

systemID

String systemID
Use serialVersionUID for interoperability.

tableLocation

float tableLocation
DOCUMENT ME!

tablePosition

float tablePosition
DOCUMENT ME!

te

float te
DOCUMENT ME!

TE2

float TE2
DOCUMENT ME!

thickness

float thickness
DOCUMENT ME!

ti

float ti
DOCUMENT ME!

totalPostTriggerDelayTime

float totalPostTriggerDelayTime
DOCUMENT ME!

tr

float tr
DOCUMENT ME!

transmitAttenuatorSetting

short transmitAttenuatorSetting
DOCUMENT ME!

ts

float ts
DOCUMENT ME!

user0

float user0
DOCUMENT ME!

user1

float user1
DOCUMENT ME!

user2

float user2
DOCUMENT ME!

user3

float user3
DOCUMENT ME!

user4

float user4
DOCUMENT ME!

user5

float user5
DOCUMENT ME!

user6

float user6
DOCUMENT ME!

user7

float user7
DOCUMENT ME!

user8

float user8
DOCUMENT ME!

user9

float user9
DOCUMENT ME!

variableBandwidth

String variableBandwidth
DOCUMENT ME!

vascularImagingFlags

String vascularImagingFlags
DOCUMENT ME!

vasMode

String vasMode
DOCUMENT ME!

vencScalingFactor

float vencScalingFactor
DOCUMENT ME!

verticalAnatomicalReference

String verticalAnatomicalReference
DOCUMENT ME!

verticalLandmark

float verticalLandmark
DOCUMENT ME!

year

int year
DOCUMENT ME!

Class gov.nih.mipav.model.file.FileInfoGESigna5X extends FileInfoBase implements Serializable

serialVersionUID: -4456298776612648834L

Serialized Fields

actualDateTime

int actualDateTime
18.

addValue

int addValue
112 - value to add to pixels.

anatomicalRef

String anatomicalRef
84 - 3 bytes - Anatomical Reference.

autoXmtFreq

int autoXmtFreq
282 Auto Center Frequency (0.1 Hz).

autoXmtGain

short autoXmtGain
286 Auto Transmit Gain (0.1 dB).

calFldStr

int calFldStr
388 Calibrated Field Strength (x10 uGauss).

cellSpace

float cellSpace
54 Cell spacing.

cenFreq

short cenFreq
296 Center frequency method.

checkSum

int checkSum
54 - 16 bit end around carry sum of pixels **** (read as unsigned short).

coilName

String coilName
362 17 characters.

coilType

short coilType
360.

compress

short compress
120 image compression type for allocation.

compression

int compression
20 0 as is 1 retangular 2 packed 3 compressed 4 compressed and packed.

contig

short contig
222 Continuous slices flag.

contrastMode

short contrastMode
106.

cPhase

short cPhase
260 Total cardiac phase prescribed.

cPhaseNum

short cPhaseNum
646 Cardiac phase number.

dasType

short dasType
68 DAS type.

dateTime

int dateTime
14 allocation date time.

dbdt

float dbdt
838 peak rate of change in gradient field, tesla/sec.

dbdtPer

float dbdtPer
842 limit in units of percent of theoretical curve.

dcnDensity

short dcnDensity
74 Decon kernel density.

dcnLen

short dcnLen
72 Number of elements in Decon kernel.

dcnShiftCnt

short dcnShiftCnt
78 Decon kernel shift count.

dcnStepSize

short dcnStepSize
76 Decon kernel stepsize.

depth

int depth
16 - number of bits.

detect

short detect
44 detector type.

diagRad

String diagRad
245 - 33 bytes Diagnostician/Radiologist.

diskid

byte diskid
6 - (internal use) Disk ID.

echo1Alpha

float echo1Alpha
240.

echo1Beta

float echo1Beta
244.

echo1Level

short echo1Level
250.

echo1Window

short echo1Window
248.

echo2Alpha

float echo2Alpha
252.

echo2Beta

float echo2Beta
256.

echo2Level

short echo2Level
262.

echo2Window

short echo2Window
260.

echo3Alpha

float echo3Alpha
264.

echo3Beta

float echo3Beta
268.

echo3Level

short echo3Level
274.

echo3Window

short echo3Window
272.

echo4Alpha

float echo4Alpha
276.

echo4Beta

float echo4Beta
280.

echo4Level

short echo4Level
286.

echo4Window

short echo4Window
284.

echo5Alpha

float echo5Alpha
288.

echo5Beta

float echo5Beta
292.

echo5Level

short echo5Level
298.

echo5Window

short echo5Window
296.

echo6Alpha

float echo6Alpha
300.

echo6Beta

float echo6Beta
304.

echo6Level

short echo6Level
310.

echo6Window

short echo6Window
308.

echo7Alpha

float echo7Alpha
312.

echo7Beta

float echo7Beta
316.

echo7Level

short echo7Level
322.

echo7Window

short echo7Window
320.

echo8Alpha

float echo8Alpha
324.

echo8Beta

float echo8Beta
328.

echo8Level

short echo8Level
334.

echo8Window

short echo8Window
332.

echoNum

short echoNum
212 echo number.

echoTime

int echoTime
202 pulse echo time (usec).

effEchoSpace

short effEchoSpace
828 effective echo spacing for EPI.

endLoc

float endLoc
128 - Last scan location (L/S).

endRAS

String endRAS
126 - 1 byte - RAS letter for last scan location (L/S).

entry

int entry
80 - Patient Entry.

equipmentUID

String equipmentUID
400 - 32 bytes.

estdbdtPer

float estdbdtPer
846 PSD estimated limit in units of percent.

estdbdtts

float estdbdtts
850 PSD estimated limit in Tesla/sec.

ETL

short ETL
640 Echo train length.

exAllocKey

String exAllocKey
334 - 13 bytes Process that allocated this record.

examNum

int examNum
8 - Read as unsigned short.

examType

String examType
305 - 3 bytes i.e. "MR" or "CT"

exChecksum

int exChecksum
356 (internal use) Exam Record Checksum.

exComplete

int exComplete
360 (internal use) Exam complete flag.

exDateTime

int exDateTime
208 - Exam date/time stamp.

exDeltaCount

int exDeltaCount
348 (internal use) Number of updates to header.

exDesc

String exDesc
282 - 23 bytes Exam Description.

exDiskID

String exDiskID
6 - 1 byte (internal use) Disk ID for this exam.

exFormat

short exFormat
308 Exam format.

exLastMod

int exLastMod
328 Date/Time of Last Change.

exModelCnt

int exModelCnt
424 (internal use) Number of 3D Models.

exModelNum

int exModelNum
420 (internal use) Last Model Number Used.

exModelsData

int exModelsData
432.

exModelsLen

int exModelsLen
428.

exNumArch

int exNumArch
368 (internal use) Number of Series Archived.

exNumSeries

int exNumSeries
372 (internal use) Number of Series Existing.

exNumUnSer

int exNumUnSer
384 (internal use) Number of Unstored series.

exPadding

String exPadding
508 - 516 bytes.

exProspCnt

int exProspCnt
408 (internal use) number of Prosp/Scout Series.

exProspData

int exProspData
416.

exProspLen

int exProspLen
412 (internal use) Prosp/Scout Sers Keys in Exam.

exSeriesCt

int exSeriesCt
364 (innternl use) Last Series Number Used.

exSeriesData

int exSeriesData
380.

exSeriesLen

int exSeriesLen
376 (internal use) Series keys for this exam.

exStat

short exStat
436 Patient status.

exSysID

String exSysID
318 - 9 bytes Creator suite and host.

exToArchCnt

int exToArchCnt
396 (internal use) number of Unarchived Series.

exToArchiveData

int exToArchiveData
404.

exToArchiveLen

int exToArchiveLen
400 (internal use) Unarchived series Keys in Exam.

exUniq

short exUniq
4 (internal use) The Make_Unique Flag.

exUnSeriesData

int exUnSeriesData
392.

exUnSeriesLen

int exUnSeriesLen
388 (internal use) Unstored Sers Keys in Exam.

exVersCre

String exVersCre
352 - 2 bytes Genesis Version - Created.

exVersCur

String exVersCur
354 - 2 bytes Genesis Version - Now.

firstAxTime

long firstAxTime
310 Start time(secs) of first axial in exam.

flax

short flax
574 Phase contrast flow axis.

forImgRev

String forImgRev
190 foreign image revision.

FOVX

float FOVX
34.

FOVY

float FOVY
38.

fracEcho

short fracEcho
642 Fractional echo-effective TE flag.

freqDir

short freqDir
742 Frequency Direction.

gOffsetX

short gOffsetX
818 gradient offset in x-direction.

gOffsetY

short gOffsetY
820 gradient offset in y-direction.

gOffsetZ

short gOffsetZ
822 gradient offset in z-direction.

gpre

short gpre
400 Graphically prescribed.

heartRate

short heartRate
224 cardiac heart rate (beats per minute).

height

int height
12 - height of image.

hist

String hist
134 - 61 bytes Patient history.

hospName

String hospName
10 - 33 characters hospital name.

im_alloc_key

String im_alloc_key
506 13 characters Process that allocated this record.

im_archived

int im_archived
544 (internal use) Image Archive Flag.

im_checksum

int im_checksum
540 (internal use) AcqRecon record checksum.

im_complete

int im_complete
548 (Internal use) Image Complete Flag.

im_lastmod

int im_lastmod
520.

im_pds_a

int im_pds_a
528 PixelData size - as stored.

im_pds_c

int im_pds_c
532 PixelData size - compressed.

im_pds_u

int im_pds_u
536 PixelData size - Uncompressed.

im_verscre

String im_verscre
524 2 characters Genesis Version - Created.

im_verscur

String im_verscur
526 2 characters Genesis Version - Now.

image_type

short image_type
584 Magnitude, Phase, Imaginary, or Real.

image_uid

String image_uid
746 32 characters Image Unique ID.

imageDimX

float imageDimX
42.

imageDimY

float imageDimY
46.

imageNum

short imageNum
12.

imagesData

int imagesData
212.

imagesLen

int imagesLen
208 - (internal use) Image keys for this Series.

imgBRHC_A

float imgBRHC_A
182 Bottom Right Hand Corner Anterior.

imgBRHC_R

float imgBRHC_R
178 Bottom Right Hand Corner Right.

imgBRHC_S

float imgBRHC_S
186 Bottom Right Hand Corner Superior.

imgCtrA

float imgCtrA
134 Anterior(i.e. X positive to anterior)

imgCtrR

float imgCtrR
130 Right (i.e. X positive to right)

imgCtrS

float imgCtrS
138 Superior(i.e. X positive to superior)

imgHdrExamNum

int imgHdrExamNum
8 - Read as unsigned short.

imgHdrSeriesNum

short imgHdrSeriesNum
10.

imgHdrSuiteID

String imgHdrSuiteID
0 - 4 bytes - suite ID.

imgLevel

short imgLevel
654 Level value.

imgLoc

float imgLoc
126.

imgPCycle

short imgPCycle
246 Images per cardiac .1 cycle.

imgrx

short imgrx
110 - image from which prescribed.

imgTLHC_A

float imgTLHC_A
158 Top Left Hand Corner Anterior.

imgTLHC_R

float imgTLHC_R
154 Top Left Hand Corner Right.

imgTLHC_S

float imgTLHC_S
162 Top Left Hand Corner Superior.

imgTRHC_A

float imgTRHC_A
170 Top Right Hand Corner Anterior.

imgTRHC_R

float imgTRHC_R
166 Top Right Hand Corner Right.

imgTRHC_S

float imgTRHC_S
174 Top Right Hand Corner Superior.

imgWindow

short imgWindow
652 Window value.

iMode

short iMode
298 Imaging mode.

integrity

short integrity
736 GE Image Integrity.

intr_del

long intr_del
402 Interimage/interloc delay (uSec).

inverTime

int inverTime
198 pulse inversion time (usec).

iOptions

long iOptions
300 Imaging options.

IVCntrstAgent

String IVCntrstAgent
72 - 17 bytes.

landmarkUID

String landmarkUID
368 - 32 bytes.

lenCmprsnHdr

int lenCmprsnHdr
76 - length of.

lenDBHdr

int lenDBHdr
108 - length of.

lenExamHdr

int lenExamHdr
136 - length of.

lenGraphics

int lenGraphics
100 - length of.

lenHistoHdr

int lenHistoHdr
84 - length of.

lenImageHdr

int lenImageHdr
152 - length of.

lenSeriesHdr

int lenSeriesHdr
144 - length of.

lenSuiteHdr

int lenSuiteHdr
128 - length of.

lenTextPlane

int lenTextPlane
92 - length of.

lenUID

int lenUID
60 - length of UID.

lenUnpackHdr

int lenUnpackHdr
68 - length of.

lenUsrDefData

int lenUsrDefData
120 - length of.

lmHor

float lmHor
88 - Horizontal landmark.

loc_ras

String loc_ras
124 1 byte RAS letter of image location.

magicNumber

int magicNumber
0x494d4746 or "IMGF" or 1229801286.

magStrength

int magStrength
80 Magnet strength (in gauss).

magWgtFlag

short magWgtFlag
730 Magnitude Weighting Flag.

matrixSizeX

short matrixSizeX
30.

matrixSizeY

short matrixSizeY
32.

minDAT

int minDAT
256 minimum delay after trigger (usec).

mobileLoc

String mobileLoc
470 - 4 bytes.

monSar

short monSar
238 Monitor SAR Flag.

mr_flip

short mr_flip
254 Flip angle for grass scans (degrees).

mr_padding

String mr_padding
990 spare space.

nEchoes

short nEchoes
210 number of echoes.

negScanSpacing

float negScanSpacing
858 Negative scan spacing for overlap slices.

nEPI

short nEPI
826 number of EPI shots.

NEX

float NEX
218 Number of excitations.

norm_A

float norm_A
146 Normal A coordinate.

norm_R

float norm_R
142 Normal R coordinate.

norm_S

float norm_S
150 Normal S coordinate.

nPhase

int nPhase
738 Number of Phases.

numCells

long numCells
46 Number of cells in det.

numDcnK

short numDcnK
70 Number of Decon kernels.

numUnImg

int numUnImg
216 - (internal use) Number of Unstored Images.

obliquePlane

int obliquePlane
270.

offsetFreq

int offsetFreq
862 offset Frequency_Mag. Transfer

op

String op
278 - 4 bytes operator.

OralCntrstAgent

String OralCntrstAgent
89 - 17 bytes.

panSysID

String panSysID
59 - 9 bytes - Archiver Suite and Host.

patian

short patian
124 Patient Age notation.

patientAge

short patientAge
122.

patientID

String patientID
84 - 13 bytes.

patientName

String patientName
97 - 25 bytes.

patientSex

short patientSex
126.

patWeight

int patWeight
128 Patient Weight.

pauseInterval

short pauseInterval
264 Pause interval (slices).

pauseTime

float pauseTime
266.

pixelID

String pixelID
58 - 14 bytes.

pixelResX

float pixelResX
50.

pixelResY

float pixelResY
54.

planeType

short planeType
114.

position

int position
76 - Patient Poisition.

prepPulse

short prepPulse
644 Prepartory pulse option.

prescan_r1

short prescan_r1
288 PreScan R1-Analog.

prescan_r2

short prescan_r2
290 PreScan R2-DIgital.

preScanOpts

short preScanOpts
816 bitmap of prescan options.

proj_alg

short proj_alg
596 Projection Algorithm.

proj_name

String proj_name
598 13 characters Projection Algorithm Name.

projectAngle

float projectAngle
498 Projection Angle.

protocolFlag

short protocolFlag
332 Non-zero indicates protocol exam.

prSysID

String prSysID
50 - 9 bytes - Primary Receiver Suite and Host.

ps_flag

short ps_flag
580 Auto/Manual Prescan flag.

ps_status

short ps_status
582 Bitmap of changed values.

psd_dateTime

int psd_dateTime
342 PSD Creation Date and Time.

psd_iname

String psd_iname
346 13 characters.

pSeq

short pSeq
304 Pulse sequence.

ptrCmprsnHdr

int ptrCmprsnHdr
72 - pointer to.

ptrDBHdr

int ptrDBHdr
104 - pointer to.

ptrExamHdr

int ptrExamHdr
132 - pointer to.

ptrGraphics

int ptrGraphics
96 - pointer to.

ptrHistoHdr

int ptrHistoHdr
80 - pointer to.

ptrImage

int ptrImage
4 - byte displacement to pixel data.

ptrImageHdr

int ptrImageHdr
148 - pointer to.

ptrSeriesHdr

int ptrSeriesHdr
140 - pointer to.

ptrSuiteHdr

int ptrSuiteHdr
124 - pointer to.

ptrTextPlane

int ptrTextPlane
88 - pointer to.

ptrUID

int ptrUID
56 - pointer to unique image identifier (UID).

ptrUnpackHdr

int ptrUnpackHdr
64 - pointer to.

ptrUsrDefData

int ptrUsrDefData
116 - pointer to.

pulseRepTime

int pulseRepTime
194 pulse repetition time (usec).

pulseSeqMode

short pulseSeqMode
306.

pulseSeqName

String pulseSeqName
308 33 characters.

rawRunNum

int rawRunNum
384 RawData Run Number.

rbpm

short rbpm
832 respiratory rate, breaths per minute.

rcvGain1

short rcvGain1
250 Actual receive gain analog (.1db).

rcvGain2

short rcvGain2
252 Actual receive gain digital (.1db).

rcvType

short rcvType
836 type of receiver used.

refImg

String refImg
650 Reference image field.

refPhy

String refPhy
212 - 33 bytes Referring Physician.

repTime

float repTime
242 Cardiac repertition time.

reqnum

String reqnum
195 - 13 bytes Requisition Number.

rtPoint

short rtPoint
834 repiratory trigger point as percent of max.

sarAvg

float sarAvg
230 Average SAR.

sarAvgHead

float sarAvgHead
854 Avg head SAR.

sarPeak

float sarPeak
234 Peak SAR.

satbits

short satbits
552 Bitmap of SAT selections.

satxloc1

short satxloc1
556 R-side pulse rel to lndmrk.

satxloc2

short satxloc2
558 L-side pulse rel to lndmrk.

satxthick

short satxthick
568 Thickness of X-axis SAT pulse.

satyloc1

short satyloc1
560 A-side SAT pulse rel to lndmrk.

satyloc2

short satyloc2
562 P-side SAT pulse rel to lndmrk.

satythick

short satythick
570 Thickness of Y-axis SAT pulse.

satzloc1

short satzloc1
564 S-side SAT pulse rel to lndmrk.

satzloc2

short satzloc2
566 I-side SAT pulse rel to lndmrk.

satzthick

short satzthick
572 Thickness of Z-axis SAT pulse.

scanAcqNum

short scanAcqNum
728 Scan Acquisition Number.

scanProtocolName

String scanProtocolName
92 - 25 bytes - Scan Protocol Name.

scanSpacing

float scanSpacing
116 Spacing between scans (mm?).

scanType

short scanType
74 - Scout or Axial (for CT).

scic

short scic
554 Surface Coil Intensity Correction Flag.

scoutType

short scoutType
122 Scout Type (AP or lateral).

screenFormat

short screenFormat
112 - (8ቬ) bits.

scTime

float scTime
22 scan duration in seconds.

seActualDT

int seActualDT
16 - Actual Series Date/Time Stamp.

seAllocKey

String seAllocKey
154 - 13 bytes - Process that allocated this record.

seChecksum

int seChecksum
188 - (internal use) Series Record checksum.

seComplete

int seComplete
192 - (internal use) Series Complete Flag.

seContrast

short seContrast
118 - greater than zero if image used contrast (L/S).

seDateTime

int seDateTime
12 - Allocation series Date/Time Stamp.

seDeltaCnt

int seDeltaCnt
168 - (internal use) number of updates to header.

seDesc

String seDesc
20 - 30 bytes - Series Description.

seDiskID

byte seDiskID
6 - Disk ID for this series - GE internal.

seExamNo

short seExamNo
8 - Exam number.

seImageCt

int seImageCt
200 - (internal use) Last Image Number Used.

seLandmarkCnt

int seLandmarkCnt
136 - Landmark counter.

seLastMod

int seLastMod
150 - Date/Time of last change.

seNacq

short seNacq
140 - Number of acquisitions.

seNumArch

int seNumArch
196 - (internal use) Number of Images Archived.

seNumImages

int seNumImages
204 - (internal use) Number of Images Existing.

sePadding

String sePadding
432 - 588 bytes.

sePdsA

float sePdsA
176 - Pixel data size - as stored.

sePdsC

float sePdsC
180 - Pixel data size - Compressed.

sePdsU

float sePdsU
184 - Pixel data size - Uncompressed.

sePlane

short sePlane
72 - Most-like Plane (for L/S).

sePseq

short sePseq
132 - Last Pulse Sequence Used (L/S).

seriesNum

short seriesNum
10 - series number.

seriesUID

String seriesUID
336 - 32 bytes.

serrx

short serrx
108 - series from which prescribed.

serviceID

String serviceID
454 - 16 bytes.

seSortOrder

short seSortOrder
134 - (internal use) Image Sort Order (L/S).

seSource

short seSource
70 - Series from which prescribed.

seSuid

String seSuid
0 - 4 bytes - Suite ID for this Series.

seType

short seType
68 - Series Type.

seUniq

short seUniq
4 - The make-unique flag - GE internal.

seVersCre

String seVersCre
172 - 2 bytes - Genesis Version - Created.

seVersCur

String seVersCur
174 - 2 bytes - Genesis Version - Now.

sliceThickness

float sliceThickness
26 in mm.

slocfov

int slocfov
274 Slice offsets on frequency axis.

slop_float_1

float slop_float_1
676 Float Slop Field 1.

slop_float_2

float slop_float_2
680 Float Slop Field 2.

slop_float_3

float slop_float_3
684 Float Slop Field 3.

slop_float_4

float slop_float_4
688 Float Slop Field 4.

slop_float_5

float slop_float_5
692 Float Slop Field 5.

slop_int_1

int slop_int_1
656 Integer Slop Field 1.

slop_int_2

int slop_int_2
660 Integer Slop Field 2.

slop_int_3

int slop_int_3
664 Integer Slop Field 3.

slop_int_4

int slop_int_4
668 Integer Slop Field 4.

slop_int_5

int slop_int_5
672 Integer Slop Field 5.

slop_int_6

int slop_int_6
974 Integer Slop Field 6.

slop_int_7

int slop_int_7
978 Integer Slop Field 7.

slop_int_8

int slop_int_8
982 Integer Slop Field 8.

slop_int_9

int slop_int_9
986 Integer Slop Field 9.

slop_str_1

String slop_str_1
696 16 characters String Slop Field 1.

slop_str_2

String slop_str_2
712 16 characters String Slop Field 2.

slquant

short slquant
398 Number of slices in this scan group.

sop_uid

String sop_uid
778 32 characters Service Obj Clas Unique ID.

srcToDet

float srcToDet
58 Distance from source to detector.

srcToIso

float srcToIso
62 Distance from source to iso.

startLoc

float startLoc
122 - First scan location (L/S).

startRAS

String startRAS
120 - 1 byte - RAS letter for first scan location (L/S).

studyStatus

short studyStatus
506 Indicates if study has complete info (DICOM/genesis).

studyUID

String studyUID
474 - 32 bytes.

suiteID

String suiteID
0 - 4 bytes.

sumImg

String sumImg
651 Summary image field.

supp_tech

short supp_tech
392 SAT fat/water/none.

surfaceCoilType

short surfaceCoilType
380.

surfcext

short surfcext
382 Extremity Coil Flag.

swapPF

short swapPF
262 Swap phase-frequency axis.

tableDelta

float tableDelta
214.

tDel

int tDel
226 Delay time after trigger (msec).

te2

int te2
206 second echo echo (usec).

thk_disclmr

short thk_disclmr
578 Slice Thickness.

threshMax1

int threshMax1
628 Upper range of pixels 1.

threshMax2

int threshMax2
636 Upper range of pixels 2.

threshMin1

int threshMin1
624 Lower range of pixels 1.

threshMin2

int threshMin2
632 Lower range of pixels 2.

toArchiveCnt

int toArchiveCnt
228 - (internal use) number of Unarchived images.

toArchiveData

int toArchiveData
236.

toArchiveLen

int toArchiveLen
232 - (internal use) Unarchived images keys in Series.

trauma

short trauma
132 Trauma Flag.

trgWindow

short trgWindow
240 Trigger window (% of R-R interval).

tubeType

short tubeType
66.

unImagesData

int unImagesData
224.

unImagesLen

int unImagesLen
220 - (internal use) Unstored Image keys in Series.

uniq

short uniq
4 - (internal use) Make-Unique Flag.

uniqSysID

String uniqSysID
438 - 16 bytes.

unOriginal

short unOriginal
824 identifies image as original or unoriginal.

user0

float user0
406 User Variable 0.

user1

float user1
410 User Variable 1.

user10

float user10
446 User Variable 10.

user11

float user11
450 User Variable 11.

user12

float user12
454 User Variable 12.

user13

float user13
458 User Variable 13.

user14

float user14
462 User Variable 14.

user15

float user15
466 User Variable 15.

user16

float user16
470 User Variable 16.

user17

float user17
474 User Variable 17.

user18

float user18
478 User Variable 18.

user19

float user19
482 User Variable 19.

user2

float user2
414 User Variable 2.

user20

float user20
486 User Variable 20.

user21

float user21
490 User Variable 21.

user22

float user22
494 User Variable 22.

user23n

float user23n
588 User Variable 23.

user24

float user24
502 Concat Sat Type Flag.

user24n

float user24n
592 User Variable 24.

user25

float user25
878 User Variable 25.

user26

float user26
882 User Variable 26.

user27

float user27
886 User Variable 27.

user28

float user28
890 User Variable 28.

user29

float user29
894 User Variable 29.

user3

float user3
418 User Variable 3.

user30

float user30
898 User Variable 30.

user31

float user31
902 User Variable 31.

user32

float user32
906 User Variable 32.

user33

float user33
910 User Variable 33.

user34

float user34
914 User Variable 34.

user35

float user35
918 User Variable 35.

user36

float user36
922 User Variable 36.

user37

float user37
926 User Variable 37.

user38

float user38
930 User Variable 38.

user39

float user39
934 User Variable 39.

user4

float user4
422 User Variable 4.

user40

float user40
938 User Variable 40.

user41

float user41
942 User Variable 41.

user42

float user42
946 User Variable 42.

user43

float user43
950 User Variable 43.

user44

float user44
954 User Variable 44.

user45

float user45
958 User Variable 45.

user46

float user46
962 User Variable 46.

user47

float user47
966 User Variable 47.

user48

float user48
970 User variable 48.

user5

float user5
426 User Variable 5.

user6

float user6
430 User Variable 6.

user7

float user7
434 User Variable 7.

user8

float user8
438 User Variable 8.

user9

float user9
442 User Variable 9.

user_bitmap

int user_bitmap
292 Bitmap defining user Cvs.

userFillMapLSW

int userFillMapLSW
874 Describes what process fills in the user CVs, ifcc or TIR.

userFillMapMSW

int userFillMapMSW
870 Describes what process fills in the user CVs, ifcc or TIR.

userUsageTag

int userUsageTag
866 Defines how following user CVs are to be filled in.

valueBg

int valueBg
32 - background value of non image locations.

varEcho

short varEcho
648 Variable echo flag.

vas_collapse

short vas_collapse
586 Collapse image.

vasMode

short vasMode
744 Vascular Mode.

vbw

float vbw
394 Variable Bandwidth (Hz).

venc

short venc
576 Phase contrast velocity encoding (mm/sec).

vencScale

float vencScale
732 Scale Weighting Venc (Velocity Encoding/PI).

viewsPerSeg

short viewsPerSeg
830 views per segment.

width

int width
8 - width of image.

xAxisRot

float xAxisRot
612 X axis rotation.

xBaseEnd

short xBaseEnd
144 - Ending number for baselines.

xBaseSt

short xBaseSt
142 - Starting number for baselines.

xenhEnd

short xenhEnd
148 - Ending number for enhanced scans.

xenhSt

short xenhSt
146 - Starting number for enhanced scans.

xmtFreq

int xmtFreq
278 Center Frequency (0.1 Hz).

xmtGain

short xmtGain
248 Actual transmit gain (.1 db).

yAxisRot

float yAxisRot
616 Yaxis rotation.

zAxisRot

float zAxisRot
620 Z axis rotation.

zeroCell

float zeroCell
50 Cell number at theta.

currentSeconds

long currentSeconds
DOCUMENT ME!

day

int day
DOCUMENT ME!

hour

int hour
DOCUMENT ME!

minute

int minute
DOCUMENT ME!

month

String month
DOCUMENT ME!

monthIndex

int monthIndex
DOCUMENT ME!

seconds

int seconds
DOCUMENT ME!

year

int year
DOCUMENT ME!

Class gov.nih.mipav.model.file.FileInfoICS extends FileInfoBase implements Serializable

serialVersionUID: -4859517795116658689L

Serialized Fields

captureVersion

String captureVersion
DOCUMENT ME!

channels

String[] channels
DOCUMENT ME!

dataSetFileName

String dataSetFileName
DOCUMENT ME!

exPhotonCnt

String[] exPhotonCnt
DOCUMENT ME!

filterExposureTimeX

String filterExposureTimeX
DOCUMENT ME!

filterFluorophoreX

String[] filterFluorophoreX
DOCUMENT ME!

history

String[] history
DOCUMENT ME!

labels

String[] labels
DOCUMENT ME!

lambdaEm

String[] lambdaEm
DOCUMENT ME!

lambdaEx

String[] lambdaEx
DOCUMENT ME!

mapchannel

String[] mapchannel
DOCUMENT ME!

numAperture

String[] numAperture
DOCUMENT ME!

pinholeRadius

String[] pinholeRadius
DOCUMENT ME!

plateChamberID

String plateChamberID
DOCUMENT ME!

plateVesselID

String plateVesselID
DOCUMENT ME!

probe

String[] probe
DOCUMENT ME!

refrInxLensMedium

String[] refrInxLensMedium
DOCUMENT ME!

refrInxMedium

String[] refrInxMedium
DOCUMENT ME!

scilType

String scilType
DOCUMENT ME!

sensorModel

String sensorModel
DOCUMENT ME!

sensorType

String sensorType
DOCUMENT ME!

specimen

String[] specimen
DOCUMENT ME!

specimenSpecies

String[] specimenSpecies
DOCUMENT ME!

version

String version
DOCUMENT ME!

Class gov.nih.mipav.model.file.FileInfoImageXML extends FileInfoXML implements Serializable

serialVersionUID: -6296437302928259711L

Serialized Fields

bodyPart

String bodyPart
DOCUMENT ME!

currentPName

String currentPName
Used to keep track of the current parameter name.

currentPSetDesc

String currentPSetDesc
String for the current PSet description (for key).

currentSurfacePath

String currentSurfacePath
Used to keep track of the current surface.

currentVOIPath

String currentVOIPath
Used to keep track of the current VOI.

diagnosis

String diagnosis
DOCUMENT ME!

DOB

String DOB
DOCUMENT ME!

equipmentName

String equipmentName
Scan attributes. Optional XML tag.

height

int height
DOCUMENT ME!

invest

boolean[] invest
DOCUMENT ME!

investigators

FileInfoImageXML.Investigator[] investigators
Investigators (up to 3). Optional XML tag.

linkedFilePath

String linkedFilePath
Full path to an image that is linked to this image file. It is typically used to load a second image into the same frame. Optional XML tag.

linkedImagePath

String linkedImagePath
linked image path (optional).

matrix

TransMatrix matrix
Transformation matrix.

protocol

String protocol
DOCUMENT ME!

race

String race
DOCUMENT ME!

scanDate

String scanDate
DOCUMENT ME!

scanID

String scanID
DOCUMENT ME!

scanTime

String scanTime
DOCUMENT ME!

setTable

Hashtable<K,V> setTable
Hashtable for holding sets of parameters.

sex

String sex
DOCUMENT ME!

subjectID

String subjectID
DOCUMENT ME!

subjectName

String subjectName
Subject's information.

surfaces

Hashtable<K,V> surfaces
List of files which describe surfaces attached to this image.

VOIs

Hashtable<K,V> VOIs
List of files which describe VOIs attached to this image.

weight

int weight
DOCUMENT ME!

history

String history
The image history. Used by the NDAR meta-information generation dialog to write out the name of the zip file where the original data files are stored.

Class gov.nih.mipav.model.file.FileInfoImageXML.Investigator extends Object implements Serializable

serialVersionUID: -5267494343773142072L

Serialized Fields

affiliation

String affiliation
Affiliation of investigator.

email

String email
Investigator's email.

name

String name
Name of investigator.

phone

String phone
Investigator's phone number.

title

String title
Title of investigator.

Class gov.nih.mipav.model.file.FileInfoImageXML.Parameter extends Object implements Serializable

serialVersionUID: 4475674642754924771L

Serialized Fields

date

String date
Parameter date.

description

String description
Parameter description.

name

String name
Parameter name.

time

String time
Parameter time.

value

String value
Parameter value.

valueType

String valueType
Parameter value type.

Class gov.nih.mipav.model.file.FileInfoImageXML.PSet extends Object implements Serializable

serialVersionUID: 1087870691598758048L

Serialized Fields

currentParameterName

String currentParameterName
Current parameter name.

description

String description
Description of parameter.

parameterTable

Hashtable<K,V> parameterTable
Parameter hashtable.

Class gov.nih.mipav.model.file.FileInfoImageXML.SurfaceLink extends Object implements Serializable

serialVersionUID: -3088783811309623463L

Serialized Fields

display

boolean display
Should the surface be displayed.

opacity

float opacity
Opacity of surface.

path

String path
Path to surface.

Class gov.nih.mipav.model.file.FileInfoImageXML.VOILink extends Object implements Serializable

serialVersionUID: 3856425069094626835L

Serialized Fields

display

boolean display
Display VOI with image.

path

String path
Path to VOI.

Class gov.nih.mipav.model.file.FileInfoInterfile extends FileInfoBase implements Serializable

serialVersionUID: 1860672784494846816L

Serialized Fields

acquiredCardiacCycles

String[] acquiredCardiacCycles
DOCUMENT ME!

acquiredCardiacCyclesIndex

int acquiredCardiacCyclesIndex
DOCUMENT ME!

acquiredStudyDuration

String[] acquiredStudyDuration
DOCUMENT ME!

acquiredStudyDurationIndex

int acquiredStudyDurationIndex
DOCUMENT ME!

appliedCorrections

String appliedCorrections
DOCUMENT ME!

attenuationCorrection

String attenuationCorrection
DOCUMENT ME!

betaHalflife

String[] betaHalflife
DOCUMENT ME!

branchingFactor

String[] branchingFactor
DOCUMENT ME!

bytesPerPixel

String[] bytesPerPixel
DOCUMENT ME!

bytesPerPixelIndex

int bytesPerPixelIndex
DOCUMENT ME!

centerCenter

String centerCenter
DOCUMENT ME!

contactPerson

String contactPerson
DOCUMENT ME!

conversionProgram

String conversionProgram
DOCUMENT ME!

dataCompression

String dataCompression
DOCUMENT ME!

dataDescription

String dataDescription
DOCUMENT ME!

dataEncode

String dataEncode
DOCUMENT ME!

decayCorrected

String decayCorrected
DOCUMENT ME!

detectorHeadNumber

String detectorHeadNumber
DOCUMENT ME!

dimensionNumber

String dimensionNumber
DOCUMENT ME!

dynamicStudyGeneral

boolean dynamicStudyGeneral
DOCUMENT ME!

elapsedStudyDuration

String elapsedStudyDuration
DOCUMENT ME!

endianess

boolean endianess
DOCUMENT ME!

energyNumber

int energyNumber
DOCUMENT ME!

energyWindowName

String[] energyWindowName
DOCUMENT ME!

energyWindowsNumber

String energyWindowsNumber
DOCUMENT ME!

examType

String examType
DOCUMENT ME!

fGroupNumber

int fGroupNumber
DOCUMENT ME!

filterName

String filterName
DOCUMENT ME!

floodCorrected

String floodCorrected
DOCUMENT ME!

frameGroupImages

String[] frameGroupImages
DOCUMENT ME!

frameGroupImagesIndex

int frameGroupImagesIndex
DOCUMENT ME!

frameGroupNumber

String frameGroupNumber
DOCUMENT ME!

framingMethod

String[] framingMethod
DOCUMENT ME!

framingMethodIndex

int framingMethodIndex
DOCUMENT ME!

gammaHalflife

String[] gammaHalflife
DOCUMENT ME!

gatedStudyGeneral

boolean gatedStudyGeneral
DOCUMENT ME!

generalData

boolean generalData
DOCUMENT ME!

generalImageData

boolean generalImageData
DOCUMENT ME!

haveGated

boolean haveGated
DOCUMENT ME!

haveReconstructed

boolean haveReconstructed
DOCUMENT ME!

haveStaticStudy

boolean haveStaticStudy
DOCUMENT ME!

haveTomographic

boolean haveTomographic
DOCUMENT ME!

i

int i
DOCUMENT ME!

imageDataDescription

boolean imageDataDescription
DOCUMENT ME!

imageDuration

String[] imageDuration
DOCUMENT ME!

imageDurationIndex

int imageDurationIndex
DOCUMENT ME!

imageRelativeStartTime

String[] imageRelativeStartTime
DOCUMENT ME!

imageRelativeStartTimeIndex

int imageRelativeStartTimeIndex
DOCUMENT ME!

imagesPerEWindow

String imagesPerEWindow
DOCUMENT ME!

imageStartTime

String[] imageStartTime
DOCUMENT ME!

imageStartTimeIndex

int imageStartTimeIndex
DOCUMENT ME!

imagingModality

String imagingModality
DOCUMENT ME!

indexNestingLevel

String indexNestingLevel
DOCUMENT ME!

interfileDataType

String interfileDataType
DOCUMENT ME!

iNumber

int iNumber
DOCUMENT ME!

isoNumber

int isoNumber
DOCUMENT ME!

isotopeName

String[] isotopeName
DOCUMENT ME!

isotopeNumber

String isotopeNumber
DOCUMENT ME!

keysDate

String keysDate
DOCUMENT ME!

keysVersion

String keysVersion
DOCUMENT ME!

label

String[] label
DOCUMENT ME!

labelIndex

int labelIndex
DOCUMENT ME!

lowerLevel

String[] lowerLevel
DOCUMENT ME!

matrixSize1

String[] matrixSize1
DOCUMENT ME!

matrixSize1Index

int matrixSize1Index
DOCUMENT ME!

matrixSize2

String[] matrixSize2
DOCUMENT ME!

matrixSize2Index

int matrixSize2Index
DOCUMENT ME!

maximumPixelCount

String[] maximumPixelCount
DOCUMENT ME!

maximumPixelCountIndex

int maximumPixelCountIndex
DOCUMENT ME!

maximumPixelCountInGroup

String[] maximumPixelCountInGroup
DOCUMENT ME!

maximumPixelCountInGroupIndex

int maximumPixelCountInGroupIndex
DOCUMENT ME!

numberFormat

String[] numberFormat
DOCUMENT ME!

numberFormatIndex

int numberFormatIndex
DOCUMENT ME!

numberImages

int numberImages
DOCUMENT ME!

numberImagesPerEWindow

int numberImagesPerEWindow
DOCUMENT ME!

obliqueReconstruction

String obliqueReconstruction
DOCUMENT ME!

observedCardiacCycles

String observedCardiacCycles
DOCUMENT ME!

originalInstitution

String originalInstitution
DOCUMENT ME!

originatingSystem

String originatingSystem
DOCUMENT ME!

patientDOB

String patientDOB
DOCUMENT ME!

patientID

String patientID
DOCUMENT ME!

patientName

String patientName
DOCUMENT ME!

patientOrientation

String patientOrientation
DOCUMENT ME!

patientRotation

String patientRotation
DOCUMENT ME!

patientSex

String patientSex
DOCUMENT ME!

pauseBetweenFrameGroups

String[] pauseBetweenFrameGroups
DOCUMENT ME!

pauseBetweenFrameGroupsIndex

int pauseBetweenFrameGroupsIndex
DOCUMENT ME!

pauseBetweenImages

String[] pauseBetweenImages
DOCUMENT ME!

pauseBetweenImagesIndex

int pauseBetweenImagesIndex
DOCUMENT ME!

PETDataType

String PETDataType
DOCUMENT ME!

PETStudyGeneral

boolean PETStudyGeneral
DOCUMENT ME!

PETStudyImageData

boolean PETStudyImageData
DOCUMENT ME!

processStatus

String processStatus
DOCUMENT ME!

programAuthor

String programAuthor
DOCUMENT ME!

programDate

String programDate
DOCUMENT ME!

programVersion

String programVersion
DOCUMENT ME!

projectionNumber

String projectionNumber
DOCUMENT ME!

projectionTime

String projectionTime
DOCUMENT ME!

quantificationUnits

String quantificationUnits
DOCUMENT ME!

radiopharmaceutical

String radiopharmaceutical
DOCUMENT ME!

reconstructionMethod

String reconstructionMethod
DOCUMENT ME!

referenceFrameNumber

String referenceFrameNumber
DOCUMENT ME!

rotationExtent

String rotationExtent
DOCUMENT ME!

RRCycles

String[] RRCycles
DOCUMENT ME!

RRCyclesIndex

int RRCyclesIndex
DOCUMENT ME!

RRHistogram

String[] RRHistogram
DOCUMENT ME!

RRHistogramIndex

int RRHistogramIndex
DOCUMENT ME!

scalingFactor1

String[] scalingFactor1
DOCUMENT ME!

scalingFactor1Index

int scalingFactor1Index
DOCUMENT ME!

scalingFactor2

String[] scalingFactor2
DOCUMENT ME!

scalingFactor2Index

int scalingFactor2Index
DOCUMENT ME!

scannerQuantificationFactor

String scannerQuantificationFactor
DOCUMENT ME!

scatterCorrected

String scatterCorrected
DOCUMENT ME!

scatterCorrectionMethod

String scatterCorrectionMethod
DOCUMENT ME!

sliceNumber

String sliceNumber
DOCUMENT ME!

spectStudyGeneral

boolean spectStudyGeneral
DOCUMENT ME!

spectStudyReconstructedData

boolean spectStudyReconstructedData
DOCUMENT ME!

startHorizontalBedPosition

String startHorizontalBedPosition
DOCUMENT ME!

staticStudyGeneral

boolean staticStudyGeneral
DOCUMENT ME!

studyDate

String studyDate
DOCUMENT ME!

studyDuration

String studyDuration
DOCUMENT ME!

studyID

String studyID
DOCUMENT ME!

studyTime

String studyTime
DOCUMENT ME!

tFrame

int tFrame
DOCUMENT ME!

timeFrameNumber

int timeFrameNumber
DOCUMENT ME!

timeFrames

String timeFrames
DOCUMENT ME!

timeWindowImages

String[] timeWindowImages
DOCUMENT ME!

timeWindowImagesIndex

int timeWindowImagesIndex
DOCUMENT ME!

timeWindowLowerLimit

String[] timeWindowLowerLimit
DOCUMENT ME!

timeWindowLowerLimitIndex

int timeWindowLowerLimitIndex
DOCUMENT ME!

timeWindows

String timeWindows
DOCUMENT ME!

timeWindowsNumber

int timeWindowsNumber
DOCUMENT ME!

timeWindowUpperLimit

String[] timeWindowUpperLimit
DOCUMENT ME!

timeWindowUpperLimitIndex

int timeWindowUpperLimitIndex
DOCUMENT ME!

totalCounts

String[] totalCounts
DOCUMENT ME!

totalCountsIndex

int totalCountsIndex
DOCUMENT ME!

totalImageNumber

String totalImageNumber
DOCUMENT ME!

upperLevel

String[] upperLevel
DOCUMENT ME!

wNumber

int wNumber
DOCUMENT ME!

zAxisFilter

String zAxisFilter
DOCUMENT ME!

organ

String organ

gatedFrameMode

String[] gatedFrameMode

oldGatedFrameMode

String[] oldGatedFrameMode

gatedFrameModeIndex

int gatedFrameModeIndex

windowA

String windowA

windowB

String windowB

windowC

String windowC

sliceOrientation

String sliceOrientation

Class gov.nih.mipav.model.file.FileInfoJP2 extends FileInfoBase implements Serializable

Serialized Fields

imageDescription

String imageDescription
DOCUMENT ME!

Class gov.nih.mipav.model.file.FileInfoLattice extends FileInfoBase implements Serializable

serialVersionUID: 6546787758481646181L

Class gov.nih.mipav.model.file.FileInfoLIFF extends FileInfoBase implements Serializable

Serialized Fields

layerString

String[] layerString
Use serialVersionUID for interoperability.

bitDepth

short bitDepth

autoContrast

double autoContrast

binning

double binning

camera

String camera

channelArray

String[] channelArray

colorization

double colorization

cooling

double cooling

CRIRGBFilter

double CRIRGBFilter

digitalGain

double digitalGain

emissionFilterChangerArray

double[] emissionFilterChangerArray

channelNumber

int channelNumber

excitationArray

double[] excitationArray

exposureArray

double[] exposureArray

filterTurretArray

double[] filterTurretArray

focusPosition

double focusPosition

gain

double gain

leicaCondenserTurret

double leicaCondenserTurret

leicaFilterCubeArray

double[] leicaFilterCubeArray

leicaFIMArray

double[] leicaFIMArray

leicaICTurret

double leicaICTurret

leicaMagnificationChanger

double leicaMagnificationChanger

lightMode

double lightMode

ludlAuxWheel1

double ludlAuxWheel1

ludlMainWheel1Array

double[] ludlMainWheel1Array

microscope

String microscope

microfocusPosition

double microfocusPosition

objectiveName

double objectiveName

objectivePosition

double objectivePosition

offset

double offset

sensitivityArray

double[] sensitivityArray

SutterDG4Filter

double SutterDG4Filter

SutterL10Filter1Array

double[] SutterL10Filter1Array

SutterL10Filter2Array

double[] SutterL10Filter2Array

wavelengthArray

double[] wavelengthArray

xPosition

double xPosition

yPosition

double yPosition

zPosition

double zPosition

Class gov.nih.mipav.model.file.FileInfoLSM extends FileInfoBase implements Serializable

serialVersionUID: 4011175280016387707L

Serialized Fields

bleachedROIShape

int bleachedROIShape
DOCUMENT ME!

blueArray

int[] blueArray
DOCUMENT ME!

channelDataTypes

int[] channelDataTypes
DOCUMENT ME!

channelNames

String[] channelNames
DOCUMENT ME!

channels

int channels
DOCUMENT ME!

displayAspectTime

double displayAspectTime
DOCUMENT ME!

displayAspectX

double displayAspectX
DOCUMENT ME!

displayAspectY

double displayAspectY
DOCUMENT ME!

displayAspectZ

double displayAspectZ
DOCUMENT ME!

eventDescription

String[] eventDescription
DOCUMENT ME!

eventTime

double[] eventTime
DOCUMENT ME!

eventType

int[] eventType
DOCUMENT ME!

firstSliceAfterBleach

int firstSliceAfterBleach
DOCUMENT ME!

greenArray

int[] greenArray
DOCUMENT ME!

imageDescription

String imageDescription
DOCUMENT ME!

knotX

double[] knotX
DOCUMENT ME!

knotY

double[] knotY
DOCUMENT ME!

lastSliceBeforeBleach

int lastSliceBeforeBleach
DOCUMENT ME!

LSMDataType

int LSMDataType
DOCUMENT ME!

LSMDataType2

int LSMDataType2
DOCUMENT ME!

mono

int mono
DOCUMENT ME!

objectiveSphereCorrection

double objectiveSphereCorrection
DOCUMENT ME!

redArray

int[] redArray
DOCUMENT ME!

scanType

int scanType
DOCUMENT ME!

spectralScan

int spectralScan
DOCUMENT ME!

timeDim

int timeDim
DOCUMENT ME!

timeInterval

double timeInterval
DOCUMENT ME!

timeStamp

double[] timeStamp
DOCUMENT ME!

wavelengths

double[] wavelengths
DOCUMENT ME!

Class gov.nih.mipav.model.file.FileInfoMagnetomVision extends FileInfoBase implements Serializable

serialVersionUID: -7248419259071769004L

Serialized Fields

AcquisitionDateDD

int AcquisitionDateDD
DOCUMENT ME!

AcquisitionDateMM

int AcquisitionDateMM
DOCUMENT ME!

AcquisitionDateYYYY

int AcquisitionDateYYYY
DOCUMENT ME!

AcquisitionTimeHH

int AcquisitionTimeHH
DOCUMENT ME!

AcquisitionTimeMM

int AcquisitionTimeMM
DOCUMENT ME!

AcquisitionTimeSS

int AcquisitionTimeSS
DOCUMENT ME!

Annotation

String Annotation
DOCUMENT ME!

CalibrationDateDD

int CalibrationDateDD
DOCUMENT ME!

CalibrationDateMM

int CalibrationDateMM
DOCUMENT ME!

CalibrationDateYYYY

int CalibrationDateYYYY
DOCUMENT ME!

CalibrationTimeHH

int CalibrationTimeHH
DOCUMENT ME!

CalibrationTimeMM

int CalibrationTimeMM
DOCUMENT ME!

CalibrationTimeSS

int CalibrationTimeSS
DOCUMENT ME!

CenterPointX

double CenterPointX
DOCUMENT ME!

CenterPointY

double CenterPointY
DOCUMENT ME!

CenterPointZ

double CenterPointZ
DOCUMENT ME!

ColumnVectorX

double ColumnVectorX
DOCUMENT ME!

ColumnVectorY

double ColumnVectorY
DOCUMENT ME!

ColumnVectorZ

double ColumnVectorZ
DOCUMENT ME!

DisplayMatrixSize

int DisplayMatrixSize
DOCUMENT ME!

DistanceFromIsocenter

double DistanceFromIsocenter
DOCUMENT ME!

DOBDD

int DOBDD
DOCUMENT ME!

DOBMM

int DOBMM
DOCUMENT ME!

DOBYYYY

int DOBYYYY
DOCUMENT ME!

EchoTime

double EchoTime
DOCUMENT ME!

FlipAngle

double FlipAngle
DOCUMENT ME!

FOVColumn

double FOVColumn
DOCUMENT ME!

FOVRow

double FOVRow
DOCUMENT ME!

FrequencyMHz

double FrequencyMHz
DOCUMENT ME!

ImageDateDD

int ImageDateDD
DOCUMENT ME!

ImageDateMM

int ImageDateMM
DOCUMENT ME!

ImageDateYYYY

int ImageDateYYYY
DOCUMENT ME!

ImagedNucleus

String ImagedNucleus
DOCUMENT ME!

ImageTimeHH

int ImageTimeHH
DOCUMENT ME!

ImageTimeMM

int ImageTimeMM
DOCUMENT ME!

ImageTimeSS

int ImageTimeSS
DOCUMENT ME!

InstitutionName

String InstitutionName
DOCUMENT ME!

LastMoveDateDD

int LastMoveDateDD
DOCUMENT ME!

LastMoveDateMM

int LastMoveDateMM
DOCUMENT ME!

LastMoveDateYYYY

int LastMoveDateYYYY
DOCUMENT ME!

LastMoveTimeHH

int LastMoveTimeHH
DOCUMENT ME!

LastMoveTimeMM

int LastMoveTimeMM
DOCUMENT ME!

LastMoveTimeSS

int LastMoveTimeSS
DOCUMENT ME!

MagneticFieldStrength

double MagneticFieldStrength
DOCUMENT ME!

Manufacturer

String Manufacturer
DOCUMENT ME!

ModelName

String ModelName
DOCUMENT ME!

NormalVectorX

double NormalVectorX
DOCUMENT ME!

NormalVectorY

double NormalVectorY
DOCUMENT ME!

NormalVectorZ

double NormalVectorZ
DOCUMENT ME!

OrientationSet1Back

String OrientationSet1Back
DOCUMENT ME!

OrientationSet1Left

String OrientationSet1Left
DOCUMENT ME!

OrientationSet1Top

String OrientationSet1Top
DOCUMENT ME!

OrientationSet2Down

String OrientationSet2Down
DOCUMENT ME!

OrientationSet2Front

String OrientationSet2Front
DOCUMENT ME!

OrientationSet2Right

String OrientationSet2Right
DOCUMENT ME!

PatientAge

String PatientAge
DOCUMENT ME!

PatientAgeUnits

String PatientAgeUnits
DOCUMENT ME!

PatientID

String PatientID
DOCUMENT ME!

PatientName

String PatientName
DOCUMENT ME!

ReceivingCoil

String ReceivingCoil
DOCUMENT ME!

RegistrationDateDD

int RegistrationDateDD
DOCUMENT ME!

RegistrationDateMM

int RegistrationDateMM
DOCUMENT ME!

RegistrationDateYYYY

int RegistrationDateYYYY
DOCUMENT ME!

RegistrationTimeHH

int RegistrationTimeHH
DOCUMENT ME!

RegistrationTimeMM

int RegistrationTimeMM
DOCUMENT ME!

RegistrationTimeSS

int RegistrationTimeSS
DOCUMENT ME!

RepetitionTime

double RepetitionTime
DOCUMENT ME!

RowVectorX

double RowVectorX
DOCUMENT ME!

RowVectorY

double RowVectorY
DOCUMENT ME!

RowVectorZ

double RowVectorZ
DOCUMENT ME!

SequenceAuthor

String SequenceAuthor
DOCUMENT ME!

SequenceName

String SequenceName
DOCUMENT ME!

SequencePrgName

String SequencePrgName
DOCUMENT ME!

SequenceType

String SequenceType
DOCUMENT ME!

SequenceWkcName

String SequenceWkcName
DOCUMENT ME!

SiemensStudyDateDD

int SiemensStudyDateDD
DOCUMENT ME!

SiemensStudyDateMM

int SiemensStudyDateMM
DOCUMENT ME!

SiemensStudyDateYYYY

int SiemensStudyDateYYYY
DOCUMENT ME!

SiemensStudyTimeHH

int SiemensStudyTimeHH
DOCUMENT ME!

SiemensStudyTimeMM

int SiemensStudyTimeMM
DOCUMENT ME!

SiemensStudyTimeSS

int SiemensStudyTimeSS
DOCUMENT ME!

Station

String Station
DOCUMENT ME!

TextAcquisitionMatrixFreq

String TextAcquisitionMatrixFreq
DOCUMENT ME!

TextAcquisitionMatrixFreqO

String TextAcquisitionMatrixFreqO
DOCUMENT ME!

TextAcquisitionMatrixFreqS

String TextAcquisitionMatrixFreqS
DOCUMENT ME!

TextAcquisitionMatrixPhase

String TextAcquisitionMatrixPhase
DOCUMENT ME!

TextAcquisitionMatrixPhaseAxis

String TextAcquisitionMatrixPhaseAxis
DOCUMENT ME!

TextAcquisitionTimeMM

String TextAcquisitionTimeMM
DOCUMENT ME!

TextAcquisitionTimeSS

String TextAcquisitionTimeSS
DOCUMENT ME!

TextAngle

String TextAngle
DOCUMENT ME!

TextAngleFlag1

String TextAngleFlag1
DOCUMENT ME!

TextAngleFlag2

String TextAngleFlag2
DOCUMENT ME!

TextAngleFlag3

String TextAngleFlag3
DOCUMENT ME!

TextAnnotation

String TextAnnotation
DOCUMENT ME!

TextDateDD

String TextDateDD
DOCUMENT ME!

TextDateMM

String TextDateMM
DOCUMENT ME!

TextDateYYYY

String TextDateYYYY
DOCUMENT ME!

TextDOBDD

String TextDOBDD
DOCUMENT ME!

TextDOBMM

String TextDOBMM
DOCUMENT ME!

TextDOBYYYY

String TextDOBYYYY
DOCUMENT ME!

TextEchoNumber

String TextEchoNumber
DOCUMENT ME!

TextEchoTime

String TextEchoTime
DOCUMENT ME!

TextFlipAngle

String TextFlipAngle
DOCUMENT ME!

TextFOVH

String TextFOVH
DOCUMENT ME!

TextFOVV

String TextFOVV
DOCUMENT ME!

TextImageNumber

String TextImageNumber
DOCUMENT ME!

TextImageNumber2

String TextImageNumber2
DOCUMENT ME!

TextModelName

String TextModelName
DOCUMENT ME!

TextOrganization

String TextOrganization
DOCUMENT ME!

TextPatientAge

String TextPatientAge
DOCUMENT ME!

TextPatientAgeUnits

String TextPatientAgeUnits
DOCUMENT ME!

TextPatientID

String TextPatientID
DOCUMENT ME!

TextPatientName

String TextPatientName
DOCUMENT ME!

TextPatientPosition

String TextPatientPosition
DOCUMENT ME!

TextPatientSex

String TextPatientSex
DOCUMENT ME!

TextRepetitionTime

String TextRepetitionTime
DOCUMENT ME!

TextScanNumberA

String TextScanNumberA
DOCUMENT ME!

TextScanNumberB

String TextScanNumberB
DOCUMENT ME!

TextScanStartTimeHH

String TextScanStartTimeHH
DOCUMENT ME!

TextScanStartTimeMM

String TextScanStartTimeMM
DOCUMENT ME!

TextScanStartTimeSS

String TextScanStartTimeSS
DOCUMENT ME!

TextSequence

String TextSequence
DOCUMENT ME!

TextSlicePosition

String TextSlicePosition
DOCUMENT ME!

TextSliceThickness

String TextSliceThickness
DOCUMENT ME!

TextStation

String TextStation
DOCUMENT ME!

TextStudyImageNumber3

String TextStudyImageNumber3
DOCUMENT ME!

TextStudyNumber

String TextStudyNumber
DOCUMENT ME!

TextStudyNumber2

String TextStudyNumber2
DOCUMENT ME!

TextTablePosition

String TextTablePosition
DOCUMENT ME!

TextTimeHH

String TextTimeHH
DOCUMENT ME!

TextTimeMM

String TextTimeMM
DOCUMENT ME!

Class gov.nih.mipav.model.file.FileInfoMedVision extends FileInfoBase implements Serializable

serialVersionUID: -88313565378572414L

Serialized Fields

cineRate

double cineRate
DOCUMENT ME!

cols

short cols
DOCUMENT ME!

dataType

short dataType
DOCUMENT ME!

dateOfBirth

String dateOfBirth
DOCUMENT ME!

eqManuf

String eqManuf
DOCUMENT ME!

eqType

String eqType
DOCUMENT ME!

fileType

String fileType
File header data structure format.

frameRefNum

short frameRefNum
DOCUMENT ME!

imageOffset

int imageOffset
DOCUMENT ME!

imageScale

double imageScale
DOCUMENT ME!

institution

String institution
DOCUMENT ME!

modality

String modality
DOCUMENT ME!

patientName

String patientName
Info data structure format.

pixelSizeH

double pixelSizeH
DOCUMENT ME!

pixelSizeV

double pixelSizeV
hDat dataStructure format public long version;.

referringPhys

String referringPhys
DOCUMENT ME!

rows

short rows
Slice Header data structure format.

sex

String sex
DOCUMENT ME!

sliceHdrSize

short sliceHdrSize
DOCUMENT ME!

slicePosition

double slicePosition
DOCUMENT ME!

sliceRefNum

short sliceRefNum
DOCUMENT ME!

sliceThickness

double sliceThickness
DOCUMENT ME!

sliceTime

double sliceTime
DOCUMENT ME!

standardCols

short standardCols
DOCUMENT ME!

standardRows

short standardRows
DOCUMENT ME!

studyDate

String studyDate
DOCUMENT ME!

studyName

String studyName
DOCUMENT ME!

studyTime

String studyTime
DOCUMENT ME!

totalSlices

short totalSlices
DOCUMENT ME!

version

int version
DOCUMENT ME!

Class gov.nih.mipav.model.file.FileInfoMGH extends FileInfoBase implements Serializable

Serialized Fields

version

int version
Currently version number is 1

dof

int dof

leftCenter

float leftCenter

posteriorCenter

float posteriorCenter

superiorCenter

float superiorCenter

tr

float tr

flipAngle

float flipAngle

te

float te

ti

float ti

fov

float fov

transformFileName

String transformFileName

cmdlines

String[] cmdlines

matrix

TransMatrix matrix

Class gov.nih.mipav.model.file.FileInfoMicroCat extends FileInfoBase implements Serializable

serialVersionUID: -388246456500624487L

Serialized Fields

autoStartCBREngine

String autoStartCBREngine
DOCUMENT ME!

baseNameforReconstructedSlices

String baseNameforReconstructedSlices
DOCUMENT ME!

CATFileName

String CATFileName
DOCUMENT ME!

CBRHostName

String CBRHostName
DOCUMENT ME!

CBRImageDirectory

String CBRImageDirectory
DOCUMENT ME!

CBRProjectionDirectory

String CBRProjectionDirectory
DOCUMENT ME!

cylinderReconstruction

int cylinderReconstruction
DOCUMENT ME!

enableStepSize

int enableStepSize
DOCUMENT ME!

filterType

String filterType
DOCUMENT ME!

imageDestinationDirectory

String imageDestinationDirectory
DOCUMENT ME!

logScale

float logScale
DOCUMENT ME!

numberOfProjections

int numberOfProjections
DOCUMENT ME!

projectionDataAlreadyOnCBR

String projectionDataAlreadyOnCBR
DOCUMENT ME!

projectionUSize

int projectionUSize
DOCUMENT ME!

projectionVSize

int projectionVSize
DOCUMENT ME!

rotationDirection

int rotationDirection
DOCUMENT ME!

RPCPortNum

String RPCPortNum
DOCUMENT ME!

startAngle

float startAngle
DOCUMENT ME!

stepSizeFile

String stepSizeFile
DOCUMENT ME!

timeoutBetweenProjectionTransfers

int timeoutBetweenProjectionTransfers
DOCUMENT ME!

UCenterOffset

int UCenterOffset
DOCUMENT ME!

VCenterOffset

int VCenterOffset
DOCUMENT ME!

volumeOriginX

float volumeOriginX
DOCUMENT ME!

volumeOriginY

float volumeOriginY
DOCUMENT ME!

volumeOriginZ

float volumeOriginZ
DOCUMENT ME!

volumeSizeX

int volumeSizeX
DOCUMENT ME!

volumeSizeY

int volumeSizeY
DOCUMENT ME!

volumeSizeZ

int volumeSizeZ
DOCUMENT ME!

voxelSizeX

float voxelSizeX
DOCUMENT ME!

voxelSizeY

float voxelSizeY
DOCUMENT ME!

voxelSizeZ

float voxelSizeZ
DOCUMENT ME!

Class gov.nih.mipav.model.file.FileInfoMinc extends FileInfoBase implements Serializable

serialVersionUID: 6804935230803731941L

Serialized Fields

numrecs

int numrecs
DOCUMENT ME!

vmax

double vmax
Valid image maximum value. Default = -1.

vmin

double vmin
Valid image minimum value. Default = -1.

dimArray

FileMincDimElem[] dimArray
DOCUMENT ME!

gattArray

FileMincAttElem[] gattArray
DOCUMENT ME!

varArray

FileMincVarElem[] varArray
DOCUMENT ME!

Class gov.nih.mipav.model.file.FileInfoMincHDF extends FileInfoBase implements Serializable

serialVersionUID: 1372818551072422068L

Serialized Fields

validRange

double[] validRange
The valid range for image pixel values

Class gov.nih.mipav.model.file.FileInfoMRC extends FileInfoBase implements Serializable

serialVersionUID: 4677697781087324517L

Serialized Fields

alpha

float alpha
DOCUMENT ME!

beta

float beta
DOCUMENT ME!

gamma

float gamma
DOCUMENT ME!

creatorID

short creatorID
DOCUMENT ME!

idType

short idType
DOCUMENT ME!

impliedFlagBytes

int impliedFlagBytes
DOCUMENT ME!

ispg

short ispg
DOCUMENT ME!

nSymbt

short nSymbt
DOCUMENT ME!

label

String[] label
DOCUMENT ME!

lens

short lens
DOCUMENT ME!

mapC

int mapC
DOCUMENT ME!

mapR

int mapR
DOCUMENT ME!

mapS

int mapS
DOCUMENT ME!

nd1

short nd1
DOCUMENT ME!

nd2

short nd2
DOCUMENT ME!

vd1

short vd1
DOCUMENT ME!

vd2

short vd2
DOCUMENT ME!

next

int next
DOCUMENT ME!

nint

short nint
DOCUMENT ME!

nreal

short nreal
DOCUMENT ME!

nwave

short nwave
DOCUMENT ME!

rms

float rms
DOCUMENT ME!

tiltAngles

float[] tiltAngles
DOCUMENT ME!

wave1

short wave1
DOCUMENT ME!

wave2

short wave2
DOCUMENT ME!

wave3

short wave3
DOCUMENT ME!

wave4

short wave4
DOCUMENT ME!

wave5

short wave5
DOCUMENT ME!

Class gov.nih.mipav.model.file.FileInfoNIFTI extends FileInfoBase implements Serializable

serialVersionUID: -5506021019885109431L

Serialized Fields

aux_file

String aux_file
auxiliary file

bitpix

short bitpix
Bits per pixel

cal_max

float cal_max
The cal_min and cal_max fields (if nonzero) are used for mapping (possibly scaled) dataset values to display colors: - Minimum display intensity (black) corresponds to dataset value cal_min. - Maximum display intensity (white) corresponds to dataset value cal_max. - Dataset values below cal_min should display as black also, and values above cal_max as white. - Colors "black" and "white", of course, may refer to any scalar display scheme (e.g., a color lookup table specified via aux_file). - cal_min and cal_max only make sense when applied to scalar-valued datasets (i.e., dim[0] < 5 or dim[5] = 1).

cal_min

float cal_min
values of 0.0 for both fields imply that no calibration min and max values are used !

coord_code

short coord_code
If qform_code > 0, coord_code = qform_code. If qform_code <= 0 and sform_code > 0, coord_code = sform_code. coord_code has values for "Arbitrary X,Y,Z coordinate system", "Scanner based anatomical coordinates", "Coordinates aligned to another file's or to anatomical truth", "Talairach X,Y,Z coordinate system", and "MNI 152 normalized X,Y,Z coordinates".

coord_code2

short coord_code2
If qform_code > 0 and sform_code > 0, coord_code = qform_code and coord_code2 = sform_code. coord_code has values for "Arbitrary X,Y,Z coordinate system", "Scanner based anatomical coordinates", "Coordinates aligned to another file's or to anatomical truth", "Talairach X,Y,Z coordinate system", and "MNI 152 normalized X,Y,Z coordinates".

descrip

String descrip
Any text you like

freq_dim

int freq_dim
Bits 0 and 1 of the dim_info character contain the freq_dim information. 0 for "No frequency encoding direction is present", 1 for "Frequency encoding in the x direction", 2 for "Frequency encoding in the y direction", and 3 for "Frequency encoding in the z direction".

intentCode

short intentCode
The intent_code field can be used to indicate that the voxel data has some particular meaning. In particular, a large number of codes is given to indicate that the the voxel data should be interpreted as being drawn from a given probability distribution.

intentName

String intentName
The intent_name field provides space for a 15 character (plus 0 byte) name string for the type of data stored. Examples: - intent_code = NIFTI_INTENT_ESTIMATE; intent_name = "T1"; could be used to signify that the voxel values are estimates of the NMR parameter T1. - intent_code = NIFTI_INTENT_TTEST; intent_name = "House"; could be used to signify that the voxel values are t-statistics for the significance of activation response to a House stimulus. - intent_code = NIFTI_INTENT_DISPVECT; intent_name = "ToMNI152"; could be used to signify that the voxel values are a displacement vector that transforms each voxel (x,y,z) location to the corresponding location in the MNI152 standard brain. - intent_code = NIFTI_INTENT_SYMMATRIX; intent_name = "DTI"; could be used to signify that the voxel values comprise a diffusion tensor image.

intentP1

float intentP1
If present, first auxiliary parameter used with intentCode

intentP2

float intentP2
If present, second auxiliary parameter used with intentCode

intentP3

float intentP3
If present, third auxiliary parameter used with intentCode

phase_dim

int phase_dim
Bits 2 and 3 of the dim_info character contain the phase_dim information. 0 for "No phase encoding direction is present", 1 for "Phase encoding in the x direction", 2 for "Phase encoding in the y direction", and 3 for "Phase encoding in the z direction".

scl_slope

float scl_slope
If the scl_slope field is nonzero, then each voxel value in the dataset should be scaled as y = scl_slope * x + scl_inter where x = voxel value stored y = "true" voxel value Normally, we would expect this scaling to be used to store "true" floating values in a smaller integer datatype, but that is not required. That is, it is legal to use scaling even if the datatype is a float type (crazy, perhaps, but legal). - However, the scaling is to be ignored if datatype is DT_RGB24. - If datatype is a complex type, then the scaling is to be applied to both the real and imaginary parts.

scl_inter

float scl_inter

sizeof_hdr

int sizeof_hdr
Should always be a length of 348.

slice_dim

int slice_dim
Bits 4 and 5 of the dim_info character contain the slice_dim information. 0 for "No slice acquisition direction is present", 1 for "Slice acquisition in the x direction", 2 for "Slice acquisition in the y direction", and 3 for "Slice acquisition in the z direction".

sliceCode

byte sliceCode
If this is nonzero, AND if slice_dim is nonzero, AND if slice_duration is positive, indicates the timing pattern of the slice acquisition. The following codes are defined: "Slice timing order is sequentially increasing", "Slice timing order is sequentially decreasing", "Slice timing order is alternately increasing", "Slice timing order is alternately decreasing", "Slice timing order is alternately increasing #2", "Slice timing order is alternately decreasing #2".

sliceDuration

float sliceDuration
Time used to acquire 1 slice.

sliceEnd

short sliceEnd
Slice timing pattern ends with slice = (sliceEnd + 1)

sliceStart

short sliceStart
Slice timing pattern starts with slice = (sliceStart + 1)

sourceBitPix

short sourceBitPix
Source bits per pixel : 1,8,16,32,64,128 24(rgb).

sourceType

short sourceType
Original unscaled source data type

vox_offset

float vox_offset
If the magic field is "n+1", then the voxel data is stored in the same file as the header. In this case, the voxel data starts at offset (int)vox_offset into the header file. Thus, vox_offset=352.0 means that the data starts immediately after the NIFTI-1 header. If vox_offset is greater than 352, the NIFTI-1 format does not say much about the contents of the dataset file between the end of the header and the start of the data. If the magic field is "ni1", then the voxel data is stored in the associated ".img" file, starting at offset 0 (i.e., vox_offset is not used in this case, and should be set to 0.0). In a .nii file, the vox_offset field value is interpreted as the start location of the image data bytes in that file. In a .hdr/.img file pair, the vox_offset field value is the start location of the image data bytes in the .img file. If vox_offset is less than 352 in a .nii file, it is equivalent to 352 (i.e., image data never starts before byte #352 in a .nii file). The default value for vox_offset in a .nii file is 352. In a .hdr file, the default value for vox_offset is 0. * vox_offset should be an integer multiple of 16; otherwise, some programs may not work properly (e.g., SPM). This is to allow memory-mapped input to be properly byte-aligned.

extendedHeaderPresence

String extendedHeaderPresence

esize

int esize

ecode

int ecode

esize2

int esize2

ecode2

int ecode2

esize3

int esize3

ecode3

int ecode3

Class gov.nih.mipav.model.file.FileInfoNRRD extends FileInfoBase implements Serializable

Serialized Fields

matrix

TransMatrix matrix
Transformation matrix.

versionNumber

float versionNumber
Version of the NRRD file format being used.

encodingString

String encodingString
Data compression - raw, gzip

contentString

String contentString
Concise textual description of the information in the array

labelString

String[] labelString
Axis names such as X, Y, or Z

sliceThickness

float sliceThickness

modalityString

String modalityString
Diffusion weighted MRI is currently the only value that has been seen for modality in our samples.

DWMRI_B_VALUE

String DWMRI_B_VALUE
"DWMRI_b-value:=b " : This key/value pair gives the (scalar) diffusion-weighting value, in units of s/mm^2. Example: "DWMRI_b-value:=1000". The effective magnitude of diffusion-weighting for each DWI is determined with some simple calculations based on the individual per-DWI gradient directions or B-matrices.

dwmriGradient

String[][] dwmriGradient
For every index position NNNN along the DWI axis (whichever is the non-spatial axis identified by the "list" or "vector" kind field), either "DWMRI_gradient_NNNN:=x y z " or "DWMRI_B-matrix_NNNN:=xx xy xz yy yz zz " must be given (except if "DWMRI_NEX_NNNN:= M " is used).

spaceString

String spaceString
Possible values are "right-anterior-superior", "left-anterior-superior", "left-posterior-superior", "right-anterior-superior-time", "left-anterior-superior-time", "left-posterior-superior-time", "scanner-xyz", "scanner-xyz-time", "3d-right-handed", "3d-left-handed", "3d-right-handed-time", "3d-left-handed-time"

Class gov.nih.mipav.model.file.FileInfoOME extends FileInfoBase implements Serializable

serialVersionUID: -4798053431303160065L

Serialized Fields

headerFileName

String headerFileName
DOCUMENT ME!

matrix

TransMatrix matrix
DOCUMENT ME!

ome

FileInfoOME.OME ome
DOCUMENT ME!

Class gov.nih.mipav.model.file.FileInfoOSM extends FileInfoBase implements Serializable

serialVersionUID: -5125356994727655396L

Serialized Fields

alpha

float alpha
DOCUMENT ME!

beta

float beta
DOCUMENT ME!

gamma

float gamma
DOCUMENT ME!

footerSize

int footerSize
DOCUMENT ME!

idType

short idType
DOCUMENT ME!

ispg

int ispg
DOCUMENT ME!

nSymbt

int nSymbt
DOCUMENT ME!

label

String[] label
DOCUMENT ME!

lens

short lens
DOCUMENT ME!

mapC

int mapC
DOCUMENT ME!

mapR

int mapR
DOCUMENT ME!

mapS

int mapS
DOCUMENT ME!

tiltAngles

float[] tiltAngles
DOCUMENT ME!

wave1

int wave1
DOCUMENT ME!

wave2

int wave2
DOCUMENT ME!

wave3

int wave3
DOCUMENT ME!

Class gov.nih.mipav.model.file.FileInfoPARREC extends FileInfoBase implements Serializable

Serialized Fields

sliceInfo

String sliceInfo
slice specific info

Class gov.nih.mipav.model.file.FileInfoProject extends FileInfoBase implements Serializable

serialVersionUID: -8242251068336660670L

Serialized Fields

currentImageFileName

String currentImageFileName
Used to keep track of the current image.

currentPName

String currentPName
Used to keep track of the current parameter name.

currentPSetDesc

String currentPSetDesc
String for the current PSet description (for key).

dataType

int dataType
Type of Data.

images

Hashtable<K,V> images
List of images attached to this project.

invest

boolean[] invest
DOCUMENT ME!

investigators

FileInfoProject.Investigator[] investigators
Investigators (up to 3). Optional XML tag.

projectDescription

String projectDescription
Brief description of the image.

projectFileName

String projectFileName
Name (not path) of the project file.

saveNeededFlag

boolean saveNeededFlag
Flag to indicate whether the project info has been changed and should be saved.

setTable

Hashtable<K,V> setTable
Hashtable for holding sets of parameters.

Class gov.nih.mipav.model.file.FileInfoProject.ImageInfo extends Object implements Serializable

serialVersionUID: 1057184447893258773L

Serialized Fields

description

String description
DOCUMENT ME!

name

String name
DOCUMENT ME!

value

String value
DOCUMENT ME!

valueType

String valueType
DOCUMENT ME!

Class gov.nih.mipav.model.file.FileInfoProject.Investigator extends Object implements Serializable

serialVersionUID: -2326251180154056395L

Serialized Fields

affiliation

String affiliation
DOCUMENT ME!

email

String email
DOCUMENT ME!

name

String name
DOCUMENT ME!

phone

String phone
DOCUMENT ME!

title

String title
DOCUMENT ME!

Class gov.nih.mipav.model.file.FileInfoProject.Parameter extends Object implements Serializable

serialVersionUID: 7867185997827250638L

Serialized Fields

date

String date
DOCUMENT ME!

description

String description
DOCUMENT ME!

name

String name
DOCUMENT ME!

time

String time
DOCUMENT ME!

value

String value
DOCUMENT ME!

valueType

String valueType
DOCUMENT ME!

Class gov.nih.mipav.model.file.FileInfoProject.ProjectImage extends Object implements Serializable

serialVersionUID: -3382758798506490222L

Serialized Fields

currentInfoName

String currentInfoName
DOCUMENT ME!

fileName

String fileName
DOCUMENT ME!

infoTable

Hashtable<K,V> infoTable
DOCUMENT ME!

Class gov.nih.mipav.model.file.FileInfoProject.PSet extends Object implements Serializable

serialVersionUID: 524931106461981593L

Serialized Fields

currentParameterName

String currentParameterName
DOCUMENT ME!

description

String description
DOCUMENT ME!

parameterTable

Hashtable<K,V> parameterTable
DOCUMENT ME!

Class gov.nih.mipav.model.file.FileInfoRaw extends FileInfoBase implements Serializable

serialVersionUID: -1470168847948086226L

Class gov.nih.mipav.model.file.FileInfoSPM extends FileInfoBase implements Serializable

serialVersionUID: -3655260345861989046L

Serialized Fields

aux_file

String aux_file
DOCUMENT ME!

bitpix

short bitpix
DOCUMENT ME!

cal_max

float cal_max
DOCUMENT ME!

cal_min

float cal_min
DOCUMENT ME!

cal_units

String cal_units
DOCUMENT ME!

compressed

float compressed
DOCUMENT ME!

data_type

String data_type
DOCUMENT ME!

datatype

short datatype
DOCUMENT ME!

db_name

String db_name
DOCUMENT ME!

descrip

String descrip
DOCUMENT ME!

dim_un0

short dim_un0
DOCUMENT ME!

exp_date

String exp_date
DOCUMENT ME!

exp_time

String exp_time
DOCUMENT ME!

extents

int extents
DOCUMENT ME!

field_skip

int field_skip
DOCUMENT ME!

generated

String generated
DOCUMENT ME!

glmax

int glmax
DOCUMENT ME!

glmin

int glmin
DOCUMENT ME!

hist_un0

String hist_un0
DOCUMENT ME!

hkey_un0

char hkey_un0
DOCUMENT ME!

omax

int omax
DOCUMENT ME!

omin

int omin
DOCUMENT ME!

orient

byte orient
DOCUMENT ME!

origin

short[] origin
DOCUMENT ME!

patient_id

String patient_id
DOCUMENT ME!

regular

char regular
DOCUMENT ME!

scale

float scale
a floating point scale factor used during memory mapping.

scannum

String scannum
DOCUMENT ME!

session_error

short session_error
DOCUMENT ME!

sizeof_hdr

int sizeof_hdr
DOCUMENT ME!

smax

int smax
DOCUMENT ME!

smin

int smin
DOCUMENT ME!

start_field

int start_field
DOCUMENT ME!

verified

float verified
DOCUMENT ME!

views

int views
DOCUMENT ME!

vols_added

int vols_added
DOCUMENT ME!

vox_offset

float vox_offset
public float pixdim = new float[8]; // image resolutions info mm or ms stored in FileInfoBase pixdim[0] = number of dimensions pixdim[1] = voxel width pixdim[2] = voxel height pixdim[3] = voxel thickness pixdim[4] = time.

vox_units

String vox_units
public short dim[] = new short[8]; // image dimension data stored in FileInfoBase dim[0] = number of dimensions; usally 4 dim[1] = image width dim[2] = image height dim[3] = image depth (# of slices) dim[4] = volumes in image --- must be one for 3D image.

Class gov.nih.mipav.model.file.FileInfoSTK extends FileInfoBase implements Serializable

serialVersionUID: 4681901066117260212L

Serialized Fields

imageDescription

String imageDescription
DOCUMENT ME!

sameZPosition

boolean sameZPosition
DOCUMENT ME!

Class gov.nih.mipav.model.file.FileInfoSurfaceRefXML extends FileInfoXML implements Serializable

serialVersionUID: 6815854469776062772L

Serialized Fields

m_iUnique_ID

int m_iUnique_ID
Unique ID, for the surface:.

filename

String filename
.sur file name.

m_kType

String m_kType
Type keyword for the surface:.

m_kOpacity

float m_kOpacity
surface opacity:.

m_kLevelDetail

int m_kLevelDetail
surface level of detail:.

meshIndex

int meshIndex
mesh index.

Class gov.nih.mipav.model.file.FileInfoSurfaceXML extends FileInfoXML implements Serializable

serialVersionUID: 6815854469776062772L

Serialized Fields

m_iUnique_ID

int m_iUnique_ID
Unique ID, for the surface:.

m_kType

String m_kType
Type keyword for the surface:.

m_kOpacity

float m_kOpacity
surface opacity:.

m_kLevelDetail

int m_kLevelDetail
surface level of detail:.

meshIndex

int meshIndex
mesh index.

Class gov.nih.mipav.model.file.FileInfoTiff extends FileInfoBase implements Serializable

serialVersionUID: 7421068113479441629L

Serialized Fields

imageDescription

String imageDescription
DOCUMENT ME!

Class gov.nih.mipav.model.file.FileInfoTMG extends FileInfoBase implements Serializable

serialVersionUID: 652378870162150500L

Serialized Fields

commentStr

String commentStr
DOCUMENT ME!

nameStr

String nameStr
DOCUMENT ME!

timeStr

String timeStr
DOCUMENT ME!

titleStr

String titleStr
DOCUMENT ME!

Class gov.nih.mipav.model.file.FileInfoXML extends FileInfoBase implements Serializable

serialVersionUID: -7709467226605763815L

Serialized Fields

imageDataFileName

String imageDataFileName
Name (not path) of the (usually raw) image data file. The name of the image xml header file is stored in FileInfoBase.getFileName().

See Also:
FileInfoBase.getFileName(), FileInfoBase.setFileName(String)

imageDescription

String imageDescription
Brief description of the image - optional XML tag.

Class gov.nih.mipav.model.file.FileMincAttElem extends ModelSerialCloneable implements Serializable

serialVersionUID: -4847649204791713924L

Serialized Fields

name

String name
DOCUMENT ME!

nc_type

int nc_type
DOCUMENT ME!

nelems

int nelems
DOCUMENT ME!

values

Object[] values
DOCUMENT ME!

Class gov.nih.mipav.model.file.FileMincDimElem extends ModelSerialCloneable implements Serializable

serialVersionUID: -8677079575179802672L

Serialized Fields

length

int length
DOCUMENT ME!

name

String name
DOCUMENT ME!

Class gov.nih.mipav.model.file.FileMincHDF.HDFNode extends DefaultMutableTreeNode implements Serializable

serialVersionUID: 240L

Class gov.nih.mipav.model.file.FileMincVarElem extends ModelSerialCloneable implements Serializable

serialVersionUID: -3229377471887553687L

Serialized Fields

begin

int begin
DOCUMENT ME!

comments

String comments
DOCUMENT ME!

cosines

double[] cosines
DOCUMENT ME!

dimid

int[] dimid
DOCUMENT ME!

name

String name
DOCUMENT ME!

nc_type

int nc_type
DOCUMENT ME!

nelems

int nelems
DOCUMENT ME!

step

double step
in zspace, step == slice gap, not necessarily slice thickness

signtype

String signtype
DOCUMENT ME!

start

double start
DOCUMENT ME!

trueStart

double trueStart
DOCUMENT ME!

units

String units
DOCUMENT ME!

values

Vector<E> values
DOCUMENT ME!

vattArray

FileMincAttElem[] vattArray
DOCUMENT ME!

vmax

double vmax
DOCUMENT ME!

vmin

double vmin
DOCUMENT ME!

vsize

int vsize
DOCUMENT ME!

Class gov.nih.mipav.model.file.FileTiff.ModHuffmanInputStream.ModHuffmanCodingException extends IOException implements Serializable

Package gov.nih.mipav.model.provenance

Class gov.nih.mipav.model.provenance.ProvenanceChangeEvent extends ChangeEvent implements Serializable

Serialized Fields

entry

ProvenanceEntry entry

Class gov.nih.mipav.model.provenance.ProvenanceEntry extends ModelSerialCloneable implements Serializable

Serialized Fields

programName

String programName

timeStamp

String timeStamp
The timestamp

action

String action
action describing the event

platform

String platform
the name of the operating system

platformVersion

String platformVersion
the operating system's version

user

String user
the user name

hostName

String hostName
the machine host name

mipavVersion

String mipavVersion
mipav's version

mipavBuild

String mipavBuild
probably unused

mipavInputs

String mipavInputs
mipav cmd line arguments

mipavOutputs

String mipavOutputs
probably unused

compilerVersion

String compilerVersion
java's version

architecture

String architecture

Class gov.nih.mipav.model.provenance.ProvenanceHolder extends Vector<ProvenanceEntry> implements Serializable

Serialized Fields

listenerList

EventListenerList listenerList
A list of the ChangeListeners which are interested in the ChangeEvent.

Package gov.nih.mipav.model.scripting

Class gov.nih.mipav.model.scripting.ImageVariableTable extends Hashtable<String,String> implements Serializable

serialVersionUID: 4108175711902767830L

Serialized Fields

currentImageNumber

int currentImageNumber
The number to use for the next image placeholder variable to be added to the table. Starts at 1.

Class gov.nih.mipav.model.scripting.ParserException extends Exception implements Serializable

serialVersionUID: -7330285082866837830L

Serialized Fields

lineNumber

int lineNumber
The line number in the script where this error occurred.

parsedFileName

String parsedFileName
The file name of the script where this error occurred ('-' if no corresponding file on disk).

Class gov.nih.mipav.model.scripting.VariableTable extends Hashtable implements Serializable

serialVersionUID: 4108175711902767830L

Package gov.nih.mipav.model.scripting.parameters

Class gov.nih.mipav.model.scripting.parameters.ParameterException extends RuntimeException implements Serializable

Serialized Fields

parameterLabel

String parameterLabel
The label of the parameter which there was an error retrieving.

Package gov.nih.mipav.model.srb

Class gov.nih.mipav.model.srb.SRBFileTransferer.JDialogPickFiles extends JDialog implements Serializable

Serialized Fields

cancelButton

JButton cancelButton
DOCUMENT ME!

helpButton

JButton helpButton
DOCUMENT ME!

defaultDialogTitle

String defaultDialogTitle
The default dialog title.

sourceBrowseButton

JButton sourceBrowseButton
DOCUMENT ME!

sourceFilesField

JTextField sourceFilesField
Instance variables.

sourceSchemaComboBox

JComboBox sourceSchemaComboBox
DOCUMENT ME!

targetBrowseButton

JButton targetBrowseButton
DOCUMENT ME!

targetFilesField

JTextField targetFilesField
DOCUMENT ME!

targetSchemaComboBox

JComboBox targetSchemaComboBox
DOCUMENT ME!

transferButton

JButton transferButton
DOCUMENT ME!

Package gov.nih.mipav.model.structures

Class gov.nih.mipav.model.structures.BufferBase extends Object implements Serializable

serialVersionUID: -5379757071350175311L

Class gov.nih.mipav.model.structures.BufferBoolean extends BufferBase implements Serializable

serialVersionUID: 588861892470975804L

Serialized Fields

dataArray

BitSet dataArray
1D Data array of boolean stored in the BitSet object.

Class gov.nih.mipav.model.structures.BufferByte extends BufferBase implements Serializable

serialVersionUID: -4876739041350991776L

Serialized Fields

dataArray

byte[] dataArray
1D Data array of bytes.

Class gov.nih.mipav.model.structures.BufferDouble extends BufferBase implements Serializable

serialVersionUID: 3953733643360606122L

Serialized Fields

dataArray

double[] dataArray
1D Data array of doubles.

Class gov.nih.mipav.model.structures.BufferFloat extends BufferBase implements Serializable

serialVersionUID: -3011094039945269732L

Serialized Fields

dataArray

float[] dataArray
1D Data array of floats.

Class gov.nih.mipav.model.structures.BufferInt extends BufferBase implements Serializable

serialVersionUID: -2929615702424425376L

Serialized Fields

dataArray

int[] dataArray
1D Data array of integers.

Class gov.nih.mipav.model.structures.BufferLong extends BufferBase implements Serializable

serialVersionUID: -7762001591051273716L

Serialized Fields

dataArray

long[] dataArray
1D Data array of longs.

Class gov.nih.mipav.model.structures.BufferShort extends BufferBase implements Serializable

serialVersionUID: 784194545397056669L

Serialized Fields

dataArray

short[] dataArray
1D Data array of shorts.

Class gov.nih.mipav.model.structures.BufferUByte extends BufferBase implements Serializable

serialVersionUID: -3712379512280992650L

Serialized Fields

dataArray

byte[] dataArray
1D Data array of unsigned bytes (bytes).

Class gov.nih.mipav.model.structures.BufferUInt extends BufferBase implements Serializable

serialVersionUID: 1794760958290773461L

Serialized Fields

dataArray

int[] dataArray
1D Data array of unsigned integers.

Class gov.nih.mipav.model.structures.BufferUShort extends BufferBase implements Serializable

serialVersionUID: -5218443296426650180L

Serialized Fields

dataArray

short[] dataArray
1D Data array of unsigned shorts.

Class gov.nih.mipav.model.structures.CustomHashtable extends Hashtable<String,V> implements Serializable

serialVersionUID: -8592617112282655416L

Class gov.nih.mipav.model.structures.ExceptionAllocateData extends Exception implements Serializable

serialVersionUID: -6698640528995532404L

Class gov.nih.mipav.model.structures.MatrixHolder extends ModelSerialCloneable implements Serializable

serialVersionUID: 6886161945452841455L

Serialized Fields

compositeMatrix

TransMatrix compositeMatrix
The composite matrix formed by multiplying (in reverse order) all stored matrices.

matrixMap

LinkedHashMap<K,V> matrixMap
Linked hash map that will store all of the images associated matrices.

Class gov.nih.mipav.model.structures.ModelHistogram extends ModelStorageBase implements Serializable

serialVersionUID: 3128722138789734543L

Serialized Fields

histogramFrameVector

Vector<E> histogramFrameVector
DOCUMENT ME!

maxEntropyThreshold

int maxEntropyThreshold
DOCUMENT ME!

mean

float mean
DOCUMENT ME!

mode

int mode
DOCUMENT ME!

otsuThreshold

int otsuThreshold
DOCUMENT ME!

stRange

int stRange
DOCUMENT ME!

endRange

int endRange
DOCUMENT ME!

totalPixels

int totalPixels
DOCUMENT ME!

Class gov.nih.mipav.model.structures.ModelImage extends ModelStorageBase implements Serializable

serialVersionUID: 1234298038008494667L

Serialized Fields

imageName

String imageName
ImageName is patient's name when using DICOM images. It is filename for any other image something other than filename must be used for DICOM because one DICOM image is made of many seperate files. ** Not necessarily the file name.

imageOrder

int imageOrder
Indicates the image order when two images are displayed in the same frame.

mask

BitSet mask
Mask is a binary object that is true interior to a VOI and false otherwise used in algorithms to process only on VOIs if indicated by the user.

maskBU

BitSet maskBU
Backup of mask for undoing.

matrixHolder

MatrixHolder matrixHolder
Holds all of the images associated matrices.

talairach

TalairachTransformInfo talairach
Reference to talairach transform information.

voiVector

VOIVector voiVector
List of VOIs that are displayed with this image.

Class gov.nih.mipav.model.structures.ModelLUT extends ModelStorageBase implements Serializable

serialVersionUID: 5061105716563814614L

Serialized Fields

alphaLine

TransferFunction alphaLine
Fucntion that attenuates image values.

blueLine

TransferFunction blueLine
Function that maps the blue function of the LUT.

greenLine

TransferFunction greenLine
Function that maps the green function of the LUT.

indexedLUT

int[] indexedLUT
Special int array where the LUT is packed with alpha in the most significant byte of the int, followed red, green, and blue.

nColors

int nColors
Number of colors in the LUT.

redLine

TransferFunction redLine
Function that maps the red function of the LUT.

remappedLUT

int[] remappedLUT
DOCUMENT ME!

transferLine

TransferFunction transferLine
Function that maps image values into the LUT. The x coord. ranges [image.min, image.max];

type

int type
DOCUMENT ME!

x

float[] x
The X coordinates of the transfer functions.

Class gov.nih.mipav.model.structures.ModelRGB extends ModelStorageBase implements Serializable

serialVersionUID: -718098067552795698L

Serialized Fields

blueLine

TransferFunction blueLine
Function that maps the blue function of the LUT.

BOn

boolean BOn
Flag indicating whether the blue channel should be displayed.

GOn

boolean GOn
Flag indicating whether the green channel should be displayed.

greenLine

TransferFunction greenLine
Function that maps the green function of the LUT.

indexedRGB

int[] indexedRGB
DOCUMENT ME!

nColors

int nColors
Number of colors in the LUT.

redLine

TransferFunction redLine
Function that maps the red function of the LUT.

ROn

boolean ROn
Flag indicating whether the red channel should be displayed.

x

float[] x
The X coordinates of the transfer functions.

y

float[] y
The Y coordinates of the transfer functions.

Class gov.nih.mipav.model.structures.ModelSerialCloneable extends Object implements Serializable

serialVersionUID: 7436115594993339188L

Class gov.nih.mipav.model.structures.ModelSimpleImage extends ModelSerialCloneable implements Serializable

serialVersionUID: 7953112445452821048L

Serialized Fields

cMassX

float cMassX
X coordinate value of the center of mass for the image.

cMassY

float cMassY
Y coordinate value of the center of mass for the image.

cMassZ

float cMassZ
Z coordinate value of the center of mass for the image.

data

float[] data
Data buffer that is used to store the image.

dataSize

int dataSize
Size of the data buffer (number of pixels in image).

extents

int[] extents
The dimensionality of the dataset.

isColor

boolean isColor
Indicates whether is image is a color image or not.

max

float max
Maximum intensity values of image.

maxR

float maxR
Maximum intensity values of image.

maxG

float maxG
Maximum intensity values of image.

maxB

float maxB
Maximum intensity values of image.

min

float min
Minimum intensity values of image.

minR

float minR
Minimum intensity values of image.

minG

float minG
Minimum intensity values of image.

minB

float minB
Minimum intensity values of image.

nDims

int nDims
Number of dimensions of the image.

resolutions

float[] resolutions
Voxel resolutions (typically x,y,z(slice spacing),t).

tDim

int tDim
Number of volumes in the dataset. Typically t represents time.

tRes

float tRes
Resolution in the time dimension.

xDim

int xDim
Number of pixels in x dimension.

xRes

float xRes
X pixel resolution.

yDim

int yDim
Number of pixels in y dimension.

yRes

float yRes
Y pixel resolution.

zDim

int zDim
Number of pixels in z dimension.

zRes

float zRes
Z voxel resolution.

Class gov.nih.mipav.model.structures.ModelStorageBase extends ModelSerialCloneable implements Serializable

serialVersionUID: -3710345290762731636L

Serialized Fields

fileInfo

FileInfoBase[] fileInfo
Each image slice has a information that describes aspects of each slice of an image.

lastMin

double lastMin
lastMin and lastMax store the last min and max values for an image. these are used as a trigger for resetting the transfer function.

lastMax

double lastMax
lastMin and lastMax store the last min and max values for an image. these are used as a trigger for resetting the transfer function.

projectInfo

FileInfoProject projectInfo
Information about the project which the image is a part of (or null if the image was not opened as part of a project).

bufferType

int bufferType
Type of image buffer (i.e. BOOLEAN, BYTE, UBYTE, SHORT ...)

data

BufferBase data
Storage location of image data.

dataSize

int dataSize
Total buffer length.

dimExtents

int[] dimExtents
Bounds of the image where.

dimOriginalExtents

int[] dimOriginalExtents
Bounds of the image where.

filterType

int filterType
DOCUMENT ME! - TO BE MOVED - redesigned

freq1

float freq1
DOCUMENT ME! - TO BE MOVED - redesigned

freq2

float freq2
DOCUMENT ME! - TO BE MOVED - redesigned

freqU

float freqU
5 variables used in Gabor transform. - should be removed - redesigned

freqV

float freqV
DOCUMENT ME! - TO BE MOVED - redesigned

haveWindowed

boolean haveWindowed
DOCUMENT ME! - TO BE MOVED - redesigned

image25D

boolean image25D
Boolean telling if 3D images are processed 1 slice at a time.

lockStatus

int lockStatus
Locking status of the image. Default = UNLOCKED

logMagDisp

boolean logMagDisp
Boolean telling if log magnitude display is used in complex image. - TO BE MOVED - redesigned

m_bConvolve

boolean m_bConvolve
Set to true when the image is the product of the ffts of two images, so that on an inverse_fft this image will be centered properly. Default is false.

m_bRadiologicalView

boolean m_bRadiologicalView
When true, display the data in the Radiological View, when false display the Neurological View:.

m_kColorVector

Vector<E> m_kColorVector
Surface color vector. - TO BE MOVED - redesigned

m_kMaskColorVector

Vector<E> m_kMaskColorVector
Surface mask color vector. - TO BE MOVED - redesigned

m_kMaskVector

Vector<E> m_kMaskVector
Surface mask vector.- TO BE MOVED - redesigned.

min

double min
Minimum and maximum image intensity.

max

double max
Minimum and maximum image intensity.

minR

double minR
Minimum and maximum for a color image.

maxR

double maxR
Minimum and maximum for a color image.

minG

double minG
Minimum and maximum for a color image.

maxG

double maxG
Minimum and maximum for a color image.

minB

double minB
Minimum and maximum for a color image.

maxB

double maxB
Minimum and maximum for a color image.

nDims

int nDims
Number of dimensions of the data.

noLogMin

double noLogMin
Minimum and maximum image intensity with log magnitude operation removed. - TO BE MOVED

noLogMax

double noLogMax
Minimum and maximum image intensity with log magnitude operation removed. - TO BE MOVED

noLogMinNonZero

double noLogMinNonZero
Minimum and maximum image intensity with log magnitude operation removed. - TO BE MOVED

nonZeroMin

double nonZeroMin
Minimum and maximum nonzero intensity. - TO BE MOVED - redesigned

nonZeroMax

double nonZeroMax
Minimum and maximum nonzero intensity. - TO BE MOVED - redesigned

nonZeroMinR

double nonZeroMinR
Minimum and maximum nonzero image RGB. - TO BE MOVED - redesigned

nonZeroMaxR

double nonZeroMaxR
Minimum and maximum nonzero image RGB. - TO BE MOVED - redesigned

nonZeroMinG

double nonZeroMinG
Minimum and maximum nonzero image RGB. - TO BE MOVED - redesigned

nonZeroMaxG

double nonZeroMaxG
Minimum and maximum nonzero image RGB. - TO BE MOVED - redesigned

nonZeroMinB

double nonZeroMinB
Minimum and maximum nonzero image RGB. - TO BE MOVED - redesigned

nonZeroMaxB

double nonZeroMaxB
Minimum and maximum nonzero image RGB. - TO BE MOVED - redesigned

originalButterworthOrder

int originalButterworthOrder
DOCUMENT ME!- TO BE MOVED - redesigned.

originalCropCheckbox

boolean originalCropCheckbox
DOCUMENT ME!- TO BE MOVED - redesigned.

originalDoCrop

boolean originalDoCrop
DOCUMENT ME! - TO BE MOVED - redesigned

originalEnd

int[] originalEnd
DOCUMENT ME!- TO BE MOVED - redesigned.

originalFilterConstruction

int originalFilterConstruction
DOCUMENT ME! - TO BE MOVED- redesigned

originalKernelDimension

int originalKernelDimension
This are variables used by the FFT filter algorithm. - should be removed - redesigned

originalMaximum

float originalMaximum
DOCUMENT ME! - TO BE MOVED - redesigned

originalMinimum

float originalMinimum
DOCUMENT ME! - TO BE MOVED - redesigned

originalStart

int[] originalStart
DOCUMENT ME! - TO BE MOVED - redesigned

sigmaU

float sigmaU
DOCUMENT ME! - TO BE MOVED - redesigned

sigmaV

float sigmaV
DOCUMENT ME! - should be removed - redesigned

smallestMagnitudeNegative

double smallestMagnitudeNegative
smallest magnitude negative and positive.

smallestMagnitudePositive

double smallestMagnitudePositive
smallest magnitude negative and positive.

smallestMagnitudeNegativeR

double smallestMagnitudeNegativeR
smallest magnitude negative and positive.

smallestMagnitudePositiveR

double smallestMagnitudePositiveR
smallest magnitude negative and positive.

smallestMagnitudeNegativeG

double smallestMagnitudeNegativeG
smallest magnitude negative and positive.

smallestMagnitudePositiveG

double smallestMagnitudePositiveG
smallest magnitude negative and positive.

smallestMagnitudeNegativeB

double smallestMagnitudeNegativeB
smallest magnitude negative and positive.

smallestMagnitudePositiveB

double smallestMagnitudePositiveB
smallest magnitude negative and positive.

theta

float theta
DOCUMENT ME! - TO BE MOVED - redesigned

unequalDim

boolean unequalDim
Boolean telling if unequal dimensions are allowed in the FFT image. TO BE MOVED

writeLockCount

int writeLockCount
Locking write count.

avgInten

float avgInten

avgIntenR

float avgIntenR

avgIntenG

float avgIntenG

avgIntenB

float avgIntenB

stdDeviation

float stdDeviation

stdDeviationR

float stdDeviationR

stdDeviationG

float stdDeviationG

stdDeviationB

float stdDeviationB

numPixels

int numPixels

sumPixelInten

double sumPixelInten

sumPixelIntenR

double sumPixelIntenR

sumPixelIntenG

double sumPixelIntenG

sumPixelIntenB

double sumPixelIntenB

Class gov.nih.mipav.model.structures.SortingTableModel extends DefaultTableModel implements Serializable

serialVersionUID: -1782879801334035117L

Serialized Fields

htColumnClass

Hashtable<K,V> htColumnClass
DOCUMENT ME!

Class gov.nih.mipav.model.structures.TableSorter extends AbstractTableModel implements Serializable

serialVersionUID: 3279717528747239046L

Serialized Fields

tableModel

TableModel tableModel
DOCUMENT ME!

columnComparators

Map<K,V> columnComparators
DOCUMENT ME!

modelToView

int[] modelToView
DOCUMENT ME!

mouseListener

MouseListener mouseListener
DOCUMENT ME!

sortingColumns

List<E> sortingColumns
DOCUMENT ME!

tableHeader

JTableHeader tableHeader
DOCUMENT ME!

tableModelListener

TableModelListener tableModelListener
DOCUMENT ME!

viewToModel

gov.nih.mipav.model.structures.TableSorter.Row[] viewToModel
DOCUMENT ME!

Class gov.nih.mipav.model.structures.TalairachTransformInfo extends Object implements Serializable

serialVersionUID: 5791995578653926105L

Serialized Fields

acpcAC

WildMagic.LibFoundation.Mathematics.Vector3f acpcAC
Anterior Comissure in acpc space.

acpcDim

int[] acpcDim
image dimensions.

acpcMax

WildMagic.LibFoundation.Mathematics.Vector3f acpcMax
DOCUMENT ME!

acpcMin

WildMagic.LibFoundation.Mathematics.Vector3f acpcMin
ACPC min and max extents of the brain.

acpcPC

WildMagic.LibFoundation.Mathematics.Vector3f acpcPC
Posterior Comissure in acpc space.

acpcRes

float acpcRes
voxel resolution (cubic).

isAcpc

boolean isAcpc
true if we have the data to compute orig <-> acpc.

isTlrc

boolean isTlrc
true if we ahve the data to compute acpc <-> tlrc.

origAC

WildMagic.LibFoundation.Mathematics.Vector3f origAC
Anterior Comissure in original space.

origDim

int[] origDim
Original image dimensions.

origOrient

float[][] origOrient
ACPC orientation in original image.

origPC

WildMagic.LibFoundation.Mathematics.Vector3f origPC
Posterior Comissure in original space.

origRes

float[] origRes
Original image voxel resolutions.

tlrcAC

WildMagic.LibFoundation.Mathematics.Vector3f tlrcAC
Anterior Comissure in Talairach space.

tlrcDim

int[] tlrcDim
image dimensions.

tlrcPC

WildMagic.LibFoundation.Mathematics.Vector3f tlrcPC
Posterior Comissure in Talairach space.

tlrcRes

float[] tlrcRes
voxel resolutions for the sub-boxes.

Class gov.nih.mipav.model.structures.TokenizerException extends Exception implements Serializable

serialVersionUID: -5430332821046122039L

Class gov.nih.mipav.model.structures.TransferFunction extends ModelSerialCloneable implements Serializable

serialVersionUID: -6859218214454354638L

Serialized Fields

capacity

int capacity
The total capacity of the 2D point array. Intial capapcity = 10

endPtr

int endPtr
Points to the next available storage location for the point.

pts

WildMagic.LibFoundation.Mathematics.Vector2f[] pts
The array of 2D points that define the line.

slopes

float[] slopes
The array of pre-calculated slope values.

Class gov.nih.mipav.model.structures.TransMatrix extends WildMagic.LibFoundation.Mathematics.Matrix4f implements Serializable

serialVersionUID: 5604493833934574127L

Serialized Fields

m_TransformID

int m_TransformID
Transform ID associated with the matrix.

m_IsNIFTI

boolean m_IsNIFTI
boolean indicating whether this matrix is associated with a NIFTI image (special case handling)

m_IsQform

boolean m_IsQform
If true, nifti matrix codes for a qform matrix If false, nifti matrix codes for a sform matrix Value has no effect if not a nifti matrix

m_Is2D

boolean m_Is2D
Transform was constructed to transform 2D vectors, instead of 3D

Class gov.nih.mipav.model.structures.UneditableTableModel extends DefaultTableModel implements Serializable

serialVersionUID: 6185277710154266940L

Class gov.nih.mipav.model.structures.UpdateVOIEvent extends EventObject implements Serializable

serialVersionUID: 8233713497226707057L

Serialized Fields

curve

VOIBase curve
DOCUMENT ME!

source

Object source
DOCUMENT ME!

usedCurve

boolean usedCurve
DOCUMENT ME!

voi

VOI voi
DOCUMENT ME!

Class gov.nih.mipav.model.structures.VOI extends ModelSerialCloneable implements Serializable

serialVersionUID: 4045424525937515770L

Serialized Fields

NOT_A_POINT

int NOT_A_POINT
int indictating that no point was found.

active

boolean active
If true indicates tha the VOI is selected (active).

activePolylineSlicePoint

int activePolylineSlicePoint
DOCUMENT ME!

boundingBox

boolean boundingBox
If true the bounding box of the VOI should be displayed.

color

Color color
Indicates the color or the VOI.

thickness

int thickness
The thickness of the VOI lines

curves

Vector<E>[] curves
A vector array of curves per slice.

curveType

int curveType
Indicates the type of VOI (i.e. CONTOUR, POLYLINE, LINE, POINT, PROTRACTOR, etc. ... )

displayMode

int displayMode
Indicates if the VOI should be shown as a boundary or a solid.

elementLabel

short elementLabel
The label (numbering) of the curve, displayed when curve is highlighted.

fixed

boolean fixed
If true the VOI can be moved, if false this VOI cannot be moved.

ID

short ID
ID of the VOI, also used when choosing the display color.

ignoreMax

float ignoreMax
DOCUMENT ME!

ignoreMin

float ignoreMin
DOCUMENT ME!

intensity

float[] intensity
DOCUMENT ME!

level

float level
DOCUMENT ME!

name

String name
Name of the VOI stored as a string.

nearBoundPoint

int nearBoundPoint
DOCUMENT ME!

opacity

float opacity
When in the solid display mode indicates how opaque the VOI should be. Zero is transparent and one is opaque.

pLineSliceIndex

int pLineSliceIndex
DOCUMENT ME!

polarity

int polarity
Indicates if the VOI should mask ones or mask as zeros.

polygonIndex

int polygonIndex
DOCUMENT ME!

position

float[] position
DOCUMENT ME!

process

boolean process
If true this flag indicates that the VOI should be included (applied) when processing the image.

resizeIndex

int resizeIndex
DOCUMENT ME!

rgbIntensities

float[][] rgbIntensities
DOCUMENT ME!

rgbPositions

float[][] rgbPositions
DOCUMENT ME!

stats

ViewList[] stats
DOCUMENT ME!

totalIntensity

boolean totalIntensity
DOCUMENT ME!

UID

int UID
Unique ID for saving & retrieving.

visible

boolean visible
If true the VOI is visible.

voiUpdate

VOIEvent voiUpdate
DOCUMENT ME!

watershedID

short watershedID
Used to objects a label or ID inconjuction with the watershed algorithm.

xBounds

float[] xBounds
The x - dimension bounds: xBounds [0] = min and xBounds[1] = max.

yBounds

float[] yBounds
The y - dimension bounds: yBounds [0] = min and yBounds[1] = max.

zBounds

float[] zBounds
The z - dimension bounds: zBounds [0] = min and zBounds[1] = max.

zDim

int zDim
DOCUMENT ME!

Class gov.nih.mipav.model.structures.VOIBase extends Vector<WildMagic.LibFoundation.Mathematics.Vector3f> implements Serializable

serialVersionUID: -3872480526036224600L

Serialized Fields

active

boolean active
Flag indicating whether or not a VOI is active (selected). If the VOI is selected then the flag is true else it is false

black

Color black
General use color (black) used in VOI.

gcPt

WildMagic.LibFoundation.Mathematics.Vector3f gcPt
Stores the geometric center of the contour of a VOI.

cenMassPt

WildMagic.LibFoundation.Mathematics.Vector3f cenMassPt
Stores the black and white center of mass of the contour of a VOI.

cenMassPtR

WildMagic.LibFoundation.Mathematics.Vector3f cenMassPtR
Stores the red center of mass of the contour of a VOI.

cenMassPtG

WildMagic.LibFoundation.Mathematics.Vector3f cenMassPtG
Stores the green center of mass of the contour of a VOI.

cenMassPtB

WildMagic.LibFoundation.Mathematics.Vector3f cenMassPtB
Stores the blue center of mass of the contour of a VOI.

doName

boolean doName
DOCUMENT ME!

fixed

boolean fixed
Flag that indicates if the VOI is movable.

label

String label
Label (Name) for this member of the VOI.

lastPoint

int lastPoint
Keeps track of the last near point value (for keyboard moving of individual pts.

name

String name
VOI Name (for group of contours, not specific to this base).

nearPoint

int nearPoint
Flag used to inidicate if the cursor is near a point of the VOI member.

red

Color red
General use color (red) used in VOI.

white

Color white
General use color (white) used in VOI.

Class gov.nih.mipav.model.structures.VOICardiology extends VOIBase implements Serializable

serialVersionUID: -2406308173924990457L

Serialized Fields

activeArray

boolean[] activeArray
DOCUMENT ME!

centerPt

VOICardiology.CardioVector3f centerPt
DOCUMENT ME!

closed

boolean closed
Indicates whether or not the contour is closed.

flagRetrace

boolean flagRetrace
DOCUMENT ME!

indexRetrace

int indexRetrace
These four variables are used in the retrace mode of the Contour.

infarctionGons

Polygon[] infarctionGons
DOCUMENT ME!

nearBoundPoint

int nearBoundPoint
Saves the vertex point of bounding box. See nearBoundPoint method in this class.

numInfarctions

int numInfarctions
DOCUMENT ME!

numPixels

int numPixels
Number of pixels in the array used in graphing intensity along the boundary.

numSections

int numSections
DOCUMENT ME!

oldContour

VOIContour oldContour
DOCUMENT ME!

showCenter

boolean showCenter
DOCUMENT ME!

showPoints

boolean showPoints
DOCUMENT ME!

wholeInfarction

VOIContour wholeInfarction
DOCUMENT ME!

xBounds

float[] xBounds
Stores the x coordinates for the bounding box. The upper left corner and the lower right corner, respectively.

xPts

float[] xPts
Used in contains method so that memory doesn't constantly need to be reallocated.

yBounds

float[] yBounds
Stores the y coordinates for the bounding box. The upper left corner and the lower right corner, respectively.

yPts

float[] yPts
Used in contains method so that memory doesn't constantly need to be reallocated.

zBounds

float[] zBounds
Stores the z coordinates for the bounding box. The upper left corner and the lower right corner, respectively.

Class gov.nih.mipav.model.structures.VOICardiology.CardioVector3f extends WildMagic.LibFoundation.Mathematics.Vector3f implements Serializable

serialVersionUID: -8047244892701374896L

Serialized Fields

intersection

boolean intersection
DOCUMENT ME!

isShared

boolean isShared
DOCUMENT ME!

sectionNum

int sectionNum
DOCUMENT ME!

type

int type
DOCUMENT ME!

Class gov.nih.mipav.model.structures.VOIContour extends VOIBase implements Serializable

serialVersionUID: -6479418081230834617L

Serialized Fields

closed

boolean closed
Indicates whether or not the contour is closed.

flagRetrace

boolean flagRetrace
DOCUMENT ME!

indexRetrace

int indexRetrace
These four variables are used in the retrace mode of the Contour.

nearBoundPoint

int nearBoundPoint
Saves the vertex point of bounding box. See nearBoundPoint method in this class.

numPixels

int numPixels
Number of pixels in the array used in graphing intensity along the boundary.

oldContour

VOIContour oldContour
DOCUMENT ME!

xBounds

float[] xBounds
Stores the x coordinates for the bounding box. The upper left corner and the lower right corner, respectively.

xPts

float[] xPts
Used in contains method so that memory doesn't constantly need to be reallocated.

yBounds

float[] yBounds
Stores the y coordinates for the bounding box. The upper left corner and the lower right corner, respectively.

yPts

float[] yPts
Used in contains method so that memory doesn't constantly need to be reallocated.

zBounds

float[] zBounds
Stores the z coordinates for the bounding box. The upper left corner and the lower right corner, respectively.

doGeometricCenterLabel

boolean doGeometricCenterLabel
If doGeometricCenterLabel = true and if active == false and if closed = true, execute drawGeometricCenterLabel when in drawSelf

Class gov.nih.mipav.model.structures.VOILine extends VOIBase implements Serializable

serialVersionUID: -2836164853862289329L

Serialized Fields

coordinates

float[] coordinates
Scratch buffer to speed access.

coords

float[] coords
Scratch buffer to speed access.

theta

double theta
Angle of line.

x

float[] x
Scratch buffers that are allocated once at construction to speed access. stores the x coordinate of the two end points.

xDim

int xDim
X Dimension of the image.

y

float[] y
Scratch buffers that are allocated once at construction to speed access. stores the y coordinate of the two end points.

yDim

int yDim
Y Dimension of the image.

z

float[] z
Scratch buffers that are allocated once at construction to speed access. stores the z coordinate of the two end points.

Class gov.nih.mipav.model.structures.VOIPoint extends VOIBase implements Serializable

Serialized Fields

str

String str
Label of the point (e.g. 1, or 2 or 3... )

isPolySlice

boolean isPolySlice
True if this point is part of a Polyline_Slice structure

firstSlicePoint

boolean firstSlicePoint
True if this point is the 1st point in a slice/frame of Polyline_Slice

totalDistanceString

String totalDistanceString
Distance is calculated and passed in by VOI for polyline_slices

distanceString

String distanceString
Distance between segments shown only for active point in polyline_slices

isActivePoint

boolean isActivePoint
True only for the active point of a polyline_slice structure (display's coordinates)

Class gov.nih.mipav.model.structures.VOIProtractor extends VOIBase implements Serializable

serialVersionUID: 4213485128976585397L

Serialized Fields

color

Color color
Color of the protractor.

coordinates

float[] coordinates
Stores coordinates of protractor to speed the process of access.

coords

float[] coords
Stores coordinates of protractor to speed the process of access.

seg1Length

float seg1Length
Length of first protractor segment.

showLength

boolean showLength
DOCUMENT ME!

snap

boolean snap
First segment of PROTRACTOR snaps into horizontal or vertical on mouseRelease.

theta

double theta
Angle of first protractor segment with respect to x axis.

theta2

double theta2
Angle of second protractor segment with respect to first.

xDim

int xDim
X dimension of the image where the protractor is displayed.

xPts

float[] xPts
Used in contains method. Memory allocated once here as a class variable.

yDim

int yDim
Y dimension of the image where the protractor is displayed.

yPts

float[] yPts
Used in contains method. Memory allocated once here as a class variable.

Class gov.nih.mipav.model.structures.VOIText extends VOIBase implements Serializable

serialVersionUID: -6408262409409720727L

Serialized Fields

fontDescriptors

int fontDescriptors
The descriptors for the font which start at PLAIN and are additive (PLAIN + BOLD = bold) (BOLD+ITALIC = bold and italic) etc.

fontName

String fontName
The name (or type) of the font.

fontSize

int fontSize
The size of the font (half-sizes not allowed...int).

origin

float[] origin
not used except as dummy float.

textColor

Color textColor
This must be kept separate (but parallel) to the VOI color.

backgroundColor

Color backgroundColor
The color used to draw behind the main text (so that the text will stand out)

textFont

Font textFont
The font is stored here so that it does not have to be reallocated on each redraw. It is only new'd at the beginning or if the fontDescriptors variable changes

textString

String textString
The String to be displayed.

noteString

String noteString
The note stored in VOIText, has same font as textString

useMarker

boolean useMarker
If this is set to true, a draggable arrow will be displayed

Class gov.nih.mipav.model.structures.VOIVector extends ViewVOIVector implements Serializable

serialVersionUID: -7391734288216133947L

Serialized Fields

listenerList

EventListenerList listenerList
holds all interfaces listening to this vector.

voiUpdate

VOIVectorEvent voiUpdate
an instnace of the VOI update event.

Package gov.nih.mipav.model.structures.event

Class gov.nih.mipav.model.structures.event.VOIEvent extends EventObject implements Serializable

serialVersionUID: -5542473955796520517L

Serialized Fields

mostRecentUpdate

VOIBase mostRecentUpdate
holds reference because referring to a VOI held by the ViewVOIVector would cause all kinds of memory clean-up concerns. may be null.

Class gov.nih.mipav.model.structures.event.VOIVectorEvent extends EventObject implements Serializable

serialVersionUID: -2033500015284877824L

Serialized Fields

mostRecentUpdate

VOI mostRecentUpdate
holds reference because referring to a VOI held by the ViewVOIVector would cause all kinds of memory clean-up concerns. may be null.

Package gov.nih.mipav.model.structures.jama

Class gov.nih.mipav.model.structures.jama.GeneralizedEigenvalue extends Object implements Serializable

serialVersionUID: 3809017135250813360L

Serialized Fields

base

double base
DOCUMENT ME!

emax

double emax
DOCUMENT ME!

emin

double emin
DOCUMENT ME!

eps

double eps
DOCUMENT ME!

first

boolean first
------------------------ Class variables ------------------------ Double precision machine parameters found in routine dlamch.

first_dlartg

boolean first_dlartg
Double precison machine variables found in routine dlartg.

iparms

int[] iparms
DOCUMENT ME!

prec

double prec
DOCUMENT ME!

rmax

double rmax
DOCUMENT ME!

rmin

double rmin
DOCUMENT ME!

rnd

double rnd
DOCUMENT ME!

safmin

double safmin
DOCUMENT ME!

safmn2

double safmn2
DOCUMENT ME!

safmx2

double safmx2
DOCUMENT ME!

sfmin

double sfmin
DOCUMENT ME!

t

double t
DOCUMENT ME!

UI

ViewUserInterface UI
Common variables in testing routines.

Package gov.nih.mipav.plugins

Class gov.nih.mipav.plugins.JDialogStandalonePlugin extends JDialogBase implements Serializable

Class gov.nih.mipav.plugins.JDialogStandaloneScriptablePlugin extends JDialogScriptableBase implements Serializable

Package gov.nih.mipav.view

Class gov.nih.mipav.view.AlternatingTableCellRenderer extends DefaultTableCellRenderer implements Serializable

serialVersionUID: 3028551564787955672L

Serialized Fields

alternateRowCount

int alternateRowCount
DOCUMENT ME!

color1

Color color1
DOCUMENT ME!

color2

Color color2
DOCUMENT ME!

Class gov.nih.mipav.view.BarMeter extends JPanel implements Serializable

serialVersionUID: -560671300642650806L

Serialized Fields

boxHeight

int boxHeight
DOCUMENT ME!

boxWidth

int boxWidth
DOCUMENT ME!

g2d

Graphics2D g2d
DOCUMENT ME!

h

int h
DOCUMENT ME!

img

BufferedImage img
DOCUMENT ME!

unusedColor

Color unusedColor
DOCUMENT ME!

unusedRect

Rectangle2D unusedRect
DOCUMENT ME!

usedColor

Color usedColor
DOCUMENT ME!

usedRect

Rectangle2D usedRect
DOCUMENT ME!

w

int w
DOCUMENT ME!

whitespaceH

int whitespaceH
DOCUMENT ME!

whitespaceW

int whitespaceW
DOCUMENT ME!

amplitude

int amplitude
DOCUMENT ME!

divisions

int divisions
DOCUMENT ME!

Class gov.nih.mipav.view.BorderedButton extends JButton implements Serializable

serialVersionUID: -5566213886996905888L

Serialized Fields

borderColor

Color borderColor
DOCUMENT ME!

borderOn

boolean borderOn
DOCUMENT ME!

Class gov.nih.mipav.view.ColorIcon extends ModelSerialCloneable implements Serializable

Serialized Fields

color

Color color
DOCUMENT ME!

w

int w
DOCUMENT ME!

h

int h
DOCUMENT ME!

Class gov.nih.mipav.view.ColorWheel extends Canvas implements Serializable

Serialized Fields

offImage

Image offImage
offscreen image

offGraphics

Graphics offGraphics
offscreen graphics handle

r1

int r1
radii of all the circles...r6 is the outermost radius

r2

int r2
radii of all the circles...r6 is the outermost radius

r3

int r3
radii of all the circles...r6 is the outermost radius

r4

int r4
radii of all the circles...r6 is the outermost radius

r5

int r5
radii of all the circles...r6 is the outermost radius

r6

int r6
radii of all the circles...r6 is the outermost radius

type

String type
type of color wheel ABSVAL, NOSYMM, ROTATIONALSYMM, MIRRORSYMM

pS

float pS
sat vs theta

pC

float pC
color range

pB

float pB
blue saturation

gamma

float gamma
gamma correction

pG

float pG
green adj

stevensBeta

float stevensBeta
Stevens Beta

blueShiftColors

float[] blueShiftColors
array of r,g,b values after blue shifting

redShiftColors

float[] redShiftColors
array of r,g,b values after red shifting

greenAdjColors

float[] greenAdjColors
array of r,g,b values after green adj

Class gov.nih.mipav.view.DICOMDisplayer extends JTable implements Serializable

serialVersionUID: -3693967365082796271L

Serialized Fields

columnNames

String[] columnNames
DOCUMENT ME!

model

ViewTableModel model
DOCUMENT ME!

Class gov.nih.mipav.view.JPanelAnonymizeImage extends JPanelChecklist implements Serializable

serialVersionUID: -2842282459266721252L

Serialized Fields

dicomInfo

FileInfoDicom dicomInfo
all the tags that contain personal info:.

mincInfo

FileInfoMinc mincInfo
DOCUMENT ME!

Class gov.nih.mipav.view.JPanelChecklist extends JPanel implements Serializable

serialVersionUID: -6168461302590312089L

Serialized Fields

checkboxLabels

String[] checkboxLabels
must be same size as listLength.

checkboxList

JCheckBox[] checkboxList
DOCUMENT ME!

checkboxPanel

JPanel checkboxPanel
DOCUMENT ME!

checkButton

JButton checkButton
DOCUMENT ME!

chkUnchkPanel

JPanel chkUnchkPanel
DOCUMENT ME!

listLength

int listLength
must be given a nonzero number on instantiation. must be of same size as checkboxLabels.

removeList

boolean[] removeList
notice that for the next two lists, ith entry on one corresponds to the ith entry on the other. the entire list of choices possible.

scrollPane

JScrollPane scrollPane
DOCUMENT ME!

unCheckButton

JButton unCheckButton
DOCUMENT ME!

visibleList

boolean[] visibleList
the list of the choices that can be selected.

Class gov.nih.mipav.view.JPanelEdit extends JPanel implements Serializable

serialVersionUID: -8206200502096634672L

Serialized Fields

errorComponent

Component errorComponent
when necessary To CheckFields, and there is a problem with the panel such that a valid panel value cannot be made, the particular component which has a bad value will be pointed to here.

errorString

String errorString
when necessary To CheckFields, and there is a problem with the panel such that a valid panel value cannot be made, the problem will be reported in this String.

propertyName

String propertyName
A changable property name for firing PropertyChangeEvents. A panel has but one unique property associated with it, that is the file it references, but in a situation where more than one such panel may be listened to by a PropertyChangeListener, each of these panels may be given a unique name to help the Listener. Be careful when using this feature, however, because if there is more than one listener which is interested in changes in the PropertyChangeEvent, changing the property name will cause conflicts (and likely ignored events).

Class gov.nih.mipav.view.JPanelEditAxisOrientation extends JPanelEdit implements Serializable

serialVersionUID: -6931501818687637674L

Serialized Fields

orientationBox

JComboBox orientationBox
DOCUMENT ME!

Class gov.nih.mipav.view.JPanelEditBoolean extends JPanelEdit implements Serializable

serialVersionUID: 6795672926611666135L

Serialized Fields

booleanBox

JComboBox booleanBox
DOCUMENT ME!

Class gov.nih.mipav.view.JPanelEditChar extends JPanelEdit implements Serializable

serialVersionUID: 216110617521213885L

Serialized Fields

editTextField

JTextField editTextField
DOCUMENT ME!

Class gov.nih.mipav.view.JPanelEditDate extends JPanelEdit implements Serializable

serialVersionUID: 3504702516257604573L

Serialized Fields

dayCombobox

JComboBox dayCombobox
DOCUMENT ME!

monthCombobox

JComboBox monthCombobox
DOCUMENT ME!

noFutureDates

boolean noFutureDates
DOCUMENT ME!

noPastDates

boolean noPastDates
DOCUMENT ME!

xml

boolean xml
DOCUMENT ME!

yearTextField

JTextField yearTextField
DOCUMENT ME!

Class gov.nih.mipav.view.JPanelEditDefault extends JPanelEdit implements Serializable

serialVersionUID: -2218748402204415345L

Serialized Fields

maxLength

int maxLength
DOCUMENT ME!

editTextField

JTextField editTextField
DOCUMENT ME!

Class gov.nih.mipav.view.JPanelEditImageOrientation extends JPanelEdit implements Serializable

serialVersionUID: 155707351575492439L

Serialized Fields

orientationBox

JComboBox orientationBox
DOCUMENT ME!

Class gov.nih.mipav.view.JPanelEditModality extends JPanelEdit implements Serializable

serialVersionUID: -7456502877292143209L

Serialized Fields

modalityBox

JComboBox modalityBox
DOCUMENT ME!

Class gov.nih.mipav.view.JPanelEditOrientation extends JPanelEdit implements Serializable

serialVersionUID: -2127377398183049555L

Serialized Fields

orientationBox

JComboBox orientationBox
DOCUMENT ME!

Class gov.nih.mipav.view.JPanelEditRace extends JPanelEdit implements Serializable

serialVersionUID: 6499425054292194113L

Serialized Fields

raceBox

JComboBox raceBox
DOCUMENT ME!

Class gov.nih.mipav.view.JPanelEditSetOrParam extends JPanelEdit implements Serializable

serialVersionUID: 2261232133976028312L

Serialized Fields

maxLength

int maxLength
DOCUMENT ME!

editTextField

JTextField editTextField
DOCUMENT ME!

isSet

boolean isSet
DOCUMENT ME!

table

Hashtable<K,V> table
DOCUMENT ME!

Class gov.nih.mipav.view.JPanelEditSex extends JPanelEdit implements Serializable

serialVersionUID: -3767740357915707674L

Serialized Fields

sexComboBox

JComboBox sexComboBox
DOCUMENT ME!

Class gov.nih.mipav.view.JPanelEditTime extends JPanelEdit implements Serializable

serialVersionUID: -1541002811257405137L

Serialized Fields

secFraction

JTextField secFraction
DOCUMENT ME!

secCheckBox

JCheckBox secCheckBox
permits whether or not to set this field.

minCheckBox

JCheckBox minCheckBox
permits whether or not to set this field.

hourCheckBox

JCheckBox hourCheckBox
permits whether or not to set this field.

secComboBox

JComboBox secComboBox
value to add to this time field.

minComboBox

JComboBox minComboBox
value to add to this time field.

hourComboBox

JComboBox hourComboBox
value to add to this time field.

xml

boolean xml
DOCUMENT ME!

Class gov.nih.mipav.view.JPanelEditValueType extends JPanelEdit implements Serializable

serialVersionUID: 2306780604257062424L

Serialized Fields

valueTypeBox

JComboBox valueTypeBox
DOCUMENT ME!

Class gov.nih.mipav.view.JPanelFileSelection extends JPanelEdit implements Serializable

serialVersionUID: 5350976001384182834L

Serialized Fields

chooser

JFileChooser chooser
DOCUMENT ME!

chosenFile

File chosenFile
DOCUMENT ME!

fileBrowse

JButton fileBrowse
DOCUMENT ME!

fileTextField

JTextField fileTextField
DOCUMENT ME!

imageInfo

boolean imageInfo
DOCUMENT ME!

Class gov.nih.mipav.view.JPanelListController extends JPanel implements Serializable

serialVersionUID: -3060198445145485002L

Serialized Fields

listA

JList listA
upper or left-most list.

listB

JList listB
lower or right-most list.

deleteSelection

JButton deleteSelection
'X'.

listLayout

int listLayout
DOCUMENT ME!

sendAllToListA

JButton sendAllToListA
DOCUMENT ME!

sendAllToListB

JButton sendAllToListB
DOCUMENT ME!

sendSelectionToListA

JButton sendSelectionToListA
left arrow or up arrow.

sendSelectionToListB

JButton sendSelectionToListB
right arrow or down arrow.

Class gov.nih.mipav.view.JPanelProgressBar extends JPanel implements Serializable

serialVersionUID: -6963733511040621440L

Serialized Fields

pBar

JProgressBar pBar
Actual bar which fills with color as the percentage of completion increases.

Class gov.nih.mipav.view.JPanelStatisticsList extends JPanelChecklist implements Serializable

serialVersionUID: -5517669600349449423L

Serialized Fields

singleSlice

boolean singleSlice
just so the thing is non-null.

Class gov.nih.mipav.view.JVOIChecklist extends JPanel implements Serializable

serialVersionUID: 1481985505949073115L

Serialized Fields

list

JList list
DOCUMENT ME!

Class gov.nih.mipav.view.LineMeter extends JPanel implements Serializable

serialVersionUID: -7794163419733734911L

Serialized Fields

amplitude

int amplitude
DOCUMENT ME!

animationCycle

int animationCycle
DOCUMENT ME!

animationFrame

int animationFrame
DOCUMENT ME!

animationThread

Thread animationThread
monitor animation happens in its own thread.

aniSampleRate

int aniSampleRate
DOCUMENT ME!

chartWidth

int chartWidth
DOCUMENT ME!

chartHeight

int chartHeight
DOCUMENT ME!

chartXend

int chartXend
DOCUMENT ME!

chartYend

int chartYend
DOCUMENT ME!

chartXstart

int chartXstart
DOCUMENT ME!

chartYstart

int chartYstart
DOCUMENT ME!

counterLock

boolean counterLock
DOCUMENT ME!

countSinceLastUpdate

int countSinceLastUpdate
DOCUMENT ME!

dim

Dimension dim
DOCUMENT ME!

divisions

int divisions
DOCUMENT ME!

drawingWidth

int drawingWidth
DOCUMENT ME!

drawingHeight

int drawingHeight
DOCUMENT ME!

g2d

Graphics2D g2d
DOCUMENT ME!

graphLine

Line2D graphLine
DOCUMENT ME!

horizImg

BufferedImage horizImg
DOCUMENT ME!

horizLine

Line2D horizLine
DOCUMENT ME!

insets

Insets insets
DOCUMENT ME!

lineColor

Color lineColor
DOCUMENT ME!

lineSpacing

int lineSpacing
DOCUMENT ME!

numberOfDivisions

int numberOfDivisions
DOCUMENT ME!

numberOfSamplesDisplayed

int numberOfSamplesDisplayed
DOCUMENT ME!

numberOfSamplesPerDivision

int numberOfSamplesPerDivision
DOCUMENT ME!

panelWidth

int panelWidth
DOCUMENT ME!

panelHeight

int panelHeight
DOCUMENT ME!

paperColor

Color paperColor
DOCUMENT ME!

penColor

Color penColor
DOCUMENT ME!

pixelsPerDivision

int pixelsPerDivision
DOCUMENT ME!

pixelsWidePerSample

int pixelsWidePerSample
DOCUMENT ME!

recentSamples

float[] recentSamples
DOCUMENT ME!

sampleRate

int sampleRate
DOCUMENT ME!

samplesPerUpdate

int samplesPerUpdate
DOCUMENT ME!

vertLine

Line2D vertLine
DOCUMENT ME!

w

int w
DOCUMENT ME!

h

int h
DOCUMENT ME!

whitespaceH

int whitespaceH
DOCUMENT ME!

whitespaceW

int whitespaceW
DOCUMENT ME!

yLocHistory

float[] yLocHistory
DOCUMENT ME!

Class gov.nih.mipav.view.MIPAVTableCellRenderer extends DefaultTableCellRenderer implements Serializable

serialVersionUID: 2587142275980890594L

Class gov.nih.mipav.view.MipavUtil extends JComponent implements Serializable

serialVersionUID: 4180127127881019813L

Class gov.nih.mipav.view.ProgressChangeEvent extends ChangeEvent implements Serializable

Serialized Fields

message

String message
The message which will be shown with the progress bar

title

String title
The title of the progress dialog

value

int value
The value of the progress bar, the range is from 0~100

Class gov.nih.mipav.view.Rubberband extends Component implements Serializable

serialVersionUID: 7016153369248687772L

Serialized Fields

anchorPt

Point anchorPt
DOCUMENT ME!

component

Component component
DOCUMENT ME!

endPt

Point endPt
DOCUMENT ME!

lastPt

Point lastPt
DOCUMENT ME!

presetHue

float presetHue
DOCUMENT ME!

stretchedPt

Point stretchedPt
DOCUMENT ME!

usableComponent

boolean usableComponent
DOCUMENT ME!

xMax

int xMax
DOCUMENT ME!

xS

int xS
DOCUMENT ME!

yMax

int yMax
DOCUMENT ME!

yS

int yS
DOCUMENT ME!

active

boolean active
DOCUMENT ME!

firstStretch

boolean firstStretch
DOCUMENT ME!

Class gov.nih.mipav.view.RubberbandEllipse extends Rubberband implements Serializable

serialVersionUID: -3765430195677943807L

Serialized Fields

endAngle

int endAngle
DOCUMENT ME!

startAngle

int startAngle
DOCUMENT ME!

Class gov.nih.mipav.view.RubberbandLine extends Rubberband implements Serializable

serialVersionUID: 6355805256478756437L

Serialized Fields

x

int[] x
DOCUMENT ME!

y

int[] y
DOCUMENT ME!

z

int[] z
DOCUMENT ME!

doSplit

boolean doSplit
boolean for if this is a VOI Splitter (not line drawer)

Class gov.nih.mipav.view.RubberbandLivewire extends Rubberband implements Serializable

serialVersionUID: -2803229062633426608L

Serialized Fields

currContourCost

float currContourCost
DOCUMENT ME!

prevContourCost

float prevContourCost
DOCUMENT ME!

prevXPoints

float[] prevXPoints
DOCUMENT ME!

prevYPoints

float[] prevYPoints
DOCUMENT ME!

progressBar

ViewJProgressBar progressBar
DOCUMENT ME!

activeTree

gov.nih.mipav.view.RubberbandLivewire.ActiveTree activeTree
DOCUMENT ME!

clickPoints

Vector<E> clickPoints
DOCUMENT ME!

contour

VOIContour contour
DOCUMENT ME!

costGraph

byte[] costGraph
DOCUMENT ME!

count

int count
DOCUMENT ME!

firstPoint

boolean firstPoint
DOCUMENT ME!

grad_weight

float grad_weight
DOCUMENT ME!

localCosts

float[] localCosts
DOCUMENT ME!

mod

int mod
DOCUMENT ME!

presetHue

float presetHue
DOCUMENT ME!

processedIndicies

BitSet processedIndicies
DOCUMENT ME!

seededCosts

float[] seededCosts
DOCUMENT ME!

seedPoint

int seedPoint
DOCUMENT ME!

selection

int selection
DOCUMENT ME!

smoothVOIFlag

boolean smoothVOIFlag
DOCUMENT ME!

tmpPt

Point tmpPt
DOCUMENT ME!

waitCursor

Cursor waitCursor
DOCUMENT ME!

xDim

int xDim
DOCUMENT ME!

yDim

int yDim
DOCUMENT ME!

xDirections

float[] xDirections
DOCUMENT ME!

xPoints

float[] xPoints
DOCUMENT ME!

xPointsDraw

int[] xPointsDraw
DOCUMENT ME!

yDirections

float[] yDirections
DOCUMENT ME!

yPoints

float[] yPoints
DOCUMENT ME!

yPointsDraw

int[] yPointsDraw
DOCUMENT ME!

Class gov.nih.mipav.view.RubberbandPolyline extends Rubberband implements Serializable

serialVersionUID: -9153642132322433825L

Serialized Fields

contour

VOIContour contour
DOCUMENT ME!

cpt

WildMagic.LibFoundation.Mathematics.Vector3f cpt
DOCUMENT ME!

firstPoint

boolean firstPoint
DOCUMENT ME!

mouseDragged

boolean mouseDragged
DOCUMENT ME!

tmpPt

Point tmpPt
DOCUMENT ME!

Class gov.nih.mipav.view.RubberbandProtractor extends Rubberband implements Serializable

serialVersionUID: 808272437770323870L

Serialized Fields

x

int[] x
DOCUMENT ME!

y

int[] y
DOCUMENT ME!

z

int[] z
DOCUMENT ME!

Class gov.nih.mipav.view.RubberbandRectangle extends Rubberband implements Serializable

serialVersionUID: -6519290525624847778L

Class gov.nih.mipav.view.RubberbandRectangleVOI extends RubberbandRectangle implements Serializable

serialVersionUID: 3071762927070207288L

Class gov.nih.mipav.view.ViewControlsImage extends JPanel implements Serializable

serialVersionUID: 3317301000984234468L

Serialized Fields

alphaSlider

JSlider alphaSlider
DOCUMENT ME!

borderActiveImage

TitledBorder borderActiveImage
DOCUMENT ME!

borderImageSlider

TitledBorder borderImageSlider
DOCUMENT ME!

frame

ViewJFrameBase frame
DOCUMENT ME!

gbc

GridBagConstraints gbc
DOCUMENT ME!

generalPanel

JPanel generalPanel
DOCUMENT ME!

group1

ButtonGroup group1
DOCUMENT ME!

imageSize

int imageSize
DOCUMENT ME!

majorSpacing

int majorSpacing
JSlider.majorSpacing/minorSpacing.

minorSpacing

int minorSpacing
DOCUMENT ME!

paintToolBar

JToolBar paintToolBar
Paint toolbar.

panelActiveImage

JPanel panelActiveImage
DOCUMENT ME!

panelImageSlider

JPanel panelImageSlider
DOCUMENT ME!

panelOptionToolbars

JPanel panelOptionToolbars
DOCUMENT ME!

panelToolbars

JPanel panelToolbars
DOCUMENT ME!

radioImageA

JRadioButton radioImageA
DOCUMENT ME!

radioImageB

JRadioButton radioImageB
DOCUMENT ME!

registrationToolBar

JToolBar registrationToolBar
Registration toolbar.

scriptToolBar

JToolBar scriptToolBar
DOCUMENT ME!

sliderResolutionInt

int sliderResolutionInt
the slice slider is a JSlider defining an integer number of steps. That number of steps is given by sliderResolution. Although the major&minor tick marks will not necessarily align with any particular slice, there is built-in ability to have the tick-marks correspond to a particular percentage of an image set. ie, distance between each major tick will represent 1/10 of image-set, and the minor ticks will be 1/5 of that 1/10. Should the number of slices the slider must refer to be larger than the resolution the slider will not always refer to the correct slice when moved.

sliderResolutionFloat

float sliderResolutionFloat
DOCUMENT ME!

tImageSlider

JSlider tImageSlider
DOCUMENT ME!

tImageSliderDictionary

Hashtable<K,V> tImageSliderDictionary
DOCUMENT ME!

toolBar

JToolBar toolBar
Main toolbar .

toolBarObj

ViewToolBarBuilder toolBarObj
Object builds and controls the toolbars.

zImageSlider

JSlider zImageSlider
DOCUMENT ME!

zImageSliderDictionary

Hashtable<K,V> zImageSliderDictionary
DOCUMENT ME!

Class gov.nih.mipav.view.ViewDICOMDoubleListPanel extends ViewSelectableDoubleListPanel implements Serializable

serialVersionUID: 3583232599838861716L

Serialized Fields

btnMoveDown

JButton btnMoveDown
DOCUMENT ME!

btnMoveUp

JButton btnMoveUp
DOCUMENT ME!

leftTableModel

SortingTableModel leftTableModel
DOCUMENT ME!

leftTableSorter

TableSorter leftTableSorter
DOCUMENT ME!

rightTableModel

SortingTableModel rightTableModel
DOCUMENT ME!

rightTableSorter

TableSorter rightTableSorter
DOCUMENT ME!

Class gov.nih.mipav.view.ViewFileChooserSubsample extends JFileChooser implements Serializable

serialVersionUID: -5946259539592286508L

Serialized Fields

chkSave

JCheckBox chkSave
DOCUMENT ME!

txtResampleHeight

JTextField txtResampleHeight
DOCUMENT ME!

txtResampleWidth

JTextField txtResampleWidth
DOCUMENT ME!

Class gov.nih.mipav.view.ViewFileTreeNode extends DefaultMutableTreeNode implements Serializable

serialVersionUID: 2761808148905905365L

Serialized Fields

directoriesOnly

boolean directoriesOnly
DOCUMENT ME!

explored

boolean explored
DOCUMENT ME!

rootfile

boolean rootfile
DOCUMENT ME!

Class gov.nih.mipav.view.ViewImageDirectory extends JFrame implements Serializable

serialVersionUID: -1262294439731204344L

Serialized Fields

directory

String directory
DOCUMENT ME!

directoryTree

JTree directoryTree
DOCUMENT ME!

file

File file
DOCUMENT ME!

imageFilter

ViewImageFileFilter imageFilter
DOCUMENT ME!

imagePanel

JPanel imagePanel
DOCUMENT ME!

img

ViewJComponentPreviewImage img
DOCUMENT ME!

node

ViewFileTreeNode node
DOCUMENT ME!

serif12

Font serif12
DOCUMENT ME!

serif12B

Font serif12B
DOCUMENT ME!

thumbnail

FileImageXML.Thumbnail thumbnail
DOCUMENT ME!

treePanel

JPanel treePanel
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

brightness

int brightness
DOCUMENT ME!

brightPanel

JPanel brightPanel
DOCUMENT ME!

brightSlider

JSlider brightSlider
DOCUMENT ME!

contSlider

JSlider contSlider
DOCUMENT ME!

contrast

float contrast
DOCUMENT ME!

current

JLabel current
DOCUMENT ME!

current2

JLabel current2
DOCUMENT ME!

defaultImageSize

Dimension defaultImageSize
DOCUMENT ME!

imageSliderPane

JSplitPane imageSliderPane
DOCUMENT ME!

nfc

NumberFormat nfc
DOCUMENT ME!

openSeparate

boolean openSeparate
DOCUMENT ME!

openSeparateOption

JCheckBoxMenuItem openSeparateOption
DOCUMENT ME!

origBrightness

int origBrightness
DOCUMENT ME!

origContrast

float origContrast
DOCUMENT ME!

otherLabel

JLabel otherLabel
DOCUMENT ME!

placeHolder

JPanel placeHolder
DOCUMENT ME!

primaryModel

ViewTableModel primaryModel
DOCUMENT ME!

primaryTable

JTable primaryTable
DOCUMENT ME!

secondaryModel

ViewTableModel secondaryModel
DOCUMENT ME!

secondaryTable

JTable secondaryTable
DOCUMENT ME!

shift

boolean shift
DOCUMENT ME!

showXMLThumbnail

boolean showXMLThumbnail
DOCUMENT ME!

sliderPanel

JPanel sliderPanel
DOCUMENT ME!

thumbnailOption

JCheckBoxMenuItem thumbnailOption
DOCUMENT ME!

Class gov.nih.mipav.view.ViewJColorChooser extends JColorChooser implements Serializable

serialVersionUID: -7062915703384786855L

Serialized Fields

colorDialog

JDialog colorDialog
DOCUMENT ME!

Class gov.nih.mipav.view.ViewJComponentAnimate extends ViewJComponentBase implements Serializable

serialVersionUID: -2707021974594065054L

Serialized Fields

OPACITY

float OPACITY
Opacity value used by the paint brush. value = 1.0 - opaque value = 0.25 - default (mostly see through)

alphaBlend

float alphaBlend
alphaBlending values for compositing two images.

frame

ViewJFrameBase frame
frame - frame where the component image is displayed.

imageA

ModelImage imageA
imageA - model for image A.

imageB

ModelImage imageB
imageB - model for image B.

img

Image[] img
the image rendered in 2D graphics:

paintImageBuffer

int[] paintImageBuffer

slice

int slice
current slice for 3D images:

brightness

int brightness
offset ranging from -255 to 255 add to each scaled red, green, and blue

contrast

float contrast
scale factor ranging from 0.1 to 10.0 by which to multiply each red, green, and blue

disposeImage

boolean disposeImage
whether or not to dispose of imageA and imageB true unless ViewJFrameAnimate was passed an unscaled 3D image

haveFiltered

boolean haveFiltered
whether or not the brightness/contrast filter has been invoked

ignoreSlice

boolean[] ignoreSlice
set true if deleteSlice hit in ViewJFrameAnimate

imageActive

ModelImage imageActive
Which image is currently active

mt

MediaTracker mt
DOCUMENT ME!

nRow

int nRow
in 4D row and column numbers for z slices

nColumn

int nColumn
in 4D row and column numbers for z slices

nVOI

int nVOI
number of vois

originalZDim

int originalZDim
the number of z slices in a 4D image equal to zDim before the JDialogAnimate 4D to 3D conversion

paintBitmap

BitSet paintBitmap
Buffer used to indicate if the pixel location is painted (true) or unpainted (false).

paintBuffer

int[] paintBuffer
Buffer that displays the combined paintBitmap and pixBuffer buffers.

red

int red
Border color, red, green, and blue components:

green

int green
Border color, red, green, and blue components:

blue

int blue
Border color, red, green, and blue components:

showNumbers

boolean showNumbers
whether to number each z slice for 4D

VOIs

ViewVOIVector VOIs
DOCUMENT ME!

xDim

int xDim
image x, y, z dimensions in FileCoordinates

yDim

int yDim
image x, y, z dimensions in FileCoordinates

zDim

int zDim
image x, y, z dimensions in FileCoordinates

xLabel

int[] xLabel
in 4D x location of slice numbering string

yLabel

int[] yLabel
in 4D y location of slice numbering string

zString

String[] zString
string for displaying slice number

m_kPatientSlice

PatientSlice m_kPatientSlice
PatientSlice contains all the Patient Coordinate system view-specific data for rendering this component:

Class gov.nih.mipav.view.ViewJComponentAnimateClip extends ViewJComponentBase implements Serializable

serialVersionUID: -3162752418756566668L

Serialized Fields

OPACITY

float OPACITY
Opacity value used by the paint brush. value = 1.0 - opaque value = 0.25 - default (mostly see through)

alphaBlend

float alphaBlend
alphaBlending values for compositing two images.

alphaPrime

float alphaPrime
DOCUMENT ME!

img

Image[] img
DOCUMENT ME!

interpMode

int interpMode
DOCUMENT ME!

mode

int mode
mode - used to describe the cursor mode.

slice

int slice
DOCUMENT ME!

string

String string
DOCUMENT ME!

time

long time
DOCUMENT ME!

timeSlice

int timeSlice
DOCUMENT ME!

copy

BufferedImage copy
DOCUMENT ME!

ignoreSlice

boolean[] ignoreSlice
DOCUMENT ME!

mt

MediaTracker mt
DOCUMENT ME!

nRow

int nRow
DOCUMENT ME!

nColumn

int nColumn
DOCUMENT ME!

originalZDim

int originalZDim
DOCUMENT ME!

red

int red
DOCUMENT ME!

green

int green
DOCUMENT ME!

blue

int blue
DOCUMENT ME!

resX

float resX
DOCUMENT ME!

resY

float resY
DOCUMENT ME!

showNumbers

boolean showNumbers
DOCUMENT ME!

showSliceNumber

boolean showSliceNumber
DOCUMENT ME!

xDim

int xDim
DOCUMENT ME!

yDim

int yDim
DOCUMENT ME!

zDim

int zDim
DOCUMENT ME!

xLabel

int[] xLabel
DOCUMENT ME!

yLabel

int[] yLabel
DOCUMENT ME!

zoomX

float zoomX
DOCUMENT ME!

zoomY

float zoomY
DOCUMENT ME!

zString

String[] zString
DOCUMENT ME!

Class gov.nih.mipav.view.ViewJComponentBase extends JComponent implements Serializable

serialVersionUID: -1024094346997939797L

Serialized Fields

imageDim

Dimension imageDim
DOCUMENT ME!

img

Image img
DOCUMENT ME!

imgB

Image imgB
DOCUMENT ME!

interpMode

int interpMode
DOCUMENT ME!

memImageA

MemoryImageSource memImageA
DOCUMENT ME!

memImageB

MemoryImageSource memImageB
DOCUMENT ME!

resolutionX

float resolutionX
resolutionX and Y are used to correct difference in intra and inter plane voxel resolution These represent the aspect ratio of the image These are NOT to be confused with the pixel resolutions.

resolutionY

float resolutionY
DOCUMENT ME!

showSliceNumber

boolean showSliceNumber
DOCUMENT ME!

sliceString

String sliceString
DOCUMENT ME!

textColor

Color textColor
DOCUMENT ME!

zoomX

float zoomX
DOCUMENT ME!

zoomY

float zoomY
DOCUMENT ME!

OUT_OF_BOUNDS

int OUT_OF_BOUNDS
DOCUMENT ME!

lastMouseX

int lastMouseX
used by the repaintPaintBrushCursorFast method

lastMouseY

int lastMouseY
used by the repaintPaintBrushCursorFast method

Class gov.nih.mipav.view.ViewJComponentCardiology extends ViewJComponentEditImage implements Serializable

serialVersionUID: 7846145645892843524L

Serialized Fields

opacity

float opacity
opacity value used by the paint brush. The opacity value may range from 0 to 1, where 1 is completely opaque, and 0 is completely invisible.

Opacity definitions:

    • Opaque is 1.0
    • default is 0.25
    • Invisible is 0.0

Values outside the bounds of 0.0 to 1.0 are not defined.

overlayOn

boolean overlayOn
Flag to indicate if DICOM overlay should be displayed.

popupCard

ViewJPopupCardiologyVOI popupCard
DOCUMENT ME!

Class gov.nih.mipav.view.ViewJComponentColocalizationEM extends ViewJComponentBase implements Serializable

serialVersionUID: 6577659651877049839L

Serialized Fields

OPACITY

float OPACITY
Opacity value used by the paint brush. value = 1.0 - opaque value = 0.25 - default (mostly see through)

frame

ViewJFrameBase frame
frame - frame where the component image is displayed.

imageA

ModelImage imageA
imageA - model for image A.

imageB

ModelImage imageB
imageB - model for image B.

interpMode

int interpMode
Creates histogram with ellipses around most prominent clusters.

RGBTA

ModelRGB RGBTA
true if selected red, green, blue components present in RGB image.

RGBTB

ModelRGB RGBTB
DOCUMENT ME!

bin2

int bin2
DOCUMENT ME!

bottomPad

int bottomPad
DOCUMENT ME!

brightness

int brightness
DOCUMENT ME!

contrast

float contrast
DOCUMENT ME!

destImage

ModelImage destImage
DOCUMENT ME!

halfMajor

double[] halfMajor
DOCUMENT ME!

halfMinor

double[] halfMinor
DOCUMENT ME!

haveFiltered

boolean haveFiltered
DOCUMENT ME!

haveThresholded

boolean haveThresholded
DOCUMENT ME!

imageBufferDest

float[] imageBufferDest
DOCUMENT ME!

imgDest

Image imgDest
DOCUMENT ME!

leftPad

int leftPad
DOCUMENT ME!

logMagDisplay

boolean logMagDisplay
DOCUMENT ME!

lutBufferRemappedDest

int[] lutBufferRemappedDest
DOCUMENT ME!

LUTdest

ModelLUT LUTdest
LUTa - lookup table for destImage.

mean

double[][] mean
DOCUMENT ME!

memImageDest

MemoryImageSource memImageDest
DOCUMENT ME!

min1

double min1
DOCUMENT ME!

max1

double max1
DOCUMENT ME!

min2

double min2
DOCUMENT ME!

max2

double max2
DOCUMENT ME!

paintBitmapDest

BitSet paintBitmapDest
Buffer used to indicate if the pixel location is painted (true) or unpainted (false).

paintBufferDest

int[] paintBufferDest
Buffer that displays the combined paintBitmap and pixBuffer buffers.

pixBufferDest

int[] pixBufferDest
Buffer used to store ARGB images of the image presently being displayed.

red

int red
DOCUMENT ME!

green

int green
DOCUMENT ME!

blue

int blue
DOCUMENT ME!

resX

float resX
DOCUMENT ME!

resY

float resY
DOCUMENT ME!

rightPad

int rightPad
DOCUMENT ME!

scale1

double scale1
DOCUMENT ME!

scale2

double scale2
DOCUMENT ME!

theta

double[] theta
DOCUMENT ME!

topPad

int topPad
DOCUMENT ME!

useBlue

boolean useBlue
DOCUMENT ME!

useGreen

boolean useGreen
DOCUMENT ME!

useRed

boolean useRed
DOCUMENT ME!

xDim

int xDim
Note that xDim and yDim refer to destImage, while zDim and tDim refer to imageA.

yDim

int yDim
Note that xDim and yDim refer to destImage, while zDim and tDim refer to imageA.

zDim

int zDim
Note that xDim and yDim refer to destImage, while zDim and tDim refer to imageA.

tDim

int tDim
Note that xDim and yDim refer to destImage, while zDim and tDim refer to imageA.

zoomX

float zoomX
DOCUMENT ME!

zoomY

float zoomY
DOCUMENT ME!

Class gov.nih.mipav.view.ViewJComponentColocalizationRegression extends ViewJComponentBase implements Serializable

serialVersionUID: -2295519432253254184L

Serialized Fields

OPACITY

float OPACITY
Opacity value used by the paint brush. value = 1.0 - opaque value = 0.25 - default (mostly see through)

frame

ViewJFrameBase frame
frame - frame where the component image is displayed.

imageA

ModelImage imageA
imageA - model for image A.

imageB

ModelImage imageB
imageB - model for image B.

interpMode

int interpMode
DOCUMENT ME!

RGBTA

ModelRGB RGBTA
true if selected red, green, blue components present in RGB image.

RGBTB

ModelRGB RGBTB
DOCUMENT ME!

alg

AlgorithmColocalizationRegression alg
DOCUMENT ME!

bin1

int bin1
DOCUMENT ME!

bin2

int bin2
DOCUMENT ME!

bottomPad

int bottomPad
DOCUMENT ME!

brightness

int brightness
DOCUMENT ME!

colocIntensity1

float[] colocIntensity1
DOCUMENT ME!

colocIntensity2

float[] colocIntensity2
DOCUMENT ME!

colocSize

float[] colocSize
DOCUMENT ME!

contrast

float contrast
DOCUMENT ME!

destImage

ModelImage destImage
DOCUMENT ME!

doSecondIteration

boolean doSecondIteration
DOCUMENT ME!

editImageFrameA

ViewJComponentEditImage editImageFrameA
DOCUMENT ME!

editImageFrameB

ViewJComponentEditImage editImageFrameB
DOCUMENT ME!

firstIndex

float firstIndex
DOCUMENT ME!

freeRangeColocIntensity1

float[] freeRangeColocIntensity1
DOCUMENT ME!

freeRangeColocIntensity2

float[] freeRangeColocIntensity2
DOCUMENT ME!

freeRangeColocSize

float[] freeRangeColocSize
DOCUMENT ME!

freeRangeMode

boolean freeRangeMode
DOCUMENT ME!

freeRangeRThreshold

float[] freeRangeRThreshold
DOCUMENT ME!

haveFiltered

boolean haveFiltered
DOCUMENT ME!

haveFreeRangeThreshold

boolean[] haveFreeRangeThreshold
DOCUMENT ME!

haveThreshold

boolean[] haveThreshold
DOCUMENT ME!

haveThresholded

boolean haveThresholded
DOCUMENT ME!

imageBufferDest

float[] imageBufferDest
DOCUMENT ME!

imgDest

Image imgDest
DOCUMENT ME!

leftPad

int leftPad
DOCUMENT ME!

linearCorrelation

float linearCorrelation
DOCUMENT ME!

lineMin

int lineMin
DOCUMENT ME!

lineMin1

double lineMin1
DOCUMENT ME!

lineMax1

double lineMax1
DOCUMENT ME!

lineMin2

double lineMin2
DOCUMENT ME!

lineMax2

double lineMax2
DOCUMENT ME!

lineOffset

double lineOffset
DOCUMENT ME!

lineSlope

double lineSlope
DOCUMENT ME!

lineVOI

VOI lineVOI
DOCUMENT ME!

localizeFrame

ViewJFrameColocalizationRegression localizeFrame
DOCUMENT ME!

logMagDisplay

boolean logMagDisplay
DOCUMENT ME!

lutBufferRemappedDest

int[] lutBufferRemappedDest
DOCUMENT ME!

LUTdest

ModelLUT LUTdest
LUTa - lookup table for destImage.

memImageDest

MemoryImageSource memImageDest
DOCUMENT ME!

min1

double min1
DOCUMENT ME!

max1

double max1
DOCUMENT ME!

min2

double min2
DOCUMENT ME!

max2

double max2
DOCUMENT ME!

minimumx

double minimumx
DOCUMENT ME!

maximumx

double maximumx
DOCUMENT ME!

nVOI

int nVOI
DOCUMENT ME!

originalLineOffset

float originalLineOffset
DOCUMENT ME!

originalLineSlope

float originalLineSlope
DOCUMENT ME!

paintBitmapDest

BitSet paintBitmapDest
Buffer used to indicate if the pixel location is painted (true) or unpainted (false).

paintBufferDest

int[] paintBufferDest
Buffer that displays the combined paintBitmap and pixBuffer buffers.

pixBufferDest

int[] pixBufferDest
Buffer used to store ARGB images of the image presently being displayed.

pointVOI

VOI pointVOI
DOCUMENT ME!

red

int red
DOCUMENT ME!

green

int green
DOCUMENT ME!

blue

int blue
DOCUMENT ME!

regionLinesDisplay

boolean regionLinesDisplay
DOCUMENT ME!

resX

float resX
DOCUMENT ME!

resY

float resY
DOCUMENT ME!

rightPad

int rightPad
DOCUMENT ME!

rThreshold

float[] rThreshold
DOCUMENT ME!

scale1

double scale1
DOCUMENT ME!

scale2

double scale2
DOCUMENT ME!

secondIndex

float secondIndex
DOCUMENT ME!

thresholdOn1

boolean thresholdOn1
DOCUMENT ME!

topPad

int topPad
DOCUMENT ME!

useBlue

boolean useBlue
DOCUMENT ME!

useGreen

boolean useGreen
DOCUMENT ME!

useRed

boolean useRed
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

VOIs

ViewVOIVector VOIs
DOCUMENT ME!

xArray

float[] xArray
DOCUMENT ME!

xdiff

double xdiff
DOCUMENT ME!

ydiff

double ydiff
DOCUMENT ME!

xDim

int xDim
Note that xDim and yDim refer to destImage, while zDim and tDim refer to imageA.

yDim

int yDim
Note that xDim and yDim refer to destImage, while zDim and tDim refer to imageA.

zDim

int zDim
Note that xDim and yDim refer to destImage, while zDim and tDim refer to imageA.

tDim

int tDim
Note that xDim and yDim refer to destImage, while zDim and tDim refer to imageA.

yArray

float[] yArray
DOCUMENT ME!

zArray

float[] zArray
DOCUMENT ME!

zoomX

float zoomX
DOCUMENT ME!

zoomY

float zoomY
DOCUMENT ME!

Class gov.nih.mipav.view.ViewJComponentDTIImage extends ViewJComponentEditImage implements Serializable

Serialized Fields

type

String type
type of color wheel ABSVAL, NOSYMM, ROTATIONALSYMM, MIRRORSYMM *

imageA

ModelImage imageA
model image *

pS

float pS
sat vs theta *

pC

float pC
color range *

pB

float pB
blue saturation *

pG

float pG
green adj *

gamma

float gamma
gamma correction *

twoPi

float twoPi
two pi *

piDivTwo

float piDivTwo
pi div two *

blueShiftColors

float[] blueShiftColors
arry of r,g,b after blue shift *

redShiftColors

float[] redShiftColors
array of r,g,b values after red shifting *

greenAdjColors

float[] greenAdjColors
arry of r,g,b after green adj *

anisotropyMax

float anisotropyMax
anisotropy max *

anisotropyMin

float anisotropyMin
anisotropy min *

anisotropyBuffer

float[] anisotropyBuffer
anisotropy file data buffer *

clippedBuffer

float[] clippedBuffer
anisotropy file data buffer *

stevensBeta

float stevensBeta
Stevens Beta *

adjustExp

float adjustExp
adjust exp *

isMultiply

boolean isMultiply
boolean for truncate/multiply *

truncMultColors

float[] truncMultColors
arry of r,g,b after scaling/truncating *

Class gov.nih.mipav.view.ViewJComponentEditImage extends ViewJComponentBase implements Serializable

serialVersionUID: -3799092616373463766L

Serialized Fields

checkerDialog

JDialogCheckerBoard checkerDialog
Dialog used to set properties of the checkerboard display:(Image A displayed in alternating squares with Image B.

growDialog

RegionGrowDialog growDialog
Dialog used to control region growing of the paint tool.

intensityDropper

float intensityDropper
Used in paint to indicate intensity painted into the image.

MAGR_HEIGHT

int MAGR_HEIGHT
Default size of magnifier window = 120 pixels.

MAGR_MAG

float MAGR_MAG
Magnification value of magnifier window -- default = 4.0.

MAGR_WIDTH

int MAGR_WIDTH
default = 120 pixels.

allActive

boolean allActive
Set to true when all contours of a VOI are active.

alphaBlend

float alphaBlend
Value used to control the display when compositing two images. Usually = 1 - alphaPrime.

alphaPrime

float alphaPrime
Value used to control the display when compositing two images. It is the amount of image A to display and is has a range of [0,1]

rgbString

String rgbString
String representing RGB components used in applied paint

cleanImageBufferA

int[] cleanImageBufferA
Buffer used to store ARGB images of the image presently being displayed.

cleanImageBufferB

int[] cleanImageBufferB
Buffer used to store ARGB images of the image presently being displayed.

crosshairCursor

Cursor crosshairCursor
Crosshair cursor that can be changed per user preference (in Mipav Options).

cursorMode

int cursorMode
Used to describe the cursor mode.

displayFuzzy

boolean displayFuzzy
DOCUMENT ME!

drawVOIs

boolean drawVOIs
Flag used ONLY by ViewJComponentRegistration to prohibit VOI drawing.

frame

ViewJFrameBase frame
Frame where the component image is displayed.

frameControls

ViewControlsImage frameControls
Controls having color and opacity.

fuzzyThreshold

float fuzzyThreshold
Region grow parameters fuzzyConnectedness is not used if fuzzyThreshold is less than 0. When fuzzyConnectedness is used, fuzzyThreshold ranges from 0 to 1.

imageA

ModelImage imageA
Model for image A.

imageActive

ModelImage imageActive
Active image.

imageB

ModelImage imageB
Model for image B.

imageBufferA

float[] imageBufferA
Buffer for image A, raw intensity.

imageBufferActive

float[] imageBufferActive
Buffer for active image.

imageBufferB

float[] imageBufferB
Buffer for image B, raw intensity.

imageExtents

int[] imageExtents
The dimensionality of the image.

imageStatList

JDialogVOIStatistics imageStatList
DOCUMENT ME!

less

float less
DOCUMENT ME!

lessB

float lessB
DOCUMENT ME!

lessG

float lessG
DOCUMENT ME!

lessR

float lessR
DOCUMENT ME!

logMagDisplay

boolean logMagDisplay
Flag for displaying logMag.

LUTa

ModelLUT LUTa
Lookup table for image A.

LUTb

ModelLUT LUTb
Lookup table for image B.

m_kPatientSlice

PatientSlice m_kPatientSlice
PatientSlice contains all the Patient Coordinate system view-specific data for rendering this component:.

magSettings

JDialogMagnificationControls magSettings
Dialog used to control the magnification of the image.

maxDistance

float maxDistance
DOCUMENT ME!

maxExtents

int[] maxExtents
DOCUMENT ME!

modifyFlag

boolean modifyFlag
Used to "lock" display when an algorithm is in the calculation process.

more

float more
DOCUMENT ME!

moreB

float moreB
DOCUMENT ME!

moreG

float moreG
DOCUMENT ME!

moreR

float moreR
DOCUMENT ME!

mousePressIsShiftDown

boolean mousePressIsShiftDown
Keep track of state of shift for mouse Pressed events.

nColumnCheckers

int nColumnCheckers
The number columns when two images are displayed in the checker board mode.

nRowCheckers

int nRowCheckers
Checkerboard display parameters. The number of rows to display.

onTop

boolean onTop
for the use of the user-notifier.

orientation

int orientation
orientation of the slice, may be AXIAL, CORONAL, SAGITTAL, or UNKNOWN_ORIENT.

paintBitmap

BitSet paintBitmap
Buffer used to indicate if the pixel location is painted (true) or unpainted (false).

paintBitmapBU

BitSet paintBitmapBU
Backup of paint buffer for undo.

paintBitmapSwitch

boolean paintBitmapSwitch
if true do not getMask on a setActiveImage command so as to keep the mask from the old active image.

paintBrush

BitSet paintBrush
BitSet used for painting (brushes on/off).

paintBrushDim

Dimension paintBrushDim
Dimension of the paint.

paintBrushDimPrevious

Dimension paintBrushDimPrevious
DOCUMENT ME!

paintBrushPrevious

BitSet paintBrushPrevious
DOCUMENT ME!

paintBrushSize

int paintBrushSize
Paint brush size.

paintImage

BufferedImage paintImage
buffered image that is transparent to show the paintbrush cursor.

paintImagePrevious

BufferedImage paintImagePrevious
DOCUMENT ME!

pixBuffer

int[] pixBuffer
The buffer used to store the ARGB image of the image presently being displayed.

pixBufferB

int[] pixBufferB
Buffer used to store ARGB image of the windowed imageB.

previousPaintBrush

int previousPaintBrush
The previous paint brush we were using when the user temporarily changes the paint brush size using keyboard shortcuts (by pressing 1, 2, 3, 4).

RGBTA

ModelRGB RGBTA
DOCUMENT ME!

RGBTB

ModelRGB RGBTB
DOCUMENT ME!

saveValue

float saveValue
Used with commitMask(int imagesDone), to save the value.

saveValueB

float saveValueB
DOCUMENT ME!

saveValueG

float saveValueG
DOCUMENT ME!

saveValueR

float saveValueR
DOCUMENT ME!

saveX

short saveX
Used with commitMask(int imagesDone), to save positions.

saveY

short saveY
Used with commitMask(int imagesDone), to save positions.

saveZ

short saveZ
Used with commitMask(int imagesDone), to save positions.

seedPaintBitmap

BitSet seedPaintBitmap
Buffer used to remember the area painted around the last seed point for region growing.

seedVal

float seedVal
Seed value to start the region grow.

seedValB

float seedValB
DOCUMENT ME!

seedValG

float seedValG
DOCUMENT ME!

seedValR

float seedValR
DOCUMENT ME!

sizeLimit

int sizeLimit
DOCUMENT ME!

slice

int slice
DOCUMENT ME!

stringOverride

String stringOverride
String used to override the slice number in the lower left corner.

time

long time
DOCUMENT ME!

timeSlice

int timeSlice
DOCUMENT ME!

toppedColor

Color toppedColor
DOCUMENT ME!

useVOI

boolean useVOI
This flag is used by the fuzzy connectedness to indicate that a VOI should be used to calculate certain values to initialize the process.

variableThresholds

boolean variableThresholds
DOCUMENT ME!

visRect

Rectangle visRect
Visible rectangle to draw topped.

voiHandler

VOIHandler voiHandler
Handles all aspects of VOIs, including mouse responses, movements, VOI graphing etc.

winLevelSet

boolean winLevelSet
User invokes window and level adjustment with right mouse drag in DEFAULT mode.

xPG

short xPG
X coord of seed point.

yPG

short yPG
Y coord of seed point.

zPG

short zPG
Z coord of seed point.

cleanImageB

Image cleanImageB
DOCUMENT ME!

intensityLabel

boolean intensityLabel
If true then the x,y location and pixel/voxel intensity should be displayed (x,y: intensity).

lastWinRegionSlice

int lastWinRegionSlice
Last slice the image was at when win region was ON. its necessary because otherwise, a new cleanImageB would have to be created upon every repaint. should be initialized to a negative number

m_kWinLevel

WindowLevel m_kWinLevel
window / level mouse control:.

offscreenImage

Image offscreenImage
DOCUMENT ME!

paintImageBuffer

int[] paintImageBuffer
This image indicates which images have been painted.

shiftDown

boolean shiftDown
Flag used to indicate if the shift key is depressed. True indicates the shift key is depressed.

showMagIntensity

boolean showMagIntensity
Flag used to indicate that the intensity values of the image should be displayed in the magnified portion of the image. The intensity values can only be shown if the magnification is high enough to fit the text representation of the value in the magnified voxel/pixel.

wasDragging

boolean wasDragging
Boolean to determine if the mouse had been dragging before mouse release (for moving and setting active).

windowedRegionSize

int windowedRegionSize
The window region size of used when two images are displayed in the same frame. The size of the window indicates how much of image B is displayed.

useRComp

boolean useRComp

useGComp

boolean useGComp

useBComp

boolean useBComp

zeroToOneLUTAdj

boolean zeroToOneLUTAdj
flag indicating whether there is 0 to 1 LUT Adjustment *

paintBuffer

int[] paintBuffer

Class gov.nih.mipav.view.ViewJComponentFunct extends JComponent implements Serializable

serialVersionUID: -2525400551576940334L

Serialized Fields

X

float[] X
DOCUMENT ME!

Y

float[] Y
DOCUMENT ME!

functName

String functName
DOCUMENT ME!

lineColor

Color lineColor
DOCUMENT ME!

newX

int[] newX
DOCUMENT ME!

newXLength

int newXLength
DOCUMENT ME!

newY

int[] newY
DOCUMENT ME!

newYLength

int newYLength
DOCUMENT ME!

originalX

float[] originalX
DOCUMENT ME!

originalY

float[] originalY
DOCUMENT ME!

showFitFunction

boolean showFitFunction
DOCUMENT ME!

showFunction

boolean showFunction
DOCUMENT ME!

voi

VOI voi
DOCUMENT ME!

Class gov.nih.mipav.view.ViewJComponentGraph extends JComponent implements Serializable

serialVersionUID: 4064300190247654824L

Serialized Fields

backgroundColor

Color backgroundColor
DOCUMENT ME!

bounds

Rectangle bounds
DOCUMENT ME!

colorBox

JComboBox colorBox
DOCUMENT ME!

crosshairCursor

Cursor crosshairCursor
DOCUMENT ME!

defaultCursor

Cursor defaultCursor
DOCUMENT ME!

defaultMaxDomain

float defaultMaxDomain
DOCUMENT ME!

defaultMaxRange

float defaultMaxRange
DOCUMENT ME!

defaultMinDomain

float defaultMinDomain
DOCUMENT ME!

defaultMinRange

float defaultMinRange
DOCUMENT ME!

fittedFunctions

ViewJComponentFunct[] fittedFunctions
DOCUMENT ME!

font10

Font font10
DOCUMENT ME!

font12

Font font12
DOCUMENT ME!

font12B

Font font12B
DOCUMENT ME!

fun1PrintIcon

ImageIcon fun1PrintIcon
DOCUMENT ME!

fun2Icon

ImageIcon fun2Icon
DOCUMENT ME!

fun2PrintIcon

ImageIcon fun2PrintIcon
DOCUMENT ME!

fun3Icon

ImageIcon fun3Icon
DOCUMENT ME!

fun3PrintIcon

ImageIcon fun3PrintIcon
DOCUMENT ME!

fun4Icon

ImageIcon fun4Icon
DOCUMENT ME!

fun4PrintIcon

ImageIcon fun4PrintIcon
DOCUMENT ME!

fun5Icon

ImageIcon fun5Icon
DOCUMENT ME!

fun5PrintIcon

ImageIcon fun5PrintIcon
DOCUMENT ME!

functions

ViewJComponentFunct[] functions
DOCUMENT ME!

graphBounds

Rectangle graphBounds
DOCUMENT ME!

maxDomain

float maxDomain
DOCUMENT ME!

maxRange

float maxRange
DOCUMENT ME!

minDomain

float minDomain
DOCUMENT ME!

minRange

float minRange
DOCUMENT ME!

newX

int[] newX
DOCUMENT ME!

newY

int[] newY
DOCUMENT ME!

oldRubberband

Rectangle oldRubberband
DOCUMENT ME!

parentFrame

JFrame parentFrame
DOCUMENT ME!

rubberbandRect

RubberbandRectangle rubberbandRect
DOCUMENT ME!

showFittedFunctions

boolean showFittedFunctions
DOCUMENT ME!

showFunctions

boolean showFunctions
DOCUMENT ME!

showGridLines

boolean showGridLines
DOCUMENT ME!

showLegend

boolean showLegend
DOCUMENT ME!

showMinorTickMarks

boolean showMinorTickMarks
DOCUMENT ME!

showPoints

boolean showPoints
DOCUMENT ME!

title

String title
DOCUMENT ME!

xGridLines

int xGridLines
DOCUMENT ME!

xLabel

String xLabel
DOCUMENT ME!

xScale

double xScale
DOCUMENT ME!

xTick

double xTick
DOCUMENT ME!

yGridLines

int yGridLines
DOCUMENT ME!

yLabel

String yLabel
DOCUMENT ME!

yScale

double yScale
DOCUMENT ME!

yTick

double yTick
DOCUMENT ME!

Class gov.nih.mipav.view.ViewJComponentHistoLUT extends ViewJComponentHLUTBase implements Serializable

serialVersionUID: -1320755809299024115L

Serialized Fields

lut

ModelLUT lut
DOCUMENT ME!

Class gov.nih.mipav.view.ViewJComponentHistoRGB extends ViewJComponentHLUTBase implements Serializable

serialVersionUID: 288314366500212340L

Serialized Fields

RGBT

ModelRGB RGBT
DOCUMENT ME!

Class gov.nih.mipav.view.ViewJComponentHLUTBase extends JComponent implements Serializable

serialVersionUID: 3244043088343763762L

Serialized Fields

addPointFlag

boolean addPointFlag
DOCUMENT ME!

componentDim

Dimension componentDim
The outer dimension of the histogram component we will be drawing.

dim

Dimension dim
The histogram image dimension.

histogram

ModelHistogram histogram
The image histogram.

histogramBuffer

int[] histogramBuffer
DOCUMENT ME!

histogramMax

double histogramMax
DOCUMENT ME!

histogramMaxLog

double histogramMaxLog
DOCUMENT ME!

histogramParent

HistoLUTParent histogramParent
The container of this histogram component.

image

ModelImage image
The image whose histo lut we are displaying.

img

Image img
DOCUMENT ME!

index

int index
DOCUMENT ME!

logFlag

boolean logFlag
Whether to transform the histogram data by log10.

lutIndexBuffer

int[] lutIndexBuffer
DOCUMENT ME!

mode

int mode
The current mode of the histogram component.

offsetX

int offsetX
DOCUMENT ME!

offsetY

int offsetY
DOCUMENT ME!

pixBuffer

int[] pixBuffer
DOCUMENT ME!

range

int range
DOCUMENT ME!

stRange

int stRange
DOCUMENT ME!

thresholdMode

int thresholdMode
The current threshold mode (dual or dual inverse) or NO_THRESHOLD if not in theshold mode.

x

float[] x
DOCUMENT ME!

xN

int[] xN
DOCUMENT ME!

y

float[] y
DOCUMENT ME!

yN

int[] yN
DOCUMENT ME!

z

float[] z
DOCUMENT ME!

zN

int[] zN
DOCUMENT ME!

Class gov.nih.mipav.view.ViewJComponentLUT extends ViewJComponentBase implements Serializable

serialVersionUID: 5027534629757769708L

Serialized Fields

LUT

ModelLUT LUT
DOCUMENT ME!

LUTDims

Dimension LUTDims
DOCUMENT ME!

LUTIndexBuffer

int[] LUTIndexBuffer
DOCUMENT ME!

orientation

int orientation
DOCUMENT ME!

Class gov.nih.mipav.view.ViewJComponentLUTTable extends ViewJComponentBase implements Serializable

serialVersionUID: 4862175635665317557L

Serialized Fields

offsetX

int offsetX
Offset to draw the tick mark and value label.

offsetY

int offsetY
DOCUMENT ME!

x

float[] x
control points coordinate of LUT transfer function .

xN

int[] xN
DOCUMENT ME!

y

float[] y
DOCUMENT ME!

yN

int[] yN
DOCUMENT ME!

z

float[] z
DOCUMENT ME!

zN

int[] zN
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

LUT

ModelLUT LUT
DOCUMENT ME!

LUTDims

Dimension LUTDims
DOCUMENT ME!

LUTIndexBuffer

int[] LUTIndexBuffer
DOCUMENT ME!

orientation

int orientation
DOCUMENT ME!

Class gov.nih.mipav.view.ViewJComponentPreviewImage extends ViewJComponentBase implements Serializable

serialVersionUID: 5183033960229966439L

Serialized Fields

brightness

int brightness
DOCUMENT ME!

contrast

float contrast
DOCUMENT ME!

imageSize

int imageSize
DOCUMENT ME!

imgHeight

int imgHeight
DOCUMENT ME!

imgWidth

int imgWidth
DOCUMENT ME!

memImage

MemoryImageSource memImage
DOCUMENT ME!

paintBuffer

int[] paintBuffer
DOCUMENT ME!

panelHeight

int panelHeight
DOCUMENT ME!

panelWidth

int panelWidth
DOCUMENT ME!

parent

PreviewImageContainer parent
DOCUMENT ME!

m_kPatientSlice

PatientSlice m_kPatientSlice
PatientSlice interfaces with the ModelImage class to render the image w/LUT changes for this component. Slices are rendered in FileCoordinates.

Class gov.nih.mipav.view.ViewJComponentRegistration extends ViewJComponentEditImage implements Serializable

serialVersionUID: 4961820290271772572L

Serialized Fields

OPACITY

float OPACITY
Opacity value used by the paint brush. value = 1.0 - opaque value = 0.25 - default (mostly see through)

addPointCursor

Cursor addPointCursor
DOCUMENT ME!

defaultCursor

Cursor defaultCursor
DOCUMENT ME!

magRegionCursor

Cursor magRegionCursor
Custom cursor: magnify region.

moveCursor

Cursor moveCursor
DOCUMENT ME!

pointCursor

Cursor pointCursor
DOCUMENT ME!

rectCursor

Cursor rectCursor
DOCUMENT ME!

removePointCursor

Cursor removePointCursor
DOCUMENT ME!

waitCursor

Cursor waitCursor
DOCUMENT ME!

wandCursor

Cursor wandCursor
DOCUMENT ME!

toolFrame

ViewJFrameRegistrationTool toolFrame
Frame where component image is displayed (only for new RegistrationTool).

memCount

int memCount
DOCUMENT ME!

adjMark

int adjMark
number of VOIs for adjustable slice

anchorPt

Point anchorPt
DOCUMENT ME!

centerid

short centerid
id of rotation center

centerVOI

VOI centerVOI
center rotation VOI

doAdjMark

boolean doAdjMark
DOCUMENT ME!

doCenter

boolean doCenter
DOCUMENT ME!

doDrag

boolean doDrag
no adjusted slice movements with mouseDrag

doRefMark

boolean doRefMark
DOCUMENT ME!

hue

float hue
DOCUMENT ME!

id

short id
DOCUMENT ME!

markerType

int[] markerType
DOCUMENT ME!

newVOI

VOI newVOI
DOCUMENT ME!

newX

int newX
adjustable slice VOI.

newY

int newY
adjustable slice VOI.

nMovingVOI

int nMovingVOI
number of rotation center and

nPts

int nPts
DOCUMENT ME!

oldFrame

boolean oldFrame
Used to set old or new mode of registration.

ptCoord

float[] ptCoord
DOCUMENT ME!

red

int red
DOCUMENT ME!

green

int green
DOCUMENT ME!

blue

int blue
DOCUMENT ME!

refMark

int refMark
number of VOIs for reference slice

rotCenterMark

int rotCenterMark
number of VOIs for rotation center

showVOIs

boolean showVOIs
DOCUMENT ME!

useDualVOIs

boolean useDualVOIs
to use VOIs from both imageA and imageB

x

int[] x
DOCUMENT ME!

y

int[] y
DOCUMENT ME!

xFinish

float xFinish
values obtained when mouseReleased

yFinish

float yFinish
values obtained when mouseReleased

xOrg

int[] xOrg
DOCUMENT ME!

xPres

int[] xPres
DOCUMENT ME!

xRotation

float xRotation
DOCUMENT ME!

xStart

float xStart
values obtained when mousePressed

yStart

float yStart
values obtained when mousePressed

yOrg

int[] yOrg
DOCUMENT ME!

yPres

int[] yPres
DOCUMENT ME!

yRotation

float yRotation
DOCUMENT ME!

Class gov.nih.mipav.view.ViewJComponentSingleRegistration extends ViewJComponentEditImage implements Serializable

serialVersionUID: -6751136899996457162L

Serialized Fields

centerPtLocation

int centerPtLocation
location of the center pt VOI (for registration rotation).

isReference

boolean isReference
if the image is in a registration window, is the image the reference (and not the adjusted).

ptCoord

float[] ptCoord
Temporary buffer used when extracting points from a VOI. Save reallocating memory often.

xCoords

int[] xCoords
Buffers used to save the X coordinates fo the points that make up a VOI.

yCoords

int[] yCoords
Buffers used to save the Y coordinates fo the points that make up a VOI.

Class gov.nih.mipav.view.ViewJComponentTriImage extends ViewJComponentEditImage implements Serializable

serialVersionUID: -389214941507734031L

Serialized Fields

dragCenterPt

boolean dragCenterPt
DOCUMENT ME!

intensityLineVisible

boolean intensityLineVisible
DOCUMENT ME!

protractorVisible

boolean protractorVisible
DOCUMENT ME!

anchorPt

Point anchorPt
anchorPt is used to determine movements. mousePressed() establishes the coordinates of anchorPt. mouseDragged() calculates distance from the anchorPt to the present location and uses this distance to move an object. Then it sets anchorPt to the new location to repeat the process.

axisLabels

String[][] axisLabels
Labels for the axes:.

cornerCropPt

WildMagic.LibFoundation.Mathematics.Vector3f[] cornerCropPt
Crop Bounding Box Corners in Screen Coordinates:.

cropColor

Color[] cropColor
Crop Bounding Box Colors:.

cropPoints

WildMagic.LibFoundation.Mathematics.Vector2f[] cropPoints
Crop Bounding Box in Screen Coordinates:.

crosshairPt

WildMagic.LibFoundation.Mathematics.Vector3f crosshairPt
The x and y coordinate of the cursor position in screen space of this component.

doCenter

boolean doCenter
Whether to show the center of rotation point in the volume and allow the user to change it. doCenter is set true by center command and set false by DEFAULT and CUBE_BOUNDS modes.

dragBBpt

int dragBBpt
DOCUMENT ME!

hasOrientation

boolean hasOrientation
true if the imageActive has an orientation, false if imageActive is of FileInfoBase.UNKNOWN_ORIENT.

horizontalTalGridPts

int[] horizontalTalGridPts
DOCUMENT ME!

intensityLine

VOI intensityLine
VOI line used to measure distance and show intensity value graphs.

lastZOrg

int lastZOrg
In mousePressed, in mode == DEFAULT for a VOI point, the z value is saved as lastZOrg. In mouseDragged, in mode == MOVE_VOIPOINT the points at the lastZOrg value can be removed and replaced with points at the new z value. The new z value is then saved in lastZOrg. The z values are all in image volume space.

localImageExtents

int[] localImageExtents
imageActive extents in the local (Patient) coordinate system:.

m_kLocalCropLower

WildMagic.LibFoundation.Mathematics.Vector3f m_kLocalCropLower
Lower Crop Bounding Box in Patient Coordinates:.

m_kLocalCropUpper

WildMagic.LibFoundation.Mathematics.Vector3f m_kLocalCropUpper
Upper Crop Bounding Box in Patient Coordinates:.

m_kVolumePoint

WildMagic.LibFoundation.Mathematics.Vector3f m_kVolumePoint
Cursor 3D point in FileCoordinates.

moveLine

boolean moveLine
Together with moveProtractor, ensures that the user can either move the protractor or the line VOI, but not both at the same time. Which one can be moved depends on which one the mouse is closer to.

See Also:
ViewJComponentTriImage.moveProtractor

moveLineEndpoint

boolean moveLineEndpoint
DOCUMENT ME!

moveProtractor

boolean moveProtractor
Together with moveLine, ensures that the user can either move the protractor or the line VOI, but not both at the same time. Which one can be moved depends on which one the mouse is closer to.

See Also:
ViewJComponentTriImage.moveLine

res

float[] res
Reordered resolutions according to orientation. See ModelStorageBase.getResolutions( int index, int orientation ). The orientation parameter may be either: FileInfoBase.AXIAL, FileInfoBase.CORONAL, FileInfoBase.SAGITTAL for oriented slices, or FileInfoBase.UNKNOWN_ORIENT for the default slice orientation.

seg1Length

float seg1Length
DOCUMENT ME!

showAxes

boolean showAxes
If true, show XY, XZ, or ZY orientation axes in a corner of the component.

showBoundingRect

boolean showBoundingRect
Specifies whether the user wants to show the cropping / paint bounds rectangle.

showCrosshairs

boolean showCrosshairs
If true, show crosshairs indicating the currently position within the component.

showTalairachGrid

boolean showTalairachGrid
Whether to show the talairach grid on the component.

showTalairachGridmarkers

boolean showTalairachGridmarkers
Whether to show the talairach gridmarkers on the component.

snapProtractor90

boolean snapProtractor90
Flag for snapping protractor to nearest multiple of 90 degrees.

talairachMajorLineColor

Color talairachMajorLineColor
DOCUMENT ME!

talairachMinorLineColor

Color talairachMinorLineColor
DOCUMENT ME!

theta

double theta
Protractor angle, ranging from -180 to 180 degrees.

theta2

double theta2
DOCUMENT ME!

triImageFrame

ViewJFrameTriImage triImageFrame
The tri image frame of which this object is a component.

unitsOfMeasure

int[] unitsOfMeasure
Reordered unitsOfMeasure according to orientation. See ModelStorageBase.getUnitsOfMeasure( int indes, int orientation ). The orientation parameter may be either: FileInfoBase.AXIAL, FileInfoBase.CORONAL, FileInfoBase.SAGITTAL for oriented slices, or FileInfoBase.UNKNOWN_ORIENT for the default slice orientation.

verticalTalGridPts

int[] verticalTalGridPts
DOCUMENT ME!

voiProtractor

VOI voiProtractor
The protractor VOI.

xColor

Color[] xColor
color of the crosshairs.

yColor

Color[] yColor
DOCUMENT ME!

zColor

Color[] zColor
DOCUMENT ME!

crosshairPixelGap

int crosshairPixelGap
the gap (in one direction) between the center of the crosshair and the actual crosshair line

Class gov.nih.mipav.view.ViewJFrameAnimate extends ViewJFrameBase implements Serializable

serialVersionUID: -2372670418729121051L

Serialized Fields

toggleArray

JToggleButton[] toggleArray
DOCUMENT ME!

progressBar

ViewJProgressBar progressBar
currently running.

actualPerSecond

float actualPerSecond
DOCUMENT ME!

alphaBlend

float alphaBlend
DOCUMENT ME!

aps

String aps
set to give 2 digits to the right of the decimal.

backForthButton

JToggleButton backForthButton
DOCUMENT ME!

bfRun

boolean bfRun
DOCUMENT ME!

borderCol

Color borderCol
z slice.

buttonArray

JButton[] buttonArray
DOCUMENT ME!

cForwardButton

JToggleButton cForwardButton
DOCUMENT ME!

cfRun

boolean cfRun
DOCUMENT ME!

componentImage

ViewJComponentAnimate componentImage
with complex images.

componentY

int componentY
DOCUMENT ME!

controlFrame

ViewJFrameBase controlFrame
DOCUMENT ME!

controlPanel

JPanel controlPanel
DOCUMENT ME!

controls

ViewControlsImage controls
DOCUMENT ME!

cpGBC

GridBagConstraints cpGBC
DOCUMENT ME!

cpGBL

GridBagLayout cpGBL
DOCUMENT ME!

cReverseButton

JToggleButton cReverseButton
DOCUMENT ME!

crRun

boolean crRun
DOCUMENT ME!

cycleTime

long cycleTime
DOCUMENT ME!

deleteButton

JButton deleteButton
DOCUMENT ME!

disposeImage

boolean disposeImage
DOCUMENT ME!

etchedBorder

Border etchedBorder
DOCUMENT ME!

extents

int[] extents
DOCUMENT ME!

fileMenu

JMenu fileMenu
DOCUMENT ME!

font12

Font font12
DOCUMENT ME!

font12B

Font font12B
DOCUMENT ME!

forwardButton

JToggleButton forwardButton
DOCUMENT ME!

fpsSlider

JSlider fpsSlider
DOCUMENT ME!

framesPerSecond

float framesPerSecond
DOCUMENT ME!

fRun

boolean fRun
DOCUMENT ME!

gbc

GridBagConstraints gbc
DOCUMENT ME!

gbcTP

GridBagConstraints gbcTP
DOCUMENT ME!

gbl

GridBagLayout gbl
DOCUMENT ME!

imageA

ModelImage imageA
DOCUMENT ME!

imageB

ModelImage imageB
DOCUMENT ME!

imageBufferA

float[] imageBufferA
DOCUMENT ME!

imageBufferB

float[] imageBufferB
DOCUMENT ME!

innerPanel

JPanel innerPanel
DOCUMENT ME!

labelActualPerSecond

JLabel labelActualPerSecond
DOCUMENT ME!

labelAnimationFrame

JLabel labelAnimationFrame
DOCUMENT ME!

labelFramesPerSecond

JLabel labelFramesPerSecond
DOCUMENT ME!

labelTable

Hashtable<K,V> labelTable
DOCUMENT ME!

localTime

long localTime
newmsWait = msWait - msElapsed is passed to the sleep function.

localTime2

long localTime2
DOCUMENT ME!

logMagDisplay

boolean logMagDisplay
DOCUMENT ME!

LUTa

ModelLUT LUTa
DOCUMENT ME!

LUTb

ModelLUT LUTb
DOCUMENT ME!

menuItemVector

Vector<E> menuItemVector
for each individual z Slice for 4D, 1 number for frame for 3D.

menuObj

ViewMenuBuilder menuObj
DOCUMENT ME!

minimumHeight

int minimumHeight
DOCUMENT ME!

minimumToolBarWidth

int minimumToolBarWidth
DOCUMENT ME!

mjpegQuality

float mjpegQuality
DOCUMENT ME!

msElapsed

long msElapsed
DOCUMENT ME!

msWait

long msWait
DOCUMENT ME!

nColumn

int nColumn
DOCUMENT ME!

newmsWait

long newmsWait
DOCUMENT ME!

nf

NumberFormat nf
DOCUMENT ME!

nImage

int nImage
DOCUMENT ME!

nRow

int nRow
DOCUMENT ME!

openingMenuBar

JMenuBar openingMenuBar
DOCUMENT ME!

origBrightness

int origBrightness
DOCUMENT ME!

origContrast

float origContrast
red, green, and blue origBrightness remains constant until applyButton is pressed, restores brightness if cancelButton is pressed.

originalZDim

int originalZDim
for 4D originalXDim and originalYDim are xDim and yDim before 4D to 3D conversion.

paintBuffer

int[] paintBuffer
DOCUMENT ME!

pause

boolean pause
DOCUMENT ME!

pauseButton

JToggleButton pauseButton
DOCUMENT ME!

pixBuffer

int[] pixBuffer
DOCUMENT ME!

pressedBorder

Border pressedBorder
DOCUMENT ME!

recordButton

JButton recordButton
DOCUMENT ME!

reverseButton

JToggleButton reverseButton
DOCUMENT ME!

RGBTA

ModelRGB RGBTA
DOCUMENT ME!

RGBTB

ModelRGB RGBTB
DOCUMENT ME!

rRun

boolean rRun
currently running.

scrollPane

JScrollPane scrollPane
DOCUMENT ME!

scrollPaneSize

int scrollPaneSize
DOCUMENT ME!

showFrameBorder

boolean showFrameBorder
DOCUMENT ME!

showNumbers

boolean showNumbers
equals zDim of original 4D before 4D to 3D conversion.

sliceOldNumber

int[] sliceOldNumber
red, green, and blue origContrast remains constant until applyButton is pressed, restores contrast if cancelButton is pressed.

slider

JSlider slider
DOCUMENT ME!

startTime

long startTime
= localTime2 - localTime.

stopTime

long stopTime
= localTime2 - localTime.

stop

boolean stop
containing only 5 msec. sleep commands.

stopButton

JToggleButton stopButton
DOCUMENT ME!

structureY

int structureY
DOCUMENT ME!

textActualPerSecond

JTextField textActualPerSecond
DOCUMENT ME!

textAnimationFrame

JTextField textAnimationFrame
Note that an attempt to have DocumentListener for textAnimationFrame set the slider value was unsuccessful.

textFramesPerSecond

JTextField textFramesPerSecond
DOCUMENT ME!

toolBar

JToolBar toolBar
DOCUMENT ME!

toolBarObj

ViewToolBarBuilder toolBarObj
DOCUMENT ME!

topPanel

JPanel topPanel
and innerPanel placed in scrollPane.

xDim

int xDim
DOCUMENT ME!

yDim

int yDim
DOCUMENT ME!

originalXDim

int originalXDim
DOCUMENT ME!

originalYDim

int originalYDim
DOCUMENT ME!

xScreen

int xScreen
DOCUMENT ME!

yScreen

int yScreen
DOCUMENT ME!

zoom

float zoom
DOCUMENT ME!

zShow

int zShow
DOCUMENT ME!

zSlice

int zSlice
DOCUMENT ME!

Class gov.nih.mipav.view.ViewJFrameAnimateClip extends ViewJFrameBase implements Serializable

serialVersionUID: 8057377898754491817L

Serialized Fields

toggleArray

JToggleButton[] toggleArray
DOCUMENT ME!

progressBar

ViewJProgressBar progressBar
currently running.

actualPerSecond

float actualPerSecond
DOCUMENT ME!

aps

String aps
set to give 2 digits to the right of the decimal.

backForthButton

JToggleButton backForthButton
DOCUMENT ME!

bfRun

boolean bfRun
DOCUMENT ME!

borderCol

Color borderCol
z slice.

buttonArray

JButton[] buttonArray
DOCUMENT ME!

cForwardButton

JToggleButton cForwardButton
DOCUMENT ME!

cfRun

boolean cfRun
DOCUMENT ME!

componentImage

ViewJComponentAnimateClip componentImage
with complex images.

componentY

int componentY
DOCUMENT ME!

controlPanel

JPanel controlPanel
DOCUMENT ME!

controls

ViewControlsImage controls
DOCUMENT ME!

cpGBC

GridBagConstraints cpGBC
DOCUMENT ME!

cpGBL

GridBagLayout cpGBL
DOCUMENT ME!

cReverseButton

JToggleButton cReverseButton
DOCUMENT ME!

crRun

boolean crRun
DOCUMENT ME!

cycleTime

long cycleTime
DOCUMENT ME!

deleteButton

JButton deleteButton
DOCUMENT ME!

dir

String dir
DOCUMENT ME!

etchedBorder

Border etchedBorder
DOCUMENT ME!

fileMenu

JMenu fileMenu
DOCUMENT ME!

forwardButton

JToggleButton forwardButton
DOCUMENT ME!

fpsSlider

JSlider fpsSlider
DOCUMENT ME!

framesPerSecond

float framesPerSecond
DOCUMENT ME!

fRun

boolean fRun
DOCUMENT ME!

gbc

GridBagConstraints gbc
DOCUMENT ME!

gbcTP

GridBagConstraints gbcTP
DOCUMENT ME!

gbl

GridBagLayout gbl
DOCUMENT ME!

innerPanel

JPanel innerPanel
DOCUMENT ME!

labelActualPerSecond

JLabel labelActualPerSecond
DOCUMENT ME!

labelAnimationFrame

JLabel labelAnimationFrame
DOCUMENT ME!

labelFramesPerSecond

JLabel labelFramesPerSecond
DOCUMENT ME!

labelTable

Hashtable<K,V> labelTable
DOCUMENT ME!

localTime

long localTime
newmsWait = msWait - msElapsed is passed to the sleep function.

localTime2

long localTime2
DOCUMENT ME!

menuItemVector

Vector<E> menuItemVector
for each individual z Slice for 4D, 1 number for frame for 3D.

menuObj

ViewMenuBuilder menuObj
DOCUMENT ME!

minimumHeight

int minimumHeight
DOCUMENT ME!

minimumToolBarWidth

int minimumToolBarWidth
DOCUMENT ME!

msElapsed

long msElapsed
DOCUMENT ME!

msWait

long msWait
DOCUMENT ME!

nColumn

int nColumn
DOCUMENT ME!

newmsWait

long newmsWait
DOCUMENT ME!

nf

NumberFormat nf
DOCUMENT ME!

nImage

int nImage
DOCUMENT ME!

nRow

int nRow
DOCUMENT ME!

openingMenuBar

JMenuBar openingMenuBar
DOCUMENT ME!

originalZDim

int originalZDim
for 4D originalXDim and originalYDim are xDim and yDim before 4D to 3D conversion.

pause

boolean pause
DOCUMENT ME!

pauseButton

JToggleButton pauseButton
DOCUMENT ME!

pressedBorder

Border pressedBorder
DOCUMENT ME!

recordButton

JButton recordButton
DOCUMENT ME!

reverseButton

JToggleButton reverseButton
DOCUMENT ME!

rRun

boolean rRun
currently running.

scrollPane

JScrollPane scrollPane
DOCUMENT ME!

scrollPaneSize

int scrollPaneSize
DOCUMENT ME!

showFrameBorder

boolean showFrameBorder
DOCUMENT ME!

showNumbers

boolean showNumbers
equals zDim of original 4D before 4D to 3D conversion.

sliceOldNumber

int[] sliceOldNumber
DOCUMENT ME!

slider

JSlider slider
DOCUMENT ME!

startTime

long startTime
= localTime2 - localTime.

stopTime

long stopTime
= localTime2 - localTime.

stop

boolean stop
containing only 5 msec. sleep commands.

stopButton

JToggleButton stopButton
DOCUMENT ME!

structureY

int structureY
DOCUMENT ME!

textActualPerSecond

JTextField textActualPerSecond
DOCUMENT ME!

textAnimationFrame

JTextField textAnimationFrame
Note that an attempt to have DocumentListener for textAnimationFrame set the slider value was unsuccessful.

textFramesPerSecond

JTextField textFramesPerSecond
DOCUMENT ME!

toolBar

JToolBar toolBar
DOCUMENT ME!

topPanel

JPanel topPanel
and innerPanel placed in scrollPane.

xDim

int xDim
DOCUMENT ME!

yDim

int yDim
DOCUMENT ME!

originalXDim

int originalXDim
DOCUMENT ME!

originalYDim

int originalYDim
DOCUMENT ME!

xScreen

int xScreen
DOCUMENT ME!

yScreen

int yScreen
DOCUMENT ME!

zoom

float zoom
DOCUMENT ME!

zShow

int zShow
DOCUMENT ME!

zSlice

int zSlice
DOCUMENT ME!

Class gov.nih.mipav.view.ViewJFrameBase extends JFrame implements Serializable

serialVersionUID: -3040123414501128141L

Serialized Fields

zoomMode

int zoomMode
DOCUMENT ME!

absoluteLabel

JLabel absoluteLabel
Labels for the current absolute position:.

absoluteLabelVals

JLabel[] absoluteLabelVals
Labels for the current absolute position values:.

absolutePanel

JPanel absolutePanel
JPanel containing the absoulte position labels:.

alphaBlend

float alphaBlend
Indicates the amount of blending when two images are loaded in the image frame.

displayMode

int displayMode
Indicates which image is to be acted upon when two images are displayed.

imageA

ModelImage imageA
Reference to the image A of this frame.

imageB

ModelImage imageB
Reference to the image B of this frame.

linkFrame

ViewJFrameImage linkFrame
Holds a reference (link) to another frame so that it be updated with this frame.

linkTriFrame

ViewJFrameTriImage linkTriFrame
Holds a reference (link) to another frame so that it can be updated with this frame.

LUTa

ModelLUT LUTa
Reference to LUT for image A.

LUTb

ModelLUT LUTb
Reference to LUT for image B.

progressBar

ViewJProgressBar progressBar
Reference to progress bar.

scannerLabel

JLabel scannerLabel
Labels for the current scanner position:.

scannerLabelVals

JLabel[] scannerLabelVals
Labels for the current scanner position values:.

scannerPanel

JPanel scannerPanel
JPanel containing the scanner position labels:.

tabbedPane

JTabbedPane tabbedPane
The main tabbed pane in the volume view frame.

userInterface

ViewUserInterface userInterface
Reference to the user interface.

blue

int blue
Blue channel value of the paint color.

enableCloseImageB

boolean enableCloseImageB
Tells whether the ViewMenuBuilder should allow Close Image(B) after loading image B.

green

int green
Green channel value of the paint color.

lastState

int lastState
Save if last state was iconified or normal.

opacity

float opacity
Opacity value of the paint color.

paintBitmap

BitSet paintBitmap
Reference to the BitSet map used in painting the image.

red

int red
Red channel value of the paint color.

voiSavedFileName

String voiSavedFileName
DOCUMENT ME!

linkedScrolling

boolean linkedScrolling
Variable indicating if images of like dimensions should be scrolled simult.

Class gov.nih.mipav.view.ViewJFrameCardiology extends ViewJFrameBase implements Serializable

serialVersionUID: -5959179080746432639L

Serialized Fields

componentImage

ViewJComponentCardiology componentImage
Object where DICOM image, ... is converted and displayed as a Java image

controls

ViewControlsImage controls
Reference to the toolbars located in the controls object.

fudgeFactor

int fudgeFactor
Frame adjustment to keep the frame from being just small enough for the ScrollPane to display the scroll bars. Windows seems to find an inset value needing a fudge factor of 3, but Mac OS 10 (X), doesn't, and needs a fudge factor of 7 to not require scroll bars. Either way, insets + fudge-factor must equal 7.

heightResFactor

float heightResFactor
Storage for correction parameters where datasets have non isotropic values.

imageBufferA

float[] imageBufferA
Buffer used to store image intensities the presently viewed slice of image A.

logMagDisplay

boolean logMagDisplay
Flag indicating whether or not that the image should be displayed in Log scale. Used primarily for displaying the FFT of an image.

menuBar

JMenuBar menuBar
Reference to the frame's menu bar.

menuBarMaker

ViewMenuBar menuBarMaker
Constructs the image menu bar.

menuBuilder

ViewMenuBuilder menuBuilder
This object contains a number of useful functions for building a menu and querying the state of menu items.

nImage

int nImage
Number of slices in a 3D dataset.

nTImage

int nTImage
Number of time sequences in a 4D dataset.

pixBuffer

int[] pixBuffer
Integer buffer (4 bytes that stores the concatenated Alpha (1 byte), Red (1 byte), Green ( 1 byte ), Blue (1 byte ) data. The ARGB values are generated by using the imageA intensities as a index into a LUT.

resols

float[] resols
Storage of the image voxel resolutions. One resolution value per dimension.

scrollPane

JScrollPane scrollPane
The scrollPane where the image is displayed.

tSlice

int tSlice
Image time sequence number of image that is displayed. Zero indexed based.

units

int[] units
Storage of the resolution units of measure. For example, mm, cm, inches ...

widthResFactor

float widthResFactor
Storage for correction parameters where datasets have non isotropic values.

windowLevel

JDialogWinLevel[] windowLevel
Reference to the two window and level dialogs where [0] is for imageA, [1] for imageB.

zoom

float zoom
Defaults magnification of image to 1.

zSlice

int zSlice
Image slice number of image that is displayed. Zero indexed based.

colorChooser

ViewJColorChooser colorChooser
Reference to the color chooser.

doOrigins

boolean doOrigins
When loading an image into B slot, should origins be matched?

infoDialog

JDialogImageInfo infoDialog
reference to the JDialogImageInfo for updating slice/resolutions.

lastVOI_UID

int lastVOI_UID
DOCUMENT ME!

useXOR

boolean useXOR
tells whether or not to XOR when creating binary masks (allowing holes).

zoomDialog

JDialogZoom zoomDialog
Reference to the magnification tool.

Class gov.nih.mipav.view.ViewJFrameColocalizationEM extends ViewJFrameBase implements Serializable

serialVersionUID: -7006573111870808134L

Serialized Fields

bottomPad

int bottomPad
DOCUMENT ME!

componentImage

ViewJComponentColocalizationEM componentImage
DOCUMENT ME!

componentY

int componentY
DOCUMENT ME!

controlFrame

ViewJFrameBase controlFrame
DOCUMENT ME!

controls

ViewControlsImage controls
DOCUMENT ME!

cpGBC

GridBagConstraints cpGBC
DOCUMENT ME!

cpGBL

GridBagLayout cpGBL
DOCUMENT ME!

destImage

ModelImage destImage
The image containing the 2D histogram.

etchedBorder

Border etchedBorder
DOCUMENT ME!

extents

int[] extents
DOCUMENT ME!

fileMenu

JMenu fileMenu
set to give 6 digits to the right of the decimal.

font12

Font font12
DOCUMENT ME!

font12B

Font font12B
DOCUMENT ME!

gbc

GridBagConstraints gbc
DOCUMENT ME!

gbcTP

GridBagConstraints gbcTP
DOCUMENT ME!

gbl

GridBagLayout gbl
DOCUMENT ME!

halfMajor

double[] halfMajor
DOCUMENT ME!

halfMinor

double[] halfMinor
DOCUMENT ME!

imageA

ModelImage imageA
DOCUMENT ME!

imageB

ModelImage imageB
DOCUMENT ME!

imageBufferA

float[] imageBufferA
DOCUMENT ME!

imageBufferB

float[] imageBufferB
DOCUMENT ME!

imageBufferDest

float[] imageBufferDest
DOCUMENT ME!

innerPanel

JPanel innerPanel
DOCUMENT ME!

leftPad

int leftPad
The spaces around the histogram bin area.

logDisplayButton

JToggleButton logDisplayButton
DOCUMENT ME!

logMagDisplay

boolean logMagDisplay
DOCUMENT ME!

LUTa

ModelLUT LUTa
DOCUMENT ME!

LUTb

ModelLUT LUTb
DOCUMENT ME!

LUTdest

ModelLUT LUTdest
The LUT for the 2D histogram.

mean

double[][] mean
red, green, and blue origContrast remains constant until applyButton is pressed, restores contrast if cancelButton is pressed.

menuItemVector

Vector<E> menuItemVector
DOCUMENT ME!

menuObj

ViewMenuBuilder menuObj
DOCUMENT ME!

min1

double min1
Minimum and maximum buffer and secondBuffer areas.

max1

double max1
Minimum and maximum buffer and secondBuffer areas.

min2

double min2
Minimum and maximum buffer and secondBuffer areas.

max2

double max2
Minimum and maximum buffer and secondBuffer areas.

minimumHeight

int minimumHeight
DOCUMENT ME!

minimumToolBarWidth

int minimumToolBarWidth
DOCUMENT ME!

nf

NumberFormat nf
DOCUMENT ME!

openingMenuBar

JMenuBar openingMenuBar
DOCUMENT ME!

origBrightness

int origBrightness
DOCUMENT ME!

origContrast

float origContrast
red, green, and blue origBrightness remains constant until applyButton is pressed, restores brightness if cancelButton is pressed.

paintBufferDest

int[] paintBufferDest
DOCUMENT ME!

pixBufferDest

int[] pixBufferDest
DOCUMENT ME!

pressedBorder

Border pressedBorder
DOCUMENT ME!

raisedBorder

Border raisedBorder
DOCUMENT ME!

RGBTA

ModelRGB RGBTA
DOCUMENT ME!

rightPad

int rightPad
DOCUMENT ME!

scale1

double scale1
bin1 is generated from Math.round(scale1*(buffer[i]-min1)) and bin2 is generated from Math.round(scale2*(secondBuffer[i]-min2)).

scale2

double scale2
bin1 is generated from Math.round(scale1*(buffer[i]-min1)) and bin2 is generated from Math.round(scale2*(secondBuffer[i]-min2)).

scrollPane

JScrollPane scrollPane
DOCUMENT ME!

scrollPaneSize

int scrollPaneSize
DOCUMENT ME!

structureY

int structureY
DOCUMENT ME!

theta

double[] theta
DOCUMENT ME!

toolBar

JToolBar toolBar
DOCUMENT ME!

toolBarObj

ViewToolBarBuilder toolBarObj
DOCUMENT ME!

topPad

int topPad
DOCUMENT ME!

topPanel

JPanel topPanel
and innerPanel placed in scrollPane.

useBlue

boolean useBlue
DOCUMENT ME!

useGreen

boolean useGreen
DOCUMENT ME!

useRed

boolean useRed
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

xDim

int xDim
Note that xDim and yDim refer to destImage.

yDim

int yDim
Note that xDim and yDim refer to destImage.

xScreen

int xScreen
DOCUMENT ME!

yScreen

int yScreen
DOCUMENT ME!

zoom

float zoom
DOCUMENT ME!

Class gov.nih.mipav.view.ViewJFrameColocalizationRegression extends ViewJFrameBase implements Serializable

serialVersionUID: -2084669389930362925L

Serialized Fields

alg

AlgorithmColocalizationRegression alg
DOCUMENT ME!

bottomPad

int bottomPad
DOCUMENT ME!

colocIntensity1

float[] colocIntensity1
DOCUMENT ME!

colocIntensity2

float[] colocIntensity2
DOCUMENT ME!

colocSize

float[] colocSize
DOCUMENT ME!

componentImage

ViewJComponentColocalizationRegression componentImage
DOCUMENT ME!

componentY

int componentY
DOCUMENT ME!

controlFrame

ViewJFrameBase controlFrame
DOCUMENT ME!

controls

ViewControlsImage controls
DOCUMENT ME!

cpGBC

GridBagConstraints cpGBC
DOCUMENT ME!

cpGBL

GridBagLayout cpGBL
DOCUMENT ME!

dataLine1

String dataLine1
DOCUMENT ME!

dataLine2

String dataLine2
DOCUMENT ME!

destImage

ModelImage destImage
The image containing the 2D histogram.

doSecondIteration

boolean doSecondIteration
DOCUMENT ME!

etchedBorder

Border etchedBorder
DOCUMENT ME!

extents

int[] extents
DOCUMENT ME!

freeRangeButton

JToggleButton freeRangeButton
DOCUMENT ME!

freeRangeColocIntensity1

float[] freeRangeColocIntensity1
DOCUMENT ME!

freeRangeColocIntensity2

float[] freeRangeColocIntensity2
DOCUMENT ME!

freeRangeColocSize

float[] freeRangeColocSize
DOCUMENT ME!

freeRangeMode

boolean freeRangeMode
DOCUMENT ME!

freeRangeRThreshold

float[] freeRangeRThreshold
The linear correlation coefficient for all pixels with values either below color1 for buffer or below color2 for secondBuffer.

gbc

GridBagConstraints gbc
DOCUMENT ME!

gbcTP

GridBagConstraints gbcTP
DOCUMENT ME!

gbl

GridBagLayout gbl
DOCUMENT ME!

haveFreeRangeThreshold

boolean[] haveFreeRangeThreshold
true for pixels with calculated freeRangeRThreshold values.

haveThreshold

boolean[] haveThreshold
DOCUMENT ME!

imageA

ModelImage imageA
DOCUMENT ME!

imageB

ModelImage imageB
DOCUMENT ME!

imageBufferA

float[] imageBufferA
DOCUMENT ME!

imageBufferB

float[] imageBufferB
DOCUMENT ME!

imageBufferDest

float[] imageBufferDest
DOCUMENT ME!

innerPanel

JPanel innerPanel
DOCUMENT ME!

labelCurrent

JLabel labelCurrent
DOCUMENT ME!

labelCurrentColoc

JLabel labelCurrentColoc
private JLabel labelLineFunction;.

labelCurrentIntensity1

JLabel labelCurrentIntensity1
DOCUMENT ME!

labelCurrentIntensity2

JLabel labelCurrentIntensity2
DOCUMENT ME!

labelLinearCorrelation

JLabel labelLinearCorrelation
DOCUMENT ME!

labelPValue

JLabel labelPValue
DOCUMENT ME!

leftPad

int leftPad
The spaces around the histogram bin area.

linearCorrelation

float linearCorrelation
The linear correlation coefficient for all points with either buffer[i] >= threshold1 or secondBuffer[i] >= threshold2.

lineMin1

double lineMin1
The endpoints of the line segment in (buffer,secondBuffer) values.

lineMax1

double lineMax1
The endpoints of the line segment in (buffer,secondBuffer) values.

lineMin2

double lineMin2
The endpoints of the line segment in (buffer,secondBuffer) values.

lineMax2

double lineMax2
The endpoints of the line segment in (buffer,secondBuffer) values.

logDisplayButton

JToggleButton logDisplayButton
DOCUMENT ME!

logMagDisplay

boolean logMagDisplay
DOCUMENT ME!

LUTa

ModelLUT LUTa
DOCUMENT ME!

LUTdest

ModelLUT LUTdest
The LUT for the 2D histogram.

menuItemVector

Vector<E> menuItemVector
DOCUMENT ME!

menuObj

ViewMenuBuilder menuObj
DOCUMENT ME!

min1

double min1
Minimum and maximum buffer and secondBuffer areas.

max1

double max1
Minimum and maximum buffer and secondBuffer areas.

min2

double min2
Minimum and maximum buffer and secondBuffer areas.

max2

double max2
Minimum and maximum buffer and secondBuffer areas.

minimumHeight

int minimumHeight
DOCUMENT ME!

minimumToolBarWidth

int minimumToolBarWidth
DOCUMENT ME!

nf

NumberFormat nf
DOCUMENT ME!

nVOI

int nVOI
DOCUMENT ME!

offset

float offset
DOCUMENT ME!

openingMenuBar

JMenuBar openingMenuBar
DOCUMENT ME!

origBrightness

int origBrightness
DOCUMENT ME!

origContrast

float origContrast
red, green, and blue origBrightness remains constant until applyButton is pressed, restores brightness if cancelButton is pressed.

originalX

int originalX
DOCUMENT ME!

originalY

int originalY
DOCUMENT ME!

paintBufferDest

int[] paintBufferDest
DOCUMENT ME!

pixBufferDest

int[] pixBufferDest
DOCUMENT ME!

pointCalculation

boolean pointCalculation
DOCUMENT ME!

pointVOI

VOI pointVOI
DOCUMENT ME!

pressedBorder

Border pressedBorder
DOCUMENT ME!

PValue

float PValue
statistic giving the portion of images generated with randomly scrambled blocks of pixels having a linear correlation coefficient less than that of the actual image.

raisedBorder

Border raisedBorder
DOCUMENT ME!

regionLinesDisplay

boolean regionLinesDisplay
DOCUMENT ME!

regionLinesDisplayButton

JToggleButton regionLinesDisplayButton
DOCUMENT ME!

RGBTA

ModelRGB RGBTA
set to give 6 digits to the right of the decimal.

rightPad

int rightPad
DOCUMENT ME!

rThreshold

float[] rThreshold
The linear correlation coefficients for all pixels with values either below color1 for buffer or below a*color1 + b for secondBuffer.

scale1

double scale1
bin1 is generated from Math.round(scale1*(buffer[i]-min1)) and bin2 is generated from Math.round(scale2*(secondBuffer[i]-min2)).

scale2

double scale2
bin1 is generated from Math.round(scale1*(buffer[i]-min1)) and bin2 is generated from Math.round(scale2*(secondBuffer[i]-min2)).

scrollPane

JScrollPane scrollPane
DOCUMENT ME!

scrollPaneSize

int scrollPaneSize
DOCUMENT ME!

slope

float slope
The slope and offset of the total least squares line.

statusPanel

JPanel statusPanel
DOCUMENT ME!

structureY

int structureY
DOCUMENT ME!

thresholdOn1

boolean thresholdOn1
If true, the matrix of linear correlation coefficients is taken along color 1 at unity spacings. If false, along color 2.

toolBar

JToolBar toolBar
DOCUMENT ME!

topPad

int topPad
DOCUMENT ME!

topPanel

JPanel topPanel
and innerPanel placed in scrollPane.

useBlue

boolean useBlue
DOCUMENT ME!

useGreen

boolean useGreen
DOCUMENT ME!

useRed

boolean useRed
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

VOIs

ViewVOIVector VOIs
red, green, and blue origContrast remains constant until applyButton is pressed, restores contrast if cancelButton is pressed.

xDim

int xDim
Note that xDim and yDim refer to destImage.

yDim

int yDim
Note that xDim and yDim refer to destImage.

xScreen

int xScreen
DOCUMENT ME!

yScreen

int yScreen
DOCUMENT ME!

zoom

float zoom
DOCUMENT ME!

Class gov.nih.mipav.view.ViewJFrameCreatePaint extends JFrame implements Serializable

Serialized Fields

buttonGrid

JToggleButton[][] buttonGrid
Array of toggle buttons used to create the grid

buttonSize

Dimension buttonSize
Make sure the button size is always this dimension

gridHeight

int gridHeight
grid's height

gridWidth

int gridWidth
grid's width

gridPanel

JPanel gridPanel
Panel that holds the grid (stored as private variable so as to remove/rebuild the grid as needed

gridDialog

gov.nih.mipav.view.ViewJFrameCreatePaint.JDialogGridSize gridDialog
The grid resize dialog

openItem

JMenu openItem
Menu item that holds the list of paintbrushes to open (for editing)

blackImage

ImageIcon blackImage
used to create the "selected" state of the buttons

whiteImage

ImageIcon whiteImage
used to create the "unselected" state of the buttons

wasLoaded

boolean wasLoaded
switch that tells the save-dialog that this brush was opened from disk, so brush will be re-written on save

loadName

String loadName
the name of the loaded brush (used with the above wasLoaded parameter)

Class gov.nih.mipav.view.ViewJFrameDICOMParser extends ViewImageDirectory implements Serializable

serialVersionUID: 1085995416072088026L

Serialized Fields

brightness

int brightness
DOCUMENT ME!

brightnessContrastPanel

JPanel brightnessContrastPanel
DOCUMENT ME!

brightnessSlider

JSlider brightnessSlider
DOCUMENT ME!

contrastSlider

JSlider contrastSlider
DOCUMENT ME!

columnKeyTable

Hashtable<K,V> columnKeyTable
DOCUMENT ME!

componentImageDicom

ViewJComponentPreviewImage componentImageDicom
DOCUMENT ME!

contrast

float contrast
DOCUMENT ME!

current

JLabel current
DOCUMENT ME!

current2

JLabel current2
DOCUMENT ME!

disregardSeries

boolean disregardSeries
DOCUMENT ME!

fileInfoVector

Vector<E> fileInfoVector
fileInfoVector represents images in image table but imageTableVector was needed also becasue this handles multiple series in the same dir. fileInfoVector is all the images in the dir but imageTableVector represents all the images that are in the image table at a particular instance or series

imageTableVector

Vector<E> imageTableVector
fileInfoVector represents images in image table but imageTableVector was needed also becasue this handles multiple series in the same dir. fileInfoVector is all the images in the dir but imageTableVector represents all the images that are in the image table at a particular instance or series

imageTable

JTable imageTable
DOCUMENT ME!

imageTableModel

SortingTableModel imageTableModel
DOCUMENT ME!

imageTableSorter

TableSorter imageTableSorter
DOCUMENT ME!

nfc

NumberFormat nfc
DOCUMENT ME!

origBrightness

int origBrightness
DOCUMENT ME!

origContrast

float origContrast
DOCUMENT ME!

rightPane

JSplitPane rightPane
DOCUMENT ME!

seriesNumberCounters

HashMap<K,V> seriesNumberCounters
This is a hashmasp of series numbers and corresponding counter for the number of images in each series.*

seriesOptionBox

JCheckBoxMenuItem seriesOptionBox
DOCUMENT ME!

seriesTable

JTable seriesTable
DOCUMENT ME!

seriesTableModel

SortingTableModel seriesTableModel
DOCUMENT ME!

seriesTableSorter

TableSorter seriesTableSorter
DOCUMENT ME!

studyTable

JTable studyTable
DOCUMENT ME!

studyTableModel

SortingTableModel studyTableModel
DOCUMENT ME!

studyTableSorter

TableSorter studyTableSorter
DOCUMENT ME!

Class gov.nih.mipav.view.ViewJFrameDICOMQuery extends JFrame implements Serializable

serialVersionUID: 3899062842723888728L

Serialized Fields

browseButton

JButton browseButton
DOCUMENT ME!

currentDateL

JLabel currentDateL
DOCUMENT ME!

dicomQuery

DICOM_Query dicomQuery
DOCUMENT ME!

endYearBox

JComboBox endYearBox
DOCUMENT ME!

endMonthBox

JComboBox endMonthBox
DOCUMENT ME!

endDayBox

JComboBox endDayBox
DOCUMENT ME!

font12

Font font12
DOCUMENT ME!

font12B

Font font12B
DOCUMENT ME!

font18B

Font font18B
DOCUMENT ME!

listPanel

JPanel listPanel
DOCUMENT ME!

messageTable

DICOMDisplayer messageTable
DOCUMENT ME!

monthString

String[] monthString
DOCUMENT ME!

moveRequestHash

Hashtable<K,V> moveRequestHash
DOCUMENT ME!

ptNameText

JTextField ptNameText
DOCUMENT ME!

ptIDText

JTextField ptIDText
DOCUMENT ME!

studyNOText

JTextField studyNOText
DOCUMENT ME!

physText

JTextField physText
DOCUMENT ME!

queryLev

JLabel queryLev
DOCUMENT ME!

queryLevel

int queryLevel
DOCUMENT ME!

queryMsgID

int queryMsgID
DOCUMENT ME!

queryPanel

JPanel queryPanel
DOCUMENT ME!

hostsPanel

JPanel hostsPanel
DOCUMENT ME!

setupPanel

JPanel setupPanel
DOCUMENT ME!

aboutPanel

JPanel aboutPanel
DOCUMENT ME!

sendPanel

JPanel sendPanel
DOCUMENT ME!

queryPDU

DICOM_PDUService queryPDU
DOCUMENT ME!

queryResultTable

JTable queryResultTable
DOCUMENT ME!

queryTableModel

ViewTableModel queryTableModel
DOCUMENT ME!

refreshButton

JButton refreshButton
DOCUMENT ME!

rootQueryPanel

JPanel rootQueryPanel
DOCUMENT ME!

sendButton

JButton sendButton
DOCUMENT ME!

sendDestCBox

JComboBox sendDestCBox
DOCUMENT ME!

sendModel

ViewTableModel sendModel
DOCUMENT ME!

sendQueryThread

Thread sendQueryThread
DOCUMENT ME!

sendStatusClearButton

JButton sendStatusClearButton
DOCUMENT ME!

sendStatusTArea

JTextArea sendStatusTArea
DOCUMENT ME!

sendTable

JTable sendTable
DOCUMENT ME!

seriesInstanceUID

String seriesInstanceUID
DOCUMENT ME!

serverModel

ViewTableModel serverModel
DOCUMENT ME!

serverTable

JTable serverTable
DOCUMENT ME!

set

JButton set
DOCUMENT ME!

createStore

JButton createStore
DOCUMENT ME!

editStore

JButton editStore
DOCUMENT ME!

deleteStore

JButton deleteStore
DOCUMENT ME!

setStore

JButton setStore
DOCUMENT ME!

cancel

JButton cancel
DOCUMENT ME!

help1

JButton help1
DOCUMENT ME!

help2

JButton help2
DOCUMENT ME!

help3

JButton help3
DOCUMENT ME!

help4

JButton help4
DOCUMENT ME!

SOPInstanceUID

String SOPInstanceUID
DOCUMENT ME!

sourceTextF

JTextField sourceTextF
DOCUMENT ME!

startCalendar

Calendar startCalendar
DOCUMENT ME!

endCalendar

Calendar endCalendar
DOCUMENT ME!

todayCalendar

Calendar todayCalendar
DOCUMENT ME!

startYearBox

JComboBox startYearBox
DOCUMENT ME!

startMonthBox

JComboBox startMonthBox
DOCUMENT ME!

startDayBox

JComboBox startDayBox
DOCUMENT ME!

storageModel

ViewTableModel storageModel
DOCUMENT ME!

storageTable

JTable storageTable
DOCUMENT ME!

studyInstanceUID

String studyInstanceUID
DOCUMENT ME!

subQueryPanel

JPanel subQueryPanel
DOCUMENT ME!

tabbedPane

JTabbedPane tabbedPane
DOCUMENT ME!

testButton

JButton testButton
DOCUMENT ME!

textArea

JTextArea textArea
DOCUMENT ME!

uids

DICOM_UID[] uids
DOCUMENT ME!

up

JButton up
DOCUMENT ME!

down

JButton down
DOCUMENT ME!

cancelQ

JButton cancelQ
DOCUMENT ME!

send

JButton send
DOCUMENT ME!

move

JButton move
DOCUMENT ME!

create

JButton create
DOCUMENT ME!

edit

JButton edit
DOCUMENT ME!

delete

JButton delete
DOCUMENT ME!

upDirButton

JButton upDirButton
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.ViewJFrameFastMarching2 extends ViewJFrameImage implements Serializable

serialVersionUID: -949160895087175876L

Serialized Fields

m_bIterate

boolean m_bIterate
DOCUMENT ME!

m_bNext

boolean m_bNext
DOCUMENT ME!

Class gov.nih.mipav.view.ViewJFrameFastMarching3 extends ViewJFrameImage implements Serializable

serialVersionUID: 7827645314485923857L

Serialized Fields

m_bIterate

boolean m_bIterate
DOCUMENT ME!

m_bNext

boolean m_bNext
DOCUMENT ME!

Class gov.nih.mipav.view.ViewJFrameGraph extends JFrame implements Serializable

serialVersionUID: 5127841803361813975L

Serialized Fields

autoShrinkRange

boolean autoShrinkRange
DOCUMENT ME!

autoShrinkRangeCheckbox

JCheckBox autoShrinkRangeCheckbox
DOCUMENT ME!

axisDialog

JDialog axisDialog
DOCUMENT ME!

axisPanel

JPanel axisPanel
DOCUMENT ME!

backgroundButton

JButton backgroundButton
DOCUMENT ME!

backgroundLabel

JLabel backgroundLabel
DOCUMENT ME!

backgroundPanel

JPanel backgroundPanel
DOCUMENT ME!

colorBox

JComboBox colorBox
DOCUMENT ME!

colorChooser

ViewJColorChooser colorChooser
DOCUMENT ME!

colorDialog

JDialog colorDialog
DOCUMENT ME!

copyMenu

JMenu copyMenu
DOCUMENT ME!

defaultDirectory

String defaultDirectory
DOCUMENT ME!

deleteMenu

JMenu deleteMenu
DOCUMENT ME!

editMenu

JMenu editMenu
DOCUMENT ME!

fileMenu

JMenu fileMenu
DOCUMENT ME!

fitFunctPanel

JPanel fitFunctPanel
DOCUMENT ME!

fitFunctTypePanel

JPanel fitFunctTypePanel
DOCUMENT ME!

fitFunctVisibleCheckbox

JCheckBox[] fitFunctVisibleCheckbox
DOCUMENT ME!

fitFunctVisiblePanel

JPanel fitFunctVisiblePanel
DOCUMENT ME!

fitMode

ViewJFrameGraph.FitMode fitMode
Current mode for fitting functions

frameGraphVOI

VOI frameGraphVOI
DOCUMENT ME!

functionIndex

int functionIndex
DOCUMENT ME!

functLineColorButton

JButton[] functLineColorButton
DOCUMENT ME!

functVisibleCheckbox

JCheckBox[] functVisibleCheckbox
the slope changes.

graph

ViewJComponentGraph graph
DOCUMENT ME!

gridDialog

JDialog gridDialog
DOCUMENT ME!

gridlinesCheckbox

JCheckBox gridlinesCheckbox
DOCUMENT ME!

gridPanel

JPanel gridPanel
DOCUMENT ME!

itemClose

JMenuItem itemClose
DOCUMENT ME!

itemFittedCheckbox

JCheckBox[] itemFittedCheckbox
DOCUMENT ME!

itemModifyGraph

JMenuItem itemModifyGraph
DOCUMENT ME!

itemNormalize

JMenuItem itemNormalize
DOCUMENT ME!

itemOpenNewGraph

JMenuItem itemOpenNewGraph

itemOpenSameGraph

JMenuItem itemOpenSameGraph
DOCUMENT ME!

itemPasteFunct

JMenuItem itemPasteFunct
DOCUMENT ME!

itemPrintGraph

JMenuItem itemPrintGraph
DOCUMENT ME!

itemResetGraph

JMenuItem itemResetGraph
DOCUMENT ME!

itemResetRange

JMenuItem itemResetRange
DOCUMENT ME!

itemSaveGraph

JMenuItem itemSaveGraph
DOCUMENT ME!

itemTableOutput

JMenuItem itemTableOutput

lastUnits

String lastUnits
DOCUMENT ME!

legendCheckbox

JCheckBox legendCheckbox
DOCUMENT ME!

nameField

JTextField[] nameField
DOCUMENT ME!

functionLabel

JLabel[] functionLabel
DOCUMENT ME!

legendPanel

JPanel legendPanel
DOCUMENT ME!

mainPanel

JPanel mainPanel
DOCUMENT ME!

maxRangeField

JTextField maxRangeField
DOCUMENT ME!

maxRangeLabel

JLabel maxRangeLabel
DOCUMENT ME!

menuPanel

JPanel menuPanel
DOCUMENT ME!

messageGraph

ViewJFrameMessageGraph messageGraph
DOCUMENT ME!

minorTickMarksCheckbox

JCheckBox minorTickMarksCheckbox
DOCUMENT ME!

minRangeField

JTextField minRangeField
DOCUMENT ME!

minRangeLabel

JLabel minRangeLabel
DOCUMENT ME!

modifyDialog

JDialog modifyDialog
DOCUMENT ME!

modifyGraphPanel

JPanel modifyGraphPanel
DOCUMENT ME!

modifyTabbedPane

JTabbedPane modifyTabbedPane
DOCUMENT ME!

functionPropPanel

JPanel functionPropPanel
DOCUMENT ME!

openingMenuBar

JMenuBar openingMenuBar
DOCUMENT ME!

pointsCheckbox

JCheckBox pointsCheckbox
DOCUMENT ME!

pointsVisiblePanel

JPanel pointsVisiblePanel
DOCUMENT ME!

fitType

JComboBox fitType
Combo box for selecting the fitting function type

rangeDialog

JDialog rangeDialog
DOCUMENT ME!

rangePanel

JPanel rangePanel
DOCUMENT ME!

resetRangeButton

JButton resetRangeButton
DOCUMENT ME!

showPanel

JPanel showPanel
DOCUMENT ME!

tabbedPane

JTabbedPane tabbedPane
DOCUMENT ME!

titleField

JTextField titleField
DOCUMENT ME!

titleLabel

JLabel titleLabel
DOCUMENT ME!

units

String units
DOCUMENT ME!

updateRGBIndex

int updateRGBIndex
DOCUMENT ME!

vectorCopyFunct

Vector<E> vectorCopyFunct
DOCUMENT ME!

vectorDeleteFunct

Vector<E> vectorDeleteFunct
DOCUMENT ME!

viewMenu

JMenu viewMenu
DOCUMENT ME!

voi

VOI voi
DOCUMENT ME!

xAxisLabel

JLabel xAxisLabel
DOCUMENT ME!

xAxisLabelField

JTextField xAxisLabelField
DOCUMENT ME!

xGridLineField

JTextField xGridLineField
DOCUMENT ME!

xGridLineLabel

JLabel xGridLineLabel
DOCUMENT ME!

yAxisLabel

JLabel yAxisLabel
DOCUMENT ME!

yAxisLabelField

JTextField yAxisLabelField
DOCUMENT ME!

yGridLineField

JTextField yGridLineField
DOCUMENT ME!

yGridLineLabel

JLabel yGridLineLabel
DOCUMENT ME!

Class gov.nih.mipav.view.ViewJFrameHistoLUT extends ViewJFrameBase implements Serializable

serialVersionUID: -5323312688163424096L

Serialized Fields

calcThresholdVolume

boolean calcThresholdVolume
DOCUMENT ME!

colEMFrame

ViewJFrameColocalizationEM colEMFrame
DOCUMENT ME!

colRegFrame

ViewJFrameColocalizationRegression colRegFrame
DOCUMENT ME!

entireFlag

boolean entireFlag
DOCUMENT ME!

lutPanel

ViewJPanelLUT lutPanel
DOCUMENT ME!

menuObj

ViewMenuBuilder menuObj
DOCUMENT ME!

regComponent

ViewJComponentRegistration regComponent
DOCUMENT ME!

Class gov.nih.mipav.view.ViewJFrameHistoRGB extends ViewJFrameBase implements Serializable

serialVersionUID: -4685406207107911894L

Serialized Fields

blueCheckBoxA

JCheckBox blueCheckBoxA
DOCUMENT ME!

blueCheckBoxB

JCheckBox blueCheckBoxB
DOCUMENT ME!

calcThresholdVolume

boolean calcThresholdVolume
DOCUMENT ME!

entireFlag

boolean entireFlag
DOCUMENT ME!

fillValuesA

float[] fillValuesA
DOCUMENT ME!

fillValuesB

float[] fillValuesB
DOCUMENT ME!

greenCheckBoxA

JCheckBox greenCheckBoxA
DOCUMENT ME!

greenCheckBoxB

JCheckBox greenCheckBoxB
DOCUMENT ME!

histogramABlue

ModelHistogram histogramABlue
DOCUMENT ME!

histogramAGreen

ModelHistogram histogramAGreen
DOCUMENT ME!

histogramARed

ModelHistogram histogramARed
DOCUMENT ME!

histogramBBlue

ModelHistogram histogramBBlue
DOCUMENT ME!

histogramBGreen

ModelHistogram histogramBGreen
DOCUMENT ME!

histogramBRed

ModelHistogram histogramBRed
DOCUMENT ME!

histoPanelA

ViewJPanelHistoLUT histoPanelA
DOCUMENT ME!

histoPanelB

ViewJPanelHistoLUT histoPanelB
DOCUMENT ME!

logCheckBoxA

JCheckBox logCheckBoxA
DOCUMENT ME!

logCheckBoxB

JCheckBox logCheckBoxB
DOCUMENT ME!

menuObj

ViewMenuBuilder menuObj
DOCUMENT ME!

panelA

JPanel panelA
DOCUMENT ME!

panelB

JPanel panelB
DOCUMENT ME!

redCheckBoxA

JCheckBox redCheckBoxA
DOCUMENT ME!

redCheckBoxB

JCheckBox redCheckBoxB
DOCUMENT ME!

redRGBButton

JToggleButton redRGBButton
DOCUMENT ME!

blueRGBButton

JToggleButton blueRGBButton
DOCUMENT ME!

greenRGBButton

JToggleButton greenRGBButton
DOCUMENT ME!

allRGBButton

JToggleButton allRGBButton
DOCUMENT ME!

regComponent

ViewJComponentRegistration regComponent
DOCUMENT ME!

RGBExtents

int[] RGBExtents
DOCUMENT ME!

RGBTA

ModelRGB RGBTA
DOCUMENT ME!

RGBTB

ModelRGB RGBTB
DOCUMENT ME!

tabbedPane

JTabbedPane tabbedPane
DOCUMENT ME!

threshLowerBF

JTextField threshLowerBF
DOCUMENT ME!

threshUpperBF

JTextField threshUpperBF
DOCUMENT ME!

threshFillBF

JTextField threshFillBF
DOCUMENT ME!

threshLowerF

JTextField threshLowerF
threshold related.

threshUpperF

JTextField threshUpperF
threshold related.

threshFillF

JTextField threshFillF
threshold related.

toolBar

JToolBar toolBar
DOCUMENT ME!

toolBarObj

ViewToolBarBuilder toolBarObj
Object which generates the toolbar.

updateCheckBoxA

JCheckBox updateCheckBoxA
DOCUMENT ME!

updateCheckBoxB

JCheckBox updateCheckBoxB
DOCUMENT ME!

useThresholdChannelA

boolean[] useThresholdChannelA
DOCUMENT ME!

useThresholdChannelB

boolean[] useThresholdChannelB
DOCUMENT ME!

voxelVolumeLabel

JLabel voxelVolumeLabel
DOCUMENT ME!

voxelVolumeLabelB

JLabel voxelVolumeLabelB
DOCUMENT ME!

lutAdjustCheckboxB

JCheckBox lutAdjustCheckboxB
DOCUMENT ME

Class gov.nih.mipav.view.ViewJFrameImage extends ViewJFrameBase implements Serializable

serialVersionUID: -5990635548319625443L

Serialized Fields

componentImage

ViewJComponentEditImage componentImage
Object where DICOM image, ... is converted and displayed as a Java image

controls

ViewControlsImage controls
Reference to the toolbars located in the controls object.

heightResFactor

float heightResFactor
Storage for correction parameters where datasets have non isotropic values.

imageBufferA

float[] imageBufferA
Buffer used to store image intensities the presently viewed slice of image A.

imageBufferB

float[] imageBufferB
Buffer used to store image intensities the presently viewed slice of image B.

infoDialogA

JDialogImageInfo infoDialogA
reference to the JDialogImageInfo for updating slice/resolutions.

infoDialogB

JDialogImageInfo infoDialogB
DOCUMENT ME!

logMagDisplay

boolean logMagDisplay
Flag indicating whether or not that the image should be displayed in Log scale. Used primarily for displaying the FFT of an image.

menuBar

JMenuBar menuBar
Reference to the frame's menu bar.

menuBarMaker

ViewMenuBar menuBarMaker
Constructs the image menu bar.

menuBuilder

ViewMenuBuilder menuBuilder
This object contains a number of useful functions for building a menu and querying the state of menu items.

nImage

int nImage
Number of slices in a 3D dataset.

nTImage

int nTImage
Number of time sequences in a 4D dataset.

pixBuffer

int[] pixBuffer
Integer buffer (4 bytes that stores the concatenated Alpha (1 byte), Red (1 byte), Green ( 1 byte ), Blue (1 byte ) data. The ARGB values are generated by using the imageA intensities as a index into a LUT.

pixBufferB

int[] pixBufferB
Integer buffer (4 bytes that stores the concatenated Alpha (1 byte), Red (1 byte), Green ( 1 byte ), Blue (1 byte ) data. The ARGB values are generated by using the imageB intensities as a index into a LUT.

resols

float[] resols
Storage of the image voxel resolutions. One resolution value per dimension.

scrollPane

JScrollPane scrollPane
The scrollPane where the image is displayed.

units

int[] units
Storage of the resolution units of measure. For example, mm, cm, inches ...

widthResFactor

float widthResFactor
Storage for correction parameters where datasets have non isotropic values.

windowLevel

JDialogWinLevel[] windowLevel
Reference to the two window and level dialogs where [0] is for imageA, [1] for imageB.

zoom

float zoom
Defaults magnification of image to 1.

colorChooser

ViewJColorChooser colorChooser
Reference to the color chooser.

doOrients

boolean doOrients
DOCUMENT ME!

doOrigins

boolean doOrigins
When loading an image into B slot, should origins and orients be matched?

gridOptions

JDialogGridOptions gridOptions
Only want one gridoptions dialog per jframeimage.

isShiftDown

boolean isShiftDown
boolean indicating if shift button is down.

paintBrushLocked

boolean paintBrushLocked
used in conjuction with the above variable, stating that the paint brush has been changed but will change back to previous.

previousPaintBrushIndex

int previousPaintBrushIndex
Holds the selected Paint brush index while painting in hold 0-9 key mode.

quickPaintBrushIndex

int quickPaintBrushIndex
DOCUMENT ME!

useXOR

boolean useXOR
tells whether or not to XOR when creating binary masks (allowing holes).

zoomDialog

JDialogZoom zoomDialog
Reference to the magnification tool.

dpDialog

JDialogDataProvenance dpDialog
Data provenance dialog

m_kAutoItkLoader

AutoItkLoader m_kAutoItkLoader

multipaintDialog

JDialogMultiPaint multipaintDialog
reference to the JDialogMultiPaint for shortcuts

Class gov.nih.mipav.view.ViewJFrameLightBox extends ViewJFrameBase implements Serializable

serialVersionUID: -4014825600247045462L

Serialized Fields

activeSliceButton

JButton activeSliceButton
DOCUMENT ME!

borderColor

Color borderColor
Color for the line border surrounding each image in the light-box.

borderSize

int borderSize
Spacing for the line border surrounding each image in the light-box.

componentImage

ViewJComponentEditImage[] componentImage
DOCUMENT ME!

controls

ViewControlsImage controls
DOCUMENT ME!

currentPage

int currentPage
Page information.

currentSelectedSlice

int currentSelectedSlice
DOCUMENT ME!

currentSlice

int currentSlice
Current info -- this slice info refers to the *real* slice number, not the page index for a slice on a page.

currentTSlice

int currentTSlice
DOCUMENT ME!

deleteButton

JButton deleteButton
DOCUMENT ME!

deleteSelection

JMenuItem deleteSelection
DOCUMENT ME!

extractButton

JButton extractButton
DOCUMENT ME!

extractSelection

JMenuItem extractSelection
DOCUMENT ME!

interpolateShapesButton

JButton interpolateShapesButton
DOCUMENT ME!

firstPageButton

JButton firstPageButton
DOCUMENT ME!

firstPageMenuItem

JMenuItem firstPageMenuItem
DOCUMENT ME!

frameHeight

int frameHeight
DOCUMENT ME!

frameWidth

int frameWidth
Frame information.

goToSliceText

JTextField goToSliceText
DOCUMENT ME!

gridColor

Color gridColor
Color for the region in-between the images in the light-box.

gridColumn

int gridColumn
DOCUMENT ME!

gridRow

int gridRow
Value for the number of rows (number of images along the y-axis) and columns (number of images along the x-axis) in the light-box.

Note that both row and column set to 1 cannot make sense, but that one or the other will be the 'dependent variable' as defined by the row_dependent boolean var.

A value of 0 means that the dependent variable will automatically be sized to its maximum size that can fit nicely on the screen.

gridSpacing

int gridSpacing
Spacing between images in the light-box.

increment

int increment

group

ButtonGroup group
DOCUMENT ME!

imageBorder

CompoundBorder[] imageBorder
DOCUMENT ME!

imageBufferA

float[] imageBufferA
DOCUMENT ME!

imageBufferB

float[] imageBufferB
DOCUMENT ME!

imageFrame

ViewJFrameImage imageFrame
DOCUMENT ME!

imageHeight

int imageHeight
DOCUMENT ME!

imagePanel

JPanel[] imagePanel
DOCUMENT ME!

imagePanelSizeX

int imagePanelSizeX
Per num visible images information.

imagePanelSizeY

int imagePanelSizeY
Per num visible images information.

imageWidth

int imageWidth
DOCUMENT ME!

lastPageButton

JButton lastPageButton
DOCUMENT ME!

lastPageMenuItem

JMenuItem lastPageMenuItem
DOCUMENT ME!

lastSelectedSlice

int lastSelectedSlice
DOCUMENT ME!

lightBoxOptions

JDialogLightBox lightBoxOptions
DOCUMENT ME!

LUTa

ModelLUT LUTa
DOCUMENT ME!

LUTb

ModelLUT LUTb
DOCUMENT ME!

magMax

float magMax
DOCUMENT ME!

magMin

float magMin
DOCUMENT ME!

magnification

float magnification
Magnification of images in the light-box (mag is a percentage).

maxPagePanelSizeX

int maxPagePanelSizeX
DOCUMENT ME!

maxPagePanelSizeY

int maxPagePanelSizeY
DOCUMENT ME!

menuBar

JMenuBar menuBar
Variables for the menubar.

nextPageButton

JButton nextPageButton
elements of paging toolbar.

nextPageMenuItem

JMenuItem nextPageMenuItem
DOCUMENT ME!

numPages

int numPages
DOCUMENT ME!

numTotalSlices

int numTotalSlices
DOCUMENT ME!

numTSlices

int numTSlices
DOCUMENT ME!

numVisibleSlices

int numVisibleSlices
DOCUMENT ME!

pagePanel

JPanel pagePanel
DOCUMENT ME!

pagePanelSizeX

int pagePanelSizeX
DOCUMENT ME!

pagePanelSizeY

int pagePanelSizeY
DOCUMENT ME!

pagingTBar

JToolBar pagingTBar
DOCUMENT ME!

pixBuffer

int[] pixBuffer
DOCUMENT ME!

pixBufferB

int[] pixBufferB
DOCUMENT ME!

prevPageButton

JButton prevPageButton
DOCUMENT ME!

prevPageMenuItem

JMenuItem prevPageMenuItem
DOCUMENT ME!

repaintButton

JButton repaintButton
DOCUMENT ME!

resolutionX

float resolutionX
DOCUMENT ME!

resolutionY

float resolutionY
DOCUMENT ME!

row_dependent

boolean row_dependent
Indicates which--row or column--should be dependent on the other.

the default is the number of rows is the dependent variable, and is dependent apon the total number of images and the number of columns. Don't confuse the reading to be "This display is (t/f) dependent on the row." It -could- be read as "The display is a column-independent (t/f) matrix".

selectedBorderColor

Color selectedBorderColor
Color for the line border surrounding each selected image in the light-box.

selectedBorderSize

int selectedBorderSize
Spacing for the selected line border surrounding each image in the light-box.

selectedImages

Vector<E> selectedImages
The selectedImages contains the *real* slice numbers -- not the index of a slice on a page. So the maximum number in the vector will be numTotalSlices - 1.

selectedTimeSlices

Vector<E> selectedTimeSlices
The selected Time Slices vector contains the real slice number and time slice number in the format (slice #).(time slice #) the maximum number in the vector will be numTotalSlices * t.

selectIndividualTSlices

JCheckBoxMenuItem selectIndividualTSlices
DOCUMENT ME!

singleTSlice

boolean singleTSlice
DOCUMENT ME!

srcImage

ModelImage srcImage
DOCUMENT ME!

tBar

JToolBar tBar
DOCUMENT ME!

toolbarPanel

JPanel toolbarPanel
Variables for the toolbar.

unselectedBorderColor

Color unselectedBorderColor
DOCUMENT ME!

updatePaint

JCheckBoxMenuItem updatePaint
DOCUMENT ME!

xScreen

int xScreen
DOCUMENT ME!

yScreen

int yScreen
DOCUMENT ME!

Class gov.nih.mipav.view.ViewJFrameMemory extends JFrame implements Serializable

serialVersionUID: -8863264033308071151L

Serialized Fields

bm

BarMeter bm
DOCUMENT ME!

callGCbutton

JButton callGCbutton
DOCUMENT ME!

lm

LineMeter lm
DOCUMENT ME!

pauseButton

JButton pauseButton
DOCUMENT ME!

paused

boolean paused
DOCUMENT ME!

percentUsed

JLabel percentUsed
DOCUMENT ME!

sampleRate

JTextField sampleRate
DOCUMENT ME!

surf

ViewJFrameMemory.MemoryMonitor surf
thread.

total

JLabel total
DOCUMENT ME!

used

JLabel used
test notification of memory used.

Class gov.nih.mipav.view.ViewJFrameMessage extends JFrame implements Serializable

serialVersionUID: -1198653323631787447L

Serialized Fields

delTabButton

JButton delTabButton
DOCUMENT ME!

frameInsets

Insets frameInsets
DOCUMENT ME!

lastState

int lastState
Indicates last state of frame - NORMAL or ICONIFIED.

menu

JMenuBar menu
DOCUMENT ME!

removeCurrentTab

JMenuItem removeCurrentTab
DOCUMENT ME!

tabbedPane

JTabbedPane tabbedPane
DOCUMENT ME!

tBar

JToolBar tBar
DOCUMENT ME!

Class gov.nih.mipav.view.ViewJFrameMessage.ScrollTextArea extends JScrollPane implements Serializable

serialVersionUID: 3869765356771292936L

Serialized Fields

tArea

JTextArea tArea
DOCUMENT ME!

Class gov.nih.mipav.view.ViewJFrameMessageGraph extends JFrame implements Serializable

serialVersionUID: -3229727417859189823L

Serialized Fields

debugArea

JTextArea debugArea
DOCUMENT ME!

debugSPane

JScrollPane debugSPane
DOCUMENT ME!

font12

Font font12
DOCUMENT ME!

font12B

Font font12B
DOCUMENT ME!

frameInsets

Insets frameInsets
DOCUMENT ME!

menu

JMenuBar menu
DOCUMENT ME!

tBar

JToolBar tBar
DOCUMENT ME!

Class gov.nih.mipav.view.ViewJFrameMultiple extends ViewJFrameImage implements Serializable

serialVersionUID: -1374582208019835548L

Serialized Fields

states

ViewJFrameMultiple.StateList states
The state keys used to store/retrieve the image states, (optionally) in order.

componentTable

Hashtable<K,V> componentTable
Table of ComponentImages to be displayed on various frames. The current component image is stored in componentImage.

controlsTable

Hashtable<K,V> controlsTable
Table of toolbar image controls. The current controls are stored in controls.

currentKey

String currentKey
The last key used to access one of the images of this frame.

imageATable

Hashtable<K,V> imageATable
Table of images being used in this frame. The key for each image indicates which tab it should be used for. Stored in imageA.

imageBTable

Hashtable<K,V> imageBTable
Table of images being used in this frame. The key for each image indicates which tab it should be used for. Stored in imageB.

LUTaTable

Hashtable<K,V> LUTaTable
Table of LUTs to accompany the image table. Stored in LUTa.

LUTbTable

Hashtable<K,V> LUTbTable
Table of LUTs to accompany the image table. Stored in LUTb.

projectInfo

FileInfoProject projectInfo
Contains parameters and images to be used by the frame.

scrollPaneTable

Hashtable<K,V> scrollPaneTable
Table of the scroll panes, which hold the component images. The current scroll pane is stored in scrollPane.

Class gov.nih.mipav.view.ViewJFrameMultiple.StateList extends Vector implements Serializable

serialVersionUID: 7118784852919366358L

Class gov.nih.mipav.view.ViewJFramePaintVasculature extends ViewJFrameBase implements Serializable

serialVersionUID: 1332576394417707204L

Serialized Fields

componentImage

ViewJComponentEditImage componentImage
Display of the MIP image.

fudgeFactor

int fudgeFactor
Frame adjustment to keep the frame from being just small enough for the ScrollPane to display the scroll bars. Windows seems to find an inset value needing a fudge factor of 3, but Mac OS 10 (X), doesn't, and needs a fudge factor of 7 to not require scroll bars. Either way, insets + fudge-factor must equal 7.

heightResFactor

float heightResFactor
Storage for correction parameters where datasets have non isotropic values.

imageBuffer

float[] imageBuffer
Buffer used to store image intensities the presently viewed slice of image.

logMagDisplay

boolean logMagDisplay
Flag indicating whether or not that the image should be displayed in Log scale. Used primarily for displaying the FFT of an image.

mipBuffer

float[] mipBuffer
Buffer to store the MIP image that results from the raytrace.

mipExtents

int[] mipExtents
The dimensions of the MIP image.

mipImage

ModelImage mipImage
MIP image generated from the volume.

mipZTable

Hashtable<K,V> mipZTable
Table which holds the z coordinate on the 3D volume for a point (x,y) on the 2D MIP image.

paintDialog

JDialogPaintVasculature paintDialog
Dialog to facilitate vasculature painting.

parent

ViewJFrameBase parent
Parent frame of this frame.

pixBuffer

int[] pixBuffer
Integer buffer (4 bytes that stores the concatenated Alpha (1 byte), Red (1 byte), Green ( 1 byte ), Blue (1 byte ) data. The ARGB values are generated by using the mipImage intensities as a index into a LUT.

resols

float[] resols
Storage of the image voxel resolutions. One resolution value per dimension.

seedPoints

VOI seedPoints
VOI containing the possible seed points.

units

int[] units
Storage of the resolution units of measure. For example, mm, cm, inches ...

widthResFactor

float widthResFactor
Storage for correction parameters where datasets have non isotropic values.

xScreen

int xScreen
Width of the display screen.

yScreen

int yScreen
Height of the display screen.

zoom

float zoom
Defaults magnification of image to 1.

scrollPane

JScrollPane scrollPane
The scrollPane where the image is displayed.

Class gov.nih.mipav.view.ViewJFrameRegisteredImages extends JFrame implements Serializable

serialVersionUID: -4417297294466318211L

Serialized Fields

callDeletebutton

JButton callDeletebutton
DOCUMENT ME!

callGCbutton

JButton callGCbutton
DOCUMENT ME!

callToFrontbutton

JButton callToFrontbutton
DOCUMENT ME!

imageList

JList imageList
DOCUMENT ME!

pauseButton

JButton pauseButton
DOCUMENT ME!

paused

boolean paused
DOCUMENT ME!

sampleRate

JTextField sampleRate
DOCUMENT ME!

scrollPane

JScrollPane scrollPane
DOCUMENT ME!

surf

ImageRegistryMonitor surf
thread to watch image registry.

UI

ViewUserInterface UI
DOCUMENT ME!

Class gov.nih.mipav.view.ViewJFrameRegistration extends ViewJFrameBase implements Serializable

serialVersionUID: 229266911029610324L

Serialized Fields

toggleArray

JToggleButton[] toggleArray
DOCUMENT ME!

serif12

Font serif12
DOCUMENT ME!

adjMark

int adjMark
DOCUMENT ME!

adjMarkButton

JToggleButton adjMarkButton
DOCUMENT ME!

adjMarkMinusButton

JButton adjMarkMinusButton
DOCUMENT ME!

alphaSlider

JSlider alphaSlider
DOCUMENT ME!

bufferFactor

int bufferFactor
DOCUMENT ME!

bufferSize

int bufferSize
DOCUMENT ME!

buttonArray

JButton[] buttonArray
DOCUMENT ME!

ccwButton

JButton ccwButton
DOCUMENT ME!

componentImage

ViewJComponentRegistration componentImage
DOCUMENT ME!

componentY

int componentY
DOCUMENT ME!

controlPanel

JPanel controlPanel
DOCUMENT ME!

controls

ViewControlsImage controls
DOCUMENT ME!

cpGBC

GridBagConstraints cpGBC
DOCUMENT ME!

cpGBL

GridBagLayout cpGBL
DOCUMENT ME!

curAdjMark

int curAdjMark
DOCUMENT ME!

curRefMark

int curRefMark
DOCUMENT ME!

cwButton

JButton cwButton
DOCUMENT ME!

defaultModeButton

JToggleButton defaultModeButton
DOCUMENT ME!

degreeIncrement

float degreeIncrement
DOCUMENT ME!

degreeIncrementButton

JButton degreeIncrementButton
DOCUMENT ME!

doDrag

boolean doDrag
DOCUMENT ME!

doneLeastSquares

boolean doneLeastSquares
DOCUMENT ME!

doRegionB

boolean doRegionB
DOCUMENT ME!

downButton

JButton downButton
DOCUMENT ME!

dragButton

JToggleButton dragButton
DOCUMENT ME!

etchedBorder

Border etchedBorder
DOCUMENT ME!

extents

int[] extents
DOCUMENT ME!

fileMenu

JMenu fileMenu
DOCUMENT ME!

font12

Font font12
DOCUMENT ME!

gbc

GridBagConstraints gbc
DOCUMENT ME!

haveVOIPoints

boolean haveVOIPoints
DOCUMENT ME!

helpMenu

JMenu helpMenu
DOCUMENT ME!

i

int i
DOCUMENT ME!

j

int j
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

imageBufferA

float[] imageBufferA
DOCUMENT ME!

imageBufferB

float[] imageBufferB
DOCUMENT ME!

imageBufferOriginalB

float[] imageBufferOriginalB
DOCUMENT ME!

imageSize

int imageSize
DOCUMENT ME!

itemClose

JMenuItem itemClose
DOCUMENT ME!

itemHelp

JMenuItem itemHelp
DOCUMENT ME!

labelReferenceSlice

JLabel labelReferenceSlice
DOCUMENT ME!

labelAdjustedSlice

JLabel labelAdjustedSlice
DOCUMENT ME!

labelTable

Hashtable<K,V> labelTable
DOCUMENT ME!

labelTable2

Hashtable<K,V> labelTable2
DOCUMENT ME!

leftButton

JButton leftButton
DOCUMENT ME!

linkedXMLName

String linkedXMLName
DOCUMENT ME!

logMagDisplay

boolean logMagDisplay
DOCUMENT ME!

markerType

int[] markerType
DOCUMENT ME!

minimumToolBarWidth

int minimumToolBarWidth
DOCUMENT ME!

mode

int mode
DOCUMENT ME!

movementGroup

ButtonGroup movementGroup
DOCUMENT ME!

n

int n
DOCUMENT ME!

newAlphaBlend

int newAlphaBlend
DOCUMENT ME!

newExtents

int[] newExtents
DOCUMENT ME!

nImage

int nImage
DOCUMENT ME!

nVOI

int nVOI
DOCUMENT ME!

openingMenuBar

JMenuBar openingMenuBar
DOCUMENT ME!

paintBuffer

int[] paintBuffer
DOCUMENT ME!

pixBuffer

int[] pixBuffer
DOCUMENT ME!

pixBufferB

int[] pixBufferB
DOCUMENT ME!

pixelIncrement

float pixelIncrement
DOCUMENT ME!

pixelIncrementButton

JButton pixelIncrementButton
DOCUMENT ME!

pointSetA

double[][] pointSetA
DOCUMENT ME!

pointSetB

double[][] pointSetB
DOCUMENT ME!

pressedBorder

Border pressedBorder
DOCUMENT ME!

refMark

int refMark
DOCUMENT ME!

refMarkButton

JToggleButton refMarkButton
DOCUMENT ME!

refMarkMinusButton

JButton refMarkMinusButton
DOCUMENT ME!

rightButton

JButton rightButton
DOCUMENT ME!

rotateButton

JToggleButton rotateButton
DOCUMENT ME!

scrollPane

JScrollPane scrollPane
DOCUMENT ME!

scrollPaneSize

int scrollPaneSize
DOCUMENT ME!

secondImage

ModelImage secondImage
DOCUMENT ME!

slider

JSlider slider
DOCUMENT ME!

slider2

JSlider slider2
DOCUMENT ME!

structureY

int structureY
DOCUMENT ME!

textReferenceSlice

JTextField textReferenceSlice
DOCUMENT ME!

textAdjustedSlice

JTextField textAdjustedSlice
DOCUMENT ME!

toolBar

JToolBar toolBar
DOCUMENT ME!

toolBar2

JToolBar toolBar2
DOCUMENT ME!

toolBarObj

ViewToolBarBuilder toolBarObj
DOCUMENT ME!

toolBarObj2

ViewToolBarBuilder toolBarObj2
DOCUMENT ME!

topPanel

JPanel topPanel
DOCUMENT ME!

translateButton

JToggleButton translateButton
DOCUMENT ME!

upButton

JButton upButton
DOCUMENT ME!

voi

VOI voi
DOCUMENT ME!

VOIPoints

WildMagic.LibFoundation.Mathematics.Vector3f[] VOIPoints
DOCUMENT ME!

xDim

int xDim
DOCUMENT ME!

xfrm

TransMatrix xfrm
DOCUMENT ME!

xfrmBA

TransMatrix xfrmBA
DOCUMENT ME!

xfrmD

TransMatrix xfrmD
DOCUMENT ME!

xfrmH

TransMatrix xfrmH
DOCUMENT ME!

xOrg

int[] xOrg
DOCUMENT ME!

xPres

int[] xPres
DOCUMENT ME!

xRes

float xRes
DOCUMENT ME!

xRotation

float xRotation
DOCUMENT ME!

xScreen

int xScreen
DOCUMENT ME!

yScreen

int yScreen
DOCUMENT ME!

yDim

int yDim
DOCUMENT ME!

yOrg

int[] yOrg
DOCUMENT ME!

yPres

int[] yPres
DOCUMENT ME!

yRes

float yRes
DOCUMENT ME!

yRotation

float yRotation
DOCUMENT ME!

zoom

float zoom
DOCUMENT ME!

zSlice

int zSlice
DOCUMENT ME!

zSlice2

int zSlice2
DOCUMENT ME!

zLastSlice

int zLastSlice
DOCUMENT ME!

zLastSlice2

int zLastSlice2
DOCUMENT ME!

Class gov.nih.mipav.view.ViewJFrameRegistrationTool extends ViewJFrameBase implements Serializable

serialVersionUID: 5476210706978180244L

Serialized Fields

toggleArray

JToggleButton[] toggleArray
DOCUMENT ME!

serif12

Font serif12
DOCUMENT ME!

adjMark

int adjMark
DOCUMENT ME!

adjMarkButton

JToggleButton adjMarkButton
DOCUMENT ME!

adjMarkMinusButton

JButton adjMarkMinusButton
DOCUMENT ME!

alphaSlider

JSlider alphaSlider
DOCUMENT ME!

bothPanel

JPanel bothPanel
DOCUMENT ME!

bufferFactor

int bufferFactor
DOCUMENT ME!

bufferSize

int bufferSize
DOCUMENT ME!

buttonArray

JButton[] buttonArray
DOCUMENT ME!

ccwButton

JButton ccwButton
DOCUMENT ME!

componentImage

ViewJComponentRegistration componentImage
for both images displayed together.

componentImageA

ViewJComponentSingleRegistration componentImageA
for images to be displayed separately.

componentImageB

ViewJComponentSingleRegistration componentImageB
DOCUMENT ME!

componentY

int componentY
DOCUMENT ME!

controlPanel

JPanel controlPanel
DOCUMENT ME!

controls

ViewControlsImage controls
DOCUMENT ME!

copyAdjToRefButton

JButton copyAdjToRefButton
DOCUMENT ME!

copyRefToAdjButton

JButton copyRefToAdjButton
DOCUMENT ME!

cpGBC

GridBagConstraints cpGBC
DOCUMENT ME!

cpGBL

GridBagLayout cpGBL
DOCUMENT ME!

curAdjMark

int curAdjMark
DOCUMENT ME!

curRefMark

int curRefMark
DOCUMENT ME!

cwButton

JButton cwButton
DOCUMENT ME!

defaultModeButton

JToggleButton defaultModeButton
DOCUMENT ME!

degreeIncrement

float degreeIncrement
DOCUMENT ME!

degreeIncrementButton

JButton degreeIncrementButton
DOCUMENT ME!

doDrag

boolean doDrag
DOCUMENT ME!

doneLeastSquares

boolean doneLeastSquares
DOCUMENT ME!

doRegionB

boolean doRegionB
DOCUMENT ME!

downButton

JButton downButton
DOCUMENT ME!

etchedBorder

Border etchedBorder
DOCUMENT ME!

extents

int[] extents
DOCUMENT ME!

fileMenu

JMenu fileMenu
DOCUMENT ME!

firstDraw

boolean firstDraw
DOCUMENT ME!

font12

Font font12
DOCUMENT ME!

gbc

GridBagConstraints gbc
DOCUMENT ME!

helpMenu

JMenu helpMenu
DOCUMENT ME!

i

int i
DOCUMENT ME!

j

int j
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

imageBufferA

float[] imageBufferA
DOCUMENT ME!

imageBufferB

float[] imageBufferB
DOCUMENT ME!

imageBufferOriginalB

float[] imageBufferOriginalB
DOCUMENT ME!

imageSize

int imageSize
DOCUMENT ME!

itemClose

JMenuItem itemClose
DOCUMENT ME!

itemHelp

JMenuItem itemHelp
DOCUMENT ME!

leftButton

JButton leftButton
DOCUMENT ME!

logMagDisplay

boolean logMagDisplay
DOCUMENT ME!

lsPerformed

boolean lsPerformed
DOCUMENT ME!

mode

int mode
DOCUMENT ME!

movementGroup

ButtonGroup movementGroup
DOCUMENT ME!

n

int n
DOCUMENT ME!

newAlphaBlend

int newAlphaBlend
DOCUMENT ME!

newExtents

int[] newExtents
DOCUMENT ME!

openingMenuBar

JMenuBar openingMenuBar
DOCUMENT ME!

pixBuffer

int[] pixBuffer
DOCUMENT ME!

pixBufferB

int[] pixBufferB
DOCUMENT ME!

pixBufferCompA

int[] pixBufferCompA
DOCUMENT ME!

pixBufferCompB

int[] pixBufferCompB
DOCUMENT ME!

pixelIncrement

float pixelIncrement
DOCUMENT ME!

pixelIncrementButton

JButton pixelIncrementButton
DOCUMENT ME!

pointSetA

double[][] pointSetA
DOCUMENT ME!

pointSetB

double[][] pointSetB
DOCUMENT ME!

pointSetBT

double[][] pointSetBT
DOCUMENT ME!

refMark

int refMark
DOCUMENT ME!

refMarkButton

JToggleButton refMarkButton
DOCUMENT ME!

refMarkMinusButton

JButton refMarkMinusButton
DOCUMENT ME!

regButton

JToggleButton regButton
DOCUMENT ME!

RGBa

ModelRGB RGBa
DOCUMENT ME!

RGBb

ModelRGB RGBb
DOCUMENT ME!

rightButton

JButton rightButton
DOCUMENT ME!

rotateButton

JToggleButton rotateButton
DOCUMENT ME!

scrollPane

JScrollPane scrollPane
DOCUMENT ME!

scrollPaneSeparateA

JScrollPane scrollPaneSeparateA
DOCUMENT ME!

scrollPaneSeparateB

JScrollPane scrollPaneSeparateB
DOCUMENT ME!

scrollPaneSize

int scrollPaneSize
DOCUMENT ME!

secondImage

ModelImage secondImage
DOCUMENT ME!

separatePanel

JPanel separatePanel
DOCUMENT ME!

showVOIs

JCheckBoxMenuItem showVOIs
DOCUMENT ME!

structureY

int structureY
DOCUMENT ME!

tabbedPane

JTabbedPane tabbedPane
DOCUMENT ME!

toolBar

JToolBar toolBar
DOCUMENT ME!

toolBar2

JToolBar toolBar2
DOCUMENT ME!

toolBarSep

JToolBar toolBarSep
DOCUMENT ME!

topPanel

JPanel topPanel
DOCUMENT ME!

translateButton

JToggleButton translateButton
DOCUMENT ME!

upButton

JButton upButton
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

xCoords

int[] xCoords
DOCUMENT ME!

xDim

int xDim
DOCUMENT ME!

xfrm

TransMatrix xfrm
DOCUMENT ME!

xfrmBA

TransMatrix xfrmBA
DOCUMENT ME!

xfrmD

TransMatrix xfrmD
DOCUMENT ME!

xfrmH

TransMatrix xfrmH
DOCUMENT ME!

xOrg

int[] xOrg
DOCUMENT ME!

xRes

float xRes
DOCUMENT ME!

xRotation

float xRotation
DOCUMENT ME!

xScreen

int xScreen
DOCUMENT ME!

yScreen

int yScreen
DOCUMENT ME!

yCoords

int[] yCoords
DOCUMENT ME!

yDim

int yDim
DOCUMENT ME!

yOrg

int[] yOrg
DOCUMENT ME!

yRes

float yRes
DOCUMENT ME!

yRotation

float yRotation
DOCUMENT ME!

zoom

float zoom
DOCUMENT ME!

Class gov.nih.mipav.view.ViewJFrameTriImage extends ViewJFrameBase implements Serializable

serialVersionUID: -7588617549055746009L

Serialized Fields

scrollPane

JScrollPane[] scrollPane
DOCUMENT ME!

triImage

ViewJComponentTriImage[] triImage
DOCUMENT ME!

triImagePanel

JPanel[] triImagePanel
DOCUMENT ME!

btnInvisible

JToggleButton[] btnInvisible
DOCUMENT ME!

bufferFactor

int bufferFactor
1 for black and white, 4 for color.

centerButtonSelected

boolean centerButtonSelected
DOCUMENT ME!

chkShowTalairachGrid

JCheckBox chkShowTalairachGrid
"Show talairach grid" checkbox.

chkShowTalairachGridMarkers

JCheckBox chkShowTalairachGridMarkers
"Show talairach gridmarkers" checkbox.

color

Color color
Color of the paint.

colorChooser

ViewJColorChooser colorChooser
Color chooser to use when selecting paint color.

colorPaintButton

JButton colorPaintButton
Button for changing the color of the paint.

controls

ViewControlsImage controls
Used to obtain initial paint opacity and color.

coordinateListeners

Vector<E> coordinateListeners
A list of CoordinateChangeListeners who want to know about changes to the coordinate currently pointed to by the tri-image frame's crosshairs.

crosshairSpinner

JSpinner crosshairSpinner
Spinner component for the crosshair gap size.

currentAbsolutePositionLabels

Point3D currentAbsolutePositionLabels
The current values of the absolute position labels.

defaultPreferredHeight

int defaultPreferredHeight
The default hight of the window, if it cannot be calculated.

extents

int[] extents
Extents of image.

imageToolBar

JToolBar imageToolBar
Image control toolbar.

intensitySpinner

JSpinner intensitySpinner
Spinner component for the paint intensity.

labelXTal

JTextField labelXTal
Label the Talairach position x value in the image volume.

labelYTal

JTextField labelYTal
Label the Talairach position y value in the image volume.

labelZTal

JTextField labelZTal
Label the Talairach position z value in the image volume.

menuObj

ViewMenuBuilder menuObj
Menu items storage.

oldLayout

boolean oldLayout
DOCUMENT ME!

OPACITY

float OPACITY
Opacity of paint.

paintBrushNames

String[] paintBrushNames
List of built-in and user-defined paint brushes.

paintToolBar

JToolBar paintToolBar
Paint tool bar.

borderPaintButton

JToggleButton borderPaintButton

bogusBorderPaintButton

JToggleButton bogusBorderPaintButton

panelActiveImage

JPanel panelActiveImage
Panel for deciding which image is active; appears when 2 images are loaded.

panelToolbar

JPanel panelToolbar
Panel that holds the toolbars.

parentFrame

ViewJFrameImage parentFrame
Reference to the parent window.

pluginPanel

Component pluginPanel
Reference to the plug-in panel in the 2x2 (old) layout.

radioImageA

JRadioButton radioImageA
Radio button for selecting image A as active.

radioImageB

JRadioButton radioImageB
Radio button for selecting image B as active.

radioImageBoth

JRadioButton radioImageBoth
Radio button for selecting both images as active.

resols

float[] resols
Resolutions of image.

scrollOriginalCrosshair

boolean scrollOriginalCrosshair
Flag telling the crosshair movement to update slice in original image frame.

showTalairachGrid

boolean showTalairachGrid
Flag for showing the Talairach grid on the component images.

showTalairachPosition

boolean showTalairachPosition
Flag for showing the Talairach position on the component images.

tDim

int tDim
Time dimension of the original image.

tImageSlider

JSlider tImageSlider
Slider for 4D images, time dimension.

traverseButton

JToggleButton traverseButton
Button for traversing the images.

tSlice

int tSlice
Time slice that this image is on.

units

int[] units
Units of image - mm, inches, etc.

useInfNew

boolean useInfNew
if true use cerebellum-adjusted static variable.

volumeCenter

int[] volumeCenter
The point to become center of transformed image.

volumePositionFrame

VolumePositionFrame volumePositionFrame
Reference to the volume coordinate frame.

volumePositionPanel

JPanel volumePositionPanel
Reference to the volume coordinate panel when it is in the plug-in position.

zoom

float zoom
Magnification for image.

addPointToggleButton

JToggleButton addPointToggleButton
DOCUMENT ME!

dropperPaintToggleButton

JToggleButton dropperPaintToggleButton
DOCUMENT ME!

indivMagButton

JToggleButton indivMagButton
refs to indiviadual frame zooming in and out buttons.

indivMinButton

JToggleButton indivMinButton
refs to indiviadual frame zooming in and out buttons.

leastSquaresButton

JButton leastSquaresButton
DOCUMENT ME!

magButton

JButton magButton
refs to the magnify and minimize button.*

minButton

JButton minButton
refs to the magnify and minimize button.*

paintBox

JComboBox paintBox
Box holding the list of available paint brushes.

paintBrushLocked

boolean paintBrushLocked
used with the above to say the paint brush has been changed, waiting to change back.

paintCanToggleButton

JToggleButton paintCanToggleButton
DOCUMENT ME!

quickPaintBrushIndex

int quickPaintBrushIndex
int used for quick-key painting for speedier paint brush access.

snapProtractor90

boolean snapProtractor90
Flag for snapping protractor to nearest multiple of 90 degrees.

spinnerDefaultValue

double spinnerDefaultValue
Used to setup the paint spinner.

spinnerMin

double spinnerMin
Used to setup the paint spinner.

spinnerMax

double spinnerMax
Used to setup the paint spinner.

spinnerStep

double spinnerStep
Used to setup the paint spinner.

talairachVoxelLabel

JLabel talairachVoxelLabel
DOCUMENT ME!

toolbarBuilder

ViewToolBarBuilder toolbarBuilder
Toolbar builder reference.

tpSplineButton

JButton tpSplineButton
DOCUMENT ME!

volumeBounds

CubeBounds volumeBounds
Volume Boundary may be changed for cropping the volume.

Class gov.nih.mipav.view.ViewJPanelHistoLUT extends JPanel implements Serializable

serialVersionUID: -3873204112932340987L

Serialized Fields

colorChooser

ViewJColorChooser colorChooser
The LUT color chooser.

componentHistogram

ViewJComponentHLUTBase componentHistogram
The histogram LUT of the image. The square one.

componentLUT

ViewJComponentLUT componentLUT
Lookup table of image. The narrow rectangular one.

histogram

ModelHistogram histogram
Model histogram.

histoLUTType

int histoLUTType
The type of histogram component to show.

image

ModelImage image
The image.

lut

ModelLUT lut
The grayscale lookup table for the image.

LUTIndex

int LUTIndex
The LUT index used when chaning the LUT color by clicking on the ViewJComponentLUT.

lutRecorder

JDialogRecordLUT lutRecorder
LUT recorder.

parent

HistoLUTParent parent
The component containing this panel.

RGBT

ModelRGB RGBT
The RGB lookup table.

Class gov.nih.mipav.view.ViewJPanelLUT extends JPanel implements Serializable

serialVersionUID: -1769974472965867218L

Serialized Fields

ctDialogA

JDialogCT ctDialogA
DOCUMENT ME!

ctDialogB

JDialogCT ctDialogB
DOCUMENT ME!

cursorIndex

int cursorIndex
Active mouse cursor index of the imageA, B and GM image A, B.

cursorIndexB

int cursorIndexB
Active mouse cursor index of the imageA, B and GM image A, B.

entireFlag

boolean entireFlag
DOCUMENT ME!

histogramA

ModelHistogram histogramA
DOCUMENT ME!

histogramB

ModelHistogram histogramB
DOCUMENT ME!

histoPanelA

ViewJPanelHistoLUT histoPanelA
DOCUMENT ME!

histoPanelB

ViewJPanelHistoLUT histoPanelB
DOCUMENT ME!

indexColorATextF

JTextField indexColorATextF
DOCUMENT ME!

indexColorBTextF

JTextField indexColorBTextF
DOCUMENT ME!

interpCheckBoxA

JCheckBox interpCheckBoxA
DOCUMENT ME!

interpCheckBoxB

JCheckBox interpCheckBoxB
DOCUMENT ME!

labelsTable

Hashtable<K,V> labelsTable
Histogram dialog slider labels of the imageA, B and GM imageA, B.

labelsTableB

Hashtable<K,V> labelsTableB
Histogram dialog slider labels of the imageA, B and GM imageA, B.

logCheckBoxA

JCheckBox logCheckBoxA
DOCUMENT ME!

logCheckBoxB

JCheckBox logCheckBoxB
DOCUMENT ME!

mouseLabel

JLabel mouseLabel
The opacity slider label.

mouseLabelB

JLabel mouseLabelB
The opacity slider label.

mouseSlider

JSlider mouseSlider
Opacity X scale sliders.

mouseSliderB

JSlider mouseSliderB
Opacity X scale sliders.

mouseSliderLabels

JLabel[] mouseSliderLabels
The labels below the opacity slider.

mouseSliderLabelsB

JLabel[] mouseSliderLabelsB
The labels below the opacity slider.

nColorsATextF

JTextField nColorsATextF
DOCUMENT ME!

nColorsBTextF

JTextField nColorsBTextF
DOCUMENT ME!

oneBasedLUTCheckBoxImageB

JCheckBox oneBasedLUTCheckBoxImageB
DOCUMENT ME!

outputBox

JComboBox outputBox
DOCUMENT ME!

outputBoxB

JComboBox outputBoxB
DOCUMENT ME!

panelA

JPanel panelA
DOCUMENT ME!

panelB

JPanel panelB
DOCUMENT ME!

panelParent

ViewJFrameHistoLUT panelParent
DOCUMENT ME!

rangeText

JTextField rangeText
X range text field in the imageA, B histogram dialog.

rangeTextB

JTextField rangeTextB
X range text field in the imageA, B histogram dialog.

rangeX

float rangeX
X range value of the imageA, B and GM imageA, B.

rangeXB

float rangeXB
X range value of the imageA, B and GM imageA, B.

scaleRangeA

int scaleRangeA
Scale range value according to the image min and max.

scaleRangeB

int scaleRangeB
Scale range value according to the image min and max.

tabbedPane

JTabbedPane tabbedPane
DOCUMENT ME!

threshLowerBF

JTextField threshLowerBF
DOCUMENT ME!

threshUpperBF

JTextField threshUpperBF
DOCUMENT ME!

threshFillBF

JTextField threshFillBF
DOCUMENT ME!

threshLowerF

JTextField threshLowerF
threshold related.

threshUpperF

JTextField threshUpperF
threshold related.

threshFillF

JTextField threshFillF
threshold related.

toolBarBottom

JToolBar toolBarBottom
DOCUMENT ME!

toolBarCenter

JToolBar toolBarCenter
center toolbar

toolBarObj

ViewToolBarBuilder toolBarObj
DOCUMENT ME!

toolBarThreshold

JToolBar toolBarThreshold
DOCUMENT ME!

toolBarTop

JToolBar toolBarTop
DOCUMENT ME!

updateCheckBoxA

JCheckBox updateCheckBoxA
DOCUMENT ME!

updateCheckBoxB

JCheckBox updateCheckBoxB
DOCUMENT ME!

voxelVolumeLabel

JLabel voxelVolumeLabel
Used to display the volume or area of the voxels/pixels between the upper and lower bounds.

xRangeTextA

JTextField xRangeTextA
X range text field in the imageA, B and GM image A, B histogram dialog. Following text fields are used by the tri-planar volume view.

xRangeTextB

JTextField xRangeTextB
X range text field in the imageA, B and GM image A, B histogram dialog. Following text fields are used by the tri-planar volume view.

yRangeTextA

JTextField yRangeTextA
Y range text field in the imageA, B and GM image A, B histogram dialog. Following text fields are used by the tri-planar volume view.

yRangeTextB

JTextField yRangeTextB
Y range text field in the imageA, B and GM image A, B histogram dialog. Following text fields are used by the tri-planar volume view.

Class gov.nih.mipav.view.ViewJPopupCardiologyVOI extends JPanel implements Serializable

serialVersionUID: -5496458990593918502L

Serialized Fields

calcSubMenu

JMenu calcSubMenu
DOCUMENT ME!

component

ViewJComponentCardiology component
DOCUMENT ME!

popup

JPopupMenu popup
DOCUMENT ME!

sectionSubMenu

JMenu sectionSubMenu
DOCUMENT ME!

voiSubMenu

JMenu voiSubMenu
DOCUMENT ME!

Class gov.nih.mipav.view.ViewJPopupPt extends JPanel implements Serializable

serialVersionUID: 393929198484576018L

Serialized Fields

voiHandler

VOIHandler voiHandler
DOCUMENT ME!

itemBuildPolyline

JMenuItem itemBuildPolyline
DOCUMENT ME!

itemProps

JMenuItem itemProps
DOCUMENT ME!

itemShowGraph

JMenuItem itemShowGraph
DOCUMENT ME!

itemShowPAAIDialog

JMenuItem itemShowPAAIDialog
DOCUMENT ME!

propSubMenu

JMenu propSubMenu
DOCUMENT ME!

ptPopup

JPopupMenu ptPopup
DOCUMENT ME!

Class gov.nih.mipav.view.ViewJPopupVOI extends JPanel implements Serializable

serialVersionUID: -7134535981914560813L

Serialized Fields

contourOrderSubMenu

JMenu contourOrderSubMenu
DOCUMENT ME!

editSubMenu

JMenu editSubMenu
DOCUMENT ME!

flipSubMenu

JMenu flipSubMenu
DOCUMENT ME!

graphSubMenu

JMenu graphSubMenu
DOCUMENT ME!

itemClose

JMenuItem itemClose
DOCUMENT ME!

itemCrop

JMenuItem itemCrop
DOCUMENT ME!

itemOutputDistance

JMenuItem itemOutputDistance
DOCUMENT ME!

itemProps

JMenuItem itemProps
DOCUMENT ME!

orderSubMenu

JMenu orderSubMenu
DOCUMENT ME!

popup

JPopupMenu popup
DOCUMENT ME!

propSubMenu

JMenu propSubMenu
DOCUMENT ME!

selectionMenu

JMenu selectionMenu
DOCUMENT ME!

voiHandler

VOIHandler voiHandler
DOCUMENT ME!

Class gov.nih.mipav.view.ViewJProgressBar extends JFrame implements Serializable

serialVersionUID: -4893646677987678693L

Serialized Fields

cancelButton

JButton cancelButton
Cancel button, if applicable.

messagePBar

JLabel messagePBar
Label directly above the bar that is updated during operation if necessary.

pBar

JProgressBar pBar
Actual bar which fills with color as the percentage of completion increases.

percentage

JLabel percentage
Percentage label, puts a number next to the bar with the actual percent completed.

readyToDispose

boolean readyToDispose
For users wanting to override the automatic closing option when progress reaches 100.

separateThread

boolean separateThread
DOCUMENT ME!

title

String title
Title of the frame for the progress bar.

messageLocked

boolean messageLocked
indicates if the message string (in the progress bar) is locked so that it wont be updated

Class gov.nih.mipav.view.ViewList extends Object implements Serializable

serialVersionUID: 3493522274714412775L

Serialized Fields

state

boolean state
DOCUMENT ME!

string

String string
DOCUMENT ME!

Class gov.nih.mipav.view.ViewMenuBuilder.QuickList extends JComponent implements Serializable

serialVersionUID: -4787325627153954566L

Serialized Fields

listener

ActionListener listener
DOCUMENT ME!

quickListItems

Vector<E> quickListItems
DOCUMENT ME!

Class gov.nih.mipav.view.ViewOpenImageSequence extends JFrame implements Serializable

serialVersionUID: 5007701357886039L

Serialized Fields

brightnessSlider

JSlider brightnessSlider
DOCUMENT ME!

cellRenderer

AlternatingTableCellRenderer cellRenderer
DOCUMENT ME!

chkForceUBYTE

JCheckBox chkForceUBYTE
DOCUMENT ME!

cmbFilter

JComboBox cmbFilter
DOCUMENT ME!

contrastSlider

JSlider contrastSlider
DOCUMENT ME!

currentPath

File currentPath
DOCUMENT ME!

enableCheckbox

JCheckBox enableCheckbox
DOCUMENT ME!

fileListData

File[] fileListData
DOCUMENT ME!

lblOrigDim

JLabel lblOrigDim
DOCUMENT ME!

previewFilename

String previewFilename
DOCUMENT ME!

previewPanel

JPanel previewPanel
DOCUMENT ME!

radCTZ

JRadioButton radCTZ
Radio button for CTZ sequence

radCZT

JRadioButton radCZT
Radio button for CZT sequence

radTCZ

JRadioButton radTCZ
Radio button for TCZ sequence

radTZC

JRadioButton radTZC
Radio button for TZC sequence

radZCT

JRadioButton radZCT
Radio button for ZCT sequence

radZTC

JRadioButton radZTC
Radio button for ZTC sequence

table

JTable table
DOCUMENT ME!

tableModel

UneditableTableModel tableModel
DOCUMENT ME!

txtChannels

JTextField txtChannels
DOCUMENT ME!

txtDirectory

JTextField txtDirectory
DOCUMENT ME!

txtHeight

JTextField txtHeight
DOCUMENT ME!

txtSlices

JTextField txtSlices
DOCUMENT ME!

txtTimePoints

JTextField txtTimePoints
DOCUMENT ME!

txtWidth

JTextField txtWidth
DOCUMENT ME!

CZT

int CZT
Int denoting CZT sequence

TCZ

int TCZ
Int denoting TCZ sequence

CTZ

int CTZ
Int denoting CTZ sequence

TZC

int TZC
Int denoting TZC sequence

ZCT

int ZCT
Int denoting ZCT sequence

ZTC

int ZTC
Int denoting ZTC sequence

channelMap

int[] channelMap
DOCUMENT ME!

filenameTableModel

SortingTableModel filenameTableModel
DOCUMENT ME!

filenameTableSorter

TableSorter filenameTableSorter
DOCUMENT ME!

filenameTable

JTable filenameTable
DOCUMENT ME!

Class gov.nih.mipav.view.ViewSelectableDoubleListPanel extends JPanel implements Serializable

serialVersionUID: -7066171606587907360L

Serialized Fields

btnAdd

JButton btnAdd
DOCUMENT ME!

btnRemove

JButton btnRemove
DOCUMENT ME!

gbConstraints

GridBagConstraints gbConstraints
DOCUMENT ME!

gbLayout

GridBagLayout gbLayout
DOCUMENT ME!

leftTable

JTable leftTable
DOCUMENT ME!

rightTable

JTable rightTable
DOCUMENT ME!

Class gov.nih.mipav.view.ViewSplashScreen extends JFrame implements Serializable

serialVersionUID: 924235664168779459L

Serialized Fields

image

Image image
The splash screen image.

loadOK

boolean loadOK
Whether the splash screen was loaded from disk successfully.

Class gov.nih.mipav.view.ViewTableModel extends DefaultTableModel implements Serializable

serialVersionUID: 487484434950231158L

Class gov.nih.mipav.view.ViewToolBarBuilder.JScriptToolBar extends JToolBar implements Serializable

serialVersionUID: 6205577015710803423L

Serialized Fields

recordScriptButton

JButton recordScriptButton
The recording button.

Class gov.nih.mipav.view.ViewToolBarBuilder.VOIColorButton extends JButton implements Serializable

Class gov.nih.mipav.view.ViewVOIVector extends Vector<VOI> implements Serializable

serialVersionUID: 6003086288473157573L

Class gov.nih.mipav.view.VOIFrameNode extends DefaultMutableTreeNode implements Serializable

serialVersionUID: -6795049606234900885L

Serialized Fields

frameNumber

int frameNumber
DOCUMENT ME!

Class gov.nih.mipav.view.VOIGroupNode extends DefaultMutableTreeNode implements Serializable

serialVersionUID: 2278502889235734935L

Class gov.nih.mipav.view.VOIGroupTree extends JTree implements Serializable

serialVersionUID: -6853661393602487962L

Class gov.nih.mipav.view.VOIHandler extends JComponent implements Serializable

serialVersionUID: -6198406879690675965L

Serialized Fields

allActive

boolean allActive
Whether all counters of the currently selected VOI are active.

anchorPt

Point anchorPt
Anchor point used in calculated VOI movement distances.

compImage

ViewJComponentEditImage compImage
The component image that owns this class.

graphImgBuff

float[] graphImgBuff
Buffer for holding VOI graphing information.

gridColor

Color gridColor
color of grid.

gridLabelingOn

boolean gridLabelingOn
if number/lettering should be displayed for grid boxes.

gridLabelOrientation

boolean gridLabelOrientation
boolean to determine the orientation: true is x-axis numbered false is x-axis lettered.

gridOverlayOn

boolean gridOverlayOn
Flag to indicate if NEI grid overlay should be displayed.

gridSpacingX

float gridSpacingX
spacing of the grid (horizontal) in terms of resolution.

gridSpacingY

float gridSpacingY
spacing of the grid (vertical) in terms of resolution.

listenerList

EventListenerList listenerList
created to handle VOI updates. Must fireVOIUpdate(...) to get listeners to handle the update. Perhaps better location for the VOIupdate is in ViewJCompoenentEditImage, but this listenerlist will handle listeners of more than one type.

mode

int mode
Current mode for mouse behavior (VOI manipulation).

mousePressIsShiftDown

boolean mousePressIsShiftDown
Keep track of state of shift for mouse Pressed events.

newPolySliceVOI

VOI newPolySliceVOI
New polyline slice VOI.

overlayOn

boolean overlayOn
Flag to indicate if DICOM overlay should be displayed.

popup

ViewJPopupVOI popup
Popup Menu for VOIs (non-point).

popupPt

ViewJPopupPt popupPt
Popup Menu for VOIPoints.

presetHue

float presetHue
The preset hue for the livewire VOI rubberband.

ptIntensity

float[] ptIntensity
Buffer for holding intensities at specific points.

ptPosition

float[] ptPosition
buffer used when graphing a VOIPoint on a grayscale image.

ptRGBIntensities

float[][] ptRGBIntensities
Buffer for holding RGB intensities [0,1,2] at specific points.

ptRGBPositions

float[][] ptRGBPositions
Buffer used for graphing VOIPoints for an RGB image.

rbLevelSet

RubberbandLevelSet rbLevelSet
Rubberband tool for VOIs.

rbRect

Rubberband rbRect
Rubberband tool for VOIs.

rbPolyline

Rubberband rbPolyline
Rubberband tool for VOIs.

rbEllipse

Rubberband rbEllipse
Rubberband tool for VOIs.

rbLine

Rubberband rbLine
Rubberband tool for VOIs.

rbRectQuick

Rubberband rbRectQuick
Rubberband tool for VOIs.

rbProtractor

Rubberband rbProtractor
Rubberband tool for VOIs.

rbLivewire

Rubberband rbLivewire
Rubberband tool for VOIs.

rubberband

Rubberband rubberband
Rubberband tool for VOIs.

undoVOI

VOI undoVOI
VOI clipboard used to undo the VOI. This VOI is a copy of last VOI selected.

voiDialog

JDialogVOIStats voiDialog
Dialog for displaying/calculating VOI statistics as well as the VOI Browser.

voiID

int voiID
Active VOI's ID.

voiIDa

int voiIDa
VOI ID for image A.

voiIDb

int voiIDb
VOI ID for image B.

voiUpdate

UpdateVOIEvent voiUpdate
an update event for the VOI.

wasDragging

boolean wasDragging
Whether the VOI was being dragged.

lastVOI_UID

int lastVOI_UID

colorChooser

ViewJColorChooser colorChooser
Color chooser for VOI color (outside of the properties dialog)

Class gov.nih.mipav.view.VOINode extends DefaultMutableTreeNode implements Serializable

serialVersionUID: -1101994985217434811L

Class gov.nih.mipav.view.VOIRegistrationHandler extends VOIHandler implements Serializable

Class gov.nih.mipav.view.VolumePositionFrame extends JFrame implements Serializable

serialVersionUID: 3115465399315063208L

Serialized Fields

parentFrame

ViewJFrameTriImage parentFrame
Reference to the parentFrame, to notify when this window closes:.

Package gov.nih.mipav.view.components

Class gov.nih.mipav.view.components.JPanelAlgorithmOutputOptions extends JPanel implements Serializable

serialVersionUID: -5964491506018618684L

Serialized Fields

newImageRadio

JRadioButton newImageRadio
DOCUMENT ME!

replaceImageRadio

JRadioButton replaceImageRadio
DOCUMENT ME!

srcImage

ModelImage srcImage
DOCUMENT ME!

voiRegionsRadio

JRadioButton voiRegionsRadio
DOCUMENT ME!

wholeImageRadio

JRadioButton wholeImageRadio
DOCUMENT ME!

Class gov.nih.mipav.view.components.JPanelColorChannels extends JPanel implements Serializable

serialVersionUID: 3679634471868989877L

Serialized Fields

blueCheckbox

JCheckBox blueCheckbox
DOCUMENT ME!

greenCheckbox

JCheckBox greenCheckbox
DOCUMENT ME!

redCheckbox

JCheckBox redCheckbox
DOCUMENT ME!

srcImage

ModelImage srcImage
DOCUMENT ME!

Class gov.nih.mipav.view.components.JPanelItkFilterParams extends JPanel implements Serializable

Serialized Fields

m_DimensionTab

JTabbedPane m_DimensionTab
tabbed pane to choose 2D, 2.5D or 3D filter.

m_ParamPanel2D

JPanel m_ParamPanel2D
Main panel that contains input widgets for 2D filter.

m_ParamPanel3D

JPanel m_ParamPanel3D
Main panel that contains input widgets for 3D filter.

m_FilterObj2D

Object m_FilterObj2D
2D Itk filter object to manipulate.

m_FilterObj3D

Object m_FilterObj3D
3D Itk filter object to manipulate.

m_MethodList2D

List<E> m_MethodList2D
Discovered list of the filter's 'set' methods

m_MethodList3D

List<E> m_MethodList3D
Discovered list of the filter's 'set' methods

m_ParamList

List<E> m_ParamList
Parameters to send to the script recorder, if active.

Class gov.nih.mipav.view.components.JPanelSigmas extends JPanel implements Serializable

serialVersionUID: 4032897701053956108L

Serialized Fields

correctionFactorCheckbox

JCheckBox correctionFactorCheckbox
gui

correctionFactorLabel

JLabel correctionFactorLabel
label

labelGaussZ

JLabel labelGaussZ
label

srcImage

ModelImage srcImage
the input image which will be processed

textGaussX

JTextField textGaussX
gui, sigma value

textGaussY

JTextField textGaussY
gui, sigma value

textGaussZ

JTextField textGaussZ
gui, sigma value

Class gov.nih.mipav.view.components.JPanelWaterShedITK extends JPanel implements Serializable

Serialized Fields

textConductance

JTextField textConductance
Use serialVersionUID for interoperability.

textIterations

JTextField textIterations

textThreshold

JTextField textThreshold

textLevel

JTextField textLevel

textTimeStep

JTextField textTimeStep

conductance

float conductance

iterations

int iterations

threshold

float threshold

level

float level

timeStep

float timeStep

principleCheckBox

JCheckBox principleCheckBox

principleComponents

boolean principleComponents

parametersPanel

JPanel parametersPanel
Parameter panel contains the WaterShed parameters.

Class gov.nih.mipav.view.components.WidgetFactory.ScrollTextArea extends JScrollPane implements Serializable

serialVersionUID: 3869765356771292936L

Serialized Fields

tArea

JTextArea tArea
accessible JTextArea

Package gov.nih.mipav.view.dialogs

Class gov.nih.mipav.view.dialogs.DialogDTIColorDisplay extends ViewJFrameBase implements Serializable

serialVersionUID: 7511908857729035381L

Serialized Fields

title

String title
dialog title and version *

mainPanel

JPanel mainPanel
panels *

bottomPanel

JPanel bottomPanel
panels *

refPanel

JPanel refPanel
panels *

colorPanel

JPanel colorPanel
panels *

colorWheelPanel

JPanel colorWheelPanel
panels *

resultImagePanel

JPanel resultImagePanel
panels *

optionsPanel

JPanel optionsPanel
panels *

colorWheelChoicesPanel

JPanel colorWheelChoicesPanel
panels *

heuristicParametersPanel

JPanel heuristicParametersPanel
panels *

anisotropyMaxPanel

JPanel anisotropyMaxPanel
panels *

anisotropyMinPanel

JPanel anisotropyMinPanel
panels *

gammaPanel

JPanel gammaPanel
panels *

stevensBetaPanel

JPanel stevensBetaPanel
panels *

satBluePanel

JPanel satBluePanel
panels *

dimGreenPanel

JPanel dimGreenPanel
panels *

colorRangePanel

JPanel colorRangePanel
panels *

satVsThetaPanel

JPanel satVsThetaPanel
panels *

resultPanel

JPanel resultPanel
panels *

resultImageSliderPanel

JPanel resultImageSliderPanel
panels *

tempPanel

JPanel tempPanel
panels *

toolbarPanel

JPanel toolbarPanel
panels *

adjustExpPanel

JPanel adjustExpPanel
panels *

truncMultPanel

JPanel truncMultPanel
panels *

restoreDefaultsPanel

JPanel restoreDefaultsPanel
panels *

saveLoadPanel

JPanel saveLoadPanel
panels *

minAnisotropyMaxLabel

JLabel minAnisotropyMaxLabel
labels *

maxAnisotropyMaxLabel

JLabel maxAnisotropyMaxLabel
labels *

minAnisotropyMinLabel

JLabel minAnisotropyMinLabel
labels *

maxAnisotropyMinLabel

JLabel maxAnisotropyMinLabel
labels *

minGammaLabel

JLabel minGammaLabel
labels *

maxGammaLabel

JLabel maxGammaLabel
labels *

minStevensBetaLabel

JLabel minStevensBetaLabel
labels *

maxStevensBetaLabel

JLabel maxStevensBetaLabel
labels *

minSatBlueLabel

JLabel minSatBlueLabel
labels *

maxSatBlueLabel

JLabel maxSatBlueLabel
labels *

minDimGreenLabel

JLabel minDimGreenLabel
labels *

maxDimGreenLabel

JLabel maxDimGreenLabel
labels *

minColorRangeLabel

JLabel minColorRangeLabel
labels *

maxColorRangeLabel

JLabel maxColorRangeLabel
labels *

minSatVsThetaLabel

JLabel minSatVsThetaLabel
labels *

maxSatVsThetaLabel

JLabel maxSatVsThetaLabel
labels *

minResultImageSlicesLabel

JLabel minResultImageSlicesLabel
labels *

maxResultImageSlicesLabel

JLabel maxResultImageSlicesLabel
labels *

currentResultImageSlicesLabel

JLabel currentResultImageSlicesLabel
labels *

magLabel

JLabel magLabel
labels *

refLabel1

JLabel refLabel1
labels *

refLabel2

JLabel refLabel2
labels *

refLabel3

JLabel refLabel3
labels *

minAdjustExpLabel

JLabel minAdjustExpLabel
labels *

maxAdjustExpLabel

JLabel maxAdjustExpLabel
labels *

minAnisotropyMax

float minAnisotropyMax
mins and maxes for heuristic parameters*

maxAnisotropyMax

float maxAnisotropyMax
mins and maxes for heuristic parameters*

minAnisotropyMin

float minAnisotropyMin
mins and maxes for heuristic parameters*

maxAnisotropyMin

float maxAnisotropyMin
mins and maxes for heuristic parameters*

minGamma

float minGamma
mins and maxes for heuristic parameters*

maxGamma

float maxGamma
mins and maxes for heuristic parameters*

minStevensBeta

float minStevensBeta
mins and maxes for heuristic parameters*

maxStevensBeta

float maxStevensBeta
mins and maxes for heuristic parameters*

minSatBlue

float minSatBlue
mins and maxes for heuristic parameters*

maxSatBlue

float maxSatBlue
mins and maxes for heuristic parameters*

minDimGreen

float minDimGreen
mins and maxes for heuristic parameters*

maxDimGreen

float maxDimGreen
mins and maxes for heuristic parameters*

minColorRange

float minColorRange
mins and maxes for heuristic parameters*

maxColorRange

float maxColorRange
mins and maxes for heuristic parameters*

minSatVsTheta

float minSatVsTheta
mins and maxes for heuristic parameters*

maxSatVsTheta

float maxSatVsTheta
mins and maxes for heuristic parameters*

minAdjustExp

float minAdjustExp
mins and maxes for heuristic parameters*

maxAdjustExp

float maxAdjustExp
mins and maxes for heuristic parameters*

resultScrollPanel

JScrollPane resultScrollPanel
scroll pane for result image *

anisotropyMaxTextField

JTextField anisotropyMaxTextField
textfields *

anisotropyMinTextField

JTextField anisotropyMinTextField
textfields *

gammaTextField

JTextField gammaTextField
textfields *

stevensBetaTextField

JTextField stevensBetaTextField
textfields *

satBlueTextField

JTextField satBlueTextField
textfields *

dimGreenTextField

JTextField dimGreenTextField
textfields *

colorRangeTextField

JTextField colorRangeTextField
textfields *

satVsThetaTextField

JTextField satVsThetaTextField
textfields *

adjustExpTextField

JTextField adjustExpTextField
textfields *

magButton

JButton magButton
buttons *

unMagButton

JButton unMagButton
buttons *

zoomOneButton

JButton zoomOneButton
buttons *

captureImageButton

JButton captureImageButton
buttons *

restoreDefaultsButton

JButton restoreDefaultsButton
buttons *

saveButton

JButton saveButton
buttons *

loadButton

JButton loadButton
buttons *

eigvecSrcImage

ModelImage eigvecSrcImage
eigenvector src image *

anisotropyImage

ModelImage anisotropyImage
anisotropy src image *

eigvecFilename

String eigvecFilename
names of eigenvector and anisotropy files*

anisotropyFilename

String anisotropyFilename
names of eigenvector and anisotropy files*

resultImage

ModelImage resultImage
result image *

LUTa

ModelLUT LUTa
LUT of input image *

colorWheel

ColorWheel colorWheel
Color Wheels *

alg

AlgorithmDTIColorDisplay alg
handle to the algorithm *

gbl

GridBagLayout gbl
GridBagLayout *

gbc

GridBagConstraints gbc
GridbagConstraints *

anisotropyMaxSlider

JSlider anisotropyMaxSlider
various sliders in dialog *

anisotropyMinSlider

JSlider anisotropyMinSlider
various sliders in dialog *

gammaSlider

JSlider gammaSlider
various sliders in dialog *

stevensBetaSlider

JSlider stevensBetaSlider
various sliders in dialog *

satBlueSlider

JSlider satBlueSlider
various sliders in dialog *

dimGreenSlider

JSlider dimGreenSlider
various sliders in dialog *

colorRangeSlider

JSlider colorRangeSlider
various sliders in dialog *

satVsThetaSlider

JSlider satVsThetaSlider
various sliders in dialog *

resultImageSlider

JSlider resultImageSlider
various sliders in dialog *

adjustExpSlider

JSlider adjustExpSlider
various sliders in dialog *

titledBorder

TitledBorder titledBorder
titled border for certain components *

colorWheelComboBox

JComboBox colorWheelComboBox
color wheel choices combo box *

anisotropyMax

float anisotropyMax
anisotropy max *

anisotropyMin

float anisotropyMin
anisotropy min *

adjustExp

float adjustExp
adjust exp *

gamma

float gamma
gamma correction *

stevensBeta

float stevensBeta
steven's beta *

pB

float pB
blue saturation *

pG

float pG
green saturation *

pC

float pC
color range *

pS

float pS
saturation vs theta *

componentImage

ViewJComponentDTIImage componentImage
ViewJComponentDTIImage *

imageBufferA

float[] imageBufferA
Buffer used to store image intensities the presently viewed slice of image A.

resols

float[] resols
Storage of the image voxel resolutions. One resolution value per dimension.

pixBuffer

int[] pixBuffer
Integer buffer (4 bytes that stores the concatenated Alpha (1 byte), Red (1 byte), Green ( 1 byte ), Blue (1 byte ) data. The ARGB values are generated by using the imageA intensities as a index into a LUT.

units

int[] units
Storage of the resolution units of measure. For example, mm, cm, inches ...

zSlice

int zSlice
current z slice *

widthResFactor

float widthResFactor
Storage for correction parameters where datasets have non isotropic values.

heightResFactor

float heightResFactor
Storage for correction parameters where datasets have non isotropic values.

tSlice

int tSlice
Image time sequence number of image that is displayed. Zero indexed based.

nImage

int nImage
Number of slices in a 3D dataset.

nTImage

int nTImage
Number of time sequences in a 4D dataset.

type

String type
type of color wheel ABSVAL, NOSYMM, ROTATIONALSYMM, MIRRORSYMM *

toolbarBuilder

ViewToolBarBuilder toolbarBuilder
ViewToolBarBuilder *

zoom

float zoom
current zoom for result image *

numSlices

int numSlices
num slices for result image *

currentRectangle

Rectangle currentRectangle
rectangle for screen capture*

truncMultRadioGroup

ButtonGroup truncMultRadioGroup
radio group for truncate/multiply *

truncRadio

JRadioButton truncRadio
radio buttons for truncate/multiply *

multRadio

JRadioButton multRadio
radio buttons for truncate/multiply *

isMultiply

boolean isMultiply
boolean for truncate/multiply *

flag

boolean flag
flag needed when performing restore defaults *

in

BufferedReader in
Buffered Reader for loading params *

out

BufferedWriter out
Buffered Writer for saving params *

currentColorWheelType

String currentColorWheelType
String indicating current color wheel type *

m_afScreenResolutions

float[] m_afScreenResolutions
Sets the correct resolutions for the image that is created by captureImage.

m_fSliceThickness

float m_fSliceThickness
Sets the correct slice thickness

Class gov.nih.mipav.view.dialogs.JDialogACPC extends JDialogBase implements Serializable

Serialized Fields

comboBoxOrientX

JComboBox comboBoxOrientX

comboBoxOrientY

JComboBox comboBoxOrientY

comboBoxOrientZ

JComboBox comboBoxOrientZ

ACPCGroup

ButtonGroup ACPCGroup

applyACPCButton

JButton applyACPCButton

cancelACPCButton

JButton cancelACPCButton

setACPCButton

JButton setACPCButton

clearACPCButton

JButton clearACPCButton

superiorEdge

JRadioButton superiorEdge

posteriorMargin

JRadioButton posteriorMargin

inferiorEdge

JRadioButton inferiorEdge

firstPt

JRadioButton firstPt

anotherPt

JRadioButton anotherPt

frame

ViewJFrameTriImage frame

image

ModelImage image

transform

TalairachTransformInfo transform

textVoxelLength

JTextField textVoxelLength

haveSuperiorEdge

boolean haveSuperiorEdge

havePosteriorMargin

boolean havePosteriorMargin

haveInferiorEdge

boolean haveInferiorEdge

haveFirstPt

boolean haveFirstPt

haveAnotherPt

boolean haveAnotherPt

orient

int[] orient

superiorEdgePt

WildMagic.LibFoundation.Mathematics.Vector3f superiorEdgePt

posteriorMarginPt

WildMagic.LibFoundation.Mathematics.Vector3f posteriorMarginPt

inferiorEdgePt

WildMagic.LibFoundation.Mathematics.Vector3f inferiorEdgePt

firstMidSagPt

WildMagic.LibFoundation.Mathematics.Vector3f firstMidSagPt

anotherMidSagPt

WildMagic.LibFoundation.Mathematics.Vector3f anotherMidSagPt

interpolation

int interpolation

originalSuperiorEdge

WildMagic.LibFoundation.Mathematics.Vector3f originalSuperiorEdge

originalPosteriorMargin

WildMagic.LibFoundation.Mathematics.Vector3f originalPosteriorMargin

voxelLength

float voxelLength

ACPCImage

ModelImage ACPCImage

Class gov.nih.mipav.view.dialogs.JDialogAdaptiveNR extends JDialogScriptableBase implements Serializable

serialVersionUID: 1276771512966999332L

Serialized Fields

adaptiveNRAlgo

AlgorithmAdaptiveNR adaptiveNRAlgo
DOCUMENT ME!

destinationGroup

ButtonGroup destinationGroup
DOCUMENT ME!

destinationPanel

JPanel destinationPanel
DOCUMENT ME!

displayLoc

int displayLoc
DOCUMENT ME!

distWeight

float distWeight
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

labelDistWeight

JLabel labelDistWeight
DOCUMENT ME!

labelRadiusCb

JLabel labelRadiusCb
DOCUMENT ME!

labelRadiusCr

JLabel labelRadiusCr
DOCUMENT ME!

labelRadiusY

JLabel labelRadiusY
DOCUMENT ME!

newImage

JRadioButton newImage
DOCUMENT ME!

paramPanel

JPanel paramPanel
DOCUMENT ME!

radiusCb

float radiusCb
DOCUMENT ME!

radiusCr

float radiusCr
DOCUMENT ME!

radiusY

float radiusY
DOCUMENT ME!

reduce

boolean reduce
DOCUMENT ME!

reduceCheckBox

JCheckBox reduceCheckBox
DOCUMENT ME!

replaceImage

JRadioButton replaceImage
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

textDistWeight

JTextField textDistWeight
DOCUMENT ME!

textRadiusCb

JTextField textRadiusCb
DOCUMENT ME!

textRadiusCr

JTextField textRadiusCr
DOCUMENT ME!

textRadiusY

JTextField textRadiusY
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogAdaptivePathSmooth extends JDialogScriptableBase implements Serializable

serialVersionUID: 3709702364792587183L

Serialized Fields

adaptivePathSmoothAlgo

AlgorithmAdaptivePathSmooth adaptivePathSmoothAlgo
DOCUMENT ME!

destinationGroup

ButtonGroup destinationGroup
DOCUMENT ME!

destinationPanel

JPanel destinationPanel
DOCUMENT ME!

diff

float diff
DOCUMENT ME!

displayLoc

int displayLoc
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

image25D

boolean image25D
DOCUMENT ME!

image25DCheckBox

JCheckBox image25DCheckBox
DOCUMENT ME!

includeNeighbors

boolean includeNeighbors
DOCUMENT ME!

labelRadiusCb

JLabel labelRadiusCb
DOCUMENT ME!

labelRadiusCr

JLabel labelRadiusCr
DOCUMENT ME!

labelRadiusY

JLabel labelRadiusY
DOCUMENT ME!

labelThreshold

JLabel labelThreshold
DOCUMENT ME!

neighborCheckBox

JCheckBox neighborCheckBox
DOCUMENT ME!

newImage

JRadioButton newImage
DOCUMENT ME!

paramPanel

JPanel paramPanel
DOCUMENT ME!

radiusCb

float radiusCb
DOCUMENT ME!

radiusCr

float radiusCr
DOCUMENT ME!

radiusY

float radiusY
DOCUMENT ME!

reduce

boolean reduce
DOCUMENT ME!

reduceCheckBox

JCheckBox reduceCheckBox
DOCUMENT ME!

replaceImage

JRadioButton replaceImage
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

textRadiusCb

JTextField textRadiusCb
DOCUMENT ME!

textRadiusCr

JTextField textRadiusCr
DOCUMENT ME!

textRadiusY

JTextField textRadiusY
DOCUMENT ME!

textThreshold

JTextField textThreshold
DOCUMENT ME!

threshold

float threshold
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogAddMargins extends JDialogScriptableBase implements Serializable

serialVersionUID: 8624253753510650511L

Serialized Fields

back

int back
DOCUMENT ME!

backInput

JTextField backInput
DOCUMENT ME!

blueValue

double blueValue
DOCUMENT ME!

bottomInput

JTextField bottomInput
DOCUMENT ME!

bottomSide

int bottomSide
DOCUMENT ME!

colorFactor

int colorFactor
DOCUMENT ME!

defaultBlueInput

JTextField defaultBlueInput
DOCUMENT ME!

defaultGreenInput

JTextField defaultGreenInput
DOCUMENT ME!

defaultRedInput

JTextField defaultRedInput
DOCUMENT ME!

defaultValue

double defaultValue
DOCUMENT ME!

defaultValueInput

JTextField defaultValueInput
DOCUMENT ME!

destinationGroup

ButtonGroup destinationGroup
DOCUMENT ME!

displayLoc

int displayLoc
DOCUMENT ME!

front

int front
DOCUMENT ME!

frontInput

JTextField frontInput
DOCUMENT ME!

greenValue

double greenValue
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

imageMarginsAlgo

AlgorithmAddMargins imageMarginsAlgo
DOCUMENT ME!

leftSide

int leftSide
DOCUMENT ME!

leftSideInput

JTextField leftSideInput
DOCUMENT ME!

loopingGroup

ButtonGroup loopingGroup
DOCUMENT ME!

newImage

JRadioButton newImage
DOCUMENT ME!

noBuffer

JRadioButton noBuffer
DOCUMENT ME!

redValue

double redValue
DOCUMENT ME!

replaceImage

JRadioButton replaceImage
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

rightSide

int rightSide
DOCUMENT ME!

rightSideInput

JTextField rightSideInput
DOCUMENT ME!

topInput

JTextField topInput
DOCUMENT ME!

topSide

int topSide
DOCUMENT ME!

usingBuffer

JRadioButton usingBuffer
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogAGVF extends JDialogBase implements Serializable

serialVersionUID: -3328779751424483654L

Serialized Fields

agvfAlgo

AlgorithmAGVF agvfAlgo
DOCUMENT ME!

boundaryIterations

int boundaryIterations
DOCUMENT ME!

checkboxDisplay

JCheckBox checkboxDisplay
DOCUMENT ME!

dilation

float dilation
default dilation:.

do25D

boolean do25D
DOCUMENT ME!

do25DCheckBox

JCheckBox do25DCheckBox
DOCUMENT ME!

doCellTracking

boolean doCellTracking
When true, do a Cell-tracking version of Active GVF Contours:.

doCellTrackingCheckBox

JCheckBox doCellTrackingCheckBox
Checkbox to turn cell-tracking on/off:.

doDilate

boolean doDilate
When true, dilate the cell radius before finding the next contour:.

doDilateCheckBox

JCheckBox doDilateCheckBox
Checkbox to turn cell-tracking on/off:.

groupNum

int groupNum
DOCUMENT ME!

gvfIterations

int gvfIterations
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

kValue

float kValue
DOCUMENT ME!

labelDilation

JLabel labelDilation
user-interface for setting the cell-radius dilation (multiple of cell expected radius).

labelGaussZ

JLabel labelGaussZ
DOCUMENT ME!

labelGVFIterations

JLabel labelGVFIterations
DOCUMENT ME!

labelRadius

JLabel labelRadius
user-interface for setting the estimated cell-radius (pixels).

labelResampling

JLabel labelResampling
user-interface for setting the uniform-resampling constraint contribution:.

labelShape

JLabel labelShape
user-interface for setting the shape constraint contribution:.

labelSize

JLabel labelSize
user-interface for setting the size constraint contribution:.

labelVelocity

JLabel labelVelocity
user-interface for setting the initial cell velocity:.

propagate

JRadioButton propagate
DOCUMENT ME!

propagationFlag

boolean propagationFlag
DOCUMENT ME!

radiusConstraint

float radiusConstraint
Default cell radius (pixels).

removeOriginal

boolean removeOriginal
DOCUMENT ME!

removeOriginalCheckBox

JCheckBox removeOriginalCheckBox
DOCUMENT ME!

resamplingConstraint

float resamplingConstraint
default sampling constraint contribution:.

resultImage

ModelImage resultImage
DOCUMENT ME!

scaleX

float scaleX
DOCUMENT ME!

scaleY

float scaleY
DOCUMENT ME!

scaleZ

float scaleZ
DOCUMENT ME!

shapeConstraint

float shapeConstraint
default shape constraint contribution:.

sigmas

float[] sigmas
DOCUMENT ME!

singleSlice

JRadioButton singleSlice
DOCUMENT ME!

sizeConstraint

float sizeConstraint
default size constraint contribution:.

smoothness

float smoothness
DOCUMENT ME!

srcVOI

VOI srcVOI
DOCUMENT ME!

textBoundaryIterations

JTextField textBoundaryIterations
DOCUMENT ME!

textDilation

JTextField textDilation
DOCUMENT ME!

textDx

JTextField textDx
DOCUMENT ME!

textDy

JTextField textDy
DOCUMENT ME!

textGaussX

JTextField textGaussX
DOCUMENT ME!

textGaussY

JTextField textGaussY
DOCUMENT ME!

textGaussZ

JTextField textGaussZ
DOCUMENT ME!

textGVFIterations

JTextField textGVFIterations
DOCUMENT ME!

textK

JTextField textK
DOCUMENT ME!

textRadius

JTextField textRadius
DOCUMENT ME!

textResampling

JTextField textResampling
DOCUMENT ME!

textShape

JTextField textShape
DOCUMENT ME!

textSize

JTextField textSize
DOCUMENT ME!

textSmoothness

JTextField textSmoothness
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

velocityDx

float velocityDx
default initial velocity (dx):.

velocityDy

float velocityDy
default initial velocity (dx):.

voiColor

Color voiColor
DOCUMENT ME!

VOIs

ViewVOIVector VOIs
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogAHE extends JDialogScriptableBase implements Serializable

serialVersionUID: -6408786765504411315L

Serialized Fields

aheAlgo

AlgorithmAHE aheAlgo
DOCUMENT ME!

clamp

boolean clamp
DOCUMENT ME!

clampImage

JCheckBox clampImage
DOCUMENT ME!

clampingValue

JTextField clampingValue
DOCUMENT ME!

clampValue

int clampValue
DOCUMENT ME!

clampValueLabel

JLabel clampValueLabel
DOCUMENT ME!

colorPanel

JPanelColorChannels colorPanel
DOCUMENT ME!

comboBoxHeightDiv

JComboBox comboBoxHeightDiv
DOCUMENT ME!

comboBoxWidthDiv

JComboBox comboBoxWidthDiv
DOCUMENT ME!

destinationGroup

ButtonGroup destinationGroup
or if the source image is to be replaced.

displayLoc

int displayLoc
DOCUMENT ME!

heightDivisions

int heightDivisions
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

newImage

JRadioButton newImage
DOCUMENT ME!

replaceImage

JRadioButton replaceImage
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

widthDivisions

int widthDivisions
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogAHElocal extends JDialogScriptableBase implements Serializable

serialVersionUID: -6607139120847474768L

Serialized Fields

aheAlgo

AlgorithmAHElocal aheAlgo
DOCUMENT ME!

clamp

boolean clamp
DOCUMENT ME!

clampCheckBox

JCheckBox clampCheckBox
DOCUMENT ME!

clampLabel

JLabel clampLabel
DOCUMENT ME!

clampValue

int clampValue
DOCUMENT ME!

clampValueText

JTextField clampValueText
DOCUMENT ME!

colorPanel

JPanelColorChannels colorPanel
DOCUMENT ME!

comboBoxKernelShape

JComboBox comboBoxKernelShape
DOCUMENT ME!

comboBoxKernelSize

JComboBox comboBoxKernelSize
DOCUMENT ME!

comboBoxScaleMax

JComboBox comboBoxScaleMax
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

kernelShape

int kernelShape
DOCUMENT ME!

kernelSize

int kernelSize
DOCUMENT ME!

minThresholdLabel

JLabel minThresholdLabel
DOCUMENT ME!

minThresholdText

JTextField minThresholdText
DOCUMENT ME!

minThresholdValue

float minThresholdValue
DOCUMENT ME!

outputPanel

JPanelAlgorithmOutputOptions outputPanel
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

scaleMaxValue

int scaleMaxValue
DOCUMENT ME!

threshold

boolean threshold
DOCUMENT ME!

thresholdCheckBox

JCheckBox thresholdCheckBox
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogAnalyzeNIFTIChoice extends JDialogBase implements Serializable

serialVersionUID: 4588130080855618027L

Serialized Fields

analyzeFile

JRadioButton analyzeFile
Radio button to indicate that an analyze img file should be written out.

interfileFile

JRadioButton interfileFile
Radio button to indicate that an Interfile img file should be written out.

niftiFile

JRadioButton niftiFile
Radio button to indicate that a nifti img file should be written out.

okayPressed

boolean okayPressed
Whether the window was closed through the user clicking the OK button (and not just killing the dialog).

comboBoxSaveMethod

JComboBox comboBoxSaveMethod
Whether to save as selected by dialog or always as analyze, interfile, or nifti.

Class gov.nih.mipav.view.dialogs.JDialogAnimate extends JDialogBase implements Serializable

serialVersionUID: 3763989468823480229L

Serialized Fields

algoTrans

AlgorithmTransform algoTrans
DOCUMENT ME!

algoTransB

AlgorithmTransform algoTransB
DOCUMENT ME!

borderB

JButton borderB
false if column radio button selected.

borderCol

Color borderCol
DOCUMENT ME!

colorChooser

ViewJColorChooser colorChooser
DOCUMENT ME!

comboBoxImage

JComboBox comboBoxImage
DOCUMENT ME!

comboBoxInterp

JComboBox comboBoxInterp
DOCUMENT ME!

controlFrame

ViewJFrameBase controlFrame
DOCUMENT ME!

DIM

int DIM
DOCUMENT ME!

frameAnimate

ViewJFrameAnimate frameAnimate
DOCUMENT ME!

frameBorderCheckBox

JCheckBox frameBorderCheckBox
DOCUMENT ME!

imageA

ModelImage imageA
DOCUMENT ME!

imageB

ModelImage imageB
DOCUMENT ME!

isVisible

boolean isVisible
Is dialog visible or not.

LUTa

ModelLUT LUTa
DOCUMENT ME!

LUTb

ModelLUT LUTb
DOCUMENT ME!

radioColumn

JRadioButton radioColumn
DOCUMENT ME!

radioRow

JRadioButton radioRow
DOCUMENT ME!

rcText

JTextField rcText
DOCUMENT ME!

resultImageA

ModelImage resultImageA
DOCUMENT ME!

resultImageB

ModelImage resultImageB
DOCUMENT ME!

RGBTA

ModelRGB RGBTA
DOCUMENT ME!

RGBTB

ModelRGB RGBTB
DOCUMENT ME!

rowBFlag

boolean rowBFlag
each z slice in 4D images.

scaleText

JTextField scaleText
DOCUMENT ME!

showFrameBorder

boolean showFrameBorder
DOCUMENT ME!

ui

ViewUserInterface ui
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogAnisotropicDiffusion extends JDialogScriptableBase implements Serializable

serialVersionUID: -7624088316240843823L

Serialized Fields

diffusionAlgo

AlgorithmAnisotropicDiffusion diffusionAlgo
DOCUMENT ME!

image

ModelImage image
Source image.

image25D

boolean image25D
DOCUMENT ME!

image25DCheckbox

JCheckBox image25DCheckbox
DOCUMENT ME!

iters

int iters
DOCUMENT ME!

konst

float konst
DOCUMENT ME!

resultImage

ModelImage resultImage
Result image.

textIters

JTextField textIters
DOCUMENT ME!

textK

JTextField textK
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

sigmaPanel

JPanelSigmas sigmaPanel

outputPanel

JPanelAlgorithmOutputOptions outputPanel

Class gov.nih.mipav.view.dialogs.JDialogAnnotation extends JDialogBase implements Serializable

serialVersionUID: 2171038314100102783L

Serialized Fields

activeImage

ModelImage activeImage
The image that contains the VOI text.

backgroundColorButton

JButton backgroundColorButton
button to bring up the background color chooser.

boldBox

JCheckBox boldBox
checkbox for bold style.

buttonPanel

JPanel buttonPanel
Panel to contain the okay/cancel/help buttons.

colorButton

JButton colorButton
button to bring up color chooser.

colorChooser

ViewJColorChooser colorChooser
color chooser to select text color.

fontDescriptors

int fontDescriptors
descriptors for font (BOLD, PLAIN, ITALIC).

fontName

String fontName
name/style of the font.

fontSize

int fontSize
size of font (int).

fontSizeField

JTextField fontSizeField
textfield for font size (int only).

fontTypeBox

JComboBox fontTypeBox
combobox to hold the names of all available fonts.

isBackground

boolean isBackground
toggle between background and text color changing.

isRegistered

boolean isRegistered
whether this is an existing or new VOIText (isRegistered = existing).

italicBox

JCheckBox italicBox
checkbox for italic style.

slice

int slice
slice of image where the VOI resides.

nameField

JTextField nameField
NameField that will contain the string to be displayed.

noteField

JTextArea noteField
NoteField for providing a note about this marker. Note only displayed when clicked.

textVOI

VOI textVOI
the VOI that contains the VOIText.

useMarkerBox

JCheckBox useMarkerBox
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogAnnotation.UpdateTextAction extends AbstractAction implements Serializable

serialVersionUID: -7210907002611412247L

Class gov.nih.mipav.view.dialogs.JDialogAnonymizeDirectory extends JDialogBase implements Serializable

serialVersionUID: -6606891655523582196L

Serialized Fields

actOnPath

TreePath[] actOnPath
for the files selected ...

anonymizer

Thread anonymizer
Access to the running thread which is anonymising directories.

changeFilenameBox

JCheckBox changeFilenameBox
DOCUMENT ME!

checkBoxPanel

JPanelAnonymizeImage checkBoxPanel
DOCUMENT ME!

directoryTree

JTree directoryTree
Actual things we can see...

everything

JTabbedPane everything
Onscreen objects.

filePanel

JPanel filePanel
Logical construct to reuild a source tree...

genericImageName

String genericImageName
Used as part of the image name; used in all processed image-sets.

grouping

ButtonGroup grouping
DOCUMENT ME!

imageDestBrowse

JButton imageDestBrowse
DOCUMENT ME!

imageDestDirectory

File imageDestDirectory
private File srcDirectory; // Defined by the.

imageDestDirText

JTextField imageDestDirText
DOCUMENT ME!

imageNameText

JTextField imageNameText
DOCUMENT ME!

keyLog

String keyLog
Translation key, stored in "patient.key.doc".

logPane

JTextArea logPane
holds output log; updated as processed.

noisyProcess

boolean noisyProcess
Noisy means notifying the user of stupid errors.

noRandButton

JRadioButton noRandButton
DOCUMENT ME!

outputLog

String outputLog
String to hold all file checks, changes and ignores.

rand

Random rand
To generate wierd, unrecoverable names for anon images.

randChildButton

JRadioButton randChildButton
DOCUMENT ME!

randTopButton

JRadioButton randTopButton
DOCUMENT ME!

recursiveCheckBox

JCheckBox recursiveCheckBox
private JButton srcBrowse;.

selectedList

JTextArea selectedList
All directory-tree selected directories are listed for user-consumption in this whitespace.

sequenceStart

int sequenceStart
Used as part of the image name; represents beginning of sequence for all processed image sets.

sequenceText

JTextField sequenceText
DOCUMENT ME!

sourcePanel

JPanel sourcePanel
DOCUMENT ME!

stopButton

JButton stopButton
stops the thread from continuing its processing. on same panel as OK and Cancel.

toplevelOnly

int toplevelOnly
DOCUMENT ME!

xlatDestBrowse

JButton xlatDestBrowse
DOCUMENT ME!

xlatDestDirectory

File xlatDestDirectory
DOCUMENT ME!

xlatDestDirText

JTextField xlatDestDirText
DOCUMENT ME!

xlatDestinationUsage

int xlatDestinationUsage
Defines options for WRITE, OVERWRITE, APPEND for the xlat file.

Class gov.nih.mipav.view.dialogs.JDialogAnonymizeImage extends JDialogBase implements Serializable

serialVersionUID: -5845185607194185354L

Serialized Fields

checkboxPanel

JPanelAnonymizeImage checkboxPanel
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogAutoCorrelation extends JDialogScriptableBase implements Serializable

serialVersionUID: 5909303016264063087L

Serialized Fields

algoAutoCorrelation

AlgorithmAutoCorrelation algoAutoCorrelation
DOCUMENT ME!

haveBlue

boolean haveBlue
DOCUMENT ME!

haveGreen

boolean haveGreen
DOCUMENT ME!

haveRed

boolean haveRed
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

maxR

double maxR
DOCUMENT ME!

maxG

double maxG
DOCUMENT ME!

maxB

double maxB
DOCUMENT ME!

minR

double minR
DOCUMENT ME!

minG

double minG
DOCUMENT ME!

minB

double minB
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

resultImageB

ModelImage resultImageB
DOCUMENT ME!

resultImageG

ModelImage resultImageG
DOCUMENT ME!

resultImageR

ModelImage resultImageR
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

UI

ViewUserInterface UI
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogAutoCovariance extends JDialogScriptableBase implements Serializable

serialVersionUID: 5044633994224797404L

Serialized Fields

algoAutoCovariance

AlgorithmAutoCovariance algoAutoCovariance
DOCUMENT ME!

haveBlue

boolean haveBlue
DOCUMENT ME!

haveGreen

boolean haveGreen
DOCUMENT ME!

haveRed

boolean haveRed
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

maxR

double maxR
DOCUMENT ME!

maxG

double maxG
DOCUMENT ME!

maxB

double maxB
DOCUMENT ME!

minR

double minR
DOCUMENT ME!

minG

double minG
DOCUMENT ME!

minB

double minB
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

resultImageB

ModelImage resultImageB
DOCUMENT ME!

resultImageG

ModelImage resultImageG
DOCUMENT ME!

resultImageR

ModelImage resultImageR
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

UI

ViewUserInterface UI
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogAVIChoice extends JDialogBase implements Serializable

serialVersionUID: 4858762290060675316L

Serialized Fields

compressionBox

JComboBox compressionBox
Combo box to select compression.

okayPressed

boolean okayPressed
DOCUMENT ME!

operating_system

int operating_system
DOCUMENT ME!

qualityField

JTextField qualityField
Text Field for M-JPEG quality.

Class gov.nih.mipav.view.dialogs.JDialogBarrelDistortion extends JDialogScriptableBase implements Serializable

Serialized Fields

bdAlgo

AlgorithmBarrelDistortion bdAlgo
DOCUMENT ME!

image

ModelImage image
Source image.

resultImage

ModelImage resultImage
Result image.

paramsPanel

JPanel paramsPanel
DOCUMENT ME!

a

float a

b

float b

c

float c

d

float d

mainLabel

JLabel mainLabel

mainLabel2

JLabel mainLabel2

mainLabel3

JLabel mainLabel3

aLabel

JLabel aLabel

bLabel

JLabel bLabel

cLabel

JLabel cLabel

dLabel

JLabel dLabel

aText

JTextField aText

bText

JTextField bText

cText

JTextField cText

dText

JTextField dText

noScalingDCheckBox

JCheckBox noScalingDCheckBox

noScalingD

boolean noScalingD

Class gov.nih.mipav.view.dialogs.JDialogBase extends JDialog implements Serializable

serialVersionUID: -6802105487936807310L

Serialized Fields

cancelFlag

boolean cancelFlag
Flag indicating if the dialog had been cancelled or not.

applyButton

JButton applyButton
Apply button is used to apply the setting of the dialog.

cancelButton

JButton cancelButton
Cancel button is used on most dialogs. Defining it in the base allows default actions if the user presses return and the button is in focus.

closeButton

JButton closeButton
Close button is used to close the dialog.

helpButton

JButton helpButton
Help button is used on most dialogs. Defining it in the base allows default actions if the user presses return and the button is in focus.

mainDialogPanel

JPanel mainDialogPanel
The main panel of the dialog. To be filled by inheriting classes. Defaults to BorderLayout since that's what the contentPane defaults to (makes it easier to change over to using mainDialogPanel without messing up the layout).

OKButton

JButton OKButton
OK button is used on most dialogs. Defining it in the base allows default actions if the user presses return and the button is in focus.

parentFrame

Frame parentFrame
Parent frame of this dialog, usually of type ViewJFrameImage.

runInSeparateThread

boolean runInSeparateThread
Flag indicating if the algorithm should run in a separate thread. Default is true.

runningScriptFlag

boolean runningScriptFlag
Whether we are using this dialog as part of a script.

serif12

Font serif12
Fonts, same as MipavUtil.font12 and MipavUtil.font12B.

serif12B

Font serif12B
Fonts, same as MipavUtil.font12 and MipavUtil.font12B.

progressBar

ViewJProgressBar progressBar
Progress bar that will listen to a dialog's algorithm (and reflect current progress)

Class gov.nih.mipav.view.dialogs.JDialogBase.CancelAction extends AbstractAction implements Serializable

serialVersionUID: 8763437075181255552L

Class gov.nih.mipav.view.dialogs.JDialogBase.HelpAction extends AbstractAction implements Serializable

serialVersionUID: -1362974760098666480L

Class gov.nih.mipav.view.dialogs.JDialogBase.OKAction extends AbstractAction implements Serializable

serialVersionUID: -7409235372458546982L

Class gov.nih.mipav.view.dialogs.JDialogBGAndFGDistanceMap extends JDialogScriptableBase implements Serializable

Serialized Fields

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

outputPanel

JPanelAlgorithmOutputOptions outputPanel

distanceMapAlgo2D

AlgorithmMorphology2D distanceMapAlgo2D

distanceMapAlgo3D

AlgorithmMorphology3D distanceMapAlgo3D

titles

String[] titles
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogBGDistanceMap extends JDialogScriptableBase implements Serializable

serialVersionUID: 8286579547782268746L

Serialized Fields

distanceMapAlgo2D

AlgorithmMorphology2D distanceMapAlgo2D
DOCUMENT ME!

distanceMapAlgo3D

AlgorithmMorphology3D distanceMapAlgo3D
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

outputPanel

JPanelAlgorithmOutputOptions outputPanel

Class gov.nih.mipav.view.dialogs.JDialogBlankImage extends JDialogBase implements Serializable

serialVersionUID: 8301756369819912860L

Serialized Fields

dataType

int dataType
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

radioBool

JRadioButton radioBool
DOCUMENT ME!

radioByte

JRadioButton radioByte
DOCUMENT ME!

radioDouble

JRadioButton radioDouble
DOCUMENT ME!

radioFloat

JRadioButton radioFloat
DOCUMENT ME!

radioInt

JRadioButton radioInt
DOCUMENT ME!

radioLong

JRadioButton radioLong
DOCUMENT ME!

radioShort

JRadioButton radioShort
DOCUMENT ME!

radioUByte

JRadioButton radioUByte
DOCUMENT ME!

radioUInt

JRadioButton radioUInt
DOCUMENT ME!

radioUShort

JRadioButton radioUShort
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogBoundaryAttenuation extends JDialogScriptableBase implements Serializable

serialVersionUID: -7736447447170989384L

Serialized Fields

attenuationAlgo

AlgorithmBoundaryAttenuation attenuationAlgo
The attenuation algorithm.

destImage

ModelImage destImage
The attenuated image.

maxAttenuation

float maxAttenuation
The maximum amount of attenuation to apply to the image (0 = no attenuation, 1 = full attenuation).

maxAttenuationTF

JTextField maxAttenuationTF
Maximum attenuation text field.

numErosions

int numErosions
The number of levels of attenuation to perform (done through morphological erosion).

numErosionsTF

JTextField numErosionsTF
Number of erosions text field.

srcImage

ModelImage srcImage
The image to attenuate.

userInterface

ViewUserInterface userInterface
The MIPAV user interface.

Class gov.nih.mipav.view.dialogs.JDialogBrainSurfaceExtractor extends JDialogScriptableBase implements Serializable

serialVersionUID: -4594568089644651497L

Serialized Fields

closeKernelSize

float closeKernelSize
Size of the kernel used in the closing operations.

closeKernelSizeTF

JTextField closeKernelSizeTF
Text field used to enter the number of closings to perform.

edgeKernelSize

float edgeKernelSize
Edge detection kernel size (.6 in Shattuck paper).

edgeKernelSizeTF

JTextField edgeKernelSizeTF
Text field used to enter the edge detection kernel size.

erosion25D

boolean erosion25D
Whether to process the slices of the 3D image separately while performing the erosion / dilation.

erosion25DCB

JCheckBox erosion25DCB
Check box for indicating whether erosion / dilation should process slices independently.

erosionIterations

int erosionIterations
Number of erosion / dilation operations to perform (2 in Shattuck paper).

erosionIterationsTF

JTextField erosionIterationsTF
Text field used to enter the number of erosions / dilations.

extractBrainAlgo

AlgorithmBrainSurfaceExtractor extractBrainAlgo
Reference to the algorithm we will be running.

extractPaint

boolean extractPaint
Whether to extract the brain to paint instead of removing image data.

extractPaintCheckBox

JCheckBox extractPaintCheckBox
Checkbox to extract the brain to paint instead of removing image data.

fillHoles

boolean fillHoles
Whether to fill in all internal holes in the extracted brain.

fillHolesCB

JCheckBox fillHolesCB
Checkbox for indicating whether to close all of the interior holes in the extracted brain.

filterGaussianStdDev

float filterGaussianStdDev
Standard deviation of the filter's gaussian kernel.

filterGaussianStdDevTF

JTextField filterGaussianStdDevTF
Text field used to enter the standard deviation of the filter's gaussian kernel.

filterIterations

int filterIterations
Number of filter iterations.

filterIterationsTF

JTextField filterIterationsTF
Text field used to enter the number of filter iterations.

image

ModelImage image
The source image.

imageCopy

ModelImage imageCopy
A copy of the source image to run the algorithm on.

imgName

String imgName
The original image name.

resultImage

ModelImage resultImage
The result image.

showIntermediateImages

boolean showIntermediateImages
Whether to show images from intermediate steps of the BSE algorithm.

showIntermediateImagesCB

JCheckBox showIntermediateImagesCB
Checkbox to show images which can help in paramater tweaking.

userInterface

ViewUserInterface userInterface
Reference to the main user interface.

useSeparable

boolean useSeparable
Whether to use a separable convolver during edge detection.

useSeparableCB

JCheckBox useSeparableCB
Checkbox to elect to use the separable convolver in the edge detection algorithm.

Class gov.nih.mipav.view.dialogs.JDialogBrightness extends JDialogBase implements Serializable

serialVersionUID: -1222614304368736757L

Serialized Fields

brightness

int brightness
DOCUMENT ME!

brightnessSlider

JSlider brightnessSlider
DOCUMENT ME!

contrastSlider

JSlider contrastSlider
DOCUMENT ME!

componentImage

ViewJComponentAnimate componentImage
DOCUMENT ME!

componentImageColEM

ViewJComponentColocalizationEM componentImageColEM
DOCUMENT ME!

componentImageColReg

ViewJComponentColocalizationRegression componentImageColReg
DOCUMENT ME!

contrast

float contrast
DOCUMENT ME!

current

JLabel current
DOCUMENT ME!

current2

JLabel current2
DOCUMENT ME!

nfc

NumberFormat nfc
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogBSmooth extends JDialogBase implements Serializable

serialVersionUID: -2582311598077394632L

Serialized Fields

defaultPts

int defaultPts
DOCUMENT ME!

elementNum

int elementNum
DOCUMENT ME!

gons

Polygon[] gons
DOCUMENT ME!

groupNum

int groupNum
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

nPts

int nPts
DOCUMENT ME!

removeOriginal

boolean removeOriginal
DOCUMENT ME!

removeOriginalCheckBox

JCheckBox removeOriginalCheckBox
DOCUMENT ME!

smoothAlgo

AlgorithmBSmooth smoothAlgo
DOCUMENT ME!

textInterpNPts

JTextField textInterpNPts
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

trim

boolean trim
DOCUMENT ME!

trimCheckBox

JCheckBox trimCheckBox
DOCUMENT ME!

voiColor

Color voiColor
DOCUMENT ME!

VOIs

ViewVOIVector VOIs
DOCUMENT ME!

zSlice

int zSlice
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogBSnake extends JDialogBase implements Serializable

serialVersionUID: 6813632326437983422L

Serialized Fields

boundaryIterations

int boundaryIterations
DOCUMENT ME!

groupNum

int groupNum
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

labelCorrected

JLabel labelCorrected
DOCUMENT ME!

normFactor

float normFactor
DOCUMENT ME!

propagate

JRadioButton propagate
DOCUMENT ME!

propagationType

int propagationType
DOCUMENT ME!

removeOriginal

boolean removeOriginal
DOCUMENT ME!

removeOriginalCheckBox

JCheckBox removeOriginalCheckBox
DOCUMENT ME!

resolutionCheckbox

JCheckBox resolutionCheckbox
difference between x,y resolutions (in plane) and z resolution (between planes).

scaleX

float scaleX
DOCUMENT ME!

scaleY

float scaleY
DOCUMENT ME!

scaleZ

float scaleZ
DOCUMENT ME!

singleSlice

JRadioButton singleSlice
DOCUMENT ME!

snakeAlgo

AlgorithmBSnake snakeAlgo
DOCUMENT ME!

srcVOI

VOI srcVOI
DOCUMENT ME!

textBoundaryIterations

JTextField textBoundaryIterations
DOCUMENT ME!

textGaussX

JTextField textGaussX
DOCUMENT ME!

textGaussY

JTextField textGaussY
DOCUMENT ME!

textGaussZ

JTextField textGaussZ
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

voiColor

Color voiColor
DOCUMENT ME!

VOIs

ViewVOIVector VOIs
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogBulkImageCalculator extends JDialogScriptableBase implements Serializable

Serialized Fields

imageA

ModelImage imageA
source image.

resultImage

ModelImage resultImage
result image

isColor

boolean isColor
is color boolean

comboBoxOperator

JComboBox comboBoxOperator
operator combo box

srcTableModel

ViewTableModel srcTableModel
table model for the srcimages.

srcImagesTable

JTable srcImagesTable
table to display the src image names.

srcImagesList

ArrayList<E> srcImagesList
list of images to send to algorithm

additionalImagesList

ArrayList<E> additionalImagesList
list of any additional images browsed to

clipMode

int clipMode
clip mode

alg

AlgorithmImageCalculator alg
handle to algorithm

opType

int opType
operation type....for now set to ADD

displayLoc

int displayLoc
result image in new frame

additionalImagesLabel

JLabel additionalImagesLabel
label for browsing for additional images

addImageBrowseButton

JButton addImageBrowseButton
browse button

removeSelectedImagesLabel

JLabel removeSelectedImagesLabel
label for removing selected images

removeSelectedButton

JButton removeSelectedButton
remove button

isMultifile

boolean isMultifile
boolean isMultifile

selectedRows

int[] selectedRows
indices of selcted rows to remove

Class gov.nih.mipav.view.dialogs.JDialogCaptureScreen extends JDialogBase implements Serializable

serialVersionUID: -2364847865242983737L

Serialized Fields

currentRectangle

Rectangle currentRectangle
The rectangle that will be captured from the screen to save to a file.

instructions

JLabel instructions
Instructions on how to use screen capture, line 1.

instructions2

JLabel instructions2
Instructions on how to use screen capture, line 2.

mode

int mode
Mode - region, window, or none.

myGlassPanes

gov.nih.mipav.view.dialogs.JDialogCaptureScreen.MyGlassPane[] myGlassPanes
Special glass panes for all the valid frames in the GUI so that the user can draw rectangles on top of objects in the GUI.

oldFrames

JFrame[] oldFrames
All the valid JFrames in the GUI.

oldPanes

Component[] oldPanes
Old glass panes to reset to after drawing is done.

regionButton

JRadioButton regionButton
Button for selecting region mode.

save

boolean save
Flag that indicates whether to save capture as file or put it in new frame on screen.

saveCheck

JCheckBox saveCheck
Checkbox for selecting display in window.

userInterface

ViewUserInterface userInterface
Pointer to the user interface.

windowButton

JRadioButton windowButton
Button for selecting window mode.

activeFrame

ViewJFrameImage activeFrame
Active frame

Class gov.nih.mipav.view.dialogs.JDialogCaptureScreens extends JDialogBase implements Serializable

serialVersionUID: 5133757391495903883L

Serialized Fields

currentRectangle

Rectangle currentRectangle
The rectangle that will be captured from the screen to save to a file.

imageFrame

ViewJFrameImage imageFrame
The parent image frame.

numSlices

int numSlices
Number of slices in the image.

Class gov.nih.mipav.view.dialogs.JDialogCardiology extends JDialogBase implements Serializable

serialVersionUID: 4074062695729029005L

Serialized Fields

currentSlice

int currentSlice
DOCUMENT ME!

dimX

int dimX
DOCUMENT ME!

dimY

int dimY
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

infarctionVOIIndex

int infarctionVOIIndex
DOCUMENT ME!

innerVOIIndex

int innerVOIIndex
DOCUMENT ME!

numSections

int numSections
DOCUMENT ME!

numSectionsField

JTextField numSectionsField
DOCUMENT ME!

outerVOIIndex

int outerVOIIndex
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogCenterOfMass extends JDialogScriptableBase implements Serializable

Serialized Fields

image

ModelImage image
DOCUMENT ME!

labelThres2

JLabel labelThres2
DOCUMENT ME!

min

float min
DOCUMENT ME!

max

float max
DOCUMENT ME!

regionFlag

boolean regionFlag
or if the source image is to be replaced.

textThres1

JTextField textThres1
DOCUMENT ME!

textThres2

JTextField textThres2
DOCUMENT ME!

thres1

float thres1
DOCUMENT ME!

thres2

float thres2
DOCUMENT ME!

comAlgo

AlgorithmCenterOfMass comAlgo
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

VOIRegions

JRadioButton VOIRegions
DOCUMENT ME!

wholeImage

JRadioButton wholeImage
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogCenterOfMass.CheckValueAction extends AbstractAction implements Serializable

serialVersionUID: -1531686009578681460L

Class gov.nih.mipav.view.dialogs.JDialogCenterOfMassRGB extends JDialogScriptableBase implements Serializable

Serialized Fields

applyToAllBox

JCheckBox applyToAllBox
false = apply algorithm only to VOI regions apply same threshold to all.

image

ModelImage image
DOCUMENT ME!

maxs

float[] maxs
DOCUMENT ME!

mins

float[] mins
Minimum and maximum values for red/gree/blue.

regionFlag

boolean regionFlag
or if the source image is to be replaced.

textThreshold1

JTextField[] textThreshold1
Text fields for lower & upper thresholds and fill values.

textThreshold2

JTextField[] textThreshold2
DOCUMENT ME!

comAlgoRGB

AlgorithmCenterOfMassRGB comAlgoRGB
DOCUMENT ME!

thresholdB

float[] thresholdB
DOCUMENT ME!

thresholdG

float[] thresholdG
DOCUMENT ME!

thresholdLabels1

JLabel[] thresholdLabels1
DOCUMENT ME!

thresholdLabels2

JLabel[] thresholdLabels2
DOCUMENT ME!

thresholdR

float[] thresholdR
lower [0] and upper [1] thresholds for RGB.

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

VOIRegions

JRadioButton VOIRegions
DOCUMENT ME!

wholeImage

JRadioButton wholeImage
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogCentroidThreshold extends JDialogBase implements Serializable

serialVersionUID: 5102272946311012581L

Serialized Fields

centroids

float[] centroids
DOCUMENT ME!

defaultValueInput

JTextField[] defaultValueInput
DOCUMENT ME!

gbc

GridBagConstraints gbc
DOCUMENT ME!

gbl

GridBagLayout gbl
DOCUMENT ME!

i

int i
DOCUMENT ME!

imageName

String imageName
DOCUMENT ME!

minimum

float minimum
DOCUMENT ME!

maximum

float maximum
DOCUMENT ME!

nClasses

int nClasses
DOCUMENT ME!

threshold

float threshold
DOCUMENT ME!

thresholdValueInput

JTextField thresholdValueInput
DOCUMENT ME!

tmpStr

String tmpStr
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogChangeMaskNumber extends JDialogBase implements Serializable

Serialized Fields

changeLabel

JLabel changeLabel
this is the text in the Dialog

numberField

JTextField numberField
this is the input for the user to enter what number they want to change to

changeButton

JButton changeButton
this is the action button to change

srcButton

JButton srcButton
this is a ref to the source button so that the text on the button can be changed

correspButton

JButton correspButton
this is a ref to the corresponding button becasue they need to be in sync

btArrayList

ArrayList<E> btArrayList
this is the array list of the texts on the buttons

currentMaskNumberIndex

int currentMaskNumberIndex
this represents the current index of the btArrayList

color

Color[] color
re f to Color array

lutB

ModelLUT lutB
lutB

image

ModelImage image
ref to image

intensityLockVector

Vector<E> intensityLockVector
ref to IntensityLockVector

srcValue

int srcValue
src button text number

Class gov.nih.mipav.view.dialogs.JDialogCheckerBoard extends JDialogBase implements Serializable

serialVersionUID: 4180573157937289440L

Serialized Fields

closeButton

JButton closeButton
DOCUMENT ME!

compImage

ViewJComponentEditImage compImage
DOCUMENT ME!

doCheckbox

JCheckBox doCheckbox
DOCUMENT ME!

doReg

boolean doReg
DOCUMENT ME!

labelColumnNumber

JLabel labelColumnNumber
DOCUMENT ME!

labelRowNumber

JLabel labelRowNumber
DOCUMENT ME!

labelTable

Hashtable<K,V> labelTable
DOCUMENT ME!

labelTable2

Hashtable<K,V> labelTable2
DOCUMENT ME!

maxColumn

int maxColumn
DOCUMENT ME!

maxRow

int maxRow
DOCUMENT ME!

regImage

ViewJComponentRegistration regImage
DOCUMENT ME!

slider

JSlider slider
DOCUMENT ME!

slider2

JSlider slider2
DOCUMENT ME!

textRowNumber

JTextField textRowNumber
DOCUMENT ME!

textColumnNumber

JTextField textColumnNumber
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogCircleToRectangle extends JDialogBase implements Serializable

serialVersionUID: 0L

Serialized Fields

extents

int[] extents
DOCUMENT ME!

cAlgo

AlgorithmCircleToRectangle cAlgo
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

xDim

int xDim
DOCUMENT ME!

xSource

double[] xSource
DOCUMENT ME!

xText

JTextField xText
DOCUMENT ME!

yDim

int yDim
DOCUMENT ME!

ySource

double[] ySource
DOCUMENT ME!

yText

JTextField yText
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogCircularSectorToRectangle extends JDialogBase implements Serializable

serialVersionUID: 0L

Serialized Fields

extents

int[] extents
DOCUMENT ME!

cAlgo

AlgorithmCircularSectorToRectangle cAlgo
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

xDim

int xDim
DOCUMENT ME!

xSource

double[] xSource
DOCUMENT ME!

xText

JTextField xText
DOCUMENT ME!

yDim

int yDim
DOCUMENT ME!

ySource

double[] ySource
DOCUMENT ME!

yText

JTextField yText
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogClose extends JDialogScriptableBase implements Serializable

serialVersionUID: -8489706932459076773L

Serialized Fields

closeAlgo25D

AlgorithmMorphology25D closeAlgo25D
DOCUMENT ME!

closeAlgo2D

AlgorithmMorphology2D closeAlgo2D
DOCUMENT ME!

closeAlgo3D

AlgorithmMorphology3D closeAlgo3D
DOCUMENT ME!

comboBoxKernel

JComboBox comboBoxKernel
DOCUMENT ME!

do25D

boolean do25D
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

image25D

JCheckBox image25D
DOCUMENT ME!

itersD

int itersD
or if the source image is to be replaced.

itersE

int itersE
DOCUMENT ME!

kernel

int kernel
DOCUMENT ME!

kernelSize

float kernelSize
DOCUMENT ME!

labelKernel

JLabel labelKernel
DOCUMENT ME!

labelKernelSize

JLabel labelKernelSize
DOCUMENT ME!

labelNIterD

JLabel labelNIterD
DOCUMENT ME!

labelNIterE

JLabel labelNIterE
DOCUMENT ME!

maskPanel

JPanel maskPanel
DOCUMENT ME!

outputPanel

JPanelAlgorithmOutputOptions outputPanel
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

textKernelSize

JTextField textKernelSize
DOCUMENT ME!

textNIterD

JTextField textNIterD
DOCUMENT ME!

textNIterE

JTextField textNIterE
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogCoherenceEnhancingDiffusion extends JDialogScriptableBase implements Serializable

serialVersionUID: 1141466038513737001L

Serialized Fields

checkBox25D

JCheckBox checkBox25D
DOCUMENT ME!

coherenceEnhancingDiffusionAlgo

AlgorithmCoherenceEnhancingDiffusion coherenceEnhancingDiffusionAlgo
DOCUMENT ME!

derivativeScale

float derivativeScale
DOCUMENT ME!

diffusitivityDenom

float diffusitivityDenom
DOCUMENT ME!

do25D

boolean do25D
DOCUMENT ME!

entireImage

boolean entireImage
DOCUMENT ME!

gaussianScale

float gaussianScale
DOCUMENT ME!

numIterations

int numIterations
DOCUMENT ME!

radioEntireImage

JRadioButton radioEntireImage
DOCUMENT ME!

radioVOIRegion

JRadioButton radioVOIRegion
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

srcImage

ModelImage srcImage
DOCUMENT ME!

textDerivative

JTextField textDerivative
DOCUMENT ME!

textGaussian

JTextField textGaussian
DOCUMENT ME!

textNumberIterations

JTextField textNumberIterations
DOCUMENT ME!

textDiffusitivity

JTextField textDiffusitivity
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogColocalizationEM extends JDialogScriptableBase implements Serializable

serialVersionUID: -2241466976779150747L

Serialized Fields

andButton

JRadioButton andButton
DOCUMENT ME!

bin1

int bin1
DOCUMENT ME!

bin1Default

boolean bin1Default
DOCUMENT ME!

bin1Label

JLabel bin1Label
DOCUMENT ME!

bin1Text

JTextField bin1Text
DOCUMENT ME!

bin2

int bin2
DOCUMENT ME!

bin2Default

boolean bin2Default
DOCUMENT ME!

bin2Label

JLabel bin2Label
DOCUMENT ME!

bin2Text

JTextField bin2Text
DOCUMENT ME!

blueCheckBox

JCheckBox blueCheckBox
DOCUMENT ME!

bottomPad

int bottomPad
DOCUMENT ME!

buffer

float[] buffer
DOCUMENT ME!

colocalizationAlgo

AlgorithmColocalizationEM colocalizationAlgo
DOCUMENT ME!

colorsPresent

int colorsPresent
DOCUMENT ME!

comboBoxCostFunct

JComboBox comboBoxCostFunct
DOCUMENT ME!

cost

int cost
DOCUMENT ME!

doOr

boolean doOr
DOCUMENT ME!

entireImage

boolean entireImage
DOCUMENT ME!

firstImage

ModelImage firstImage
DOCUMENT ME!

gaussianLabel

JLabel gaussianLabel
DOCUMENT ME!

gaussians

int gaussians
DOCUMENT ME!

gaussianText

JTextField gaussianText
DOCUMENT ME!

greenCheckBox

JCheckBox greenCheckBox
DOCUMENT ME!

imageComboBox

JComboBox imageComboBox
DOCUMENT ME!

imageLength

int imageLength
DOCUMENT ME!

iterationLabel

JLabel iterationLabel
DOCUMENT ME!

iterations

int iterations
DOCUMENT ME!

iterationText

JTextField iterationText
DOCUMENT ME!

labelCost

JLabel labelCost
DOCUMENT ME!

labelImage

JLabel labelImage
DOCUMENT ME!

leftPad

int leftPad
DOCUMENT ME!

mask

BitSet mask
DOCUMENT ME!

maxR

double maxR
DOCUMENT ME!

maxG

double maxG
DOCUMENT ME!

maxB

double maxB
DOCUMENT ME!

maxRV

double maxRV
DOCUMENT ME!

maxGV

double maxGV
DOCUMENT ME!

maxBV

double maxBV
DOCUMENT ME!

minR

double minR
DOCUMENT ME!

minG

double minG
DOCUMENT ME!

minB

double minB
DOCUMENT ME!

minRV

double minRV
DOCUMENT ME!

minGV

double minGV
DOCUMENT ME!

minBV

double minBV
DOCUMENT ME!

minV

double minV
DOCUMENT ME!

maxV

double maxV
DOCUMENT ME!

nBoundingVOIs

int nBoundingVOIs
DOCUMENT ME!

orButton

JRadioButton orButton
DOCUMENT ME!

possibleInt2Values

double possibleInt2Values
DOCUMENT ME!

possibleIntValues

double possibleIntValues
DOCUMENT ME!

redCheckBox

JCheckBox redCheckBox
DOCUMENT ME!

regCheckBox

JCheckBox regCheckBox
DOCUMENT ME!

register

boolean register
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

rightPad

int rightPad
DOCUMENT ME!

secondImage

ModelImage secondImage
DOCUMENT ME!

secondMinV

double secondMinV
DOCUMENT ME!

secondMaxV

double secondMaxV
DOCUMENT ME!

secondName

String secondName
DOCUMENT ME!

segImage

ModelImage segImage
Class segmentation shown.

threshold1

float threshold1
DOCUMENT ME!

threshold1Label

JLabel threshold1Label
DOCUMENT ME!

threshold1Text

JTextField threshold1Text
DOCUMENT ME!

threshold2

float threshold2
DOCUMENT ME!

threshold2Label

JLabel threshold2Label
DOCUMENT ME!

threshold2Text

JTextField threshold2Text
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

topPad

int topPad
DOCUMENT ME!

UI

ViewUserInterface UI
DOCUMENT ME!

useBlue

boolean useBlue
DOCUMENT ME!

useGreen

boolean useGreen
DOCUMENT ME!

useRed

boolean useRed
DOCUMENT ME!

VOIRegions

JRadioButton VOIRegions
DOCUMENT ME!

wholeImage

JRadioButton wholeImage
DOCUMENT ME!

xDim

int xDim
DOCUMENT ME!

yDim

int yDim
DOCUMENT ME!

zDim

int zDim
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogColocalizationRegression extends JDialogScriptableBase implements Serializable

serialVersionUID: 2982353729666791012L

Serialized Fields

point1

float point1
DOCUMENT ME!

point2

float point2
DOCUMENT ME!

background1

float background1
DOCUMENT ME!

background2

float background2
DOCUMENT ME!

bin1

int bin1
DOCUMENT ME!

bin1Default

boolean bin1Default
DOCUMENT ME!

bin1Label

JLabel bin1Label
DOCUMENT ME!

bin1Text

JTextField bin1Text
DOCUMENT ME!

bin2

int bin2
DOCUMENT ME!

bin2Default

boolean bin2Default
DOCUMENT ME!

bin2Label

JLabel bin2Label
DOCUMENT ME!

bin2Text

JTextField bin2Text
DOCUMENT ME!

blueCheckBox

JCheckBox blueCheckBox
DOCUMENT ME!

bottomPad

int bottomPad
DOCUMENT ME!

buffer

float[] buffer
DOCUMENT ME!

colocalizationAlgo

AlgorithmColocalizationRegression colocalizationAlgo
DOCUMENT ME!

colocCheckBox

JCheckBox colocCheckBox
DOCUMENT ME!

colorsPresent

int colorsPresent
DOCUMENT ME!

comboBoxCostFunct

JComboBox comboBoxCostFunct
DOCUMENT ME!

componentImage1

ViewJComponentEditImage componentImage1
DOCUMENT ME!

componentImage2

ViewJComponentEditImage componentImage2
DOCUMENT ME!

cost

int cost
DOCUMENT ME!

directory

String directory
DOCUMENT ME!

doColocWithThresholds

boolean doColocWithThresholds
DOCUMENT ME!

doSecondIteration

boolean doSecondIteration
DOCUMENT ME!

doVOISubtraction

boolean doVOISubtraction
DOCUMENT ME!

entireImage

boolean entireImage
DOCUMENT ME!

fileName

String fileName
DOCUMENT ME!

firstImage

ModelImage firstImage
DOCUMENT ME!

firstName

String firstName
DOCUMENT ME!

greenCheckBox

JCheckBox greenCheckBox
DOCUMENT ME!

imageComboBox

JComboBox imageComboBox
DOCUMENT ME!

imageLength

int imageLength
DOCUMENT ME!

labelCost

JLabel labelCost
DOCUMENT ME!

labelImage

JLabel labelImage
DOCUMENT ME!

leftPad

int leftPad
DOCUMENT ME!

mask

BitSet mask
DOCUMENT ME!

maskButton

JButton maskButton
DOCUMENT ME!

maskFileDir

String maskFileDir
DOCUMENT ME!

maskFileName

String maskFileName
DOCUMENT ME!

maskImage

ModelImage maskImage
DOCUMENT ME!

maskName

String maskName
DOCUMENT ME!

maskRadio

JRadioButton maskRadio
DOCUMENT ME!

maskText

JTextField maskText
DOCUMENT ME!

maxR

double maxR
DOCUMENT ME!

maxG

double maxG
DOCUMENT ME!

maxB

double maxB
DOCUMENT ME!

minR

double minR
DOCUMENT ME!

minG

double minG
DOCUMENT ME!

minB

double minB
DOCUMENT ME!

nBoundingVOIs

int nBoundingVOIs
DOCUMENT ME!

point1Label

JLabel point1Label
DOCUMENT ME!

point1Text

JTextField point1Text
DOCUMENT ME!

point2Label

JLabel point2Label
DOCUMENT ME!

point2Text

JTextField point2Text
DOCUMENT ME!

pointCalculation

boolean pointCalculation
DOCUMENT ME!

pointCheckBox

JCheckBox pointCheckBox
DOCUMENT ME!

possibleInt2Values

double possibleInt2Values
DOCUMENT ME!

possibleIntValues

double possibleIntValues
DOCUMENT ME!

redCheckBox

JCheckBox redCheckBox
DOCUMENT ME!

regCheckBox

JCheckBox regCheckBox
DOCUMENT ME!

register

boolean register
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

rightPad

int rightPad
DOCUMENT ME!

secondImage

ModelImage secondImage
DOCUMENT ME!

secondIterationCheckBox

JCheckBox secondIterationCheckBox
DOCUMENT ME!

secondName

String secondName
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

topPad

int topPad
DOCUMENT ME!

UI

ViewUserInterface UI
DOCUMENT ME!

useBlue

boolean useBlue
DOCUMENT ME!

useGreen

boolean useGreen
DOCUMENT ME!

useRed

boolean useRed
DOCUMENT ME!

VOICheckBox

JCheckBox VOICheckBox
DOCUMENT ME!

VOIRegions

JRadioButton VOIRegions
DOCUMENT ME!

wholeImage

JRadioButton wholeImage
DOCUMENT ME!

xDim

int xDim
DOCUMENT ME!

yDim

int yDim
DOCUMENT ME!

zDim

int zDim
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogColorEdge extends JDialogScriptableBase implements Serializable

serialVersionUID: -5364017650931720063L

Serialized Fields

algoColorEdge

AlgorithmColorEdge algoColorEdge
DOCUMENT ME!

displayLoc

int displayLoc
DOCUMENT ME!

red1

int red1
DOCUMENT ME!

green1

int green1
DOCUMENT ME!

blue1

int blue1
DOCUMENT ME!

red1Text

JTextField red1Text
DOCUMENT ME!

green1Text

JTextField green1Text
DOCUMENT ME!

blue1Text

JTextField blue1Text
DOCUMENT ME!

red2

int red2
DOCUMENT ME!

green2

int green2
DOCUMENT ME!

blue2

int blue2
DOCUMENT ME!

red2Text

JTextField red2Text
DOCUMENT ME!

green2Text

JTextField green2Text
DOCUMENT ME!

blue2Text

JTextField blue2Text
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

sourceImage

ModelImage sourceImage
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogConcat extends JDialogScriptableBase implements Serializable

serialVersionUID: 3284724231720657011L

Serialized Fields

comboBoxImage

JComboBox comboBoxImage
DOCUMENT ME!

displayLoc

int displayLoc
DOCUMENT ME!

do3D

boolean do3D
DOCUMENT ME!

imageA

ModelImage imageA
DOCUMENT ME!

imageB

ModelImage imageB
DOCUMENT ME!

mathAlgo

AlgorithmConcat mathAlgo
DOCUMENT ME!

radio3D

JRadioButton radio3D
DOCUMENT ME!

radio4D

JRadioButton radio4D
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

selectedName

String selectedName
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogConstrainedOAR3D extends JDialogScriptableBase implements Serializable

serialVersionUID: -5867077647353095805L

Serialized Fields

advancedDialog

JDialog advancedDialog
Variables for Advanced Settings dialog.

bracketBoundText

JTextField bracketBoundText
DOCUMENT ME!

maxIterationsText

JTextField maxIterationsText
DOCUMENT ME!

numMinText

JTextField numMinText
DOCUMENT ME!

buttonWeightInput

JButton buttonWeightInput
DOCUMENT ME!

buttonWeightRef

JButton buttonWeightRef
DOCUMENT ME!

calcCOG

boolean calcCOG
DOCUMENT ME!

calcCOGCheckbox

JCheckBox calcCOGCheckbox
DOCUMENT ME!

coarsePanelX

JPanel coarsePanelX
DOCUMENT ME!

coarsePanelY

JPanel coarsePanelY
DOCUMENT ME!

coarsePanelZ

JPanel coarsePanelZ
DOCUMENT ME!

comboBoxCostFunct

JComboBox comboBoxCostFunct
DOCUMENT ME!

comboBoxDOF

JComboBox comboBoxDOF
DOCUMENT ME!

comboBoxImage

JComboBox comboBoxImage
DOCUMENT ME!

comboBoxInterp

JComboBox comboBoxInterp
DOCUMENT ME!

comboBoxInterp2

JComboBox comboBoxInterp2
DOCUMENT ME!

cost

int cost
DOCUMENT ME!

interp

int interp
DOCUMENT ME!

interp2

int interp2
DOCUMENT ME!

DOF

int DOF
DOCUMENT ME!

costName

String costName
DOCUMENT ME!

displayTransform

boolean displayTransform
DOCUMENT ME!

doColor

boolean doColor
DOCUMENT ME!

doSubsample

boolean doSubsample
DOCUMENT ME!

fastMode

boolean fastMode
DOCUMENT ME!

fastModeCheckbox

JCheckBox fastModeCheckbox
DOCUMENT ME!

fileNameWRef

String fileNameWRef
DOCUMENT ME!

directoryWRef

String directoryWRef
DOCUMENT ME!

fileNameWInput

String fileNameWInput
DOCUMENT ME!

directoryWInput

String directoryWInput
DOCUMENT ME!

gbc

GridBagConstraints gbc
DOCUMENT ME!

inputWeightImage

ModelImage inputWeightImage
DOCUMENT ME!

refWeightImage

ModelImage refWeightImage
DOCUMENT ME!

labelInterp2

JLabel labelInterp2
DOCUMENT ME!

labelTranslateRangeX

JLabel labelTranslateRangeX
DOCUMENT ME!

labelTranslateRangeY

JLabel labelTranslateRangeY
DOCUMENT ME!

labelTranslateRangeZ

JLabel labelTranslateRangeZ
DOCUMENT ME!

limitTranslation

boolean limitTranslation
DOCUMENT ME!

oneTransLimit

boolean oneTransLimit
DOCUMENT ME!

limitTranslationCheckbox

JCheckBox limitTranslationCheckbox
DOCUMENT ME!

matchImage

ModelImage matchImage
DOCUMENT ME!

maxIterations_def

int maxIterations_def
DOCUMENT ME!

bracketBound_def

int bracketBound_def
DOCUMENT ME!

numMinima_def

int numMinima_def
DOCUMENT ME!

maxIterations

int maxIterations
DOCUMENT ME!

bracketBound

int bracketBound
DOCUMENT ME!

maxLimits

float[][] maxLimits
when done debugging: private boolean limitTranslation = false, oneTransLimit = false;.

maxOfMinResol

boolean maxOfMinResol
DOCUMENT ME!

maxTransTextX

JTextField maxTransTextX
DOCUMENT ME!

maxTransTextY

JTextField maxTransTextY
DOCUMENT ME!

maxTransTextZ

JTextField maxTransTextZ
DOCUMENT ME!

minMaxCheckbox

JCheckBox minMaxCheckbox
DOCUMENT ME!

minTransTextX

JTextField minTransTextX
DOCUMENT ME!

minTransTextY

JTextField minTransTextY
DOCUMENT ME!

minTransTextZ

JTextField minTransTextZ
DOCUMENT ME!

mmLabelX

JLabel mmLabelX
DOCUMENT ME!

mmLabelY

JLabel mmLabelY
DOCUMENT ME!

mmLabelZ

JLabel mmLabelZ
DOCUMENT ME!

noneRadio

JRadioButton noneRadio
DOCUMENT ME!

numberCoarseTextX

JTextField numberCoarseTextX
DOCUMENT ME!

numberCoarseTextY

JTextField numberCoarseTextY
DOCUMENT ME!

numberCoarseTextZ

JTextField numberCoarseTextZ
DOCUMENT ME!

numCoarseX

int numCoarseX
DOCUMENT ME!

numCoarseY

int numCoarseY
DOCUMENT ME!

numCoarseZ

int numCoarseZ
DOCUMENT ME!

numMinima

int numMinima
DOCUMENT ME!

refImage

ModelImage refImage
DOCUMENT ME!

reg3

AlgorithmConstrainedOAR3D reg3
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

rotateBeginTextX

JTextField rotateBeginTextX
DOCUMENT ME!

rotateBeginTextY

JTextField rotateBeginTextY
DOCUMENT ME!

rotateBeginTextZ

JTextField rotateBeginTextZ
DOCUMENT ME!

rotateBeginX

float rotateBeginX
private JTextField fineRateTextX, fineRateTextY, fineRateTextZ;.

rotateEndX

float rotateEndX
private JTextField fineRateTextX, fineRateTextY, fineRateTextZ;.

rotateRangeX

float rotateRangeX
private JTextField fineRateTextX, fineRateTextY, fineRateTextZ;.

rotateBeginY

float rotateBeginY
DOCUMENT ME!

rotateEndY

float rotateEndY
DOCUMENT ME!

rotateRangeY

float rotateRangeY
DOCUMENT ME!

rotateBeginZ

float rotateBeginZ
DOCUMENT ME!

rotateEndZ

float rotateEndZ
DOCUMENT ME!

rotateRangeZ

float rotateRangeZ
DOCUMENT ME!

rotateEndTextX

JTextField rotateEndTextX
DOCUMENT ME!

rotateEndTextY

JTextField rotateEndTextY
DOCUMENT ME!

rotateEndTextZ

JTextField rotateEndTextZ
DOCUMENT ME!

rotatePanel

JPanel rotatePanel
Variables for Rotation and Translation bounds.

rotateRangePanelX

JPanel rotateRangePanelX
DOCUMENT ME!

rotateRangePanelY

JPanel rotateRangePanelY
DOCUMENT ME!

rotateRangePanelZ

JPanel rotateRangePanelZ
DOCUMENT ME!

sampleCheckbox

JCheckBox sampleCheckbox
DOCUMENT ME!

textInput

JTextField textInput
DOCUMENT ME!

textRef

JTextField textRef
DOCUMENT ME!

toLabelX

JLabel toLabelX
DOCUMENT ME!

toLabelY

JLabel toLabelY
DOCUMENT ME!

toLabelZ

JLabel toLabelZ
DOCUMENT ME!

transformCheckbox

JCheckBox transformCheckbox
DOCUMENT ME!

translatePanel

JPanel translatePanel
DOCUMENT ME!

translateRangePanelX

JPanel translateRangePanelX
private JPanel finePanelX, finePanelY, finePanelZ;.

translateRangePanelY

JPanel translateRangePanelY
private JPanel finePanelX, finePanelY, finePanelZ;.

translateRangePanelZ

JPanel translateRangePanelZ
private JPanel finePanelX, finePanelY, finePanelZ;.

transLimits

float[][] transLimits
DOCUMENT ME!

UI

ViewUserInterface UI
DOCUMENT ME!

universalRotationCheckbox

JCheckBox universalRotationCheckbox
DOCUMENT ME!

universalTranslationCheckbox

JCheckBox universalTranslationCheckbox
DOCUMENT ME!

voiRadio

JRadioButton voiRadio
DOCUMENT ME!

voisOnly

boolean voisOnly
DOCUMENT ME!

weighted

boolean weighted
DOCUMENT ME!

weightRadio

JRadioButton weightRadio
DOCUMENT ME!

xRRadio

JRadioButton xRRadio
DOCUMENT ME!

yRRadio

JRadioButton yRRadio
DOCUMENT ME!

zRRadio

JRadioButton zRRadio
DOCUMENT ME!

xRSelected

boolean xRSelected
DOCUMENT ME!

yRSelected

boolean yRSelected
DOCUMENT ME!

zRSelected

boolean zRSelected
DOCUMENT ME!

outOfBoundsLabel

JLabel outOfBoundsLabel

outOfBoundsComboBox

JComboBox outOfBoundsComboBox

valueLabel

JLabel valueLabel

valueText

JTextField valueText

imageMin

double imageMin

imageMax

double imageMax

dataType

int dataType

outOfBoundsIndex

int outOfBoundsIndex
Tells how to select fill value for out of bounds data 0 for image minimum 1 for NaN for float, zero otherwise. 2 for user defined 3 for image maximum

fillValue

float fillValue

Class gov.nih.mipav.view.dialogs.JDialogConvert3Dto4D extends JDialogScriptableBase implements Serializable

serialVersionUID: 5353653644655035651L

Serialized Fields

comboBoxUnitOfMeasure3

JComboBox comboBoxUnitOfMeasure3
DOCUMENT ME!

comboBoxUnitOfMeasure4

JComboBox comboBoxUnitOfMeasure4
DOCUMENT ME!

convert3Dto4DAlgo

AlgorithmConvert3Dto4D convert3Dto4DAlgo
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

imageName

String imageName
DOCUMENT ME!

labelVolumeLength

JLabel labelVolumeLength
DOCUMENT ME!

measure3

int measure3
DOCUMENT ME!

measure4

int measure4
DOCUMENT ME!

res3

float res3
DOCUMENT ME!

res4

float res4
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

textRes3

JTextField textRes3
DOCUMENT ME!

textRes4

JTextField textRes4
DOCUMENT ME!

textVolumeLength

JTextField textVolumeLength
DOCUMENT ME!

volumeLength

int volumeLength
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogConvert4Dto3D extends JDialogScriptableBase implements Serializable

serialVersionUID: -4079283618961189766L

Serialized Fields

convert4Dto3DAlgo

AlgorithmConvert4Dto3D convert4Dto3DAlgo
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogConvert4DtoRGB extends JDialogScriptableBase implements Serializable

Serialized Fields

image

ModelImage image
src image

destExtents

int[] destExtents
extents for extracted 3D subset

xSlices

int xSlices
num x slices of src image

ySlices

int ySlices
num y slices of src image

zSlices

int zSlices
num z slices for src image

channelImages

ModelImage[] channelImages
extraced 3D Model Images from src image

channelColorsComboBoxes

JComboBox[] channelColorsComboBoxes
corresponding dropdown for each channel image

subsetAlgo

AlgorithmSubset subsetAlgo
ref to AlgorithmSubset

mainPanel

JPanel mainPanel
main panel of dialog

inputPanel

JPanel inputPanel
input panel of dialog

OKCancelPanel

JPanel OKCancelPanel
ok/cancel panel of dialog

remapCheckBox

JCheckBox remapCheckBox
re-map checkbox

imageB

ModelImage imageB
blue channel image

imageG

ModelImage imageG
green channel image

imageR

ModelImage imageR
red channel image

resultImage

ModelImage resultImage
result image

remapMode

boolean remapMode
boolean for remap

mathAlgo

AlgorithmRGBConcat mathAlgo
ref to AlgorithmRGBConcat

blank

ModelImage blank
blank image

vol1Channel

String vol1Channel
vol 1 channel for scripting

vol2Channel

String vol2Channel
vol 2 channel for scripting

vol3Channel

String vol3Channel
vol 3 channel for scriptin

Class gov.nih.mipav.view.dialogs.JDialogConvertDicom extends JDialogBase implements Serializable

serialVersionUID: 61852307944098120L

Serialized Fields

browseButton

JButton browseButton
DOCUMENT ME!

browseOutputButton

JButton browseOutputButton
DOCUMENT ME!

compression

int compression
DOCUMENT ME!

compressionBox

JComboBox compressionBox
DOCUMENT ME!

dirField

JTextField dirField
DOCUMENT ME!

fieldChanged

boolean fieldChanged
DOCUMENT ME!

outputBox

JComboBox outputBox
DOCUMENT ME!

outputField

JTextField outputField
DOCUMENT ME!

outputPanel

JPanel outputPanel
DOCUMENT ME!

qualityField

JTextField qualityField
DOCUMENT ME!

qualityLabel

JLabel qualityLabel
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogConvertType extends JDialogScriptableBase implements Serializable

serialVersionUID: -6815107682654273857L

Serialized Fields

bigEnd

JRadioButton bigEnd
DOCUMENT ME!

changeTypeAlgo

AlgorithmChangeType changeTypeAlgo
DOCUMENT ME!

dataType

int dataType
DOCUMENT ME!

displayLoc

int displayLoc
DOCUMENT ME!

endianess

boolean endianess
DOCUMENT ME!

fullRangeRadio

JRadioButton fullRangeRadio
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

inEnd

JLabel inEnd
DOCUMENT ME!

inMin

double inMin
DOCUMENT ME!

inMax

double inMax
DOCUMENT ME!

inputRangeGroup

ButtonGroup inputRangeGroup
DOCUMENT ME!

inStart

JLabel inStart
DOCUMENT ME!

inTempMin

double inTempMin
DOCUMENT ME!

inTempMax

double inTempMax
DOCUMENT ME!

littleEnd

JRadioButton littleEnd
DOCUMENT ME!

newImage

JRadioButton newImage
DOCUMENT ME!

outEnd

JLabel outEnd
DOCUMENT ME!

outMin

double outMin
DOCUMENT ME!

outMax

double outMax
DOCUMENT ME!

outStart

JLabel outStart
DOCUMENT ME!

outTempMin

double outTempMin
DOCUMENT ME!

outTempMax

double outTempMax
DOCUMENT ME!

processIndep

boolean processIndep
DOCUMENT ME!

processIndepBox

JCheckBox processIndepBox
DOCUMENT ME!

radioARGB

JRadioButton radioARGB
DOCUMENT ME!

radioARGB_FLOAT

JRadioButton radioARGB_FLOAT
DOCUMENT ME!

radioARGB_USHORT

JRadioButton radioARGB_USHORT
DOCUMENT ME!

radioBool

JRadioButton radioBool
DOCUMENT ME!

radioByte

JRadioButton radioByte
DOCUMENT ME!

radioDouble

JRadioButton radioDouble
DOCUMENT ME!

radioFloat

JRadioButton radioFloat
DOCUMENT ME!

radioInt

JRadioButton radioInt
DOCUMENT ME!

radioLong

JRadioButton radioLong
DOCUMENT ME!

radioShort

JRadioButton radioShort
DOCUMENT ME!

radioUByte

JRadioButton radioUByte
DOCUMENT ME!

radioUInt

JRadioButton radioUInt
DOCUMENT ME!

radioUShort

JRadioButton radioUShort
DOCUMENT ME!

replaceImage

JRadioButton replaceImage
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

textInEnd

JTextField textInEnd
DOCUMENT ME!

textInStart

JTextField textInStart
DOCUMENT ME!

textOutEnd

JTextField textOutEnd
DOCUMENT ME!

textOutStart

JTextField textOutStart
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

useDefaultRanges

boolean useDefaultRanges
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

userRangeRadio

JRadioButton userRangeRadio
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogCorrectSpacing extends JDialogScriptableBase implements Serializable

serialVersionUID: 6267255098982835652L

Serialized Fields

correctSpaceAlgo

AlgorithmCorrectSpacing correctSpaceAlgo
DOCUMENT ME!

extents

int[] extents
DOCUMENT ME!

fileFormat

int fileFormat
DOCUMENT ME!

fileInfoBuffer

FileInfoBase fileInfoBuffer
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

numIm

int numIm
DOCUMENT ME!

numRepIm

int numRepIm
DOCUMENT ME!

numBlank

int numBlank
DOCUMENT ME!

newNumIm

int newNumIm
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

thick

float thick
DOCUMENT ME!

space

float space
DOCUMENT ME!

gap

float gap
DOCUMENT ME!

newThick

float newThick
DOCUMENT ME!

zStart

float zStart
DOCUMENT ME!

newZStart

float newZStart
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogCreateRtable extends JDialogScriptableBase implements Serializable

Serialized Fields

binNumber

int binNumber
Number of bins for gradient direction, normal to the tangent angle, going from 0 to 2*PI radians. The gradient direction is defined as going into the object.

binText

JTextField binText

createRtableAlgo

AlgorithmCreateRtable createRtableAlgo
DOCUMENT ME!

fileButton

JButton fileButton
DOCUMENT ME!

fileName

String fileName
DOCUMENT ME!

fileTF

JTextField fileTF
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

sideText

JTextField sideText

sidePointsForTangent

int sidePointsForTangent
Number of points to take from each side of a point on a curve in determining a tangent

Class gov.nih.mipav.view.dialogs.JDialogCrop extends JDialogScriptableBase implements Serializable

serialVersionUID: 9000755868801202116L

Serialized Fields

borderSize

int borderSize
DOCUMENT ME!

cropAlgo

AlgorithmCrop cropAlgo
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

imgRes

float[] imgRes
DOCUMENT ME!

startPos

float[] startPos
DOCUMENT ME!

lowXmm

float lowXmm
DOCUMENT ME!

lowYmm

float lowYmm
DOCUMENT ME!

lowZmm

float lowZmm
DOCUMENT ME!

nDims

int nDims
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

resXUnit

int resXUnit
DOCUMENT ME!

resYUnit

int resYUnit
DOCUMENT ME!

textBorderSize

JTextField textBorderSize
DOCUMENT ME!

textWidth

JTextField textWidth
DOCUMENT ME!

textHeight

JTextField textHeight
DOCUMENT ME!

textDepth

JTextField textDepth
DOCUMENT ME!

textXmin

JTextField textXmin
DOCUMENT ME!

textYmin

JTextField textYmin
DOCUMENT ME!

textZmin

JTextField textZmin
DOCUMENT ME!

textLowerXmm

JTextField textLowerXmm
DOCUMENT ME!

textLowerYmm

JTextField textLowerYmm
DOCUMENT ME!

textLowerZmm

JTextField textLowerZmm
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

xBounds

int[] xBounds
DOCUMENT ME!

yBounds

int[] yBounds
DOCUMENT ME!

zBounds

int[] zBounds
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogCropParam extends JDialogScriptableBase implements Serializable

serialVersionUID: -2434000521271688512L

Serialized Fields

back

int back
DOCUMENT ME!

backInput

JTextField backInput
DOCUMENT ME!

borderSize

int borderSize
DOCUMENT ME!

bottomInput

JTextField bottomInput
DOCUMENT ME!

bottomSide

int bottomSide
DOCUMENT ME!

cropAlgo

AlgorithmCrop cropAlgo
DOCUMENT ME!

destinationGroup

ButtonGroup destinationGroup
DOCUMENT ME!

displayLoc

int displayLoc
DOCUMENT ME!

front

int front
DOCUMENT ME!

frontInput

JTextField frontInput
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

leftSide

int leftSide
DOCUMENT ME!

leftSideInput

JTextField leftSideInput
DOCUMENT ME!

newImage

JRadioButton newImage
DOCUMENT ME!

replaceImage

JRadioButton replaceImage
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

rightSide

int rightSide
DOCUMENT ME!

rightSideInput

JTextField rightSideInput
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

topInput

JTextField topInput
DOCUMENT ME!

topSide

int topSide
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

xBounds

int[] xBounds
DOCUMENT ME!

yBounds

int[] yBounds
DOCUMENT ME!

zBounds

int[] zBounds
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogCT extends JDialogBase implements Serializable

serialVersionUID: 8061222665925432857L

Serialized Fields

abdomenLabel

JLabel abdomenLabel
Preset labels.

abdomenMin

int abdomenMin
Preset min, max values. Min presents the min window value. Max presents the max window value.

abdomenMax

int abdomenMax
Preset min, max values. Min presents the min window value. Max presents the max window value.

headLabel

JLabel headLabel
DOCUMENT ME!

headMin

int headMin
DOCUMENT ME!

headMax

int headMax
DOCUMENT ME!

lungLabel

JLabel lungLabel
DOCUMENT ME!

lungMin

int lungMin
DOCUMENT ME!

lungMax

int lungMax
DOCUMENT ME!

mediastinumLabel

JLabel mediastinumLabel
DOCUMENT ME!

mediastinumMin

int mediastinumMin
DOCUMENT ME!

mediastinumMax

int mediastinumMax
DOCUMENT ME!

minLabel

JLabel minLabel
DOCUMENT ME!

maxLabel

JLabel maxLabel
DOCUMENT ME!

minText

JTextField minText
Min, max text fields.

maxText

JTextField maxText
Min, max text fields.

origNPts

int origNPts
Single Transfer Line size.

origX

float[] origX
x, y, z arrays of the LUT transfer function.

origY

float[] origY
x, y, z arrays of the LUT transfer function.

origZ

float[] origZ
x, y, z arrays of the LUT transfer function.

radioAbdomen

JRadioButton radioAbdomen
Preset radio buttons.

radioHead

JRadioButton radioHead
DOCUMENT ME!

radioLung

JRadioButton radioLung
DOCUMENT ME!

radioMediastinum

JRadioButton radioMediastinum
DOCUMENT ME!

radioSpine

JRadioButton radioSpine
DOCUMENT ME!

radioVertebrae

JRadioButton radioVertebrae
DOCUMENT ME!

resetButton

JButton resetButton
Reset button to reset the default preset values.

setButton

JButton setButton
When user change the window, level values, setButton sets the min, max of the window values.

spineLabel

JLabel spineLabel
DOCUMENT ME!

spineMin

int spineMin
DOCUMENT ME!

spineMax

int spineMax
DOCUMENT ME!

vertebraeLabel

JLabel vertebraeLabel
DOCUMENT ME!

vertebraeMin

int vertebraeMin
DOCUMENT ME!

vertebraeMax

int vertebraeMax
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogCTHistoLUT extends JDialogBase implements Serializable

serialVersionUID: 8061222665925432857L

Serialized Fields

abdomenLabel

JLabel abdomenLabel
Preset labels.

abdomenMin

int abdomenMin
Preset min, max values. Min presents the min window value. Max presents the max window value.

abdomenMax

int abdomenMax
Preset min, max values. Min presents the min window value. Max presents the max window value.

headLabel

JLabel headLabel
DOCUMENT ME!

headMin

int headMin
DOCUMENT ME!

headMax

int headMax
DOCUMENT ME!

lungLabel

JLabel lungLabel
DOCUMENT ME!

lungMin

int lungMin
DOCUMENT ME!

lungMax

int lungMax
DOCUMENT ME!

mediastinumLabel

JLabel mediastinumLabel
DOCUMENT ME!

mediastinumMin

int mediastinumMin
DOCUMENT ME!

mediastinumMax

int mediastinumMax
DOCUMENT ME!

minLabel

JLabel minLabel
DOCUMENT ME!

maxLabel

JLabel maxLabel
DOCUMENT ME!

minText

JTextField minText
Min, max text fields.

maxText

JTextField maxText
Min, max text fields.

origNPts

int origNPts
Single Transfer Line size.

origX

float[] origX
x, y, z arrays of the LUT transfer function.

origY

float[] origY
x, y, z arrays of the LUT transfer function.

origZ

float[] origZ
x, y, z arrays of the LUT transfer function.

radioAbdomen

JRadioButton radioAbdomen
Preset radio buttons.

radioHead

JRadioButton radioHead
DOCUMENT ME!

radioLung

JRadioButton radioLung
DOCUMENT ME!

radioMediastinum

JRadioButton radioMediastinum
DOCUMENT ME!

radioSpine

JRadioButton radioSpine
DOCUMENT ME!

radioVertebrae

JRadioButton radioVertebrae
DOCUMENT ME!

resetButton

JButton resetButton
Reset button to reset the default preset values.

setButton

JButton setButton
When user change the window, level values, setButton sets the min, max of the window values.

spineLabel

JLabel spineLabel
DOCUMENT ME!

spineMin

int spineMin
DOCUMENT ME!

spineMax

int spineMax
DOCUMENT ME!

vertebraeLabel

JLabel vertebraeLabel
DOCUMENT ME!

vertebraeMin

int vertebraeMin
DOCUMENT ME!

vertebraeMax

int vertebraeMax
DOCUMENT ME!

componentHistogram

ViewJComponentHistoLUT componentHistogram
Histogram component reference inside the JPanelHistoLUT.

Class gov.nih.mipav.view.dialogs.JDialogCTPreset extends JDialogBase implements Serializable

serialVersionUID: 3709628941183114805L

Serialized Fields

dim

Dimension dim
DOCUMENT ME!

abdomenLabel

JLabel abdomenLabel
Preset labels.

abdomenMin

int abdomenMin
Preset min, max values. Min presents the min window value. Max presents the max window value.

abdomenMax

int abdomenMax
Preset min, max values. Min presents the min window value. Max presents the max window value.

dataSlice

float[] dataSlice
Reference to the image data of the slice presently displayed. Needed to calculate the max/min of the slice used to adjust the transfer function.

headLabel

JLabel headLabel
DOCUMENT ME!

headMin

int headMin
DOCUMENT ME!

headMax

int headMax
DOCUMENT ME!

image

ModelImage image
Reference to the image that will be affected by the adjust of the window and level.

lungLabel

JLabel lungLabel
DOCUMENT ME!

lungMin

int lungMin
DOCUMENT ME!

lungMax

int lungMax
DOCUMENT ME!

LUT

ModelLUT LUT
Reference to the LUT used to display the image.

maxImage

float maxImage
Image's maximum intensity.

mediastinumLabel

JLabel mediastinumLabel
DOCUMENT ME!

mediastinumMin

int mediastinumMin
DOCUMENT ME!

mediastinumMax

int mediastinumMax
DOCUMENT ME!

minImage

float minImage
Image's minimum intensity.

minLabel

JLabel minLabel
DOCUMENT ME!

maxLabel

JLabel maxLabel
DOCUMENT ME!

minText

JTextField minText
Min, max text fields.

maxText

JTextField maxText
Min, max text fields.

radioAbdomen

JRadioButton radioAbdomen
Preset radio buttons.

radioHead

JRadioButton radioHead
DOCUMENT ME!

radioLung

JRadioButton radioLung
DOCUMENT ME!

radioMediastinum

JRadioButton radioMediastinum
DOCUMENT ME!

radioSpine

JRadioButton radioSpine
DOCUMENT ME!

radioVertebrae

JRadioButton radioVertebrae
DOCUMENT ME!

resetButton

JButton resetButton
Reset button to reset the default preset values.

setButton

JButton setButton
When user change the window, level values, setButton sets the min, max of the window values.

spineLabel

JLabel spineLabel
DOCUMENT ME!

spineMin

int spineMin
DOCUMENT ME!

spineMax

int spineMax
DOCUMENT ME!

vertebraeLabel

JLabel vertebraeLabel
DOCUMENT ME!

vertebraeMin

int vertebraeMin
DOCUMENT ME!

vertebraeMax

int vertebraeMax
DOCUMENT ME!

x

float[] x
Three arrays to save the coordinates of the LUT's transfer fucntion. z[] not used.

y

float[] y
DOCUMENT ME!

z

float[] z
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogCumulativeHistogram extends JDialogBase implements Serializable

serialVersionUID: -2835835380784019616L

Serialized Fields

hist

ModelHistogram hist
MoelHistogram object.*

histoBuffer

int[] histoBuffer
int array of histogram values.

image

ModelImage image
Source Image.

RGBValue

int RGBValue
int vlaue indicating RGB channel.

Class gov.nih.mipav.view.dialogs.JDialogDataProvenance extends JDialogBase implements Serializable

serialVersionUID: 3861014709972568409L

Serialized Fields

DEFAULT_SIZE

Dimension DEFAULT_SIZE
Describes the initial size of the textual display area when the dialog is created. The value is given in pixel size rather than the number of characters since the display area has no characters to display.

buttonPanel

JPanel buttonPanel
DOCUMENT ME!

scrollPane

JScrollPane scrollPane
DOCUMENT ME!

textArea

JTextArea textArea
DOCUMENT ME!

pHolder

ProvenanceHolder pHolder
The provenance holder to display (or inject provenance data for "open provenance")

dpModel

ViewTableModel dpModel
The table model

isSystem

boolean isSystem
boolean determining if this is the system's data provenance, or an open image's

name

String name
The name of the provenance (system or image name)

path

String path
The path to the provenance file

Class gov.nih.mipav.view.dialogs.JDialogDCCIEConversion extends JDialogBase implements Serializable

serialVersionUID: 8180947616779037172L

Serialized Fields

aviField

JTextField aviField
DOCUMENT ME!

aviPanel

JPanel aviPanel
DOCUMENT ME!

browseButton

JButton browseButton
DOCUMENT ME!

browseOutputButton

JButton browseOutputButton
DOCUMENT ME!

compression

int compression
DOCUMENT ME!

compressionBox

JComboBox compressionBox
DOCUMENT ME!

dirField

JTextField dirField
DOCUMENT ME!

inputBox

JComboBox inputBox
DOCUMENT ME!

inputPanel

JPanel inputPanel
DOCUMENT ME!

mjpegButton

JRadioButton mjpegButton
DOCUMENT ME!

mp4Button

JRadioButton mp4Button
DOCUMENT ME!

qualityField

JTextField qualityField
DOCUMENT ME!

qualityLabel

JLabel qualityLabel
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogDeleteObjects extends JDialogScriptableBase implements Serializable

serialVersionUID: -5905410727732570098L

Serialized Fields

deleteAlgo2D

AlgorithmMorphology2D deleteAlgo2D
DOCUMENT ME!

deleteAlgo3D

AlgorithmMorphology3D deleteAlgo3D
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

labelMax

JLabel labelMax
DOCUMENT ME!

labelMin

JLabel labelMin
DOCUMENT ME!

max

int max
or if the source image is to be replaced.

min

int min
or if the source image is to be replaced.

outputPanel

JPanelAlgorithmOutputOptions outputPanel
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

textMax

JTextField textMax
DOCUMENT ME!

textMin

JTextField textMin
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogDENCLUE extends JDialogScriptableBase implements Serializable

serialVersionUID: -8761669177340930135L

Serialized Fields

arbitraryButton

JRadioButton arbitraryButton
DOCUMENT ME!

centerButton

JRadioButton centerButton
DOCUMENT ME!

clusterGroup

ButtonGroup clusterGroup
DOCUMENT ME!

denAlgo

AlgorithmDENCLUE denAlgo
DOCUMENT ME!

distance

float distance
DOCUMENT ME!

distanceLabel

JLabel distanceLabel
DOCUMENT ME!

distanceText

JTextField distanceText
DOCUMENT ME!

gaussianButton

JRadioButton gaussianButton
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

influenceGroup

ButtonGroup influenceGroup
DOCUMENT ME!

isArbitrary

boolean isArbitrary
DOCUMENT ME!

isGaussian

boolean isGaussian
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

squareButton

JRadioButton squareButton
DOCUMENT ME!

threshold

float threshold
DOCUMENT ME!

thresholdLabel

JLabel thresholdLabel
DOCUMENT ME!

thresholdText

JTextField thresholdText
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogDenoisingBLS_GSM extends JDialogScriptableBase implements Serializable

serialVersionUID: -8519961604071482971L

Serialized Fields

blockSizeX

int blockSizeX
DOCUMENT ME!

blockSizeY

int blockSizeY
DOCUMENT ME!

boundaryCheckBox

JCheckBox boundaryCheckBox
DOCUMENT ME!

comboBoxFilter

JComboBox comboBoxFilter
DOCUMENT ME!

covarianceCheckBox

JCheckBox covarianceCheckBox
DOCUMENT ME!

deAlgo

AlgorithmDenoisingBLS_GSM deAlgo
DOCUMENT ME!

destinationGroup

ButtonGroup destinationGroup
DOCUMENT ME!

destinationPanel

JPanel destinationPanel
DOCUMENT ME!

displayLoc

int displayLoc
DOCUMENT ME!

filter

int filter
DOCUMENT ME!

filterPanel

JPanel filterPanel
DOCUMENT ME!

fullButton

JRadioButton fullButton
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

includeCovar

boolean includeCovar
DOCUMENT ME!

localXLabel

JLabel localXLabel
DOCUMENT ME!

localXText

JTextField localXText
DOCUMENT ME!

localYLabel

JLabel localYLabel
DOCUMENT ME!

localYText

JTextField localYText
DOCUMENT ME!

mainPanel

JPanel mainPanel
DOCUMENT ME!

method

int method
DOCUMENT ME!

methodGroup

ButtonGroup methodGroup
DOCUMENT ME!

newImage

JRadioButton newImage
DOCUMENT ME!

noiseGroup

ButtonGroup noiseGroup
DOCUMENT ME!

noiseLabel

JLabel noiseLabel
DOCUMENT ME!

noiseText

JTextField noiseText
DOCUMENT ME!

nOrientations

int nOrientations
DOCUMENT ME!

nScales

int nScales
DOCUMENT ME!

optimize

boolean optimize
DOCUMENT ME!

optimizeCheckBox

JCheckBox optimizeCheckBox
DOCUMENT ME!

orientLabel

JLabel orientLabel
DOCUMENT ME!

orientText

JTextField orientText
DOCUMENT ME!

orthogonalButton

JRadioButton orthogonalButton
DOCUMENT ME!

parentCheckBox

JCheckBox parentCheckBox
DOCUMENT ME!

psdButton

JRadioButton psdButton
DOCUMENT ME!

replaceImage

JRadioButton replaceImage
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

scaleLabel

JLabel scaleLabel
DOCUMENT ME!

scaleText

JTextField scaleText
DOCUMENT ME!

sig

float sig
DOCUMENT ME!

steerableButton

JRadioButton steerableButton
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

undecimatedButton

JRadioButton undecimatedButton
DOCUMENT ME!

useBoundary

boolean useBoundary
DOCUMENT ME!

useParent

boolean useParent
DOCUMENT ME!

usePSD

boolean usePSD
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

whiteButton

JRadioButton whiteButton
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogDicom2XMLSelection extends JDialogListSaveSelection implements Serializable

serialVersionUID: -1864581773877529737L

Serialized Fields

wasOkay

boolean wasOkay
Boolean that determines if the window was closed (hitting the X) wasOkay = true means the [x] was not clicked.

destFormatStr

String destFormatStr

sourceInfo

FileInfoDicom sourceInfo
FileInfoDicom for source image

Class gov.nih.mipav.view.dialogs.JDialogDICOMTagEditor extends JDialogBase implements Serializable

serialVersionUID: 8765963102638731411L

Serialized Fields

applyToAllSlicesCheckBox

JCheckBox applyToAllSlicesCheckBox
DOCUMENT ME!

newInputPanel

JPanelEdit[] newInputPanel
DOCUMENT ME!

originalTextField

JTextField originalTextField
DOCUMENT ME!

struckOkayButton

boolean struckOkayButton
DOCUMENT ME!

tagKey

String tagKey
DOCUMENT ME!

tagTable

FileDicomTagTable tagTable
A reference to the tag table containing the tag we will be editing.

Class gov.nih.mipav.view.dialogs.JDialogDICOMtoAVI extends JDialogBase implements Serializable

serialVersionUID: 4954811111242576089L

Serialized Fields

aviField

JTextField aviField
DOCUMENT ME!

browseButton

JButton browseButton
DOCUMENT ME!

browseOutputButton

JButton browseOutputButton
DOCUMENT ME!

compression

int compression
DOCUMENT ME!

compressionBox

JComboBox compressionBox
DOCUMENT ME!

dirField

JTextField dirField
DOCUMENT ME!

mjpegButton

JRadioButton mjpegButton
DOCUMENT ME!

mp4Button

JRadioButton mp4Button
DOCUMENT ME!

qualityField

JTextField qualityField
DOCUMENT ME!

qualityLabel

JLabel qualityLabel
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogDilate extends JDialogScriptableBase implements Serializable

serialVersionUID: -2780388883449887106L

Serialized Fields

comboBoxKernel

JComboBox comboBoxKernel
DOCUMENT ME!

dilateAlgo25D

AlgorithmMorphology25D dilateAlgo25D
DOCUMENT ME!

dilateAlgo2D

AlgorithmMorphology2D dilateAlgo2D
DOCUMENT ME!

dilateAlgo3D

AlgorithmMorphology3D dilateAlgo3D
DOCUMENT ME!

do25D

boolean do25D
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

image25D

JCheckBox image25D
DOCUMENT ME!

iters

int iters
or if the source image is to be replaced.

kernel

int kernel
DOCUMENT ME!

kernelSize

float kernelSize
DOCUMENT ME!

labelKernel

JLabel labelKernel
DOCUMENT ME!

labelKernelSize

JLabel labelKernelSize
DOCUMENT ME!

labelNIter

JLabel labelNIter
DOCUMENT ME!

maskPanel

JPanel maskPanel
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

textKernelSize

JTextField textKernelSize
DOCUMENT ME!

textNIter

JTextField textNIter
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

outputPanel

JPanelAlgorithmOutputOptions outputPanel

Class gov.nih.mipav.view.dialogs.JDialogDirectResample extends JDialogScriptableBase implements Serializable

serialVersionUID: 2885627426314170051L

Serialized Fields

algoTransform

AlgorithmTransform algoTransform
The algorithm.

dim

int dim
Number of available dimension.

enableVolRender

boolean enableVolRender
Boolean flag to enable volume render button.

extents

int[] extents
Original dimensions extents value array.

extXInput

JTextField extXInput
Original X, Y, Z dimension extents values.

extYInput

JTextField extYInput
Original X, Y, Z dimension extents values.

extZInput

JTextField extZInput
Original X, Y, Z dimension extents values.

extXOutput

JTextField extXOutput
Power of 2 X, Y, Z dimension extents values.

extYOutput

JTextField extYOutput
Power of 2 X, Y, Z dimension extents values.

extZOutput

JTextField extZOutput
Power of 2 X, Y, Z dimension extents values.

forceResample

boolean forceResample
Boolean flag to do resample images.

image

ModelImage image
Model images A and B.

imageB

ModelImage imageB
Model images A and B.

leftPanel

JPanel leftPanel
Left panel and right panels corresponding to original and expected extents.

rightPanel

JPanel rightPanel
Left panel and right panels corresponding to original and expected extents.

newRes

float[] newRes
Resample resolutioin corresponding to Power of 2.

originalVolPowerOfTwo

boolean originalVolPowerOfTwo
Boolean flag to indicate the original image is in Power of 2.

res

float[] res
Original resolutioin arrray.

resampledImageFrame

ViewJFrameImage resampledImageFrame
DOCUMENT ME!

resultImage

ModelImage resultImage
Temp Model image.

resultImageB

ModelImage resultImageB
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
Parent ui.

volExtents

int[] volExtents
Resampled dimension value in Power of 2.

volSize

int volSize
Volume size X*Y*Z.

comboBoxInterp

JComboBox comboBoxInterp
DOCUMENT ME!

interp

int interp
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogDistanceMap extends JDialogScriptableBase implements Serializable

serialVersionUID: -5952815004874741476L

Serialized Fields

distanceMapAlgo2D

AlgorithmMorphology2D distanceMapAlgo2D
DOCUMENT ME!

distanceMapAlgo3D

AlgorithmMorphology3D distanceMapAlgo3D
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

outputPanel

JPanelAlgorithmOutputOptions outputPanel

Class gov.nih.mipav.view.dialogs.JDialogDTICreateListFile extends JDialogBase implements Serializable

Serialized Fields

dwiPathTextField

JTextField dwiPathTextField
path to dwi file/dir

dwiPathBrowseButton

JButton dwiPathBrowseButton
browse button for dwi file/folder

interleavedCheckbox

JCheckBox interleavedCheckbox
checkbox for interleaved dataset

optionsGroup

ButtonGroup optionsGroup
button group for radio buttons

gradFileRadio

JRadioButton gradFileRadio
gradient file option

bmtxtFileRadio

JRadioButton bmtxtFileRadio
b-matrix file option

gradientFilePathTextField

JTextField gradientFilePathTextField
path to gradient file

dwiLabel

JLabel dwiLabel
dwi data label

gradientFileBrowseButton

JButton gradientFileBrowseButton
browse button

bmtxtFilePathTextField

JTextField bmtxtFilePathTextField
path to bmatrix file

bmtxtFileBrowseButton

JButton bmtxtFileBrowseButton
browse button

outputTextArea

JTextArea outputTextArea
output text area

scrollPane

JScrollPane scrollPane
Scroll Pane for the Text Area

currDir

String currDir
current directory

studyName

String studyName
study name string

prFileDir

String prFileDir
par/rec file directory

prFileName

String prFileName
par/rec file name

alg

AlgorithmDTICreateListFile alg
handle to the algorithm

gradientPath

String gradientPath
gradient path

bmatrixPath

String bmatrixPath
bmatrix path

studyPath

String studyPath
study path

isInterleaved

boolean isInterleaved
boolean if interleaved

isDICOM

boolean isDICOM
boolean indicating if we are dealing with dicom or par/rec

performRegistrationCheckbox

JCheckBox performRegistrationCheckbox
checkbox for performing registration

registrationSettingsButton

JButton registrationSettingsButton
button to launch the registration settings

regOptions

JDialogDTICreateListFileRegOAR35DOptions regOptions
handle to JDialogDTICreateListFileRegOAR35DOptions

dicomB0VolumeLabel

JLabel dicomB0VolumeLabel
label for dicom b0 volume if doing registration

dicomB0VolumeTextField

JTextField dicomB0VolumeTextField
path to dicom b0 volume if doing registration

dicomB0VolumePath

String dicomB0VolumePath

dicomB0VolumeBrowseButton

JButton dicomB0VolumeBrowseButton
browse button to locate the dicom b0 volume if doing registration

Class gov.nih.mipav.view.dialogs.JDialogDTICreateListFileRegOAR35DOptions extends JDialogBase implements Serializable

serialVersionUID: -4309868934393418962L

Serialized Fields

advancedDialog

JDialog advancedDialog
Variables for Advanced Settings dialog.

bracketBoundText

JTextField bracketBoundText
DOCUMENT ME!

maxIterationsText

JTextField maxIterationsText
DOCUMENT ME!

numMinText

JTextField numMinText
DOCUMENT ME!

comboBoxCostFunct

JComboBox comboBoxCostFunct
DOCUMENT ME!

comboBoxDOF

JComboBox comboBoxDOF
DOCUMENT ME!

comboBoxInterp

JComboBox comboBoxInterp
DOCUMENT ME!

comboBoxInterp2

JComboBox comboBoxInterp2
DOCUMENT ME!

cost

int cost
DOCUMENT ME!

interp

int interp
DOCUMENT ME!

interp2

int interp2
DOCUMENT ME!

DOF

int DOF
DOCUMENT ME!

doSubsample

boolean doSubsample
DOCUMENT ME!

fastMode

boolean fastMode
DOCUMENT ME!

fastModeCheckbox

JCheckBox fastModeCheckbox
DOCUMENT ME!

fileNameWInput

String fileNameWInput
DOCUMENT ME!

directoryWInput

String directoryWInput
DOCUMENT ME!

maxOfMinResol

boolean maxOfMinResol
DOCUMENT ME!

graphCheckBox

JCheckBox graphCheckBox
DOCUMENT ME!

inputWeightImage

ModelImage inputWeightImage
DOCUMENT ME!

isScript

boolean isScript
DOCUMENT ME!

labelInterp2

JLabel labelInterp2
DOCUMENT ME!

gbc

GridBagConstraints gbc
DOCUMENT ME!

xSelected

boolean xSelected
DOCUMENT ME!

ySelected

boolean ySelected
DOCUMENT ME!

zSelected

boolean zSelected
DOCUMENT ME!

rotatePanel

JPanel rotatePanel

calcCOG

boolean calcCOG
DOCUMENT ME!

maxIterations_def

int maxIterations_def
DOCUMENT ME!

bracketBound_def

int bracketBound_def
DOCUMENT ME!

numMinima_def

int numMinima_def
DOCUMENT ME!

maxIterations

int maxIterations
DOCUMENT ME!

bracketBound

int bracketBound
DOCUMENT ME!

numMinima

int numMinima
DOCUMENT ME!

registerTo

int registerTo

isDICOM

boolean isDICOM

universalCheckbox

JCheckBox universalCheckbox
DOCUMENT ME!

xRadio

JRadioButton xRadio
DOCUMENT ME!

yRadio

JRadioButton yRadio
DOCUMENT ME!

zRadio

JRadioButton zRadio
DOCUMENT ME!

rotateRangePanelX

JPanel rotateRangePanelX
DOCUMENT ME!

rotateRangePanelY

JPanel rotateRangePanelY
DOCUMENT ME!

rotateRangePanelZ

JPanel rotateRangePanelZ
DOCUMENT ME!

finePanelX

JPanel finePanelX
DOCUMENT ME!

finePanelY

JPanel finePanelY
DOCUMENT ME!

finePanelZ

JPanel finePanelZ
DOCUMENT ME!

coarsePanelX

JPanel coarsePanelX
DOCUMENT ME!

coarsePanelY

JPanel coarsePanelY
DOCUMENT ME!

coarsePanelZ

JPanel coarsePanelZ
DOCUMENT ME!

rotateBegin

float rotateBegin
DOCUMENT ME!

rotateEnd

float rotateEnd
DOCUMENT ME!

coarseRate

float coarseRate
DOCUMENT ME!

fineRate

float fineRate
DOCUMENT ME!

rotateBeginX

float rotateBeginX
DOCUMENT ME!

rotateEndX

float rotateEndX
DOCUMENT ME!

coarseRateX

float coarseRateX
DOCUMENT ME!

fineRateX

float fineRateX
DOCUMENT ME!

rotateBeginY

float rotateBeginY
DOCUMENT ME!

rotateEndY

float rotateEndY
DOCUMENT ME!

coarseRateY

float coarseRateY
DOCUMENT ME!

fineRateY

float fineRateY
DOCUMENT ME!

rotateBeginZ

float rotateBeginZ
DOCUMENT ME!

rotateEndZ

float rotateEndZ
DOCUMENT ME!

coarseRateZ

float coarseRateZ
DOCUMENT ME!

fineRateZ

float fineRateZ
DOCUMENT ME!

rotateBeginText

JTextField rotateBeginText
DOCUMENT ME!

rotateEndText

JTextField rotateEndText
DOCUMENT ME!

coarseRateText

JTextField coarseRateText
DOCUMENT ME!

fineRateText

JTextField fineRateText
DOCUMENT ME!

rotateBeginTextX

JTextField rotateBeginTextX
DOCUMENT ME!

rotateEndTextX

JTextField rotateEndTextX
DOCUMENT ME!

coarseRateTextX

JTextField coarseRateTextX
DOCUMENT ME!

fineRateTextX

JTextField fineRateTextX
DOCUMENT ME!

rotateBeginTextY

JTextField rotateBeginTextY
DOCUMENT ME!

rotateEndTextY

JTextField rotateEndTextY
DOCUMENT ME!

coarseRateTextY

JTextField coarseRateTextY
DOCUMENT ME!

fineRateTextY

JTextField fineRateTextY
DOCUMENT ME!

rotateBeginTextZ

JTextField rotateBeginTextZ
DOCUMENT ME!

rotateEndTextZ

JTextField rotateEndTextZ
DOCUMENT ME!

coarseRateTextZ

JTextField coarseRateTextZ
DOCUMENT ME!

fineRateTextZ

JTextField fineRateTextZ
DOCUMENT ME!

sampleCheckBox

JCheckBox sampleCheckBox
DOCUMENT ME!

minMaxCheckbox

JCheckBox minMaxCheckbox
DOCUMENT ME!

UI

ViewUserInterface UI
DOCUMENT ME!

useOutsideReferenceVolume

boolean useOutsideReferenceVolume
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogEdgeLaplacian extends JDialogScriptableBase implements Serializable

serialVersionUID: -4875093981299828397L

Serialized Fields

edgeImage

ModelImage edgeImage
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

image25D

boolean image25D
false = apply algorithm only to VOI regions.

image25DCheckbox

JCheckBox image25DCheckbox
DOCUMENT ME!

laplacianAlgo

AlgorithmEdgeLaplacian laplacianAlgo
DOCUMENT ME!

laplacianSepAlgo

AlgorithmEdgeLaplacianSep laplacianSepAlgo
DOCUMENT ME!

outputPanel

JPanelAlgorithmOutputOptions outputPanel
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

separable

boolean separable
DOCUMENT ME!

sepCheckBox

JCheckBox sepCheckBox
DOCUMENT ME!

sigmaPanel

JPanelSigmas sigmaPanel
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogEdgeNMSuppression extends JDialogScriptableBase implements Serializable

serialVersionUID: -7682705151759726551L

Serialized Fields

edgeImage

ModelImage edgeImage
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

image25D

boolean image25D
false = apply algorithm only to VOI regions.

image25DCheckbox

JCheckBox image25DCheckbox
DOCUMENT ME!

nmSupAlgo

AlgorithmEdgeNMSuppression nmSupAlgo
DOCUMENT ME!

outputPanel

JPanelAlgorithmOutputOptions outputPanel
DOCUMENT ME!

sigmaPanel

JPanelSigmas sigmaPanel
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogEditor extends JDialogBase implements Serializable

serialVersionUID: 1979336171963042575L

Serialized Fields

closedOkay

boolean closedOkay
DOCUMENT ME!

key

Object key
the representative key of this object; must be unique.

newValue

JPanelEdit[] newValue
DOCUMENT ME!

oldValue

JTextField oldValue
DOCUMENT ME!

imageFileName

String imageFileName
DOCUMENT ME!

psetDesc

String psetDesc
DOCUMENT ME!

row

int row
DOCUMENT ME!

serif12B

Font serif12B
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogEditUserDefinedFileTypes extends JDialogBase implements Serializable

Serialized Fields

displayPanel

JPanel displayPanel
The panels that make up this Dialog

applyClosePanel

JPanel applyClosePanel
The panels that make up this Dialog

checkBoxArrList

ArrayList<E> checkBoxArrList
This is the ArrayList of JCheckBoxes

checkboxNames

ArrayList<E> checkboxNames
This is a list of the checkbox names that is used for validation of user input to make sure there are no duplicates

checkedFileTypes

ArrayList<E> checkedFileTypes
This a list is the list of checked check boxes that is populated when user hits apply

fileExtensionsTS

TreeSet<E> fileExtensionsTS
This is the alphabetically sorted collection of supported file extension names

userInput

JTextField userInput
This is the user input for additional file extensions

userInputFileTypes

String[] userInputFileTypes
This array is the list of additional file extensions that user typed in that is populated when user hits apply

preferencesFileTypes

String[] preferencesFileTypes
This array is the list of file extensions that is pulled from the Preferences. We need this in order to check the appropriate check boxes and the user input text field when the user opens up this dialog initailly

Class gov.nih.mipav.view.dialogs.JDialogEllipseToCircle extends JDialogBase implements Serializable

serialVersionUID: 0L

Serialized Fields

extents

int[] extents
DOCUMENT ME!

ecAlgo

AlgorithmEllipseToCircle ecAlgo
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

UI

ViewUserInterface UI
DOCUMENT ME!

xDim

int xDim
DOCUMENT ME!

xText

JTextField xText
DOCUMENT ME!

yDim

int yDim
DOCUMENT ME!

yText

JTextField yText
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogEntropyMinimization extends JDialogScriptableBase implements Serializable

serialVersionUID: -417774372547972740L

Serialized Fields

displayLoc

int displayLoc
DOCUMENT ME!

emAlgo

AlgorithmEntropyMinimization emAlgo
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

m2Button

JRadioButton m2Button
DOCUMENT ME!

m3Button

JRadioButton m3Button
DOCUMENT ME!

ma2Button

JRadioButton ma2Button
DOCUMENT ME!

newImage

JRadioButton newImage
DOCUMENT ME!

noiseGroup

ButtonGroup noiseGroup
DOCUMENT ME!

noiseType

int noiseType
DOCUMENT ME!

replaceImage

JRadioButton replaceImage
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

subsample

boolean subsample
DOCUMENT ME!

subsampleCheckbox

JCheckBox subsampleCheckbox
DOCUMENT ME!

thresholdCheckbox

JCheckBox thresholdCheckbox
DOCUMENT ME!

thresholdLabel

JLabel thresholdLabel
DOCUMENT ME!

thresholdLevel

float thresholdLevel
DOCUMENT ME!

thresholdSelected

boolean thresholdSelected
DOCUMENT ME!

thresholdText

JTextField thresholdText
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogErode extends JDialogScriptableBase implements Serializable

serialVersionUID: -3069882376396094338L

Serialized Fields

comboBoxKernelErode

JComboBox comboBoxKernelErode
DOCUMENT ME!

do25D

boolean do25D
DOCUMENT ME!

erodeAlgo25D

AlgorithmMorphology25D erodeAlgo25D
DOCUMENT ME!

erodeAlgo2D

AlgorithmMorphology2D erodeAlgo2D
DOCUMENT ME!

erodeAlgo3D

AlgorithmMorphology3D erodeAlgo3D
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

image25D

JCheckBox image25D
DOCUMENT ME!

iters

int iters
or if the source image is to be replaced.

kernelErode

int kernelErode
DOCUMENT ME!

kernelSizeErode

float kernelSizeErode
DOCUMENT ME!

labelKernelErode

JLabel labelKernelErode
DOCUMENT ME!

labelKernelSizeErode

JLabel labelKernelSizeErode
DOCUMENT ME!

labelNIterErode

JLabel labelNIterErode
DOCUMENT ME!

maskPanelErode

JPanel maskPanelErode
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

textKernelSizeErode

JTextField textKernelSizeErode
DOCUMENT ME!

textNIterErode

JTextField textNIterErode
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

outputPanel

JPanelAlgorithmOutputOptions outputPanel

Class gov.nih.mipav.view.dialogs.JDialogEvaluateMaskSegmentation extends JDialogScriptableBase implements Serializable

serialVersionUID: -1381945839499712050L

Serialized Fields

comboBoxImage

JComboBox comboBoxImage
Combo box with image names for choosing test image.

evalSeg

AlgorithmEvaluateMaskSegmentation evalSeg
Algorithm to run from this dialog.

testImage

ModelImage testImage
DOCUMENT ME!

titles

String[] titles
Used to lock and unlock images.

trueImage

ModelImage trueImage
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
Reference to userface.

Class gov.nih.mipav.view.dialogs.JDialogEvaluateSegmentation extends JDialogScriptableBase implements Serializable

serialVersionUID: -6446476110592386369L

Serialized Fields

comboBoxImage

JComboBox comboBoxImage
Combo box with image names for choosing test image.

evalSeg

AlgorithmEvaluateSegmentation evalSeg
Algorithm to run from this dialog.

imagesFound

int imagesFound
DOCUMENT ME!

testImage

ModelImage testImage
DOCUMENT ME!

titles

String[] titles
Used to lock and unlock images.

trueBoundingVOIs

int trueBoundingVOIs
DOCUMENT ME!

trueID

int[] trueID
DOCUMENT ME!

trueImage

ModelImage trueImage
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
Reference to userface.

Class gov.nih.mipav.view.dialogs.JDialogExtractBrain extends JDialogScriptableBase implements Serializable

serialVersionUID: 7723410343739118755L

Serialized Fields

aboveMedian

float aboveMedian
The factor above which second stage edge erosion occurs.

centerOfMass

WildMagic.LibFoundation.Mathematics.Vector3f centerOfMass
The volume's center of mass computed from computeCenter(ModelImage, int, boolean)

depth

int depth
The maximum depth within the brain's surface to sample image intensities, by default set to 5.

depthTF

JTextField depthTF
Field for entering the maximum depth. The dialog box suggests a value between 3 - 19 and requires a value from 3 - 33.

erosionLabel

JLabel erosionLabel
Label for the percentage entered for second stage edge erosion.

erosionTF

JTextField erosionTF
Defines the allowable percentage for edge intensity values ub second stage edge erosion, default is 50 percent.

extractBrainAlgo

AlgorithmBrainExtractor extractBrainAlgo
Algorithm used for brain extraction.

extractToPaint

boolean extractToPaint
When true, mask of extracted brain is painted over the source image.

extractToPaintCheckBox

JCheckBox extractToPaintCheckBox
When checked, mask of extracted brain is painted over the source image.

image

ModelImage image
Source image for extracting brain, default image is null.

imageRatio

float imageRatio
Image influence ratio for controlling the sampling depth used to calculate intensity extrema, by default set to .1.

imageRatioTF

JTextField imageRatioTF
Field for entering the image influence ratio. The dialog box requires that a value from .01 - .51 be entered.

initCenterPoint

WildMagic.LibFoundation.Mathematics.Vector3f initCenterPoint
Either the volume's center of mass or a user indicated point depending on the value of useCenterOfMass.

initCenterX

float initCenterX
Used to denote the brain's center of mass y-coordinate. By default set to zero.

initCenterXLabel

JLabel initCenterXLabel
Label for the x-coordinate of the user-defined center.

initCenterXTF

JTextField initCenterXTF
An optional field for denoting a desired initial x-corrdinate for the mesh. Editable if and only if useCenterOfMass is set to false

initCenterY

float initCenterY
Used to denote the brain's center of mass y-coordinate. By default set to zero.

initCenterYLabel

JLabel initCenterYLabel
Label for the y-coordinate of the user-defined center.

initCenterYTF

JTextField initCenterYTF
An optional field for denoting a desired initial y-corrdinate for the mesh. Editable if and only if useCenterOfMass is set to false

initCenterZ

float initCenterZ
Used to denote the brain's center of mass y-coordinate. By default set to zero.

initCenterZLabel

JLabel initCenterZLabel
Label for the z-coordinate of the user-defined center.

initCenterZTF

JTextField initCenterZTF
An optional field for denoting a desired initial z-corrdinate for the mesh. Editable if and only if useCenterOfMass is set to false

justEllipse

boolean justEllipse
When true, image mask is set to the initial ellipsoid approximation of the brain calculated from the volume's center of mass.

justInitEllipsoidCheckbox

JCheckBox justInitEllipsoidCheckbox
When checked, justEllipse is set to true.

nIterations

int nIterations
Number of surface evolutions to perform, by default set to 500.

nIterationsTF

JTextField nIterationsTF
Field for inputting the number of surface evolutions to perform. This requests, but does not require, a value from 100 - 2000

orientation

int orientation
Orientation value corresponding to not the value of AlgorithmBrainExtractor.SAT_COR

orientCheckbox

JCheckBox orientCheckbox
When checked, denotes that the images orientation does not correspond to AlgorithmBrainExtractor.SAT_COR

secondStageCheckBox

JCheckBox secondStageCheckBox
Initially unchecked, determined whether this algorithm performs secondStageErosion

secondStageErosion

boolean secondStageErosion
When true, sets edge values which are greater than the median intensity by a user-defined factor of aboveMedian to zero.

stiffness

float stiffness
Allows for variable motion of the mesh in the surface normal direction, default value of .15

stiffnessTF

JTextField stiffnessTF
Field for specifing stiffness of the mesh. The dialog box suggests, but does not require that a value between .01 and .5 entered.

titles

String[] titles
DOCUMENT ME!

useCenterOfMass

boolean useCenterOfMass
By default true, parameter indicates that the center position of the brain should be calculated using JDialogExtractBrain.computeCenter(ModelImage, int, boolean)

useCenterOfMassCheckBox

JCheckBox useCenterOfMassCheckBox
By default checked, yields a true value for useCenterOfMass

userInterface

ViewUserInterface userInterface
The user interface for this dialog box.

useSphere

boolean useSphere
When true estimates that boundary of the VOI by a sphere.

useSphereCheckbox

JCheckBox useSphereCheckbox
Initially not checked, estimates the boundary by a sphere rather than an ellipse.

Class gov.nih.mipav.view.dialogs.JDialogExtractObject extends JDialogBase implements Serializable

serialVersionUID: -4587834627195392398L

Serialized Fields

chooserButton

JButton chooserButton
DOCUMENT ME!

chooserButton2

JButton chooserButton2
DOCUMENT ME!

extractObjectAlgo

AlgorithmObjectExtractor extractObjectAlgo
DOCUMENT ME!

groupNum

int groupNum
DOCUMENT ME!

gvfImage

ModelImage[] gvfImage
DOCUMENT ME!

gvfIndex

int gvfIndex
DOCUMENT ME!

gvfModel

DefaultListModel gvfModel
DOCUMENT ME!

gvfName

String gvfName
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

justInit

boolean justInit
DOCUMENT ME!

justInitCheckbox

JCheckBox justInitCheckbox
DOCUMENT ME!

model

DefaultListModel model
DOCUMENT ME!

removeButton

JButton removeButton
DOCUMENT ME!

removeButton2

JButton removeButton2
DOCUMENT ME!

saveGVF

boolean saveGVF
DOCUMENT ME!

saveGVFCheckBox

JCheckBox saveGVFCheckBox
DOCUMENT ME!

srcVOI

VOI srcVOI
DOCUMENT ME!

surIndex

int surIndex
DOCUMENT ME!

surName

String surName
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

triMesh

WildMagic.LibGraphics.SceneGraph.TriMesh triMesh
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

voiColor

Color voiColor
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogExtractSlices extends JDialogScriptableBase implements Serializable

serialVersionUID: 5258936423490848172L

Serialized Fields

convert4Dto3D

boolean convert4Dto3D
DOCUMENT ME!

extractList

Vector<E> extractList
DOCUMENT ME!

extractSlicesAlgo

AlgorithmExtractSlices extractSlicesAlgo
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

srcImage

ModelImage srcImage
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogExtractSlicesVolumes extends JDialogScriptableBase implements Serializable

serialVersionUID: -2217089541745539442L

Serialized Fields

checkboxList

JCheckBox[] checkboxList
DOCUMENT ME!

checkboxPanel

JPanel checkboxPanel
DOCUMENT ME!

checkButton

JButton checkButton
DOCUMENT ME!

checkEvenButton

JButton checkEvenButton
DOCUMENT ME!

checkListExtract

boolean[] checkListExtract
DOCUMENT ME!

checkOddButton

JButton checkOddButton
DOCUMENT ME!

exampleLabel

JLabel exampleLabel
DOCUMENT ME!

exampleLabel2

JLabel exampleLabel2
DOCUMENT ME!

extractedImages

ModelImage[] extractedImages
DOCUMENT ME!

extractSlicesAlgo

AlgorithmExtractSlicesVolumes extractSlicesAlgo
DOCUMENT ME!

nSlices

int nSlices
DOCUMENT ME!

numChecked

int numChecked
DOCUMENT ME!

rangeField

JTextField rangeField
DOCUMENT ME!

scrollPane

JScrollPane scrollPane
DOCUMENT ME!

srcImage

ModelImage srcImage
DOCUMENT ME!

unCheckButton

JButton unCheckButton
DOCUMENT ME!

useRange

JCheckBox useRange
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogExtractSurfaceCubes extends JDialogScriptableBase implements Serializable

serialVersionUID: 7919553320035488503L

Serialized Fields

blurCheck

JCheckBox blurCheck
DOCUMENT ME!

blurFlag

boolean blurFlag
DOCUMENT ME!

blurTF

JTextField blurTF
DOCUMENT ME!

blurValue

float blurValue
DOCUMENT ME!

decimateFlag

boolean decimateFlag
DOCUMENT ME!

decimateSurfaceCB

JCheckBox decimateSurfaceCB
DOCUMENT ME!

directory

String directory
DOCUMENT ME!

extractSurAlgo

AlgorithmExtractSurfaceCubes extractSurAlgo
DOCUMENT ME!

fileButton

JButton fileButton
DOCUMENT ME!

fileName

String fileName
DOCUMENT ME!

fileTF

JTextField fileTF
DOCUMENT ME!

fileTypeList

JComboBox fileTypeList
surface file format list.

fileTypes

String[] fileTypes
surface file formats.

image

ModelImage image
DOCUMENT ME!

intensityLevelRB

JRadioButton intensityLevelRB
DOCUMENT ME!

intensityTF

JTextField intensityTF
DOCUMENT ME!

level

int level
DOCUMENT ME!

maskImageRB

JRadioButton maskImageRB
DOCUMENT ME!

mode

int mode
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

VOIRegionsRB

JRadioButton VOIRegionsRB
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogFaceAnonymizerBET extends JDialogScriptableBase implements Serializable

serialVersionUID: -1027127665518969757L

Serialized Fields

defaceAlgo

AlgorithmFaceAnonymizerBET defaceAlgo
The algorithm corresponding to this dialog box.

estimateWithSphereBET

boolean estimateWithSphereBET
Flag indicates BET should approximate initial brain by sphere. Initially set to false.

estimateWithSphereCheckbox

JCheckBox estimateWithSphereCheckbox
Check box corresponding to estimateSphereBET.

extraBrainPaddingField

JTextField extraBrainPaddingField
Text field corresponding to brain padding parameter.

extraMMsToPad

int extraMMsToPad
FaceAnonymizer parameter. Guarantees that the extracted brain will be avoided by the specified number of millimeters. Initially set to 20.

faceOrientation

int faceOrientation
Indicates face orientation of the image.

facingDownRadio

JRadioButton facingDownRadio
Button for facing down image.

facingIntoRadio

JRadioButton facingIntoRadio
Button for facing into the screen image.

facingLeftRadio

JRadioButton facingLeftRadio
Button for facing left image.

facingOutRadio

JRadioButton facingOutRadio
Button for facing out image.

facingRightRadio

JRadioButton facingRightRadio
Button for facing right image.

facingUpRadio

JRadioButton facingUpRadio
Button for facing up image.

imageInfluenceBET

float imageInfluenceBET
the depth to calculate in approximating brain maximum and minimum intensities. Initially set to .1

imageInfluenceField

JTextField imageInfluenceField
The text field corresponding to imageInfluenceField.

srcImage

ModelImage srcImage
The image that face anonymization will be performed on.

stiffnessBET

float stiffnessBET
Controls the stiffness of the brain approximation mesh. Initially set to 0.15.

stiffnessField

JTextField stiffnessField
The text field corresponding to stiffnessBET.

Class gov.nih.mipav.view.dialogs.JDialogFFT extends JDialogScriptableBase implements Serializable

serialVersionUID: -7969114857894881595L

Serialized Fields

bandPass

JRadioButton bandPass
DOCUMENT ME!

bandStop

JRadioButton bandStop
DOCUMENT ME!

butterworthFilter

JRadioButton butterworthFilter
DOCUMENT ME!

butterworthOrder

int butterworthOrder
DOCUMENT ME!

buttonPanel

JPanel buttonPanel
DOCUMENT ME!

constructionGroup

ButtonGroup constructionGroup
DOCUMENT ME!

constructionMethod

int constructionMethod
DOCUMENT ME!

constructionPanel

JPanel constructionPanel
DOCUMENT ME!

destinationGroup

ButtonGroup destinationGroup
DOCUMENT ME!

destinationPanel

JPanel destinationPanel
DOCUMENT ME!

directionGroup

ButtonGroup directionGroup
DOCUMENT ME!

directionPanel

JPanel directionPanel
DOCUMENT ME!

displayLoc

int displayLoc
DOCUMENT ME!

FFTAlgo

AlgorithmFFT FFTAlgo
DOCUMENT ME!

filterPanel

JPanel filterPanel
DOCUMENT ME!

filterType

int filterType
DOCUMENT ME!

filterTypeGroup

ButtonGroup filterTypeGroup
DOCUMENT ME!

forwardFFT

JRadioButton forwardFFT
DOCUMENT ME!

freq1

float freq1
DOCUMENT ME!

freq2

float freq2
DOCUMENT ME!

frequencyFilter

JRadioButton frequencyFilter
DOCUMENT ME!

gaussianFilter

JRadioButton gaussianFilter
DOCUMENT ME!

highPass

JRadioButton highPass
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

image25D

boolean image25D
DOCUMENT ME!

image25DCheckbox

JCheckBox image25DCheckbox
DOCUMENT ME!

imageCrop

boolean imageCrop
DOCUMENT ME!

imageCropCheckbox

JCheckBox imageCropCheckbox
DOCUMENT ME!

inverseFFT

JRadioButton inverseFFT
DOCUMENT ME!

kernelDiameter

int kernelDiameter
DOCUMENT ME!

labelF1

JLabel labelF1
DOCUMENT ME!

labelF2

JLabel labelF2
DOCUMENT ME!

labelKernelDiameter

JLabel labelKernelDiameter
DOCUMENT ME!

labelOrder

JLabel labelOrder
DOCUMENT ME!

logDisplayCheckbox

JCheckBox logDisplayCheckbox
private JPanel optionsPanel;.

logMagDisplay

boolean logMagDisplay
DOCUMENT ME!

lowPass

JRadioButton lowPass
DOCUMENT ME!

mainPanel

JPanel mainPanel
DOCUMENT ME!

newImage

JRadioButton newImage
DOCUMENT ME!

replaceImage

JRadioButton replaceImage
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

textF1

JTextField textF1
DOCUMENT ME!

textF2

JTextField textF2
DOCUMENT ME!

textKernelDiameter

JTextField textKernelDiameter
DOCUMENT ME!

textOrder

JTextField textOrder
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

transformDir

int transformDir
DOCUMENT ME!

unequalDim

boolean unequalDim
DOCUMENT ME!

unequalDimCheckbox

JCheckBox unequalDimCheckbox
DOCUMENT ME!

windowFilter

JRadioButton windowFilter
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogFileInfo extends JDialogBase implements Serializable

serialVersionUID: 1629395651992086059L

Serialized Fields

edit

JButton edit
DOCUMENT ME!

editorDialog

JDialogEditor editorDialog
DOCUMENT ME!

editorDialogTable

Hashtable<K,V> editorDialogTable
DOCUMENT ME!

fileinfo

FileInfoBase fileinfo
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

listSelector

ListSelectionModel listSelector
DOCUMENT ME!

primaryModel

ViewTableModel primaryModel
DOCUMENT ME!

primaryTable

JTable primaryTable
DOCUMENT ME!

primaryTypeHolder

Hashtable<K,V> primaryTypeHolder
tpe holds the type of editor to be used; editor holds the editor dialog.

primaryEditorHolder

Hashtable<K,V> primaryEditorHolder
tpe holds the type of editor to be used; editor holds the editor dialog.

scrollPane

JScrollPane scrollPane
DOCUMENT ME!

secondaryModel

ViewTableModel secondaryModel
DOCUMENT ME!

secondaryTable

JTable secondaryTable
DOCUMENT ME!

secondaryTypeHolder

Hashtable<K,V> secondaryTypeHolder
DOCUMENT ME!

secondaryEditorHolder

Hashtable<K,V> secondaryEditorHolder
DOCUMENT ME!

selectedRow

int selectedRow
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogFileInfoDICOM extends JDialogScriptableBase implements Serializable

serialVersionUID: 7337962386655472087L

Serialized Fields

DicomInfo

FileInfoDicom DicomInfo
DOCUMENT ME!

editorDialogDicom

JDialogDICOMTagEditor editorDialogDicom
DOCUMENT ME!

editorDialogDicomList

Vector<E> editorDialogDicomList
DOCUMENT ME!

imageA

ModelImage imageA
DOCUMENT ME!

listSelectorDicom

ListSelectionModel listSelectorDicom
DOCUMENT ME!

scrollPaneDicom

JScrollPane scrollPaneDicom
DOCUMENT ME!

selectedRowDicom

int selectedRowDicom
DOCUMENT ME!

showPrivate

boolean showPrivate
DOCUMENT ME!

tagsModel

ViewTableModel tagsModel
DOCUMENT ME!

tagsTable

JTable tagsTable
DOCUMENT ME!

isAppend

boolean isAppend
DOCUMENT ME!

toolbarPanel

JPanel toolbarPanel
DOCUMENT ME!

toolbarBuilder

ViewToolBarBuilder toolbarBuilder
DOCUMENT ME !

saveCheckedButton

JButton saveCheckedButton
buttons for toolbar

saveCheckedAppendButton

JButton saveCheckedAppendButton
buttons for toolbar

checkAllButton

JButton checkAllButton
buttons for toolbar

uncheckAllButton

JButton uncheckAllButton
buttons for toolbar

editTagButton

JButton editTagButton
buttons for toolbar

overlayButton

JButton overlayButton
buttons for toolbar

anonymizeButton

JButton anonymizeButton
buttons for toolbar

toolBar

JToolBar toolBar
tool bar

showPrivateButton

JToggleButton showPrivateButton

bogusShowPrivateButton

JToggleButton bogusShowPrivateButton

fileName

String fileName
fileName of where dicom tags are save to

directory

String directory
directory of where dicom tags are save to

sliceIndex

int sliceIndex
slice index for which fileInfo is saved

launchFileChooser

boolean launchFileChooser

Class gov.nih.mipav.view.dialogs.JDialogFileInfoMinc extends JDialogText implements Serializable

serialVersionUID: -966963254580510543L

Class gov.nih.mipav.view.dialogs.JDialogFileInfoMincHDF extends JDialogBase implements Serializable

Serialized Fields

mincInfo

FileInfoMincHDF mincInfo
DOCUMENT ME!

imageA

ModelImage imageA
DOCUMENT ME!

scrollPaneDicom

JScrollPane scrollPaneDicom
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogFileInfoProject extends JDialogBase implements Serializable

serialVersionUID: 2059007700162379513L

Serialized Fields

addImage

JButton addImage
DOCUMENT ME!

addInfo

JMenuItem addInfo
DOCUMENT ME!

addParam

JMenuItem addParam
DOCUMENT ME!

addSet

JButton addSet
DOCUMENT ME!

edit

JButton edit
DOCUMENT ME!

editorDialog

JDialogEditor editorDialog
DOCUMENT ME!

editorDialogTable

Hashtable<K,V> editorDialogTable
DOCUMENT ME!

fileinfo

FileInfoProject fileinfo
DOCUMENT ME!

imageFileNameforAddInfo

String imageFileNameforAddInfo
DOCUMENT ME!

imageHashtable

Hashtable<K,V> imageHashtable
DOCUMENT ME!

infoColumnNames

String[] infoColumnNames
DOCUMENT ME!

infoModel

ViewTableModel infoModel
DOCUMENT ME!

infoTable

JTable infoTable
DOCUMENT ME!

investigatorModel

ViewTableModel investigatorModel
DOCUMENT ME!

investigatorTable

JTable investigatorTable
DOCUMENT ME!

investigatorTypeHolder

Hashtable<K,V> investigatorTypeHolder
DOCUMENT ME!

investigatorEditorHolder

Hashtable<K,V> investigatorEditorHolder
DOCUMENT ME!

listSelector

ListSelectionModel listSelector
DOCUMENT ME!

masterScrollPane

JScrollPane masterScrollPane
DOCUMENT ME!

numImages

int numImages
DOCUMENT ME!

numSets

int numSets
DOCUMENT ME!

parameterColumnNames

String[] parameterColumnNames
DOCUMENT ME!

parameterModel

ViewTableModel parameterModel
DOCUMENT ME!

parameterTable

JTable parameterTable
DOCUMENT ME!

primaryModel

ViewTableModel primaryModel
DOCUMENT ME!

primaryTable

JTable primaryTable
DOCUMENT ME!

primaryTypeHolder

Hashtable<K,V> primaryTypeHolder
tpe holds the type of editor to be used; editor holds the editor dialog.

primaryEditorHolder

Hashtable<K,V> primaryEditorHolder
tpe holds the type of editor to be used; editor holds the editor dialog.

removeInfo

JButton removeInfo
DOCUMENT ME!

removeParam

JButton removeParam
DOCUMENT ME!

scrollingBox

Box scrollingBox
DOCUMENT ME!

scrollPane

JScrollPane scrollPane
DOCUMENT ME!

selectedRow

int selectedRow
DOCUMENT ME!

setDescforAddParam

String setDescforAddParam
DOCUMENT ME!

setHashtable

Hashtable<K,V> setHashtable
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogFileInfoXML extends JDialogBase implements Serializable

serialVersionUID: -8790820691884630599L

Serialized Fields

addParam

JMenuItem addParam
menu item for adding parameter.

addSet

JButton addSet
button for adding sets.

addSurface

JButton addSurface
button for adding surfaces.

edit

JButton edit
edit button.

editorDialogTable

Hashtable<K,V> editorDialogTable
hashtable to store editor dialogs associated with the table.

fileinfo

FileInfoImageXML fileinfo
file info xml to be displayed.

image

ModelImage image
model image associated with the FileInfo.

investigatorModel

ViewTableModel investigatorModel
model associated with investigator information.

investigatorTable

JTable investigatorTable
investigator information table.

masterScrollPane

JScrollPane masterScrollPane
master scroll pane in which to display all information.

numSets

int numSets
counter for number of sets within file info.

parameterColumnNames

String[] parameterColumnNames
array of strings for parameter column names.

primaryModel

ViewTableModel primaryModel
model associated with primary image information.

primaryTable

JTable primaryTable
primary image information table.

primaryTypeHolder

Hashtable<K,V> primaryTypeHolder
Type holds the type of editor, editor holds the actual editor dialog.

primaryEditorHolder

Hashtable<K,V> primaryEditorHolder
Type holds the type of editor, editor holds the actual editor dialog.

subjectTypeHolder

Hashtable<K,V> subjectTypeHolder
Type holds the type of editor, editor holds the actual editor dialog.

subjectEditorHolder

Hashtable<K,V> subjectEditorHolder
Type holds the type of editor, editor holds the actual editor dialog.

scanTypeHolder

Hashtable<K,V> scanTypeHolder
Type holds the type of editor, editor holds the actual editor dialog.

scanEditorHolder

Hashtable<K,V> scanEditorHolder
Type holds the type of editor, editor holds the actual editor dialog.

investigatorTypeHolder

Hashtable<K,V> investigatorTypeHolder
Type holds the type of editor, editor holds the actual editor dialog.

investigatorEditorHolder

Hashtable<K,V> investigatorEditorHolder
Type holds the type of editor, editor holds the actual editor dialog.

removeParam

JButton removeParam
button for removing parameters.

removeSurface

JButton removeSurface
button for removing surfaces.

scanModel

ViewTableModel scanModel
model associated with scan information.

scanTable

JTable scanTable
scan infomation table.

scrollingBox

Box scrollingBox
Box to hold table information.

setDescforAddParam

String setDescforAddParam
string holding set description when adding a parameter.

setHashtable

Hashtable<K,V> setHashtable
hash table holding set information.

subjectModel

ViewTableModel subjectModel
model associated with subject information.

subjectTable

JTable subjectTable
subject information table.

surfaceColumnNames

String[] surfaceColumnNames
array of strings for surface column names.

surfaces

JDialogFileInfoXML.SurfaceDisplay surfaces
for displaying surfaces.

Class gov.nih.mipav.view.dialogs.JDialogFillObjects extends JDialogScriptableBase implements Serializable

serialVersionUID: 3464349858386521845L

Serialized Fields

destinationGroup

ButtonGroup destinationGroup
use later.

destinationPanel

JPanel destinationPanel
panel that hold the new image radio button.

displayLoc

int displayLoc
Flag indicating if a new image is to be generated.

idObjectsAlgo2D

AlgorithmMorphology2D idObjectsAlgo2D
Morphology2D algorithm reference.

idObjectsAlgo25D

AlgorithmMorphology25D idObjectsAlgo25D
Morphology25D algorithm reference.

idObjectsAlgo3D

AlgorithmMorphology3D idObjectsAlgo3D
Morphology3D algorithm reference.

image

ModelImage image
source image.

image25D

JCheckBox image25D
DOCUMENT ME!

do25D

boolean do25D
DOCUMENT ME!

imageVOIGroup

ButtonGroup imageVOIGroup
DOCUMENT ME!

imageVOIPanel

JPanel imageVOIPanel
used later.

newImage

JRadioButton newImage
new image radio button.

regionFlag

boolean regionFlag
DOCUMENT ME!

replaceImage

JRadioButton replaceImage
use later.

titles

String[] titles
DOCUMENT ME!

ubyteImage

ModelImage ubyteImage
Usigned byte image, the actual image to do the morphology calculation.

userInterface

ViewUserInterface userInterface
user interface renference.

VOIRegions

JRadioButton VOIRegions
DOCUMENT ME!

wholeImage

JRadioButton wholeImage
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogFilterChoice extends JDialogBase implements Serializable

serialVersionUID: 3198970819287117617L

Serialized Fields

checkImages

JCheckBox[] checkImages
DOCUMENT ME!

imageFilter

ViewImageFileFilter imageFilter
DOCUMENT ME!

fileTypeDescriptions

String[] fileTypeDescriptions

fileTypeInts

int[] fileTypeInts

fileTypeExtensions

String[] fileTypeExtensions

Class gov.nih.mipav.view.dialogs.JDialogFindEdges extends JDialogScriptableBase implements Serializable

serialVersionUID: 8141787725573550699L

Serialized Fields

edgingType

int edgingType
DOCUMENT ME!

edgingTypeGroup

ButtonGroup edgingTypeGroup
DOCUMENT ME!

edgingTypePanel

JPanel edgingTypePanel
DOCUMENT ME!

findEdgesAlgo2D

AlgorithmMorphology2D findEdgesAlgo2D
DOCUMENT ME!

findEdgesAlgo3D

AlgorithmMorphology3D findEdgesAlgo3D
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

innerEdging

JRadioButton innerEdging
DOCUMENT ME!

outerEdging

JRadioButton outerEdging
DOCUMENT ME!

outputPanel

JPanelAlgorithmOutputOptions outputPanel
Contains radio buttons used to indicate whether the whole image/just VOI regions should be processed, and whether a new image should be produced.

resultImage

ModelImage resultImage
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogFindRtableObject extends JDialogScriptableBase implements Serializable

serialVersionUID: 0L

Serialized Fields

chooserButton

JButton chooserButton
DOCUMENT ME!

findAlgo

AlgorithmFindRtableObject findAlgo
DOCUMENT ME!

fileList

JList fileList
DOCUMENT ME!

filePanel

JPanel filePanel
DOCUMENT ME!

model

DefaultListModel model
DOCUMENT ME!

paramPanel

JPanel paramPanel
DOCUMENT ME!

removeButton

JButton removeButton
DOCUMENT ME!

srcImage

ModelImage srcImage

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

omegaRBetaList

LinkedList<E>[] omegaRBetaList
For each omega angle index, a linked list of R and B values is present omega is the gradient angle to the curve, with the gradient defined as going into the object, and R and B give the distance and angle from the center of the VOI to the tangent point

omegaBins

int omegaBins
Number of bins for gradient angle omega going from 0 to 2*PI

sidePointsForTangent

int sidePointsForTangent
Number of points to take from each side of a point on a curve in determining a tangent

maxPixelBinWidth

float maxPixelBinWidth
Desired maximum pixel bin width for x, y center value

pixelWidthText

JTextField pixelWidthText

maxBufferSize

int maxBufferSize
The maximum Hough transform size in megabytes - default is currently 256

maxBufferText

JTextField maxBufferText

rotationCheckBox

JCheckBox rotationCheckBox

degreesWidthLabel

JLabel degreesWidthLabel

degreesWidthText

JTextField degreesWidthText

allowRotation

boolean allowRotation
If true, allow rotation of R-table object

maxDegreesBinWidth

float maxDegreesBinWidth
Desired maximum rotation angle.

allowScaling

boolean allowScaling
If true, allow scaling of R-table object

scalingCheckBox

JCheckBox scalingCheckBox

minScaleFactor

float minScaleFactor

minScaleLabel

JLabel minScaleLabel

minScaleText

JTextField minScaleText

maxScaleFactor

float maxScaleFactor

maxScaleLabel

JLabel maxScaleLabel

maxScaleText

JTextField maxScaleText

scaleBins

int scaleBins
Desired number of scaling bins

scalingLabel

JLabel scalingLabel

scalingText

JTextField scalingText

objectsToFind

int objectsToFind
Number of instances of R-table of to find in the image

numObjectsText

JTextField numObjectsText
Minimum pixel distances between instances of R-table objects

parametersFile

String parametersFile
File containing omegaBins, sidePointsForTangent, and omegaRBetaList, the R-table

endianess

boolean endianess

raFile

RandomAccessFile raFile

Class gov.nih.mipav.view.dialogs.JDialogFlip extends JDialogScriptableBase implements Serializable

serialVersionUID: -5672670158596197276L

Serialized Fields

flipAlgo

AlgorithmFlip flipAlgo
Algorithm used by the dialog.

flipAxis

int flipAxis
Axis to flip around.

flipObject

int flipObject
The object to be flipped

image

ModelImage image
Source image.

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

flipVoiCheckbox

JCheckBox flipVoiCheckbox
When checked, VOIs are flipped when image is flipped.

flipAxisZRadioButton

JRadioButton flipAxisZRadioButton
Image is flipped by depth when selected

flipAxisYRadioButton

JRadioButton flipAxisYRadioButton
Image is flipped horizontally when selected

flipAxisXRadioButton

JRadioButton flipAxisXRadioButton
Image is flipped vertically when selected

Class gov.nih.mipav.view.dialogs.JDialogFrameLinker extends JDialogBase implements Serializable

serialVersionUID: 8115834657630127291L

Serialized Fields

comboBoxImage

JComboBox comboBoxImage
DOCUMENT ME!

frameB

ViewJFrameImage frameB
DOCUMENT ME!

imageA

ModelImage imageA
DOCUMENT ME!

imageB

ModelImage imageB
DOCUMENT ME!

imageRef

int imageRef
DOCUMENT ME!

linkButton

JButton linkButton
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogFRAP extends JDialogBase implements Serializable

serialVersionUID: 6390017817188485094L

Serialized Fields

analysisGroup

ButtonGroup analysisGroup
DOCUMENT ME!

backgroundButton

JRadioButton backgroundButton
DOCUMENT ME!

backgroundIndex

int backgroundIndex
DOCUMENT ME!

bandButton

JRadioButton bandButton
DOCUMENT ME!

bleachedROIShape

int bleachedROIShape
DOCUMENT ME!

blueButton

JRadioButton blueButton
DOCUMENT ME!

circleButton

JRadioButton circleButton
DOCUMENT ME!

colorGroup

ButtonGroup colorGroup
DOCUMENT ME!

colorsPresent

int colorsPresent
DOCUMENT ME!

comboBoxCostFunct

JComboBox comboBoxCostFunct
DOCUMENT ME!

componentImage

ViewJComponentEditImage componentImage
DOCUMENT ME!

cost

int cost
DOCUMENT ME!

createInfoLine

boolean createInfoLine
DOCUMENT ME!

createRegCheckBox

JCheckBox createRegCheckBox
DOCUMENT ME!

createRegImage

boolean createRegImage
DOCUMENT ME!

diffusion

float diffusion
DOCUMENT ME!

fileInfo

FileInfoLSM fileInfo
DOCUMENT ME!

fileInfoImageXML

FileInfoImageXML fileInfoImageXML
DOCUMENT ME!

firstSliceAfterBleach

int firstSliceAfterBleach
DOCUMENT ME!

firstSliceNum

int firstSliceNum
DOCUMENT ME!

firstSliceNumText

JTextField firstSliceNumText
DOCUMENT ME!

frapAlgo

AlgorithmFRAP frapAlgo
DOCUMENT ME!

greenButton

JRadioButton greenButton
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

infoPanel

JPanel infoPanel
DOCUMENT ME!

knotX

double[] knotX
DOCUMENT ME!

labelCost

JLabel labelCost
DOCUMENT ME!

labelDiffusion

JLabel labelDiffusion
DOCUMENT ME!

labelFirstSlice

JLabel labelFirstSlice
DOCUMENT ME!

labelImage

JLabel labelImage
DOCUMENT ME!

labelRadius

JLabel labelRadius
DOCUMENT ME!

labelRef

JLabel labelRef
DOCUMENT ME!

labelShape

JLabel labelShape
DOCUMENT ME!

maxR

double maxR
DOCUMENT ME!

maxG

double maxG
DOCUMENT ME!

maxB

double maxB
DOCUMENT ME!

minR

double minR
DOCUMENT ME!

minG

double minG
DOCUMENT ME!

minB

double minB
DOCUMENT ME!

model

int model
DOCUMENT ME!

nBoundingVOIs

int nBoundingVOIs
DOCUMENT ME!

oneDButton

JRadioButton oneDButton
DOCUMENT ME!

paramPanel

JPanel paramPanel
DOCUMENT ME!

paramVary

boolean paramVary
DOCUMENT ME!

paramVaryCheckBox

JCheckBox paramVaryCheckBox
DOCUMENT ME!

photoBleachedButton

JRadioButton photoBleachedButton
DOCUMENT ME!

photoBleachedIndex

int photoBleachedIndex
DOCUMENT ME!

radius

float radius
DOCUMENT ME!

redButton

JRadioButton redButton
DOCUMENT ME!

regCheckBox

JCheckBox regCheckBox
DOCUMENT ME!

register

boolean register
DOCUMENT ME!

singleExpButton

JRadioButton singleExpButton
DOCUMENT ME!

textDiffusion

JTextField textDiffusion
DOCUMENT ME!

textRadius

JTextField textRadius
DOCUMENT ME!

useBlue

boolean useBlue
DOCUMENT ME!

useGreen

boolean useGreen
DOCUMENT ME!

useRed

boolean useRed
DOCUMENT ME!

VOIGroup

ButtonGroup VOIGroup
DOCUMENT ME!

VOIIndex1

int VOIIndex1
DOCUMENT ME!

VOIIndex2

int VOIIndex2
DOCUMENT ME!

VOIIndex3

int VOIIndex3
DOCUMENT ME!

VOIs

ViewVOIVector VOIs
DOCUMENT ME!

wholeOrganButton

JRadioButton wholeOrganButton
DOCUMENT ME!

wholeOrganCheckBox

JCheckBox wholeOrganCheckBox
DOCUMENT ME!

wholeOrganIndex

int wholeOrganIndex
DOCUMENT ME!

wholeOrganNormalize

boolean wholeOrganNormalize
DOCUMENT ME!

xPos

int xPos
DOCUMENT ME!

yPos

int yPos
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogFrequencyFilter extends JDialogScriptableBase implements Serializable

serialVersionUID: 4979580288393418858L

Serialized Fields

bandPass

JRadioButton bandPass
DOCUMENT ME!

bandStop

JRadioButton bandStop
DOCUMENT ME!

butterworthFilter

JRadioButton butterworthFilter
DOCUMENT ME!

butterworthOrder

int butterworthOrder
DOCUMENT ME!

constructionGroup

ButtonGroup constructionGroup
DOCUMENT ME!

constructionMethod

int constructionMethod
DOCUMENT ME!

constructionPanel

JPanel constructionPanel
DOCUMENT ME!

destinationGroup

ButtonGroup destinationGroup
DOCUMENT ME!

destinationPanel

JPanel destinationPanel
DOCUMENT ME!

displayLoc

int displayLoc
DOCUMENT ME!

filterPanel

JPanel filterPanel
DOCUMENT ME!

filterType

int filterType
DOCUMENT ME!

filterTypeGroup

ButtonGroup filterTypeGroup
DOCUMENT ME!

freq1

float freq1
DOCUMENT ME!

freq2

float freq2
DOCUMENT ME!

FrequencyFilterAlgo

AlgorithmFrequencyFilter FrequencyFilterAlgo
DOCUMENT ME!

gaussianFilter

JRadioButton gaussianFilter
DOCUMENT ME!

highPass

JRadioButton highPass
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

image25D

boolean image25D
DOCUMENT ME!

image25DCheckbox

JCheckBox image25DCheckbox
DOCUMENT ME!

imageCrop

boolean imageCrop
DOCUMENT ME!

imageCropCheckbox

JCheckBox imageCropCheckbox
DOCUMENT ME!

kernelDiameter

int kernelDiameter
DOCUMENT ME!

labelF1

JLabel labelF1
DOCUMENT ME!

labelF2

JLabel labelF2
DOCUMENT ME!

labelKernelDiameter

JLabel labelKernelDiameter
DOCUMENT ME!

labelOrder

JLabel labelOrder
DOCUMENT ME!

lowPass

JRadioButton lowPass
DOCUMENT ME!

mainPanel

JPanel mainPanel
DOCUMENT ME!

newImage

JRadioButton newImage
DOCUMENT ME!

replaceImage

JRadioButton replaceImage
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

textF1

JTextField textF1
DOCUMENT ME!

textF2

JTextField textF2
DOCUMENT ME!

textKernelDiameter

JTextField textKernelDiameter
DOCUMENT ME!

textOrder

JTextField textOrder
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

windowFilter

JRadioButton windowFilter
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogFRET extends JDialogBase implements Serializable

serialVersionUID: 1026032715678640392L

Serialized Fields

backgroundButton

JRadioButton backgroundButton
DOCUMENT ME!

backgroundIndex

int backgroundIndex
DOCUMENT ME!

blueButton

JRadioButton blueButton
DOCUMENT ME!

colorGroup

ButtonGroup colorGroup
DOCUMENT ME!

colorsPresent

int colorsPresent
DOCUMENT ME!

comboBoxCostFunct

JComboBox comboBoxCostFunct
DOCUMENT ME!

componentImage

ViewJComponentEditImage componentImage
DOCUMENT ME!

componentPostImage

ViewJComponentEditImage componentPostImage
DOCUMENT ME!

cost

int cost
DOCUMENT ME!

createRegCheckBox

JCheckBox createRegCheckBox
DOCUMENT ME!

createRegImage

boolean createRegImage
DOCUMENT ME!

donorButton

JRadioButton donorButton
DOCUMENT ME!

donorIndex

int donorIndex
DOCUMENT ME!

fretAlgo

AlgorithmFRETAcceptorPhotobleach fretAlgo
DOCUMENT ME!

greenButton

JRadioButton greenButton
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

imageComboBox

JComboBox imageComboBox
DOCUMENT ME!

labelCost

JLabel labelCost
DOCUMENT ME!

maxR

double maxR
DOCUMENT ME!

maxG

double maxG
DOCUMENT ME!

maxB

double maxB
DOCUMENT ME!

minR

double minR
DOCUMENT ME!

minG

double minG
DOCUMENT ME!

minB

double minB
DOCUMENT ME!

nBoundingVOIs

int nBoundingVOIs
DOCUMENT ME!

postImage

ModelImage postImage
DOCUMENT ME!

redButton

JRadioButton redButton
DOCUMENT ME!

regCheckBox

JCheckBox regCheckBox
DOCUMENT ME!

register

boolean register
DOCUMENT ME!

signalButton

JRadioButton signalButton
DOCUMENT ME!

signalIndex

int signalIndex
DOCUMENT ME!

UI

ViewUserInterface UI
DOCUMENT ME!

useBlue

boolean useBlue
DOCUMENT ME!

useGreen

boolean useGreen
DOCUMENT ME!

useRed

boolean useRed
DOCUMENT ME!

VOIGroup

ButtonGroup VOIGroup
DOCUMENT ME!

VOIs

ViewVOIVector VOIs
DOCUMENT ME!

yPos

int yPos
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogFRETBleedThrough extends JDialogScriptableBase implements Serializable

serialVersionUID: 8726771970079234501L

Serialized Fields

acceptorButton

JRadioButton acceptorButton
DOCUMENT ME!

acceptorRun

boolean acceptorRun
DOCUMENT ME!

activeButton

JRadioButton activeButton
DOCUMENT ME!

activeIndex

int activeIndex
DOCUMENT ME!

backgroundButton

JRadioButton backgroundButton
DOCUMENT ME!

backgroundIndex

int backgroundIndex
DOCUMENT ME!

blueButton

JRadioButton blueButton
DOCUMENT ME!

chooserButton

JButton chooserButton
DOCUMENT ME!

chooserButton2

JButton chooserButton2
DOCUMENT ME!

colorGroup

ButtonGroup colorGroup
DOCUMENT ME!

colorPanel

JPanel colorPanel
DOCUMENT ME!

componentImage

ViewJComponentEditImage componentImage
DOCUMENT ME!

doColor

boolean doColor
DOCUMENT ME!

donorButton

JRadioButton donorButton
DOCUMENT ME!

dyeGroup

ButtonGroup dyeGroup
DOCUMENT ME!

fbtAlgo

AlgorithmFRETBleedThrough fbtAlgo
DOCUMENT ME!

FP2Image

ModelImage FP2Image
DOCUMENT ME!

FRETImage

ModelImage FRETImage
DOCUMENT ME!

greenButton

JRadioButton greenButton
DOCUMENT ME!

imageList

JList imageList
DOCUMENT ME!

imageList2

JList imageList2
DOCUMENT ME!

imagePanel

JPanel imagePanel
DOCUMENT ME!

imagePanel2

JPanel imagePanel2
DOCUMENT ME!

model

DefaultListModel model
DOCUMENT ME!

model2

DefaultListModel model2
DOCUMENT ME!

nBoundingVOIs

int nBoundingVOIs
DOCUMENT ME!

paramPanel

JPanel paramPanel
DOCUMENT ME!

redButton

JRadioButton redButton
DOCUMENT ME!

removeButton

JButton removeButton
DOCUMENT ME!

removeButton2

JButton removeButton2
DOCUMENT ME!

srcImage

ModelImage srcImage
The source image must be either an image with donor dye only taken with a donor fluorescent peak filter or an image with acceptor dye only taken with a acceptor fluorescent peak filter.

useBlue

boolean useBlue
DOCUMENT ME!

useGreen

boolean useGreen
DOCUMENT ME!

useRed

boolean useRed
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

VOIGroup

ButtonGroup VOIGroup
DOCUMENT ME!

VOIs

ViewVOIVector VOIs
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogFRETEfficiency extends JDialogScriptableBase implements Serializable

serialVersionUID: 156910291527442369L

Serialized Fields

acceptorImage

ModelImage acceptorImage
DOCUMENT ME!

activeButton

JRadioButton activeButton
DOCUMENT ME!

activeIndex

int activeIndex
DOCUMENT ME!

AFPintoDFP

float AFPintoDFP
DOCUMENT ME!

AFPintoFRET

float AFPintoFRET
DOCUMENT ME!

backgroundButton

JRadioButton backgroundButton
DOCUMENT ME!

backgroundIndex

int backgroundIndex
DOCUMENT ME!

blueButton

JRadioButton blueButton
DOCUMENT ME!

chooserButton

JButton chooserButton
DOCUMENT ME!

chooserButton2

JButton chooserButton2
DOCUMENT ME!

colorGroup

ButtonGroup colorGroup
DOCUMENT ME!

colorPanel

JPanel colorPanel
DOCUMENT ME!

componentImage

ViewJComponentEditImage componentImage
DOCUMENT ME!

createEfficiencyImage

boolean createEfficiencyImage
DOCUMENT ME!

createFDivAImage

boolean createFDivAImage
DOCUMENT ME!

createFDivDImage

boolean createFDivDImage
DOCUMENT ME!

DFPintoAFP

float DFPintoAFP
DOCUMENT ME!

DFPintoFRET

float DFPintoFRET
DOCUMENT ME!

doColor

boolean doColor
DOCUMENT ME!

efficiencyImage

ModelImage efficiencyImage
DOCUMENT ME!

effImageCheckBox

JCheckBox effImageCheckBox
DOCUMENT ME!

fDivACheckBox

JCheckBox fDivACheckBox
DOCUMENT ME!

fDivAImage

ModelImage fDivAImage
DOCUMENT ME!

fDivDCheckBox

JCheckBox fDivDCheckBox
DOCUMENT ME!

fDivDImage

ModelImage fDivDImage
DOCUMENT ME!

feffAlgo

AlgorithmFRETEfficiency feffAlgo
DOCUMENT ME!

FRETImage

ModelImage FRETImage
DOCUMENT ME!

greenButton

JRadioButton greenButton
DOCUMENT ME!

imageList

JList imageList
DOCUMENT ME!

imageList2

JList imageList2
DOCUMENT ME!

imagePanel

JPanel imagePanel
DOCUMENT ME!

imagePanel2

JPanel imagePanel2
DOCUMENT ME!

model

DefaultListModel model
DOCUMENT ME!

model2

DefaultListModel model2
DOCUMENT ME!

nBoundingVOIs

int nBoundingVOIs
DOCUMENT ME!

paramPanel

JPanel paramPanel
DOCUMENT ME!

redButton

JRadioButton redButton
DOCUMENT ME!

removeButton

JButton removeButton
DOCUMENT ME!

removeButton2

JButton removeButton2
DOCUMENT ME!

srcImage

ModelImage srcImage
The source image must be the image taken with the donor fluorescent peak filter.

textAFPintoDFP

JTextField textAFPintoDFP
DOCUMENT ME!

textAFPintoFRET

JTextField textAFPintoFRET
DOCUMENT ME!

textDFPintoAFP

JTextField textDFPintoAFP
DOCUMENT ME!

textDFPintoFRET

JTextField textDFPintoFRET
DOCUMENT ME!

useBlue

boolean useBlue
DOCUMENT ME!

useGreen

boolean useGreen
DOCUMENT ME!

useRed

boolean useRed
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

VOIGroup

ButtonGroup VOIGroup
DOCUMENT ME!

VOIs

ViewVOIVector VOIs
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogFuzzyCMeans extends JDialogScriptableBase implements Serializable

serialVersionUID: 7191124209694457297L

Serialized Fields

centroids

float[] centroids
DOCUMENT ME!

cropBackground

boolean cropBackground
DOCUMENT ME!

cropCheckbox

JCheckBox cropCheckbox
DOCUMENT ME!

destExtents

int[] destExtents
DOCUMENT ME!

endTol

float endTol
DOCUMENT ME!

fcmAlgo

AlgorithmFuzzyCMeans fcmAlgo
DOCUMENT ME!

fuzzyOnly

JRadioButton fuzzyOnly
DOCUMENT ME!

hardFuzzyBoth

JRadioButton hardFuzzyBoth
DOCUMENT ME!

hardOnly

JRadioButton hardOnly
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

imageVOIGroup

ButtonGroup imageVOIGroup
DOCUMENT ME!

imageVOIPanel

JPanel imageVOIPanel
DOCUMENT ME!

labelEndTol

JLabel labelEndTol
DOCUMENT ME!

labelExpo

JLabel labelExpo
DOCUMENT ME!

labelJacobi

JLabel labelJacobi
DOCUMENT ME!

labelMaxIter

JLabel labelMaxIter
DOCUMENT ME!

labelNClasses

JLabel labelNClasses
DOCUMENT ME!

labelNPyramid

JLabel labelNPyramid
DOCUMENT ME!

labelSignal

JLabel labelSignal
DOCUMENT ME!

labelSmooth

JLabel labelSmooth
DOCUMENT ME!

maxIter

int maxIter
DOCUMENT ME!

nClasses

int nClasses
DOCUMENT ME!

nPyramid

int nPyramid
DOCUMENT ME!

oneJacobiIter

int oneJacobiIter
DOCUMENT ME!

oneSmooth

float oneSmooth
DOCUMENT ME!

outputGainField

boolean outputGainField
private JCheckBox calcGainFieldCheckbox;.

paramPanel

JPanel paramPanel
DOCUMENT ME!

presentNumber

int presentNumber
DOCUMENT ME!

q

float q
DOCUMENT ME!

regionFlag

boolean regionFlag
DOCUMENT ME!

resultImage

ModelImage[] resultImage
DOCUMENT ME!

resultNumber

int resultNumber
DOCUMENT ME!

segmentation

int segmentation
DOCUMENT ME!

segmentationGroup

ButtonGroup segmentationGroup
DOCUMENT ME!

segmentationPanel

JPanel segmentationPanel
DOCUMENT ME!

textEndTol

JTextField textEndTol
DOCUMENT ME!

textExpo

JTextField textExpo
DOCUMENT ME!

textMaxIter

JTextField textMaxIter
DOCUMENT ME!

textNClasses

JTextField textNClasses
DOCUMENT ME!

textNPyramid

JTextField textNPyramid
DOCUMENT ME!

textOneJacobiIter

JTextField textOneJacobiIter
DOCUMENT ME!

textOneSmooth

JTextField textOneSmooth
DOCUMENT ME!

textSignal

JTextField textSignal
DOCUMENT ME!

textTwoJacobiIter

JTextField textTwoJacobiIter
DOCUMENT ME!

textTwoSmooth

JTextField textTwoSmooth
DOCUMENT ME!

threshold

float threshold
DOCUMENT ME!

twoJacobiIter

int twoJacobiIter
DOCUMENT ME!

twoSmooth

float twoSmooth
DOCUMENT ME!

VOIRegions

JRadioButton VOIRegions
DOCUMENT ME!

wholeImage

JRadioButton wholeImage
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogGaborFilter extends JDialogScriptableBase implements Serializable

serialVersionUID: -7693130193527088045L

Serialized Fields

createGabor

boolean createGabor
DOCUMENT ME!

createGaborCheckBox

JCheckBox createGaborCheckBox
DOCUMENT ME!

destinationGroup

ButtonGroup destinationGroup
DOCUMENT ME!

destinationPanel

JPanel destinationPanel
DOCUMENT ME!

displayLoc

int displayLoc
DOCUMENT ME!

filterPanel

JPanel filterPanel
DOCUMENT ME!

freqU

float freqU
DOCUMENT ME!

FrequencyFilterAlgo

AlgorithmFrequencyFilter FrequencyFilterAlgo
DOCUMENT ME!

freqV

float freqV
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

labelFU

JLabel labelFU
DOCUMENT ME!

labelFV

JLabel labelFV
DOCUMENT ME!

labelSU

JLabel labelSU
DOCUMENT ME!

labelSV

JLabel labelSV
DOCUMENT ME!

labelTheta

JLabel labelTheta
DOCUMENT ME!

mainPanel

JPanel mainPanel
DOCUMENT ME!

newImage

JRadioButton newImage
DOCUMENT ME!

replaceImage

JRadioButton replaceImage
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

sigmaU

float sigmaU
DOCUMENT ME!

sigmaV

float sigmaV
DOCUMENT ME!

textFU

JTextField textFU
DOCUMENT ME!

textFV

JTextField textFV
DOCUMENT ME!

textSU

JTextField textSU
DOCUMENT ME!

textSV

JTextField textSV
DOCUMENT ME!

textTheta

JTextField textTheta
DOCUMENT ME!

theta

float theta
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogGaussianBlur extends JDialogScriptableBase implements Serializable

serialVersionUID: -5074546334694615886L

Serialized Fields

colorChannelPanel

JPanelColorChannels colorChannelPanel
DOCUMENT ME!

gaussianBlurAlgo

AlgorithmGaussianBlur gaussianBlurAlgo
DOCUMENT ME!

gaussianBlurSepAlgo

AlgorithmGaussianBlurSep gaussianBlurSepAlgo
DOCUMENT ME!

image

ModelImage image
Source image.

image25D

boolean image25D
Flag indicating if slices should be blurred independently.

image25DCheckbox

JCheckBox image25DCheckbox
DOCUMENT ME!

outputOptionsPanel

JPanelAlgorithmOutputOptions outputOptionsPanel
DOCUMENT ME!

resultImage

ModelImage resultImage
Result image.

separable

boolean separable
DOCUMENT ME!

sepCheckbox

JCheckBox sepCheckbox
DOCUMENT ME!

sigmaPanel

JPanelSigmas sigmaPanel
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogGaussianBlurITK extends JDialogScriptableBase implements Serializable

serialVersionUID: -4057161307906161677L

Serialized Fields

colorChannelPanel

JPanelColorChannels colorChannelPanel
Which color channels to filter

gaussianBlurAlgo

AlgorithmGaussianBlurITK gaussianBlurAlgo
filter algorithm

image

ModelImage image
source image

image25D

boolean image25D
flag indicating if slices should be blurred independently

image25DCheckbox

JCheckBox image25DCheckbox
gui for image25D

outputOptionsPanel

JPanelAlgorithmOutputOptions outputOptionsPanel
new image or replace current

resultImage

ModelImage resultImage
result image

sigmaPanel

JPanelSigmas sigmaPanel
sigmas of kernel

titles

String[] titles
saved window titles

userInterface

ViewUserInterface userInterface
UI to hang from

Class gov.nih.mipav.view.dialogs.JDialogGradientMagnitude extends JDialogScriptableBase implements Serializable

serialVersionUID: 2890654165880748219L

Serialized Fields

colorChannelPanel

JPanelColorChannels colorChannelPanel
DOCUMENT ME!

gradientMagAlgo

AlgorithmGradientMagnitude gradientMagAlgo
DOCUMENT ME!

gradientMagSepAlgo

AlgorithmGradientMagnitudeSep gradientMagSepAlgo
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

image25D

boolean image25D
DOCUMENT ME!

image25DCheckbox

JCheckBox image25DCheckbox
DOCUMENT ME!

outputOptionsPanel

JPanelAlgorithmOutputOptions outputOptionsPanel
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

separable

boolean separable
DOCUMENT ME!

sepCheckbox

JCheckBox sepCheckbox
DOCUMENT ME!

sigmaPanel

JPanelSigmas sigmaPanel
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogGraphBasedSegmentation extends JDialogScriptableBase implements Serializable

serialVersionUID: -5153750542245396807L

Serialized Fields

destinationGroup

ButtonGroup destinationGroup
DOCUMENT ME!

destinationPanel

JPanel destinationPanel
DOCUMENT ME!

displayLoc

int displayLoc
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

minComponentSize

int minComponentSize
DOCUMENT ME!

newImage

JRadioButton newImage
DOCUMENT ME!

paramPanel

JPanel paramPanel
DOCUMENT ME!

replaceImage

JRadioButton replaceImage
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

segAlgo

AlgorithmGraphBasedSegmentation segAlgo
DOCUMENT ME!

sigma

float sigma
DOCUMENT ME!

textGauss

JTextField textGauss
DOCUMENT ME!

textMinComponentSize

JTextField textMinComponentSize
DOCUMENT ME!

textThreshold

JTextField textThreshold
DOCUMENT ME!

threshold

float threshold
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogGridOptions extends JDialogBase implements Serializable

serialVersionUID: 1869680780124245552L

Serialized Fields

chooser

ViewJColorChooser chooser
DOCUMENT ME!

color

Color color
DOCUMENT ME!

colorButton

JButton colorButton
DOCUMENT ME!

comp

ViewJComponentEditImage comp
DOCUMENT ME!

height

float height
DOCUMENT ME!

heightField

JTextField heightField
DOCUMENT ME!

labelBox

JCheckBox labelBox
DOCUMENT ME!

labelXAlphaButton

JRadioButton labelXAlphaButton
DOCUMENT ME!

labelXNumButton

JRadioButton labelXNumButton
DOCUMENT ME!

unitsStr

String unitsStr
DOCUMENT ME!

width

float width
DOCUMENT ME!

widthField

JTextField widthField
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogGUIDClient extends JDialog implements Serializable

Serialized Fields

doubleEntryBox

JCheckBox doubleEntryBox

guidField

JTextField guidField

mainFields

JTextField[] mainFields

secondaryFields

JTextField[] secondaryFields

mainPanel

JPanel mainPanel

gbc

GridBagConstraints gbc

helpButton

JButton helpButton

cancelButton

JButton cancelButton

OKButton

JButton OKButton

fieldNames

String[] fieldNames

Class gov.nih.mipav.view.dialogs.JDialogGVF extends JDialogBase implements Serializable

serialVersionUID: -7812609363025907144L

Serialized Fields

boundaryIterations

int boundaryIterations
DOCUMENT ME!

checkboxDisplay

JCheckBox checkboxDisplay
DOCUMENT ME!

do25D

boolean do25D
DOCUMENT ME!

do25DCheckBox

JCheckBox do25DCheckBox
DOCUMENT ME!

extents

int[] extents
DOCUMENT ME!

gons

Polygon[] gons
DOCUMENT ME!

groupNum

int groupNum
DOCUMENT ME!

gvfAlgo

AlgorithmGVF gvfAlgo
DOCUMENT ME!

gvfIterations

int gvfIterations
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

kValue

float kValue
DOCUMENT ME!

labelGaussZ

JLabel labelGaussZ
DOCUMENT ME!

propagate

JRadioButton propagate
DOCUMENT ME!

propagationFlag

boolean propagationFlag
DOCUMENT ME!

removeOriginal

boolean removeOriginal
DOCUMENT ME!

removeOriginalCheckBox

JCheckBox removeOriginalCheckBox
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

scaleX

float scaleX
DOCUMENT ME!

scaleY

float scaleY
DOCUMENT ME!

scaleZ

float scaleZ
DOCUMENT ME!

singleSlice

JRadioButton singleSlice
DOCUMENT ME!

srcVOI

VOI srcVOI
DOCUMENT ME!

textBoundaryIterations

JTextField textBoundaryIterations
DOCUMENT ME!

textGaussX

JTextField textGaussX
DOCUMENT ME!

textGaussY

JTextField textGaussY
DOCUMENT ME!

textGaussZ

JTextField textGaussZ
DOCUMENT ME!

textGVFIterations

JTextField textGVFIterations
DOCUMENT ME!

textK

JTextField textK
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

voiColor

Color voiColor
DOCUMENT ME!

VOIs

ViewVOIVector VOIs
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogHaralickTexture extends JDialogScriptableBase implements Serializable

serialVersionUID: 2408406330754526954L

Serialized Fields

colorPanel

JPanel colorPanel
DOCUMENT ME!

colorGroup

ButtonGroup colorGroup
DOCUMENT ME!

redButton

JRadioButton redButton
DOCUMENT ME!

greenButton

JRadioButton greenButton
DOCUMENT ME!

blueButton

JRadioButton blueButton
DOCUMENT ME!

RGBOffset

int RGBOffset
DOCUMENT ME!

asm

boolean asm
DOCUMENT ME!

asmCheckBox

JCheckBox asmCheckBox
DOCUMENT ME!

contrast

boolean contrast
DOCUMENT ME!

contrastCheckBox

JCheckBox contrastCheckBox
DOCUMENT ME!

correlation

boolean correlation
DOCUMENT ME!

correlationCheckBox

JCheckBox correlationCheckBox
DOCUMENT ME!

dissimilarity

boolean dissimilarity
DOCUMENT ME!

dissimilarityCheckBox

JCheckBox dissimilarityCheckBox
DOCUMENT ME!

energy

boolean energy
DOCUMENT ME!

energyCheckBox

JCheckBox energyCheckBox
DOCUMENT ME!

entropy

boolean entropy
DOCUMENT ME!

entropyCheckBox

JCheckBox entropyCheckBox
DOCUMENT ME!

ew

boolean ew
DOCUMENT ME!

ewCheckBox

JCheckBox ewCheckBox
DOCUMENT ME!

homogeneity

boolean homogeneity
DOCUMENT ME!

homogeneityCheckBox

JCheckBox homogeneityCheckBox
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

invariantCheckBox

JCheckBox invariantCheckBox
DOCUMENT ME!

invariantDir

boolean invariantDir
DOCUMENT ME!

inverseOrder1

boolean inverseOrder1
DOCUMENT ME!

inverseOrder1CheckBox

JCheckBox inverseOrder1CheckBox
DOCUMENT ME!

labelOffsetDistance

JLabel labelOffsetDistance
DOCUMENT ME!

labelWindowSize

JLabel labelWindowSize
DOCUMENT ME!

maxProbability

boolean maxProbability
DOCUMENT ME!

maxProbabilityCheckBox

JCheckBox maxProbabilityCheckBox
DOCUMENT ME!

mean

boolean mean
DOCUMENT ME!

meanCheckBox

JCheckBox meanCheckBox
DOCUMENT ME!

nesw

boolean nesw
DOCUMENT ME!

neswCheckBox

JCheckBox neswCheckBox
DOCUMENT ME!

ns

boolean ns
DOCUMENT ME!

nsCheckBox

JCheckBox nsCheckBox
DOCUMENT ME!

numDirections

int numDirections
DOCUMENT ME!

numOperators

int numOperators
DOCUMENT ME!

offsetDistance

int offsetDistance
DOCUMENT ME!

resultImage

ModelImage[] resultImage
DOCUMENT ME!

resultNumber

int resultNumber
DOCUMENT ME!

scalePanel

JPanel scalePanel
DOCUMENT ME!

senw

boolean senw
DOCUMENT ME!

senwCheckBox

JCheckBox senwCheckBox
DOCUMENT ME!

standardDeviation

boolean standardDeviation
DOCUMENT ME!

standardDeviationCheckBox

JCheckBox standardDeviationCheckBox
DOCUMENT ME!

textOffsetDistance

JTextField textOffsetDistance
DOCUMENT ME!

textureAlgo

AlgorithmHaralickTexture textureAlgo
DOCUMENT ME!

textWindowSize

JTextField textWindowSize
DOCUMENT ME!

variance

boolean variance
DOCUMENT ME!

varianceCheckBox

JCheckBox varianceCheckBox
DOCUMENT ME!

windowSize

int windowSize
DOCUMENT ME!

labelRescaling

JLabel labelRescaling

textRescaling

JTextField textRescaling

greyLevels

int greyLevels
Number of grey levels used if data must be rescaled

Class gov.nih.mipav.view.dialogs.JDialogHessian extends JDialogBase implements Serializable

serialVersionUID: -8129223463637379259L

Serialized Fields

gaussianScale

float gaussianScale
DOCUMENT ME!

hess00

JLabel hess00
DOCUMENT ME!

hess01

JLabel hess01
DOCUMENT ME!

hess02

JLabel hess02
DOCUMENT ME!

hess10

JLabel hess10
DOCUMENT ME!

hess11

JLabel hess11
DOCUMENT ME!

hess12

JLabel hess12
DOCUMENT ME!

hess20

JLabel hess20
DOCUMENT ME!

hess21

JLabel hess21
DOCUMENT ME!

hess22

JLabel hess22
DOCUMENT ME!

locationX

int locationX
DOCUMENT ME!

locationY

int locationY
DOCUMENT ME!

locationZ

int locationZ
DOCUMENT ME!

runItButton

JButton runItButton
DOCUMENT ME!

runItAllButton

JButton runItAllButton
DOCUMENT ME!

runBatchButton

JButton runBatchButton
DOCUMENT ME!

runMethod

int runMethod
DOCUMENT ME!

textLocX

JTextField textLocX
DOCUMENT ME!

textLocY

JTextField textLocY
DOCUMENT ME!

textLocZ

JTextField textLocZ
DOCUMENT ME!

textGaussScale

JTextField textGaussScale
DOCUMENT ME!

eigenSystemAlgo

AlgorithmEigensolver eigenSystemAlgo
DOCUMENT ME!

hessianAlgo

AlgorithmHessian hessianAlgo
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

imgHessianAlgor

AlgorithmImageHessian imgHessianAlgor
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogHistogram2Dim extends JDialogScriptableBase implements Serializable

serialVersionUID: -2641827384253148080L

Serialized Fields

bin1

int bin1
Number of bins for first image.

bin1Default

boolean bin1Default
Default number of bins for first image. Default is 256.

bin1Label

JLabel bin1Label
Label description for bin1.

bin1Text

JTextField bin1Text
Textfield for bin1.

bin2

int bin2
Number of bins for second image.

bin2Default

boolean bin2Default
Default number of bins for first image. Default is 256.

bin2Label

JLabel bin2Label
Label description for bin1.

bin2Text

JTextField bin2Text
Textfield for bin2.

blueCheckBox

JCheckBox blueCheckBox
Checkbox to select blue image.

colorsPresent

int colorsPresent
Number of colors present.

doLinearRescale

boolean doLinearRescale
If true, the range of second image is same as the range of the first image.

doLogResult

boolean doLogResult
If true, calculates the log of the result image for better visualization.

firstImage

ModelImage firstImage
First image (Source image).

greenCheckBox

JCheckBox greenCheckBox
Checkbox to select green image.

histogram2DimAlgo

AlgorithmHistogram2Dim histogram2DimAlgo
Instance of AlgorithmHistogram2Dim.

imageComboBox

JComboBox imageComboBox
Combobox to select the second image.

labelImage

JLabel labelImage
Image label.

linearCheckbox

JCheckBox linearCheckbox
Checkbox to select linear rescaling of second image.

maxR

double maxR
Max intensity values in Red, Green and Blue images respectively.

maxG

double maxG
Max intensity values in Red, Green and Blue images respectively.

maxB

double maxB
Max intensity values in Red, Green and Blue images respectively.

minR

double minR
Min. intensity values in Red, Green and Blue images respectively

minG

double minG
Min. intensity values in Red, Green and Blue images respectively

minB

double minB
Min. intensity values in Red, Green and Blue images respectively

possibleInt2Values

double possibleInt2Values
Possible intensity values for second image.

possibleIntValues

double possibleIntValues
Possible intensity values for first image.

redCheckBox

JCheckBox redCheckBox
Checkbox to select Red image.

resultCheckbox

JCheckBox resultCheckbox
Checkbox to display the log of result image.

resultImage

ModelImage resultImage
Image where the result is stored.

secondImage

ModelImage secondImage
Second image (Base image).

titles

String[] titles
String titles for the new windows.

useBlue

boolean useBlue
If true, blue image is selected as of the two images for calculating histogram.

useGreen

boolean useGreen
If true, green image is selected as of the two images for calculating histogram.

useRed

boolean useRed
If true, red image is selected as of the two images for calculating histogram.

userInterface

ViewUserInterface userInterface
Keeps record of the present structure of the application.

Class gov.nih.mipav.view.dialogs.JDialogHistogramLUT extends JDialogBase implements Serializable

serialVersionUID: 1863683975229524849L

Serialized Fields

colocalizationEMFrame

boolean colocalizationEMFrame
DOCUMENT ME!

colocalizationRegFrame

boolean colocalizationRegFrame
DOCUMENT ME!

imageA

ModelImage imageA
DOCUMENT ME!

imageB

ModelImage imageB
DOCUMENT ME!

LUTa

ModelLUT LUTa
DOCUMENT ME!

LUTb

ModelLUT LUTb
DOCUMENT ME!

regComponent

ViewJComponentRegistration regComponent
false = apply algorithm only to VOI regions.

regionFlag

boolean regionFlag
DOCUMENT ME!

RGBa

ModelRGB RGBa
DOCUMENT ME!

RGBb

ModelRGB RGBb
DOCUMENT ME!

VOIRegions

JRadioButton VOIRegions
DOCUMENT ME!

wholeImage

JRadioButton wholeImage
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogHistogramMatch extends JDialogScriptableBase implements Serializable

serialVersionUID: -4835888925289199854L

Serialized Fields

baseImage

ModelImage baseImage
DOCUMENT ME!

comboBoxImage

JComboBox comboBoxImage
DOCUMENT ME!

displayLoc

int displayLoc
DOCUMENT ME!

matchHistogramAlgo

AlgorithmHistogramMatch matchHistogramAlgo
DOCUMENT ME!

matchImage

ModelImage matchImage
DOCUMENT ME!

newImage

JRadioButton newImage
DOCUMENT ME!

replaceImage

JRadioButton replaceImage
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

titles

String[] titles
or if the source image is to be replaced.

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogHistogramSummary extends JDialogScriptableBase implements Serializable

serialVersionUID: -1570864449910121911L

Serialized Fields

imageMax

double imageMax
DOCUMENT ME!

imageMin

double imageMin
DOCUMENT ME!

bins

int bins
DOCUMENT ME!

binText

JTextField binText
DOCUMENT ME!

blueButton

JRadioButton blueButton
DOCUMENT ME!

colorGroup

ButtonGroup colorGroup
DOCUMENT ME!

colorPanel

JPanel colorPanel
DOCUMENT ME!

error

String error
DOCUMENT ME!

greenButton

JRadioButton greenButton
DOCUMENT ME!

histAlgo

AlgorithmHistogram histAlgo
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

radVOIs

JRadioButton radVOIs
DOCUMENT ME!

radWholeImage

JRadioButton radWholeImage
DOCUMENT ME!

redButton

JRadioButton redButton
DOCUMENT ME!

RGBOffset

int RGBOffset
DOCUMENT ME!

displayGraph

boolean displayGraph

userLimitsCheckBox

JCheckBox userLimitsCheckBox

userLimits

boolean userLimits

userMinText

JTextField userMinText

userMinLabel

JLabel userMinLabel

userMin

float userMin

userMaxText

JTextField userMaxText

userMaxLabel

JLabel userMaxLabel

userMax

float userMax

Class gov.nih.mipav.view.dialogs.JDialogHomomorphicFilter extends JDialogScriptableBase implements Serializable

serialVersionUID: 1061706659841470806L

Serialized Fields

butterworthOrder

int butterworthOrder
DOCUMENT ME!

destinationGroup

ButtonGroup destinationGroup
DOCUMENT ME!

destinationPanel

JPanel destinationPanel
DOCUMENT ME!

displayLoc

int displayLoc
DOCUMENT ME!

filterPanel

JPanel filterPanel
DOCUMENT ME!

freq1

float freq1
DOCUMENT ME!

FrequencyFilterAlgo

AlgorithmFrequencyFilter FrequencyFilterAlgo
DOCUMENT ME!

highGain

float highGain
DOCUMENT ME!

highTruncated

float highTruncated
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

image25D

boolean image25D
DOCUMENT ME!

image25DCheckbox

JCheckBox image25DCheckbox
DOCUMENT ME!

labelF1

JLabel labelF1
DOCUMENT ME!

labelHighGain

JLabel labelHighGain
DOCUMENT ME!

labelHighTruncated

JLabel labelHighTruncated
DOCUMENT ME!

labelLowGain

JLabel labelLowGain
DOCUMENT ME!

labelLowTruncated

JLabel labelLowTruncated
DOCUMENT ME!

labelOrder

JLabel labelOrder
DOCUMENT ME!

lowGain

float lowGain
DOCUMENT ME!

lowTruncated

float lowTruncated
DOCUMENT ME!

mainPanel

JPanel mainPanel
DOCUMENT ME!

newImage

JRadioButton newImage
DOCUMENT ME!

nf

DecimalFormat nf
DOCUMENT ME!

replaceImage

JRadioButton replaceImage
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

textF1

JTextField textF1
DOCUMENT ME!

textHighGain

JTextField textHighGain
DOCUMENT ME!

textHighTruncated

JTextField textHighTruncated
DOCUMENT ME!

textLowGain

JTextField textLowGain
DOCUMENT ME!

textLowTruncated

JTextField textLowTruncated
DOCUMENT ME!

textOrder

JTextField textOrder
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogHoughCircle extends JDialogBase implements Serializable

serialVersionUID: 0L

Serialized Fields

hAlgo

AlgorithmHoughCircle hAlgo
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

x0

int x0
DOCUMENT ME!

x0Text

JTextField x0Text
DOCUMENT ME!

y0

int y0
DOCUMENT ME!

y0Text

JTextField y0Text

rad

int rad

radText

JTextField radText
DOCUMENT ME!

numCircles

int numCircles

numCirclesText

JTextField numCirclesText

Class gov.nih.mipav.view.dialogs.JDialogHoughCircleChoice extends JDialogBase implements Serializable

serialVersionUID: 0L

Serialized Fields

x0Array

double[] x0Array

xDimSource

int xDimSource

y0Array

double[] y0Array

yDimSource

int yDimSource

radArray

double[] radArray

maxRad

double maxRad

countArray

int[] countArray

selectedCircle

boolean[] selectedCircle

numCirclesFound

int numCirclesFound

selectedArray

JCheckBox[] selectedArray

okayPressed

boolean okayPressed
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogHoughEllipse extends JDialogBase implements Serializable

serialVersionUID: 0L

Serialized Fields

hAlgo

AlgorithmHoughEllipse hAlgo
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

minCoverage

double minCoverage
Minimum percentage of the perimiter of a found ellipse that must be covered by points for it to be valid.

minCoverageText

JTextField minCoverageText
DOCUMENT ME!

sidePointsForTangent

int sidePointsForTangent
Maximum number of points to take from each side of a point on a curve in determining a tangent

sideText

JTextField sideText

pixelWidthText

JTextField pixelWidthText

maxPixelBinWidth

double maxPixelBinWidth
For xCenter, yCenter, r1, and r2 must bin width <= maxPixelBinWidth

degreesWidthText

JTextField degreesWidthText

maxDegreesBinWidth

double maxDegreesBinWidth
For theta must have bin width <= maxDegreesBinWidth

numEllipses

int numEllipses
number of ellipses to be found

numEllipsesText

JTextField numEllipsesText

minPointDistance

double minPointDistance
Smallest allowable distance between 2 of 3 picked points

minPointText

JTextField minPointText

maxPointDistance

double maxPointDistance
Largest allowable distance between 2 of 3 picked points

maxPointText

JTextField maxPointText

pointSetsRequired

int pointSetsRequired
Number of point triplets required before each ellipse find is performed

pointSetsText

JTextField pointSetsText

countThreshold

int countThreshold
Number of counts required to find an ellipse

countText

JTextField countText

ellipseRangeTolerance

double ellipseRangeTolerance
Maximum percent by which perimiter pixels can deviate from the ellipse equation

toleranceText

JTextField toleranceText

maxCyclesText

JTextField maxCyclesText

maxEllipseFindCycles

int maxEllipseFindCycles
Maximum number of pointSetsRequired triplet point acqusitions that is allowed to occur

maxBufferText

JTextField maxBufferText

maxBufferSize

int maxBufferSize
The maximum Hough transform size in megabytes - default is currently 256

Class gov.nih.mipav.view.dialogs.JDialogHoughEllipseChoice extends JDialogBase implements Serializable

serialVersionUID: 0L

Serialized Fields

xCenter

float[] xCenter

xDimSource

int xDimSource

yCenter

float[] yCenter

yDimSource

int yDimSource

r1

float[] r1

r2

float[] r2

theta

float[] theta

minR1

double minR1

maxR1

double maxR1

minR2

double minR2

maxR2

double maxR2

count

short[] count

selectedEllipse

boolean[] selectedEllipse

numEllipsesFound

int numEllipsesFound

selectedArray

JCheckBox[] selectedArray

okayPressed

boolean okayPressed
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogHoughLine extends JDialogBase implements Serializable

serialVersionUID: 0L

Serialized Fields

hAlgo

AlgorithmHoughLine hAlgo
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

n1

int n1
Number of rho cells

xText

JTextField xText
DOCUMENT ME!

n2

int n2
Number of theta cells

yText

JTextField yText
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogHoughLineChoice extends JDialogBase implements Serializable

serialVersionUID: 0L

Serialized Fields

rhoArray

int[] rhoArray

n1

int n1

thetaArray

int[] thetaArray

n2

int n2

countArray

int[] countArray

selectedLine

boolean[] selectedLine

maxDistance

float[] maxDistance

numLinesFound

int numLinesFound

selectedArray

JCheckBox[] selectedArray

distanceArray

JTextField[] distanceArray

okayPressed

boolean okayPressed
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogHoughParabola extends JDialogBase implements Serializable

serialVersionUID: 0L

Serialized Fields

hAlgo

AlgorithmHoughParabola hAlgo
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

xvBins

int xvBins
DOCUMENT ME!

xvText

JTextField xvText
DOCUMENT ME!

yvBins

int yvBins
DOCUMENT ME!

yvText

JTextField yvText

phiBins

int phiBins

phiText

JTextField phiText
DOCUMENT ME!

phiConstant

double phiConstant

phiConstantText

JTextField phiConstantText

pBins

int pBins

pText

JTextField pText

pMin

float pMin

pMinText

JTextField pMinText

pMax

float pMax

pMaxText

JTextField pMaxText

maxBufferText

JTextField maxBufferText

maxBufferSize

int maxBufferSize
The maximum Hough transform size in megabytes - default is currently 256

numParabolas

int numParabolas

numParabolasText

JTextField numParabolasText

sidePointsForTangent

int sidePointsForTangent
Maximum number of points to take from each side of a point on a curve in determining a tangent

sideText

JTextField sideText

Class gov.nih.mipav.view.dialogs.JDialogHoughParabolaChoice extends JDialogBase implements Serializable

serialVersionUID: 0L

Serialized Fields

xvTable

float[] xvTable

xDim

int xDim

yvTable

float[] yvTable

yDim

int yDim

phiTable

double[] phiTable

phiBins

int phiBins

pTable

float[] pTable

pMin

float pMin

pMax

float pMax

countTable

int[] countTable

selectedParabola

boolean[] selectedParabola

numParabolasFound

int numParabolasFound

selectedArray

JCheckBox[] selectedArray

okayPressed

boolean okayPressed
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogIDObjects extends JDialogScriptableBase implements Serializable

serialVersionUID: -6478138973143988561L

Serialized Fields

idObjectsAlgo2D

AlgorithmMorphology2D idObjectsAlgo2D
DOCUMENT ME!

idObjectsAlgo3D

AlgorithmMorphology3D idObjectsAlgo3D
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

labelMax

JLabel labelMax
DOCUMENT ME!

labelMin

JLabel labelMin
DOCUMENT ME!

max

int max
DOCUMENT ME!

min

int min
DOCUMENT ME!

outputPanel

JPanelAlgorithmOutputOptions outputPanel
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

textMax

JTextField textMax
DOCUMENT ME!

textMin

JTextField textMin
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogIHN3Correction extends JDialogScriptableBase implements Serializable

serialVersionUID: 9210373092056571003L

Serialized Fields

autoThreshold

boolean autoThreshold
DOCUMENT ME!

autoThresholdCheckbox

JCheckBox autoThresholdCheckbox
DOCUMENT ME!

convertTomm

float convertTomm
DOCUMENT ME!

createField

boolean createField
DOCUMENT ME!

createFieldCheckbox

JCheckBox createFieldCheckbox
DOCUMENT ME!

destExtents

int[] destExtents
DOCUMENT ME!

endTol

float endTol
DOCUMENT ME!

fieldDistance

float fieldDistance
DOCUMENT ME!

fieldImage

ModelImage fieldImage
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

kernelfwhm

float kernelfwhm
DOCUMENT ME!

labelDistance

JLabel labelDistance
DOCUMENT ME!

labelEndTol

JLabel labelEndTol
DOCUMENT ME!

labelKernel

JLabel labelKernel
DOCUMENT ME!

labelMaxIter

JLabel labelMaxIter
DOCUMENT ME!

labelNoise

JLabel labelNoise
DOCUMENT ME!

labelShrink

JLabel labelShrink
DOCUMENT ME!

labelSignal

JLabel labelSignal
DOCUMENT ME!

maxIter

int maxIter
DOCUMENT ME!

N3Algo

AlgorithmIHN3Correction N3Algo
DOCUMENT ME!

noise

float noise
DOCUMENT ME!

orgResol

float[] orgResol
DOCUMENT ME!

regionFlag

boolean regionFlag
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

resXUnit

int resXUnit
DOCUMENT ME!

resYUnit

int resYUnit
DOCUMENT ME!

resZUnit

int resZUnit
DOCUMENT ME!

shrink

float shrink
DOCUMENT ME!

textDistance

JTextField textDistance
DOCUMENT ME!

textEndTol

JTextField textEndTol
DOCUMENT ME!

textKernel

JTextField textKernel
DOCUMENT ME!

textMaxIter

JTextField textMaxIter
DOCUMENT ME!

textNoise

JTextField textNoise
DOCUMENT ME!

textShrink

JTextField textShrink
DOCUMENT ME!

textSignal

JTextField textSignal
DOCUMENT ME!

threshold

float threshold
DOCUMENT ME!

useScript

boolean useScript
DOCUMENT ME!

VOIRegions

JRadioButton VOIRegions
DOCUMENT ME!

wholeImage

JRadioButton wholeImage
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogImageCalculator extends JDialogScriptableBase implements Serializable

serialVersionUID: -7373755862535613674L

Serialized Fields

adOpString

String adOpString
Advanced function string.

advancedButton

JButton advancedButton
DOCUMENT ME!

clipMode

int clipMode
DOCUMENT ME!

comboBoxImage

JComboBox comboBoxImage
DOCUMENT ME!

comboBoxOperator

JComboBox comboBoxOperator
DOCUMENT ME!

displayLoc

int displayLoc
DOCUMENT ME!

imageA

ModelImage imageA
source image.

imageB

ModelImage imageB
DOCUMENT ME!

isColor

boolean isColor
DOCUMENT ME!

mathAlgo

AlgorithmImageCalculator mathAlgo
DOCUMENT ME!

opType

int opType
DOCUMENT ME!

radioClip

JRadioButton radioClip
DOCUMENT ME!

radioNew

JRadioButton radioNew
DOCUMENT ME!

radioPromote

JRadioButton radioPromote
DOCUMENT ME!

radioReplace

JRadioButton radioReplace
DOCUMENT ME!

resultImage

ModelImage resultImage
result image.

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogImageInfo extends JDialogBase implements Serializable

serialVersionUID: -3239665202530115877L

Serialized Fields

acpcACFields

JTextField[] acpcACFields
DOCUMENT ME!

acpcDimFields

JTextField[] acpcDimFields
DOCUMENT ME!

acpcMaxFields

JTextField[] acpcMaxFields
DOCUMENT ME!

acpcMinFields

JTextField[] acpcMinFields
TLRC Specific info.

acpcPCFields

JTextField[] acpcPCFields
DOCUMENT ME!

acpcResField

JTextField acpcResField
DOCUMENT ME!

addReplaceMatrix

JButton addReplaceMatrix
Add as New/Replace button (depending on selected matrix type).

applyButton

JButton applyButton
DOCUMENT ME!

bigEnd

JRadioButton bigEnd
Radio button to denote image is big endian.

buttonPanel

JPanel buttonPanel
DOCUMENT ME!

changeTypeAlgo

AlgorithmChangeType changeTypeAlgo
DOCUMENT ME!!

comboBoxUnitOfMeasure1

JComboBox comboBoxUnitOfMeasure1
DOCUMENT ME!

comboBoxUnitOfMeasure3

JComboBox comboBoxUnitOfMeasure3
DOCUMENT ME!

comboBoxUnitOfMeasure4

JComboBox comboBoxUnitOfMeasure4
DOCUMENT ME!

comboBoxUnitOfMeasure5

JComboBox comboBoxUnitOfMeasure5
DOCUMENT ME!

DIM

int DIM
DOCUMENT ME!

endianess

boolean endianess
Indicates the endianess of the image.

fileTransMatrix

TransMatrix fileTransMatrix
DOCUMENT ME!

font12B

Font font12B
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

isTLRCBox

JCheckBox isTLRCBox
DOCUMENT ME!

leftHandSystem

boolean leftHandSystem
If true change matrix to the left-hand coordinate system.

linkedImageButton

JButton linkedImageButton
DOCUMENT ME!

linkedImageField

JTextField linkedImageField
DOCUMENT ME!

littleEnd

JRadioButton littleEnd
Radio button to denote image is little endian.

loadButton

JButton loadButton
DOCUMENT ME!

matrix

double[][] matrix
DOCUMENT ME!

matrixBox

JComboBox matrixBox
Box to hold the matrices parsed from the MatrixHolder.

matrixFile

String matrixFile
DOCUMENT ME!

measure1

int measure1
DOCUMENT ME!

measure3

int measure3
DOCUMENT ME!

measure4

int measure4
DOCUMENT ME!

measure5

int measure5
DOCUMENT ME!

modality

int modality
DOCUMENT ME!

modalityBox

JComboBox modalityBox
DOCUMENT ME!

modalityStr

String[] modalityStr
DOCUMENT ME!

nameText

JTextField nameText
DOCUMENT ME!

newImageName

String newImageName
DOCUMENT ME!

orient

int orient
DOCUMENT ME!

orientationBox1

JComboBox orientationBox1
DOCUMENT ME!

orientationBox2

JComboBox orientationBox2
DOCUMENT ME!

orientationBox3

JComboBox orientationBox3
DOCUMENT ME!

orientAxis

int[] orientAxis
DOCUMENT ME!

orientBox

JComboBox orientBox
DOCUMENT ME!

orientFields

JTextField[] orientFields
DOCUMENT ME!

origACFields

JTextField[] origACFields
ACPC Specific info.

origDimFields

JTextField[] origDimFields
DOCUMENT ME!

origin

float[] origin
DOCUMENT ME!

origPCFields

JTextField[] origPCFields
DOCUMENT ME!

origResFields

JTextField[] origResFields
DOCUMENT ME!

resampleImage

ModelImage resampleImage
DOCUMENT ME!

resIndex

int resIndex
DOCUMENT ME!

resolutionBox

JCheckBox resolutionBox
DOCUMENT ME!

resolutions

float[] resolutions
DOCUMENT ME!

saveButton

JButton saveButton
DOCUMENT ME!

sliceThickness

float sliceThickness
DOCUMENT ME!

tabbedPane

JTabbedPane tabbedPane
DOCUMENT ME!

tBar

JToolBar tBar
DOCUMENT ME!

textMatrix

JTextField[][] textMatrix
DOCUMENT ME!

textRes1

JTextField textRes1
DOCUMENT ME!

textRes2

JTextField textRes2
DOCUMENT ME!

textRes3

JTextField textRes3
DOCUMENT ME!

textRes4

JTextField textRes4
DOCUMENT ME!

textRes5

JTextField textRes5
DOCUMENT ME!

textSt1

JTextField textSt1
DOCUMENT ME!

textSt2

JTextField textSt2
DOCUMENT ME!

textSt3

JTextField textSt3
DOCUMENT ME!

textSt4

JTextField textSt4
DOCUMENT ME!

textSliceThickness

JTextField textSliceThickness
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

tlrcACFields

JTextField[] tlrcACFields
DOCUMENT ME!

tlrcDimFields

JTextField[] tlrcDimFields
DOCUMENT ME!

tlrcPCFields

JTextField[] tlrcPCFields
DOCUMENT ME!

tlrcResFields

JTextField[] tlrcResFields
DOCUMENT ME!

transformIDBox

JComboBox transformIDBox
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

wcSystem

boolean wcSystem
If true change matrix to the world coordinate system.

provenanceArea

JTextArea provenanceArea
text area showing the

Class gov.nih.mipav.view.dialogs.JDialogImageMath extends JDialogScriptableBase implements Serializable

serialVersionUID: -2720105824431405427L

Serialized Fields

clipMode

int clipMode
DOCUMENT ME!

comboBoxOperator

JComboBox comboBoxOperator
DOCUMENT ME!

group

ButtonGroup group
DOCUMENT ME!

image

ModelImage image
source image.

imaginaryValue

double imaginaryValue
Used as both imaginary value and blue value

blueValue

double blueValue

inputPanel

JPanel inputPanel
DOCUMENT ME!

labelOperator

JLabel labelOperator
DOCUMENT ME!

labelValue

JLabel labelValue
Used for single value, real part of complex, and red part of color

labelValueI

JLabel labelValueI
Used for imaginary part of complex and green part of color

labelValueB

JLabel labelValueB
Used for blue part of color

mathAlgo

AlgorithmImageMath mathAlgo
DOCUMENT ME!

opType

int opType
DOCUMENT ME!

outputPanel

JPanelAlgorithmOutputOptions outputPanel
DOCUMENT ME!

radioClip

JRadioButton radioClip
DOCUMENT ME!

radioPromote

JRadioButton radioPromote
DOCUMENT ME!

radioFloat

JRadioButton radioFloat
DOCUMENT ME!

realValue

double realValue
DOCUMENT ME!

resultImage

ModelImage resultImage
result image.

textValue

JTextField textValue
Used for single value, real part of complex, and red part of color

textValueI

JTextField textValueI
Use for imaginary part of complex and green part of color

textValueB

JTextField textValueB
Used for blue part of color

titles

String[] titles
DOCUMENT ME!

useComplex

boolean useComplex
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogInitialCentroids extends JDialogBase implements Serializable

serialVersionUID: -7070007899490674843L

Serialized Fields

centroids

float[] centroids
DOCUMENT ME!

defaultValueInput

JTextField[] defaultValueInput
DOCUMENT ME!

gbc

GridBagConstraints gbc
DOCUMENT ME!

gbl

GridBagLayout gbl
DOCUMENT ME!

i

int i
DOCUMENT ME!

minimum

float minimum
DOCUMENT ME!

maximum

float maximum
DOCUMENT ME!

nClasses

int nClasses
DOCUMENT ME!

tmpStr

String tmpStr
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogInsertMissingSlices extends JDialogScriptableBase implements Serializable

serialVersionUID: -5205189127854148892L

Serialized Fields

allPresent

boolean allPresent
true if no slices are missing.

average

JRadioButton average
Radio button selected if inserted slices are a weighted average of surrounding slices.

blank

JRadioButton blank
Radio button selected if inserted slices are blank.

checkListInsert

boolean[] checkListInsert
Array of length totalSlices, false where slice is already present, true where slice must be inserted.

destFlag

boolean destFlag
DOCUMENT ME!

destinationGroup

ButtonGroup destinationGroup
DOCUMENT ME!

displayLoc

int displayLoc
Flag indicating if a new image is to be generated.

image

ModelImage image
source image.

insertBlank

boolean insertBlank
If true insert blank slices, if false insert weighted average slices.

missingNumberArray

int[] missingNumberArray
DOCUMENT ME!

missingPositions

int missingPositions
DOCUMENT ME!

missingSliceArray

int[] missingSliceArray
DOCUMENT ME!

missingSlices

int missingSlices
DOCUMENT ME!

newImage

JRadioButton newImage
DOCUMENT ME!

nSlices

int nSlices
Number of slices in original 3D image.

replaceImage

JRadioButton replaceImage
DOCUMENT ME!

resultImage

ModelImage resultImage
image create if new image button is selected.

rSliceAlgo

AlgorithmReplaceRemovedSlices rSliceAlgo
DOCUMENT ME!

totalSlices

int totalSlices
Number of slices that will be present in the 3D image after the missing slices have been inserted.

Class gov.nih.mipav.view.dialogs.JDialogInsertSlice extends JDialogScriptableBase implements Serializable

serialVersionUID: 7157371462824445245L

Serialized Fields

adjacentDown

JRadioButton adjacentDown
DOCUMENT ME!

adjacentUp

JRadioButton adjacentUp
DOCUMENT ME!

average

JRadioButton average
DOCUMENT ME!

blank

JRadioButton blank
DOCUMENT ME!

comboBoxImage

JComboBox comboBoxImage
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

insertedImage

ModelImage insertedImage
DOCUMENT ME!

insertSlice

int insertSlice
DOCUMENT ME!

insertSliceAlgo

AlgorithmInsertSlice insertSliceAlgo
DOCUMENT ME!

nSlices

int nSlices
DOCUMENT ME!

original

JRadioButton original
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

sliceType

int sliceType
DOCUMENT ME!

textSlice

JTextField textSlice
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogInstallPlugin extends JDialogBase implements Serializable

serialVersionUID: -8736744495208652866L

Serialized Fields

browseButton

JButton browseButton
DOCUMENT ME!

files

Vector<E> files
DOCUMENT ME!

pluginDir

String pluginDir
DOCUMENT ME!

textName

JTextField textName
DOCUMENT ME!

ui

ViewUserInterface ui
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogIntensityPaint extends JDialogBase implements Serializable

serialVersionUID: -736880761566398344L

Serialized Fields

inputLabel

JLabel inputLabel
DOCUMENT ME!

inputText

JTextField inputText
DOCUMENT ME!

intensityDouble

double intensityDouble
DOCUMENT ME!

intensityStringValue

String intensityStringValue
DOCUMENT ME!

outMax

double outMax
DOCUMENT ME!

outMin

double outMin
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogIntensityThreshold extends JDialogBase implements Serializable

serialVersionUID: 988706874933899996L

Serialized Fields

component

ViewJComponentEditImage component
DOCUMENT ME!

doAverage

boolean doAverage
DOCUMENT ME!

threshField

JTextField threshField
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogInvert extends JDialogScriptableBase implements Serializable

serialVersionUID: 6770504320836953902L

Serialized Fields

changeTypeAlgo

AlgorithmChangeType changeTypeAlgo
DOCUMENT ME!

dataType

int dataType
DOCUMENT ME!

displayLoc

int displayLoc
DOCUMENT ME!

endianess

boolean endianess
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

inTempMin

double inTempMin
DOCUMENT ME!

inTempMax

double inTempMax
DOCUMENT ME!

newImage

JRadioButton newImage
DOCUMENT ME!

outTempMin

double outTempMin
DOCUMENT ME!

outTempMax

double outTempMax
DOCUMENT ME!

replaceImage

JRadioButton replaceImage
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogItkFilter extends JDialogScriptableBase implements Serializable

serialVersionUID: -4057161307906161677L

Serialized Fields

m_itkFilterAlgo

AlgorithmItkFilter m_itkFilterAlgo
filter algorithm

m_itkFilter2D

PItkFilter m_itkFilter2D
itk filter container, 2D

m_itkFilter3D

PItkFilter m_itkFilter3D
itk filter container, 3D

m_srcImage

ModelImage m_srcImage
source image

m_resultImage

ModelImage m_resultImage
result image

m_image25D

boolean m_image25D
flag indicating if slices should be blurred independently

m_filterParamPanel

JPanelItkFilterParams m_filterParamPanel
widgets for all the filter's parameters.

m_colorChannelPanel

JPanelColorChannels m_colorChannelPanel
Which color channels to filter

m_outputOptionsPanel

JPanelAlgorithmOutputOptions m_outputOptionsPanel
new image or replace current, option to apply algorithm only to VOI regions.

m_titles

String[] m_titles
saved window titles

m_userInterface

ViewUserInterface m_userInterface
UI to hang from

Class gov.nih.mipav.view.dialogs.JDialogLaplacian extends JDialogScriptableBase implements Serializable

serialVersionUID: 2631054897246586311L

Serialized Fields

ampFactor

float ampFactor
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

image25D

boolean image25D
DOCUMENT ME!

image25DCheckbox

JCheckBox image25DCheckbox
DOCUMENT ME!

labelAmpFact

JLabel labelAmpFact
DOCUMENT ME!

laplacianAlgo

AlgorithmLaplacian laplacianAlgo
DOCUMENT ME!

outputPanel

JPanelAlgorithmOutputOptions outputPanel
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

sigmasPanel

JPanelSigmas sigmasPanel
DOCUMENT ME!

textAmpFact

JTextField textAmpFact
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogLevelSet extends JDialogBase implements Serializable

serialVersionUID: -1593443884995027289L

Serialized Fields

image25D

boolean image25D
Flag indicating if slices should be blurred independently.

image25DCheckbox

JCheckBox image25DCheckbox
DOCUMENT ME!

contractButton

JRadioButton contractButton
DOCUMENT ME!

deltaT

float deltaT
DOCUMENT ME!

edgeAttract

float edgeAttract
DOCUMENT ME!

epsilon

float epsilon
DOCUMENT ME!

expandButton

JRadioButton expandButton
DOCUMENT ME!

expandContractButton

JRadioButton expandContractButton
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

iters

int iters
DOCUMENT ME!

itersCheckBox

JCheckBox itersCheckBox
DOCUMENT ME!

label3D

JLabel label3D
difference between x,y resolutions (in plane) and z resolution (between planes).

labelCorrected

JLabel labelCorrected
DOCUMENT ME!

labelDeltaT

JLabel labelDeltaT
DOCUMENT ME!

labelEdgeAttract

JLabel labelEdgeAttract
DOCUMENT ME!

labelEpsilon

JLabel labelEpsilon
DOCUMENT ME!

labelGaussX

JLabel labelGaussX
DOCUMENT ME!

labelGaussY

JLabel labelGaussY
DOCUMENT ME!

labelGaussZ

JLabel labelGaussZ
DOCUMENT ME!

labelIters

JLabel labelIters
DOCUMENT ME!

labelTestIters

JLabel labelTestIters
DOCUMENT ME!

levelSetAlgo

AlgorithmLevelSet levelSetAlgo
DOCUMENT ME!

movement

int movement
DOCUMENT ME!

movementGroup

ButtonGroup movementGroup
DOCUMENT ME!

normFactor

float normFactor
DOCUMENT ME!

paintMask

BitSet paintMask
DOCUMENT ME!

resolutionCheckbox

JCheckBox resolutionCheckbox
DOCUMENT ME!

scaleX

float scaleX
DOCUMENT ME!

scaleY

float scaleY
DOCUMENT ME!

scaleZ

float scaleZ
DOCUMENT ME!

testIters

int testIters
DOCUMENT ME!

textDeltaT

JTextField textDeltaT
DOCUMENT ME!

textEdgeAttract

JTextField textEdgeAttract
DOCUMENT ME!

textEpsilon

JTextField textEpsilon
DOCUMENT ME!

textGaussX

JTextField textGaussX
DOCUMENT ME!

textGaussY

JTextField textGaussY
DOCUMENT ME!

textGaussZ

JTextField textGaussZ
DOCUMENT ME!

textIters

JTextField textIters
DOCUMENT ME!

textTestIters

JTextField textTestIters
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogLevelSetDiffusion extends JDialogBase implements Serializable

serialVersionUID: -6530047904436344937L

Serialized Fields

image25D

boolean image25D
Flag indicating if slices should be blurred independently.

image25DCheckbox

JCheckBox image25DCheckbox
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

iters

int iters
DOCUMENT ME!

kValue

float kValue
DOCUMENT ME!

labelCorrected

JLabel labelCorrected
DOCUMENT ME!

labelGaussX

JLabel labelGaussX
DOCUMENT ME!

labelGaussY

JLabel labelGaussY
DOCUMENT ME!

labelGaussZ

JLabel labelGaussZ
DOCUMENT ME!

labelIters

JLabel labelIters
DOCUMENT ME!

labelK

JLabel labelK
DOCUMENT ME!

levelSetAlgo

AlgorithmLevelSetDiffusion levelSetAlgo
DOCUMENT ME!

normFactor

float normFactor
DOCUMENT ME!

paintMask

BitSet paintMask
DOCUMENT ME!

resolutionCheckbox

JCheckBox resolutionCheckbox
DOCUMENT ME!

scaleX

float scaleX
DOCUMENT ME!

scaleY

float scaleY
DOCUMENT ME!

scaleZ

float scaleZ
DOCUMENT ME!

textGaussX

JTextField textGaussX
DOCUMENT ME!

textGaussY

JTextField textGaussY
DOCUMENT ME!

textGaussZ

JTextField textGaussZ
DOCUMENT ME!

textIters

JTextField textIters
difference between x,y resolutions (in plane) and z resolution (between planes).

textK

JTextField textK
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogLightBox extends JDialogBase implements Serializable

serialVersionUID: -4983517621211045288L

Serialized Fields

bgColor

Color bgColor
DOCUMENT ME!

borderB

JButton borderB
DOCUMENT ME!

backgroundB

JButton backgroundB
DOCUMENT ME!

borderColor

Color borderColor
DOCUMENT ME!

borderSize

int borderSize
DOCUMENT ME!

bordersizeL

JLabel bordersizeL
DOCUMENT ME!

bordersizeText

JTextField bordersizeText
DOCUMENT ME!

incrementText

JTextField incrementText

incrementLabel

JLabel incrementLabel

increment

int increment

lastIncrement

int lastIncrement

col

int col
DOCUMENT ME!

colLabel

JLabel colLabel
DOCUMENT ME!

colorChooser

ViewJColorChooser colorChooser
DOCUMENT ME!

colorPanel

JPanel colorPanel
DOCUMENT ME!

colPanel

JPanel colPanel
DOCUMENT ME!

colText

JTextField colText
DOCUMENT ME!

font12

Font font12
DOCUMENT ME!

font12B

Font font12B
DOCUMENT ME!

frame

ViewJFrameLightBox frame
DOCUMENT ME!

gridSize

int gridSize
DOCUMENT ME!

gridsizeL

JLabel gridsizeL
DOCUMENT ME!

gridsizeText

JTextField gridsizeText
DOCUMENT ME!

lastBgColor

Color lastBgColor
DOCUMENT ME!

lastBorderColor

Color lastBorderColor
DOCUMENT ME!

lastBorderSize

int lastBorderSize
DOCUMENT ME!

lastCol

int lastCol
DOCUMENT ME!

lastGridSize

int lastGridSize
DOCUMENT ME!

lastMagnification

float lastMagnification
DOCUMENT ME!

lastRow

int lastRow
DOCUMENT ME!

lastRowBFlag

boolean lastRowBFlag
DOCUMENT ME!

lastTSlice

int lastTSlice
DOCUMENT ME!

magnification

float magnification
DOCUMENT ME!

magniWindow

JWindow magniWindow
DOCUMENT ME!

magSlider

JSlider magSlider
DOCUMENT ME!

magSliderDictionary

Hashtable<K,V> magSliderDictionary
DOCUMENT ME!

magSliderPanel

JPanel magSliderPanel
DOCUMENT ME!

panelRowColumn

JPanel panelRowColumn
DOCUMENT ME!

radioColumn

JRadioButton radioColumn
DOCUMENT ME!

radioRow

JRadioButton radioRow
DOCUMENT ME!

resetButton

JButton resetButton
DOCUMENT ME!

row

int row
DOCUMENT ME!

row_dependent

boolean row_dependent
DOCUMENT ME!

rowBFlag

boolean rowBFlag
values obtained from settings.

rowLabel

JLabel rowLabel
DOCUMENT ME!

rowPanel

JPanel rowPanel
DOCUMENT ME!

rowText

JTextField rowText
DOCUMENT ME!

toolTip

JLabel toolTip
DOCUMENT ME!

tSlice

int tSlice
DOCUMENT ME!

tSlider

JSlider tSlider
DOCUMENT ME!

tSliderDictionary

Hashtable<K,V> tSliderDictionary
DOCUMENT ME!

tSliderPanel

JPanel tSliderPanel
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogListSaveSelection extends JDialogBase implements Serializable

serialVersionUID: -5740263457469223226L

Serialized Fields

selectFileA

JPanelFileSelection selectFileA
Indicates the source file for list A. The Default property name given to this file selector is "SelectFileA"

selectFileB

JPanelFileSelection selectFileB
Indicates the source file for list B. The Default property name given to this file selector is "SelectFileB"

selector

JDialogListSaveSelection.JPanelListSelection selector
Allows the user to modify listB based on either the file provided in selectFileA or selectFileB.

selectedList

JList selectedList
List of selected VOIs.

sourceList

JList sourceList
List of available VOIs.

Class gov.nih.mipav.view.dialogs.JDialogListSaveSelection.JPanelListSelection extends JPanelListController implements Serializable

serialVersionUID: -4660560256657187754L

Serialized Fields

comp

JDialogListSaveSelection.TagComparator comp
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogLivewire extends JDialogBase implements Serializable

serialVersionUID: -5986380794955471822L

Serialized Fields

radioGradient

JRadioButton radioGradient
DOCUMENT ME!

radioIntensity

JRadioButton radioIntensity
DOCUMENT ME!

radioMedial

JRadioButton radioMedial
DOCUMENT ME!

selection

int selection
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogLoadImage extends JDialogScriptableBase implements Serializable

serialVersionUID: -8455082719816268161L

Serialized Fields

browseButton

JButton browseButton
DOCUMENT ME!

dataType

int dataType
If blank image is to be loaded...need the type (for non-color images).

doOrigins

boolean doOrigins
DOCUMENT ME!

doOrients

boolean doOrients
DOCUMENT ME!

image

ModelImage image
Source image.

imageChooser

JComboBox imageChooser
DOCUMENT ME!

importImage

ModelImage importImage
image taken from the frame to be imported:.

importLUT

ModelLUT importLUT

importRGB

ModelRGB importRGB

loadType

int loadType
are we loading from frame, file, or blank.

matchOrigins

JCheckBox matchOrigins
DOCUMENT ME!

matchOrients

JCheckBox matchOrients
DOCUMENT ME!

picListingPanel

JPanel picListingPanel
DOCUMENT ME!

radioBool

JRadioButton radioBool
DOCUMENT ME!

radioByte

JRadioButton radioByte
DOCUMENT ME!

radioDouble

JRadioButton radioDouble
DOCUMENT ME!

radioFloat

JRadioButton radioFloat
DOCUMENT ME!

radioInt

JRadioButton radioInt
DOCUMENT ME!

radioLong

JRadioButton radioLong
DOCUMENT ME!

radioShort

JRadioButton radioShort
DOCUMENT ME!

radioUByte

JRadioButton radioUByte
DOCUMENT ME!

radioUInt

JRadioButton radioUInt
DOCUMENT ME!

radioUShort

JRadioButton radioUShort
DOCUMENT ME!

resultImage

ModelImage resultImage
a cloned version of importImage that will be inserted into the source images's B slot.

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogLoadImageForRegistration extends JDialogBase implements Serializable

serialVersionUID: 3843075015237096037L

Serialized Fields

browseButton

JButton browseButton
DOCUMENT ME!

directory

String directory
DOCUMENT ME!

fileButton

JRadioButton fileButton
DOCUMENT ME!

fileName

String fileName
DOCUMENT ME!

fileTFld

JTextField fileTFld
DOCUMENT ME!

frameButton

JRadioButton frameButton
DOCUMENT ME!

imageA

ModelImage imageA
DOCUMENT ME!

imageChooser

JComboBox imageChooser
DOCUMENT ME!

importImage

ModelImage importImage
image taken from the frame to be imported:.

isFrame

boolean isFrame
DOCUMENT ME!

LUTb

ModelLUT LUTb
DOCUMENT ME!

masterImage

ViewJFrameImage masterImage
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogLoadLeica extends JDialogBase implements Serializable

serialVersionUID: 5662541302525039992L

Serialized Fields

headerFile

File headerFile
DOCUMENT ME!

scrollPane

JScrollPane scrollPane
DOCUMENT ME!

seriesList

JList seriesList
DOCUMENT ME!

successful

boolean successful
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogLoadLeica.LeicaSeries extends JComponent implements Serializable

serialVersionUID: 1101169071873919736L

Serialized Fields

channels

int[] channels
DOCUMENT ME!

extents

int[] extents
DOCUMENT ME!

fileNames

Vector<E> fileNames
DOCUMENT ME!

numImages

int numImages
DOCUMENT ME!

resolutions

float[] resolutions
DOCUMENT ME!

seriesName

String seriesName
DOCUMENT ME!

description

String description
DOCUMENT ME!

units

int[] units
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogLocalNormalization extends JDialogScriptableBase implements Serializable

serialVersionUID: 4460969182116331919L

Serialized Fields

algoLocal

AlgorithmLocalNormalization algoLocal
DOCUMENT ME!

blurringDiameter

int blurringDiameter
DOCUMENT ME!

blurringDiameterText

JTextField blurringDiameterText
DOCUMENT ME!

blurringFreq

float blurringFreq
user-selectable variables used in the FFT-blurring operation used as interim variables in starting the algorithm op.

blurringFreqText

JTextField blurringFreqText
DOCUMENT ME!

colorPanel

JPanelColorChannels colorPanel
DOCUMENT ME!

displayLoc

int displayLoc
DOCUMENT ME!

errorComponent

JTextField errorComponent
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

sourceImage

ModelImage sourceImage
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

unsharp

float[] unsharp
user-selectable variables used in the unsharping operation. used as interim variables in starting the algorithm op.

unsharpWeight

float unsharpWeight
DOCUMENT ME!

unsharpWeightText

JTextField unsharpWeightText
DOCUMENT ME!

unsharpXtext

JTextField unsharpXtext
DOCUMENT ME!

unsharpYtext

JTextField unsharpYtext
DOCUMENT ME!

unsharpZtext

JTextField unsharpZtext
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogMagnificationControls extends JDialogBase implements Serializable

serialVersionUID: 2838490243455666340L

Serialized Fields

box_width

int box_width
DOCUMENT ME!

componentImage

ViewJComponentEditImage componentImage
DOCUMENT ME!

current

JLabel current
DOCUMENT ME!

intensityCheckbox

JCheckBox intensityCheckbox
DOCUMENT ME!

magSlider

JSlider magSlider
DOCUMENT ME!

max

int max
DOCUMENT ME!

min

int min
DOCUMENT ME!

widthText

JTextField widthText
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogMask extends JDialogScriptableBase implements Serializable

serialVersionUID: 7339956453691640420L

Serialized Fields

displayLoc

int displayLoc
DOCUMENT ME!

exteriorFill

JRadioButton exteriorFill
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

interiorFill

JRadioButton interiorFill
DOCUMENT ME!

maskAlgo

AlgorithmMask maskAlgo
DOCUMENT ME!

max

double max
DOCUMENT ME!

min

double min
DOCUMENT ME!

newImage

JRadioButton newImage
DOCUMENT ME!

polarity

boolean polarity
or if the source image is to be replaced.

replaceImage

JRadioButton replaceImage
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

textValue

JTextField textValue
DOCUMENT ME!

textValueB

JTextField textValueB
DOCUMENT ME!

textValueG

JTextField textValueG
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

value

float value
DOCUMENT ME!

valueB

float valueB
DOCUMENT ME!

valueG

float valueG
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogMask3D4D extends JDialogBase implements Serializable

serialVersionUID: 7339956453691640420L

Serialized Fields

threeD

JRadioButton threeD
Radio button indicating that the image should only be masked in 3D

fourD

JRadioButton fourD
Radio button indicating that the image should be masked in 4D

saveMasksAs4D

boolean saveMasksAs4D

Class gov.nih.mipav.view.dialogs.JDialogMatchImages extends JDialogScriptableBase implements Serializable

serialVersionUID: -4508090288311270016L

Serialized Fields

checkOrigins

JCheckBox checkOrigins
DOCUMENT ME!

checkDimensions

JCheckBox checkDimensions
DOCUMENT ME!

comboBoxImageA

JComboBox comboBoxImageA
DOCUMENT ME!

comboBoxImageB

JComboBox comboBoxImageB
DOCUMENT ME!

doOrigins

boolean doOrigins
DOCUMENT ME!

doDimensions

boolean doDimensions
DOCUMENT ME!

imageA

ModelImage imageA
DOCUMENT ME!

imageB

ModelImage imageB
DOCUMENT ME!

matchAlgo

AlgorithmMatchImages matchAlgo
DOCUMENT ME!

padValTxt

JTextField padValTxt
DOCUMENT ME!

padValue

int padValue
DOCUMENT ME!

resultImageA

ModelImage resultImageA
DOCUMENT ME!

resultImageB

ModelImage resultImageB
DOCUMENT ME!

selectedNameA

String selectedNameA
DOCUMENT ME!

selectedNameB

String selectedNameB
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogMaximumIntensityProjection extends JDialogScriptableBase implements Serializable

serialVersionUID: -586175799570928868L

Serialized Fields

image

ModelImage image
Source Image.

borderSize

int borderSize
Dialog border size

minInput

JTextField minInput
Jtextfield for minimum value of threshold.

maxInput

JTextField maxInput
Jtextfield for maximum value of threshold.

minIntensity

float minIntensity
Minimum intensity.

maxIntensity

float maxIntensity
Maximum intensity.

minInputR

JTextField minInputR

maxInputR

JTextField maxInputR

minInputG

JTextField minInputG

maxInputG

JTextField maxInputG

minInputB

JTextField minInputB

maxInputB

JTextField maxInputB

minIntensityR

float minIntensityR

maxIntensityR

float maxIntensityR

minIntensityG

float minIntensityG

maxIntensityG

float maxIntensityG

minIntensityB

float minIntensityB

maxIntensityB

float maxIntensityB

mipAlgo

AlgorithmMaximumIntensityProjection mipAlgo
Algorithm instance.

Class gov.nih.mipav.view.dialogs.JDialogMaximumLikelihoodIteratedBlindDeconvolution extends JDialogScriptableBase implements Serializable

serialVersionUID: 7390265931793649147L

Serialized Fields

ibdAlgor

AlgorithmMaximumLikelihoodIteratedBlindDeconvolution ibdAlgor
The MaximumLikelihood Blind Deconvolution algorithm:

numberIterations

int numberIterations
The number of iterations for calculating the deconvolution:

showProgress

int showProgress
Display the deconvolved image every X images to show progress:

objectiveNumericalAperature

float objectiveNumericalAperature
The object numerical aperature, a property of the lens used to image the sample:

wavelength

float wavelength
The reflected or fluorescence wavelength of the sample:

refractiveIndex

float refractiveIndex
The index of refraction of the sample:

useMicroscopeSettings

boolean useMicroscopeSettings
When true the lens NA, wavelength, and refractive index are used in the deconvolution process

originalImage

ModelImage originalImage
The original data image to be reconstructed:

extents

int[] extents
The extents of original image

dim

int dim
Number of dimensions in an image e.g 2D, 3D

newExtents

int[] newExtents
The extents of transformed (to the power of 2) image

doResample

boolean doResample
The boolean value to determine whether to resample the original image or not.

textNumberIterations

JTextField textNumberIterations
User-Interface for entering the number of deconvolution iterations:

textShowProgress

JTextField textShowProgress
User-Interface for entering the number of intermediate images to show:

textObjectiveNumericalAperature

JTextField textObjectiveNumericalAperature
User-Interface for entering the objective numerical aperature:

textWavelength

JTextField textWavelength
User-Interface for entering the sample wavelength:

textRefractiveIndex

JTextField textRefractiveIndex
User-Interface for entering the index of refraction:

textOriginalExtentX

JTextField textOriginalExtentX
User-Interface for displaying the original extent X

textOriginalExtentY

JTextField textOriginalExtentY
User-Interface for displaying the original extent Y

textOriginalExtentZ

JTextField textOriginalExtentZ
User-Interface for displaying the original extent Z

textExpectedExtentX

JTextField textExpectedExtentX
User-Interface for entering the expected extent X

textExpectedExtentY

JTextField textExpectedExtentY
User-Interface for entering the expected extent Y

textExpectedExtentZ

JTextField textExpectedExtentZ
User-Interface for entering the expected extent Z

Class gov.nih.mipav.view.dialogs.JDialogMean extends JDialogScriptableBase implements Serializable

serialVersionUID: -5373013772234532691L

Serialized Fields

adaptiveVectorButton

JRadioButton adaptiveVectorButton
DOCUMENT ME!

blue

boolean blue
DOCUMENT ME!

blueChannel

JCheckBox blueChannel
DOCUMENT ME!

blueLabel

JLabel blueLabel
DOCUMENT ME!

blueText

JTextField blueText
DOCUMENT ME!

blueVector

int blueVector
DOCUMENT ME!

bySlice

JRadioButton bySlice
DOCUMENT ME!

comboBoxKernelSize

JComboBox comboBoxKernelSize
DOCUMENT ME!

filterType

int filterType
DOCUMENT ME!

green

boolean green
DOCUMENT ME!

greenChannel

JCheckBox greenChannel
DOCUMENT ME!

greenLabel

JLabel greenLabel
DOCUMENT ME!

greenText

JTextField greenText
DOCUMENT ME!

greenVector

int greenVector
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

image25D

boolean image25D
false = apply algorithm only to VOI regions.

kernelSize

int kernelSize
DOCUMENT ME!

meanAlgo

AlgorithmMean meanAlgo
DOCUMENT ME!

outputPanel

JPanelAlgorithmOutputOptions outputPanel
DOCUMENT ME!

parallelVectorButton

JRadioButton parallelVectorButton
DOCUMENT ME!

red

boolean red
DOCUMENT ME!

redChannel

JCheckBox redChannel
DOCUMENT ME!

redLabel

JLabel redLabel
DOCUMENT ME!

redText

JTextField redText
DOCUMENT ME!

redVector

int redVector
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

separateButton

JRadioButton separateButton
DOCUMENT ME!

separateVectorGroup

ButtonGroup separateVectorGroup
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

wholeVolume

JRadioButton wholeVolume
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogMedian extends JDialogScriptableBase implements Serializable

serialVersionUID: -7749097890204237664L

Serialized Fields

adaptiveSize

boolean adaptiveSize
DOCUMENT ME!

adaptiveSizeBox

JCheckBox adaptiveSizeBox
DOCUMENT ME!

blue

boolean blue
DOCUMENT ME!

blueChannel

JCheckBox blueChannel
DOCUMENT ME!

bySlice

JRadioButton bySlice
DOCUMENT ME!

comboBoxKernelShape

JComboBox comboBoxKernelShape
DOCUMENT ME!

comboBoxKernelSize

JComboBox comboBoxKernelSize
DOCUMENT ME!

comboBoxMaximumSize

JComboBox comboBoxMaximumSize
DOCUMENT ME!

componentButton

JRadioButton componentButton
DOCUMENT ME!

filterType

int filterType
DOCUMENT ME!

green

boolean green
DOCUMENT ME!

greenChannel

JCheckBox greenChannel
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

image25D

boolean image25D
false = apply algorithm only to VOI regions.

iters

int iters
DOCUMENT ME!

kernelShape

int kernelShape
DOCUMENT ME!

kernelSize

int kernelSize
DOCUMENT ME!

labelMaximumSize

JLabel labelMaximumSize
DOCUMENT ME!

labelSTDDeviation

JLabel labelSTDDeviation
DOCUMENT ME!

maximumSize

int maximumSize
DOCUMENT ME!

medianAlgo

AlgorithmMedian medianAlgo
DOCUMENT ME!

outputPanel

JPanelAlgorithmOutputOptions outputPanel
DOCUMENT ME!

red

boolean red
DOCUMENT ME!

redChannel

JCheckBox redChannel
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

stdDev

float stdDev
DOCUMENT ME!

textNIter

JTextField textNIter
DOCUMENT ME!

textSTDDeviation

JTextField textSTDDeviation
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

vectorDirectionButton

JRadioButton vectorDirectionButton
DOCUMENT ME!

vectorGroup

ButtonGroup vectorGroup
DOCUMENT ME!

vectorMagnitudeButton

JRadioButton vectorMagnitudeButton
DOCUMENT ME!

wholeVolume

JRadioButton wholeVolume
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogMemoryAllocation extends JDialogBase implements Serializable

serialVersionUID: -1470759041555523857L

Serialized Fields

filename

String filename
filename based on the application name: mipav.lax or iaso.lax.

fileType

String fileType
DOCUMENT ME!

initHeapText

JTextField initHeapText
DOCUMENT ME!

laxContents

Vector<E> laxContents
DOCUMENT ME!

maxHeapText

JTextField maxHeapText
DOCUMENT ME!

startupFile

File startupFile
Contains all java properties of the MIPAV app (used at least when loading!)

usePreferencesButton

JButton usePreferencesButton
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogMidsagittal extends JDialogScriptableBase implements Serializable

serialVersionUID: -2594860465921132823L

Serialized Fields

alignAlgo

AlgorithmMidsagittal alignAlgo
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogMipavOptions extends JDialogBase implements Serializable

serialVersionUID: 6756915900242085699L

Serialized Fields

labels

JLabel[] labels
DOCUMENT ME!

activeColor

JButton activeColor
DOCUMENT ME!

checkOnFrameClose

JCheckBox checkOnFrameClose
DOCUMENT ME!

colorChooser

JColorChooser colorChooser
DOCUMENT ME!

crosshairChoices

JComboBox crosshairChoices
DOCUMENT ME!

crosshairNames

String[] crosshairNames
DOCUMENT ME!

debugAlgorithmBox

JCheckBox debugAlgorithmBox
DOCUMENT ME!

debugCommsBox

JCheckBox debugCommsBox
DOCUMENT ME!

multiThreadingEnabledCheckBox

JCheckBox multiThreadingEnabledCheckBox
Multi-Threading Enabled Check Box

debugFileIOBox

JCheckBox debugFileIOBox
DOCUMENT ME!

debugMinorBox

JCheckBox debugMinorBox
DOCUMENT ME!

debugScriptingBox

JCheckBox debugScriptingBox

dicomCatcher

JCheckBox dicomCatcher
DOCUMENT ME!

displayColorPanel

JPanel displayColorPanel
DOCUMENT ME!

displayPanel

JPanel displayPanel
MIPAV global options private JPanel globalChangesPanel;.

displaySplash

JCheckBox displaySplash
DOCUMENT ME!

displayUserInterfacePanel

JPanel displayUserInterfacePanel
DOCUMENT ME!

enableLoggingBox

JCheckBox enableLoggingBox
DOCUMENT ME!

fileFilter

int fileFilter
DOCUMENT ME!

fileMiscPanel

JPanel fileMiscPanel
DOCUMENT ME!

filePanel

JPanel filePanel
DOCUMENT ME!

fileSavePanel

JPanel fileSavePanel
DOCUMENT ME!

filterButton

JButton filterButton
DOCUMENT ME!

editUserDefButton

JButton editUserDefButton
Button to lasunch the Edit User Defined File Types Dialog

fontChooser

JComboBox fontChooser
DOCUMENT ME!

fontNames

String[] fontNames
DOCUMENT ME!

fontSizeField

JTextField fontSizeField
DOCUMENT ME!

frameRateField

JTextField frameRateField
DOCUMENT ME!

imageChooser

JComboBox imageChooser
DOCUMENT ME!

logFileButton

JButton logFileButton
DOCUMENT ME!

logFilename

String logFilename
DOCUMENT ME!

provenanceCheckBox

JCheckBox provenanceCheckBox
DOCUMENT ME!

provenanceFilename

String provenanceFilename

provenanceFileButton

JButton provenanceFileButton

provenanceImageCheckBox

JCheckBox provenanceImageCheckBox

otherPanel

JPanel otherPanel
DOCUMENT ME!

performLaxCheck

JCheckBox performLaxCheck
DOCUMENT ME!

pointVOIChoices

JComboBox pointVOIChoices
DOCUMENT ME!

preferredActiveColor

Color preferredActiveColor
DOCUMENT ME!

preferredCrosshair

String preferredCrosshair
DOCUMENT ME!

quickListLevel

JComboBox quickListLevel
DOCUMENT ME!

saveAllCheckBox

JCheckBox saveAllCheckBox
DOCUMENT ME!

saveDefaultsCheckBox

JCheckBox saveDefaultsCheckBox
DOCUMENT ME!

saveLabel

JLabel saveLabel
Label before combBoxSaveMethod

comboBoxSaveImgMethod

JComboBox comboBoxSaveImgMethod
Whether to save .img files as selected by dialog or always as analyze, interfile, or nifti.

comboBoxSaveMncMethod

JComboBox comboBoxSaveMncMethod
Whether to save .mnc files as selected by dialog or always as minc1 or minc2.

savePromptOverwriteBox

JCheckBox savePromptOverwriteBox
DOCUMENT ME!

saveThumbnailCheckBox

JCheckBox saveThumbnailCheckBox
DOCUMENT ME!

saveXMLOnHDRSaveCheckBox

JCheckBox saveXMLOnHDRSaveCheckBox
DOCUMENT ME!

fileTempDirField

JTextField fileTempDirField

fileTempDirBrowseButton

JButton fileTempDirBrowseButton

showLineVOIAngleBox

JCheckBox showLineVOIAngleBox
DOCUMENT ME!

continuousVOIBox

JCheckBox continuousVOIBox

saveVOILPSBox

JCheckBox saveVOILPSBox

showOutputWindow

JCheckBox showOutputWindow
DOCUMENT ME!

showPaintBorderBox

JCheckBox showPaintBorderBox
DOCUMENT ME!

tabbedPane

JTabbedPane tabbedPane
DOCUMENT ME!

useAWTBox

JCheckBox useAWTBox
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
ui must be set to access the list of images to set image-specfic options (ie,. log mode)

voiColorChoices

JComboBox voiColorChoices
DOCUMENT ME!

voiColorNames

String[] voiColorNames
DOCUMENT ME!

voiColors

Color[] voiColors
DOCUMENT ME!

voiDrawButton

JButton voiDrawButton
DOCUMENT ME!

intensityLabelColorButton

JButton intensityLabelColorButton
DOCUMENT ME!

intensityLabelBackgroundButton

JButton intensityLabelBackgroundButton
DOCUMENT ME!

voiDrawColor

Color voiDrawColor
DOCUMENT ME!

intensityLabelColor

Color intensityLabelColor
DOCUMENT ME!

intensityLabelBackgroundColor

Color intensityLabelBackgroundColor
DOCUMENT ME!

srbPanel

JPanel srbPanel

srbVersionComboBox

JComboBox srbVersionComboBox

srbTransferModeComboBox

JComboBox srbTransferModeComboBox

srbBaseTempDirField

JTextField srbBaseTempDirField

srbTempDirBrowseButton

JButton srbTempDirBrowseButton

Class gov.nih.mipav.view.dialogs.JDialogMode extends JDialogScriptableBase implements Serializable

serialVersionUID: 4183545541629455949L

Serialized Fields

bySlice

JRadioButton bySlice
DOCUMENT ME!

comboBoxKernelShape

JComboBox comboBoxKernelShape
DOCUMENT ME!

comboBoxKernelSize

JComboBox comboBoxKernelSize
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

image25D

boolean image25D
DOCUMENT ME!

kernelShape

int kernelShape
DOCUMENT ME!

kernelSize

int kernelSize
DOCUMENT ME!

modeAlgo

AlgorithmMode modeAlgo
DOCUMENT ME!

outputPanel

JPanelAlgorithmOutputOptions outputPanel
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

wholeVolume

JRadioButton wholeVolume
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogMorphologicalFilter extends JDialogScriptableBase implements Serializable

serialVersionUID: -523142924576794921L

Serialized Fields

image

ModelImage image
DOCUMENT ME!

image25D

boolean image25D
DOCUMENT ME!

image25DCheckbox

JCheckBox image25DCheckbox
DOCUMENT ME!

labelSizeX

JLabel labelSizeX
DOCUMENT ME!

labelSizeY

JLabel labelSizeY
DOCUMENT ME!

labelSizeZ

JLabel labelSizeZ
DOCUMENT ME!

mfAlgo

AlgorithmMorphologicalFilter mfAlgo
DOCUMENT ME!

outputPanel

JPanelAlgorithmOutputOptions outputPanel
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

sizePanel

JPanel sizePanel
DOCUMENT ME!

sizeX

int sizeX
DOCUMENT ME!

sizeY

int sizeY
DOCUMENT ME!

sizeZ

int sizeZ
DOCUMENT ME!

textSizeX

JTextField textSizeX
DOCUMENT ME!

textSizeY

JTextField textSizeY
DOCUMENT ME!

textSizeZ

JTextField textSizeZ
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogMRIShadingCorrection extends JDialogScriptableBase implements Serializable

serialVersionUID: 2132712619224805730L

Serialized Fields

destinationGroup

ButtonGroup destinationGroup
DOCUMENT ME!

destinationPanel

JPanel destinationPanel
DOCUMENT ME!

displayLoc

int displayLoc
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

iters

int iters
DOCUMENT ME!

labelGaussX

JLabel labelGaussX
DOCUMENT ME!

labelGaussY

JLabel labelGaussY
DOCUMENT ME!

labelIters

JLabel labelIters
DOCUMENT ME!

labelNorm

JLabel labelNorm
DOCUMENT ME!

mAlgo

AlgorithmMRIShadingCorrection mAlgo
DOCUMENT ME!

newImage

JRadioButton newImage
DOCUMENT ME!

norm

float norm
DOCUMENT ME!

paramPanel

JPanel paramPanel
DOCUMENT ME!

replaceImage

JRadioButton replaceImage
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

scaleX

float scaleX
DOCUMENT ME!

scaleY

float scaleY
DOCUMENT ME!

textGaussX

JTextField textGaussX
DOCUMENT ME!

textGaussY

JTextField textGaussY
DOCUMENT ME!

textIters

JTextField textIters
DOCUMENT ME!

textNorm

JTextField textNorm
DOCUMENT ME!

thresholdCheckbox

JCheckBox thresholdCheckbox
DOCUMENT ME!

thresholdLabel

JLabel thresholdLabel
DOCUMENT ME!

thresholdLevel

float thresholdLevel
DOCUMENT ME!

thresholdSelected

boolean thresholdSelected
DOCUMENT ME!

thresholdText

JTextField thresholdText
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogMSFuzzyCMeans extends JDialogScriptableBase implements Serializable

serialVersionUID: 5469772983205216898L

Serialized Fields

afcmAlgo

AlgorithmMSpectralFuzzyCMeans afcmAlgo
DOCUMENT ME!

centroids

float[] centroids
DOCUMENT ME!

changeRemoveIndex

boolean changeRemoveIndex
DOCUMENT ME!

chooserButton

JButton chooserButton
DOCUMENT ME!

colorPanel

JPanelColorChannels colorPanel
DOCUMENT ME!

cropBackground

boolean cropBackground
DOCUMENT ME!

cropCheckbox

JCheckBox cropCheckbox
DOCUMENT ME!

destExtents

int[] destExtents
DOCUMENT ME!

endTol

float endTol
DOCUMENT ME!

fuzzyOnly

JRadioButton fuzzyOnly
DOCUMENT ME!

hardFuzzyBoth

JRadioButton hardFuzzyBoth
DOCUMENT ME!

hardOnly

JRadioButton hardOnly
DOCUMENT ME!

imageList

JList imageList
DOCUMENT ME!

imagePanel

JPanel imagePanel
DOCUMENT ME!

imageVOIGroup

ButtonGroup imageVOIGroup
DOCUMENT ME!

imageVOIPanel

JPanel imageVOIPanel
DOCUMENT ME!

labelEndTol

JLabel labelEndTol
DOCUMENT ME!

labelExpo

JLabel labelExpo
DOCUMENT ME!

labelJacobi

JLabel labelJacobi
DOCUMENT ME!

labelLoaded

JLabel labelLoaded
DOCUMENT ME!

labelMaxIter

JLabel labelMaxIter
DOCUMENT ME!

labelNClasses

JLabel labelNClasses
DOCUMENT ME!

labelNPyramid

JLabel labelNPyramid
DOCUMENT ME!

labelSmooth

JLabel labelSmooth
DOCUMENT ME!

maxIter

int maxIter
DOCUMENT ME!

model

DefaultListModel model
DOCUMENT ME!

nClasses

int nClasses
DOCUMENT ME!

nPyramid

int nPyramid
DOCUMENT ME!

oneJacobiIter

int oneJacobiIter
DOCUMENT ME!

oneSmooth

float oneSmooth
DOCUMENT ME!

outputGainField

boolean outputGainField
private JCheckBox calcGainFieldCheckbox;.

paramPanel

JPanel paramPanel
DOCUMENT ME!

presentNumber

int presentNumber
DOCUMENT ME!

q

float q
DOCUMENT ME!

regionFlag

boolean regionFlag
DOCUMENT ME!

removeButton

JButton removeButton
DOCUMENT ME!

removeIndex

int removeIndex
DOCUMENT ME!

resultImage

ModelImage[] resultImage
DOCUMENT ME!

resultNumber

int resultNumber
DOCUMENT ME!

segmentation

int segmentation
DOCUMENT ME!

segmentationGroup

ButtonGroup segmentationGroup
DOCUMENT ME!

segmentationPanel

JPanel segmentationPanel
DOCUMENT ME!

srcImage

ModelImage[] srcImage
DOCUMENT ME!

srcNumber

int srcNumber
DOCUMENT ME!

tempImage

ModelImage[] tempImage
DOCUMENT ME!

textEndTol

JTextField textEndTol
DOCUMENT ME!

textExpo

JTextField textExpo
DOCUMENT ME!

textMaxIter

JTextField textMaxIter
DOCUMENT ME!

textNClasses

JTextField textNClasses
DOCUMENT ME!

textNPyramid

JTextField textNPyramid
DOCUMENT ME!

textOneJacobiIter

JTextField textOneJacobiIter
DOCUMENT ME!

textOneSmooth

JTextField textOneSmooth
DOCUMENT ME!

textTwoJacobiIter

JTextField textTwoJacobiIter
DOCUMENT ME!

textTwoSmooth

JTextField textTwoSmooth
DOCUMENT ME!

threshold

float[] threshold
DOCUMENT ME!

twoJacobiIter

int twoJacobiIter
DOCUMENT ME!

twoSmooth

float twoSmooth
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

VOIRegions

JRadioButton VOIRegions
DOCUMENT ME!

wholeImage

JRadioButton wholeImage
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogMultiPaint extends JDialogBase implements Serializable

serialVersionUID: -7497259210728078264L

Serialized Fields

alphaBlend

int alphaBlend
DOCUMENT ME!

triPlanarAlphaBlend

int triPlanarAlphaBlend
DOCUMENT ME!

bottomPanel

JPanel bottomPanel
DOCUMENT ME!

closePanel

JPanel closePanel
DOCUMENT ME!

buttonShortkeys

JToggleButton buttonShortkeys
DOCUMENT ME!

buttonTextArrayList

ArrayList<E> buttonTextArrayList
this is the array list of texts for the mask number buttons.

changeMaskNumberDialog

JDialogChangeMaskNumber changeMaskNumberDialog
Ref to JDialogChangeMaskNumber.*

collapseButton

JButton collapseButton
Button that allows user to collapse masks/paint to single value.*

saveAs3DMaskRadio

JRadioButton saveAs3DMaskRadio
radio buttons for commmiting masks as 3d or 4d if image is 4d

saveAs4DMaskRadio

JRadioButton saveAs4DMaskRadio
radio buttons for commmiting masks as 3d or 4d if image is 4d

radioGroup

ButtonGroup radioGroup
button group for radio buttons

saveMasksAs4D

boolean saveMasksAs4D
this boolean is needed for commiting masks for a 4d image

color

Color[] color
array of colors to use for the labels.

currentOpacity

float currentOpacity
saved opacity parameter when hiding the paint

displayMasksButton

JToggleButton displayMasksButton
display masks toggle button.

displayModeButton

JToggleButton displayModeButton
DOCUMENT ME!

displayPaintButton

JToggleButton displayPaintButton
DOCUMENT ME!

displayPanel

JPanel displayPanel
DOCUMENT ME!

editBox

JCheckBox editBox
DOCUMENT ME!

exportVoiButton

JButton exportVoiButton
button VOI export.

filePanel

JPanel filePanel
DOCUMENT ME!

image

ModelImage image
source image.

imgBSize

int imgBSize
The size, in voxels, of the mask.

importVoiButton

JButton importVoiButton
button VOI import.

indeterminateProgressBar

JProgressBar indeterminateProgressBar
DOCUMENT ME!

intensityLockVector

Vector<E> intensityLockVector
DOCUMENT ME!

label

String[] label
labels for the painted objects.

labelField

JTextField[] labelField
DOCUMENT ME!

listButton

BorderedButton[] listButton
DOCUMENT ME!

listPanel

JPanel listPanel
DOCUMENT ME!

loadDialog

JFileChooser loadDialog
DOCUMENT ME!

loadLabelsButton

JButton loadLabelsButton
DOCUMENT ME!

loadMaskButton

JButton loadMaskButton
DOCUMENT ME!

checkAutosave

JToggleButton checkAutosave

save

gov.nih.mipav.view.dialogs.MultiPaintAutoSave save
DOCUMENT ME!

saver

Timer saver
DOCUMENT ME!

mainPanel

JPanel mainPanel
dialog elements.

maskPanel

JPanel maskPanel
DOCUMENT ME!

miscPanel

JPanel miscPanel
DOCUMENT ME!

multiButton

BorderedButton[] multiButton
DOCUMENT ME!

multiPanel

JPanel multiPanel
DOCUMENT ME!

nbx

int nbx
number of paint masks initially.

nby

int nby
number of paint masks initially.

newSelection

int newSelection
This represents the button the user selects to..initally at 1.*

numberLabel

JLabel numberLabel
DOCUMENT ME!

numberPanel

JPanel numberPanel
DOCUMENT ME!

numberXField

JTextField numberXField
resize x value.

numberYField

JTextField numberYField
resize y value.

optionPanel

JPanel optionPanel
DOCUMENT ME!

preserveBox

JCheckBox[] preserveBox
DOCUMENT ME!

preserved

boolean[] preserved
check whether the mask can be affected by new paint or not.

resizeButton

JButton resizeButton
resize button.

saveDialog

JFileChooser saveDialog
DOCUMENT ME!

saveLabelsButton

JButton saveLabelsButton
save labels button.

saveMaskButton

JButton saveMaskButton
save mask button.

scrollPane

JScrollPane scrollPane
This is the scroll pane for the label list panel.*

selected

int selected
id for the selected paint mask.

userInterface

ViewUserInterface userInterface
private int destExtents[];.

voiPanel

JPanel voiPanel
DOCUMENT ME!

leftPanel

JPanel leftPanel
DOCUMENT ME!

rightPanel

JPanel rightPanel
DOCUMENT ME!

leftRightPanel

JPanel leftRightPanel
DOCUMENT ME!

xDim

int xDim
The mask size in the x dimension.

yDim

int yDim
The mask size in the y dimension.

zDim

int zDim
The mask size in the z dimension.

lockAllButton

JButton lockAllButton
lock all masks checkbox *

unlockAllButton

JButton unlockAllButton
unlock all masks checkbox *

lockPanel

JPanel lockPanel
lock panel

isVisibleMask

boolean isVisibleMask

isVisiblePaint

boolean isVisiblePaint

isCompactDisplay

boolean isCompactDisplay

Class gov.nih.mipav.view.dialogs.JDialogNColors extends JDialogBase implements Serializable

serialVersionUID: -2280005601447558064L

Serialized Fields

field

JTextField field
DOCUMENT ME!

nColors

int nColors
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogNDARGenomics extends JDialogBase implements Serializable

Serialized Fields

privateField

JTextField privateField

irbField

JTextField irbField

abstractTitleField

JTextField abstractTitleField

piNameField

JTextField piNameField

piEmailField

JTextField piEmailField

piPhoneField

JTextField piPhoneField

piTitleField

JTextField piTitleField

abstractArea

WidgetFactory.ScrollTextArea abstractArea
Scrolling text area for abstract

logOutputArea

WidgetFactory.ScrollTextArea logOutputArea
Scrolling text area for log output

metaListPane

JScrollPane metaListPane

rawListPane

JScrollPane rawListPane

metaSourceList

JList metaSourceList

rawSourceList

JList rawSourceList

metaSourceModel

DefaultListModel metaSourceModel

rawSourceModel

DefaultListModel rawSourceModel

nextButton

JButton nextButton

previousButton

JButton previousButton

addMetaSourceButton

JButton addMetaSourceButton

addRawSourceButton

JButton addRawSourceButton

removeSourceButton

JButton removeSourceButton

privateBrowseButton

JButton privateBrowseButton

openAbstractButton

JButton openAbstractButton

publicButton

JRadioButton publicButton

privateButton

JRadioButton privateButton

tabbedPane

JTabbedPane tabbedPane

anonConfirmBox

JCheckBox anonConfirmBox

privacyTextArea

JTextArea privacyTextArea

Class gov.nih.mipav.view.dialogs.JDialogNearlyCircleToCircle extends JDialogBase implements Serializable

serialVersionUID: 0L

Serialized Fields

extents

int[] extents
DOCUMENT ME!

ncAlgo

AlgorithmNearlyCircleToCircle ncAlgo
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

UI

ViewUserInterface UI
DOCUMENT ME!

xDim

int xDim
DOCUMENT ME!

xText

JTextField xText
DOCUMENT ME!

yDim

int yDim
DOCUMENT ME!

yText

JTextField yText
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogNIFTIChoice extends JDialogBase implements Serializable

serialVersionUID: 5469246588202892297L

Serialized Fields

okayPressed

boolean okayPressed
DOCUMENT ME!

oneFile

JRadioButton oneFile
DOCUMENT ME!

twoFiles

JRadioButton twoFiles
DOCUMENT ME!

writeGroup

ButtonGroup writeGroup
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogNLNoiseReduction extends JDialogScriptableBase implements Serializable

serialVersionUID: -6988226818561396907L

Serialized Fields

bt

double bt
DOCUMENT ME!

destinationGroup

ButtonGroup destinationGroup
DOCUMENT ME!

destinationPanel

JPanel destinationPanel
DOCUMENT ME!

displayLoc

int displayLoc
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

image25D

boolean image25D
DOCUMENT ME!

image25DCheckbox

JCheckBox image25DCheckbox
of similar brightness voxels is empty, a local median filter is used. This allows the correction of impulse ("salt-and-pepper") noise. If false, when no neighborhood is found, the original intensity of the voxel of interest remains unchanged.

labelMaskSD

JLabel labelMaskSD
DOCUMENT ME!

labelThreshold

JLabel labelThreshold
DOCUMENT ME!

maskSD

float maskSD
DOCUMENT ME!

maximumThresholdDouble

double maximumThresholdDouble
DOCUMENT ME!

defaultThresholdDouble

double defaultThresholdDouble
DOCUMENT ME!

medianCheckbox

JCheckBox medianCheckbox
The mask is basically Gaussian with standard deviation in image units - e.g. mm set by the user. However, for a small, fast, flat response with a 3x3 or 3x3x3 voxel mask, set maskSD to 0.

minimumThreshold

long minimumThreshold
DOCUMENT ME!

maximumThreshold

long maximumThreshold
DOCUMENT ME!

defaultThreshold

long defaultThreshold
DOCUMENT ME!

newImage

JRadioButton newImage
DOCUMENT ME!

nlnrAlgo

AlgorithmNLNoiseReduction nlnrAlgo
DOCUMENT ME!

optionsPanel

JPanel optionsPanel
DOCUMENT ME!

replaceImage

JRadioButton replaceImage
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

textMaskSD

JTextField textMaskSD
discriminate between noise and the underlying image. Ideally, the value should be set greater than the noise level and less than the contrast of the underlying image. Edges of contrast smaller than this threshold will tend to be blurred whereas those of greater contrast will not be.

textThreshold

JTextField textThreshold
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

useMedian

boolean useMedian
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogNMSuppression extends JDialogScriptableBase implements Serializable

serialVersionUID: 3261350233947714913L

Serialized Fields

image

ModelImage image
DOCUMENT ME!

image25D

boolean image25D
DOCUMENT ME!

image25DCheckbox

JCheckBox image25DCheckbox
DOCUMENT ME!

nmSuppressionAlgo

AlgorithmNMSuppression nmSuppressionAlgo
DOCUMENT ME!

outputPanel

JPanelAlgorithmOutputOptions outputPanel
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

sigmaPanel

JPanelSigmas sigmaPanel
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogNoise extends JDialogScriptableBase implements Serializable

serialVersionUID: 3214808660601346651L

Serialized Fields

destinationGroup

ButtonGroup destinationGroup
DOCUMENT ME!

destinationPanel

JPanel destinationPanel
DOCUMENT ME!

displayLoc

int displayLoc
DOCUMENT ME!

group1

ButtonGroup group1
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

imageRangeLabel

JLabel imageRangeLabel
DOCUMENT ME!

maximumNoise

double maximumNoise
DOCUMENT ME!

min

double min
DOCUMENT ME!

max

double max
DOCUMENT ME!

newImage

JRadioButton newImage
DOCUMENT ME!

noiseType

int noiseType
DOCUMENT ME!

panelImageType

JPanel panelImageType
DOCUMENT ME!

panelGU

JPanel panelGU
DOCUMENT ME!

panelPO

JPanel panelPO

radioGaussian

JRadioButton radioGaussian
DOCUMENT ME!

radioUniform

JRadioButton radioUniform
DOCUMENT ME!

radioPoisson

JRadioButton radioPoisson

randomAlgo

AlgorithmNoise randomAlgo
DOCUMENT ME!

replaceImage

JRadioButton replaceImage
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

start

JLabel start
DOCUMENT ME!

backgroundText

JTextField backgroundText

background

double background

gainText

JTextField gainText

gain

double gain

textStart

JTextField textStart
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogOpacityControls extends JDialogBase implements Serializable

serialVersionUID: 844490628214011726L

Serialized Fields

controls

ViewControlsImage controls
Controls affected by opacity changes.

current

JLabel current
Label that gives current value of slider.

opacity

float opacity
Opacity number.

opacitySlider

JSlider opacitySlider
Opacity slider.

surfacePaint

SurfacePaint surfacePaint
SurfacePaint reference

surfacePaint_WM

SurfacePaint_WM surfacePaint_WM
SurfacePaint reference

Class gov.nih.mipav.view.dialogs.JDialogOpen extends JDialogScriptableBase implements Serializable

serialVersionUID: -9116067564431404676L

Serialized Fields

comboBoxKernel

JComboBox comboBoxKernel
DOCUMENT ME!

do25D

boolean do25D
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

image25D

JCheckBox image25D
DOCUMENT ME!

itersD

int itersD
or if the source image is to be replaced.

itersE

int itersE
DOCUMENT ME!

kernel

int kernel
DOCUMENT ME!

kernelSize

float kernelSize
DOCUMENT ME!

labelKernel

JLabel labelKernel
DOCUMENT ME!

labelKernelSize

JLabel labelKernelSize
DOCUMENT ME!

labelNIterD

JLabel labelNIterD
DOCUMENT ME!

labelNIterE

JLabel labelNIterE
DOCUMENT ME!

maskPanel

JPanel maskPanel
DOCUMENT ME!

openAlgo25D

AlgorithmMorphology25D openAlgo25D
DOCUMENT ME!

openAlgo2D

AlgorithmMorphology2D openAlgo2D
DOCUMENT ME!

openAlgo3D

AlgorithmMorphology3D openAlgo3D
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

textKernelSize

JTextField textKernelSize
DOCUMENT ME!

textNIterD

JTextField textNIterD
DOCUMENT ME!

textNIterE

JTextField textNIterE
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

outputPanel

JPanelAlgorithmOutputOptions outputPanel

Class gov.nih.mipav.view.dialogs.JDialogOrder extends JDialogBase implements Serializable

serialVersionUID: 670499188247272869L

Serialized Fields

datasetOrder

JRadioButton datasetOrder
DOCUMENT ME!

dicomOrder

JRadioButton dicomOrder
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogOrientMatrix extends JDialogBase implements Serializable

serialVersionUID: -5386555201530113228L

Serialized Fields

image

ModelImage image
DOCUMENT ME!

leftHandRuleCheckbox

JCheckBox leftHandRuleCheckbox
DOCUMENT ME!

matrix

TransMatrix matrix
DOCUMENT ME!

panelAxisMode

JPanel panelAxisMode
DOCUMENT ME!

pFrame

JDialogBase pFrame
DOCUMENT ME!

worldCoordCheckbox

JCheckBox worldCoordCheckbox
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogOverlay extends JDialogBase implements Serializable

serialVersionUID: -2470981064995748425L

Serialized Fields

borderTitles

String[] borderTitles
DOCUMENT ME!

buttonArray

JButton[] buttonArray
DOCUMENT ME!

headerString

String headerString
DOCUMENT ME!

isDicom

boolean isDicom
DOCUMENT ME!

nameArray

JTextField[] nameArray
DOCUMENT ME!

overlayNames

String[] overlayNames
DOCUMENT ME!

overlayValues

String[] overlayValues
DOCUMENT ME!

tagDialog

gov.nih.mipav.view.dialogs.JDialogOverlay.JDialogChooseOverlay tagDialog
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogPad extends JDialogScriptableBase implements Serializable

serialVersionUID: -2434000521271688512L

Serialized Fields

back

int back
Number of slices to be padded at back.

backInput

JTextField backInput
Textfield for number of slices to be padded at back.

borderSize

int borderSize
Border size

bottomInput

JTextField bottomInput
Textfield for number of pixels padded at the bottom.

valueInput

JTextField valueInput
Textfield for the pad value.

bottomSide

int bottomSide
Number of pixels to be padded at the bottom.

padAlgo

AlgorithmPad padAlgo
Instance of AlgorithmPad

destinationGroup

ButtonGroup destinationGroup
Buttons in Destination box.

displayLoc

int displayLoc
Flag indicating whether new image is to be generated or source image is to be replaced

front

int front
Number of slices to be padded in front.

frontInput

JTextField frontInput
Textfield for the slices to be padded in front.

image

ModelImage image
Source image

leftSide

int leftSide
Number of pixels to be padded on the left side.

leftSideInput

JTextField leftSideInput
Textfield for the pixels to be padded on left side.

newImage

JRadioButton newImage
Radio button to select new image.

replaceImage

JRadioButton replaceImage
Radio button to replace the source image.

resultImage

ModelImage resultImage
Result image

rightSide

int rightSide
Number of pixels to be padded on the right side.

rightSideInput

JTextField rightSideInput
Textfield for the nunber of pixels on the right side.

titles

String[] titles
Title of the frame shown when image is NULL

topInput

JTextField topInput
Textfield for the pixels to be padded on top.

topSide

int topSide
Number of pixels to be padded on top.

padValue

int padValue
Value to be padded.

userInterface

ViewUserInterface userInterface
Instance of ViewUserInterface.

xBounds

int[] xBounds
xBounds indicating the number of pixels to be padded on left and the total length of X dimension

yBounds

int[] yBounds
yBounds indicating the number of pixels to be padded on top and the total length of Y dimension

zBounds

int[] zBounds
zBounds indicating the number of slices to be padded in front and the total length of Y dimension

Class gov.nih.mipav.view.dialogs.JDialogPadImages extends JDialogScriptableBase implements Serializable

serialVersionUID: 4451162492289524768L

Serialized Fields

destinationGroup

ButtonGroup destinationGroup
DOCUMENT ME!

displayLoc

int displayLoc
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

newImage

JRadioButton newImage
DOCUMENT ME!

nSlices

int nSlices
DOCUMENT ME!

paddedSlices

int paddedSlices
DOCUMENT ME!

paddingGroup

ButtonGroup paddingGroup
DOCUMENT ME!

padMode

int padMode
DOCUMENT ME!

padSlicesAlgo

AlgorithmPadWithSlices padSlicesAlgo
DOCUMENT ME!

padToBack

JRadioButton padToBack
DOCUMENT ME!

padToFront

JRadioButton padToFront
DOCUMENT ME!

padToHalf

JRadioButton padToHalf
DOCUMENT ME!

replaceImage

JRadioButton replaceImage
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogPaintGrow extends JDialogBase implements Serializable

serialVersionUID: -165750503127683051L

Serialized Fields

constrainBoundsCheckbox

JCheckBox constrainBoundsCheckbox
DOCUMENT ME!

currentFuzzy

JLabel currentFuzzy
DOCUMENT ME!

displayFuzzy

boolean displayFuzzy
DOCUMENT ME!

distanceCheckbox

JCheckBox distanceCheckbox
DOCUMENT ME!

enableVariableCheckbox

boolean enableVariableCheckbox
DOCUMENT ME!

frame

Frame frame
DOCUMENT ME!

fuzzyCheckbox

JCheckBox fuzzyCheckbox
DOCUMENT ME!

fuzzyImageCheckbox

JCheckBox fuzzyImageCheckbox
DOCUMENT ME!

fuzzySlider

JSlider fuzzySlider
DOCUMENT ME!

fuzzyThreshold

float fuzzyThreshold
DOCUMENT ME!

haveBlue

boolean haveBlue
DOCUMENT ME!

haveColor

boolean haveColor
DOCUMENT ME!

haveGreen

boolean haveGreen
DOCUMENT ME!

haveRed

boolean haveRed
DOCUMENT ME!

initialDelta

int initialDelta
DOCUMENT ME!

initialDeltaB

int initialDeltaB
DOCUMENT ME!

initialDeltaG

int initialDeltaG
DOCUMENT ME!

initialDeltaR

int initialDeltaR
DOCUMENT ME!

leadString

String leadString
DOCUMENT ME!

less

float less
DOCUMENT ME!

more

float more
DOCUMENT ME!

lowerMid

JLabel lowerMid
DOCUMENT ME!

lowerMidB

JLabel lowerMidB
DOCUMENT ME!

lowerMidG

JLabel lowerMidG
DOCUMENT ME!

lowerMidR

JLabel lowerMidR
DOCUMENT ME!

lowSlider

JSlider lowSlider
DOCUMENT ME!

lowSliderB

JSlider lowSliderB
DOCUMENT ME!

lowSliderField

JTextField lowSliderField
DOCUMENT ME!

lowSliderFieldB

JTextField lowSliderFieldB
DOCUMENT ME!

lowSliderFieldG

JTextField lowSliderFieldG
DOCUMENT ME!

lowSliderFieldR

JTextField lowSliderFieldR
DOCUMENT ME!

lowSliderG

JSlider lowSliderG
DOCUMENT ME!

lowSliderR

JSlider lowSliderR
DOCUMENT ME!

max

float max
DOCUMENT ME!

maxB

float maxB
DOCUMENT ME!

maxDistLabel

JLabel maxDistLabel
DOCUMENT ME!

maxDistTextF

JTextField maxDistTextF
DOCUMENT ME!

maxG

float maxG
DOCUMENT ME!

maximumFuzzy

JLabel maximumFuzzy
DOCUMENT ME!

maximumL

JLabel maximumL
DOCUMENT ME!

maximumLB

JLabel maximumLB
DOCUMENT ME!

maximumLG

JLabel maximumLG
DOCUMENT ME!

maximumLR

JLabel maximumLR
DOCUMENT ME!

maximumU

JLabel maximumU
DOCUMENT ME!

maximumUB

JLabel maximumUB
DOCUMENT ME!

maximumUG

JLabel maximumUG
DOCUMENT ME!

maximumUR

JLabel maximumUR
DOCUMENT ME!

maximumValue

double maximumValue
DOCUMENT ME!

maximumValueButton

JButton maximumValueButton
DOCUMENT ME!

maximumValueField

JTextField maximumValueField
DOCUMENT ME!

maxR

float maxR
DOCUMENT ME!

maxSizeLabel

JLabel maxSizeLabel
DOCUMENT ME!

maxSizeTextF

JTextField maxSizeTextF
DOCUMENT ME!

maxValue

double maxValue
DOCUMENT ME!

minValue

double minValue
DOCUMENT ME!

maxValueB

double maxValueB
DOCUMENT ME!

minValueB

double minValueB
DOCUMENT ME!

maxValueG

double maxValueG
DOCUMENT ME!

minValueG

double minValueG
DOCUMENT ME!

maxValueR

double maxValueR
DOCUMENT ME!

minValueR

double minValueR
DOCUMENT ME!

min

float min
DOCUMENT ME!

minB

float minB
DOCUMENT ME!

minG

float minG
DOCUMENT ME!

minimumFuzzy

JLabel minimumFuzzy
DOCUMENT ME!

minimumL

JLabel minimumL
DOCUMENT ME!

minimumLB

JLabel minimumLB
DOCUMENT ME!

minimumLG

JLabel minimumLG
DOCUMENT ME!

minimumLR

JLabel minimumLR
DOCUMENT ME!

minimumU

JLabel minimumU
DOCUMENT ME!

minimumUB

JLabel minimumUB
DOCUMENT ME!

minimumUG

JLabel minimumUG
DOCUMENT ME!

minimumUR

JLabel minimumUR
DOCUMENT ME!

minR

float minR
DOCUMENT ME!

paintGrowListeners

Vector<E> paintGrowListeners
DOCUMENT ME!

posTextF

JTextField posTextF
DOCUMENT ME!

range

double range
DOCUMENT ME!

rangeB

double rangeB
DOCUMENT ME!

rangeG

double rangeG
DOCUMENT ME!

rangeR

double rangeR
DOCUMENT ME!

regionGrowAlgo

AlgorithmRegionGrow regionGrowAlgo
DOCUMENT ME!

setRadioBoth

boolean setRadioBoth
DOCUMENT ME!

sizeCheckbox

JCheckBox sizeCheckbox
DOCUMENT ME!

upperMid

JLabel upperMid
DOCUMENT ME!

upperMidB

JLabel upperMidB
DOCUMENT ME!

upperMidG

JLabel upperMidG
DOCUMENT ME!

upperMidR

JLabel upperMidR
DOCUMENT ME!

upSlider

JSlider upSlider
DOCUMENT ME!

upSliderB

JSlider upSliderB
DOCUMENT ME!

upSliderField

JTextField upSliderField
DOCUMENT ME!

upSliderFieldB

JTextField upSliderFieldB
DOCUMENT ME!

upSliderFieldG

JTextField upSliderFieldG
DOCUMENT ME!

upSliderFieldR

JTextField upSliderFieldR
DOCUMENT ME!

upSliderG

JSlider upSliderG
DOCUMENT ME!

upSliderR

JSlider upSliderR
DOCUMENT ME!

useVOI

boolean useVOI
DOCUMENT ME!

variableDeltasCheckbox

JCheckBox variableDeltasCheckbox
DOCUMENT ME!

variableThresholds

boolean variableThresholds
DOCUMENT ME!

voiCheckbox

JCheckBox voiCheckbox
DOCUMENT ME!

disableSliders

boolean disableSliders
DOCUMENT ME!

disableSlidersB

boolean disableSlidersB
DOCUMENT ME!

disableSlidersG

boolean disableSlidersG
DOCUMENT ME!

disableSlidersR

boolean disableSlidersR
DOCUMENT ME!

font12B

Font font12B
DOCUMENT ME!

imageType

int imageType
DOCUMENT ME!

lowSetFromField

boolean lowSetFromField
DOCUMENT ME!

lowSetFromFieldB

boolean lowSetFromFieldB
DOCUMENT ME!

lowSetFromFieldG

boolean lowSetFromFieldG
DOCUMENT ME!

lowSetFromFieldR

boolean lowSetFromFieldR
DOCUMENT ME!

tabbedPane

JTabbedPane tabbedPane
DOCUMENT ME!

upSetFromField

boolean upSetFromField
DOCUMENT ME!

upSetFromFieldB

boolean upSetFromFieldB
DOCUMENT ME!

upSetFromFieldG

boolean upSetFromFieldG
DOCUMENT ME!

upSetFromFieldR

boolean upSetFromFieldR
DOCUMENT ME!

surfacePaint

SurfacePaint surfacePaint
SurfacePaint reference

surfacePaint_WM

SurfacePaint_WM surfacePaint_WM
SurfacePaint reference

Class gov.nih.mipav.view.dialogs.JDialogPaintRGBComponents extends JDialogBase implements Serializable

serialVersionUID: 844490628214011726L

Serialized Fields

useRBox

JCheckBox useRBox

useGBox

JCheckBox useGBox

useBBox

JCheckBox useBBox

Class gov.nih.mipav.view.dialogs.JDialogPaintVasculature extends JDialogBase implements Serializable

serialVersionUID: -7746172110383193434L

Serialized Fields

deltaSetFromField

boolean deltaSetFromField
Boolean which indicates that the seed point intensity bounds were changed from one of the text fields and not from one of the sliders.

doneButton

JButton doneButton
Button to indicate that the painting is finished and the dialog and attached image frame should be closed.

growButton

JButton growButton
Button which indicates that a region grow has been initiated / is being adjusted.

intensityTF

JTextField intensityTF
Text field containing the seed value intensity.

intensityValue

int intensityValue
The value of seed points to use.

isCloseOkay

boolean isCloseOkay
Indicates that we are done with the current grow, and can close the MIP when the done button is next clicked.

lowerDeltaSlider

JSlider lowerDeltaSlider
Slider which adjusts the lower bound of the region grow.

lowerDeltaTF

JTextField lowerDeltaTF
Text field containing the lower bound of the region grow.

maxDelta

int maxDelta
The most we can get away from the initial seed point intensity value (151).

mouseIntensityLabel

JLabel mouseIntensityLabel
The intensity of the current mouse position within the mip.

mouseXLabel

JLabel mouseXLabel
The x position of the current mouse position within the mip.

mouseYLabel

JLabel mouseYLabel
The y position of the current mouse position within the mip.

mouseZLabel

JLabel mouseZLabel
The z position of the current mouse position within the mip (the z position of the volume voxel put into the mip).

oldSeedIntensity

int oldSeedIntensity
The intensity value to use to recalculate the possible seed points when switching from CLICK_POINT mode back to AUTO_MODE.

paintGrowListeners

Vector<E> paintGrowListeners
List of frames that want to know about paint updates.

paintGrowMode

int paintGrowMode
The point selection mode.

rfastFrame

ViewJFrameImage rfastFrame
The main RFAST frame.

seedPoints

Vector<E> seedPoints
List of points where we have grown a region from.

toolbarPanel

JPanel toolbarPanel
The dialog's toolbar panel.

undoButton

JButton undoButton
Button to undo the last region grow change (either a click of the grow button, or an adjustment of the threshold sliders).

upperDeltaSlider

JSlider upperDeltaSlider
Slider which adjusts the upper bound of the region grow.

upperDeltaTF

JTextField upperDeltaTF
Text field containing the upper bound of the region grow.

Class gov.nih.mipav.view.dialogs.JDialogParticleAnalysisNew extends JDialogScriptableBase implements Serializable

serialVersionUID: 7849492525308767787L

Serialized Fields

comboBoxKernelClose

JComboBox comboBoxKernelClose
DOCUMENT ME!

comboBoxKernelOpen

JComboBox comboBoxKernelOpen
DOCUMENT ME!

do25D

boolean do25D
DOCUMENT ME!

erodePanel

JPanel erodePanel
Erode panel.

image

ModelImage image
DOCUMENT ME!

image25D

JCheckBox image25D
DOCUMENT ME!

itersClose

int itersClose

itersOpen

int itersOpen

itersErode

int itersErode

kernelClose

int kernelClose
DOCUMENT ME!

kernelOpen

int kernelOpen
DOCUMENT ME!

kernelSizeClose

float kernelSizeClose
DOCUMENT ME!

kernelSizeOpen

float kernelSizeOpen
DOCUMENT ME!

labelKernelClose

JLabel labelKernelClose
DOCUMENT ME!

labelKernelOpen

JLabel labelKernelOpen
DOCUMENT ME!

labelKernelSizeClose

JLabel labelKernelSizeClose
DOCUMENT ME!

labelKernelSizeOpen

JLabel labelKernelSizeOpen
DOCUMENT ME!

labelNIterClose

JLabel labelNIterClose
DOCUMENT ME!

labelNIterErode

JLabel labelNIterErode
DOCUMENT ME!

labelNIterOpen

JLabel labelNIterOpen
DOCUMENT ME!

maskPanelClose

JPanel maskPanelClose
Close declearation.

maskPanelOpen

JPanel maskPanelOpen
DOCUMENT ME!

particleAlgo25D

AlgorithmMorphology25D particleAlgo25D
DOCUMENT ME!

particleAlgo2D

AlgorithmMorphology2D particleAlgo2D
DOCUMENT ME!

particleAlgo3D

AlgorithmMorphology3D particleAlgo3D
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

showFrame

boolean showFrame
DOCUMENT ME!

showResultCB

JCheckBox showResultCB
DOCUMENT ME!

textErode

JTextField textErode
DOCUMENT ME!

textKernelSizeClose

JTextField textKernelSizeClose
DOCUMENT ME!

textKernelSizeOpen

JTextField textKernelSizeOpen
DOCUMENT ME!

textNIterClose

JTextField textNIterClose
DOCUMENT ME!

textNIterOpen

JTextField textNIterOpen
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

outputPanel

JPanelAlgorithmOutputOptions outputPanel

Class gov.nih.mipav.view.dialogs.JDialogPointArea extends JDialogScriptableBase implements Serializable

serialVersionUID: -2157089114762708039L

Serialized Fields

averageIntensities

float[] averageIntensities
DOCUMENT ME!

rgbAverageIntensities

float[][] rgbAverageIntensities
DOCUMENT ME!

constrainBox

JCheckBox constrainBox
DOCUMENT ME!

leftPad

boolean leftPad
DOCUMENT ME!

leftPadBox

JCheckBox leftPadBox
DOCUMENT ME!

locationField

JTextField locationField
DOCUMENT ME!

pointAlgo

AlgorithmPointArea pointAlgo
DOCUMENT ME!

showGraph

boolean showGraph
DOCUMENT ME!

srcImage

ModelImage srcImage
DOCUMENT ME!

threshold

float threshold
DOCUMENT ME!

thresholdBox

JCheckBox thresholdBox
DOCUMENT ME!

thresholdField

JTextField thresholdField
DOCUMENT ME!

topPad

boolean topPad
DOCUMENT ME!

topPadBox

JCheckBox topPadBox
DOCUMENT ME!

useThreshold

boolean useThreshold
DOCUMENT ME!

xLoc

int xLoc
DOCUMENT ME!

xSpaceField

JTextField xSpaceField
DOCUMENT ME!

xSpacing

int xSpacing
DOCUMENT ME!

yLoc

int yLoc
DOCUMENT ME!

ySpaceField

JTextField ySpaceField
DOCUMENT ME!

ySpacing

int ySpacing
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogPointArea.JTextFieldFilter extends PlainDocument implements Serializable

serialVersionUID: -4552252563901427164L

Serialized Fields

acceptedChars

String acceptedChars
DOCUMENT ME!

negativeAccepted

boolean negativeAccepted
DOCUMENT ME!

box

JCheckBox box
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogPointArea.UpdateYSpaceAction extends AbstractAction implements Serializable

serialVersionUID: 578406985180315919L

Class gov.nih.mipav.view.dialogs.JDialogPowerPaint extends JDialogBase implements Serializable

serialVersionUID: 6175130808453006120L

Serialized Fields

backgroundDim

int backgroundDim
DOCUMENT ME!

backgroundsDim

int backgroundsDim
DOCUMENT ME!

botPanel

JPanel botPanel
DOCUMENT ME!

buttonDilate

JButton buttonDilate
DOCUMENT ME!

buttonErode

JButton buttonErode
DOCUMENT ME!

buttonExportToMask

JButton buttonExportToMask
DOCUMENT ME!

buttonExportToVOI

JButton buttonExportToVOI
DOCUMENT ME!

buttonFillBackground

JButton buttonFillBackground
DOCUMENT ME!

buttonFillBackgrounds

JButton buttonFillBackgrounds
DOCUMENT ME!

buttonGrowRegion

JButton buttonGrowRegion
DOCUMENT ME!

buttonImportFromMask

JButton buttonImportFromMask
DOCUMENT ME!

buttonImportFromVOI

JButton buttonImportFromVOI
DOCUMENT ME!

buttonRevert

JButton buttonRevert
DOCUMENT ME!

buttonRmObject

JButton buttonRmObject
DOCUMENT ME!

buttonRmObjects

JButton buttonRmObjects
DOCUMENT ME!

buttonShortkeys

JToggleButton buttonShortkeys
DOCUMENT ME!

c2x

int c2x
DOCUMENT ME!

c2y

int c2y
DOCUMENT ME!

c2z

int c2z
DOCUMENT ME!

c3x

int c3x
DOCUMENT ME!

c3y

int c3y
DOCUMENT ME!

c3z

int c3z
DOCUMENT ME!

checkSave

JCheckBox checkSave
DOCUMENT ME!

checkThreshold

JCheckBox checkThreshold
handling of intensity threshold.

comboConnectType

JComboBox comboConnectType
DOCUMENT ME!

comboDilateDimType

JComboBox comboDilateDimType
DOCUMENT ME!

comboErodeDimType

JComboBox comboErodeDimType
DOCUMENT ME!

comboStructureType

JComboBox comboStructureType
DOCUMENT ME!

connectType

String connectType
DOCUMENT ME!

connectTypes

String[] connectTypes
DOCUMENT ME!

dilateDimType

String dilateDimType
DOCUMENT ME!

dimTypes

String[] dimTypes
DOCUMENT ME!

erodeDimType

String erodeDimType
DOCUMENT ME!

exportPanel

JPanel exportPanel
DOCUMENT ME!

getMouseInput

int getMouseInput
DOCUMENT ME!

groupBackground

ButtonGroup groupBackground
DOCUMENT ME!

groupBackgrounds

ButtonGroup groupBackgrounds
DOCUMENT ME!

groupGrowRegion

ButtonGroup groupGrowRegion
DOCUMENT ME!

groupObject

ButtonGroup groupObject
DOCUMENT ME!

groupObjects

ButtonGroup groupObjects
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

labelConnectType

JLabel labelConnectType
DOCUMENT ME!

labelO2D

JLabel labelO2D
DOCUMENT ME!

labelO3D

JLabel labelO3D
DOCUMENT ME!

labelStructureType

JLabel labelStructureType
DOCUMENT ME!

labelStructuring

JLabel labelStructuring
DOCUMENT ME!

lowerThreshold

float lowerThreshold
handling of intensity threshold.

mainPanel

JPanel mainPanel
dialog elements.

morphoPanel

JPanel morphoPanel
DOCUMENT ME!

movePanel

JPanel movePanel
DOCUMENT ME!

multiPaintDialog

JDialogMultiPaint multiPaintDialog
DOCUMENT ME!

nx

int nx
DOCUMENT ME!

ny

int ny
DOCUMENT ME!

nz

int nz
DOCUMENT ME!

objectPanel

JPanel objectPanel
DOCUMENT ME!

panelThreshold

JPanel panelThreshold
DOCUMENT ME!

previous

BitSet previous
internal objects.

radioBackground2D

JRadioButton radioBackground2D
DOCUMENT ME!

radioBackground3D

JRadioButton radioBackground3D
DOCUMENT ME!

radioBackgrounds2D

JRadioButton radioBackgrounds2D
DOCUMENT ME!

radioBackgrounds3D

JRadioButton radioBackgrounds3D
DOCUMENT ME!

radioGrowRegion2D

JRadioButton radioGrowRegion2D
DOCUMENT ME!

radioGrowRegion3D

JRadioButton radioGrowRegion3D
DOCUMENT ME!

radioObject2D

JRadioButton radioObject2D
DOCUMENT ME!

radioObject3D

JRadioButton radioObject3D
DOCUMENT ME!

radioObjects2D

JRadioButton radioObjects2D
DOCUMENT ME!

radioObjects3D

JRadioButton radioObjects3D
DOCUMENT ME!

regionGrowDim

int regionGrowDim
parameters.

resultImage

ModelImage resultImage
DOCUMENT ME!

rmObjDim

int rmObjDim
DOCUMENT ME!

rmObjsDim

int rmObjsDim
DOCUMENT ME!

save

gov.nih.mipav.view.dialogs.PaintAutoSave save
DOCUMENT ME!

saver

Timer saver
DOCUMENT ME!

se2xy

BitSet se2xy
DOCUMENT ME!

se2yz

BitSet se2yz
DOCUMENT ME!

se2xz

BitSet se2xz
DOCUMENT ME!

se3

BitSet se3
DOCUMENT ME!

spinLower

JSpinner spinLower
handling of intensity threshold.

spinUpper

JSpinner spinUpper
DOCUMENT ME!

structureSize

float structureSize
DOCUMENT ME!

structureType

String structureType
DOCUMENT ME!

structureTypes

String[] structureTypes
DOCUMENT ME!

textSave

JTextField textSave
DOCUMENT ME!

textStructuring

JTextField textStructuring
DOCUMENT ME!

upperThreshold

float upperThreshold
handling of intensity threshold.

Class gov.nih.mipav.view.dialogs.JDialogPrincipalComponents extends JDialogScriptableBase implements Serializable

serialVersionUID: 7032654276398964355L

Serialized Fields

averagedImageCheckbox

JCheckBox averagedImageCheckbox
DOCUMENT ME!

displayAndAsk

boolean displayAndAsk
DOCUMENT ME!

displayPCheckbox

JCheckBox displayPCheckbox
DOCUMENT ME!

doAveraging

boolean doAveraging
DOCUMENT ME!

doFilter

boolean doFilter
DOCUMENT ME!

filteredImageCheckbox

JCheckBox filteredImageCheckbox
DOCUMENT ME!

imageFrame

ViewJFrameImage[] imageFrame
DOCUMENT ME!

imageNumber

int imageNumber
DOCUMENT ME!

imageType

int imageType
DOCUMENT ME!

iNumber

int iNumber
DOCUMENT ME!

labelNumber

JLabel labelNumber
DOCUMENT ME!

nPlanes

int nPlanes
DOCUMENT ME!

pComponentAlgo

AlgorithmPrincipalComponents pComponentAlgo
DOCUMENT ME!

pNumber

int pNumber
DOCUMENT ME!

resultImage

ModelImage[] resultImage
DOCUMENT ME!

srcImage

ModelImage srcImage
DOCUMENT ME!

textNumber

JTextField textNumber
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogQuantify extends JDialogScriptableBase implements Serializable

serialVersionUID: 412669652447327059L

Serialized Fields

algoQuantify

AlgorithmQuantify algoQuantify
DOCUMENT ME!

directory

String directory
DOCUMENT ME!

fileName

String fileName
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

maskImage

ModelImage maskImage
DOCUMENT ME!

textFile

JTextField textFile
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

buttonFile

JButton buttonFile

comboBoxImage

JComboBox comboBoxImage

loadCheckBox

JCheckBox loadCheckBox

Class gov.nih.mipav.view.dialogs.JDialogQuantifyMask extends JDialogScriptableBase implements Serializable

Serialized Fields

image

ModelImage image

Class gov.nih.mipav.view.dialogs.JDialogRandomizeSliceOrder extends JDialogScriptableBase implements Serializable

serialVersionUID: 8562091054505687054L

Serialized Fields

image

ModelImage image
DOCUMENT ME!

orderAlgo

AlgorithmRandSliceOrder orderAlgo
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogRawIO extends JDialogBase implements Serializable

serialVersionUID: -1588091095156376702L

Serialized Fields

checkboxEnd

JCheckBox checkboxEnd
DOCUMENT ME!

comboBoxUnitOfMeasure1

JComboBox comboBoxUnitOfMeasure1
DOCUMENT ME!

comboBoxUnitOfMeasure2

JComboBox comboBoxUnitOfMeasure2
DOCUMENT ME!

comboBoxUnitOfMeasure3

JComboBox comboBoxUnitOfMeasure3
DOCUMENT ME!

comboBoxUnitOfMeasure4

JComboBox comboBoxUnitOfMeasure4
DOCUMENT ME!

comboBoxUnitOfMeasure5

JComboBox comboBoxUnitOfMeasure5
DOCUMENT ME!

dataType

int dataType
DOCUMENT ME!

dimExtents

int[] dimExtents
DOCUMENT ME!

endianess

boolean endianess
DOCUMENT ME!

extents

int[] extents
DOCUMENT ME!

labelOffset

JLabel labelOffset
DOCUMENT ME!

offset

int offset
DOCUMENT ME!

radioARGB

JRadioButton radioARGB
DOCUMENT ME!

radioARGB_USHORT

JRadioButton radioARGB_USHORT
DOCUMENT ME!

radioBool

JRadioButton radioBool
DOCUMENT ME!

radioByte

JRadioButton radioByte
DOCUMENT ME!

radioDouble

JRadioButton radioDouble
DOCUMENT ME!

radioFloat

JRadioButton radioFloat
DOCUMENT ME!

radioInt

JRadioButton radioInt
DOCUMENT ME!

radioLong

JRadioButton radioLong
DOCUMENT ME!

radioShort

JRadioButton radioShort
DOCUMENT ME!

radioUByte

JRadioButton radioUByte
DOCUMENT ME!

radioUInt

JRadioButton radioUInt
DOCUMENT ME!

radioUShort

JRadioButton radioUShort
DOCUMENT ME!

resolution

JLabel resolution
DOCUMENT ME!

resolutions

float[] resolutions
DOCUMENT ME!

textDim1

JTextField textDim1
DOCUMENT ME!

textDim2

JTextField textDim2
DOCUMENT ME!

textDim3

JTextField textDim3
DOCUMENT ME!

textDim4

JTextField textDim4
DOCUMENT ME!

textDim5

JTextField textDim5
DOCUMENT ME!

textOffset

JTextField textOffset
DOCUMENT ME!

textRes1

JTextField textRes1
DOCUMENT ME!

textRes2

JTextField textRes2
DOCUMENT ME!

textRes3

JTextField textRes3
DOCUMENT ME!

textRes4

JTextField textRes4
DOCUMENT ME!

textRes5

JTextField textRes5
DOCUMENT ME!

unitsOfMeasure

int[] unitsOfMeasure
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogRecordLUT extends JDialogBase implements Serializable

serialVersionUID: 2240336763327716473L

Serialized Fields

offsetX

int offsetX
Offset to draw the tick mark and value label.

offsetY

int offsetY
DOCUMENT ME!

x

float[] x
control points coordinate of LUT transfer function .

xN

int[] xN
DOCUMENT ME!

y

float[] y
DOCUMENT ME!

yN

int[] yN
DOCUMENT ME!

z

float[] z
DOCUMENT ME!

zN

int[] zN
DOCUMENT ME!

compLUT

ViewJComponentLUTTable compLUT
Lookup table of image. The rectangular LUT table.

image

ModelImage image
ModelImage reference.

lut

ModelLUT lut
LUT table renference.

lutTablePanel

JPanel lutTablePanel
LUT table panel.

tBarPanel

JPanel tBarPanel
Panel to hold the toolbar.

toolBar

JToolBar toolBar
Toolbar.

Class gov.nih.mipav.view.dialogs.JDialogRegistrationBSpline extends JDialogScriptableBase implements Serializable

serialVersionUID: 8193864043052368084L

Serialized Fields

kStringDimension

String kStringDimension
DOCUMENT ME.*

m_akNamesCompatibleTargetImages

String[] m_akNamesCompatibleTargetImages
Contains names of compatible target images that can be registered to the input source image for 2D/3D registration. Null reference for 2.5D registration.

m_bCreateDeformationImage

boolean m_bCreateDeformationImage
Flag set if the deformation computation is to be performed. Reflects the state of the associated check box in the dialog.

m_iTargetSlice

int m_iTargetSlice
Index of the slice from the source image to use for 2.5 registration. The index may be -1 to indicate registration is with adjacent slice. Reflects the state of the target slice radio buttons and the combo box if a particular reference slice is to be used.

m_kAlgorithmReg

AlgorithmRegBSpline m_kAlgorithmReg
Flag set if the deformation computation is to be performed.

m_kCheckCreateDeformationImage

JCheckBox m_kCheckCreateDeformationImage
DOCUMENT ME!

m_kCheckMultiPass

JCheckBox m_kCheckMultiPass
DOCUMENT ME!

m_kComboBoxCostFunction

JComboBox m_kComboBoxCostFunction
DOCUMENT ME!

m_kComboBoxTargetImage

JComboBox m_kComboBoxTargetImage
Controls displayed in the dialog box. All of these controls are always displayed unless otherwise noted.

m_kComboBoxTargetSlice

JComboBox m_kComboBoxTargetSlice
DOCUMENT ME!

m_kControlsPass1

gov.nih.mipav.view.dialogs.JDialogRegistrationBSpline.Controls m_kControlsPass1
Container for controls to select the parameters for the first pass of registration. These controls are always displayed.

m_kControlsPass2

gov.nih.mipav.view.dialogs.JDialogRegistrationBSpline.Controls m_kControlsPass2
Container for controls to select the parameters for the optional second pass of registration. These controls are created but are only displayed when the check box is selected for two-pass registration.

m_kImageDef

ModelImage m_kImageDef
Reference to new image creatd with computed deformation resulting from registration. Null reference is deformation computation is not selected.

m_kImageReg

ModelImage m_kImageReg
Reference to new image created with result of registration of source image. Cannot be null.

m_kImageSrc

ModelImage m_kImageSrc
Reference to the input source image. Cannot be null.

m_kImageTrg

ModelImage m_kImageTrg
Reference to the selected target image. Null reference for 2.5D registration.

m_kLabelIterationsPass1

JLabel m_kLabelIterationsPass1
DOCUMENT ME!

m_kLabelIterationsPass2

JLabel m_kLabelIterationsPass2
DOCUMENT ME!

m_kLabelOptionsPass1

JLabel m_kLabelOptionsPass1
DOCUMENT ME!

m_kLabelOptionsPass2

JLabel m_kLabelOptionsPass2
DOCUMENT ME!

m_kOptionsPass1

AlgorithmRegBSpline.Options m_kOptionsPass1
Reference to parameters to use for first pass of registration. Cannot be null.

m_kOptionsPass2

AlgorithmRegBSpline.Options m_kOptionsPass2
Reference to parameters to use for optional second pass of registration. Null reference if only a single pass of registration is to be performed.

m_kRadioSliceAdjacent

JRadioButton m_kRadioSliceAdjacent
DOCUMENT ME!

m_kRadioSliceReference

JRadioButton m_kRadioSliceReference
DOCUMENT ME!

m_kRegMeasure

RegistrationMeasure m_kRegMeasure
Reference to concrete implementation of the RegistrationMeasure abstract class which defines the particular measure to use during registration. Cannot be null. Reflects the selection in the associated combo box in the dialog.

m_kUI

ViewUserInterface m_kUI
Used for scripting and to access the currently registered images.

Class gov.nih.mipav.view.dialogs.JDialogRegistrationChamfer extends JDialogBase implements Serializable

serialVersionUID: 8391544557885381489L

Serialized Fields

baseImage

ModelImage baseImage
Register match image to base image.

chamfer

AlgorithmRegChamfer chamfer
Algorithm this dialog will call.

comboBox2or3D

JComboBox comboBox2or3D
GUI components.

comboBoxEdge

JComboBox comboBoxEdge
DOCUMENT ME!

comboBoxOriginal

JComboBox comboBoxOriginal
DOCUMENT ME!

edge

JLabel edge
DOCUMENT ME!

image25D

boolean image25D
true means do each slice individually, false means do them all together.

matchImage

ModelImage matchImage
Register match image to base image.

original

JLabel original
DOCUMENT ME!

regionFlag

boolean regionFlag
true means apply algorithm to whole image, false means to just the VOI.

register25D

JRadioButton register25D
DOCUMENT ME!

register2Dor3D

JRadioButton register2Dor3D
DOCUMENT ME!

titles

String[] titles
Used for setting image to locked and unlocked.

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

voiRegions

JRadioButton voiRegions
DOCUMENT ME!

wholeImage

JRadioButton wholeImage
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogRegistrationLeastSquares extends JDialogScriptableBase implements Serializable

serialVersionUID: -2171665599919057675L

Serialized Fields

baseImage

ModelImage baseImage
Base image - register match image to base image.

comboBoxImage

JComboBox comboBoxImage
Combo box with image names for choosing base image.

DIM

int DIM
Number of dimensions in match image.

fromOAR3D

boolean fromOAR3D
DOCUMENT ME!

lsCompleted

boolean lsCompleted
DOCUMENT ME!

LSMatch

AlgorithmRegLeastSquares LSMatch
Algorithm to run from this dialog.

matchImage

ModelImage matchImage
Match image - register match image to base image.

resultImage

ModelImage resultImage
Result image - image returned from registration algorithm.

resultMatrix

TransMatrix resultMatrix
DOCUMENT ME!

titles

String[] titles
Used to lock and unlock images.

userInterface

ViewUserInterface userInterface
Reference to userface.

xdimA

int xdimA
Dimensions of match image and base image.

ydimA

int ydimA
Dimensions of match image and base image.

zdimA

int zdimA
Dimensions of match image and base image.

xresA

float xresA
Resolutions of match image and base image.

yresA

float yresA
Resolutions of match image and base image.

zresA

float zresA
Resolutions of match image and base image.

xresB

float xresB
Resolutions of match image and base image.

yresB

float yresB
Resolutions of match image and base image.

zresB

float zresB
Resolutions of match image and base image.

outOfBoundsLabel

JLabel outOfBoundsLabel

outOfBoundsComboBox

JComboBox outOfBoundsComboBox

valueLabel

JLabel valueLabel

valueText

JTextField valueText

imageMin

double imageMin

imageMax

double imageMax

dataType

int dataType

outOfBoundsIndex

int outOfBoundsIndex
Tells how to select fill value for out of bounds data 0 for image minimum 1 for NaN for float, zero otherwise. 2 for user defined 3 for image maximum

fillValue

float fillValue

Class gov.nih.mipav.view.dialogs.JDialogRegistrationOAR25D extends JDialogScriptableBase implements Serializable

serialVersionUID: -8324270868997072706L

Serialized Fields

doGraph

boolean doGraph
DOCUMENT ME!

adjacentImageRButton

JRadioButton adjacentImageRButton
DOCUMENT ME!

advancedDialog

JDialog advancedDialog
Variables for Advanced Settings dialog.

bracketBoundText

JTextField bracketBoundText
DOCUMENT ME!

maxIterationsText

JTextField maxIterationsText
DOCUMENT ME!

numMinText

JTextField numMinText
DOCUMENT ME!

buttonWeightInput

JButton buttonWeightInput
DOCUMENT ME!

coarseRateText

JTextField coarseRateText
DOCUMENT ME!

comboBoxCostFunct

JComboBox comboBoxCostFunct
DOCUMENT ME!

comboBoxDOF

JComboBox comboBoxDOF
DOCUMENT ME!

comboBoxInterp

JComboBox comboBoxInterp
DOCUMENT ME!

comboBoxInterp2

JComboBox comboBoxInterp2
DOCUMENT ME!

cost

int cost
DOCUMENT ME!

interp

int interp
DOCUMENT ME!

interp2

int interp2
DOCUMENT ME!

DOF

int DOF
DOCUMENT ME!

doAdjacent

boolean doAdjacent
DOCUMENT ME!

doColor

boolean doColor
DOCUMENT ME!

doSubsample

boolean doSubsample
DOCUMENT ME!

fileNameWInput

String fileNameWInput
DOCUMENT ME!

directoryWInput

String directoryWInput
DOCUMENT ME!

fineRateText

JTextField fineRateText
DOCUMENT ME!

graphCheckBox

JCheckBox graphCheckBox
DOCUMENT ME!

inputWeightImage

ModelImage inputWeightImage
DOCUMENT ME!

labelCoarse

JLabel labelCoarse
DOCUMENT ME!

labelCoarseDegrees

JLabel labelCoarseDegrees
DOCUMENT ME!

labelFine

JLabel labelFine
DOCUMENT ME!

labelFineDegrees

JLabel labelFineDegrees
DOCUMENT ME!

labelInterp2

JLabel labelInterp2
DOCUMENT ME!

labelRotateDegrees

JLabel labelRotateDegrees
DOCUMENT ME!

labelRotateRange

JLabel labelRotateRange
DOCUMENT ME!

labelRotateRangeTo

JLabel labelRotateRangeTo
DOCUMENT ME!

matchImage

ModelImage matchImage
DOCUMENT ME!

maxIterations_def

int maxIterations_def
DOCUMENT ME!

bracketBound_def

int bracketBound_def
DOCUMENT ME!

numMinima_def

int numMinima_def
DOCUMENT ME!

maxIterations

int maxIterations
DOCUMENT ME!

bracketBound

int bracketBound
DOCUMENT ME!

noneRadio

JRadioButton noneRadio
DOCUMENT ME!

numMinima

int numMinima
DOCUMENT ME!

refImageNum

int refImageNum
DOCUMENT ME!

refImageNumText

JTextField refImageNumText
DOCUMENT ME!

refImageRButton

JRadioButton refImageRButton
DOCUMENT ME!

refSlice

ModelImage refSlice
DOCUMENT ME!

reg25

AlgorithmRegOAR25D2 reg25
DOCUMENT ME!

rotateBegin

float rotateBegin
DOCUMENT ME!

rotateEnd

float rotateEnd
DOCUMENT ME!

coarseRate

float coarseRate
DOCUMENT ME!

fineRate

float fineRate
DOCUMENT ME!

rotateBeginText

JTextField rotateBeginText
DOCUMENT ME!

rotateEndText

JTextField rotateEndText
DOCUMENT ME!

sampleCheckBox

JCheckBox sampleCheckBox
DOCUMENT ME!

textInput

JTextField textInput
DOCUMENT ME!

transformVOIs

boolean transformVOIs
DOCUMENT ME!

transformVOIsBox

JCheckBox transformVOIsBox
DOCUMENT ME!

UI

ViewUserInterface UI
DOCUMENT ME!

useOutsideReferenceSlice

boolean useOutsideReferenceSlice
DOCUMENT ME!

voiRadio

JRadioButton voiRadio
DOCUMENT ME!

voisOnly

boolean voisOnly
DOCUMENT ME!

weighted

boolean weighted
DOCUMENT ME!

weightRadio

JRadioButton weightRadio
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogRegistrationOAR2D extends JDialogScriptableBase implements Serializable

serialVersionUID: -688716905705879638L

Serialized Fields

advancedDialog

JDialog advancedDialog
Variables for Advanced Settings dialog.

bracketBoundText

JTextField bracketBoundText
DOCUMENT ME!

maxIterationsText

JTextField maxIterationsText
DOCUMENT ME!

numMinText

JTextField numMinText
DOCUMENT ME!

bruteForceCheckBox

JCheckBox bruteForceCheckBox
CheckBox to turn brute-force registration on or off:.

bruteForceDialog

JDialog bruteForceDialog
Dialog to set the brute-force registration parameters:.

buttonWeightInput

JButton buttonWeightInput
DOCUMENT ME!

buttonWeightRef

JButton buttonWeightRef
DOCUMENT ME!

coarseRateText

JTextField coarseRateText
DOCUMENT ME!

comboBoxCostFunct

JComboBox comboBoxCostFunct
DOCUMENT ME!

comboBoxDOF

JComboBox comboBoxDOF
DOCUMENT ME!

comboBoxImage

JComboBox comboBoxImage
DOCUMENT ME!

comboBoxInterp

JComboBox comboBoxInterp
DOCUMENT ME!

comboBoxInterp2

JComboBox comboBoxInterp2
DOCUMENT ME!

cost

int cost
DOCUMENT ME!

interp

int interp
DOCUMENT ME!

interp2

int interp2
DOCUMENT ME!

DOF

int DOF
DOCUMENT ME!

displayTransform

boolean displayTransform
DOCUMENT ME!

doColor

boolean doColor
DOCUMENT ME!

doColorCheckBox

JCheckBox doColorCheckBox
CheckBox to turn color registration on or off:.

doSubsample

boolean doSubsample
DOCUMENT ME!

fileNameWRef

String fileNameWRef
DOCUMENT ME!

directoryWRef

String directoryWRef
DOCUMENT ME!

fileNameWInput

String fileNameWInput
DOCUMENT ME!

directoryWInput

String directoryWInput
DOCUMENT ME!

fineRateText

JTextField fineRateText
DOCUMENT ME!

inputWeightImage

ModelImage inputWeightImage
DOCUMENT ME!

refWeightImage

ModelImage refWeightImage
DOCUMENT ME!

labelCoarse

JLabel labelCoarse
DOCUMENT ME!

labelCoarseDegrees

JLabel labelCoarseDegrees
DOCUMENT ME!

labelFine

JLabel labelFine
DOCUMENT ME!

labelFineDegrees

JLabel labelFineDegrees
DOCUMENT ME!

labelInterp2

JLabel labelInterp2
DOCUMENT ME!

labelRotateDegrees

JLabel labelRotateDegrees
DOCUMENT ME!

labelRotateRange

JLabel labelRotateRange
DOCUMENT ME!

labelRotateRangeTo

JLabel labelRotateRangeTo
DOCUMENT ME!

m_bSubsetDialog

boolean m_bSubsetDialog
If true the dialog for this instance of JDialogRegistrationOAR2D will not activate the AlgorithmRegOAR2D:.

matchImage

ModelImage matchImage
DOCUMENT ME!

maxIterations_def

int maxIterations_def
DOCUMENT ME!

bracketBound_def

int bracketBound_def
DOCUMENT ME!

numMinima_def

int numMinima_def
DOCUMENT ME!

maxIterations

int maxIterations
DOCUMENT ME!

bracketBound

int bracketBound
DOCUMENT ME!

noneRadio

JRadioButton noneRadio
DOCUMENT ME!

numMinima

int numMinima
DOCUMENT ME!

refImage

ModelImage refImage
DOCUMENT ME!

reg2

AlgorithmRegOAR2D reg2
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

rotateBegin

float rotateBegin
DOCUMENT ME!

rotateEnd

float rotateEnd
DOCUMENT ME!

coarseRate

float coarseRate
DOCUMENT ME!

fineRate

float fineRate
DOCUMENT ME!

rotateBeginText

JTextField rotateBeginText
DOCUMENT ME!

rotateEndText

JTextField rotateEndText
DOCUMENT ME!

rotationBF

float rotationBF
DOCUMENT ME!

xscaleBF

float xscaleBF
DOCUMENT ME!

yscaleBF

float yscaleBF
DOCUMENT ME!

rotationText

JTextField rotationText
Brute-force registration parameters:.

translationText

JTextField translationText
Brute-force registration parameters:.

xscaleText

JTextField xscaleText
Brute-force registration parameters:.

yscaleText

JTextField yscaleText
Brute-force registration parameters:.

scaleStepsText

JTextField scaleStepsText
Brute-force registration parameters:.

sampleCheckBox

JCheckBox sampleCheckBox
DOCUMENT ME!

scaleStepsBF

int scaleStepsBF
DOCUMENT ME!

textInput

JTextField textInput
DOCUMENT ME!

textRef

JTextField textRef
DOCUMENT ME!

transformCheckbox

JCheckBox transformCheckbox
DOCUMENT ME!

translationBF

int translationBF
DOCUMENT ME!

UI

ViewUserInterface UI
DOCUMENT ME!

voiRadio

JRadioButton voiRadio
DOCUMENT ME!

voisOnly

boolean voisOnly
DOCUMENT ME!

weighted

boolean weighted
DOCUMENT ME!

weightRadio

JRadioButton weightRadio
DOCUMENT ME!

comAlgo

AlgorithmCenterOfMass comAlgo

threshold

float[] threshold

outOfBoundsLabel

JLabel outOfBoundsLabel

outOfBoundsComboBox

JComboBox outOfBoundsComboBox

valueLabel

JLabel valueLabel

valueText

JTextField valueText

imageMin

double imageMin

imageMax

double imageMax

dataType

int dataType

outOfBoundsIndex

int outOfBoundsIndex
Tells how to select fill value for out of bounds data 0 for image minimum 1 for NaN for float, zero otherwise. 2 for user defined 3 for image maximum

fillValue

float fillValue

Class gov.nih.mipav.view.dialogs.JDialogRegistrationOAR35D extends JDialogScriptableBase implements Serializable

serialVersionUID: -4309868934393418962L

Serialized Fields

doGraph

boolean doGraph
DOCUMENT ME!

adjacentImageRButton

JRadioButton adjacentImageRButton
DOCUMENT ME!

advancedDialog

JDialog advancedDialog
Variables for Advanced Settings dialog.

averageImageRButton

JRadioButton averageImageRButton
DOCUMENT ME!

bracketBoundText

JTextField bracketBoundText
DOCUMENT ME!

maxIterationsText

JTextField maxIterationsText
DOCUMENT ME!

numMinText

JTextField numMinText
DOCUMENT ME!

buttonWeightInput

JButton buttonWeightInput
DOCUMENT ME!

coarseRateText

JTextField coarseRateText
DOCUMENT ME!

comboBoxCostFunct

JComboBox comboBoxCostFunct
DOCUMENT ME!

comboBoxDOF

JComboBox comboBoxDOF
DOCUMENT ME!

comboBoxInterp

JComboBox comboBoxInterp
DOCUMENT ME!

comboBoxInterp2

JComboBox comboBoxInterp2
DOCUMENT ME!

cost

int cost
DOCUMENT ME!

interp

int interp
DOCUMENT ME!

interp2

int interp2
DOCUMENT ME!

DOF

int DOF
DOCUMENT ME!

doColor

boolean doColor
DOCUMENT ME!

doSubsample

boolean doSubsample
DOCUMENT ME!

fastMode

boolean fastMode
DOCUMENT ME!

fastModeCheckbox

JCheckBox fastModeCheckbox
DOCUMENT ME!

fileNameWInput

String fileNameWInput
DOCUMENT ME!

directoryWInput

String directoryWInput
DOCUMENT ME!

fineRateText

JTextField fineRateText
DOCUMENT ME!

graphCheckBox

JCheckBox graphCheckBox
DOCUMENT ME!

inputWeightImage

ModelImage inputWeightImage
DOCUMENT ME!

labelInterp2

JLabel labelInterp2
DOCUMENT ME!

matchImage

ModelImage matchImage
DOCUMENT ME!

maxIterations_def

int maxIterations_def
DOCUMENT ME!

bracketBound_def

int bracketBound_def
DOCUMENT ME!

numMinima_def

int numMinima_def
DOCUMENT ME!

maxIterations

int maxIterations
DOCUMENT ME!

bracketBound

int bracketBound
DOCUMENT ME!

noneRadio

JRadioButton noneRadio
DOCUMENT ME!

numMinima

int numMinima
DOCUMENT ME!

refImageNum

int refImageNum
DOCUMENT ME!

refImageNumText

JTextField refImageNumText
DOCUMENT ME!

refImageRButton

JRadioButton refImageRButton
DOCUMENT ME!

refVolume

ModelImage refVolume
DOCUMENT ME!

reg35

AlgorithmRegOAR35D reg35
DOCUMENT ME!

registerTo

int registerTo
DOCUMENT ME!

rotateBegin

float rotateBegin
DOCUMENT ME!

rotateEnd

float rotateEnd
DOCUMENT ME!

coarseRate

float coarseRate
DOCUMENT ME!

fineRate

float fineRate
DOCUMENT ME!

rotateBeginText

JTextField rotateBeginText
DOCUMENT ME!

rotateEndText

JTextField rotateEndText
DOCUMENT ME!

sampleCheckBox

JCheckBox sampleCheckBox
DOCUMENT ME!

textInput

JTextField textInput
DOCUMENT ME!

UI

ViewUserInterface UI
DOCUMENT ME!

useOutsideReferenceVolume

boolean useOutsideReferenceVolume
DOCUMENT ME!

voiRadio

JRadioButton voiRadio
DOCUMENT ME!

voisOnly

boolean voisOnly
DOCUMENT ME!

weighted

boolean weighted
DOCUMENT ME!

weightRadio

JRadioButton weightRadio
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogRegistrationOAR3D extends JDialogScriptableBase implements Serializable

serialVersionUID: -1461819906844299206L

Serialized Fields

advancedDialog

JDialog advancedDialog
Variables for Advanced Settings dialog.

bracketBoundText

JTextField bracketBoundText
DOCUMENT ME!

maxIterationsText

JTextField maxIterationsText
DOCUMENT ME!

numMinText

JTextField numMinText
DOCUMENT ME!

buttonWeightInput

JButton buttonWeightInput
DOCUMENT ME!

buttonWeightRef

JButton buttonWeightRef
DOCUMENT ME!

calcCOG

boolean calcCOG
DOCUMENT ME!

calcCOGCheckbox

JCheckBox calcCOGCheckbox
DOCUMENT ME!

calcLSBox

JCheckBox calcLSBox
DOCUMENT ME!

coarsePanelX

JPanel coarsePanelX
DOCUMENT ME!

coarsePanelY

JPanel coarsePanelY
DOCUMENT ME!

coarsePanelZ

JPanel coarsePanelZ
DOCUMENT ME!

coarseRateTextX

JTextField coarseRateTextX
DOCUMENT ME!

coarseRateTextY

JTextField coarseRateTextY
DOCUMENT ME!

coarseRateTextZ

JTextField coarseRateTextZ
DOCUMENT ME!

comboBoxCostFunct

JComboBox comboBoxCostFunct
DOCUMENT ME!

comboBoxDOF

JComboBox comboBoxDOF
DOCUMENT ME!

comboBoxImage

JComboBox comboBoxImage
DOCUMENT ME!

comboBoxInterp

JComboBox comboBoxInterp
DOCUMENT ME!

comboBoxInterp2

JComboBox comboBoxInterp2
DOCUMENT ME!

cost

int cost
DOCUMENT ME!

interp

int interp
DOCUMENT ME!

interp2

int interp2
DOCUMENT ME!

DOF

int DOF
DOCUMENT ME!

costName

String costName
DOCUMENT ME!

displayTransform

boolean displayTransform
DOCUMENT ME!

doColor

boolean doColor
DOCUMENT ME!

doLS

boolean doLS
DOCUMENT ME!

doSubsample

boolean doSubsample
DOCUMENT ME!

fastMode

boolean fastMode
DOCUMENT ME!

fastModeCheckbox

JCheckBox fastModeCheckbox
DOCUMENT ME!

fileNameWRef

String fileNameWRef
DOCUMENT ME!

directoryWRef

String directoryWRef
DOCUMENT ME!

fileNameWInput

String fileNameWInput
DOCUMENT ME!

directoryWInput

String directoryWInput
DOCUMENT ME!

finePanelX

JPanel finePanelX
DOCUMENT ME!

finePanelY

JPanel finePanelY
DOCUMENT ME!

finePanelZ

JPanel finePanelZ
DOCUMENT ME!

fineRateTextX

JTextField fineRateTextX
DOCUMENT ME!

fineRateTextY

JTextField fineRateTextY
DOCUMENT ME!

fineRateTextZ

JTextField fineRateTextZ
DOCUMENT ME!

gbc

GridBagConstraints gbc
DOCUMENT ME!

inputWeightImage

ModelImage inputWeightImage
DOCUMENT ME!

refWeightImage

ModelImage refWeightImage
DOCUMENT ME!

labelInterp2

JLabel labelInterp2
DOCUMENT ME!

lsCompleted

boolean lsCompleted
DOCUMENT ME!

lsImage

ModelImage lsImage
DOCUMENT ME!

lsMatrix

TransMatrix lsMatrix
DOCUMENT ME!

matchImage

ModelImage matchImage
DOCUMENT ME!

maxIterations_def

int maxIterations_def
DOCUMENT ME!

bracketBound_def

int bracketBound_def
DOCUMENT ME!

numMinima_def

int numMinima_def
DOCUMENT ME!

maxIterations

int maxIterations
DOCUMENT ME!

bracketBound

int bracketBound
DOCUMENT ME!

maxOfMinResol

boolean maxOfMinResol
DOCUMENT ME!

minMaxCheckbox

JCheckBox minMaxCheckbox
DOCUMENT ME!

noneRadio

JRadioButton noneRadio
DOCUMENT ME!

numMinima

int numMinima
DOCUMENT ME!

refImage

ModelImage refImage
DOCUMENT ME!

reg3

AlgorithmRegOAR3D reg3
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

rotateBeginTextX

JTextField rotateBeginTextX
DOCUMENT ME!

rotateBeginTextY

JTextField rotateBeginTextY
DOCUMENT ME!

rotateBeginTextZ

JTextField rotateBeginTextZ
DOCUMENT ME!

rotateBeginX

float rotateBeginX
DOCUMENT ME!

rotateEndX

float rotateEndX
DOCUMENT ME!

coarseRateX

float coarseRateX
DOCUMENT ME!

fineRateX

float fineRateX
DOCUMENT ME!

rotateBeginY

float rotateBeginY
DOCUMENT ME!

rotateEndY

float rotateEndY
DOCUMENT ME!

coarseRateY

float coarseRateY
DOCUMENT ME!

fineRateY

float fineRateY
DOCUMENT ME!

rotateBeginZ

float rotateBeginZ
DOCUMENT ME!

rotateEndZ

float rotateEndZ
DOCUMENT ME!

coarseRateZ

float coarseRateZ
DOCUMENT ME!

fineRateZ

float fineRateZ
DOCUMENT ME!

rotateEndTextX

JTextField rotateEndTextX
DOCUMENT ME!

rotateEndTextY

JTextField rotateEndTextY
DOCUMENT ME!

rotateEndTextZ

JTextField rotateEndTextZ
DOCUMENT ME!

rotatePanel

JPanel rotatePanel
DOCUMENT ME!

rotateRangePanelX

JPanel rotateRangePanelX
DOCUMENT ME!

rotateRangePanelY

JPanel rotateRangePanelY
DOCUMENT ME!

rotateRangePanelZ

JPanel rotateRangePanelZ
DOCUMENT ME!

sampleCheckbox

JCheckBox sampleCheckbox
DOCUMENT ME!

textInput

JTextField textInput
DOCUMENT ME!

textRef

JTextField textRef
DOCUMENT ME!

transformCheckbox

JCheckBox transformCheckbox
DOCUMENT ME!

UI

ViewUserInterface UI
DOCUMENT ME!

universalCheckbox

JCheckBox universalCheckbox
DOCUMENT ME!

voiRadio

JRadioButton voiRadio
DOCUMENT ME!

voisOnly

boolean voisOnly
DOCUMENT ME!

weighted

boolean weighted
DOCUMENT ME!

weightRadio

JRadioButton weightRadio
DOCUMENT ME!

xRadio

JRadioButton xRadio
DOCUMENT ME!

xSelected

boolean xSelected
DOCUMENT ME!

yRadio

JRadioButton yRadio
DOCUMENT ME!

ySelected

boolean ySelected
DOCUMENT ME!

zRadio

JRadioButton zRadio
DOCUMENT ME!

outOfBoundsLabel

JLabel outOfBoundsLabel

outOfBoundsComboBox

JComboBox outOfBoundsComboBox

valueLabel

JLabel valueLabel

valueText

JTextField valueText

imageMin

double imageMin

imageMax

double imageMax

dataType

int dataType

outOfBoundsIndex

int outOfBoundsIndex
Tells how to select fill value for out of bounds data 0 for image minimum 1 for NaN for float, zero otherwise. 2 for user defined 3 for image maximum

fillValue

float fillValue

Class gov.nih.mipav.view.dialogs.JDialogRegistrationTPSpline extends JDialogScriptableBase implements Serializable

serialVersionUID: 5973812592305647222L

Serialized Fields

baseImage

ModelImage baseImage
DOCUMENT ME!

comboBoxImage

JComboBox comboBoxImage
DOCUMENT ME!

coplanar

boolean coplanar
DOCUMENT ME!

DIM

int DIM
DOCUMENT ME!

matchImage

ModelImage matchImage
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

spline

AlgorithmTPSpline spline
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

UI

ViewUserInterface UI
DOCUMENT ME!

xSource

double[] xSource
DOCUMENT ME!

xTar

double[] xTar
DOCUMENT ME!

ySource

double[] ySource
DOCUMENT ME!

yTar

double[] yTar
DOCUMENT ME!

zSource

double[] zSource
DOCUMENT ME!

zTar

double[] zTar
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogRegistrationTSOAR extends JDialogScriptableBase implements Serializable

serialVersionUID: 5174224884360217569L

Serialized Fields

algoReg

AlgorithmRegTSOAR algoReg
DOCUMENT ME!

comboBoxCostFunct

JComboBox comboBoxCostFunct
DOCUMENT ME!

comboBoxDOF

JComboBox comboBoxDOF
DOCUMENT ME!

comboBoxInterp

JComboBox comboBoxInterp
DOCUMENT ME!

comboBoxInterp2

JComboBox comboBoxInterp2
DOCUMENT ME!

cost

int cost
DOCUMENT ME!

interp

int interp
DOCUMENT ME!

interp2

int interp2
DOCUMENT ME!

DOF

int DOF
DOCUMENT ME!

displayTransform

boolean displayTransform
DOCUMENT ME!

reference

boolean reference
DOCUMENT ME!

doGraph

boolean doGraph
DOCUMENT ME!

doSubsample

boolean doSubsample
DOCUMENT ME!

finalRegistrationAtLevel2

boolean finalRegistrationAtLevel2
DOCUMENT ME!

graphCheckBox

JCheckBox graphCheckBox
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

labelInterp2

JLabel labelInterp2
DOCUMENT ME!

meanButton

JRadioButton meanButton
DOCUMENT ME!

referenceButton

JRadioButton referenceButton
DOCUMENT ME!

refImageNum

int refImageNum
DOCUMENT ME!

refImageNumText

JTextField refImageNumText
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

sampleCheckBox

JCheckBox sampleCheckBox
DOCUMENT ME!

sampleCheckBoxLevel2

JCheckBox sampleCheckBoxLevel2
DOCUMENT ME!

sincCheckBox

JCheckBox sincCheckBox
DOCUMENT ME!

sincNormalizedCrossCorrelation

boolean sincNormalizedCrossCorrelation
DOCUMENT ME!

transformCheckbox

JCheckBox transformCheckbox
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogRegistrationTurbo extends JDialogBase implements Serializable

serialVersionUID: -5462614304976325159L

Serialized Fields

automan

int automan
DOCUMENT ME!

automaticCheckBox

JCheckBox automaticCheckBox
DOCUMENT ME!

comboBoxDistort

JComboBox comboBoxDistort
DOCUMENT ME!

comboBoxImage

JComboBox comboBoxImage
DOCUMENT ME!

comboBoxInterp

JComboBox comboBoxInterp
DOCUMENT ME!

DIM

int DIM
DOCUMENT ME!

entireSource

boolean entireSource
DOCUMENT ME!

entireTarget

boolean entireTarget
DOCUMENT ME!

interpolation

int interpolation
or TRILINEAR_DISTORTION.

resultImage

ModelImage[] resultImage
DOCUMENT ME!

sourceImage

ModelImage sourceImage
DOCUMENT ME!

sourceVOICheckBox

JCheckBox sourceVOICheckBox
DOCUMENT ME!

targetImage

ModelImage targetImage
DOCUMENT ME!

targetVOICheckBox

JCheckBox targetVOICheckBox
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

transformation

int transformation
DOCUMENT ME!

turbo

AlgorithmRegTurbo turbo
DOCUMENT ME!

UI

ViewUserInterface UI
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogRegPatientPos extends JDialogScriptableBase implements Serializable

serialVersionUID: -7190471812525279048L

Serialized Fields

comboBoxImage

JComboBox comboBoxImage
DOCUMENT ME!

doMatch

boolean doMatch
DOCUMENT ME!

imageA

ModelImage imageA
DOCUMENT ME!

imageB

ModelImage imageB
DOCUMENT ME!

matchOrigBox

JCheckBox matchOrigBox
DOCUMENT ME!

RegPatPos

AlgorithmRegPatientPos RegPatPos
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

UI

ViewUserInterface UI
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogRegularizedIsotropicDiffusion extends JDialogScriptableBase implements Serializable

serialVersionUID: 781611739174870058L

Serialized Fields

checkBox25D

JCheckBox checkBox25D
DOCUMENT ME!

contrast

float contrast
DOCUMENT ME!

do25D

boolean do25D
DOCUMENT ME!

numIterations

int numIterations
DOCUMENT ME!

regIsoDiffusionAlgo

AlgorithmRegularizedIsotropicDiffusion regIsoDiffusionAlgo
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

srcImage

ModelImage srcImage
DOCUMENT ME!

stdDev

float stdDev
DOCUMENT ME!

textNumberIterations

JTextField textNumberIterations
DOCUMENT ME!

textGaussian

JTextField textGaussian
DOCUMENT ME!

textContrast

JTextField textContrast
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogRegVOILandmark extends JDialogBase implements Serializable

serialVersionUID: 1515612809506343793L

Serialized Fields

algoRegVOILankmark

AlgorithmRegVOILandmark algoRegVOILankmark
DOCUMENT ME!

comboBoxOpt

JComboBox comboBoxOpt
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

labelminTx

JLabel labelminTx
DOCUMENT ME!

labelmaxTx

JLabel labelmaxTx
DOCUMENT ME!

labelminTy

JLabel labelminTy
DOCUMENT ME!

labelmaxTy

JLabel labelmaxTy
DOCUMENT ME!

labelminRz

JLabel labelminRz
DOCUMENT ME!

labelmaxRz

JLabel labelmaxRz
DOCUMENT ME!

labelStep

JLabel labelStep
DOCUMENT ME!

minDiff

JRadioButton minDiff
DOCUMENT ME!

maxSum

JRadioButton maxSum
DOCUMENT ME!

position

WildMagic.LibFoundation.Mathematics.Vector3f[] position
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

clonedImage

ModelImage clonedImage

scaleX

float scaleX
DOCUMENT ME!

scaleY

float scaleY
DOCUMENT ME!

textGaussX

JTextField textGaussX
DOCUMENT ME!

textGaussY

JTextField textGaussY
DOCUMENT ME!

textStep

JTextField textStep
DOCUMENT ME!

textminTx

JTextField textminTx
DOCUMENT ME!

textmaxTx

JTextField textmaxTx
DOCUMENT ME!

textminTy

JTextField textminTy
DOCUMENT ME!

textmaxTy

JTextField textmaxTy
DOCUMENT ME!

textminRz

JTextField textminRz
DOCUMENT ME!

textmaxRz

JTextField textmaxRz
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

tmpIntensity

float[] tmpIntensity
DOCUMENT ME!

tmpPosition

WildMagic.LibFoundation.Mathematics.Vector3f[] tmpPosition
DOCUMENT ME!

UI

ViewUserInterface UI
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogRemovePlugin extends JDialogBase implements Serializable

serialVersionUID: -6309199966911968353L

Serialized Fields

destroyFileCheckbox

JCheckBox destroyFileCheckbox
Toggles whether or not the plugin file should be deleted from MIPAV's class directory.

list

JList list
List of installed plugins.

Class gov.nih.mipav.view.dialogs.JDialogRemoveSlices extends JDialogScriptableBase implements Serializable

serialVersionUID: 7932215505116955663L

Serialized Fields

checkboxList

JCheckBox[] checkboxList
DOCUMENT ME!

checkboxPanel

JPanel checkboxPanel
DOCUMENT ME!

checkButton

JButton checkButton
DOCUMENT ME!

checkEvenButton

JButton checkEvenButton
DOCUMENT ME!

checkListRemove

boolean[] checkListRemove
DOCUMENT ME!

checkOddButton

JButton checkOddButton
DOCUMENT ME!

destinationGroup

ButtonGroup destinationGroup
DOCUMENT ME!

displayLoc

int displayLoc
DOCUMENT ME!

dontOpenFrame

boolean dontOpenFrame
DOCUMENT ME!

doReplace

boolean doReplace
DOCUMENT ME!

exampleLabel

JLabel exampleLabel
DOCUMENT ME!

exampleLabel2

JLabel exampleLabel2
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

newImage

JRadioButton newImage
DOCUMENT ME!

nSlices

int nSlices
DOCUMENT ME!

numChecked

int numChecked
DOCUMENT ME!

origExtents

int[] origExtents
DOCUMENT ME!

origNDims

int origNDims
DOCUMENT ME!

pressedCheckEven

boolean pressedCheckEven
DOCUMENT ME!

pressedCheckOdd

boolean pressedCheckOdd
DOCUMENT ME!

rangeField

JTextField rangeField
DOCUMENT ME!

removeSlicesAlgo

AlgorithmRemoveSlices removeSlicesAlgo
DOCUMENT ME!

replaceBox

JCheckBox replaceBox
DOCUMENT ME!

replaceImage

JRadioButton replaceImage
DOCUMENT ME!

replaceSlicesAlgo

AlgorithmReplaceRemovedSlices replaceSlicesAlgo
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

scrollPane

JScrollPane scrollPane
DOCUMENT ME!

successful

boolean successful
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

unCheckButton

JButton unCheckButton
DOCUMENT ME!

useRange

JCheckBox useRange
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

insertBlank

boolean insertBlank
If true, insert a blank rather than a weighted average

Class gov.nih.mipav.view.dialogs.JDialogRemoveTSlices extends JDialogScriptableBase implements Serializable

serialVersionUID: -5187681503326982110L

Serialized Fields

checkboxList

JCheckBox[] checkboxList
DOCUMENT ME!

checkboxPanel

JPanel checkboxPanel
DOCUMENT ME!

checkButton

JButton checkButton
DOCUMENT ME!

checkListRemove

boolean[] checkListRemove
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

nChecked

int nChecked
DOCUMENT ME!

nSlices

int nSlices
DOCUMENT ME!

removeTSlicesAlgo

AlgorithmRemoveTSlices removeTSlicesAlgo
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

unCheckButton

JButton unCheckButton
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogReorient extends JDialogScriptableBase implements Serializable

Serialized Fields

algoTrans

AlgorithmTransform algoTrans

image

ModelImage image

template

ModelImage template

resultImage

ModelImage resultImage

orientTypes

String[] orientTypes

newOrientTypes

String[] newOrientTypes

resolutionTypes

String[] resolutionTypes

resolutionIndex

int resolutionIndex

interpTypes

String[] interpTypes

interpType

String interpType

orients

String[] orients

fileInfo

FileInfoBase fileInfo

mainPanel

JPanel mainPanel

labelResType

JLabel labelResType

comboResType

JComboBox comboResType

labelTemplate

JLabel labelTemplate

comboTemplate

JComboBox comboTemplate

labelInterpType

JLabel labelInterpType

comboInterpType

JComboBox comboInterpType

presentOrientLabel2

JLabel presentOrientLabel2

presentOrientBoxX

JComboBox presentOrientBoxX

presentOrientBoxY

JComboBox presentOrientBoxY

presentOrientBoxZ

JComboBox presentOrientBoxZ

or

int[] or

newOrientBox

JComboBox newOrientBox

newOrientBoxX

JComboBox newOrientBoxX

newOrientBoxY

JComboBox newOrientBoxY

newOrientBoxZ

JComboBox newOrientBoxZ

newOr

int[] newOr

Class gov.nih.mipav.view.dialogs.JDialogReplaceBlankSlicesWithAverages extends JDialogScriptableBase implements Serializable

Serialized Fields

rAlgo

AlgorithmReplaceBlankSlicesWithAverages rAlgo
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogReplaceSlice extends JDialogBase implements Serializable

serialVersionUID: -4522782534141992295L

Serialized Fields

image

ModelImage image
DOCUMENT ME!

sliceBox

JComboBox sliceBox
DOCUMENT ME!

sliceField

JTextField sliceField
DOCUMENT ME!

sliceImage

ModelImage sliceImage
DOCUMENT ME!

sliceNum

int sliceNum
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogReplaceValue extends JDialogScriptableBase implements Serializable

serialVersionUID: -4321343995269931526L

Serialized Fields

algoReplace

AlgorithmReplaceValue algoReplace
DOCUMENT ME!

displayLoc

int displayLoc
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

inputVal

double inputVal
DOCUMENT ME!

newImage

JRadioButton newImage
DOCUMENT ME!

outputField

JTextField outputField
DOCUMENT ME!

outputVal

double outputVal
DOCUMENT ME!

rangeString

String rangeString
DOCUMENT ME!

rangesVector

Vector<E> rangesVector
DOCUMENT ME!

replaceImage

JRadioButton replaceImage
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

setChoiceBox

JComboBox setChoiceBox
DOCUMENT ME!

setChoiceButton

JRadioButton setChoiceButton
DOCUMENT ME!

userDefinedButton

JRadioButton userDefinedButton
DOCUMENT ME!

userDefinedField

JTextField userDefinedField
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogReslice extends JDialogScriptableBase implements Serializable

serialVersionUID: 293226884205657186L

Serialized Fields

comboBoxInterp

JComboBox comboBoxInterp
Used for choosing interpolation.

image

ModelImage image
Image to reslice.

mode

int mode
Interpolation mode.

resliceAlgo

AlgorithmReslice resliceAlgo
Reslice algorithm.

resultImage

ModelImage resultImage
resliced image.

userInterface

ViewUserInterface userInterface
User interface pointer.

Class gov.nih.mipav.view.dialogs.JDialogRGBConcat extends JDialogScriptableBase implements Serializable

serialVersionUID: 4183252789435843400L

Serialized Fields

blank

ModelImage blank
DOCUMENT ME!

cBoxRemap

JCheckBox cBoxRemap
DOCUMENT ME!

comboBoxImageBlue

JComboBox comboBoxImageBlue
DOCUMENT ME!

comboBoxImageGreen

JComboBox comboBoxImageGreen
DOCUMENT ME!

comboBoxImageRed

JComboBox comboBoxImageRed
DOCUMENT ME!

destinationGroup

ButtonGroup destinationGroup
DOCUMENT ME!

destinationPanel

JPanel destinationPanel
DOCUMENT ME!

displayLoc

int displayLoc
DOCUMENT ME!

imageB

ModelImage imageB
DOCUMENT ME!

imageG

ModelImage imageG
DOCUMENT ME!

imageR

ModelImage imageR
DOCUMENT ME!

mathAlgo

AlgorithmRGBConcat mathAlgo
DOCUMENT ME!

newImage

JRadioButton newImage
DOCUMENT ME!

remapMode

boolean remapMode
DOCUMENT ME!

replaceImage

JRadioButton replaceImage
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogRGBtoGray extends JDialogScriptableBase implements Serializable

serialVersionUID: 3780026821781916357L

Serialized Fields

blueValue

float blueValue
DOCUMENT ME!

destinationGroup

ButtonGroup destinationGroup
DOCUMENT ME!

destinationPanel

JPanel destinationPanel
DOCUMENT ME!

displayLoc

int displayLoc
DOCUMENT ME!

equalButton

JRadioButton equalButton
DOCUMENT ME!

fInfoBase

FileInfoBase fInfoBase
DOCUMENT ME!

graphicsButton

JRadioButton graphicsButton
DOCUMENT ME!

greenValue

float greenValue
DOCUMENT ME!

imageA

ModelImage imageA
DOCUMENT ME!

intensityAverage

boolean intensityAverage
DOCUMENT ME!

labelR

JLabel labelR
DOCUMENT ME!

labelG

JLabel labelG
DOCUMENT ME!

labelB

JLabel labelB
DOCUMENT ME!

newImage

JRadioButton newImage
DOCUMENT ME!

redValue

float redValue
set the values to the defaults -- based on a default of equal values.

replaceImage

JRadioButton replaceImage
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

RGBAlgo

AlgorithmRGBtoGray RGBAlgo
DOCUMENT ME!

textR

JTextField textR
DOCUMENT ME!

textG

JTextField textG
DOCUMENT ME!

textB

JTextField textB
DOCUMENT ME!

textThreshold

JTextField textThreshold
DOCUMENT ME!

threshold

float threshold
DOCUMENT ME!

thresholdAverage

boolean thresholdAverage
DOCUMENT ME!

thresholdCheckBox

JCheckBox thresholdCheckBox
DOCUMENT ME!

userButton

JRadioButton userButton
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogRGBtoGrays extends JDialogScriptableBase implements Serializable

serialVersionUID: 540686811347959955L

Serialized Fields

imageA

ModelImage imageA
DOCUMENT ME!

resultImageB

ModelImage resultImageB
DOCUMENT ME!

resultImageG

ModelImage resultImageG
DOCUMENT ME!

resultImageR

ModelImage resultImageR
DOCUMENT ME!

RGBAlgo

AlgorithmRGBtoGrays RGBAlgo
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogRGBtoHSB extends JDialogScriptableBase implements Serializable

serialVersionUID: -3386283808285677422L

Serialized Fields

HSBAlgo

AlgorithmRGBtoHSB HSBAlgo
DOCUMENT ME!

imageA

ModelImage imageA
DOCUMENT ME!

resultImageB

ModelImage resultImageB
DOCUMENT ME!

resultImageH

ModelImage resultImageH
DOCUMENT ME!

resultImageS

ModelImage resultImageS
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogRotate extends JDialogScriptableBase implements Serializable

serialVersionUID: 8408959889101739488L

Serialized Fields

image

ModelImage image
Source image for algorithm.

resultImage

ModelImage resultImage
Result image after algorithm has completed.

rotateAlgo

AlgorithmRotate rotateAlgo
DOCUMENT ME!

rotateAxis

int rotateAxis
Rotation axis.

Class gov.nih.mipav.view.dialogs.JDialogSaveDicom extends JDialogBase implements Serializable

serialVersionUID: 7303665224054251504L

Serialized Fields

autofillButton

JButton autofillButton
DOCUMENT ME!

dicomFileInfo

FileInfoDicom dicomFileInfo
DOCUMENT ME!

fileInfo

FileInfoBase fileInfo
DOCUMENT ME!

fillButton

JButton fillButton
DOCUMENT ME!

gbc

GridBagConstraints gbc
DOCUMENT ME!

lateralities

String[] lateralities
DOCUMENT ME!

laterality

JComboBox laterality
DOCUMENT ME!

layout

GridBagLayout layout
DOCUMENT ME!

modalities

String[] modalities
DOCUMENT ME!

parts

String[] parts
DOCUMENT ME!

patientBirthDate

JTextField patientBirthDate
DOCUMENT ME!

patientBirthTime

JTextField patientBirthTime
DOCUMENT ME!

patientComments

JTextField patientComments
DOCUMENT ME!

patientEthnicGroup

JTextField patientEthnicGroup
DOCUMENT ME!

patientID

JTextField patientID
DOCUMENT ME!

patientName

JTextField patientName
DOCUMENT ME!

patientOrientation

JTextField patientOrientation
DOCUMENT ME!

patientOtherIDs

JTextField patientOtherIDs
DOCUMENT ME!

patientOtherNames

JTextField patientOtherNames
DOCUMENT ME!

patientPanel

JPanel patientPanel
DOCUMENT ME!

patientSex

JComboBox patientSex
DOCUMENT ME!

positions

String[] positions
DOCUMENT ME!

requiredPanel

JPanel requiredPanel
DOCUMENT ME!

seriesBody

JComboBox seriesBody
DOCUMENT ME!

seriesDate

JTextField seriesDate
DOCUMENT ME!

seriesDescrip

JTextField seriesDescrip
DOCUMENT ME!

seriesLarge

JTextField seriesLarge
DOCUMENT ME!

seriesMod

JComboBox seriesMod
DOCUMENT ME!

seriesNo

JTextField seriesNo
DOCUMENT ME!

seriesOp

JTextField seriesOp
DOCUMENT ME!

seriesPanel

JPanel seriesPanel
DOCUMENT ME!

seriesPerfPhy

JTextField seriesPerfPhy
DOCUMENT ME!

seriesPos

JComboBox seriesPos
DOCUMENT ME!

seriesProtocol

JTextField seriesProtocol
DOCUMENT ME!

seriesSmall

JTextField seriesSmall
DOCUMENT ME!

seriesStepDate

JTextField seriesStepDate
DOCUMENT ME!

seriesStepDescrip

JTextField seriesStepDescrip
DOCUMENT ME!

seriesStepID

JTextField seriesStepID
DOCUMENT ME!

seriesStepTime

JTextField seriesStepTime
DOCUMENT ME!

seriesTime

JTextField seriesTime
DOCUMENT ME!

seriesUID

JTextField seriesUID
DOCUMENT ME!

sexes

String[] sexes
DOCUMENT ME!

studyAccNumber

JTextField studyAccNumber
DOCUMENT ME!

studyAge

JTextField studyAge
DOCUMENT ME!

studyDate

JTextField studyDate
DOCUMENT ME!

studyDescrip

JTextField studyDescrip
DOCUMENT ME!

studyDiag

JTextField studyDiag
DOCUMENT ME!

studyHist

JTextField studyHist
DOCUMENT ME!

studyID

JTextField studyID
DOCUMENT ME!

studyOcc

JTextField studyOcc
DOCUMENT ME!

studyPanel

JPanel studyPanel
DOCUMENT ME!

studyPhyRead

JTextField studyPhyRead
DOCUMENT ME!

studyPhyRec

JTextField studyPhyRec
DOCUMENT ME!

studyRefPhy

JTextField studyRefPhy
DOCUMENT ME!

studySize

JTextField studySize
DOCUMENT ME!

studyTime

JTextField studyTime
DOCUMENT ME!

studyUID

JTextField studyUID
DOCUMENT ME!

studyWeight

JTextField studyWeight
DOCUMENT ME!

tabPane

JTabbedPane tabPane
DOCUMENT ME!

tagsImportedFromNonDicomImage

Hashtable<K,V> tagsImportedFromNonDicomImage
DICOM tags extracted from the image we want to save. Example: dicom_0xNNNN el_0xNNNN tags stored in MINC headers.

tagsList

Hashtable<K,V> tagsList
The additional tags list is a list of tags the DTI group has requested.

additionalTagsList

Hashtable<K,V> additionalTagsList
The additional tags list is a list of tags the DTI group has requested.

UI

ViewUserInterface UI
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogSaveMergedVOIs extends JDialogBase implements Serializable

Serialized Fields

labelAxialVOI

JLabel labelAxialVOI

labelSagittalVOI

JLabel labelSagittalVOI

labelCoronalVOI

JLabel labelCoronalVOI

labelPlyFile

JLabel labelPlyFile

textFieldAxialVOI

JTextField textFieldAxialVOI
Text field for each VOI and ply file.

textFieldSagittalVOI

JTextField textFieldSagittalVOI
Text field for each VOI and ply file.

textFieldCoronalVOI

JTextField textFieldCoronalVOI
Text field for each VOI and ply file.

textFieldPlyFile

JTextField textFieldPlyFile
Text field for each VOI and ply file.

buttonAxial

JButton buttonAxial
Choose button for each VOI and ply file.

buttonSagittal

JButton buttonSagittal
Choose button for each VOI and ply file.

buttonCoronal

JButton buttonCoronal
Choose button for each VOI and ply file.

buttonPly

JButton buttonPly
Choose button for each VOI and ply file.

VOIsPanel

JPanel VOIsPanel

buttonPanel

JPanel buttonPanel
Button panel to hold the OK button, Cancel button, and Help button.

msgPanel

JPanel msgPanel
Msg box to show the Prostate surface analysis related info.

AxialVOIs

gov.nih.mipav.view.dialogs.InstanceVOI AxialVOIs
Axial VOI instance

SagittalVOIs

gov.nih.mipav.view.dialogs.InstanceVOI SagittalVOIs
Sagittal VOI instance

CoronalVOIs

gov.nih.mipav.view.dialogs.InstanceVOI CoronalVOIs
Coronal VOI instance

PlyInstance

gov.nih.mipav.view.dialogs.InstanceVOI PlyInstance
Ply file instance. This instance only uses the file dir and file name.

Class gov.nih.mipav.view.dialogs.JDialogSaveMinc extends JDialogBase implements Serializable

serialVersionUID: 5951116204923790986L

Serialized Fields

comboX

JComboBox comboX
DOCUMENT ME!

comboY

JComboBox comboY
DOCUMENT ME!

comboZ

JComboBox comboZ
DOCUMENT ME!

defaultAxisOrient

int[] defaultAxisOrient
DOCUMENT ME!

defaultSet

boolean defaultSet
DOCUMENT ME!

defaultXSpace

float defaultXSpace
DOCUMENT ME!

defaultXStart

float defaultXStart
Variables for holding default values. Then if the default values are used (as in, the user hit "OK" without changing any values), that option would be set in "options". This affects the way the script records.

defaultYSpace

float defaultYSpace
DOCUMENT ME!

defaultYStart

float defaultYStart
DOCUMENT ME!

defaultZSpace

float defaultZSpace
DOCUMENT ME!

defaultZStart

float defaultZStart
DOCUMENT ME!

fileInfo

FileInfoBase fileInfo
Variables for holding and storing file information.

options

FileWriteOptions options
DOCUMENT ME!

ori

int[] ori
Axes orientations.

orient

int orient
DOCUMENT ME!

orientLabel

JLabel orientLabel
Variables for the actual GUI; not all need to be global, but just as easy. The text fields and radio buttons do need to be global.

xSpace

JTextField xSpace
DOCUMENT ME!

xStart

JTextField xStart
DOCUMENT ME!

ySpace

JTextField ySpace
DOCUMENT ME!

yStart

JTextField yStart
DOCUMENT ME!

zSpace

JTextField zSpace
DOCUMENT ME!

zStart

JTextField zStart
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogSaveMincVersionChoice extends JDialogBase implements Serializable

Serialized Fields

minc1File

JRadioButton minc1File
Radio button to indicate that an Minc1 CDF mnc file should be written out.

minc2File

JRadioButton minc2File
Radio button to indicate that a Minc2 HDF5 mnc file should be written out.

okayPressed

boolean okayPressed
Whether the window was closed through the user clicking the OK button (and not just killing the dialog).

comboBoxSaveMethod

JComboBox comboBoxSaveMethod
Whether to save as selected by dialog or always as analyze, interfile, or nifti.

Class gov.nih.mipav.view.dialogs.JDialogSaveSlices extends JDialogBase implements Serializable

serialVersionUID: 6208822935229525687L

Serialized Fields

afniEnabled

boolean afniEnabled
DOCUMENT ME!

corEnabled

boolean corEnabled
DOCUMENT ME!

enablePackBitWrite

boolean enablePackBitWrite
DOCUMENT ME!

fourDimEnabled

boolean fourDimEnabled
DOCUMENT ME!

labelDigitNumber

JLabel labelDigitNumber
DOCUMENT ME!

labelFirstSlice

JLabel labelFirstSlice
DOCUMENT ME!

labelFirstTimePeriod

JLabel labelFirstTimePeriod
DOCUMENT ME!

labelLastSlice

JLabel labelLastSlice
DOCUMENT ME!

labelLastTimePeriod

JLabel labelLastTimePeriod
DOCUMENT ME!

labelStartNumber

JLabel labelStartNumber
DOCUMENT ME!

maxTimeValue

int maxTimeValue
DOCUMENT ME!

maxValue

int maxValue
DOCUMENT ME!

minTimeValue

int minTimeValue
DOCUMENT ME!

minValue

int minValue
DOCUMENT ME!

multiFileCheckbox

JCheckBox multiFileCheckbox
DOCUMENT ME!

options

FileWriteOptions options
DOCUMENT ME!

packBitCheckbox

JCheckBox packBitCheckbox
DOCUMENT ME!

slicePanel

JPanel slicePanel
DOCUMENT ME!

textDigitNumber

JTextField textDigitNumber
DOCUMENT ME!

textFirstSlice

JTextField textFirstSlice
DOCUMENT ME!

textFirstTimePeriod

JTextField textFirstTimePeriod
DOCUMENT ME!

textLastSlice

JTextField textLastSlice
DOCUMENT ME!

textLastTimePeriod

JTextField textLastTimePeriod
DOCUMENT ME!

textStartNumber

JTextField textStartNumber
DOCUMENT ME!

tiffEnabled

boolean tiffEnabled
DOCUMENT ME!

tiffPanel

JPanel tiffPanel
DOCUMENT ME!

timeEnabled

boolean timeEnabled
DOCUMENT ME!

timePanel

JPanel timePanel
DOCUMENT ME!

encapJP2Panel

JPanel encapJP2Panel

encapJP2Checkbox

JCheckBox encapJP2Checkbox

saveAsEncapJP2

boolean saveAsEncapJP2

isDicom

boolean isDicom

Class gov.nih.mipav.view.dialogs.JDialogScriptableBase extends JDialogBase implements Serializable

serialVersionUID: 1714695069613762132L

Serialized Fields

scriptParameters

AlgorithmParameters scriptParameters
Contains parameters used to run or record the dialog action, along with some common helper methods.

displayInNewFrame

boolean displayInNewFrame

Class gov.nih.mipav.view.dialogs.JDialogScriptableTransform extends JDialogScriptableBase implements Serializable

serialVersionUID: -7786904359172693422L

Serialized Fields

algoTal

AlgorithmTalairachTransform algoTal
DOCUMENT ME!

algoTrans

AlgorithmTransform algoTrans
or if the source image is to be replaced.

clipCheckbox

JCheckBox clipCheckbox
DOCUMENT ME!

voiCheckbox

JCheckBox voiCheckbox
DOCUMENT ME!

image25DCheckbox

JCheckBox image25DCheckbox
DOCUMENT ME!

updateOriginCheckbox

JCheckBox updateOriginCheckbox
DOCUMENT ME!

invertCheckbox

JCheckBox invertCheckbox
DOCUMENT ME!

comboBoxImage

JComboBox comboBoxImage
DOCUMENT ME!

comboBoxInterp

JComboBox comboBoxInterp
DOCUMENT ME!

comboBoxTalTransform

JComboBox comboBoxTalTransform
DOCUMENT ME!

computeTImage

JRadioButton computeTImage
DOCUMENT ME!

do25D

boolean do25D
DOCUMENT ME!

doRotateCenter

boolean doRotateCenter
DOCUMENT ME!

doTalairach

boolean doTalairach
DOCUMENT ME!

doVOI

boolean doVOI
DOCUMENT ME!

doClip

boolean doClip
DOCUMENT ME!

doPad

boolean doPad
DOCUMENT ME!

setPix

boolean setPix
DOCUMENT ME!

doUpdateOrigin

boolean doUpdateOrigin
DOCUMENT ME!

doInvMat

boolean doInvMat
DOCUMENT ME!

fileTransMatrix

TransMatrix fileTransMatrix
Stores the matrix read in from a file it then can be converted to the corrected axis orientation (i.e. world coordinate and/or left-hand coordinate systems).

image

ModelImage image
DOCUMENT ME!

interp

int interp
DOCUMENT ME!

fillValue

float fillValue

labelOrigin

JLabel labelOrigin

labelResX

JLabel labelResX
DOCUMENT ME!

labelResY

JLabel labelResY
DOCUMENT ME!

labelResZ

JLabel labelResZ
DOCUMENT ME!

labelDimX

JLabel labelDimX
DOCUMENT ME!

labelDimY

JLabel labelDimY
DOCUMENT ME!

labelDimZ

JLabel labelDimZ
DOCUMENT ME!

labelTx

JLabel labelTx
DOCUMENT ME!

labelTy

JLabel labelTy
DOCUMENT ME!

labelTz

JLabel labelTz
DOCUMENT ME!

labelRx

JLabel labelRx
DOCUMENT ME!

labelRy

JLabel labelRy
DOCUMENT ME!

labelRz

JLabel labelRz
DOCUMENT ME!

labelSx

JLabel labelSx
DOCUMENT ME!

labelSy

JLabel labelSy
DOCUMENT ME!

labelSz

JLabel labelSz
DOCUMENT ME!

labelSKx

JLabel labelSKx
DOCUMENT ME!

labelSKy

JLabel labelSKy
DOCUMENT ME!

labelSKz

JLabel labelSKz
DOCUMENT ME!

leftHandSystem

boolean leftHandSystem
If true change matrix to the left-hand coordinate system.

magSlider

JSlider magSlider
DOCUMENT ME!

matrixDeterminationGroup

ButtonGroup matrixDeterminationGroup
DOCUMENT ME!

rotationAxisGroup

ButtonGroup rotationAxisGroup
DOCUMENT ME!

cropOrPad

ButtonGroup cropOrPad
DOCUMENT ME!

matrixFile

String matrixFile
DOCUMENT ME!

matrixFName

JTextField matrixFName
DOCUMENT ME!

max

int max
DOCUMENT ME!

min

int min
DOCUMENT ME!

maximum

JLabel maximum
DOCUMENT ME!

minimum

JLabel minimum
DOCUMENT ME!

current

JLabel current
DOCUMENT ME!

oXdim

int oXdim
DOCUMENT ME!

oYdim

int oYdim
DOCUMENT ME!

oZdim

int oZdim
DOCUMENT ME!

cXdim

int cXdim
DOCUMENT ME!

cYdim

int cYdim
DOCUMENT ME!

cZdim

int cZdim
DOCUMENT ME!

oXres

float oXres
DOCUMENT ME!

oYres

float oYres
DOCUMENT ME!

oZres

float oZres
DOCUMENT ME!

cXres

float cXres
DOCUMENT ME!

cYres

float cYres
DOCUMENT ME!

cZres

float cZres
DOCUMENT ME!

units

int[] units

resampleGroup

ButtonGroup resampleGroup
DOCUMENT ME!

resampleImage

ModelImage resampleImage
DOCUMENT ME!

resampletoUser

JRadioButton resampletoUser
DOCUMENT ME!

resampletoImage

JRadioButton resampletoImage
DOCUMENT ME!

resampleSlider

JRadioButton resampleSlider
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

rotCenter

JRadioButton rotCenter
DOCUMENT ME!

rotOrigin

JRadioButton rotOrigin
DOCUMENT ME!

cropRadio

JRadioButton cropRadio
DOCUMENT ME!

padRadio

JRadioButton padRadio
DOCUMENT ME!

storedMatrix

JRadioButton storedMatrix
DOCUMENT ME!

noTransform

JRadioButton noTransform
DOCUMENT ME!

userDefinedMatrix

JRadioButton userDefinedMatrix
DOCUMENT ME!

fileMatrix

JRadioButton fileMatrix
DOCUMENT ME!

storedMatrixBox

JComboBox storedMatrixBox

textResX

JTextField textResX
DOCUMENT ME!

textResY

JTextField textResY
DOCUMENT ME!

textResZ

JTextField textResZ
DOCUMENT ME!

textDimX

JTextField textDimX
DOCUMENT ME!

textDimY

JTextField textDimY
DOCUMENT ME!

textDimZ

JTextField textDimZ
DOCUMENT ME!

textTx

JTextField textTx
DOCUMENT ME!

textTy

JTextField textTy
DOCUMENT ME!

textTz

JTextField textTz
DOCUMENT ME!

textRx

JTextField textRx
DOCUMENT ME!

textRy

JTextField textRy
DOCUMENT ME!

textRz

JTextField textRz
DOCUMENT ME!

textSx

JTextField textSx
DOCUMENT ME!

textSy

JTextField textSy
DOCUMENT ME!

textSz

JTextField textSz
DOCUMENT ME!

textSKx

JTextField textSKx
DOCUMENT ME!

textSKy

JTextField textSKy
DOCUMENT ME!

textSKz

JTextField textSKz
DOCUMENT ME!

tInfo

TalairachTransformInfo tInfo
DOCUMENT ME!

transformType

int transformType
DOCUMENT ME!

tVal

String[] tVal
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

wcSystem

boolean wcSystem
If true change matrix to the world coordinate system.

xfrm

TransMatrix xfrm
DOCUMENT ME!

xyAspectRatio

JCheckBox xyAspectRatio
DOCUMENT ME!

xyzAspectRatio

JCheckBox xyzAspectRatio
DOCUMENT ME!

fieldOfView

JCheckBox fieldOfView
DOCUMENT ME!

setPixels

JCheckBox setPixels
DOCUMENT ME!

useSACenterBox

JCheckBox useSACenterBox
checkbox telling the algorithm to use the scanner coordinate center rather than the image center

useSACenter

boolean useSACenter

tabbedPane

JTabbedPane tabbedPane
Tabbed pane

isSATransform

boolean isSATransform
is this a scanner anatomical transform (->AXIAL)

enableSATransform

boolean enableSATransform

constantFOV

int constantFOV
We use the constant to preserve the FOV. Either 1 or 0;

interpFOVgroup

ButtonGroup interpFOVgroup
Button group for interpolation type, contant FOV or start, end matching.

constantFOVradio

JRadioButton constantFOVradio
Radio button for constant FOV interpolation.

endMatchFOVradio

JRadioButton endMatchFOVradio
Radio button for slice start & end matching interpolation.

dims

float[] dims

resols

float[] resols

outOfBoundsLabel

JLabel outOfBoundsLabel

outOfBoundsComboBox

JComboBox outOfBoundsComboBox

valueLabel

JLabel valueLabel

valueText

JTextField valueText

imageMin

double imageMin

imageMax

double imageMax

dataType

int dataType

outOfBoundsIndex

int outOfBoundsIndex
Tells how to select fill value for out of bounds data 0 for image minimum 1 for NaN for float, zero otherwise. 2 for user defined 3 for image maximum

Class gov.nih.mipav.view.dialogs.JDialogScriptRecorder extends JDialogBase implements Serializable

serialVersionUID: -8409175669783444792L

Serialized Fields

editButton

JButton editButton
DOCUMENT ME!

instructionLabel

JLabel instructionLabel
DOCUMENT ME!

message

String message
DOCUMENT ME!

pauseButton

JButton pauseButton
DOCUMENT ME!

pauseButton2

JButton pauseButton2
DOCUMENT ME!

scriptTextArea

JTextArea scriptTextArea
DOCUMENT ME!

scriptRecorder

ScriptRecorder scriptRecorder
A reference to the global MIPAV script recorder. This dialog listens to changes in its status and script.

Class gov.nih.mipav.view.dialogs.JDialogSelectChannelSequence extends JDialogBase implements Serializable

serialVersionUID: 7969429539433435403L

Serialized Fields

channelOrder

int[] channelOrder
DOCUMENT ME!

comboBoxes

JComboBox[] comboBoxes
DOCUMENT ME!

parent

ViewOpenImageSequence parent
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogSelectDICOMColumnHeaders extends JDialogBase implements Serializable

serialVersionUID: 5883528252352616682L

Serialized Fields

listPanel

ViewSelectableDoubleListPanel listPanel
DOCUMENT ME!

parentFrame

ViewJFrameDICOMParser parentFrame
DOCUMENT ME!

rightTable

JTable rightTable
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogServer extends JDialogBase implements Serializable

serialVersionUID: 1348641833737787663L

Serialized Fields

alias

String alias
DOCUMENT ME!

aliasField

JTextField aliasField
DOCUMENT ME!

aliasLabel

JLabel aliasLabel
DOCUMENT ME!

ip

String ip
DOCUMENT ME!

ipField

JTextField ipField
DOCUMENT ME!

ipLabel

JLabel ipLabel
DOCUMENT ME!

port

String port
DOCUMENT ME!

portField

JTextField portField
DOCUMENT ME!

portLabel

JLabel portLabel
DOCUMENT ME!

server

boolean server
DOCUMENT ME!

title

String title
DOCUMENT ME!

titleField

JTextField titleField
DOCUMENT ME!

titleLabel

JLabel titleLabel
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogShortcutEditor extends JDialogBase implements Serializable

serialVersionUID: -6964789155088488701L

Serialized Fields

addShortcut

JButton addShortcut
add shortcut button.

currentShortcut

KeyStroke currentShortcut
Keystroke built from shortcut editor dialog.

defaultShortcutModel

ViewTableModel defaultShortcutModel
DOCUMENT ME!

defaultShortcutTable

JTable defaultShortcutTable
DOCUMENT ME!

masterScrollPane

JScrollPane masterScrollPane
master scroll pane in which to display all information.

removeShortcut

JButton removeShortcut
button for removing shortcuts.

scrollingBox

Box scrollingBox
Box to hold table information.

userDefinedShortcutModel

ViewTableModel userDefinedShortcutModel
DOCUMENT ME!

userDefinedShortcutTable

JTable userDefinedShortcutTable
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogShowCosts extends JDialogBase implements Serializable

serialVersionUID: 7737847738523057492L

Serialized Fields

algoCost

AlgorithmCostFunctions algoCost
DOCUMENT ME!

algoCost2D

AlgorithmCostFunctions2D algoCost2D
DOCUMENT ME!

bin1

int bin1
DOCUMENT ME!

bin2

int bin2
DOCUMENT ME!

bin1Default

boolean bin1Default
DOCUMENT ME!

bin2Default

boolean bin2Default
DOCUMENT ME!

bin1Label

JLabel bin1Label
DOCUMENT ME!

bin2Label

JLabel bin2Label
DOCUMENT ME!

bin1Text

JTextField bin1Text
DOCUMENT ME!

bin2Text

JTextField bin2Text
DOCUMENT ME!

currentCostFunct

String currentCostFunct
DOCUMENT ME!

doLinearRescale

boolean doLinearRescale
DOCUMENT ME!

firstImage

ModelImage firstImage
DOCUMENT ME!

imageComboBox

JComboBox imageComboBox
DOCUMENT ME!

labelImage

JLabel labelImage
DOCUMENT ME!

linearCheckbox

JCheckBox linearCheckbox
DOCUMENT ME!

possibleIntValues1

double possibleIntValues1
DOCUMENT ME!

possibleIntValues2

double possibleIntValues2
DOCUMENT ME!

secondImage

ModelImage secondImage
DOCUMENT ME!

simpleImg1

ModelSimpleImage simpleImg1
DOCUMENT ME!

simpleImg2

ModelSimpleImage simpleImg2
DOCUMENT ME!

smoothSize

float smoothSize
DOCUMENT ME!

tMatrix

TransMatrix tMatrix
DOCUMENT ME!

UI

ViewUserInterface UI
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogSingleMRIImageSNR extends JDialogBase implements Serializable

serialVersionUID: 4621550176907564448L

Serialized Fields

backgroundButton

JRadioButton backgroundButton
DOCUMENT ME!

backgroundIndex

int backgroundIndex
DOCUMENT ME!

componentImage

ViewJComponentEditImage componentImage
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

labelReceiver

JLabel labelReceiver
DOCUMENT ME!

nBoundingVOIs

int nBoundingVOIs
DOCUMENT ME!

numReceivers

int numReceivers
DOCUMENT ME!

signal2Button

JRadioButton signal2Button
DOCUMENT ME!

signal2Index

int signal2Index
DOCUMENT ME!

signalButton

JRadioButton signalButton
DOCUMENT ME!

signalIndex

int signalIndex
DOCUMENT ME!

snrAlgo

AlgorithmSingleMRIImageSNR snrAlgo
DOCUMENT ME!

textReceiver

JTextField textReceiver
DOCUMENT ME!

VOIGroup

ButtonGroup VOIGroup
DOCUMENT ME!

VOIs

ViewVOIVector VOIs
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogSkeletonize extends JDialogScriptableBase implements Serializable

Serialized Fields

do25D

boolean do25D
DOCUMENT ME!

skeletonizeAlgo25D

AlgorithmMorphology25D skeletonizeAlgo25D
DOCUMENT ME!

skeletonizeAlgo2D

AlgorithmMorphology2D skeletonizeAlgo2D
DOCUMENT ME!

skeletonizeAlgo3D

AlgorithmMorphology3D skeletonizeAlgo3D
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

image25D

JCheckBox image25D
DOCUMENT ME!

labelPrune

JLabel labelPrune
DOCUMENT ME!

maskPanelSkeletonize

JPanel maskPanelSkeletonize
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

textPrune

JTextField textPrune
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

numPruningPixels

int numPruningPixels
Number of pixels to prune

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

outputPanel

JPanelAlgorithmOutputOptions outputPanel

Class gov.nih.mipav.view.dialogs.JDialogSkeletonize3D extends JDialogBase implements Serializable

serialVersionUID: 4112815251500514340L

Serialized Fields

chooserButton

JButton chooserButton
DOCUMENT ME!

distCharges

int distCharges
DOCUMENT ME!

fieldGroup

ButtonGroup fieldGroup
DOCUMENT ME!

fieldStrength

int fieldStrength
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

lineButton

JRadioButton lineButton
DOCUMENT ME!

loadButton

JRadioButton loadButton
DOCUMENT ME!

minObjectValue

float minObjectValue
DOCUMENT ME!

noLoadSaveButton

JRadioButton noLoadSaveButton
DOCUMENT ME!

outputGroup

ButtonGroup outputGroup
DOCUMENT ME!

outputPoints

boolean outputPoints
DOCUMENT ME!

perHDPoints

float perHDPoints
DOCUMENT ME!

pointButton

JRadioButton pointButton
DOCUMENT ME!

removeButton

JButton removeButton
DOCUMENT ME!

saveButton

JRadioButton saveButton
DOCUMENT ME!

saveVF

boolean saveVF
DOCUMENT ME!

skeletonize3DAlgo

AlgorithmSkeletonize3D skeletonize3DAlgo
DOCUMENT ME!

skelNumPoints

int skelNumPoints
DOCUMENT ME!

skelNumSegments

int skelNumSegments
DOCUMENT ME!

skPoints

double[][] skPoints
DOCUMENT ME!

skSegments

int[][] skSegments
DOCUMENT ME!

sliceHoleFilling

boolean sliceHoleFilling
DOCUMENT ME!

sliceHoleFillingCheckBox

JCheckBox sliceHoleFillingCheckBox
DOCUMENT ME!

textDistCharges

JTextField textDistCharges
DOCUMENT ME!

textDivergencePoints

JTextField textDivergencePoints
DOCUMENT ME!

textFieldStrength

JTextField textFieldStrength
DOCUMENT ME!

textMinObjectValue

JTextField textMinObjectValue
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

vfImage

ModelImage[] vfImage
DOCUMENT ME!

vfModel

DefaultListModel vfModel
DOCUMENT ME!

vfName

String vfName
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogSkelGeom3D extends JDialogBase implements Serializable

serialVersionUID: -2336835186270980754L

Serialized Fields

bad

boolean bad
DOCUMENT ME!

deep

float deep
DOCUMENT ME!

defer

boolean defer
DOCUMENT ME!

estR

float estR
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

minObjectValue

float minObjectValue
DOCUMENT ME!

noPropCheckBox

JCheckBox noPropCheckBox
DOCUMENT ME!

skelGeom3DAlgo

AlgorithmSkelGeom3D skelGeom3DAlgo
DOCUMENT ME!

sliceHoleFilling

boolean sliceHoleFilling
DOCUMENT ME!

sliceHoleFillingCheckBox

JCheckBox sliceHoleFillingCheckBox
DOCUMENT ME!

textMinObjectValue

JTextField textMinObjectValue
DOCUMENT ME!

textSamplingDensity

JTextField textSamplingDensity
DOCUMENT ME!

textWCosine

JTextField textWCosine
DOCUMENT ME!

throwAwayCheckBox

JCheckBox throwAwayCheckBox
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogSliceAveraging extends JDialogScriptableBase implements Serializable

serialVersionUID: -6973307260738815367L

Serialized Fields

allButton

JRadioButton allButton
DOCUMENT ME!

averagingNumber

int averagingNumber
DOCUMENT ME!

destExtents

int[] destExtents
DOCUMENT ME!

destinationGroup

ButtonGroup destinationGroup
DOCUMENT ME!

destinationPanel

JPanel destinationPanel
DOCUMENT ME!

displayLoc

int displayLoc
DOCUMENT ME!

fiveButton

JRadioButton fiveButton
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

newImage

JRadioButton newImage
DOCUMENT ME!

numberGroup

ButtonGroup numberGroup
DOCUMENT ME!

optionsPanel

JPanel optionsPanel
DOCUMENT ME!

replaceImage

JRadioButton replaceImage
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

sAverAlgo

AlgorithmSliceAveraging sAverAlgo
DOCUMENT ME!

sevenButton

JRadioButton sevenButton
DOCUMENT ME!

sliceNumber

int sliceNumber
DOCUMENT ME!

threeButton

JRadioButton threeButton
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogSmoothMesh extends JDialogBase implements Serializable

serialVersionUID: -4644401872827443236L

Serialized Fields

alpha

float alpha
Alpha smoothing factor.

alphaText

JTextField alphaText
Text field for getting alpha smoothing factor.

stiffness

float stiffness
stiffness.

stiffnessText

JTextField stiffnessText
Text field for getting stiffness for smoothing.

lambda

float lambda
positive scale factor.

lambdaText

JTextField lambdaText
Text field for getting lambda for smoothing.

mu

float mu
negative scale factor.

muText

JTextField muText
Volume text field.

mainPanel

JPanel mainPanel
main panel containing interface:

iterations

int iterations
Number of iterations for smoothing formula.

iterationsText

JTextField iterationsText
Text field for getting iterations.

limitCheckBox

JCheckBox limitCheckBox
If limitCheckBox is selected iterations stop when volume change from initial volume is greater than or equal to volumePercent.

volumeLimit

boolean volumeLimit
flag indicates volume is greater than or equal to volumePercent.

volumePercent

float volumePercent
Volume percentage.

volumeText

JTextField volumeText
Volume text field.

Class gov.nih.mipav.view.dialogs.JDialogSnake extends JDialogBase implements Serializable

serialVersionUID: -6160718529233426119L

Serialized Fields

boundaryDir

int boundaryDir
DOCUMENT ME!

boundaryDirBox

JComboBox boundaryDirBox
DOCUMENT ME!

boundaryIterations

int boundaryIterations
DOCUMENT ME!

groupNum

int groupNum
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

labelCorrected

JLabel labelCorrected
DOCUMENT ME!

normFactor

float normFactor
DOCUMENT ME!

propagate

JRadioButton propagate
DOCUMENT ME!

propagationType

int propagationType
DOCUMENT ME!

removeOriginal

boolean removeOriginal
DOCUMENT ME!

removeOriginalCheckBox

JCheckBox removeOriginalCheckBox
DOCUMENT ME!

resolutionCheckbox

JCheckBox resolutionCheckbox
DOCUMENT ME!

scaleX

float scaleX
DOCUMENT ME!

scaleY

float scaleY
DOCUMENT ME!

scaleZ

float scaleZ
DOCUMENT ME!

singleSlice

JRadioButton singleSlice
DOCUMENT ME!

smoothness

float smoothness
DOCUMENT ME!

snakeAlgo

AlgorithmSnake snakeAlgo
DOCUMENT ME!

srcVOI

VOI srcVOI
DOCUMENT ME!

textBoundaryIterations

JTextField textBoundaryIterations
DOCUMENT ME!

textGaussX

JTextField textGaussX
DOCUMENT ME!

textGaussY

JTextField textGaussY
DOCUMENT ME!

textGaussZ

JTextField textGaussZ
DOCUMENT ME!

textSmoothness

JTextField textSmoothness
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

voiColor

Color voiColor
DOCUMENT ME!

VOIs

ViewVOIVector VOIs
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogStandardDeviationThreshold extends JDialogScriptableBase implements Serializable

Serialized Fields

srcImage

ModelImage srcImage
src image, result image

resultImage

ModelImage resultImage
src image, result image

VOIs

ViewVOIVector VOIs
vois in image

groupNum

int groupNum
number for id of VOI

srcVOI

VOI srcVOI
src VOI used for thresholding ME!

algoVOI

AlgorithmVOIProps algoVOI
handle to algorithm

UI

ViewUserInterface UI
handle to UI

mainPanel

JPanel mainPanel
panels

voiStatsPanel

JPanel voiStatsPanel
panels

voiStatsLeftPanel

JPanel voiStatsLeftPanel
panels

voiStatsRightPanel

JPanel voiStatsRightPanel
panels

thresholdParametersPanel

JPanel thresholdParametersPanel
panels

thresholdParametersLeftPanel

JPanel thresholdParametersLeftPanel
panels

thresholdParametersRightPanel

JPanel thresholdParametersRightPanel
panels

destinationPanel

JPanel destinationPanel
panels

thresholdPanel

JPanel thresholdPanel
panels

stdDevTextField

JTextField stdDevTextField
text fields

stdDevTextFieldR

JTextField stdDevTextFieldR
text fields

stdDevTextFieldG

JTextField stdDevTextFieldG
text fields

stdDevTextFieldB

JTextField stdDevTextFieldB
text fields

valuesOutsideTextField

JTextField valuesOutsideTextField
text fields

valuesOutsideTextFieldR

JTextField valuesOutsideTextFieldR
text fields

valuesOutsideTextFieldG

JTextField valuesOutsideTextFieldG
text fields

valuesOutsideTextFieldB

JTextField valuesOutsideTextFieldB
text fields

inverseThresholdCheckBox

JCheckBox inverseThresholdCheckBox
checkbox for inverse threshold

setMinThresholdCheckBox

JCheckBox setMinThresholdCheckBox
checkbox for inverse threshold

setMinThresholdCheckBoxR

JCheckBox setMinThresholdCheckBoxR
checkbox for inverse threshold

setMinThresholdCheckBoxG

JCheckBox setMinThresholdCheckBoxG
checkbox for inverse threshold

setMinThresholdCheckBoxB

JCheckBox setMinThresholdCheckBoxB
checkbox for inverse threshold

setMaxThresholdCheckBox

JCheckBox setMaxThresholdCheckBox
checkbox for inverse threshold

setMaxThresholdCheckBoxR

JCheckBox setMaxThresholdCheckBoxR
checkbox for inverse threshold

setMaxThresholdCheckBoxG

JCheckBox setMaxThresholdCheckBoxG
checkbox for inverse threshold

setMaxThresholdCheckBoxB

JCheckBox setMaxThresholdCheckBoxB
checkbox for inverse threshold

maxIntensity

float maxIntensity
max intensities calculatd using std dev

maxIntensityR

float maxIntensityR
max intensities calculatd using std dev

maxIntensityG

float maxIntensityG
max intensities calculatd using std dev

maxIntensityB

float maxIntensityB
max intensities calculatd using std dev

minIntensity

float minIntensity
min intensities calculatd using std dev

minIntensityR

float minIntensityR
min intensities calculatd using std dev

minIntensityG

float minIntensityG
min intensities calculatd using std dev

minIntensityB

float minIntensityB
min intensities calculatd using std dev

avgIntensity

float avgIntensity
average intensities in VOI

avgIntensityR

float avgIntensityR
average intensities in VOI

avgIntensityG

float avgIntensityG
average intensities in VOI

avgIntensityB

float avgIntensityB
average intensities in VOI

stdDev

float stdDev
standard deviations in VOI

stdDevR

float stdDevR
standard deviations in VOI

stdDevG

float stdDevG
standard deviations in VOI

stdDevB

float stdDevB
standard deviations in VOI

numStdDev

float numStdDev
number of standard deviations used in thresholding

numStdDevR

float numStdDevR
number of standard deviations used in thresholding

numStdDevG

float numStdDevG
number of standard deviations used in thresholding

numStdDevB

float numStdDevB
number of standard deviations used in thresholding

valuesOutside

float valuesOutside
intensity values to be used in thresholding

valuesOutsideR

float valuesOutsideR
intensity values to be used in thresholding

valuesOutsideG

float valuesOutsideG
intensity values to be used in thresholding

valuesOutsideB

float valuesOutsideB
intensity values to be used in thresholding

alg

AlgorithmStandardDeviationThreshold alg
handle to algorithm

newImageRadio

JRadioButton newImageRadio
radio buttons

paintRadio

JRadioButton paintRadio
radio buttons

wholeImageRadio

JRadioButton wholeImageRadio
radio buttons

voiRegionsRadio

JRadioButton voiRegionsRadio
radio buttons

destinationRadioGroup

ButtonGroup destinationRadioGroup
radio groups

thresholdRadioGroup

ButtonGroup thresholdRadioGroup
radio groups

newImageDestination

boolean newImageDestination
flags for destination and threshold

wholeImageThreshold

boolean wholeImageThreshold
flags for destination and threshold

isColorImage

boolean isColorImage
boolean for color image

inverseThreshold

boolean inverseThreshold
boolean for inverse threshold

outMax

double outMax
image type max

outMin

double outMin
image type min

scriptFail

boolean scriptFail
boolean telling if script failed

numPixels

int numPixels

sumPixelInten

double sumPixelInten

sumPixelIntenR

double sumPixelIntenR

sumPixelIntenG

double sumPixelIntenG

sumPixelIntenB

double sumPixelIntenB

Class gov.nih.mipav.view.dialogs.JDialogSubsample extends JDialogScriptableBase implements Serializable

serialVersionUID: 3213495943646123969L

Serialized Fields

algoSub

AlgorithmSubsample algoSub
DOCUMENT ME!

by2Button

JRadioButton by2Button
DOCUMENT ME!

by4Button

JRadioButton by4Button
DOCUMENT ME!

by8Button

JRadioButton by8Button
DOCUMENT ME!

label2OriginalExtentX

JLabel label2OriginalExtentX
Label for displaying the original extent X

label2OriginalExtentY

JLabel label2OriginalExtentY
Label for displaying the original extent Y

label2OriginalExtentZ

JLabel label2OriginalExtentZ
Label for displaying the original extent Z

labelPaddedExtentX

JLabel labelPaddedExtentX
Label for displaying the padded extent X

labelPaddedExtentY

JLabel labelPaddedExtentY
Label for displaying the padded extent Y

labelPaddedExtentZ

JLabel labelPaddedExtentZ
label for displaying the padded extent Z

denom

int denom
DOCUMENT ME!

doVOI

boolean doVOI
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

dim

int dim
Number of dimensions in an image e.g 2D, 3D

doPad

boolean doPad
The boolean value to determine whether to pad the original image or not.

extents

int[] extents
The extents of original image

padExtents

int[] padExtents
The extents of padded image

newExtents

int[] newExtents
DOCUMENT ME!

oXres

float oXres
DOCUMENT ME!

oYres

float oYres
DOCUMENT ME!

oZres

float oZres
DOCUMENT ME!

processIndep

boolean processIndep
DOCUMENT ME!

processIndepBox

JCheckBox processIndepBox
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

sigmas

float[] sigmas
DOCUMENT ME!

Sx

float Sx
DOCUMENT ME!

Sy

float Sy
DOCUMENT ME!

Sz

float Sz
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

voiCheckBox

JCheckBox voiCheckBox
DOCUMENT ME!

xfrm

TransMatrix xfrm
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogSubset extends JDialogScriptableBase implements Serializable

serialVersionUID: 7757821847126335458L

Serialized Fields

destExtents

int[] destExtents
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

labelSlice

JLabel labelSlice
DOCUMENT ME!

removeDim

int removeDim
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

resultString

String resultString
DOCUMENT ME!

sliceNum

int sliceNum
DOCUMENT ME!

subsetAlgo

AlgorithmSubset subsetAlgo
DOCUMENT ME!

textSlice

JTextField textSlice
DOCUMENT ME!

textString

String textString
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

tSlices

int tSlices
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

xButton

JRadioButton xButton
DOCUMENT ME!

yButton

JRadioButton yButton
DOCUMENT ME!

zButton

JRadioButton zButton
DOCUMENT ME!

tButton

JRadioButton tButton
DOCUMENT ME!

xSlices

int xSlices
DOCUMENT ME!

ySlices

int ySlices
DOCUMENT ME!

zSlices

int zSlices
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogSubtractVOI extends JDialogScriptableBase implements Serializable

serialVersionUID: 3133054636469390689L

Serialized Fields

averageMode

int averageMode
DOCUMENT ME!

clipGroup

ButtonGroup clipGroup
DOCUMENT ME!

clipMode

int clipMode
DOCUMENT ME!

clipPanel

JPanel clipPanel
DOCUMENT ME!

destinationGroup

ButtonGroup destinationGroup
DOCUMENT ME!

destinationPanel

JPanel destinationPanel
DOCUMENT ME!

displayLoc

int displayLoc
DOCUMENT ME!

group

ButtonGroup group
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

inputPanel

JPanel inputPanel
DOCUMENT ME!

newImage

JRadioButton newImage
DOCUMENT ME!

radioClip

JRadioButton radioClip
DOCUMENT ME!

radioMean

JRadioButton radioMean
DOCUMENT ME!

radioMedian

JRadioButton radioMedian
DOCUMENT ME!

radioPromote

JRadioButton radioPromote
DOCUMENT ME!

replaceImage

JRadioButton replaceImage
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

subVOIAlgo

AlgorithmSubtractVOI subVOIAlgo
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogSwap34 extends JDialogScriptableBase implements Serializable

serialVersionUID: 8107279710815271509L

Serialized Fields

doClose

boolean doClose
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

imageName

String imageName
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

swap34Algo

AlgorithmSwap34 swap34Algo
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogSwapDims extends JDialogScriptableBase implements Serializable

serialVersionUID: 8107279710815271509L

Serialized Fields

doClose

boolean doClose
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

imageName

String imageName
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

swapDimsAlgo

AlgorithmSwapDims swapDimsAlgo
DOCUMENT ME!

swapType

int swapType

Class gov.nih.mipav.view.dialogs.JDialogTalairach extends JDialogBase implements Serializable

serialVersionUID: -2923298916025034767L

Serialized Fields

anotherPtDicom

WildMagic.LibFoundation.Mathematics.Vector3f anotherPtDicom
DOCUMENT ME!

anteriorPt

JRadioButton anteriorPt
DOCUMENT ME!

anteriorPt3Df

WildMagic.LibFoundation.Mathematics.Vector3f anteriorPt3Df
DOCUMENT ME!

applyTalairachButton

JButton applyTalairachButton
DOCUMENT ME!

cancelTalairachButton

JButton cancelTalairachButton
DOCUMENT ME!

clearTalairachButton

JButton clearTalairachButton
DOCUMENT ME!

firstPtDicom

WildMagic.LibFoundation.Mathematics.Vector3f firstPtDicom
DOCUMENT ME!

frame

ViewJFrameTriImage frame
DOCUMENT ME!

haveAnteriorPt

boolean haveAnteriorPt
DOCUMENT ME!

haveInferiorPt

boolean haveInferiorPt
DOCUMENT ME!

haveLeftPt

boolean haveLeftPt
DOCUMENT ME!

havePosteriorPt

boolean havePosteriorPt
DOCUMENT ME!

haveRightPt

boolean haveRightPt
DOCUMENT ME!

haveSuperiorPt

boolean haveSuperiorPt
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

inferiorEdgeDicom

WildMagic.LibFoundation.Mathematics.Vector3f inferiorEdgeDicom
DOCUMENT ME!

inferiorPt

JRadioButton inferiorPt
DOCUMENT ME!

inferiorPt3Df

WildMagic.LibFoundation.Mathematics.Vector3f inferiorPt3Df
DOCUMENT ME!

leftPt

JRadioButton leftPt
DOCUMENT ME!

leftPt3Df

WildMagic.LibFoundation.Mathematics.Vector3f leftPt3Df
DOCUMENT ME!

posteriorMarginDicom

WildMagic.LibFoundation.Mathematics.Vector3f posteriorMarginDicom
DOCUMENT ME!

posteriorPt

JRadioButton posteriorPt
DOCUMENT ME!

posteriorPt3Df

WildMagic.LibFoundation.Mathematics.Vector3f posteriorPt3Df
DOCUMENT ME!

rightPt

JRadioButton rightPt
DOCUMENT ME!

rightPt3Df

WildMagic.LibFoundation.Mathematics.Vector3f rightPt3Df
DOCUMENT ME!

setTalairachButton

JButton setTalairachButton
DOCUMENT ME!

superiorEdgeDicom

WildMagic.LibFoundation.Mathematics.Vector3f superiorEdgeDicom
DOCUMENT ME!

superiorPt

JRadioButton superiorPt
DOCUMENT ME!

superiorPt3Df

WildMagic.LibFoundation.Mathematics.Vector3f superiorPt3Df
DOCUMENT ME!

tOffset

int tOffset
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogTalairachTransform extends JDialogBase implements Serializable

Serialized Fields

algo

AlgorithmTalairachTransform algo

acpcDialog

JDialogACPC acpcDialog

tlrcDialog

JDialogTLRC tlrcDialog

image

ModelImage image

otherImage

ModelImage otherImage

resultImage

ModelImage resultImage

acpcImage

ModelImage acpcImage

tlrcImage

ModelImage tlrcImage

destExtents

int[] destExtents

userInterface

ViewUserInterface userInterface

title

String title

transformType

String transformType

transform

TalairachTransformInfo transform

interpolation

String interpolation

talairachPanel

JPanel talairachPanel

newImagePanel

JPanel newImagePanel

computeACPC

JButton computeACPC

computeTLRC

JButton computeTLRC

computeImage

JButton computeImage

labelImage

JLabel labelImage

comboBoxImage

JComboBox comboBoxImage

updateImage

JButton updateImage

labelTransform

JLabel labelTransform

comboBoxTransform

JComboBox comboBoxTransform

labelInterpolation

JLabel labelInterpolation

comboBoxInterpolation

JComboBox comboBoxInterpolation

loadsaveLabel

JLabel loadsaveLabel

loadButton

JButton loadButton

saveButton

JButton saveButton

botPanel

JPanel botPanel

imgPanel

JPanel imgPanel

transPanel

JPanel transPanel

interpPanel

JPanel interpPanel

loadsavePanel

JPanel loadsavePanel

loadDialog

JFileChooser loadDialog

saveDialog

JFileChooser saveDialog

Class gov.nih.mipav.view.dialogs.JDialogText extends JDialogBase implements Serializable

serialVersionUID: 3861014709972568409L

Serialized Fields

DEFAULT_SIZE

Dimension DEFAULT_SIZE
Describes the initial size of the textual display area when the dialog is created. The value is given in pixel size rather than the number of characters since the display area has no characters to display.

buttonPanel

JPanel buttonPanel
DOCUMENT ME!

followingScroll

boolean followingScroll
DOCUMENT ME!

message

StringBuffer message
DOCUMENT ME!

scrollPane

JScrollPane scrollPane
DOCUMENT ME!

textArea

JEditorPane textArea
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogTextGE extends JDialogText implements Serializable

serialVersionUID: 419753934724528702L

Serialized Fields

convertButton

JButton convertButton
DOCUMENT ME!

fileInfo

FileInfoBase[] fileInfo
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

slice

int slice
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogTextGE4X extends JDialogText implements Serializable

Serialized Fields

convertButton

JButton convertButton
DOCUMENT ME!

fileInfo

FileInfoBase[] fileInfo
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

slice

int slice
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogThreshold extends JDialogScriptableBase implements Serializable

serialVersionUID: 8143576591075984708L

Serialized Fields

displayLoc

int displayLoc
DOCUMENT ME!

fillValue

float fillValue
DOCUMENT ME!

histogram

ModelHistogram histogram
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

inverseCheckbox

JCheckBox inverseCheckbox
DOCUMENT ME!

isInverse

boolean isInverse
DOCUMENT ME!

labelThres2

JLabel labelThres2
DOCUMENT ME!

maxEntCheckbox

JCheckBox maxEntCheckbox
DOCUMENT ME!

min

float min
DOCUMENT ME!

max

float max
DOCUMENT ME!

newImage

JRadioButton newImage
DOCUMENT ME!

otsuCheckbox

JCheckBox otsuCheckbox
DOCUMENT ME!

outMax

double outMax
DOCUMENT ME!

outMin

double outMin
DOCUMENT ME!

outputBox

JComboBox outputBox
Holds the choices for the outputType.

outputType

int outputType
Same data-type, binary, or unsigned byte mask.

regionFlag

boolean regionFlag
or if the source image is to be replaced.

replaceImage

JRadioButton replaceImage
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

textFill

JTextField textFill
DOCUMENT ME!

textThres1

JTextField textThres1
DOCUMENT ME!

textThres2

JTextField textThres2
DOCUMENT ME!

thres1

float thres1
DOCUMENT ME!

thres2

float thres2
DOCUMENT ME!

thresholdAlgo

AlgorithmThresholdDual thresholdAlgo
DOCUMENT ME!

thresholdType

int thresholdType
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

VOIRegions

JRadioButton VOIRegions
DOCUMENT ME!

wholeImage

JRadioButton wholeImage
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogThreshold.CheckValueAction extends AbstractAction implements Serializable

serialVersionUID: -1531686009578681460L

Class gov.nih.mipav.view.dialogs.JDialogThresholdLUT extends JDialogBase implements Serializable

serialVersionUID: -3705234971745674752L

Serialized Fields

fillValue

float fillValue
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

labelMax

JLabel labelMax
DOCUMENT ME!

labelMin

JLabel labelMin
DOCUMENT ME!

lowerThreshold

float lowerThreshold
DOCUMENT ME!

upperThreshold

float upperThreshold
DOCUMENT ME!

outputType

int outputType
DOCUMENT ME!

radioBinary

JRadioButton radioBinary
DOCUMENT ME!

radioRange

JRadioButton radioRange
DOCUMENT ME!

radioThresh

JRadioButton radioThresh
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

textFill

JTextField textFill
DOCUMENT ME!

textMax

JTextField textMax
DOCUMENT ME!

textMin

JTextField textMin
DOCUMENT ME!

thresholdAlgo

AlgorithmThresholdDual thresholdAlgo
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogThresholdRGB extends JDialogScriptableBase implements Serializable

serialVersionUID: 1903960650432668714L

Serialized Fields

applyToAllBox

JCheckBox applyToAllBox
false = apply algorithm only to VOI regions apply same threshold to all.

applyToBlueBox

JCheckBox applyToBlueBox
enable blue threshold.

applyToGreenBox

JCheckBox applyToGreenBox
enable green threshold.

applyToRedBox

JCheckBox applyToRedBox
enable red threshold.

displayLoc

int displayLoc
DOCUMENT ME!

fillValues

float[] fillValues
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

inverseOptionBox

JCheckBox inverseOptionBox
choose inverse or no inverse threshold.

isInverse

boolean isInverse
inverse?

maxs

float[] maxs
DOCUMENT ME!

mins

float[] mins
Minimum and maximum values for red/gree/blue.

newImage

JRadioButton newImage
DOCUMENT ME!

regionFlag

boolean regionFlag
or if the source image is to be replaced.

replaceImage

JRadioButton replaceImage
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

textFills

JTextField[] textFills
DOCUMENT ME!

textThreshold1

JTextField[] textThreshold1
Text fields for lower & upper thresholds and fill values.

textThreshold2

JTextField[] textThreshold2
DOCUMENT ME!

thres1

float thres1
DOCUMENT ME!

thres2

float thres2
DOCUMENT ME!

thresholdAlgoRGB

AlgorithmThresholdDualRGB thresholdAlgoRGB
DOCUMENT ME!

thresholdB

float[] thresholdB
DOCUMENT ME!

thresholdG

float[] thresholdG
DOCUMENT ME!

thresholdLabels1

JLabel[] thresholdLabels1
DOCUMENT ME!

thresholdLabels2

JLabel[] thresholdLabels2
DOCUMENT ME!

thresholdR

float[] thresholdR
lower [0] and upper [1] thresholds for RGB.

titles

String[] titles
DOCUMENT ME!

useChannel

boolean[] useChannel
tells whether or not to use the channels (red=0, green=1, blue=2).

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

VOIRegions

JRadioButton VOIRegions
DOCUMENT ME!

wholeImage

JRadioButton wholeImage
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogTLRC extends JDialogBase implements Serializable

Serialized Fields

frame

ViewJFrameTriImage frame

originalImage

ModelImage originalImage

acpcImage

ModelImage acpcImage

talairachImage

ModelImage talairachImage

transform

TalairachTransformInfo transform

applyTalairachButton

JButton applyTalairachButton

cancelTalairachButton

JButton cancelTalairachButton

anteriorPt

JRadioButton anteriorPt

posteriorPt

JRadioButton posteriorPt

superiorPt

JRadioButton superiorPt

inferiorPt

JRadioButton inferiorPt

leftPt

JRadioButton leftPt

rightPt

JRadioButton rightPt

setTalairachButton

JButton setTalairachButton

clearTalairachButton

JButton clearTalairachButton

tOffset

int tOffset

superiorEdgeDicom

WildMagic.LibFoundation.Mathematics.Vector3f superiorEdgeDicom

posteriorMarginDicom

WildMagic.LibFoundation.Mathematics.Vector3f posteriorMarginDicom

inferiorEdgeDicom

WildMagic.LibFoundation.Mathematics.Vector3f inferiorEdgeDicom

firstPtDicom

WildMagic.LibFoundation.Mathematics.Vector3f firstPtDicom

anotherPtDicom

WildMagic.LibFoundation.Mathematics.Vector3f anotherPtDicom

anteriorPt3Df

WildMagic.LibFoundation.Mathematics.Vector3f anteriorPt3Df

posteriorPt3Df

WildMagic.LibFoundation.Mathematics.Vector3f posteriorPt3Df

superiorPt3Df

WildMagic.LibFoundation.Mathematics.Vector3f superiorPt3Df

inferiorPt3Df

WildMagic.LibFoundation.Mathematics.Vector3f inferiorPt3Df

leftPt3Df

WildMagic.LibFoundation.Mathematics.Vector3f leftPt3Df

rightPt3Df

WildMagic.LibFoundation.Mathematics.Vector3f rightPt3Df

haveAnteriorPt

boolean haveAnteriorPt

havePosteriorPt

boolean havePosteriorPt

haveSuperiorPt

boolean haveSuperiorPt

haveInferiorPt

boolean haveInferiorPt

haveLeftPt

boolean haveLeftPt

haveRightPt

boolean haveRightPt

interpolation

int interpolation

Class gov.nih.mipav.view.dialogs.JDialogTransform extends JDialogScriptableBase implements Serializable

serialVersionUID: -7786904359172693422L

Serialized Fields

algoTal

AlgorithmTalairachTransform algoTal
DOCUMENT ME!

algoTrans

AlgorithmTransform algoTrans
or if the source image is to be replaced.

clipCheckbox

JCheckBox clipCheckbox
DOCUMENT ME!

voiCheckbox

JCheckBox voiCheckbox
DOCUMENT ME!

image25DCheckbox

JCheckBox image25DCheckbox
DOCUMENT ME!

updateOriginCheckbox

JCheckBox updateOriginCheckbox
DOCUMENT ME!

invertCheckbox

JCheckBox invertCheckbox
DOCUMENT ME!

comboBoxImage

JComboBox comboBoxImage
DOCUMENT ME!

comboBoxInterp

JComboBox comboBoxInterp
DOCUMENT ME!

comboBoxTalTransform

JComboBox comboBoxTalTransform
DOCUMENT ME!

computeTImage

JRadioButton computeTImage
DOCUMENT ME!

do25D

boolean do25D
DOCUMENT ME!

doRotateCenter

boolean doRotateCenter
DOCUMENT ME!

doTalairach

boolean doTalairach
DOCUMENT ME!

doVOI

boolean doVOI
DOCUMENT ME!

doClip

boolean doClip
DOCUMENT ME!

doPad

boolean doPad
DOCUMENT ME!

setPix

boolean setPix
DOCUMENT ME!

doUpdateOrigin

boolean doUpdateOrigin
DOCUMENT ME!

doInvMat

boolean doInvMat
DOCUMENT ME!

fileTransMatrix

TransMatrix fileTransMatrix
Stores the matrix read in from a file it then can be converted to the corrected axis orientation (i.e. world coordinate and/or left-hand coordinate systems).

image

ModelImage image
DOCUMENT ME!

interp

int interp
DOCUMENT ME!

fillValue

float fillValue

labelOrigin

JLabel labelOrigin
DOCUMENT ME!

padLabel

JLabel padLabel
DOCUMENT ME!

labelResX

JLabel labelResX
DOCUMENT ME!

labelResY

JLabel labelResY
DOCUMENT ME!

labelResZ

JLabel labelResZ
DOCUMENT ME!

labelDimX

JLabel labelDimX
DOCUMENT ME!

labelDimY

JLabel labelDimY
DOCUMENT ME!

labelDimZ

JLabel labelDimZ
DOCUMENT ME!

labelTx

JLabel labelTx
DOCUMENT ME!

labelTy

JLabel labelTy
DOCUMENT ME!

labelTz

JLabel labelTz
DOCUMENT ME!

labelRx

JLabel labelRx
DOCUMENT ME!

labelRy

JLabel labelRy
DOCUMENT ME!

labelRz

JLabel labelRz
DOCUMENT ME!

labelSx

JLabel labelSx
DOCUMENT ME!

labelSy

JLabel labelSy
DOCUMENT ME!

labelSz

JLabel labelSz
DOCUMENT ME!

labelSKx

JLabel labelSKx
DOCUMENT ME!

labelSKy

JLabel labelSKy
DOCUMENT ME!

labelSKz

JLabel labelSKz
DOCUMENT ME!

leftHandSystem

boolean leftHandSystem
If true change matrix to the left-hand coordinate system.

magSlider

JSlider magSlider
DOCUMENT ME!

matrixDeterminationGroup

ButtonGroup matrixDeterminationGroup
DOCUMENT ME!

rotationAxisGroup

ButtonGroup rotationAxisGroup
DOCUMENT ME!

cropOrPad

ButtonGroup cropOrPad
DOCUMENT ME!

matrixFile

String matrixFile
DOCUMENT ME!

matrixFName

JTextField matrixFName
DOCUMENT ME!

max

int max
DOCUMENT ME!

min

int min
DOCUMENT ME!

maximum

JLabel maximum
DOCUMENT ME!

minimum

JLabel minimum
DOCUMENT ME!

current

JLabel current
DOCUMENT ME!

oXdim

int oXdim
DOCUMENT ME!

oYdim

int oYdim
DOCUMENT ME!

oZdim

int oZdim
DOCUMENT ME!

cXdim

int cXdim
DOCUMENT ME!

cYdim

int cYdim
DOCUMENT ME!

cZdim

int cZdim
DOCUMENT ME!

oXres

float oXres
DOCUMENT ME!

oYres

float oYres
DOCUMENT ME!

oZres

float oZres
DOCUMENT ME!

cXres

float cXres
DOCUMENT ME!

cYres

float cYres
DOCUMENT ME!

cZres

float cZres
DOCUMENT ME!

units

int[] units

padValTxt

JTextField padValTxt
DOCUMENT ME!

resampleGroup

ButtonGroup resampleGroup
DOCUMENT ME!

resampleImage

ModelImage resampleImage
DOCUMENT ME!

resampletoUser

JRadioButton resampletoUser
DOCUMENT ME!

resampletoImage

JRadioButton resampletoImage
DOCUMENT ME!

resampleSlider

JRadioButton resampleSlider
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

rotCenter

JRadioButton rotCenter
DOCUMENT ME!

rotOrigin

JRadioButton rotOrigin
DOCUMENT ME!

cropRadio

JRadioButton cropRadio
DOCUMENT ME!

padRadio

JRadioButton padRadio
DOCUMENT ME!

storedMatrix

JRadioButton storedMatrix
DOCUMENT ME!

noTransform

JRadioButton noTransform
DOCUMENT ME!

userDefinedMatrix

JRadioButton userDefinedMatrix
DOCUMENT ME!

fileMatrix

JRadioButton fileMatrix
DOCUMENT ME!

storedMatrixBox

JComboBox storedMatrixBox

textResX

JTextField textResX
DOCUMENT ME!

textResY

JTextField textResY
DOCUMENT ME!

textResZ

JTextField textResZ
DOCUMENT ME!

textDimX

JTextField textDimX
DOCUMENT ME!

textDimY

JTextField textDimY
DOCUMENT ME!

textDimZ

JTextField textDimZ
DOCUMENT ME!

textTx

JTextField textTx
DOCUMENT ME!

textTy

JTextField textTy
DOCUMENT ME!

textTz

JTextField textTz
DOCUMENT ME!

textRx

JTextField textRx
DOCUMENT ME!

textRy

JTextField textRy
DOCUMENT ME!

textRz

JTextField textRz
DOCUMENT ME!

textSx

JTextField textSx
DOCUMENT ME!

textSy

JTextField textSy
DOCUMENT ME!

textSz

JTextField textSz
DOCUMENT ME!

textSKx

JTextField textSKx
DOCUMENT ME!

textSKy

JTextField textSKy
DOCUMENT ME!

textSKz

JTextField textSKz
DOCUMENT ME!

tInfo

TalairachTransformInfo tInfo
DOCUMENT ME!

transformType

int transformType
DOCUMENT ME!

tVal

String[] tVal
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

wcSystem

boolean wcSystem
If true change matrix to the world coordinate system.

xfrm

TransMatrix xfrm
DOCUMENT ME!

xyAspectRatio

JCheckBox xyAspectRatio
DOCUMENT ME!

xyzAspectRatio

JCheckBox xyzAspectRatio
DOCUMENT ME!

fieldOfView

JCheckBox fieldOfView
DOCUMENT ME!

setPixels

JCheckBox setPixels
DOCUMENT ME!

useSACenterBox

JCheckBox useSACenterBox
checkbox telling the algorithm to use the scanner coordinate center rather than the image center

useSACenter

boolean useSACenter

tabbedPane

JTabbedPane tabbedPane
Tabbed pane

isSATransform

boolean isSATransform
is this a scanner anatomical transform (->AXIAL)

enableSATransform

boolean enableSATransform

outOfBoundsLabel

JLabel outOfBoundsLabel

outOfBoundsComboBox

JComboBox outOfBoundsComboBox

valueLabel

JLabel valueLabel

valueText

JTextField valueText

imageMin

double imageMin

imageMax

double imageMax

dataType

int dataType

outOfBoundsIndex

int outOfBoundsIndex
Tells how to select fill value for out of bounds data 0 for image minimum 1 for NaN for float, zero otherwise. 2 for user defined 3 for image maximum

Class gov.nih.mipav.view.dialogs.JDialogTransformBSpline extends JDialogBase implements Serializable

serialVersionUID: 3877682545436641450L

Serialized Fields

algoTrans

AlgorithmTransformBSpline algoTrans
DOCUMENT ME!

chooserButton

JButton chooserButton
DOCUMENT ME!

controlMat

float[][] controlMat
DOCUMENT ME!

controlMat25D

float[][][] controlMat25D
DOCUMENT ME!

destExtents

int[] destExtents
DOCUMENT ME!

destMinExtent

int destMinExtent
DOCUMENT ME!

have25D

boolean have25D
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

model

DefaultListModel model
DOCUMENT ME!

nDims

int nDims
DOCUMENT ME!

nltName

String nltName
DOCUMENT ME!

numberSlices

int numberSlices
DOCUMENT ME!

numControlPoints

int numControlPoints
DOCUMENT ME!

removeButton

JButton removeButton
DOCUMENT ME!

resolutions

float[] resolutions
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

splineDegree

int splineDegree
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogTransformNL extends JDialogScriptableBase implements Serializable

serialVersionUID: 6309170791275620891L

Serialized Fields

interp

int interp
DOCUMENT ME!

oXdim

int oXdim
DOCUMENT ME!

oYdim

int oYdim
DOCUMENT ME!

oZdim

int oZdim
DOCUMENT ME!

oXres

float oXres
DOCUMENT ME!

oYres

float oYres
DOCUMENT ME!

oZres

float oZres
DOCUMENT ME!

transformVOI

boolean transformVOI
DOCUMENT ME!

doClip

boolean doClip
DOCUMENT ME!

algoTrans

AlgorithmRegNonlinear algoTrans
or if the source image is to be replaced.

clipCheckbox

JCheckBox clipCheckbox
DOCUMENT ME!

voiCheckbox

JCheckBox voiCheckbox
DOCUMENT ME!

coeffp

int coeffp
DOCUMENT ME!

comboBoxInterp

JComboBox comboBoxInterp
DOCUMENT ME!

coords

int coords
DOCUMENT ME!

endianess

boolean endianess
DOCUMENT ME!

es

double[][] es
DOCUMENT ME!

fileButton

JButton fileButton
DOCUMENT ME!

fmodel

int fmodel
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

order

int order
DOCUMENT ME!

parametersFile

String parametersFile
DOCUMENT ME!

parametersFName

JTextField parametersFName
DOCUMENT ME!

raFile

RandomAccessFile raFile
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

resultResolutions

float[] resultResolutions
DOCUMENT ME!

targetUnits

int[] targetUnits
DOCUMENT ME!

targetXDim

int targetXDim
DOCUMENT ME!

targetYDim

int targetYDim
DOCUMENT ME!

targetZDim

int targetZDim
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogTriFrameLinker extends JDialogBase implements Serializable

serialVersionUID: -4546169496119216251L

Serialized Fields

comboBoxImage

JComboBox comboBoxImage
DOCUMENT ME!

frameB

ViewJFrameTriImage frameB
DOCUMENT ME!

imageA

ModelImage imageA
DOCUMENT ME!

imageB

ModelImage imageB
DOCUMENT ME!

linkButton

JButton linkButton
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogTriImageTransformation extends JDialogBase implements Serializable

serialVersionUID: -6567165297005633024L

Serialized Fields

boxIndex

int boxIndex
DOCUMENT ME!

centerX

double centerX
angles are passed to setRotate.

centerY

double centerY
angles are passed to setRotate.

centerZ

double centerZ
angles are passed to setRotate.

comboBoxInterp

JComboBox comboBoxInterp
DOCUMENT ME!

frame

ViewJFrameTriImage frame
Pointer back to frame that called this.

imageA

ModelImage imageA
Image to transform.

imageB

ModelImage imageB
Image B to transform, can be null.

progressBar

ViewJProgressBar progressBar
Progress bar.

thetaXY

double thetaXY
DOCUMENT ME!

thetaXZ

double thetaXZ
DOCUMENT ME!

thetaZY

double thetaZY
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogTrim extends JDialogBase implements Serializable

serialVersionUID: 2967441574461453380L

Serialized Fields

current

JLabel current
DOCUMENT ME!

maximum

JLabel maximum
DOCUMENT ME!

minimum

JLabel minimum
DOCUMENT ME!

trimCheckbox

JCheckBox trimCheckbox
DOCUMENT ME!

trimSlider

JSlider trimSlider
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogTwoMRIImagesSNR extends JDialogBase implements Serializable

serialVersionUID: -2992719068907961685L

Serialized Fields

comboBoxCostFunct

JComboBox comboBoxCostFunct
DOCUMENT ME!

componentImage

ViewJComponentEditImage componentImage
DOCUMENT ME!

componentImage2

ViewJComponentEditImage componentImage2
DOCUMENT ME!

cost

int cost
DOCUMENT ME!

createRegCheckBox

JCheckBox createRegCheckBox
DOCUMENT ME!

createRegImage

boolean createRegImage
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

image2

ModelImage image2
DOCUMENT ME!

imageComboBox

JComboBox imageComboBox
DOCUMENT ME!

labelCost

JLabel labelCost
DOCUMENT ME!

nBoundingVOIs

int nBoundingVOIs
DOCUMENT ME!

regCheckBox

JCheckBox regCheckBox
DOCUMENT ME!

register

boolean register
DOCUMENT ME!

signal2Button

JRadioButton signal2Button
DOCUMENT ME!

signal2Image

int signal2Image
DOCUMENT ME!

signal2Index

int signal2Index
DOCUMENT ME!

signalButton

JRadioButton signalButton
DOCUMENT ME!

signalImage

int signalImage
DOCUMENT ME!

signalIndex

int signalIndex
DOCUMENT ME!

snrAlgo

AlgorithmTwoMRIImagesSNR snrAlgo
DOCUMENT ME!

UI

ViewUserInterface UI
DOCUMENT ME!

VOIGroup

ButtonGroup VOIGroup
DOCUMENT ME!

VOIs

ViewVOIVector VOIs
DOCUMENT ME!

VOIs2

ViewVOIVector VOIs2
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogUltErode extends JDialogScriptableBase implements Serializable

serialVersionUID: -7439335499053110688L

Serialized Fields

dist

float dist
DOCUMENT ME!

erodeAlgo2D

AlgorithmMorphology2D erodeAlgo2D
DOCUMENT ME!

erodeAlgo3D

AlgorithmMorphology3D erodeAlgo3D
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

outputPanel

JPanelAlgorithmOutputOptions outputPanel
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

textNPix

JTextField textNPix
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogUnknownIO extends JDialogBase implements Serializable

serialVersionUID: 960085709232971480L

Serialized Fields

imageType

int imageType
DOCUMENT ME!

list

JList list
DOCUMENT ME!

suffix

String suffix
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogUnsharpMask extends JDialogScriptableBase implements Serializable

serialVersionUID: -3776616289889677111L

Serialized Fields

image

ModelImage image
DOCUMENT ME!

image25D

boolean image25D
DOCUMENT ME!

image25DCheckbox

JCheckBox image25DCheckbox
DOCUMENT ME!

outputPanel

JPanelAlgorithmOutputOptions outputPanel
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

sigmaPanel

JPanelSigmas sigmaPanel
DOCUMENT ME!

textWeight

JTextField textWeight
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

unsharpMaskAlgo

AlgorithmUnsharpMask unsharpMaskAlgo
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

weight

float weight
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogVOIExtraction extends JDialogBase implements Serializable

serialVersionUID: 6131165470681736959L

Serialized Fields

imageA

ModelImage imageA
DOCUMENT ME!

VOIExtractionAlgo

AlgorithmVOIExtraction VOIExtractionAlgo
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogVOIShapeInterpolation extends JDialogBase implements Serializable

Serialized Fields

imageA

ModelImage imageA
src image

alg

AlgorithmVOIShapeInterpolation alg
algorithm

Class gov.nih.mipav.view.dialogs.JDialogVOISplitter extends JDialogBase implements Serializable

serialVersionUID: 4074062695729029005L

Serialized Fields

currentSlice

int currentSlice
DOCUMENT ME!

dimX

int dimX
DOCUMENT ME!

dimY

int dimY
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

allSlicesBox

JCheckBox allSlicesBox
DOCUMENT ME!

onlyActiveBox

JCheckBox onlyActiveBox

startPt

WildMagic.LibFoundation.Mathematics.Vector3f startPt

endPt

WildMagic.LibFoundation.Mathematics.Vector3f endPt

slope

float slope

b

float b

tol

float tol

Class gov.nih.mipav.view.dialogs.JDialogVOIStatistics extends JDialogScriptableBase implements Serializable

serialVersionUID: -1354965054401181781L

Serialized Fields

addremove

JDialogVOIStatistics.JPanelAddRemoveVOI addremove
Panel to push/pull VOIs from full list to selectable list.

calculator

AlgorithmVOIProps calculator
DOCUMENT ME!

checkBoxPanel

JPanelStatisticsList checkBoxPanel
Panel holding statistics options.

checkList

boolean[] checkList
boolean array mirroring checkbox panel's selection.

doForce

boolean doForce
force precision to display at maximum.

everything

JTabbedPane everything
Tabbed pane that holds all components.

fileSelectorPanel

JPanelFileSelection fileSelectorPanel
Panel to select files.

highlighter

JDialogVOIStatistics.VOIHighlighter highlighter
Operator to provide listener access... could be done by /this/

image

ModelImage image
Global image reference to the currently active image during script running and recording.

logFileText

StringBuffer logFileText
The text of the log process to be written to file.

logModel

ViewTableModel logModel
Model where data is stored for the table.

logTable

JTable logTable
Table holding log of statistics calculated.

noisyProcess

boolean noisyProcess
Flag where true means notifying the user of stupid errors.

outputOptionsPanel

JDialogVOIStatistics.JPanelStatisticsOptions outputOptionsPanel
Panel holding statistics output options.

overwriteBox

JCheckBoxMenuItem overwriteBox
Check box item indicating if we're to always overwriteBox the statistics file.

precision

int precision
Number of digits after decimal place to allow.

processType

int processType
DOCUMENT ME!

rangeFlag

int rangeFlag
DOCUMENT ME!

rangeMaximum

float rangeMaximum
DOCUMENT ME!

rangeMinimum

float rangeMinimum
DOCUMENT ME!

selectedList

JList selectedList
List of selected VOIs.

showTotals

boolean showTotals
DOCUMENT ME!

tableDestination

File tableDestination
Log file destination.

tableDestinationUsage

int tableDestinationUsage
Indicates options for OVERWRITE, APPEND for the xlat file.

toolBar

JToolBar toolBar
Toolbar.

userInterface

ViewUserInterface userInterface
Icon and log access.

volumesList

JList volumesList
List of available VOIs.

xUnits

int xUnits
DOCUMENT ME!

yUnits

int yUnits
DOCUMENT ME!

zUnits

int zUnits
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogVOIStatistics.JPanelAddRemoveVOI extends JPanelListController implements Serializable

serialVersionUID: -2076771728355899710L

Class gov.nih.mipav.view.dialogs.JDialogVOIStatistics.JPanelExclusionSelector extends JPanel implements Serializable

serialVersionUID: 1471564039185960351L

Serialized Fields

boundA

JTextField boundA
DOCUMENT ME!

boundB

JTextField boundB
DOCUMENT ME!

excludeSelection

JComboBox excludeSelection
DOCUMENT ME!

exclusionPanel

JPanel exclusionPanel
DOCUMENT ME!

lowerLimit

Float lowerLimit
DOCUMENT ME!

permitExclusion

JCheckBox permitExclusion
DOCUMENT ME!

upperLimit

Float upperLimit
held for switching between states of the exclusion.

Class gov.nih.mipav.view.dialogs.JDialogVOIStatistics.JPanelStatisticFileFormatOptions extends JPanel implements Serializable

serialVersionUID: -4726615904924397356L

Serialized Fields

tabDelimited

JRadioButton tabDelimited
Radio button to choose a tab-delimited file.

xml

JRadioButton xml
Radio button to choose a XML file.

Class gov.nih.mipav.view.dialogs.JDialogVOIStatistics.JPanelStatisticsOptions extends JPanel implements Serializable

serialVersionUID: 6577076069976323730L

Serialized Fields

byContour

JRadioButton byContour
A radio button to select calculation by VOI contour.

bySlice

JRadioButton bySlice
A radio button to select calculation by VOI slice.

byTotalVOI

JRadioButton byTotalVOI
A radio button to select calculation by total VOI.

excluder

JDialogVOIStatistics.JPanelExclusionSelector excluder
The Exclusion selector.

forceDecimal

JCheckBox forceDecimal
DOCUMENT ME!

precisionBox

JComboBox precisionBox
User can choose the precision to display.

showTotals

JCheckBox showTotals
A check box to opt for VOI totals.

Class gov.nih.mipav.view.dialogs.JDialogVOIStats extends JDialogBase implements Serializable

serialVersionUID: 1618733051752245417L

Serialized Fields

algoVOI

AlgorithmVOIProps algoVOI
DOCUMENT ME!

applyButton

JButton applyButton
DOCUMENT ME!

calcButton

JButton calcButton
DOCUMENT ME!

helpButton

JButton helpButton
DOCUMENT ME!

checkboxAdditiveOrSubtractive

JCheckBox checkboxAdditiveOrSubtractive
DOCUMENT ME!

checkboxBoundary

JCheckBox checkboxBoundary
DOCUMENT ME!

checkboxBoundingBox

JCheckBox checkboxBoundingBox
DOCUMENT ME!

checkboxExclude

JCheckBox checkboxExclude
DOCUMENT ME!

checkboxSaveStats

JCheckBox checkboxSaveStats
DOCUMENT ME!

checkboxIncludeForProcessing

JCheckBox checkboxIncludeForProcessing
DOCUMENT ME!

checkboxVOIName

JCheckBox checkboxVOIName
DOCUMENT ME!

colorButton

JButton colorButton
DOCUMENT ME!

colorChooser

ViewJColorChooser colorChooser
DOCUMENT ME!

colorVOI

Color colorVOI
DOCUMENT ME!

contourTextArea

JTextArea contourTextArea
DOCUMENT ME!

current

JLabel current
DOCUMENT ME!

followVOISelectionBox

JCheckBox followVOISelectionBox
DOCUMENT ME!

frameBorder

Border frameBorder
DOCUMENT ME!

frameFollowsSelection

boolean frameFollowsSelection
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

labelMax

JLabel labelMax
DOCUMENT ME!

labelMin

JLabel labelMin
DOCUMENT ME!

listPanel

JPanelStatisticsList listPanel
DOCUMENT ME!

opacitySlider

JSlider opacitySlider
DOCUMENT ME!

popup

gov.nih.mipav.view.dialogs.JDialogVOIStats.VOITreePopup popup
DOCUMENT ME!

root

DefaultMutableTreeNode root
DOCUMENT ME!

seedValue

short seedValue
DOCUMENT ME!

seedValueTF

JTextField seedValueTF
DOCUMENT ME!

statsPanel

JPanel statsPanel
DOCUMENT ME!

textMax

JTextField textMax
DOCUMENT ME!

textMin

JTextField textMin
DOCUMENT ME!

treeSelectionChange

boolean treeSelectionChange
DOCUMENT ME!

voi

VOI voi
DOCUMENT ME!

voiContourPane

JScrollPane voiContourPane
DOCUMENT ME!

voiModel

DefaultTreeModel voiModel
DOCUMENT ME!

VOIName

JTextField VOIName
DOCUMENT ME!

VOIThicknessField

JTextField VOIThicknessField
DOCUMENT ME!

voiTree

JTree voiTree
DOCUMENT ME!

voiTreePane

JScrollPane voiTreePane
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogVSMIP extends JDialogBase implements Serializable

serialVersionUID: -229974440831184567L

Serialized Fields

accumulatorFrame

ViewJFrameImage accumulatorFrame
DOCUMENT ME!

iterate

boolean iterate
DOCUMENT ME!

mipFrame

ViewJFrameImage mipFrame
DOCUMENT ME!

viewMIP

boolean viewMIP
DOCUMENT ME!

viewAccumulator

boolean viewAccumulator
DOCUMENT ME!

iterateButton

JCheckBox iterateButton
DOCUMENT ME!

mipImage

ModelImage mipImage
DOCUMENT ME!

mipInfo

MIPNode[] mipInfo
DOCUMENT ME!

mipPlaneWidth

int mipPlaneWidth
DOCUMENT ME!

mipPlaneHeight

int mipPlaneHeight
DOCUMENT ME!

resultBuffer

float[] resultBuffer
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

srcImage

ModelImage srcImage
DOCUMENT ME!

stepSize

float stepSize
DOCUMENT ME!

angleX

float angleX
DOCUMENT ME!

angleY

float angleY
DOCUMENT ME!

textAngleX

JTextField textAngleX
DOCUMENT ME!

textAngleY

JTextField textAngleY
DOCUMENT ME!

textMipPlaneWidth

JTextField textMipPlaneWidth
DOCUMENT ME!

textMipPlaneHeight

JTextField textMipPlaneHeight
DOCUMENT ME!

textMipStepSize

JTextField textMipStepSize
DOCUMENT ME!

viewMipImage

JRadioButton viewMipImage
DOCUMENT ME!

viewAccumulatorImage

JRadioButton viewAccumulatorImage
DOCUMENT ME!

vsMIPAlgo

AlgorithmVSMIP vsMIPAlgo
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogWatershed extends JDialogScriptableBase implements Serializable

serialVersionUID: -3432667720289138422L

Serialized Fields

buttonEnergyInput

JButton buttonEnergyInput
DOCUMENT ME!

choiceCheckBox

JCheckBox choiceCheckBox
DOCUMENT ME!

gmDirectory

String gmDirectory
DOCUMENT ME!

gmFileName

String gmFileName
DOCUMENT ME!

gmImage

ModelImage gmImage
DOCUMENT ME!

gmTextFile

JTextField gmTextFile
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

labelCorrected

JLabel labelCorrected
DOCUMENT ME!

labelGaussX

JLabel labelGaussX
DOCUMENT ME!

labelGaussY

JLabel labelGaussY
DOCUMENT ME!

labelGaussZ

JLabel labelGaussZ
DOCUMENT ME!

normFactor

float normFactor
DOCUMENT ME!

resolutionCheckbox

JCheckBox resolutionCheckbox
difference between x,y resolutions (in plane) and z resolution (between planes).

resultImage

ModelImage resultImage
DOCUMENT ME!

scaleX

float scaleX
DOCUMENT ME!

scaleY

float scaleY
DOCUMENT ME!

scaleZ

float scaleZ
DOCUMENT ME!

textGaussX

JTextField textGaussX
DOCUMENT ME!

textGaussY

JTextField textGaussY
DOCUMENT ME!

textGaussZ

JTextField textGaussZ
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

watershedAlgo

AlgorithmWatershed watershedAlgo
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogWaterShedITK extends JDialogScriptableBase implements Serializable

serialVersionUID: -4057161307906161677L

Serialized Fields

colorChannelPanel

JPanelColorChannels colorChannelPanel
DOCUMENT ME!

waterShedlAlgo

AlgorithmWaterShedITK waterShedlAlgo
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

image25D

boolean image25D
false = apply algorithm only to VOI regions.

image25DCheckbox

JCheckBox image25DCheckbox
DOCUMENT ME!

outputOptionsPanel

JPanelAlgorithmOutputOptions outputOptionsPanel
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

waterShedPanel

JPanelWaterShedITK waterShedPanel
WaterShed parameters panel.

Class gov.nih.mipav.view.dialogs.JDialogWaveletThreshold extends JDialogScriptableBase implements Serializable

serialVersionUID: 5536998601413644702L

Serialized Fields

cNum

int cNum
or if the source image is to be replaced.

coefficientCombo

JComboBox coefficientCombo
DOCUMENT ME!

displayLoc

int displayLoc
DOCUMENT ME!

doWaveletImage

boolean doWaveletImage
DOCUMENT ME!

garrote

JRadioButton garrote
DOCUMENT ME!

hard

JRadioButton hard
DOCUMENT ME!

image

ModelImage image
DOCUMENT ME!

newImage

JRadioButton newImage
DOCUMENT ME!

replaceImage

JRadioButton replaceImage
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

scad

JRadioButton scad
DOCUMENT ME!

soft

JRadioButton soft
DOCUMENT ME!

textThreshold

JTextField textThreshold
DOCUMENT ME!

threshold

float threshold
DOCUMENT ME!

thresholdType

int thresholdType
DOCUMENT ME!

titles

String[] titles
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

waveletAlgo

AlgorithmWaveletThreshold waveletAlgo
DOCUMENT ME!

waveletCheckBox

JCheckBox waveletCheckBox
DOCUMENT ME!

waveletImage

ModelImage waveletImage
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogWinLevel extends JDialogBase implements Serializable

serialVersionUID: -3270517526341902110L

Serialized Fields

closeButton

JButton closeButton
DOCUMENT ME!

dataSlice

float[] dataSlice
Reference to the image data of the slice presently displayed. Needed to calculate the max/min of the slice used to adjust the transfer function.

image

ModelImage image
Reference to the image that will be affected by the adjust of the window and level.

level

float level
Average of the min and max extents of the transfer window that desribes the window size.

levelLabel

JLabel levelLabel
DOCUMENT ME!

levelSlider

JSlider levelSlider
DOCUMENT ME!

levelSliderMax

int levelSliderMax
Stores the maximum slider value.

LUT

ModelLUT LUT
Reference to the LUT used to display the image.

maxImage

float maxImage
Image's maximum intensity.

minImage

float minImage
Image's minimum intensity.

sliderPanel

JPanel sliderPanel
DOCUMENT ME!

window

float window
The size of the window.

windowLabel

JLabel windowLabel
DOCUMENT ME!

windowSlider

JSlider windowSlider
DOCUMENT ME!

windowSliderMax

int windowSliderMax
Stores the minimum slider value.

winValTextField

JTextField winValTextField
textfield inputs for window and level

levelValTextField

JTextField levelValTextField
textfield inputs for window and level

winMaxFloat

float winMaxFloat
the maxes and mins for window and level

winMinFloat

float winMinFloat
the maxes and mins for window and level

levelMaxFloat

float levelMaxFloat
the maxes and mins for window and level

levelMinFloat

float levelMinFloat
the maxes and mins for window and level

x

float[] x
Three arrays to save the coordinates of the LUT's transfer fucntion. z[] not used.

y

float[] y
DOCUMENT ME!

z

float[] z
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogXcosmEM extends JDialogScriptableBase implements Serializable

serialVersionUID: 981523715011352299L

Serialized Fields

percentIterationsHalfSize

int percentIterationsHalfSize
DOCUMENT ME!

percentIterationsOriginalSize

int percentIterationsOriginalSize
DOCUMENT ME!

percentIterationsQuarterSize

int percentIterationsQuarterSize
DOCUMENT ME!

xcosmEMAlgo

AlgorithmXcosmEM xcosmEMAlgo
DOCUMENT ME!

backupNumberIterations

int backupNumberIterations
DOCUMENT ME!

decayConstant

float decayConstant
DOCUMENT ME!

entireImage

boolean entireImage
DOCUMENT ME!

estimateDecay

boolean estimateDecay
DOCUMENT ME!

imageComboBox

JComboBox imageComboBox
DOCUMENT ME!

labelImage

JLabel labelImage
DOCUMENT ME!

originalImage

ModelImage originalImage
DOCUMENT ME!

penaltyIntensity

boolean penaltyIntensity
DOCUMENT ME!

penaltyValue

float penaltyValue
DOCUMENT ME!

psfImage

ModelImage psfImage
DOCUMENT ME!

radioEntireImage

JRadioButton radioEntireImage
DOCUMENT ME!

radioVOIRegion

JRadioButton radioVOIRegion
DOCUMENT ME!

radioEstimateDecay

JRadioButton radioEstimateDecay
DOCUMENT ME!

radioIntensity

JRadioButton radioIntensity
DOCUMENT ME!

radioRoughness

JRadioButton radioRoughness
DOCUMENT ME!

resultImage

ModelImage resultImage
DOCUMENT ME!

textBackupNumberIterations

JTextField textBackupNumberIterations
DOCUMENT ME!

textDecayConstant

JTextField textDecayConstant
DOCUMENT ME!

textPenaltyValue

JTextField textPenaltyValue
DOCUMENT ME!

textPercentIterationsHalfSize

JTextField textPercentIterationsHalfSize
DOCUMENT ME!

textPercentIterationsOriginalSize

JTextField textPercentIterationsOriginalSize
DOCUMENT ME!

textpercentIterationsQuarterSize

JTextField textpercentIterationsQuarterSize
DOCUMENT ME!

textTotalNumberIterations

JTextField textTotalNumberIterations
DOCUMENT ME!

textWindowLowerLimit

JTextField textWindowLowerLimit
DOCUMENT ME!

totalNumberIterations

int totalNumberIterations
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

windowLowerLimit

int windowLowerLimit
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JDialogZoom extends JDialogBase implements Serializable

serialVersionUID: 5271517126304850595L

Serialized Fields

bilinear

JRadioButton bilinear
DOCUMENT ME!

componentImage

ViewJComponentEditImage componentImage
DOCUMENT ME!

cubic

JRadioButton cubic
DOCUMENT ME!

current

JLabel current
DOCUMENT ME!

magSlider

JSlider magSlider
DOCUMENT ME!

max

int max
DOCUMENT ME!

min

int min
DOCUMENT ME!

nearest

JRadioButton nearest
DOCUMENT ME!

Class gov.nih.mipav.view.dialogs.JFrameRegistrationMosaic extends JFrame implements Serializable

serialVersionUID: 2954367270283496349L

Serialized Fields

m_aabReference

boolean[][] m_aabReference
For masking, set to true if the reference image is written into the same location:.

m_aabReferenceBackup

boolean[][] m_aabReferenceBackup
backup:.

m_akBackupBorders

javax.media.j3d.Shape3D[] m_akBackupBorders
Backup shape for Undo:.

m_akBackupImages

ModelImage[] m_akBackupImages
Backup Image for Undo:.

m_akBackupPolygons

javax.media.j3d.Shape3D[] m_akBackupPolygons
Backup shape for Undo:.

m_akBackupTG

javax.media.j3d.TransformGroup[] m_akBackupTG
Backup Transform for Undo:.

m_akBorderShapes

javax.media.j3d.Shape3D[] m_akBorderShapes
Reference to the border shape data structure for changing the color based on which image is selected:.

m_akImages

ModelImage[] m_akImages
Reference to the model images:.

m_akImageTransforms

javax.media.j3d.TransformGroup[] m_akImageTransforms
Reference and tile image transformations:.

m_akPolygonShapes

javax.media.j3d.Shape3D[] m_akPolygonShapes
Reference to the texture-mapped polygon on which the image is displayed:.

m_bBruteForce

boolean m_bBruteForce
Brute force default is off:.

m_bDisplayTransform

boolean m_bDisplayTransform
Display transfromed image in separate window: set to false (no display).

m_bDoSubsample

boolean m_bDoSubsample
Default subsample set to true:.

m_bFileLoaded

boolean m_bFileLoaded
Boolean to check that a file is loaded before mouse operations are allowed to occur.

m_bFirst

boolean m_bFirst
For blending the reference and tile images, reference image is not blended with background, reset when initData() is called.

m_bResetAlpha

boolean m_bResetAlpha
To reset m_kReferenceAlpha:.

m_bSetScale

boolean m_bSetScale
True when scale factor should be used:.

m_fCoarseRate

float m_fCoarseRate
Default rotation coarse rate, set to 2 degrees:.

m_fFineRate

float m_fFineRate
Default rotation fine rate, set to 1 degree:.

m_fRotateBegin

float m_fRotateBegin
Default rotation start, set to negative 5 degrees:.

m_fRotateEnd

float m_fRotateEnd
Default rotation end, set to postive 5 degrees:.

m_fRotationRange

float m_fRotationRange
default rotation range (0).

m_fScale

float m_fScale
Scale factor for large images:.

m_fXScaleRange

float m_fXScaleRange
default x scale range (0).

m_fYScaleRange

float m_fYScaleRange
default y scale range (0).

m_iBracketBound

int m_iBracketBound
Default bound for bracketing during optimization set to 10 units:.

m_iCost

int m_iCost
Default cost function, set to correlation ratio (smoothed, weighted):.

m_iDOF

int m_iDOF
Default degrees of freedom:.

m_iInterp

int m_iInterp
Default image interpolation, set to be bilinear interpolation:.

m_iInterp2

int m_iInterp2
Default interpolation for the transform algorithm:.

m_iMaxIterations

int m_iMaxIterations
Default number of iteration set to 2:.

m_iNumMinima

int m_iNumMinima
Default number of minima to test from level 8 at level 4 (set to 3):.

m_iOpen

int m_iOpen
index of the non-selected image:.

m_iOpenSave

int m_iOpenSave
Backup of the open index:.

m_iReference

int m_iReference
Index of the reference image:.

m_iReferenceSave

int m_iReferenceSave
Backup of the reference index:.

m_iScaleSteps

int m_iScaleSteps
default number of divisions for scale optimazation:.

m_iSelected

int m_iSelected
index of the selected image:

m_iTile

int m_iTile
Index of the tile image:.

m_iTranslationRange

int m_iTranslationRange
default x,y translation range (0).

m_iXClick

int m_iXClick
x,y positions of the mouse when one of the mouse buttons is pressed:.

m_iYClick

int m_iYClick
x,y positions of the mouse when one of the mouse buttons is pressed:.

m_kAdvancedOptionsButton

JButton m_kAdvancedOptionsButton
Launches the JDialogRegistrationOAR2D dialog to set registration options:.

m_kCanvas

javax.media.j3d.Canvas3D m_kCanvas
Drawing canvas:.

m_kCloseAllButton

JButton m_kCloseAllButton
Close all images and remove them from the scene:.

m_kCurrentTransform

javax.media.j3d.Transform3D m_kCurrentTransform
current transformation based on mouseDragged event:.

m_kMouseEvent

MouseEvent m_kMouseEvent
Reference to the mousePressed event:.

m_kOldTransform

javax.media.j3d.Transform3D m_kOldTransform
Accumulated transformation prior to current mouseDrag:.

m_kOpenReferenceButton

JButton m_kOpenReferenceButton
Open reference image:.

m_kOpenTileButton

JButton m_kOpenTileButton
Open tile image:.

m_kReferenceAlpha

ModelImage m_kReferenceAlpha
For blending between refernce and transformed tile images:.

m_kReferenceAlphaBackup

ModelImage m_kReferenceAlphaBackup
For blending between refernce and transformed tile images:.

m_kRegisterButton

JButton m_kRegisterButton
Initialize and start the registration based on how the user positioned the two images:.

m_kSaveButton

JButton m_kSaveButton
Save the mosaic image:.

m_kHelpButton

JButton m_kHelpButton
Open the mosaic image help.

m_kScene

javax.media.j3d.BranchGroup m_kScene
Scene graph root node:.

m_kTileAlpha

ModelImage m_kTileAlpha
For blending between refernce and transformed tile images:.

m_kToggleSelectedButton

JButton m_kToggleSelectedButton
Toggle which image is currently selected:.

m_kUndoButton

JButton m_kUndoButton
Undo the last registration for the mosaic image:.

m_kUniverse

com.sun.j3d.utils.universe.SimpleUniverse m_kUniverse
SimpleUniverse:.

Class gov.nih.mipav.view.dialogs.ScriptTreeNode extends DefaultMutableTreeNode implements Serializable

Serialized Fields

defaultName

String defaultName

nodeType

int nodeType

filePath

String filePath
Package gov.nih.mipav.view.renderer

Class gov.nih.mipav.view.renderer.JDialogRendererAVI extends JDialogBase implements Serializable

serialVersionUID: -1983774099020785830L

Serialized Fields

applyWindowLevel

boolean applyWindowLevel
Flag to indicate to apply window level or not.

rate

double rate
Frame rate.

rateBox

JTextField rateBox
Frame rate textbox.

windowLevelCheckBox

JCheckBox windowLevelCheckBox
Window level check box.

Class gov.nih.mipav.view.renderer.JDialogVolViewResample extends JDialogBase implements Serializable

serialVersionUID: -1966951185588087479L

Serialized Fields

RGBTA

ModelRGB RGBTA
Lookup table of the color imageA, B.

RGBTB

ModelRGB RGBTB
Lookup table of the color imageA, B.

extents

int[] extents
Original dimensions extents value array.

extXInput

JTextField extXInput
Original X, Y, Z dimension extents values.

extYInput

JTextField extYInput
Original X, Y, Z dimension extents values.

extZInput

JTextField extZInput
Original X, Y, Z dimension extents values.

extXOutput

JTextField extXOutput
Power of 2 X, Y, Z dimension extents values.

extYOutput

JTextField extYOutput
Power of 2 X, Y, Z dimension extents values.

extZOutput

JTextField extZOutput
Power of 2 X, Y, Z dimension extents values.

forcePadding

boolean forcePadding
Flag to force the padding of blank images to the end of images.

forceResample

boolean forceResample
Boolean flag to do resample images.

imageA

ModelImage imageA
Model images A and B.

imageB

ModelImage imageB
Model images A and B.

imageAOriginal

ModelImage imageAOriginal
The non-cloned image which we want to load into the renderer.

leftPanelRenderMode

int leftPanelRenderMode
The left panel renderer mode.

LUTa

ModelLUT LUTa
Lookup table of the imageA, B.

LUTb

ModelLUT LUTb
Lookup table of the imageA, B.

m_iFilter

int m_iFilter
Resample filter type, default: Trilinear Interpoloation.

m_kFilterType

JComboBox m_kFilterType
Resample filter selection box.

nDim

int nDim
Number of available dimension.

newRes

float[] newRes
Resample resolutioin corresponding to Power of 2.

padButton

JButton padButton
Pad button is used for inserting blank images to the end of the image. This approach creates the power of 2 image. Pad Button is only enabled when the power of 2 value is greater than the slices number.

radioBrainSurfaceFlattenerR

JRadioButton radioBrainSurfaceFlattenerR
Radio button of the brainsurface flattener render mode in the right panel.

radioFlythruL

JRadioButton radioFlythruL
Radio button of the fly througth mode in the left panel.

radioSurfaceView

JRadioButton radioSurfaceView
Radio button of the surface view mode in the left panel.

radioNoneR

JRadioButton radioNoneR
Radio button of the none mode in the right panel.

radioRaycastR

JRadioButton radioRaycastR
Radio button of the raycast render mode in the right panel.

radioShearwarpR

JRadioButton radioShearwarpR
Radio button of the shearwarp render mode in the right panel.

radioSurfaceL

JRadioButton radioSurfaceL
Radio button of the surface render mode int the left panel.

radioSurfaceR

JRadioButton radioSurfaceR
Radio button of the surface render mode in the right panel.

res

float[] res
Original resolutioin arrray.

resampledImage

ModelImage resampledImage
Temp Model image.

rightPanelRenderMode

int rightPanelRenderMode
The right panel renderer mode.

segmentationImage

ModelImage segmentationImage
An image with areas designated as special (vessels, etc).

sr

ViewJFrameVolumeView sr
Reference to ViewJFrameSurfaceRenderer.

startupCommand

String startupCommand
The action command to send to the volume renderer after we start it (can be used to open a tab). Used by RFAST to open up the RFA simulation immediately.

volExtents

int[] volExtents
Resampled dimension value in Power of 2.

volSize

int volSize
Volume size X*Y*Z.

m_kVolViewType

String m_kVolViewType
Type of ViewJFrameVolumeView object (using WildMagic or not)

Class gov.nih.mipav.view.renderer.JPanelAVIChoice extends JDialogBase implements Serializable

serialVersionUID: -4246819535725354623L

Serialized Fields

compressionBox

JComboBox compressionBox
Combo box to select compression.

okayPressed

boolean okayPressed
Indicator for OK button pressed.

operating_system

int operating_system
Operating system type windows or Mac.

qualityField

JTextField qualityField
Text Field for M-JPEG quality.

Class gov.nih.mipav.view.renderer.JPanelRendererBase extends JPanel implements Serializable

serialVersionUID: 7175361900854772739L

Serialized Fields

applyButton

JButton applyButton
Apply button is used to apply the setting of the dialog.

cancelButton

JButton cancelButton
Cancel button is used on most dialogs. Defining it in the base allows default actions if the user presses return and the button is in focus.

cancelFlag

boolean cancelFlag
Flag indicating if the dialog had been cancelled or not.

closeButton

JButton closeButton
Close button is used to close the dialog.

helpButton

JButton helpButton
Help button is used on most dialogs. Defining it in the base allows default actions if the user presses return and the button is in focus.

isActiveImage

boolean isActiveImage
DOCUMENT ME!

mainPanel

JPanel mainPanel
The main control.

OKButton

JButton OKButton
OK button is used on most dialogs. Defining it in the base allows default actions if the user presses return and the button is in focus.

runInSeparateThread

boolean runInSeparateThread
Flag indicating if the algorithm should run in a separate thread. Default is true.

serif12

Font serif12
Fonts, same as MipavUtil.font12 and MipavUtil.font12B.

serif12B

Font serif12B
Fonts, same as MipavUtil.font12 and MipavUtil.font12B.

Class gov.nih.mipav.view.renderer.JPanelVolOpacityRGB extends JPanelVolOpacityBase implements Serializable

serialVersionUID: 8837612116721229202L

Serialized Fields

histogramABlue

ModelHistogram histogramABlue
imageA histogram of the Blue channel.

histogramAGreen

ModelHistogram histogramAGreen
imageA histogram of the Green channel.

histogramARed

ModelHistogram histogramARed
imageA histogram of the Red channel.

histogramBBlue

ModelHistogram histogramBBlue
imageB histogram, the Blue channel.

histogramBGreen

ModelHistogram histogramBGreen
imageB histogram, the Green channel.

histogramBRed

ModelHistogram histogramBRed
imageB histogram of the Red channel.

histogramGM_ABlue

ModelHistogram histogramGM_ABlue
imageA histogram of the Blue channel.

histogramGM_AGreen

ModelHistogram histogramGM_AGreen
imageA histogram of the Green channel.

histogramGM_ARed

ModelHistogram histogramGM_ARed
imageA histogram of the Red channel.

histogramGM_BBlue

ModelHistogram histogramGM_BBlue
imageB histogram, the Blue channel.

histogramGM_BGreen

ModelHistogram histogramGM_BGreen
imageB histogram, the Green channel.

histogramGM_BRed

ModelHistogram histogramGM_BRed
imageB histogram of the Red channel.

rendererProgressBar

JProgressBar rendererProgressBar
A reference to the volume renderer frame's progress bar.

RGBTA

ModelRGB RGBTA
Tagged for deletion - Matt, Ruida, Lee, ModelRGB table for imageA, B.

RGBTA_GM

ModelRGB RGBTA_GM
Tagged for deletion - Matt, Ruida, Lee, RGB table reference of the image A, B.

RGBTB

ModelRGB RGBTB
DOCUMENT ME!

RGBTB_GM

ModelRGB RGBTB_GM
DOCUMENT ME!

toolBar

JToolBar toolBar
ToolBar that hold the linear, horizontal mode etc.

Class gov.nih.mipav.view.renderer.MouseEventVector extends Object implements Serializable

serialVersionUID: 5183229064629196522L

Serialization Methods

readObject

private void readObject(ObjectInputStream stream)
                 throws IOException,
                        ClassNotFoundException
Called by some native invokeMethod. Provides a way to read this class out as a object stream. First, the size of the vector is read, then each mouseEvent into the vector, then the name, then the view. The view is read in as a String because it is not serializable. The read method corresponds to the write method, below.

Throws:
IOException - DOCUMENT ME!
ClassNotFoundException - DOCUMENT ME!

writeObject

private void writeObject(ObjectOutputStream stream)
                  throws IOException
Called by some native invokeMethod. Provides a way to write this class out as a object stream. First, the size of the vector is written, then each mouseEvent in the vector, then the name, then the view. The view is written out as a String because it is not serializable. The write method corresponds to the read method, above.

Throws:
IOException - DOCUMENT ME!
Serialized Fields

first

boolean first
First time accessed.

mode

int mode
Current mode.

mouseEvents

Vector<E> mouseEvents
Vector to record mouse events.

name

String name
Name of the events.

state

Object state
State being recorded.

stateVector

Vector<E> stateVector
Vector to record state changes.

view

double[] view
Parent frame transform3D view.

Class gov.nih.mipav.view.renderer.SceneState extends Object implements Serializable

serialVersionUID: 9166009718509099407L

Serialized Fields

axisX

float axisX
Save the current.

axisY

float axisY
Save the current.

axisZ

float axisZ
Save the current.

axisAngle

float axisAngle
Save the current.

clipSliceX

int clipSliceX
Clipping slider values for the triplanar clipping slider x, y, z, arbitrary.

clipSliceY

int clipSliceY
Clipping slider values for the triplanar clipping slider x, y, z, arbitrary.

clipSliceZ

int clipSliceZ
Clipping slider values for the triplanar clipping slider x, y, z, arbitrary.

clipSliceA

int clipSliceA
Clipping slider values for the triplanar clipping slider x, y, z, arbitrary.

clipSliceXNeg

int clipSliceXNeg
Clipping slider values for the triplanar clipping slider x, y, z negative.

clipSliceYNeg

int clipSliceYNeg
Clipping slider values for the triplanar clipping slider x, y, z negative.

clipSliceZNeg

int clipSliceZNeg
Clipping slider values for the triplanar clipping slider x, y, z negative.

is6PlaneClipping

boolean is6PlaneClipping
Boolean flag to indicate if the 6 plane clipping mode is active.

isClipArbiPicked

boolean isClipArbiPicked
Boolean flag to indicate if the arbitary clipping mode is active.

isVolOpacityChanged

boolean isVolOpacityChanged
Boolean indicator for volume opacity changed.

isVolumeDisplayMode3D

boolean isVolumeDisplayMode3D
Boolean indicator for the current diaplay mode, volume render mode or slice render mode.

surfaceOpacity

int surfaceOpacity
Surface opacity slider value of the surface dialog.

transform

float[] transform
Current sceneRoot transform.

transformFunc

TransferFunction transformFunc
Currrent tranform function of the volume render look up table.

whichComp

int whichComp
Current active volume opacity control of the volume render.

x

int x
x, y, z triplanar slider values.

y

int y
x, y, z triplanar slider values.

z

int z
x, y, z triplanar slider values.

xClipVisible

boolean xClipVisible
Boolean visibility values for x, y, z, arbitrary clipping slider frames.

yClipVisible

boolean yClipVisible
Boolean visibility values for x, y, z, arbitrary clipping slider frames.

zClipVisible

boolean zClipVisible
Boolean visibility values for x, y, z, arbitrary clipping slider frames.

aClipVisible

boolean aClipVisible
Boolean visibility values for x, y, z, arbitrary clipping slider frames.

xNegClipVisible

boolean xNegClipVisible
Boolean visibility values for x, y, z negative clipping slider frames.

yNegClipVisible

boolean yNegClipVisible
Boolean visibility values for x, y, z negative clipping slider frames.

zNegClipVisible

boolean zNegClipVisible
Boolean visibility values for x, y, z negative clipping slider frames.

xOpacity

int xOpacity
x, y, z triplanar opacity slider values.

yOpacity

int yOpacity
x, y, z triplanar opacity slider values.

zOpacity

int zOpacity
x, y, z triplanar opacity slider values.

xVisible

boolean xVisible
Boolean visibility values for x, y, z triplanar.

yVisible

boolean yVisible
Boolean visibility values for x, y, z triplanar.

zVisible

boolean zVisible
Boolean visibility values for x, y, z triplanar.

Class gov.nih.mipav.view.renderer.ViewJComponentVolOpacityBase extends JComponent implements Serializable

serialVersionUID: 826985329858268537L

Serialized Fields

addPointFlag

boolean addPointFlag
DOCUMENT ME!

componentDim

Dimension componentDim
The outer dimension of the histogram component we will be drawing.

dim

Dimension dim
The histogram image dimension.

histogram

ModelHistogram histogram
The image histogram.

histogramBuffer

int[] histogramBuffer
DOCUMENT ME!

histogramMax

double histogramMax
DOCUMENT ME!

histogramMaxLog

double histogramMaxLog
DOCUMENT ME!

image

ModelImage image
The image whose histo lut we are displaying.

img

Image img
DOCUMENT ME!

logFlag

boolean logFlag
Whether to transform the histogram data by log10.

lutIndexBuffer

int[] lutIndexBuffer
DOCUMENT ME!

min

float min
DOCUMENT ME!

max

float max
DOCUMENT ME!

mode

int mode
The current mode of the histogram component.

newPointIndex

int newPointIndex
DOCUMENT ME!

offsetX

int offsetX
DOCUMENT ME!

offsetY

int offsetY
DOCUMENT ME!

parentPanel

JPanelVolOpacityBase parentPanel
The container of this histogram component.

pixBuffer

int[] pixBuffer
DOCUMENT ME!

range

float range
DOCUMENT ME!

stRange

int stRange
DOCUMENT ME!

tfActiveIndex

int tfActiveIndex
DOCUMENT ME!

transferFunction

TransferFunction transferFunction
DOCUMENT ME!

Class gov.nih.mipav.view.renderer.ViewJComponentVolOpacityRGB extends ViewJComponentVolOpacityBase implements Serializable

serialVersionUID: 1208349901510241151L

Serialized Fields

lutIndexBuffer

int[] lutIndexBuffer
DOCUMENT ME!

Package gov.nih.mipav.view.renderer.flythroughview

Class gov.nih.mipav.view.renderer.flythroughview.JPanelFlythruMove extends JPanelRendererBase implements Serializable

serialVersionUID: 6224214629454958231L

Serialized Fields

first

boolean first
Flag to indicate first event.

mode

int mode
Current mode, init to stop.

changedMode

boolean changedMode
flag to indicate current mode being changed.

current

int current
index to the item list.

currEventTime

long currEventTime
Current mouse press event time stamp.

isPlaying

boolean isPlaying
Flag to indicating play mouse is running or not.

mouseCount

int mouseCount
Mouse event counter.

prevEventTime

long prevEventTime
Previous mouse press event time stamp.

annotationNextButton

JButton annotationNextButton
DOCUMENT ME!

annotationPrevButton

JButton annotationPrevButton
DOCUMENT ME!

autoRunButton

JButton autoRunButton
Auto Run Button.

aviPlayButton

JToggleButton aviPlayButton
AVI Recorder Play button.

aviRecordButton

JToggleButton aviRecordButton
AVI Recorder record button.

aviStopButton

JToggleButton aviStopButton
AVI Recorder Stop button.

branchButton

JButton branchButton
DOCUMENT ME!

contButton

JToggleButton contButton
Continue play button.

endButton

JButton endButton
DOCUMENT ME!

eventVector

MouseEventVector eventVector
Seqence of mouse events ( press, shift,and release as individual mouse event).

gazeDecreaseButton

JButton gazeDecreaseButton
DOCUMENT ME!

gazeIncrButton

JButton gazeIncrButton
DOCUMENT ME!

homeButton

JButton homeButton
DOCUMENT ME!

leftRotateButton

JButton leftRotateButton
DOCUMENT ME!

mediaPlayerButton

JButton mediaPlayerButton
MS media player button to play AVI file.

middleDownButton

JButton middleDownButton
DOCUMENT ME!

middleLeftButton

JButton middleLeftButton
DOCUMENT ME!

middleLeftButtonEmpty

JButton middleLeftButtonEmpty
Empty button group.

middleRightButton

JButton middleRightButton
DOCUMENT ME!

middleUpButton

JButton middleUpButton
DOCUMENT ME!

mouseEvents

Vector<E> mouseEvents
Sequence of mouse events( press, shift and release as a whole mouse event).

mousePanel

JPanel mousePanel
Panel holds the mouse move buttons.

moviePanel

JPanel moviePanel
Movie control panel that hold mouse recorder and AVI movie control.

parentScene

FlyThroughRenderInterface parentScene
The parent fly thru render reference.

pauseButton

JToggleButton pauseButton
Pause button.

playButton

JToggleButton playButton
Display button.

playMouse

gov.nih.mipav.view.renderer.flythroughview.JPanelFlythruMove.PlayMouse playMouse
Reference to PlayMouse class object.

pressed

boolean pressed
If any of the mouse move button pressed.

quickTimeButton

JButton quickTimeButton
Apple quick time player button to play quick time movie.

recordButton

JToggleButton recordButton
Recorder button.

reverseButton

JButton reverseButton
DOCUMENT ME!

rightDownButton

JButton rightDownButton
DOCUMENT ME!

rightLeftButton

JButton rightLeftButton
DOCUMENT ME!

rightRightButton

JButton rightRightButton
DOCUMENT ME!

rightRotateButton

JButton rightRotateButton
DOCUMENT ME!

rightUpButton

JButton rightUpButton
JButton group.

scroller

JScrollPane scroller
Scroll pane.

scrollPanel

gov.nih.mipav.view.renderer.flythroughview.JPanelFlythruMove.DrawingPanel scrollPanel
Scroll panel that holding the all the control components.

stepButton

JToggleButton stepButton
Next step button.

stepDecreaseButton

JButton stepDecreaseButton
DOCUMENT ME!

stepIncrButton

JButton stepIncrButton
DOCUMENT ME!

stopButton

JToggleButton stopButton
Stop button.

time

long time
Time to wait for the next mouse event.

toolBar

JToolBar toolBar
Tool bar of the mouse recorder.

Package gov.nih.mipav.view.renderer.J3D

Class gov.nih.mipav.view.renderer.J3D.JPanelCamera extends JPanelRendererJ3D implements Serializable

serialVersionUID: 7970872222123739616L

Serialized Fields

buttonPanel

JPanel buttonPanel
Button panel.

degreeLabel

JLabel degreeLabel
Label of the rotation degree.

degreeText

JTextField degreeText
Textfield of the roation degree.

flyButton

JRadioButton flyButton
Raido Button group.

labelX

JLabel labelX
X, Y, Z labels inside the rotation panel.

labelY

JLabel labelY
X, Y, Z labels inside the rotation panel.

labelZ

JLabel labelZ
X, Y, Z labels inside the rotation panel.

leftDownButton

JButton leftDownButton
Left panel mouse button down.

leftDownButtonEmpty

JButton leftDownButtonEmpty
Left panel empty button.

leftLeftButton

JButton leftLeftButton
Left panel mouse button left.

leftRightButton

JButton leftRightButton
Left panel mouse button right.

leftUpButton

JButton leftUpButton
Left panel mouse button up.

leftUpButtonEmpty

JButton leftUpButtonEmpty
Empty button group.

middleDownButton

JButton middleDownButton
Middle panel down button.

middleLeftButton

JButton middleLeftButton
Middel panel left button.

middleLeftButtonEmpty

JButton middleLeftButtonEmpty
Middle panel empty button.

middleRightButton

JButton middleRightButton
Middle panel right button.

middleRightButtonEmpty

JButton middleRightButtonEmpty
Middle panel right button empty.

middleUpButton

JButton middleUpButton
Middel panel up button.

mode

int mode
Current mode std or fly.

mousePanel

JPanel mousePanel
Panel holds the mouse move buttons.

parentScene

RenderViewBase parentScene
Parent frame.

pressed

boolean pressed
If any of the mouse move button pressed.

radioX

JRadioButton radioX
Radio button of the X_AXIS mode option.

radioY

JRadioButton radioY
Radio button of the Y_AXIS mode option.

radioZ

JRadioButton radioZ
Radio button of the Z_AXIS mode option.

resetButton

JButton resetButton
Reset button.

rightDownButton

JButton rightDownButton
Right panel down button.

rightLeftButton

JButton rightLeftButton
Right panel left button.

rightRightButton

JButton rightRightButton
Right panel right button.

rightUpButton

JButton rightUpButton
Right panel up button.

scroller

JScrollPane scroller
Scroll pane.

scrollPanel

gov.nih.mipav.view.renderer.J3D.JPanelCamera.DrawingPanel scrollPanel
Scroll panel that holding the all the control components.

snapButton

JButton snapButton
Camera button.

startButton

JButton startButton
Start button to auto snapshooting.

stdButton

JRadioButton stdButton
Auto snapshot button.

time

long time
Time to wait for the next mouse event.

Class gov.nih.mipav.view.renderer.J3D.JPanelClip extends JPanelRendererJ3D implements Serializable

serialVersionUID: -3342110506544352170L

Serialized Fields

enables

boolean[] enables
Enable flags for the 6 ( X, Y, Z and inverse ) clipping planes.

enablesArbi

boolean[] enablesArbi
Enable flags for the arbitrary clipping planes.

enablesStatic

boolean[] enablesStatic
Enable flags for the static clipping planes.

AclipPlanePts

javax.vecmath.Vector4f[] AclipPlanePts
Arbitrary clipping plane four corners points.

arbiMouseRotateBehavior

com.sun.j3d.utils.behaviors.mouse.MouseRotate arbiMouseRotateBehavior
Mouse Rotate behavior of the arbitrary clipping plane.

arbiTG

javax.media.j3d.TransformGroup arbiTG
Tranform group for arbitrary clipping plane.

arbiTrans3d

javax.media.j3d.Transform3D arbiTrans3d
Transform3D group for clipSliceA frame box and ModelClip arbitrary clipping plane.

mcArbiTrans3D

javax.media.j3d.Transform3D mcArbiTrans3D
Transform3D group for clipSliceA frame box and ModelClip arbitrary clipping plane.

arbitrary_SG

javax.media.j3d.Switch arbitrary_SG
Arbitrary clipping plane switch group.

aSlice

int aSlice
Which arbitray clipping slice is currently displayed.

axisX

float axisX
Value attribute for the roation axis.

axisY

float axisY
Value attribute for the roation axis.

axisZ

float axisZ
Value attribute for the roation axis.

axisAngle

float axisAngle
Value attribute for the roation axis.

behaviorBG

javax.media.j3d.BranchGroup behaviorBG
The BranchGroup to which the arbitrary behaviors are attached and rotate.

boundingCheckA

JCheckBox boundingCheckA
Arbitrary and static clipping plane check box.

boundingCheckStatic

JCheckBox boundingCheckStatic
Arbitrary and static clipping plane check box.

boundingCheckStaticInv

JCheckBox boundingCheckStaticInv
Arbitrary and static clipping plane check box.

boundingCheckX

JCheckBox boundingCheckX
Check box to turn the clipping plane frame on and off.

boundingCheckY

JCheckBox boundingCheckY
Check box to turn the clipping plane frame on and off.

boundingCheckZ

JCheckBox boundingCheckZ
Check box to turn the clipping plane frame on and off.

boundingCheckXInv

JCheckBox boundingCheckXInv
X,Y,Z inverse clipping plane check box.

boundingCheckYInv

JCheckBox boundingCheckYInv
X,Y,Z inverse clipping plane check box.

boundingCheckZInv

JCheckBox boundingCheckZInv
X,Y,Z inverse clipping plane check box.

boxStatic

JCheckBox boxStatic
Static and static inverse, arbitrary clipping plane check box.

boxStaticInv

JCheckBox boxStaticInv
Static and static inverse, arbitrary clipping plane check box.

boxA

JCheckBox boxA
Static and static inverse, arbitrary clipping plane check box.

boxX

JCheckBox boxX
Check boxes that turn the image plane and the sliders on and off.

boxY

JCheckBox boxY
Check boxes that turn the image plane and the sliders on and off.

boxZ

JCheckBox boxZ
Check boxes that turn the image plane and the sliders on and off.

boxXInv

JCheckBox boxXInv
Check boxes that turn the image plane and the sliders on and off.

boxYInv

JCheckBox boxYInv
Check boxes that turn the image plane and the sliders on and off.

boxZInv

JCheckBox boxZInv
Check boxes that turn the image plane and the sliders on and off.

clipCount

int clipCount
Counters show the event number in the mouse recorder.

rotationCount

int rotationCount
Counters show the event number in the mouse recorder.

clipEvents

MouseEventVector clipEvents
Mouse event vector that record the clipping plane sliders changes.

clipSliceAIndicator

ViewJComponentBoxSlice clipSliceAIndicator
Arbitrary clipping plane yellow boundary indicator box.

clipSliceA

ViewJComponentBoxSlice clipSliceA
Arbitrary clipping plane yellow boundary indicator box.

clipSliceStatic

ViewJComponentBoxSlice clipSliceStatic
Static clipping plane boundary box.

clipSliceStaticInv

ViewJComponentBoxSlice clipSliceStaticInv
Static clipping plane boundary box.

clipSliceX

ViewJComponentBoxSlice clipSliceX
The bounding box frame around the clipping planes.

clipSliceY

ViewJComponentBoxSlice clipSliceY
The bounding box frame around the clipping planes.

clipSliceZ

ViewJComponentBoxSlice clipSliceZ
The bounding box frame around the clipping planes.

clipSliceXInv

ViewJComponentBoxSlice clipSliceXInv
X, Y, Z inverse clipping slice boundary box.

clipSliceYInv

ViewJComponentBoxSlice clipSliceYInv
X, Y, Z inverse clipping slice boundary box.

clipSliceZInv

ViewJComponentBoxSlice clipSliceZInv
X, Y, Z inverse clipping slice boundary box.

clipSliderStatic

JSlider clipSliderStatic
Static, static inverse and arbitrary clipping plane boundary box.

clipSliderStaticInv

JSlider clipSliderStaticInv
Static, static inverse and arbitrary clipping plane boundary box.

sliderA

JSlider sliderA
Static, static inverse and arbitrary clipping plane boundary box.

clipSliderX

JSlider clipSliderX
Sliders for the image planes.

clipSliderY

JSlider clipSliderY
Sliders for the image planes.

clipSliderZ

JSlider clipSliderZ
Sliders for the image planes.

sliderXInv

JSlider sliderXInv
Sliders for the image planes.

sliderYInv

JSlider sliderYInv
Sliders for the image planes.

sliderZInv

JSlider sliderZInv
Sliders for the image planes.

colorButtonA

JButton colorButtonA
Color button for the arbitrary clipping plane frame.

colorButtonStatic

JButton colorButtonStatic
Color button for the static clipping plane frame.

colorButtonStaticInv

JButton colorButtonStaticInv
Color button for the static clipping plane frame.

colorButtonX

JButton colorButtonX
Color button for X clipping plane frame.

colorButtonXInv

JButton colorButtonXInv
Color button for X clipping plane frame.

colorButtonY

JButton colorButtonY
Color button for Y clipping plane frame.

colorButtonYInv

JButton colorButtonYInv
Color button for Y clipping plane frame.

colorButtonZ

JButton colorButtonZ
Color button for Z clipping plane frame.

colorButtonZInv

JButton colorButtonZInv
Color button for Z clipping plane frame.

colorChooser

ViewJColorChooser colorChooser
Color chooser dialog.

eqnPlanes

javax.vecmath.Vector4d[] eqnPlanes
Vetor holding the clipping plane equations.

eqnPlanesArbi

javax.vecmath.Vector4d[] eqnPlanesArbi
Vetor holding the clipping plane equations.

eqnPlanesStatic

javax.vecmath.Vector4d[] eqnPlanesStatic
Vetor holding the clipping plane equations.

eqnX

javax.vecmath.Vector4d eqnX
Vector4D clipping equation of each clipping plane.

eqnXInv

javax.vecmath.Vector4d eqnXInv
Vector4D clipping equation of each clipping plane.

eqnY

javax.vecmath.Vector4d eqnY
Vector4D clipping equation of each clipping plane.

eqnYInv

javax.vecmath.Vector4d eqnYInv
Vector4D clipping equation of each clipping plane.

eqnZ

javax.vecmath.Vector4d eqnZ
Vector4D clipping equation of each clipping plane.

eqnZInv

javax.vecmath.Vector4d eqnZInv
Vector4D clipping equation of each clipping plane.

eqnA

javax.vecmath.Vector4d eqnA
Vector4D clipping equation of each clipping plane.

extractButtonA

JButton extractButtonA
Extract arbitrary cliping plane button.

extractButtonS

JButton extractButtonS
Extract static eye cliping plane button.

intersectionPts

javax.vecmath.Point3f[] intersectionPts
intersectioin points coordinate.

iNumLights

int iNumLights
12 possible intersection points.

is6PlaneClipping

boolean is6PlaneClipping
Flag to indicate 6 plane clipping is active.

isClipArbiPicked

boolean isClipArbiPicked
Arbitrary clipping plane frame being picked or not.

isFirstTimeBuildTree

boolean isFirstTimeBuildTree
First time to build the clipping plane tree.

isStateChangedEvent

boolean isStateChangedEvent
Flag to indicate StateChangeEvent invoked.

isTransformChanged

boolean isTransformChanged
Flag to indicate tranformChanged event invoked.

labelAStart

JLabel labelAStart
Arbitrary clipping slider labels.

labelAMid

JLabel labelAMid
Arbitrary clipping slider labels.

labelAEnd

JLabel labelAEnd
Arbitrary clipping slider labels.

labelStatic

JLabel labelStatic
Static cliiping slider labels.

labelStaticInv

JLabel labelStaticInv
Static cliiping slider labels.

labelA

JLabel labelA
Static cliiping slider labels.

labelStaticInvStart

JLabel labelStaticInvStart
Static inverse clipping plane labels.

labelStaticInvMid

JLabel labelStaticInvMid
Static inverse clipping plane labels.

labelStaticInvEnd

JLabel labelStaticInvEnd
Static inverse clipping plane labels.

labelStaticStart

JLabel labelStaticStart
Static clipping plane labels.

labelStaticMid

JLabel labelStaticMid
Static clipping plane labels.

labelStaticEnd

JLabel labelStaticEnd
Static clipping plane labels.

labelX

JLabel labelX
Sliders labels.

labelY

JLabel labelY
Sliders labels.

labelZ

JLabel labelZ
Sliders labels.

labelXInv

JLabel labelXInv
Sliders labels.

labelYInv

JLabel labelYInv
Sliders labels.

labelZInv

JLabel labelZInv
Sliders labels.

labelXStart

JLabel labelXStart
Slider tick labels.

labelXMid

JLabel labelXMid
Slider tick labels.

labelXEnd

JLabel labelXEnd
Slider tick labels.

labelXStartInv

JLabel labelXStartInv
X clipping slider labels.

labelXMidInv

JLabel labelXMidInv
X clipping slider labels.

labelXEndInv

JLabel labelXEndInv
X clipping slider labels.

labelYStart

JLabel labelYStart
Y clipping slider labels.

labelYMid

JLabel labelYMid
Y clipping slider labels.

labelYEnd

JLabel labelYEnd
Y clipping slider labels.

labelYStartInv

JLabel labelYStartInv
Y inverse clipping slider labels.

labelYMidInv

JLabel labelYMidInv
Y inverse clipping slider labels.

labelYEndInv

JLabel labelYEndInv
Y inverse clipping slider labels.

labelZStart

JLabel labelZStart
Z clipping slider labels.

labelZMid

JLabel labelZMid
Z clipping slider labels.

labelZEnd

JLabel labelZEnd
Z clipping slider labels.

labelZStartInv

JLabel labelZStartInv
Z clipping slider labels.

labelZMidInv

JLabel labelZMidInv
Z clipping slider labels.

labelZEndInv

JLabel labelZEndInv
Z clipping slider labels.

m_aiImageA_backup

int[] m_aiImageA_backup
Backup of the data for undo:.

m_aiImageB_backup

int[] m_aiImageB_backup
ImageB backup buffer.

m_akLightBG

javax.media.j3d.BranchGroup[] m_akLightBG
Parent of each light bulb.

m_akLightMaterials

javax.media.j3d.Material[] m_akLightMaterials
Material properties for each light bulb.

m_akLightSpheres

com.sun.j3d.utils.geometry.Sphere[] m_akLightSpheres
Shapes representing light bulbs.

m_akLightTransformGroup

javax.media.j3d.TransformGroup[] m_akLightTransformGroup
Parent transform group.

m_kLightRoot

javax.media.j3d.BranchGroup m_kLightRoot
Parent of all the light bulbs.

maxBox

float maxBox
The largest of xBox,yBox,and zBox.

maxDim

int maxDim
The largest dimension of xDim, yDim and zDim.

mc

javax.media.j3d.ModelClip mc
Global model clip object.

mcArbi

javax.media.j3d.ModelClip mcArbi
Global model clip object.

mcStatic

javax.media.j3d.ModelClip mcStatic
Global model clip object.

mcArbiBG

javax.media.j3d.BranchGroup mcArbiBG
Branch group of the arbitrary clipping plane.

mcExtendBG

javax.media.j3d.BranchGroup mcExtendBG
Branch group of the arbitrary clipping plane.

mcArbiExtendBG

javax.media.j3d.BranchGroup mcArbiExtendBG
Branch group of the arbitrary clipping plane.

mcArbiTG

javax.media.j3d.TransformGroup mcArbiTG
ModelClip arbitrary TransformGroup.

mcBG

javax.media.j3d.BranchGroup mcBG
Branch group of the 6 clipping planes.

mcStaticBG

javax.media.j3d.BranchGroup mcStaticBG
Branch group of the static clipping plane.

objClipSliceA_BG

javax.media.j3d.BranchGroup objClipSliceA_BG
Arbitrary clipping branch group.

clipSliceA_BG

javax.media.j3d.BranchGroup clipSliceA_BG
Arbitrary clipping branch group.

clipSliceAIndicator_BG

javax.media.j3d.BranchGroup clipSliceAIndicator_BG
Arbitrary clipping branch group.

objClipSlices_BG

javax.media.j3d.BranchGroup objClipSlices_BG
root of all the clipping slices branch group.

objClipSliceStatic_BG

javax.media.j3d.BranchGroup objClipSliceStatic_BG
Static clipping branch group.

objClipSliceStaticInv_BG

javax.media.j3d.BranchGroup objClipSliceStaticInv_BG
Static clipping branch group.

objClipSliceX_BG

javax.media.j3d.BranchGroup objClipSliceX_BG
Parent for each individual clip slices branch group, childen of objClipSlices_BG.

objClipSliceY_BG

javax.media.j3d.BranchGroup objClipSliceY_BG
Parent for each individual clip slices branch group, childen of objClipSlices_BG.

objClipSliceZ_BG

javax.media.j3d.BranchGroup objClipSliceZ_BG
Parent for each individual clip slices branch group, childen of objClipSlices_BG.

objClipSliceXInv_BG

javax.media.j3d.BranchGroup objClipSliceXInv_BG
Parent of the -x, -y, -z clip slices branchgroup.

objClipSliceYInv_BG

javax.media.j3d.BranchGroup objClipSliceYInv_BG
Parent of the -x, -y, -z clip slices branchgroup.

objClipSliceZInv_BG

javax.media.j3d.BranchGroup objClipSliceZInv_BG
Parent of the -x, -y, -z clip slices branchgroup.

panelA

JPanel panelA
Arbitrary and static control panels.

panelS

JPanel panelS
Arbitrary and static control panels.

panelSInv

JPanel panelSInv
Arbitrary and static control panels.

panelX

JPanel panelX
Declare each clipping plane control panel.

panelXInv

JPanel panelXInv
Declare each clipping plane control panel.

panelY

JPanel panelY
Declare each clipping plane control panel.

panelYInv

JPanel panelYInv
Declare each clipping plane control panel.

panelZ

JPanel panelZ
Declare each clipping plane control panel.

panelZInv

JPanel panelZInv
Declare each clipping plane control panel.

radicalRatio

float radicalRatio
Arbitrary clipping plane expanding ratio.

recordEventName

boolean recordEventName
Flag indicates whether to record the clip event name.

rotationAxis

javax.vecmath.AxisAngle4f rotationAxis
Rotation axis to sync up the action for both ModelClip arbitrary clipping plane and the clipSliceA frame box transformGroup.

rotationEvent

MouseEventVector rotationEvent
mouse rotation event vector for the arbitrary clipping plane.

scroller

JScrollPane scroller
The scroll pane holding the panel content. Used when the screen is small.

scrollPanel

gov.nih.mipav.view.renderer.J3D.JPanelClip.DrawingPanel scrollPanel
Scroll panel that holding all the control components.

sSlice

int sSlice
Record the current static clipping slice number.

sSliceInv

int sSliceInv
Record the current static clipping slice number.

tabbedPane

JTabbedPane tabbedPane
Tabbed Panel that hold the each clipping planes control box.

textStatic

JTextField textStatic
Static and arbitrary text field.

textStaticInv

JTextField textStaticInv
Static and arbitrary text field.

textA

JTextField textA
Static and arbitrary text field.

textX

JTextField textX
Text fields that display the slice number when slider moves.

textY

JTextField textY
Text fields that display the slice number when slider moves.

textZ

JTextField textZ
Text fields that display the slice number when slider moves.

textXInv

JTextField textXInv
X, Y, Z inverse text field.

textYInv

JTextField textYInv
X, Y, Z inverse text field.

textZInv

JTextField textZInv
X, Y, Z inverse text field.

xBox

float xBox
xBox, yBox, zBox from the parent scene.

yBox

float yBox
xBox, yBox, zBox from the parent scene.

zBox

float zBox
xBox, yBox, zBox from the parent scene.

xDim

int xDim
Image X, Y, Z dimension.

yDim

int yDim
Image X, Y, Z dimension.

zDim

int zDim
Image X, Y, Z dimension.

xSlice

int xSlice
Which slice is currently displayed in the ZY plane.

xSliceInv

int xSliceInv
Which slice is currently displayed in the ZY plane.

ySlice

int ySlice
Which slice is currently displayed in the XZ plane.

ySliceInv

int ySliceInv
Which slice is currently displayed in the XZ plane.

zSlice

int zSlice
Which slice is currently displayed in the XY plane.

zSliceInv

int zSliceInv
Which slice is currently displayed in the XY plane.

Class gov.nih.mipav.view.renderer.J3D.JPanelLights extends JPanelRendererJ3D implements Serializable

serialVersionUID: 8549491288085975699L

Serialized Fields

ambientRadio

JRadioButton ambientRadio
Radio button for different light type.

bNeedsRedraw

boolean bNeedsRedraw
Flag is set if one of the controls changed a value and the renderering needs to be redrawn when the mouse is released.

checkBoxShowLight

JCheckBox checkBoxShowLight
Check box to show the light bulb or not.

colorButton

JButton colorButton
Color button, checkBox On/Off.

colorChooser

ViewJColorChooser colorChooser
Color choose dialog reference.

colorLabel

JLabel colorLabel
Color label.

controlPanel

JPanel controlPanel
Control panel.

controlPanelBox

Box controlPanelBox
Control panel box that hold the control panel.

directionalRadio

JRadioButton directionalRadio
Directional light radio botton.

drawPanel

JPanel drawPanel
Scroll panel reference.

intensitySlider

JSlider intensitySlider
Intensity slider.

iSelect

int iSelect
index of currently selected one.

labelIntensity

JLabel labelIntensity
Light intensity label.

labelIntensityBegin

JLabel labelIntensityBegin
Light intensity label begin.

labelIntensityEnd

JLabel labelIntensityEnd
Light intensity label end.

labelIntensityMid

JLabel labelIntensityMid
Light intensity label middle.

labelShininess

JLabel labelShininess
Light shinness label.

labelShininessBegin

JLabel labelShininessBegin
Shinness label begin.

labelShininessEnd

JLabel labelShininessEnd
Shinness label end.

labelShininessMid

JLabel labelShininessMid
Shinness lable middle.

list

JList list
List of lights.

m_aiLightScale

int[] m_aiLightScale
Light scale factor array.

m_akLights

GeneralLight[] m_akLights
The structure for the light bulbs.

m_akModelLights

GeneralLight[] m_akModelLights
General light array.

m_akSoftwareLightsModel

SoftwareLight[] m_akSoftwareLightsModel
Soft light array.

m_akSoftwareLightsWorld

SoftwareLight[] m_akSoftwareLightsWorld
Lighting objects needed for software rendering.

m_akWorldLights

GeneralLight[] m_akWorldLights
World general light array.

m_kLabelPosX

JLabel m_kLabelPosX
Label for slider X position.

m_kLabelPosY

JLabel m_kLabelPosY
Label for slider Y position.

m_kLabelPosZ

JLabel m_kLabelPosZ
Label for slider Z position.

m_kLabelTrgX

JLabel m_kLabelTrgX
Label for X light target position.

m_kLabelTrgY

JLabel m_kLabelTrgY
Label for Y light target position.

m_kLabelTrgZ

JLabel m_kLabelTrgZ
Label for Z light target position.

m_kPanelSurface

JPanelSurface m_kPanelSurface
surface panel reference.

m_kRenderSurface

SurfaceRender m_kRenderSurface
Parent render frame reference.

m_kSliderPosX

JSlider m_kSliderPosX
Light x position slider.

m_kSliderPosY

JSlider m_kSliderPosY
Light y position slider.

m_kSliderPosZ

JSlider m_kSliderPosZ
Light z position slider.

m_kSliderTrgX

JSlider m_kSliderTrgX
Light x target position slider.

m_kSliderTrgY

JSlider m_kSliderTrgY
Light y target position slider.

m_kSliderTrgZ

JSlider m_kSliderTrgZ
Light z target position slider.

m_kTextPosX

JTextField m_kTextPosX
X position text field.

m_kTextPosY

JTextField m_kTextPosY
Y position text field.

m_kTextPosZ

JTextField m_kTextPosZ
Z position text field.

m_kTextTrgX

JTextField m_kTextTrgX
X target position text field.

m_kTextTrgY

JTextField m_kTextTrgY
Y target position text field.

m_kTextTrgZ

JTextField m_kTextTrgZ
Z target position text field.

onOffCheckBox

JCheckBox onOffCheckBox
Light turn on/off check box.

onOffLabel

JLabel onOffLabel
Light turn on/off label.

pointRadio

JRadioButton pointRadio
Point light radio button.

scroller

JScrollPane scroller
Scroll pane.

scrollPanel

JPanel scrollPanel
Scroll the control panel when the frame changes size.

shininessPanel

JPanel shininessPanel
Shininess panel.

shininessSlider

JSlider shininessSlider
Shininess slider.

spotRadio

JRadioButton spotRadio
Spot light radio button.

textIntensity

JTextField textIntensity
Light intensity textfield.

textShininess

JTextField textShininess
Light shinness textfield.

xBox

float xBox
x, y, z box size.

yBox

float yBox
x, y, z box size.

zBox

float zBox
x, y, z box size.

maxBox

float maxBox
x, y, z box size.

m_kGPUVolumeRender

VolumeTriPlanarRender m_kGPUVolumeRender

Class gov.nih.mipav.view.renderer.J3D.JPanelRendererJ3D extends JPanelRendererBase implements Serializable

Serialized Fields

rayBasedRender

VolumeRenderer rayBasedRender
Raycast based renderer reference, raycast renderer or shear warp renderer.

renderBase

RenderViewBase renderBase
Render base.

Class gov.nih.mipav.view.renderer.J3D.JPanelSculptor extends JPanelRendererJ3D implements Serializable

serialVersionUID: 4235930260988710821L

Serialized Fields

m_iSculptHeight

int m_iSculptHeight
DOCUMENT ME!

m_iSculptWidth

int m_iSculptWidth
Window information for Sculpting:.

lineButton

JToggleButton lineButton
Line shape button.

m_kApplySculptButton

JButton m_kApplySculptButton
Button to apply sculpt region to the volume.

m_kClearDrawOutlineButton

JButton m_kClearDrawOutlineButton
Button for clearing the sculpt region.

m_kDrawOutlineButton

JToggleButton m_kDrawOutlineButton
Toggle button is down while the mouse is used to draw the sculpt outline.

m_kInvertOutlineButton

JButton m_kInvertOutlineButton
Button for inverting the sculpt region.

m_kSaveSculptButton

JButton m_kSaveSculptButton
Button to save the sculpt image.

m_kTextureSculptor

TextureSculptor m_kTextureSculptor
DOCUMENT ME!

m_kUndoSculptButton

JButton m_kUndoSculptButton
Button to undo the sculpt and restor the original volume.

m_kVolumeSculptor

VolumeSculptor m_kVolumeSculptor
Sculptor object enables, draws and sculpts the volume based on the outline region drawn on screen. Handles drawing the sculpt region.

mainPanel

JPanel mainPanel
Control panel for volume sculpting.

rectButton

JToggleButton rectButton
Rectangle shape button.

scroller

JScrollPane scroller
The scroll pane holding the panel content. Useful when the screen is small.

scrollPanel

gov.nih.mipav.view.renderer.J3D.JPanelSculptor.DrawingPanel scrollPanel
Scroll panel that holding the all the control components.

surRender

SurfaceRender surRender
SurfaceRender reference.

toolbarBuilder

ViewToolBarBuilder toolbarBuilder
Toolbar builder reference.

m_kVolumeRendererGPU

VolumeTriPlanarRender m_kVolumeRendererGPU

Class gov.nih.mipav.view.renderer.J3D.JPanelVolOpacity extends JPanelVolOpacityBase implements Serializable

serialVersionUID: -2618795264166878795L

Serialized Fields

histogramA

ModelHistogram histogramA
Histogram reference for image A.

histogramB

ModelHistogram histogramB
Histogram reference for image B.

histogramGM_A

ModelHistogram histogramGM_A
Histogram reference for imageA GM.

histogramGM_B

ModelHistogram histogramGM_B
Histogram reference for imageB GM.

rendererProgressBar

JProgressBar rendererProgressBar
A reference to the volume renderer frame's progress bar.

Class gov.nih.mipav.view.renderer.J3D.JPanelVolOpacityBase extends JPanelRendererJ3D implements Serializable

serialVersionUID: -5320201609864903620L

Serialized Fields

blendSlider

JSlider blendSlider
Opacity slider of texture 3D volume opacity changes.

stepsSlider

JSlider stepsSlider
Steps slider of Wildmagic GPU based raytracing.

componentOpacityA

ViewJComponentVolOpacityBase componentOpacityA
Reference to compoment opacity control A.

componentOpacityB

ViewJComponentVolOpacityBase componentOpacityB
Reference to compoment opacity control B.

componentOpacityGM_A

ViewJComponentVolOpacityBase componentOpacityGM_A
Reference to compoment opacity control A GM Rescale.

componentOpacityGM_B

ViewJComponentVolOpacityBase componentOpacityGM_B
Reference to compoment opacity control B GM Rescale.

GMCheckBox

JCheckBox GMCheckBox
Gradient Magnitude Check box of the grey scale image.

gradMagRescale_A

ModelImage gradMagRescale_A
Model image of the gradient magnitude of image A rescaled to have value in the range [0:255].

gradMagRescale_B

ModelImage gradMagRescale_B
Model image of the gradient magnitude of image B rescaled to have value in the range [0:255].

imageA

ModelImage imageA
Model image A.

imageB

ModelImage imageB
Model image B.

labelsTable

Hashtable<K,V> labelsTable
Historgram dialog slider labels of the imageA, B and GM imageA, B.

labelsTableB

Hashtable<K,V> labelsTableB
Historgram dialog slider labels of the imageA, B and GM imageA, B.

labelsTableGM_A

Hashtable<K,V> labelsTableGM_A
Historgram dialog slider labels of the imageA, B and GM imageA, B.

labelsTableGM_B

Hashtable<K,V> labelsTableGM_B
Historgram dialog slider labels of the imageA, B and GM imageA, B.

middleLabelValueA

float middleLabelValueA
DOCUMENT ME!

middleLabelValueB

float middleLabelValueB
DOCUMENT ME!

middleLabelValueGM_A

float middleLabelValueGM_A
DOCUMENT ME!

middleLabelValueGM_B

float middleLabelValueGM_B
DOCUMENT ME!

mouseSlider

JSlider mouseSlider
DOCUMENT ME!

mouseSliderB

JSlider mouseSliderB
DOCUMENT ME!

mouseSliderGM_A

JSlider mouseSliderGM_A
DOCUMENT ME!

mouseSliderGM_B

JSlider mouseSliderGM_B
DOCUMENT ME!

opacitySliderLabelsA

JLabel[] opacitySliderLabelsA
The labels below the opacity slider.

opacitySliderLabelsB

JLabel[] opacitySliderLabelsB
The labels below the opacity slider.

opacitySliderLabelsGM_A

JLabel[] opacitySliderLabelsGM_A
DOCUMENT ME!

opacitySliderLabelsGM_B

JLabel[] opacitySliderLabelsGM_B
DOCUMENT ME!

panelOpacityA

JPanel panelOpacityA
Panels that hold the the control components (opacity maps).

panelOpacityB

JPanel panelOpacityB
DOCUMENT ME!

panelOpacityGM_A

JPanel panelOpacityGM_A
DOCUMENT ME!

panelOpacityGM_B

JPanel panelOpacityGM_B
DOCUMENT ME!

rangeText

JTextField rangeText
X range text field in the imageA, B histogram dialog.

rangeTextB

JTextField rangeTextB
X range text field in the imageA, B histogram dialog.

rangeTextGM_A

JTextField rangeTextGM_A
X range text field in the Gradient Magnitude imageA, B histogram dialog.

rangeTextGM_B

JTextField rangeTextGM_B
X range text field in the Gradient Magnitude imageA, B histogram dialog.

scaleRangeA

float scaleRangeA
Scale range value according to the image min and max.

scaleRangeB

float scaleRangeB
Scale range value according to the image min and max.

scaleRangeGM_A

float scaleRangeGM_A
Scale range value according to the image min and max.

scaleRangeGM_B

float scaleRangeGM_B
Scale range value according to the image min and max.

tabbedPane

JTabbedPane tabbedPane
Tabbed pane that contains the list of opacity functions.

xRangeTextA

JTextField xRangeTextA
X range text field in the imageA, B and GM image A, B histogram dialog. Following text fields are used by the tri-planar volume view.

xRangeTextB

JTextField xRangeTextB
X range text field in the imageA, B and GM image A, B histogram dialog. Following text fields are used by the tri-planar volume view.

xRangeTextGM_A

JTextField xRangeTextGM_A
X range text field in the imageA, B and GM image A, B histogram dialog. Following text fields are used by the tri-planar volume view.

xRangeTextGM_B

JTextField xRangeTextGM_B
X range text field in the imageA, B and GM image A, B histogram dialog. Following text fields are used by the tri-planar volume view.

yRangeTextA

JTextField yRangeTextA
Y range text field in the imageA, B and GM image A, B histogram dialog. Following text fields are used by the tri-planar volume view.

yRangeTextB

JTextField yRangeTextB
Y range text field in the imageA, B and GM image A, B histogram dialog. Following text fields are used by the tri-planar volume view.

yRangeTextGM_A

JTextField yRangeTextGM_A
Y range text field in the imageA, B and GM image A, B histogram dialog. Following text fields are used by the tri-planar volume view.

yRangeTextGM_B

JTextField yRangeTextGM_B
Y range text field in the imageA, B and GM image A, B histogram dialog. Following text fields are used by the tri-planar volume view.

m_kVolumeViewer

VolumeTriPlanarInterface m_kVolumeViewer
Render base.

Class gov.nih.mipav.view.renderer.J3D.PlaneRender extends VolumeCanvas3D implements Serializable

serialVersionUID: 2025132936439496099L

Serialized Fields

m_aiLocalImageExtents

int[] m_aiLocalImageExtents
The image dimensions in x,y,z:.

m_akImageComponent

javax.media.j3d.ImageComponent2D[] m_akImageComponent
Image component 2D. Used to store the ModelImage data as textures.

m_akColors

javax.vecmath.Color3f[] m_akColors
Set of colors used to draw the X and Y Bars and the Z box:.

m_bDrawAxes

boolean m_bDrawAxes
when true, the axis labels (P-> L-> S->) will be drawn

m_bDrawXHairs

boolean m_bDrawXHairs
Turns on drawing of the X,Y bars and the Axis labels:.

m_bEntryPointSelect

boolean m_bEntryPointSelect
Boolean to turn on/off the RFA probe entry point selection with mouse:.

m_bFirstDrag

boolean m_bFirstDrag
Change the mouse cursor with the first mouseDrag event

m_bLeftMousePressed

boolean m_bLeftMousePressed
True when the left mouse has been pressed, set to false when the left mouse button is released.

m_bMemoryUsage

boolean m_bMemoryUsage
Whether to store all the data in ImageComponent2D array or not:.

m_bPatientOrientation

boolean m_bPatientOrientation
Actual image orietation.

m_bRightMousePressed

boolean m_bRightMousePressed
Flag indicating if the right mouse button is currently pressed down:

m_fCenterX

float m_fCenterX
The center of the X,Y bar cross hairs, in plane coordinates:.

m_fCenterY

float m_fCenterY
The center of the X,Y bar cross hairs, in plane coordinates:.

m_kActiveLookupTable

ModelStorageBase m_kActiveLookupTable
The current active lookup table:

m_fX0

float m_fX0
lower x-bound of the texture-mapped polygon:

m_fX1

float m_fX1
upper x-bound of the texture-mapped polygon:

m_fXBox

float m_fXBox
Numbers dicatating the size of the plane based on the extents and resolutions of the image.

m_fYBox

float m_fYBox
Numbers dicatating the size of the plane based on the extents and resolutions of the image.

m_fMaxBox

float m_fMaxBox
Numbers dicatating the size of the plane based on the extents and resolutions of the image.

m_fXRange

float m_fXRange
Width of the texture-mapped polygon:

m_fXTranslate

float m_fXTranslate
X direction mouse translation.

m_fY0

float m_fY0
lower y-bound of the texture-mapped polygon:

m_fY1

float m_fY1
upper y-bound of the texture-mapped polygon:

m_fYRange

float m_fYRange
Height of the texture-mapped polygon:

m_fYTranslate

float m_fYTranslate
Y direction mouse translatioin.

m_fZoomScale

float m_fZoomScale
Image scaling from Zoom:.

m_iPlaneOrientation

int m_iPlaneOrientation
Which dimension of the ModelImage to render.

m_iSlice

int m_iSlice
Which slice is currently displayed in the XY plane.

m_kActiveImage

ModelImage m_kActiveImage
Current active image for manipulating the LUT by dragging with the right-mouse down.

m_kCanvas

VolumeCanvas3D m_kCanvas
The Canvas3D object on which the plane is drawn.

m_kCurrentTransform

javax.media.j3d.Transform3D m_kCurrentTransform
current zoom transformation

m_kDisplayedImage

javax.media.j3d.ImageComponent2D m_kDisplayedImage
The current displayed texture, based on the value of m_iSlice.

m_kImageA

ModelImage m_kImageA
Current image A.

m_kImageB

ModelImage m_kImageB
Current image B.

m_kLabelX

String m_kLabelX
x-axis label:

m_kLabelY

String m_kLabelY
y-axis label:

m_kMouseTranslate

MouseTranslation m_kMouseTranslate
Mouse translate behavior.

m_kMouseZoom

MouseZoomBehavior m_kMouseZoom
Mouse zoom behavior.

m_kObjRootBG

javax.media.j3d.BranchGroup m_kObjRootBG
The BranchGroup root of the scene managed by the simple universe. The root has a single child, a TransformGroup, that manages all of the actual objects.

m_kOrderedGroup

javax.media.j3d.OrderedGroup m_kOrderedGroup
Root order group of the image scene graph.

m_kParent

ViewJFrameVolumeView m_kParent
Reference to the parent frame:.

m_kRFA_BranchGroup

javax.media.j3d.BranchGroup m_kRFA_BranchGroup
Branch group for the RFA indicator point.

m_kTextBranchGroup

javax.media.j3d.BranchGroup m_kTextBranchGroup
Branch group to hold the texture image.

m_kTextTransformGroup

javax.media.j3d.TransformGroup m_kTextTransformGroup
Transform group to hold the texture images.

m_kTexture

javax.media.j3d.Texture2D m_kTexture
The 2D texture for the texture-mapped polygon.

m_kTranslationTG

javax.media.j3d.TransformGroup m_kTranslationTG
Group dictating how the plane is translated.

m_kUniverse

com.sun.j3d.utils.universe.SimpleUniverse m_kUniverse
The SimpleUniverse object which is the parent of everything else in the scene.

m_kPatientSlice

PatientSlice m_kPatientSlice
PatientSlice contains all the Patient Coordinate System view-specific data for rendering this component:

m_kWinLevel

WindowLevel m_kWinLevel

Class gov.nih.mipav.view.renderer.J3D.RenderViewBase extends VolumeCanvas3D implements Serializable

serialVersionUID: 2913636735677876386L

Serialized Fields

bounds

javax.media.j3d.BoundingSphere bounds
A BoundingSphere that contains the entire scene. This bound is used for all scheduling, including lighting and mouse behaviors.

background

javax.media.j3d.Background background
The background node for the canvas.

boxFrame

ViewJComponentBoxFrame boxFrame
The outside box frame.

canvas

VolumeCanvas3D canvas
The Canvas3D object on which the surfaces are drawn and where the picking happens.

captureFrame

ViewJFrameRenderCamera captureFrame
Camera snapshot frame.

captureImage

ModelImage captureImage
The resulting ModelImage of the camera snapshot.

config

GraphicsConfiguration config
The config used to extends the Canvas3D class.

displayMode

int displayMode
Indicates which image is to be acted upon when two images are displayed.

imageA

ModelImage imageA
Reference to the image A of this frame.

imageB

ModelImage imageB
Reference to the image Bof this frame.

LUTa

ModelLUT LUTa
Reference to LUT for image A.

LUTb

ModelLUT LUTb
Reference to LUT for image B.

objBehaviorBG

javax.media.j3d.BranchGroup objBehaviorBG
The BranchGroup to which the standard behaviors are attached, zoom and rotate.

objBoxFrameBG

javax.media.j3d.BranchGroup objBoxFrameBG
Parent of the whole box frame.

objRootBG

javax.media.j3d.BranchGroup objRootBG
The BranchGroup root of the scene managed by the simple universe. The root has a single child, a TransformGroup, that manages all of the actual scene objects.

rotationAngle

int rotationAngle
Rotation angle when the camera takes snapshot.

rotationAxis

int rotationAxis
Rotation axis when the camera takes snapshot.

rotationControlPanel

JPanelCamera rotationControlPanel
Camera control dialog box.

rotationTimes

int rotationTimes
Number of rotation during the camera auto snapshotting.

rotationTotal

int rotationTotal
The total rotation degree, fixing one bug.

sceneRootTG

javax.media.j3d.TransformGroup sceneRootTG
A TransformGroup object to which all the scene objects are attached, including 3D images, surface, behavior, and lights.

transRotation

javax.media.j3d.Transform3D transRotation
transform rotation of the volume image during camera snapshot.

transRotationMatrix

javax.media.j3d.Transform3D transRotationMatrix
Rotation matrix.

triPlanarViewBG

javax.media.j3d.BranchGroup triPlanarViewBG
Triplanar view branch group, which hold the three plane view and the slice box frame view.

universe

com.sun.j3d.utils.universe.SimpleUniverse universe
The SimpleUniverse object which is the parent of everything else in the scene.

viewPanel

JPanelView viewPanel
View dialog associated with surface plotter or renderer.

sliderEvents

MouseEventVector sliderEvents
Slider events used by the mouse recorder.

Class gov.nih.mipav.view.renderer.J3D.ViewJComponentVolOpacity extends ViewJComponentVolOpacityBase implements Serializable

serialVersionUID: -5441344478555285964L

Serialized Fields

myParent

RenderViewBase myParent
DOCUMENT ME!

m_kVolumeViewer

VolumeTriPlanarInterface m_kVolumeViewer

opacityCount

int opacityCount
Opacity slider event count.

opacityEvents

MouseEventVector opacityEvents
Opacity slider changed events, which is used by the mouse recorder.

Class gov.nih.mipav.view.renderer.J3D.ViewJFrameRenderCamera extends ViewJFrameBase implements Serializable

serialVersionUID: -6223794265610151148L

Serialized Fields

pBarVisible

boolean pBarVisible
Flag indicating if a whether of not the progress bar is visible.

progressBar

ViewJProgressBar progressBar
Progress bar object.

progressBarLocation

Point progressBarLocation
Progress bar default location.

progressMode

int progressMode
Progress mode - either standard, no cancel, or no progress bar.

borderColor

Color borderColor
color for the line border surrounding each image in the light-box.

borderSize

int borderSize
spacing for the line border surrounding each image in the light-box.

componentImageVector

Vector<E> componentImageVector
DOCUMENT ME!

currentSelectedSlice

int currentSelectedSlice
DOCUMENT ME!

currentSlice

int currentSlice
current info -- this slice info refers to the *real* slice number, not the page index for a slice on a page.

deleteButton

JButton deleteButton
Delete the captured image button.

deleteSelection

JMenuItem deleteSelection
Delete menu icon item.

extractButton

JButton extractButton
Extract the selected image button.

extractSelection

JMenuItem extractSelection
Extrace menu icon item.

firstTime

boolean firstTime
DOCUMENT ME!

frameHeight

int frameHeight
DOCUMENT ME!

frameStartLocation

Point frameStartLocation
DOCUMENT ME!

frameWidth

int frameWidth
frame information.

gridColor

Color gridColor
color for the region in-between the images in the light-box.

gridColumn

int gridColumn
DOCUMENT ME!

gridRow

int gridRow
value for the number of rows (number of images along the y-axis) and columns (number of images along the x-axis) in the light-box.

Note that both row and column set to 1 cannot make sense, but that one or the other will be the 'dependent variable' as defined by the row_dependent boolean var.

A value of 0 means that the dependent variable will automatically be sized to its maximum size that can fit nicely on the screen.

gridSpacing

int gridSpacing
spacing between images in the light-box.

group

ButtonGroup group
DOCUMENT ME!

imageBorderVector

Vector<E> imageBorderVector
DOCUMENT ME!

imageBufferA

float[] imageBufferA
DOCUMENT ME!

imageHeight

int imageHeight
DOCUMENT ME!

imagePanelSizeX

int imagePanelSizeX
per num visible images information.

imagePanelSizeY

int imagePanelSizeY
per num visible images information.

imagePanelVector

Vector<E> imagePanelVector
DOCUMENT ME!

imageWidth

int imageWidth
DOCUMENT ME!

lastSelectedSlice

int lastSelectedSlice
DOCUMENT ME!

magMax

float magMax
DOCUMENT ME!

magMin

float magMin
DOCUMENT ME!

magnification

float magnification
magnification of images in the light-box (mag is a percentage).

maxPagePanelSizeX

int maxPagePanelSizeX
DOCUMENT ME!

maxPagePanelSizeY

int maxPagePanelSizeY
DOCUMENT ME!

menuBar

JMenuBar menuBar
variables for the menubar.

modelImageVector

Vector<E> modelImageVector
DOCUMENT ME!

numTotalSlices

int numTotalSlices
DOCUMENT ME!

pagePanel

JPanel pagePanel
Number of pages in this frame will always be one.

pagePanelSizeX

int pagePanelSizeX
DOCUMENT ME!

pagePanelSizeY

int pagePanelSizeY
DOCUMENT ME!

pageScrollPanel

JScrollPane pageScrollPanel
Scroll panel to handle the frame scolling.

parentFrame

RenderViewBase parentFrame
DOCUMENT ME!

pixBuffer

int[] pixBuffer
DOCUMENT ME!

row_dependent

boolean row_dependent
indicates which--row or column--should be dependent on the other.

the default is the number of rows is the dependent variable, and is dependent apon the total number of images and the number of columns. Don't confuse the reading to be "This display is (t/f) dependent on the row." It -could- be read as "The display is a column-independent (t/f) matrix".

selectedBorderColor

Color selectedBorderColor
color for the line border surrounding each selected image in the light-box.

selectedBorderSize

int selectedBorderSize
spacing for the selected line border surrounding each image in the light-box.

selectedImages

Vector<E> selectedImages
the selectedImages contains the *real* slice numbers -- not the index of a slice on a page. So the maximum number in the vector will be numTotalSlices - 1.

srcImage

ModelImage srcImage
Reference to imageA.

tBar

JToolBar tBar
Frame ToolBar.

toolbarPanel

JPanel toolbarPanel
variables for the toolbar.

unselectedBorderColor

Color unselectedBorderColor
DOCUMENT ME!

xScreen

int xScreen
DOCUMENT ME!

yScreen

int yScreen
DOCUMENT ME!

Class gov.nih.mipav.view.renderer.J3D.ViewJFrameVolumeView extends ViewJFrameBase implements Serializable

serialVersionUID: 1898957906984534260L

Serialized Fields

config

GraphicsConfiguration config
Configuration param, which will pass down to each render's constructor.

isoImageA

ModelImage isoImageA
Isotropic version image A, B, used by the shear warp renderer.

isoImageB

ModelImage isoImageB
Isotropic version image A, B, used by the shear warp renderer.

menuObj

ViewMenuBuilder menuObj
Menu items storage.

modelViewLabel

JLabel modelViewLabel
Labels for the current position in 3D ModelView coordinates:.

modelViewLabelVals

JLabel[] modelViewLabelVals
DOCUMENT ME!

orient

int[] orient
Orientations of the three axes.

panelToolbar

JPanel panelToolbar
Panel that holds the toolbars.

patientSliceLabel

JLabel patientSliceLabel
Labels for the current position in PatientSlice coordinates:.

patientSliceLabelVals

JLabel[] patientSliceLabelVals
DOCUMENT ME!

RGBTA

ModelRGB RGBTA
Lookup table of the color imageA, B.

RGBTB

ModelRGB RGBTB
Lookup table of the color imageA, B.

serif12

Font serif12
Fonts, same as MipavUtil.font12 and MipavUtil.font12B.

serif12B

Font serif12B
Fonts, same as MipavUtil.font12 and MipavUtil.font12B.

panelLabels

JPanel panelLabels
Panel containing the position labels:.

axialOrientation

boolean axialOrientation
Indicates that image orientation is unknown type or not.

brainsurfaceFlattenerRender

MjCorticalAnalysis brainsurfaceFlattenerRender
Rendering the brainsurfaceFlattener objects.

cameraPanel

JPanel cameraPanel
DOCUMENT ME!

clipBox

JPanel clipBox
DOCUMENT ME!

clipButton

JButton clipButton
Button to invoke all the six clipping planes.

clipDisableButton

JButton clipDisableButton
Button to disable all the six clipping planes.

clipMaskButton

JButton clipMaskButton
Button to crop the clip volume.

clipMaskUndoButton

JButton clipMaskUndoButton
Button to undo crop the clip volume.

clipPanel

JPanel clipPanel
DOCUMENT ME!

clipPlaneButton

JButton clipPlaneButton
Button to invoke clipping planes.

clipSaveButton

JButton clipSaveButton
Button to save clipped region.

displayPanel

JPanel displayPanel
DOCUMENT ME!

dualImagePane

JSplitPane dualImagePane
dual image pane that holds the left and right panel.

dualImagePanel

JPanel dualImagePanel
The image panel to hold two Canvas3D.

dualLeftPanel

JPanel dualLeftPanel
Left panel of the dual panel view.

dualRightPanel

JPanel dualRightPanel
Right panel of the dual panel view.

firstTimeVolView

boolean firstTimeVolView
Keep track of whether we're switching to the volume renderer for the first time.

flythruControl

JPanelVirtualEndoscopySetup flythruControl
Fly through setup control panel.

flythruMoveControl

JPanelFlythruMove flythruMoveControl
Fly through movement control panel.

flythruMovePanel

JPanel flythruMovePanel
View panel contains the fly thru control panel.

flythruOptions

FlythruRender.SetupOptions flythruOptions
Fly through options.

flythruPanel

JPanel flythruPanel
Fly through panel.

flythruRender

FlythruRender flythruRender
Reference to fly through renderer.

flythruSurfaceButton

JButton flythruSurfaceButton
Surface load button.

flythruTabVector

Vector<E> flythruTabVector
DOCUMENT ME!

flyThruToolbar

JToolBar flyThruToolbar
Flythru toolbar.

histoLUTPanel

JPanel histoLUTPanel
Control panel for the surface renderer.

imageAOriginal

ModelImage imageAOriginal
Reference to the imageA original copy.

imageOrientation

int imageOrientation
Image orientation: coronal, sagittal, axial, unknown.

imagePanel

JPanel imagePanel
The image panel to hold one Canvas3D.

intensityDialog

JDialogIntensityPaint intensityDialog
DOCUMENT ME!

isBrainsurfaceFlattenerEnable

boolean isBrainsurfaceFlattenerEnable
Indicate if the brainsurface flattener render is enabled from the resample dialog or not.

isEndoscopyEnable

boolean isEndoscopyEnable
Indicate if the fly through render is enabled from the resample dialog or not.

isRayCastEnable

boolean isRayCastEnable
Indicate if the raycast render is enabled from the resample dialog or not.

isShearWarpEnable

boolean isShearWarpEnable
Indicate if the shear warp render is enabled from the resample dialog or not.

isSurfaceRenderEnable

boolean isSurfaceRenderEnable
Indicate if the surface render is enabled from the resample dialog or not.

isSurfaceViewEnable

boolean isSurfaceViewEnable
Indicate if the surface view is enabled from the resample dialog or not.

leftPanelRenderMode

int leftPanelRenderMode
The left panel renderer mode.

lightPanel

JPanel lightPanel
DOCUMENT ME!

m_akPlaneRender

PlaneRender[] m_akPlaneRender
The three slice views displayed as texture-mapped polygons:.

m_kBrainsurfaceFlattenerPanel

JPanel m_kBrainsurfaceFlattenerPanel
Control panels for the Brainsurface Flattener:.

m_kGeodesicPanel

JPanel m_kGeodesicPanel
Control panel for drawing geodesic curves.

m_kSculptPanel

JPanel m_kSculptPanel
Control panel for volume sculpting.

maxPanelWidth

int maxPanelWidth
The max width of the control panels.

menuBar

JMenuBar menuBar
Menu bar.

mousePanel

JPanel mousePanel
DOCUMENT ME!

opacityDialog

JDialogOpacityControls opacityDialog
DOCUMENT ME!

opacityPanel

JPanel opacityPanel
DOCUMENT ME!

paddingImageA

ModelImage paddingImageA
Padding imageA with blank images feeding.

paddingImageB

ModelImage paddingImageB
Padding imageB with blank images feeding.

paintGrowDialog

JDialogPaintGrow paintGrowDialog
Control panels of the triplanar view.

panelHistoLUT

JPanelHistoLUT panelHistoLUT
LUT control panel of the gray scale image.

panelHistoRGB

JPanelHistoRGB panelHistoRGB
RGB control panel of the color image.

parallelButton

JToggleButton parallelButton
Rendering parallel rotation button.

probePanel

JPanel probePanel
DOCUMENT ME!

radioCOMPOSITE

JRadioButton radioCOMPOSITE
Radio button of the COMPOSITE mode option.

radioCOMPOSITEShear

JRadioButton radioCOMPOSITEShear
Radio button of the COMPOSITE mode option.

radioMIP

JRadioButton radioMIP
Radio button of the MIP mode option.

radioMIPShear

JRadioButton radioMIPShear
Radio button of the MIP mode option.

radioSURFACE

JRadioButton radioSURFACE
Radio button of the SURFACE mode option.

radioSURFACEFAST

JRadioButton radioSURFACEFAST
Radio button of the SURFACE mode option.

radioSURFACEShear

JRadioButton radioSURFACEShear
Radio button of the SURFACE mode option.

radioSurrenderCOMPOSITE

JRadioButton radioSurrenderCOMPOSITE
Radio button of the surface render composite mode.

radioSurrenderLIGHT

JRadioButton radioSurrenderLIGHT
Radio button of the surface render lighting mode.

radioXRAY

JRadioButton radioXRAY
Radio button of the XRAY mode option.

radioXRAYShear

JRadioButton radioXRAYShear
Radio button of the XRAY mode option.

raisedbevel

Border raisedbevel
Panel Border view.

loweredbevel

Border loweredbevel
Panel Border view.

compound

Border compound
Panel Border view.

redBorder

Border redBorder
Panel Border view.

etchedBorder

Border etchedBorder
Panel Border view.

pressedBorder

Border pressedBorder
Panel Border view.

raycastCameraPanel

JPanel raycastCameraPanel
DOCUMENT ME!

raycastOptionsPanel

JPanel raycastOptionsPanel
Control panels for the raycast render.

raycastRender

VolumeRendererRayCast raycastRender
DOCUMENT ME!

raycastTabVector

Vector<E> raycastTabVector
DOCUMENT ME!

rayCastToolBar

JToolBar rayCastToolBar
Raycast toolbar.

resampleDialog

JDialogVolViewResample resampleDialog
Reference to resample dialog, use to null out the resample dialog in this frame.

rfaButton

JButton rfaButton
Button for RFA.

rfaSeparator

JButton rfaSeparator
RFA separator.

rightPane

JSplitPane rightPane
The view pane that contains the image view and tri-planar view panels.

rightPanelRenderMode

int rightPanelRenderMode
The right panel renderer mode.

screenWidth

int screenWidth
Screen width, screen height.

screenHeight

int screenHeight
Screen width, screen height.

sculptHeight

int sculptHeight
Sculpt region height.

sculptWidth

int sculptWidth
Sculpt region width.

shearwarpCameraPanel

JPanel shearwarpCameraPanel
DOCUMENT ME!

shearwarpOptionsPanel

JPanel shearwarpOptionsPanel
Control panels for the shearwarp render.

shearwarpRender

VolumeRendererShearWarp shearwarpRender
DOCUMENT ME!

shearwarpTabVector

Vector<E> shearwarpTabVector
DOCUMENT ME!

shearWarpToolBar

JToolBar shearWarpToolBar
Shearwarp toolbar.

slicePanel

JPanel slicePanel
DOCUMENT ME!

storeTabbedPaneIndex

int storeTabbedPaneIndex
Previoius tab index recorder.

surfacePanel

JPanel surfacePanel
DOCUMENT ME!

surRender

SurfaceRender surRender
Three types of renderer.

surView

SurfaceView surView
Surface View reference

surTabVector

Vector<E> surTabVector
For each render, use the vector to store the currently active tabs.

toolbarBuilder

ViewToolBarBuilder toolbarBuilder
Toolbar builder reference.

triImagePanel

JPanel triImagePanel
Tri image planar render panels.

unparallelButton

JToggleButton unparallelButton
Rendering unparallel rotaion button.

viewPanel

JPanel viewPanel
DOCUMENT ME!

viewToolBar

JToolBar viewToolBar
The top one render view switch toolbar.

volToolBar

JToolBar volToolBar
Surface Render toolbar.

Class gov.nih.mipav.view.renderer.J3D.VolumeCanvas3D extends javax.media.j3d.Canvas3D implements Serializable

serialVersionUID: 5377755312667171175L

Serialized Fields

m_bTestFrameRate

boolean m_bTestFrameRate

m_dLastTime

double m_dLastTime
Framerate Performance parameters:

m_dAccumulatedTime

double m_dAccumulatedTime
Framerate Performance parameters:

m_dFrameRate

double m_dFrameRate
Framerate Performance parameters:

m_iFrameCount

int m_iFrameCount
Framerate Performance parameters:

m_iAccumulatedFrameCount

int m_iAccumulatedFrameCount
Framerate Performance parameters:

m_iTimer

int m_iTimer
Framerate Performance parameters:

m_iMaxTimer

int m_iMaxTimer
Framerate Performance parameters:

Package gov.nih.mipav.view.renderer.J3D.model.file

Class gov.nih.mipav.view.renderer.J3D.model.file.FileInfoSurfaceRefXML_J3D extends FileInfoSurfaceRefXML implements Serializable

Serialized Fields

m_kMaterial

javax.media.j3d.Material m_kMaterial
Material properties of the surface:.

Class gov.nih.mipav.view.renderer.J3D.model.file.FileInfoSurfaceXML_J3D extends FileInfoSurfaceXML implements Serializable

Serialized Fields

m_kMaterial

javax.media.j3d.Material m_kMaterial
Material properties of the surface:.

m_kMesh

ModelTriangleMesh[] m_kMesh
Surface triangle mesh:.

Package gov.nih.mipav.view.renderer.J3D.surfaceview

Class gov.nih.mipav.view.renderer.J3D.surfaceview.JDialogSimpleText extends JDialogBase implements Serializable

serialVersionUID: 1577016550517413391L

Serialized Fields

field

JTextField field
Text field to enter name in.

name

String name
Name for the view.

Class gov.nih.mipav.view.renderer.J3D.surfaceview.JDialogSurfaceAVI extends JDialogBase implements Serializable

serialVersionUID: -475364340269669481L

Serialized Fields

rate

double rate
Frame rate per second.

rateBox

JTextField rateBox
Text field for the frame rate per second.

subSample

int subSample
Subsample flag.

subSampleCBox

JComboBox subSampleCBox
Sub sampel combo box.

Class gov.nih.mipav.view.renderer.J3D.surfaceview.JFrameSurfaceMaterialProperties extends JFrame implements Serializable

serialVersionUID: 3077827124095959620L

Serialized Fields

AFTER

int AFTER
Before/After index values for the two displayed spheres, canvases, and display panels:.

BEFORE

int BEFORE
Before/After index values for the two displayed spheres, canvases, and display panels:.

m_akMaterialPreset

javax.media.j3d.Material[] m_akMaterialPreset
Pre-defined materials

m_fShininess

float m_fShininess
specular coefficient

m_iNumPreset

int m_iNumPreset
Preset Material's examples:.

m_iSurfaceIndex

int m_iSurfaceIndex
the index of the surface that is being changed in the JPanelSurface

m_iWhichButton

int m_iWhichButton
Which button is pressed to activate the JColorChooser:.

m_kAmbient

javax.vecmath.Color3f m_kAmbient
Current color values:.

m_kAmbientColorButton

JButton m_kAmbientColorButton
Material Properties color buttons:.

m_kColorChooser

JColorChooser m_kColorChooser
Color Chooser dialog:.

m_kDiffuse

javax.vecmath.Color3f m_kDiffuse
diffuse color

m_kDiffuseColorButton

JButton m_kDiffuseColorButton
diffuse color button

m_kEmissive

javax.vecmath.Color3f m_kEmissive
emissive color

m_kEmissiveColorButton

JButton m_kEmissiveColorButton
emissive color button

m_kImagePane

JSplitPane m_kImagePane
Split pane for displaying the canvases side-by-side:.

m_kImagePanel

JPanel[] m_kImagePanel
Canvas display panels:.

m_kMainPane

JSplitPane m_kMainPane
Split pane for displaying the rendered spheres above the interface:.

m_kMaterialNew

javax.media.j3d.Material m_kMaterialNew
Materials for new vales and backup:.

m_kMaterialPanel

JPanel m_kMaterialPanel
Window display panels: Material properties buttons/slider panel:.

m_kMaterialSave

javax.media.j3d.Material m_kMaterialSave
Saved Material for backup

m_kParent

JPanelSurface m_kParent
Parent class:.

m_kShininessSlider

JSlider m_kShininessSlider
Shininess slider.

m_kSpecular

javax.vecmath.Color3f m_kSpecular
Specular color component

m_kSpecularColorButton

JButton m_kSpecularColorButton
Specular color button

m_bColorApplied

boolean m_bColorApplied
keeps track of whether or not color has been applied to surface (for backup on cancel)

Class gov.nih.mipav.view.renderer.J3D.surfaceview.JPanelDisplay extends JPanelRendererJ3D implements Serializable

serialVersionUID: 926266253314679850L

Serialized Fields

boundingCheck

JCheckBox boundingCheck
Check box for turning box on and off.

colorButton

JButton colorButton
Color button for changing color.

colorButtonBackground

JButton colorButtonBackground
Color button for changing z color.

colorChooser

ViewJColorChooser colorChooser
Color chooser dialog.

cubePanel

JPanel cubePanel
Panel for the rotation cube.

cubicCheck

JCheckBox cubicCheck
Check box for cubic control.

radioButtonGroupProjections

ButtonGroup radioButtonGroupProjections
Button group for projections.

radioButtonOrthographic

JRadioButton radioButtonOrthographic
Radio Button for Orthographic rendering.

radioButtonPerspective

JRadioButton radioButtonPerspective
Radio Button for Perspective rendering.

viewAlignedButton

JRadioButton viewAlignedButton
Radio Button for Perspective rendering.

viewButton

JRadioButton viewButton
Radio Button for Orthographic rendering.

viewTextureButtonGroup

ButtonGroup viewTextureButtonGroup
Button group for projections.

coarseValue

float coarseValue
Coarse and fine value.

fineValue

float fineValue
Coarse and fine value.

fine

JTextField fine
Coarse and fine value text field.

coarse

JTextField coarse
Coarse and fine value text field.

fineLabel

JLabel fineLabel
Coarse and fine value label.

coarseLabel

JLabel coarseLabel
Coarse and fine value label.

flag

boolean flag
Flag indicating if the red bounding box is on or off.

scroller

JScrollPane scroller
The scroll pane holding the panel content. Useful when the screen is small.

scrollPanel

gov.nih.mipav.view.renderer.J3D.surfaceview.JPanelDisplay.DrawingPanel scrollPanel
Scroll panel that holding the all the control components.

Class gov.nih.mipav.view.renderer.J3D.surfaceview.JPanelGeodesic extends JPanelRendererJ3D implements Serializable

serialVersionUID: 4382184418236793404L

Serialized Fields

drawLabel

JLabel drawLabel
Geodesic line draw control label.

flythruGeodesic

Geodesic flythruGeodesic
DOCUMENT ME!

flythruRender

FlythruRender flythruRender
FlythruRender reference.

m_bPickSetFlyThru

boolean m_bPickSetFlyThru
Initialzied to true when the the Geodesic.setPickCanvas funtion is called.

m_bPickSetSurface

boolean m_bPickSetSurface
DOCUMENT ME!

m_fDijkstraCurrent

float m_fDijkstraCurrent
DOCUMENT ME!

m_fDijkstraPrevious

float m_fDijkstraPrevious
DOCUMENT ME!

m_fDijkstraTotal

float m_fDijkstraTotal
DOCUMENT ME!

m_fEuclidianCurrent

float m_fEuclidianCurrent
Values for the current path length between the last two selected points:

m_fEuclidianPrevious

float m_fEuclidianPrevious
Values for the previous current path length between the last two selected points:

m_fEuclidianTotal

float m_fEuclidianTotal
Values for the total path lengths:.

m_fGeodesicSmoothCurrent

float m_fGeodesicSmoothCurrent
DOCUMENT ME!

m_fGeodesicSmoothPrevious

float m_fGeodesicSmoothPrevious
DOCUMENT ME!

m_fGeodesicSmoothTotal

float m_fGeodesicSmoothTotal
DOCUMENT ME!

m_kCheckLivewire

JCheckBox m_kCheckLivewire
Toggle between LiveWire Interaction and point & click interaction:.

m_kClearAllCutsButton

JButton m_kClearAllCutsButton
DOCUMENT ME!

m_kClearAllGeodesicButton

JButton m_kClearAllGeodesicButton
DOCUMENT ME!

m_kClearLastCutButton

JButton m_kClearLastCutButton
DOCUMENT ME!

m_kClearLastGeodesicButton

JButton m_kClearLastGeodesicButton
Button for deleting the geodesic.

m_kCutGeodesicButton

JButton m_kCutGeodesicButton
Button for cutting the mesh along the geodesic:.

m_kDijkstraDistance

JLabel m_kDijkstraDistance
DOCUMENT ME!

m_kDijkstraDistanceValueLast

JLabel m_kDijkstraDistanceValueLast
DOCUMENT ME!

m_kDijkstraDistanceValueTotal

JLabel m_kDijkstraDistanceValueTotal
DOCUMENT ME!

m_kDisplayButtonGroup

ButtonGroup m_kDisplayButtonGroup
DOCUMENT ME!

m_kDisplayDijkstra

JRadioButton m_kDisplayDijkstra
DOCUMENT ME!

m_kDisplayEuclidian

JRadioButton m_kDisplayEuclidian
DOCUMENT ME!

m_kDisplayGeodesic

JRadioButton m_kDisplayGeodesic
Radio buttons for displaying the smoothed geodesic, dijkstra's path, or the euclidian path:.

m_kDrawGeodesicButton

JToggleButton m_kDrawGeodesicButton
Geodesic drawing interface Toggle button is down while points are added to the curve:.

m_kEuclidianDistance

JLabel m_kEuclidianDistance
Labels to indicate the path length between the picked points, in Euclidian distance, geodesic smoothed distance, and Dijkstra's path mesh distance. Two labels each, one for the distances between the last two points picked, and one for the total length of the curve, from starting point to end point:

m_kEuclidianDistanceValueLast

JLabel m_kEuclidianDistanceValueLast
DOCUMENT ME!

m_kEuclidianDistanceValueTotal

JLabel m_kEuclidianDistanceValueTotal
DOCUMENT ME!

m_kFinishClosedGeodesicButton

JButton m_kFinishClosedGeodesicButton
DOCUMENT ME!

m_kFinishOpenGeodesicButton

JButton m_kFinishOpenGeodesicButton
DOCUMENT ME!

m_kGeodesicSmoothDistance

JLabel m_kGeodesicSmoothDistance
DOCUMENT ME!

m_kGeodesicSmoothDistanceValueLast

JLabel m_kGeodesicSmoothDistanceValueLast
DOCUMENT ME!

m_kGeodesicSmoothDistanceValueTotal

JLabel m_kGeodesicSmoothDistanceValueTotal
DOCUMENT ME!

m_kGeodesicToggleWireframe

JToggleButton m_kGeodesicToggleWireframe
DOCUMENT ME!

mainPanel

JPanel mainPanel
the main control panel.

scroller

JScrollPane scroller
The scroll pane holding the panel content. Useful when the screen is small.

scrollPanel

gov.nih.mipav.view.renderer.J3D.surfaceview.JPanelGeodesic.DrawingPanel scrollPanel
Scroll panel that holding the all the control components.

surfaceGeodesic

Geodesic surfaceGeodesic
Geodesic reference.

surPickLabel

JLabel surPickLabel
Label to indicate that enable Surface pickable before drawing geodesic line.

surRender

SurfaceRender surRender
SurfaceRender reference.

Class gov.nih.mipav.view.renderer.J3D.surfaceview.JPanelMouse extends JPanelRendererJ3D implements Serializable

serialVersionUID: -3554229077099968128L

Serialized Fields

events

Vector<E> events
Vector that holds mouse or change events.

first

boolean first
Flag to indicate first event.

listModel

DefaultListModel listModel
List to record info for each mouse, change events.

mode

int mode
Current mode, init to stop.

mouseCount

int mouseCount
Mouse event counter.

sliderCount

int sliderCount
Slider moves event counter.

changedMode

boolean changedMode
flag to indicate current mode being changed.

contButton

JToggleButton contButton
Continue play button.

currentEventVector

MouseEventVector currentEventVector
Current event vector used by the save AVI.

currentObject

Object currentObject
current SceneState object being recorded by SaveAVI.

currentTransform

javax.media.j3d.Transform3D currentTransform
Current transform3D object used in Save AVI.

eventVector

MouseEventVector eventVector
Global mouse event vector.

goButton

JButton goButton
Go to button.

isArbitraryRotation

boolean isArbitraryRotation
Flag indicates that arbitrary clipping plane is triggered or not.

isPlaying

boolean isPlaying
Flag to indicating play mouse is running or not.

mainPanel

JPanel mainPanel
The main control panel.

mjpegQuality

float mjpegQuality
Param to save AVI.

movieButton

JButton movieButton
Save AVI button .

myParent

SurfaceRender myParent
Reference to ViewJFrameSurfaceRenderer.

nameChangeVector

MouseEventVector nameChangeVector
Used by name change dialog to change name of the selected item.

newButton

JButton newButton
This button add at head of the list.

parentScene

RenderViewBase parentScene
Parent scene.

pauseButton

JToggleButton pauseButton
Pause button.

playButton

JToggleButton playButton
Display button.

playMouse

gov.nih.mipav.view.renderer.J3D.surfaceview.JPanelMouse.PlayMouse playMouse
Reference to PlayMouse class object.

process

int process
Process id used by the save AVI.

recordButton

JToggleButton recordButton
Recorder button.

recorderToAVI

gov.nih.mipav.view.renderer.J3D.surfaceview.JPanelMouse.RecordMouse recorderToAVI
Reference to RecordMouse object class.

removeAllButton

JButton removeAllButton
Remove all items in the item list.

removeButton

JButton removeButton
Remove the selected item in the item list.

resetTransform

javax.media.j3d.Transform3D resetTransform
Current transform3D object.

scroller

JScrollPane scroller
The scroll pane holding the panel content. Useful when the screen is small.

scrollPanel

gov.nih.mipav.view.renderer.J3D.surfaceview.JPanelMouse.DrawingPanel scrollPanel
Scroll panel that holding the all the control components.

setMouseVectorFlag

boolean setMouseVectorFlag
flag to indicate the first time mouse tranform event happpened.

sliceDialog

JPanelSlices sliceDialog
Dialog to turn the slices control box on and off.

stepButton

JToggleButton stepButton
Next step button.

stopButton

JToggleButton stopButton
Stop button.

toolBar

JToolBar toolBar
Tool bar of the mouse recorder.

transformChange

boolean transformChange
Flag indicates that a transform changed event is invoked.

viewList

JList viewList
View list of the mouse recorder display list.

Class gov.nih.mipav.view.renderer.J3D.surfaceview.JPanelSlices extends JPanelRendererJ3D implements Serializable

serialVersionUID: -8359831093707979536L

Serialized Fields

boxX

JCheckBox boxX
Check boxes that turn the image plane on and off.

boxY

JCheckBox boxY
Check boxes that turn the image plane on and off.

boxZ

JCheckBox boxZ
Check boxes that turn the image plane on and off.

sliderX

JSlider sliderX
Sliders for the image planes.

sliderY

JSlider sliderY
Sliders for the image planes.

sliderZ

JSlider sliderZ
Sliders for the image planes.

sliderT

JSlider sliderT
Sliders for the image planes.

tSlice

int tSlice
Which time slice is currently displayed.

slicePosition

WildMagic.LibFoundation.Mathematics.Vector3f slicePosition

xSlice

int xSlice
Which slice is currently displayed in the ZY plane.

sliceVisible

boolean[] sliceVisible
Flags indicating if the image slices are on or off.

ySlice

int ySlice
Which slice is currently displayed in the XZ plane.

zSlice

int zSlice
Which slice is currently displayed in the XY plane.

boundingBoxPanel

JPanel boundingBoxPanel
Bounding box control panel.

boundingCheck

JCheckBox[] boundingCheck
Check box for turning bounding boxes on and off.

colorButton

JButton[] colorButton
Color button for changing bounding box color.

colorChooser

ViewJColorChooser colorChooser
Color chooser dialog.

controlPanel

JPanel controlPanel
Main panel for sliders.

current

int current
Current event vector index.

labelX

JLabel labelX
Labels next to sliders.

labelY

JLabel labelY
Labels next to sliders.

labelZ

JLabel labelZ
Labels next to sliders.

labelT

JLabel labelT
Labels next to sliders.

labelX1

JLabel labelX1
Labels beneath sliders.

labelXMid

JLabel labelXMid
Labels beneath sliders.

labelXEnd

JLabel labelXEnd
Labels beneath sliders.

labelY1

JLabel labelY1
Labels beneath sliders.

labelYMid

JLabel labelYMid
Labels beneath sliders.

labelYEnd

JLabel labelYEnd
Labels beneath sliders.

labelZ1

JLabel labelZ1
Labels beneath sliders.

labelZMid

JLabel labelZMid
Labels beneath sliders.

labelZEnd

JLabel labelZEnd
Labels beneath sliders.

opacityControlPanel

JPanel opacityControlPanel
Opacity control panel.

opacityLabelX

JLabel opacityLabelX
The opacity slider label.

opacityLabelY

JLabel opacityLabelY
The opacity slider label.

opacityLabelZ

JLabel opacityLabelZ
The opacity slider label.

opacitySliderLabelsX

JLabel[] opacitySliderLabelsX
The labels below the opacity slider.

opacitySliderLabelsY

JLabel[] opacitySliderLabelsY
The labels below the opacity slider.

opacitySliderLabelsZ

JLabel[] opacitySliderLabelsZ
The labels below the opacity slider.

opacitySliderX

JSlider opacitySliderX
Opacity slider, not enabled yet.

opacitySliderY

JSlider opacitySliderY
Opacity slider, not enabled yet.

opacitySliderZ

JSlider opacitySliderZ
Opacity slider, not enabled yet.

scroller

JScrollPane scroller
The scroll pane holding the panel content. Useful when the screen is small.

scrollPanel

gov.nih.mipav.view.renderer.J3D.surfaceview.JPanelSlices.DrawingPanel scrollPanel
Scroll panel that holding the all the control components.

setSliderFlag

boolean setSliderFlag
Flag to indicate the first time slider name changes.

textX

JTextField textX
Text fields that display the slice number next to the sliders.

textY

JTextField textY
Text fields that display the slice number next to the sliders.

textZ

JTextField textZ
Text fields that display the slice number next to the sliders.

textT

JTextField textT
Text fields that display the slice number next to the sliders.

xDim

int xDim
x, y, z and time dimension values.

yDim

int yDim
x, y, z and time dimension values.

zDim

int zDim
x, y, z and time dimension values.

tDim

int tDim
x, y, z and time dimension values.

xOpacitySlice

int xOpacitySlice
x, y, z opacity slider values.

yOpacitySlice

int yOpacitySlice
x, y, z opacity slider values.

zOpacitySlice

int zOpacitySlice
x, y, z opacity slider values.

xProbe

int xProbe
Probe x, y, z position.

yProbe

int yProbe
Probe x, y, z position.

zProbe

int zProbe
Probe x, y, z position.

Class gov.nih.mipav.view.renderer.J3D.surfaceview.JPanelSurface extends JPanelRendererJ3D implements Serializable

serialVersionUID: -4600563188022683359L

Serialized Fields

activeLightBulbIndex

int activeLightBulbIndex
Record the current active index of light bulb, which is being picked.

areaLabel

JLabel areaLabel
The area label.

areaText

JTextField areaText
Displays the area of triangle.

colorButton

JButton colorButton
The color button, which calls a color chooser.

colorChooser

ViewJColorChooser colorChooser
Color chooser for when the user wants to change the color of the surface.

colorLabel

JLabel colorLabel
The color button label.

comboLabel

JLabel comboLabel
The polygon mode combo box label.

currentIndex

int currentIndex
Current surface index being highlighted.

decimateButton

JButton decimateButton
Decimate button.

detailLabel

JLabel detailLabel
The level of detail slider label.

detailSlider

JSlider detailSlider
Level of detail slider.

detailSliderLabels

JLabel[] detailSliderLabels
The labels below the detail slider.

findArbitraryClipping

boolean findArbitraryClipping
flag indicates arbitrary clpping bounding frame being picked.

findProbe

boolean findProbe
flag indicates the probe being picked.

levelSButton

JButton levelSButton
Save surface button.

levelVButton

JButton levelVButton
Save surface button.

levelWButton

JButton levelWButton
Save surface button.

levelXMLButton

JButton levelXMLButton
Save surface button.

lightArray

javax.media.j3d.Light[] lightArray
An array of eight lights that can be used for illuminating the surfaces in the scene. The lights at indices 0 and 7 are initially enabled; the other lights are initially disabled. The default positions for the lights are at the 8 corners of the cube [0,1]^3. Light 0 is at (0,0,0) and light 7 is at (1,1,1), thereby providing suitable lighting for the visible surfaces in the scene. Other lights can be enabled as desired through the light attribute dialog.

lightArrayBG

javax.media.j3d.BranchGroup[] lightArrayBG
The branch groups to which the lights are attached.

lightBulbs

ViewJComponentLightBulbs lightBulbs
The structure for the light bulbs.

m_aiMapIndexToJPanelLightsIndex

int[] m_aiMapIndexToJPanelLightsIndex
The index of the lights in JPanelLights is different from the order maintained here. This array maps from our index to JPanelLights' index.

m_aiMapJPanelLightsIndexToIndex

int[] m_aiMapJPanelLightsIndexToIndex
The index of the lights in JPanelLights is different from the order maintained here. This array maps from JPanelLights' index to our index.

m_akLights

GeneralLight[] m_akLights
The description of the lights so they can be duplicated in the "Advanced Material Properties" dialog:.

m_kAdvancedMaterialOptionsButton

JButton m_kAdvancedMaterialOptionsButton
The material options button, which launches the material editor window.

m_kGeodesicGroup

javax.media.j3d.BranchGroup m_kGeodesicGroup
For drawing the geodesic lines on the triangle mesh:.

m_kFiberTractGroup

javax.media.j3d.BranchGroup m_kFiberTractGroup
For displaying the fiber bundle tracts in the orthogonal slice view:

m_kLightsControl

JPanelLights m_kLightsControl
Light dialog for when the user clicks the light button.

m_kPathPositionTG

javax.media.j3d.TransformGroup m_kPathPositionTG
For drawing the flythru path in the triangle mesh:.

m_kStereoButton

JButton m_kStereoButton
Stereo render button, launches the JStereoWindow for viewing the ModelTriangleMesh in stereo:.

m_kSurfaceTextureButton

JButton m_kSurfaceTextureButton
Opens SurfaceTexture dialog:.

maxBox

float maxBox
ModelImage max dimension: (Extents * resolutions).

mSurfaceMask

SurfaceMask mSurfaceMask
Surface mask.

mSurfacePaint

SurfacePaint mSurfacePaint
Paint interface/algorithm for allowing the user to interactively paint the vertices of the ModelTriangleMesh.

opacityLabel

JLabel opacityLabel
The opacity slider label.

opacitySlider

JSlider opacitySlider
Opacity slider, not enabled yet.

opacitySliderLabels

JLabel[] opacitySliderLabels
The labels below the opacity slider.

parentScene

SurfaceRender parentScene
The parent object that holds necessary the structures to which the surfaces will be added and modified.

pickCanvas

com.sun.j3d.utils.picking.PickCanvas pickCanvas
The PickCanvas object that ties together the canvas and the surfaces branch group to allow pick operations on the scene.

polygonModeCB

JComboBox polygonModeCB
The combo box for the polygon mode to display.

scroller

JScrollPane scroller
The scroll pane holding the panel content. Useful when the screen is small.

setSurfaceOpacityFlag

boolean setSurfaceOpacityFlag
Indicator for the opacity slider moves.

smooth1Button

JButton smooth1Button
Smooth button.

smooth2Button

JButton smooth2Button
Smooth button.

smooth3Button

JButton smooth3Button
Smooth button.

sphere

com.sun.j3d.utils.geometry.Sphere sphere
Sphere showing where the user clicked in the surface.

sphereBranch

javax.media.j3d.BranchGroup sphereBranch
Branch group parent of the sphere.

sphereShowing

boolean sphereShowing
Flag indicating if the sphere is currently showing.

sphereTransform

javax.media.j3d.TransformGroup sphereTransform
Transform group parent of the sphere.

staticLightBehaviorBG

javax.media.j3d.BranchGroup staticLightBehaviorBG
Static light hehavior branch group.

staticLightBG

javax.media.j3d.BranchGroup staticLightBG
The branch group that holds the static light bulb.

staticLightBulb

ViewJComponentLightBulbs staticLightBulb
The structure for the static light bulb.

staticLightTG

javax.media.j3d.TransformGroup staticLightTG
The transform group that holds the static light branch group.

staticLightTranslate

com.sun.j3d.utils.behaviors.mouse.MouseTranslate staticLightTranslate
Static light translate behavior.

staticLightZoom

com.sun.j3d.utils.behaviors.mouse.MouseZoom staticLightZoom
Static light zoom behavior.

surfaceBackFaceCB

JCheckBox surfaceBackFaceCB
Check Box for surface back face culling.

surfaceClipCB

JCheckBox surfaceClipCB
Check Box for surface clpping of the volume render.

surfaceDirectoryName

String surfaceDirectoryName
The directory where a surface file was last loaded/saved. Defaults to MIPAV default directory.

surfaceList

JList surfaceList
The list box in the dialog for surfaces.

surfaceOpacityEvents

MouseEventVector surfaceOpacityEvents
Surface opacity changes event queue.

surfaceOpacitySlice

int surfaceOpacitySlice
Surface volume opacity.

surfacePickableCB

JCheckBox surfacePickableCB
Check Box for surface pickable.

surfaceRootBG

javax.media.j3d.BranchGroup surfaceRootBG
The branch group that holds all the surfaces together.

surfaceRootTG

javax.media.j3d.TransformGroup surfaceRootTG
The transform group to which the model lights are attached.

surfaceSliderCount

int surfaceSliderCount
Counter for surface opacity slider moves.

surfaceTransparencyCB

JCheckBox surfaceTransparencyCB
Check Box for surface transparency.

surfaceVector

Vector<E> surfaceVector
A list of the surfaces. The elements are of type SurfaceAttributes.

triangleLabel

JLabel triangleLabel
The number of triangles label.

triangleText

JTextField triangleText
Displays the number of triangles.

volumeLabel

JLabel volumeLabel
The volume label.

volumeText

JTextField volumeText
Displays the volume of triangle.

Class gov.nih.mipav.view.renderer.J3D.surfaceview.JPanelSurfaceTexture extends JPanelRendererJ3D implements Serializable

serialVersionUID: 7562070328632922435L

Serialized Fields

mHistoLUT

JPanelHistoLUT mHistoLUT
Display the independent LUT for Black/White images.

mHistoRGB

JPanelHistoRGB mHistoRGB
Display the independent RGB for Color Images.

mImageA

ModelImage mImageA
ModelImage used to generate the 3D texture:.

mImageALink

ModelImage mImageALink
Reference to ModelImage A for linking the texture to the imageA LUT.

mImageAsTextureRadioButton

JRadioButton mImageAsTextureRadioButton
RadioButton for turing on the surface image texture:.

mImageAsVertexColorRadioButton

JRadioButton mImageAsVertexColorRadioButton
RadioButton for turing on the surface image per-vertex color:.

mImageDirName

String mImageDirName
Stores the currently-loaded ModelImage directory name:.

mImageFileName

String mImageFileName
Stores the currently-loaded ModelImage file name:.

mImageFileNameLabel

JLabel mImageFileNameLabel
Display the currently-loaded ModelImage file name:.

mImageNoneRadioButton

JRadioButton mImageNoneRadioButton
RadioButton for turing off the surface image:.

mLoadImageButton

JButton mLoadImageButton
Load a new ModelImage:.

mLUTButtonGroup

ButtonGroup mLUTButtonGroup
Grouping the radio buttons:.

mLUTImageA

ModelImage mLUTImageA
Independent ModelImage for independent LUT.

mLUTModel

ModelLUT mLUTModel
The LUT associated with the ModelImage imageA:.

mLUTSeparate

ModelLUT mLUTSeparate
The LUT associated with the independent texture LUT:.

mModelLUTRadioButton

JRadioButton mModelLUTRadioButton
Use the ModelImage LUT.

mNewLUTRadioButton

JRadioButton mNewLUTRadioButton
Use a separate LUT.

mPatientSlice

PatientSlice mPatientSlice
Renders the ModelImage data with LUT changes.

mRGBModel

ModelRGB mRGBModel
The RGB LUT associated with the ModelImage imageA:.

mRGBSeparate

ModelRGB mRGBSeparate
The RGB LUT associated with the independent texture LUT:.

mSurfaceTextureImage

javax.media.j3d.ImageComponent3D mSurfaceTextureImage
The ModelImage texture with LUT changes, used with the Texture3D.

mTexture

javax.media.j3d.Texture3D mTexture
3D Texture used to display the ModelImage data as a texture mapped onto the ModelTriangleMesh.

mTextureButtonGroup

ButtonGroup mTextureButtonGroup
Grouping the radio buttons:.

mTextureStatus

int mTextureStatus
Currently selected ModelImage display type:.

mTextureUnitState

javax.media.j3d.TextureUnitState[] mTextureUnitState
TextureUnitState contains texture information for the rendered surfaces:.

Class gov.nih.mipav.view.renderer.J3D.surfaceview.JPanelView extends JPanelRendererJ3D implements Serializable

serialVersionUID: -8408530937731996131L

Serialized Fields

flyBehavior

FlyBehaviorRenderer flyBehavior
Fly behavior reference.

flyButton

JRadioButton flyButton
Fly behaviro radio button.

flyText

String flyText
User message explain how the mouse moves in fly mode.

labels

JLabel[] labels
speed control slider labels.

leftDownButton

JButton leftDownButton
DOCUMENT ME!

leftLeftButton

JButton leftLeftButton
DOCUMENT ME!

leftRightButton

JButton leftRightButton
DOCUMENT ME!

leftUpButton

JButton leftUpButton
Arrow button references.

middleDownButton

JButton middleDownButton
DOCUMENT ME!

middleLeftButton

JButton middleLeftButton
DOCUMENT ME!

middleRightButton

JButton middleRightButton
DOCUMENT ME!

middleUpButton

JButton middleUpButton
DOCUMENT ME!

mode

int mode
Current behavior mode.

modeGroup

ButtonGroup modeGroup
Radio button group reference.

mouseText

JTextArea mouseText
Text field reference that hold the user message.

pointerBehavior

PointerBehaviorRenderer pointerBehavior
Pointer behavior reference, not used now.

pressed

boolean pressed
Flag to indicate mouse pressed or not.

ptrButton

JRadioButton ptrButton
Point behavior button.

rightDownButton

JButton rightDownButton
DOCUMENT ME!

rightLeftButton

JButton rightLeftButton
DOCUMENT ME!

rightRightButton

JButton rightRightButton
DOCUMENT ME!

rightUpButton

JButton rightUpButton
DOCUMENT ME!

scroller

JScrollPane scroller
The scroll pane holding the panel content. Useful when the screen is small.

scrollPanel

gov.nih.mipav.view.renderer.J3D.surfaceview.JPanelView.DrawingPanel scrollPanel
Scroll panel that holding the all the control components.

stdBehavior

com.sun.j3d.utils.behaviors.vp.ViewPlatformBehavior stdBehavior
Standard behavior reference.

stdButton

JRadioButton stdButton
Standard behavior button.

stdText

String stdText
User message explain how the mouse moves in stardard mode.

time

long time
Standard mouse tread waiting time.

velocitySlider

JSlider velocitySlider
fly Speed control slider.

Class gov.nih.mipav.view.renderer.J3D.surfaceview.JStereoWindow extends JFrame implements Serializable

serialVersionUID: -2284771559648676504L

Serialized Fields

m_akUniverse

com.sun.j3d.utils.universe.SimpleUniverse[] m_akUniverse
Three SimpleUniverses, one for each canavas:.

m_dEyeSeparation

double m_dEyeSeparation
Original eye separation, read from the canvas.view.physicalbody.

m_iCurrentUniverse

int m_iCurrentUniverse
The current universe to be initialized:.

m_iStereoUpdateCount

int m_iStereoUpdateCount
First time the stereo canvas is rendered, set to true:.

m_kD

Dimension m_kD
BufferedImage Dimensions (power of two).

m_kDisplayPane

JSplitPane m_kDisplayPane
The JSplitPane displaying the left and right eye views:.

m_kEyeSep_Slider

JSlider m_kEyeSep_Slider
Focal-length, (eye separation) slider.

m_kLeftCanvas

VolumeCanvas3D m_kLeftCanvas
Left-eye view canvas:.

m_kLeftImagePanel

JPanel m_kLeftImagePanel
Left Image Panel, holds the canvas for the left-eye view:.

m_kMainPane

JSplitPane m_kMainPane
The JSplitPane displaying different views and the user-interface:.

m_kRGStereo

BufferedImage m_kRGStereo
BufferedImage containing the Anagyphy stereo image:.

m_kRightCanvas

VolumeCanvas3D m_kRightCanvas
Right-eye view canvas:.

m_kRightImagePanel

JPanel m_kRightImagePanel
Right Image Panel, holds the canvas for the right-eye view:.

m_kStereoCanvas

VolumeCanvas3D m_kStereoCanvas
Stereo canvas:.

m_kStereoPane

JSplitPane m_kStereoPane
The JSplitPane displaying the left and right eye views and the stereo view:.

m_kStereoPanel

JPanel m_kStereoPanel
Stereo Image Panel, holds the canvas for the Anaglyph stereo view:.

m_kStereoShape

javax.media.j3d.Shape3D m_kStereoShape
Texture-mapped polygon for displaying the Anaglyph stereo image as a texture:.

Class gov.nih.mipav.view.renderer.J3D.surfaceview.SurfaceRender extends RenderViewBase implements Serializable

serialVersionUID: 608959413602233595L

Serialized Fields

isViewTextureAligned

boolean isViewTextureAligned
Flag to indicate whether the view volume texture is aligned or not.

rayBasedRender

VolumeRenderer rayBasedRender
Raycast based renderer reference, raycast renderer or shear warp renderer.

isTriPlanarVolView

boolean isTriPlanarVolView
Mode is tri-planar volume view or not.

boxPanel

JPanelDisplay boxPanel
Dialog to turn bounding box of surface renderer on and off, and to change the color of the frame.

boxSlices

ViewJComponentBoxSlice[] boxSlices
The frame around the AXIAL, CORONAL, SAGITTAL slices:

boxSliceVertices

javax.vecmath.Vector3f[][] boxSliceVertices
The transformed boxSlices frames used to sample the volume data along diagonal slices:

bufferFactor

int bufferFactor
Buffer factor, 1 usually, 4 for color images.

clipPanel

JPanelClip clipPanel
Dialog to turn the clipping palne box on and off.

triSliceImages

ViewJComponentTriSliceImage[] triSliceImages
ImageRenderers for the AXIAL, CORONAL, SAGITTAL slices:

triSliceGeometry

javax.media.j3d.Shape3D[] triSliceGeometry

componentVolImage

ViewJComponentSurfaceVolume componentVolImage
Volume image object.

cubicBehaviorBG

javax.media.j3d.BranchGroup cubicBehaviorBG
The cubic roational behavior branch group.

cubicBG

javax.media.j3d.BranchGroup cubicBG
Cubic branch group.

cubicRotate

com.sun.j3d.utils.behaviors.mouse.MouseRotate cubicRotate
Cubic mouse rotation behavior.

cubicTG

javax.media.j3d.TransformGroup cubicTG
Cubic transform group.

currentTransform

javax.media.j3d.Transform3D currentTransform
Current transform matrix.

currentTransformType

int currentTransformType
Current transform changes type.

first6ClipPlane

boolean first6ClipPlane
flag indicate the first time 6 clipping plane branch switch.

firstClipArbi

boolean firstClipArbi
flag indicate the first time arbitrary clipping plane branch switch.

geodesicPanel

JPanelGeodesic geodesicPanel
Geodesic panel.

imageA

ModelImage imageA
Current image A.

imageB

ModelImage imageB
Current image B.

imageVolBufferA

float[] imageVolBufferA
Buffer that holds image A volume data.

imageVolBufferB

float[] imageVolBufferB
Buffer that holds image B volume data.

isEntryPoint

boolean isEntryPoint
Flag indicates that probe rotate around the entry point or not.

m_bRenderModeLighting

boolean m_bRenderModeLighting
Flag set when texture volume is being rendered using lights.

m_dOriginalScreenScale

double m_dOriginalScreenScale
Zoomfactor, zooming in screen scale space, and is relative to original position, this stores that original position:.

m_kObjBoxSliceProbe_TG

javax.media.j3d.TransformGroup[] m_kObjBoxSliceProbe_TG
TransformGroup[] used to rotate the AXIAL, CORONAL, SAGITTAL slice BOXES:

m_kObjPlaneProbe_TG

javax.media.j3d.TransformGroup[] m_kObjPlaneProbe_TG
TransformGroup[] used to rotate the AXIAL, CORONAL, SAGITTAL slice PLANES:

m_kProbeTransform

javax.media.j3d.Transform3D m_kProbeTransform
The Transform3D used to position the planes based on the Probe position and angle. The planes are rotates about the intersection between the probe and the plane, which may or may not be in the center of the plane. This transform allows non-origin rotations by conactenating the translation to the origin, rotation, and translation matricies into one transform, which is used to set the Transforms for the TransformGroups above and also to sample the ModelImage data on the diagonal slice:

m_kSoftwareLightSet

SoftwareLightSet m_kSoftwareLightSet
Used to compute software lighting of composite texture volume.

m_kSoftwareMaterial

SoftwareMaterial m_kSoftwareMaterial
DOCUMENT ME!

mousePanel

JPanelMouse mousePanel
Dialog for recording and playing back mouse events.

mouseRotateBehavior

MouseRotateExt mouseRotateBehavior
Mouse Rotate behavior.

mouseTranslateBehavior

com.sun.j3d.utils.behaviors.mouse.MouseTranslate mouseTranslateBehavior
Mouse Translate behavior.

mouseZoomBehavior

com.sun.j3d.utils.behaviors.mouse.MouseZoom mouseZoomBehavior
Mouse Zoom behavior.

myEyePoint

javax.vecmath.Point3d myEyePoint
Initial center viewing point of the image.

objBoxSlices_BG

javax.media.j3d.BranchGroup[] objBoxSlices_BG
BranchGroup[] containing the slice BOXES:

objTransSlices_TG

javax.media.j3d.TransformGroup[] objTransSlices_TG
Group dictating how the XY plane is translated.

objPlane_BG

javax.media.j3d.BranchGroup[] objPlane_BG
BranchGroup[] containing the image planes.

parallelRotation

boolean parallelRotation
Parallel rotation flag.

parallelScaleT3D

javax.media.j3d.Transform3D parallelScaleT3D
Transformation matrix.

parent

ViewJFrameBase parent
Controls for the image. ViewJFrameVolumeView

probePanel

JPanelProbe probePanel
Dialog for loading and displaying probes.

resols

float[] resols
Resolutions of image A.

rotationCount

int rotationCount
fix one bug from threading.

sculptorPanel

JPanelSculptor sculptorPanel
Sculptor panel.

segmentationImage

ModelImage segmentationImage
Image with areas marked with values indicating that they are special tissue types (vessels, etc).

slicePanel

JPanelSlices slicePanel
Dialog to turn the slices control box on and off.

surfacePanel

JPanelSurface surfacePanel
Dialog for loading and displaying surfaces.

surfaceTexturePanel

JPanelSurfaceTexture surfaceTexturePanel
Panel for displaying the SurfaceTexture interface:

switchGroup

javax.media.j3d.Switch switchGroup
Tri planar view and the 3D texture volume view switch group.

rotationAlpha

javax.media.j3d.Alpha rotationAlpha

sliceTransparency

javax.media.j3d.TransparencyAttributes[] sliceTransparency
ViewJComponentTriSliceImages -> Texture2D transparency values:

texture

VolumeTexture texture
Reference to 3D texture node for the volume.

sliceTextures

javax.media.j3d.Texture2D[] sliceTextures
ViewJComponentTriSliceImages -> Texture2D to display the image slices:

sliceImageComponent2D

javax.media.j3d.ImageComponent2D[] sliceImageComponent2D
Each Texture2D adds a ImageComponent2D:

m_kRFACoordMaps

javax.vecmath.Vector4f[][] m_kRFACoordMaps
Texture mapping for the RFA probe rotation:

transformCubic

javax.media.j3d.Transform3D transformCubic
Cubic tansform3D.

transformNode3d

javax.media.j3d.Transform3D transformNode3d
Setup the initial position of the image, added to ScenerootTG transform group.

view

javax.media.j3d.View view
View object in rendering a three dimensional scene from one viewpoint.

volBG

javax.media.j3d.BranchGroup volBG
Volume branch group.

volOpacityPanel

JPanelVolOpacityBase volOpacityPanel
Volume opacity control dialog.

volRenderBG

javax.media.j3d.BranchGroup volRenderBG
Volume render branch group.

volRenderNode

NodeVolumeTextureRender volRenderNode
Add here.

volRenderOG

javax.media.j3d.OrderedGroup volRenderOG
Volume render order group, specify the rendering order.

volumeDisplayMode3D

boolean volumeDisplayMode3D
If true display 3D volume as a 3D texture map or 2D array of texture maps. If false display 3 orthogonal image planes.

xBox

float xBox
Numbers dicatating the sizes of the planes based on the extents and resolutions of the image.

yBox

float yBox
Numbers dicatating the sizes of the planes based on the extents and resolutions of the image.

zBox

float zBox
Numbers dicatating the sizes of the planes based on the extents and resolutions of the image.

maxBox

float maxBox
Numbers dicatating the sizes of the planes based on the extents and resolutions of the image.

xDim

int xDim
Dimensions of image A.

yDim

int yDim
Dimensions of image A.

zDim

int zDim
Dimensions of image A.

tDim

int tDim
Dimensions of image A.

Class gov.nih.mipav.view.renderer.J3D.surfaceview.SurfaceView extends SurfaceRender implements Serializable

serialVersionUID: 608959413602233595L

Serialized Fields

boxPanel

JPanelDisplay boxPanel
Dialog to turn bounding box of surface renderer on and off, and to change the color of the frame.

boxSlices

ViewJComponentBoxSlice[] boxSlices
The frame around the AXIAL, CORONAL, SAGITTAL slices:

boxSliceVertices

javax.vecmath.Vector3f[][] boxSliceVertices
The transformed boxSlices frames used to sample the volume data along diagonal slices:

bufferFactor

int bufferFactor
Buffer factor, 1 usually, 4 for color images.

clipPanel

JPanelClip clipPanel
Dialog to turn the clipping palne box on and off.

cubicBehaviorBG

javax.media.j3d.BranchGroup cubicBehaviorBG
The cubic roational behavior branch group.

cubicBG

javax.media.j3d.BranchGroup cubicBG
Cubic branch group.

cubicRotate

com.sun.j3d.utils.behaviors.mouse.MouseRotate cubicRotate
Cubic mouse rotation behavior.

cubicTG

javax.media.j3d.TransformGroup cubicTG
Cubic transform group.

currentTransform

javax.media.j3d.Transform3D currentTransform
Current transform matrix.

currentTransformType

int currentTransformType
Current transform changes type.

first6ClipPlane

boolean first6ClipPlane
flag indicate the first time 6 clipping plane branch switch.

firstClipArbi

boolean firstClipArbi
flag indicate the first time arbitrary clipping plane branch switch.

geodesicPanel

JPanelGeodesic geodesicPanel
Geodesic panel.

imageA

ModelImage imageA
Current image A.

imageB

ModelImage imageB
Current image B.

isEntryPoint

boolean isEntryPoint
Flag indicates that probe rotate around the entry point or not.

m_bRenderModeLighting

boolean m_bRenderModeLighting
Flag set when texture volume is being rendered using lights.

m_dOriginalScreenScale

double m_dOriginalScreenScale
Zoomfactor, zooming in screen scale space, and is relative to original position, this stores that original position:.

m_kObjBoxSliceProbe_TG

javax.media.j3d.TransformGroup[] m_kObjBoxSliceProbe_TG
TransformGroup[] used to rotate the AXIAL, CORONAL, SAGITTAL slice BOXES:

m_kObjPlaneProbe_TG

javax.media.j3d.TransformGroup[] m_kObjPlaneProbe_TG
TransformGroup[] used to rotate the AXIAL, CORONAL, SAGITTAL slice PLANES:

m_kProbeTransform

javax.media.j3d.Transform3D m_kProbeTransform
The Transform3D used to position the planes based on the Probe position and angle. The planes are rotates about the intersection between the probe and the plane, which may or may not be in the center of the plane. This transform allows non-origin rotations by conactenating the translation to the origin, rotation, and translation matricies into one transform, which is used to set the Transforms for the TransformGroups above and also to sample the ModelImage data on the diagonal slice:

m_kSoftwareLightSet

SoftwareLightSet m_kSoftwareLightSet
Used to compute software lighting of composite texture volume.

m_kSoftwareMaterial

SoftwareMaterial m_kSoftwareMaterial
DOCUMENT ME!

mousePanel

JPanelMouse mousePanel
Dialog for recording and playing back mouse events.

mouseRotateBehavior

MouseRotateExt mouseRotateBehavior
Mouse Rotate behavior.

mouseTranslateBehavior

com.sun.j3d.utils.behaviors.mouse.MouseTranslate mouseTranslateBehavior
Mouse Translate behavior.

mouseZoomBehavior

com.sun.j3d.utils.behaviors.mouse.MouseZoom mouseZoomBehavior
Mouse Zoom behavior.

myEyePoint

javax.vecmath.Point3d myEyePoint
Initial center viewing point of the image.

objTransSlices_TG

javax.media.j3d.TransformGroup[] objTransSlices_TG
Group dictating how the XY plane is translated.

objPlane_BG

javax.media.j3d.BranchGroup[] objPlane_BG
BranchGroup[] containing the image planes.

parallelRotation

boolean parallelRotation
Parallel rotation flag.

parallelScaleT3D

javax.media.j3d.Transform3D parallelScaleT3D
Transformation matrix.

parent

ViewJFrameBase parent
Controls for the image. ViewJFrameVolumeView

probePanel

JPanelProbe probePanel
Dialog for loading and displaying probes.

resols

float[] resols
Resolutions of image A.

rotationCount

int rotationCount
fix one bug from threading.

segmentationImage

ModelImage segmentationImage
Image with areas marked with values indicating that they are special tissue types (vessels, etc).

slicePanel

JPanelSlices slicePanel
Dialog to turn the slices control box on and off.

surfacePanel

JPanelSurface surfacePanel
Dialog for loading and displaying surfaces.

surfaceTexturePanel

JPanelSurfaceTexture surfaceTexturePanel
Panel for displaying the SurfaceTexture interface:

switchGroup

javax.media.j3d.Switch switchGroup
Tri planar view and the 3D texture volume view switch group.

m_kRFACoordMaps

javax.vecmath.Vector4f[][] m_kRFACoordMaps
Texture mapping for the RFA probe rotation:

transformCubic

javax.media.j3d.Transform3D transformCubic
Cubic tansform3D.

transformNode3d

javax.media.j3d.Transform3D transformNode3d
Setup the initial position of the image, added to ScenerootTG transform group.

view

javax.media.j3d.View view
View object in rendering a three dimensional scene from one viewpoint.

volBG

javax.media.j3d.BranchGroup volBG
Volume branch group.

volRenderBG

javax.media.j3d.BranchGroup volRenderBG
Volume render branch group.

volRenderOG

javax.media.j3d.OrderedGroup volRenderOG
Volume render order group, specify the rendering order.

volumeDisplayMode3D

boolean volumeDisplayMode3D
If true display 3D volume as a 3D texture map or 2D array of texture maps. If false display 3 orthogonal image planes.

xBox

float xBox
Numbers dicatating the sizes of the planes based on the extents and resolutions of the image.

yBox

float yBox
Numbers dicatating the sizes of the planes based on the extents and resolutions of the image.

zBox

float zBox
Numbers dicatating the sizes of the planes based on the extents and resolutions of the image.

maxBox

float maxBox
Numbers dicatating the sizes of the planes based on the extents and resolutions of the image.

xDim

int xDim
Dimensions of image A.

yDim

int yDim
Dimensions of image A.

zDim

int zDim
Dimensions of image A.

tDim

int tDim
Dimensions of image A.

Package gov.nih.mipav.view.renderer.J3D.surfaceview.brainflattenerview

Class gov.nih.mipav.view.renderer.J3D.surfaceview.brainflattenerview.JPanelBrainSurfaceFlattener extends JPanelRendererJ3D implements Serializable

serialVersionUID: -2749305357977770854L

Serialized Fields

m_bFileLoaded

boolean m_bFileLoaded
DOCUMENT ME!

m_bFirstSurface

boolean m_bFirstSurface
DOCUMENT ME!

m_iGridY

int m_iGridY
DOCUMENT ME!

m_kButtonLoadImage

JButton m_kButtonLoadImage
DOCUMENT ME!

m_kButtonLoadSurface

JButton m_kButtonLoadSurface
DOCUMENT ME!

m_kCenter

javax.vecmath.Point3f m_kCenter
DOCUMENT ME!

m_kDisablePick

JRadioButton m_kDisablePick
DOCUMENT ME!

m_kDisplayButtonGroup

ButtonGroup m_kDisplayButtonGroup
DOCUMENT ME!

m_kDisplayPlane

JRadioButton m_kDisplayPlane
DOCUMENT ME!

m_kDisplaySphere

JRadioButton m_kDisplaySphere
DOCUMENT ME!

m_kFile

File m_kFile
DOCUMENT ME!

m_kImage

ModelImage m_kImage
DOCUMENT ME!

m_kImageDir

String m_kImageDir
DOCUMENT ME!

m_kImageFile

String m_kImageFile
DOCUMENT ME!

m_kLabelFileName

JLabel m_kLabelFileName
DOCUMENT ME!

m_kLabelFileNameImage

JLabel m_kLabelFileNameImage
DOCUMENT ME!

m_kLatLonLines

JCheckBox m_kLatLonLines
DOCUMENT ME!

m_kLUTa

ModelLUT m_kLUTa
DOCUMENT ME!

m_kLUTImageA

ModelImage m_kLUTImageA
DOCUMENT ME!

m_kNumLatText

JTextField m_kNumLatText
DOCUMENT ME!

m_kNumLonText

JTextField m_kNumLonText
DOCUMENT ME!

m_kPanelBrainsurfaceFlattenerLUT

JPanelHistoLUT m_kPanelBrainsurfaceFlattenerLUT
DOCUMENT ME!

m_kParentFrame

ViewJFrameVolumeView m_kParentFrame
DOCUMENT ME!

m_kPickButtonGroup

ButtonGroup m_kPickButtonGroup
DOCUMENT ME!

m_kPickCorrespondence

JRadioButton m_kPickCorrespondence
DOCUMENT ME!

m_kPickPuncture

JRadioButton m_kPickPuncture
DOCUMENT ME!

m_kSurfaceDir

String m_kSurfaceDir
DOCUMENT ME!

m_kTriangleMesh

ModelTriangleMesh m_kTriangleMesh
DOCUMENT ME!

m_kView

MjCorticalAnalysis m_kView
DOCUMENT ME!

Class gov.nih.mipav.view.renderer.J3D.surfaceview.brainflattenerview.MjCorticalAnalysis extends RenderViewBase implements Serializable

serialVersionUID: -6130870790192175575L

Serialized Fields

m_aiTriIndex

int[] m_aiTriIndex
DOCUMENT ME!

m_akPickColors

javax.vecmath.Color3f[] m_akPickColors
Colors for the picked points:.

m_akTriColors

javax.vecmath.Color4f[] m_akTriColors
DOCUMENT ME!

m_bCurvatureColors

boolean m_bCurvatureColors
Flag set to indicate whether curvature colors are rendered on the mesh surface. If not, then average convexity colors are rendered.

m_bInflationInitialized

boolean m_bInflationInitialized
Flag set once inflation processing has been initialized.

m_bMousePressed

boolean m_bMousePressed
Mouse events. Setting mousePressed and mouseReleased explicitly when the mouse events are received has deals with getting multiply mouse event notifications for the same mouse press.

m_bMouseReleased

boolean m_bMouseReleased
DOCUMENT ME!

m_bPickCorrespondenceEnabled

boolean m_bPickCorrespondenceEnabled
Turned on when picking with the mouse is enabled:.

m_bPickPunctureEnabled

boolean m_bPickPunctureEnabled
DOCUMENT ME!

m_iNumPicked

int m_iNumPicked
number of picked points displayed.

m_iRunningNumPicked

int m_iRunningNumPicked
DOCUMENT ME!

m_kCortical

MjCorticalMesh m_kCortical
Cortical mesh to be used in rendering scene.

m_kGeometryArrayPlane

javax.media.j3d.GeometryArray m_kGeometryArrayPlane
DOCUMENT ME!

m_kGeometryArraySphere

javax.media.j3d.GeometryArray m_kGeometryArraySphere
DOCUMENT ME!

m_kLUTConvexity

ModelLUT m_kLUTConvexity
DOCUMENT ME!

m_kLUTCurvature

ModelLUT m_kLUTCurvature
local reference to ModelLUT.

m_kMeshBranchRoot

javax.media.j3d.BranchGroup m_kMeshBranchRoot
BranchGroups for the Meshlines, for deleting and recreating the meshlines when the user changes the number of latitude and longitude lines:.

m_kMeshLinesBranchRoot

javax.media.j3d.BranchGroup m_kMeshLinesBranchRoot
DOCUMENT ME!

m_kMouseEvent

MouseEvent m_kMouseEvent
DOCUMENT ME!

m_kPanel

JPanelBrainSurfaceFlattener m_kPanel
DOCUMENT ME!

m_kPickCanvas

com.sun.j3d.utils.picking.PickCanvas m_kPickCanvas
DOCUMENT ME!

m_kShapeMesh

javax.media.j3d.Shape3D m_kShapeMesh
DOCUMENT ME!

m_kShapePlane

javax.media.j3d.Shape3D m_kShapePlane
DOCUMENT ME!

m_kShapeSphere

javax.media.j3d.Shape3D m_kShapeSphere
DOCUMENT ME!

m_kSwitchDisplay

javax.media.j3d.Switch m_kSwitchDisplay
Switch between displaying the Sphere and the Plane:.

m_kSwitchLinesMesh

javax.media.j3d.Switch m_kSwitchLinesMesh
This node contains the latitude/longitude renderings for the mesh which can be enabled/disabled.

m_kSwitchLinesPlane

javax.media.j3d.Switch m_kSwitchLinesPlane
This node contains the latitude/longitude renderings for the plane which can be enabled/disabled.

m_kSwitchLinesPlaneBranch

javax.media.j3d.BranchGroup m_kSwitchLinesPlaneBranch
DOCUMENT ME!

m_kSwitchLinesSphere

javax.media.j3d.Switch m_kSwitchLinesSphere
This node contains the latitude/longitude renderings for the sphere which can be enabled/disabled.

m_kSwitchLinesSphereBranch

javax.media.j3d.BranchGroup m_kSwitchLinesSphereBranch
DOCUMENT ME!

m_kTransformGroupActive

javax.media.j3d.TransformGroup m_kTransformGroupActive
Currently selected transform that gets modified by the handler for the keyboard behavior.

m_kTransformGroupMesh

javax.media.j3d.TransformGroup m_kTransformGroupMesh
DOCUMENT ME!

m_kTransformGroupPlane

javax.media.j3d.TransformGroup m_kTransformGroupPlane
DOCUMENT ME!

m_kTransformGroupPoseMesh

javax.media.j3d.TransformGroup m_kTransformGroupPoseMesh
This node contains all of the cortical mesh related nodes in the scene which can be manipulated as a group.

m_kTransformGroupPosePlane

javax.media.j3d.TransformGroup m_kTransformGroupPosePlane
This node contains all of the plane related nodes in the scene which can be manipulated as a group.

m_kTransformGroupPoseSphere

javax.media.j3d.TransformGroup m_kTransformGroupPoseSphere
This node contains all of the sphere related nodes in the scene which can be manipulated as a group.

m_kTransformGroupSphere

javax.media.j3d.TransformGroup m_kTransformGroupSphere
DOCUMENT ME!

m_kTriangleMesh

ModelTriangleMesh m_kTriangleMesh
Geometry for the rendering of the cortical mesh is maintained here so that the scene can be updated when the mesh is inflated.

MAX_POINTS

int MAX_POINTS
DOCUMENT ME!

MESH

int MESH
DOCUMENT ME!

PLANE

int PLANE
DOCUMENT ME!

SPHERE

int SPHERE
DOCUMENT ME!

Class gov.nih.mipav.view.renderer.J3D.surfaceview.brainflattenerview.MjVector2f extends javax.vecmath.Vector2f implements Serializable

serialVersionUID: -1076716465909115350L

Class gov.nih.mipav.view.renderer.J3D.surfaceview.brainflattenerview.MjVector3f extends javax.vecmath.Vector3f implements Serializable

serialVersionUID: -3573463090318350522L

Package gov.nih.mipav.view.renderer.J3D.surfaceview.flythruview

Class gov.nih.mipav.view.renderer.J3D.surfaceview.flythruview.FlythruRender extends SurfaceRender implements Serializable

serialVersionUID: -3255657270255875848L

Serialized Fields

buffer

short[] buffer
DOCUMENT ME!

capScreenWidth

int capScreenWidth
DOCUMENT ME!

capScreenHeight

int capScreenHeight
DOCUMENT ME!

directory

String directory
DOCUMENT ME!

extents

int[] extents
DOCUMENT ME!

fileType

String fileType
DOCUMENT ME!

imageToMovie

JpegImagesToMovie imageToMovie
DOCUMENT ME!

movieMake

MovieMaker movieMake
DOCUMENT ME!

pixels

int[] pixels
DOCUMENT ME!

rendererProgressBar

JProgressBar rendererProgressBar
A local reference to the volume renderer frame's progress bar.

robot

Robot robot
DOCUMENT ME!

imageCounter

int imageCounter
DOCUMENT ME!

kCanvas

VolumeCanvas3D kCanvas
DOCUMENT ME!

kImage

ModelImage kImage
DOCUMENT ME!

m_aiBranchIndexUnvisitedMax

int[] m_aiBranchIndexUnvisitedMax
DOCUMENT ME!

m_aiBranchIndexUnvisitedMin

int[] m_aiBranchIndexUnvisitedMin
This is the range of path samples for each branch that are unvisited.

m_aiMeshConnectivity

int[] m_aiMeshConnectivity
DOCUMENT ME!

m_iLastSelectedBranchIndex

int m_iLastSelectedBranchIndex
Keep track of the last branch that was selected (at a branch point).

m_kAnnotateList

FlyPathAnnotateList m_kAnnotateList
This is for the collection of annotation points.

m_kAnnotatePointGroup

javax.media.j3d.Group m_kAnnotatePointGroup
DOCUMENT ME!

m_kBranchConnectShape

javax.media.j3d.Shape3D m_kBranchConnectShape
DOCUMENT ME!

m_kBranchPathShape

javax.media.j3d.Shape3D m_kBranchPathShape
This is the Java3D geometry for the path.

m_kControlFrame

JPanelVirtualEndoscopySetup m_kControlFrame
This is the control frame which may need to be updated as the view changes.

m_kFlyPathBehavior

FlyPathBehavior m_kFlyPathBehavior
Keep track of the FlyPathBehavior because it knows about the view from the path.

m_kFlyPathGraphCurve

FlyPathGraphCurve m_kFlyPathGraphCurve
DOCUMENT ME!

m_kFlyPathGraphSamples

FlyPathGraphSamples m_kFlyPathGraphSamples
This is the path extracted from the skeletonization.

m_kGeodesicGroup

javax.media.j3d.Group m_kGeodesicGroup
DOCUMENT ME!

m_kMeanCurvaturesLUT

ModelLUT m_kMeanCurvaturesLUT
DOCUMENT ME!

m_kMeshCurvatures

ModelTriangleMeshCurvatures m_kMeshCurvatures
DOCUMENT ME!

m_kMouseRotateBehavior

com.sun.j3d.utils.behaviors.mouse.MouseRotate m_kMouseRotateBehavior
DOCUMENT ME!

m_kNormalColorPathUnvisited

javax.vecmath.Color3f m_kNormalColorPathUnvisited
DOCUMENT ME!

m_kNormalColorPathVisited

javax.vecmath.Color3f m_kNormalColorPathVisited
These are the colors to use when rendering the normal/selected branch that is unvisited/visited.

m_kOptions

FlythruRender.SetupOptions m_kOptions
These are the setup options passed to the constructor which we need to keep track of in case we need to use them outside the constructor.

m_kPickCanvas

com.sun.j3d.utils.picking.PickCanvas m_kPickCanvas
Used for picking.

m_kPointLight

javax.media.j3d.PointLight m_kPointLight
DOCUMENT ME!

m_kSceneRoot

javax.media.j3d.BranchGroup m_kSceneRoot
These are part of the scene and view.

m_kSelectColorPathUnvisited

javax.vecmath.Color3f m_kSelectColorPathUnvisited
DOCUMENT ME!

m_kSelectColorPathVisited

javax.vecmath.Color3f m_kSelectColorPathVisited
DOCUMENT ME!

m_kSkeleton

Skeleton3D m_kSkeleton
This it skeletonization of the binary volume.

m_kSurface

ModelTriangleMesh m_kSurface
This is the surface geometry and its properties.

m_kSurfaceCurveSegments

ModelTriangleMeshCurveSegments m_kSurfaceCurveSegments
DOCUMENT ME!

m_kSurfaceGeometry

javax.media.j3d.IndexedGeometryArray m_kSurfaceGeometry
DOCUMENT ME!

m_kSurfaceGeometryInfo

com.sun.j3d.utils.geometry.GeometryInfo m_kSurfaceGeometryInfo
This is the Java3D geometry for the surface.

m_kSurfaceMesh

ModelTriangleMesh m_kSurfaceMesh
DOCUMENT ME!

m_kSurfaceShape

javax.media.j3d.Shape3D m_kSurfaceShape
DOCUMENT ME!

m_kUniverse

com.sun.j3d.utils.universe.SimpleUniverse m_kUniverse
The simple universe contains a single canvas, a viewing platform, and a scene graph. The scene graph will contain all objects involved in the rendering.

m_kVolumeLayout

ModelImage3DLayout m_kVolumeLayout
Describes the organization of the volume data in a linear array.

parentFrame

ViewJFrameVolumeView parentFrame
DOCUMENT ME!

saveCounter

int saveCounter
DOCUMENT ME!

Class gov.nih.mipav.view.renderer.J3D.surfaceview.flythruview.JPanelVirtualEndoscopySetup extends JPanelRendererJ3D implements Serializable

serialVersionUID: 5676430934584329807L

Serialized Fields

contentBox

Box contentBox
Box layout for control panel.

continueUpdate

boolean continueUpdate
Flag indicates to continue update the surface render and plane render or not.

endoscopyImage

ModelImage endoscopyImage
Loaded endoscopy image file.

fileName

String fileName
File name and directory.

directory

String directory
File name and directory.

flythruButtonLoadImage

JButton flythruButtonLoadImage
DOCUMENT ME!

flythruLabelFileName

JLabel flythruLabelFileName
DOCUMENT ME!

kDialogSmooth

JDialogSmoothMesh kDialogSmooth
Surface smooth control panel reference.

kFile

File kFile
File to open the mask suface.

kPanelButton

JPanel kPanelButton
Button panel.

m_bShowMeanCurvatures

boolean m_bShowMeanCurvatures
Flag indicates to show pseudo color or not.

m_kButtonLoadSurface

JButton m_kButtonLoadSurface
DOCUMENT ME!

m_kCheckBoxShowCurvatures

JCheckBox m_kCheckBoxShowCurvatures
DOCUMENT ME!

m_kComboSegmentSurfaceBranchSamplesReductionFactor

JComboBox m_kComboSegmentSurfaceBranchSamplesReductionFactor
Surface sample reduction factor.

m_kContinueUpdate

JCheckBox m_kContinueUpdate
DOCUMENT ME!

m_kDecimalFormat

DecimalFormat m_kDecimalFormat
Used to create text representations of numbers.

m_kLabelBranch

JLabel m_kLabelBranch
DOCUMENT ME!

m_kLabelDirection

JLabel m_kLabelDirection
DOCUMENT ME!

m_kLabelDistance

JLabel m_kLabelDistance
DOCUMENT ME!

m_kLabelFileName

JLabel m_kLabelFileName
Automatically inserted by JBuilder Designer.

m_kLabelOrientation

JLabel m_kLabelOrientation
DOCUMENT ME!

m_kLabelPosition

JLabel m_kLabelPosition
DOCUMENT ME!

m_kLabelStepGaze

JLabel m_kLabelStepGaze
DOCUMENT ME!

m_kMeanCurvaturesLUT

ModelLUT m_kMeanCurvaturesLUT
kMean curvature LUT. Pseudo color look up table.

m_kOptions

FlythruRender.SetupOptions m_kOptions
Image option panel.

m_kTextBranch

JTextField m_kTextBranch
DOCUMENT ME!

m_kTextDirection

JTextField m_kTextDirection
DOCUMENT ME!

m_kTextDistance

JTextField m_kTextDistance
DOCUMENT ME!

m_kTextMaxNumBranches

JTextField m_kTextMaxNumBranches
maximum number of branches created for the endoscopy view.

m_kTextMinBranchLength

JTextField m_kTextMinBranchLength
minimum branch length.

m_kTextOrientation

JTextField m_kTextOrientation
DOCUMENT ME!

m_kTextPercentBSplineNumControlPoints

JTextField m_kTextPercentBSplineNumControlPoints
BSpline control points fraction of branch samples.

m_kTextPosition

JTextField m_kTextPosition
DOCUMENT ME!

m_kTextStepGaze

JTextField m_kTextStepGaze
DOCUMENT ME!

m_kTriangleMesh

ModelTriangleMesh m_kTriangleMesh
Keep a copy of the loaded triangle mesh and any other properties associated with the surface.

m_kView

FlythruRender m_kView
Applet that is associated with the controls in this frame.

parentFrame

ViewJFrameVolumeView parentFrame
Keep a reference to the ViewJFrameVolumeView.

scroller

JScrollPane scroller
Scroll pane.

scrollPanel

gov.nih.mipav.view.renderer.J3D.surfaceview.flythruview.JPanelVirtualEndoscopySetup.DrawingPanel scrollPanel
Scroll panel that holding all the control components.

surfaceDir

String surfaceDir
Loaded mask surface image directory.

updateButton

JButton updateButton
continue update button.

Class gov.nih.mipav.view.renderer.J3D.surfaceview.flythruview.ViewJSimpleProgressBar extends ViewJProgressBar implements Serializable

serialVersionUID: -8035459499734828360L

Serialized Fields

m_fRangeMax

float m_fRangeMax
DOCUMENT ME!

m_fRangeMin

float m_fRangeMin
Remember the range of input values for the progress bar. It is not required that the minimum be less than the maximum.

m_iLastValue

int m_iLastValue
Remember the value passed to the setValue method of the JProgressBar. When valid, should be in range [0,RESOLUTION).

Package gov.nih.mipav.view.renderer.J3D.surfaceview.plotterview

Class gov.nih.mipav.view.renderer.J3D.surfaceview.plotterview.JPanelMousePlotter extends JPanelRendererJ3D implements Serializable

serialVersionUID: -8105261993244718879L

Serialized Fields

changedMode

boolean changedMode
flag to indicate current mode being changed.

contButton

JToggleButton contButton
Continue play button.

current

int current
index to the item list.

currentEventVector

MouseEventVectorPlotter currentEventVector
Current event vector used by the save AVI.

currentObject

Object currentObject
current SceneState object being recorded by SaveAVI.

currentTransform

javax.media.j3d.Transform3D currentTransform
Current transform3D object used in Save AVI.

events

Vector<E> events
Vector that holds mouse or change events.

eventVector

MouseEventVectorPlotter eventVector
Global mouse event vector.

first

boolean first
Flag to indicate first event.

goButton

JButton goButton
Go to button.

isPlaying

boolean isPlaying
Flag to indicating play mouse is running or not.

listModel

DefaultListModel listModel
List to record info for each mouse, change events.

mode

int mode
Current mode, init to stop.

mouseCount

int mouseCount
Mouse event counter.

movieButton

JButton movieButton
Save AVI button .

myParentPlotter

SurfacePlotter myParentPlotter
Reference to ViewJFrameSurfacePlotter.

nameChangeVector

MouseEventVectorPlotter nameChangeVector
Used by name change dialog to change name of the selected item.

newButton

JButton newButton
This button add at head of the list.

parentScene

RenderViewBase parentScene
Parent scene.

pauseButton

JToggleButton pauseButton
Pause button.

playButton

JToggleButton playButton
Display button.

playMouse

gov.nih.mipav.view.renderer.J3D.surfaceview.plotterview.JPanelMousePlotter.PlayMouse playMouse
Reference to PlayMouse class object.

process

int process
Process id used by the save AVI.

recordButton

JToggleButton recordButton
Recorder button.

recorderToAVI

gov.nih.mipav.view.renderer.J3D.surfaceview.plotterview.JPanelMousePlotter.RecordMouse recorderToAVI
Reference to RecordMouse object class.

removeAllButton

JButton removeAllButton
Remove all items in the item list.

removeButton

JButton removeButton
Remove the selected item in the item list.

resetTransform

javax.media.j3d.Transform3D resetTransform
Current transform3D object.

sliderCount

int sliderCount
Slider moves event counter.

stepButton

JToggleButton stepButton
Next step button.

stopButton

JToggleButton stopButton
Stop button.

toolBar

JToolBar toolBar
Tool bar of the mouse recorder.

transformChange

boolean transformChange
DOCUMENT ME!

viewList

JList viewList
View list of the mouse recorder display list.

mjpegQuality

float mjpegQuality
DOCUMENT ME!

setMouseVectorFlag

boolean setMouseVectorFlag
flag to indicate the first time mouse tranform event happpened.

Class gov.nih.mipav.view.renderer.J3D.surfaceview.plotterview.JPanelSurfaceBox extends JPanelRendererJ3D implements Serializable

serialVersionUID: -1435246141584042105L

Serialized Fields

boundingCheck

JCheckBox boundingCheck
Check box for turning box on and off.

colorButton

JButton colorButton
Color button for changing color.

colorButtonBackground

JButton colorButtonBackground
Color button for changing z color.

colorChooser

ViewJColorChooser colorChooser
Color chooser dialog.

cubePanel

JPanel cubePanel
Panel for the rotation cube.

cubicCheck

JCheckBox cubicCheck
Check box for cubic control.

radioButtonGroupProjections

ButtonGroup radioButtonGroupProjections
Button group for projections.

radioButtonOrthographic

JRadioButton radioButtonOrthographic
Radio Button for Orthographic rendering.

radioButtonPerspective

JRadioButton radioButtonPerspective
Radio Button for Perspective rendering.

viewAlignedButton

JRadioButton viewAlignedButton
Radio Button for Perspective rendering.

viewButton

JRadioButton viewButton
Radio Button for Orthographic rendering.

viewTextureButtonGroup

ButtonGroup viewTextureButtonGroup
Button group for projections.

buttonPanel

JPanel buttonPanel
DOCUMENT ME!

coarseValue

float coarseValue
DOCUMENT ME!

fineValue

float fineValue
DOCUMENT ME!

fine

JTextField fine
DOCUMENT ME!

coarse

JTextField coarse
DOCUMENT ME!

fineLabel

JLabel fineLabel
DOCUMENT ME!

coarseLabel

JLabel coarseLabel
DOCUMENT ME!

flag

boolean flag
Flag indicating if box is on or off.

Class gov.nih.mipav.view.renderer.J3D.surfaceview.plotterview.MouseEventVectorPlotter extends Object implements Serializable

serialVersionUID: -6069342266407301187L

Serialization Methods

readObject

private void readObject(ObjectInputStream stream)
                 throws IOException,
                        ClassNotFoundException
Called by some native invokeMethod. Provides a way to read this class out as a object stream. First, the size of the vector is read, then each mouseEvent into the vector, then the name, then the view. The view is read in as a String because it is not serializable. The read method corresponds to the write method, below.

Throws:
IOException - If the matrix being read in by the JDialogMouseRecorder has the incorrect size.
ClassNotFoundException - DOCUMENT ME!

writeObject

private void writeObject(ObjectOutputStream stream)
                  throws IOException
Called by some native invokeMethod. Provides a way to write this class out as a object stream. First, the size of the vector is written, then each mouseEvent in the vector, then the name, then the view. The view is written out as a String because it is not serializable. The write method corresponds to the read method, above.

Throws:
IOException - DOCUMENT ME!
Serialized Fields

first

boolean first
First time accessed.

mode

int mode
Current mode.

mouseEvents

Vector<E> mouseEvents
Vector to record mouse events.

name

String name
Name of the events.

state

Object state
State being recorded.

stateVector

Vector<E> stateVector
Vector to record state changes.

view

javax.media.j3d.Transform3D view
Parent frame transform3D view.

Class gov.nih.mipav.view.renderer.J3D.surfaceview.plotterview.SceneStatePlotter extends Object implements Serializable

serialVersionUID: 5063961369724570657L

Serialized Fields

transform

javax.media.j3d.Transform3D transform
Current sceneRoot transform.

z

int z
DOCUMENT ME!

zVisible

boolean zVisible
DOCUMENT ME!

Class gov.nih.mipav.view.renderer.J3D.surfaceview.plotterview.SurfacePlotter extends RenderViewBase implements Serializable

serialVersionUID: -1650691820947415108L

Serialized Fields

boxDialog

JPanelSurfaceBox boxDialog
Dialog for recording and playing back mouse events.

componentImageXY

ViewJComponentSurface componentImageXY
Main component found in this frame.

controlPanel

JPanel controlPanel
the control panel that hold the z slider.

current

int current
Current event vector index.

extents

int[] extents
Extents of image.

imageBranch

javax.media.j3d.BranchGroup imageBranch
Branch parent of the image in the scene, needed so image can be made invisible when another surface is loaded.

isVisible

boolean isVisible
Flag indicating if the image is currently visible.

itemLine

JCheckBoxMenuItem itemLine
Check box menu item indicating if surface should be in line mode or full mode.

label1

JLabel label1
Label for slider, "1".

label100

JLabel label100
Label for slider, "100".

label50

JLabel label50
Label for slider, "50".

labelZ

JLabel labelZ
Label that says "Z (1-100)".

LUTa

ModelLUT LUTa
LUT that dictates how the vertices of the quad mesh are colored.

mainPanel

JPanel mainPanel
The main control panel.

mouseDialog

JPanelMousePlotter mouseDialog
Mouse recorder dialog associated with surface plotter.

mouseRotateBehavior

com.sun.j3d.utils.behaviors.mouse.MouseRotate mouseRotateBehavior
Mouse Rotate behavior.

mouseTranslateBehavior

com.sun.j3d.utils.behaviors.mouse.MouseTranslate mouseTranslateBehavior
Mouse Translate behavior.

mouseZoomBehavior

com.sun.j3d.utils.behaviors.mouse.MouseZoom mouseZoomBehavior
Mouse Zoom behavior.

myEyePoint

javax.vecmath.Point3d myEyePoint
Initial center viewing point of the image.

objTransXY

javax.media.j3d.TransformGroup objTransXY
Transform group guiding how image is displayed.

openingMenuBar

JMenuBar openingMenuBar
Menu bar.

panelToolbar

JPanel panelToolbar
Panel that holds the toolbars.

parallelScaleT3D

javax.media.j3d.Transform3D parallelScaleT3D
Transformation matrix.

setSliderFlag

boolean setSliderFlag
Flag to indicate the first time slider name changes.

slice

int slice
Current slice of 3D image, used to figure out XY plane to plot.

sliderEvents

MouseEventVectorPlotter sliderEvents
Slider events used by the mouse recorder.

sliderFrame

JSlider sliderFrame
Slider for frame/slice of image.

sliderZ

JSlider sliderZ
3, 1-100%, dictating where the image in the surface should be displayed.

t3d_XY_t

javax.media.j3d.Transform3D t3d_XY_t
Actual transform of the image.

textZ

JTextField textZ
Text field displaying the percentage of the slider.

texUnitStateBXY

javax.media.j3d.TextureUnitState[] texUnitStateBXY
Texture creating appearance for the "back" of the image. Needs to be array even though there will be only 1 item.

texUnitStateFXY

javax.media.j3d.TextureUnitState[] texUnitStateFXY
Texture creating appearance for the "front" of the image. Needs to be array even though there will be only 1 item.

visibleBox

JCheckBox visibleBox
Check box for whether or not the image should be visible.

xRes

float xRes
X and Y resolution.

yRes

float yRes
X and Y resolution.

zSlice

int zSlice
Z slice, which image of 1-100 are we showing.

Class gov.nih.mipav.view.renderer.J3D.surfaceview.plotterview.ViewJComponentSurface extends ViewJComponentBase implements Serializable

serialVersionUID: -870321457925828704L

Serialized Fields

cConnect

int[] cConnect
Vertex connection array.

cVertex

javax.vecmath.Point3f[] cVertex
Vertex array.

frame

RenderViewBase frame
Frame where the plotted surface is displayed.

imageA

ModelImage imageA
Structure holding image.

imageBufferA

float[] imageBufferA
Buffer which holds the pixel data.

imageExtents

int[] imageExtents
Extents of the image.

lineMode

boolean lineMode
Flag indicating if the surface is currently in line mode (true) or fill mode (false).

LUTa

ModelLUT LUTa
Lookup table for image.

lutBufferRemapped

int[] lutBufferRemapped
Used to remap the LUT appropriately.

maxBox

float maxBox
MaxBox value from the parent frame.

pixBuffer

int[] pixBuffer
Buffer used to store ARGB images of the image presently being displayed.

plottedRoot

javax.media.j3d.BranchGroup plottedRoot
Branch group that is the parent of the plotted surface.

qMesh

ModelQuadMesh qMesh
Quad mesh. This is the core of the component.

sampleSize

int sampleSize
Sample size. This determines how many triangles are used in the quad mesh.

xBox

float xBox
xBox, yBox and zBox values from the parent frame.

yBox

float yBox
xBox, yBox and zBox values from the parent frame.

zBox

float zBox
xBox, yBox and zBox values from the parent frame.

Class gov.nih.mipav.view.renderer.J3D.surfaceview.plotterview.ViewJFramePlotterView extends ViewJFrameBase implements Serializable

serialVersionUID: 8972056170229565046L

Serialized Fields

config

GraphicsConfiguration config
Configuration param, which will pass down to each render's constructor.

serif12

Font serif12
Fonts, same as MipavUtil.font12 and MipavUtil.font12B.

serif12B

Font serif12B
Fonts, same as MipavUtil.font12 and MipavUtil.font12B.

cameraPanel

JPanel cameraPanel
DOCUMENT ME!

imagePanel

JPanel imagePanel
The image panel to hold one Canvas3D.

itemLine

JCheckBoxMenuItem itemLine
Image line mode check box.

mousePanel

JPanel mousePanel
DOCUMENT ME!

openingMenuBar

JMenuBar openingMenuBar
Menu bar.

panelToolbar

JPanel panelToolbar
Toolbar panel.

plotterRender

SurfacePlotter plotterRender
Surface plotter view.

raisedbevel

Border raisedbevel
Panel Border view.

loweredbevel

Border loweredbevel
Panel Border view.

compound

Border compound
Panel Border view.

screenWidth

int screenWidth
Screen width, screen height.

screenHeight

int screenHeight
Screen width, screen height.

sliderControlPanel

JPanel sliderControlPanel
DOCUMENT ME!

surfaceBoxPanel

JPanel surfaceBoxPanel
DOCUMENT ME!

surTabVector

Vector<E> surTabVector
DOCUMENT ME!

tabbedPane

JTabbedPane tabbedPane
The main tabbed pane in the volume view frame.

tabVector

Vector<E> tabVector
For each render, use the vector to store the currently active tabs.

viewPanel

JPanel viewPanel
Control panel for the surface renderer.

Package gov.nih.mipav.view.renderer.J3D.surfaceview.rfaview

Class gov.nih.mipav.view.renderer.J3D.surfaceview.rfaview.JDialogBurnParameter extends JDialogBase implements Serializable

serialVersionUID: -1568251410627012713L

Serialized Fields

diameter

float diameter
DOCUMENT ME!

ok

boolean ok
DOCUMENT ME!

opacity

float opacity
DOCUMENT ME!

radius

float radius
DOCUMENT ME!

time

float time
DOCUMENT ME!

voltage

float voltage
DOCUMENT ME!

volume

float volume
DOCUMENT ME!

diameterField

JTextField diameterField
DOCUMENT ME!

probePanel

JPanelProbe probePanel
DOCUMENT ME!

timeField

JTextField timeField
DOCUMENT ME!

voltageField

JTextField voltageField
DOCUMENT ME!

Class gov.nih.mipav.view.renderer.J3D.surfaceview.rfaview.JPanelProbe extends JPanelRendererJ3D implements Serializable

serialVersionUID: -2467552118438070016L

Serialized Fields

bonePresetButton

JButton bonePresetButton
DOCUMENT ME!

burnBackFaceCB

JCheckBox burnBackFaceCB
burning point back face culling check box.

burnBase

BurnBase burnBase
Burn base reference.

burnClipCB

JCheckBox burnClipCB
burning point clipping check box.

burnIndex

int burnIndex
Current burning point index being hightlighted.

burningPtTransVector

javax.vecmath.Vector3f burningPtTransVector
Burning point coordinate vector in world coordinate system.

burnList

JList burnList
Burn list that hold the burning point names.

calcButton

JButton calcButton
Calculat button.

center

javax.vecmath.Point3f center
Burning point coordinate.

centerLabel

JLabel centerLabel
burning point center label.

clipping

boolean clipping
Burning surface being clipped or not.

colorButton

JButton colorButton
Burning point color button.

colorChooser

ViewJColorChooser colorChooser
Color chooser when the user changes the color of the surface.

colorLabel

JLabel colorLabel
Burning point color label.

culling

boolean culling
Burning surface being culled ( back face bulling ) or not.

cursorMode

int cursorMode
curreent cursor nevigation mode.

diffVolumeLabel

JLabel diffVolumeLabel
Volume difference label for the current treatment.

diffVolumeText

JTextField diffVolumeText
Volume difference text.

drawingPane

JPanelProbe.DrawingPane drawingPane
Associate structure of the scroll pane to resize the panel properly.

endPtTransVector

javax.vecmath.Vector3f endPtTransVector
End point coordinate vector in the world coordinate system.

entryPointLabel

JLabel entryPointLabel
entry point label.

entryPointPanel

JPanel entryPointPanel
Panel that hold the entry point roation check box.

entryPointRotationCB

JCheckBox entryPointRotationCB
entry point rotation check box.

liverPresetButton

JButton liverPresetButton
Liver segmentation preset opacity transform function control button.

loadVisualizationButton

JButton loadVisualizationButton
Load button for the opacity transform function.

m_kProbeTwistLabel

JLabel m_kProbeTwistLabel
DOCUMENT ME!

m_kProbeTwistSlider

JSlider m_kProbeTwistSlider
Rotation/Twist around the direction of the probe:.

maxBox

float maxBox
The maximum of the fram box values.

noTargetTreatment

TreatmentInformation noTargetTreatment
Treatment information to be used if the user wants to burn without any target surface.

opacity

float opacity
Burning point opacity.

opacityLabel

JLabel opacityLabel
The opacity slider label.

opacitySlider

JSlider opacitySlider
burning point surface opacity slider.

opacitySliderLabels

JLabel[] opacitySliderLabels
burning point surface opacity slider label.

paramDialog

JDialogBurnParameter paramDialog
Burning point parameter dialog to change the burning attributes, such as diameter.

parentFrame

ViewJFrameVolumeView parentFrame
Volume view frame work reference.

probe

Probe probe
Probe reference.

probeList

JList probeList
Probes list.

probeResetButton

JToggleButton probeResetButton
Reset probe nevigation mode.

probeTargetButton

JToggleButton probeTargetButton
Control the tri-planar probe nevigation mode.

radius

javax.vecmath.Point3f radius
Buring point sphere diameter.

radiusLabel

JLabel radiusLabel
burning point diameter label.

resultLabel

JLabel resultLabel
result label to show the bone, vasculature detection information message.

saveVisualizationButton

JButton saveVisualizationButton
Save button for the opacity tranform function.

scroller

JScrollPane scroller
Scroll pane that control the resizing of the panel.

semiXLabel

JLabel semiXLabel
burning point semi axis X label.

semiXText

JTextField semiXText
burning point semi axis X text field.

semiYLabel

JLabel semiYLabel
burning point semi axis Y label.

semiYText

JTextField semiYText
burning point semi axis Y text field.

semiZLabel

JLabel semiZLabel
burning point semi axis Z label.

semiZText

JTextField semiZText
burning point semi axis Z text field.

showBurning

boolean showBurning
Showing the burning process or not.

showBurnLabels

boolean showBurnLabels
Flag indicates the show burning text label or not.

showBurnLabelsCB

JCheckBox showBurnLabelsCB
Show the burning text label checkbox.

skinPresetButton

JButton skinPresetButton
Skin segmentation preset opacity transform function control button.

sliderX

JSlider sliderX
The probe X slider that control the probe push and pull movements.

snapToTarget

boolean snapToTarget
Whether to snap to center of a target surface when it is selected; defaults to true.

snapToTargetCB

JCheckBox snapToTargetCB
Checkbox indicating whether to snap to center of a target surface when it is selected.

startPtTransVector

javax.vecmath.Vector3f startPtTransVector
Start point ( invisible ) coordinate vector in world coordinate system.

tabbedPane

JTabbedPane tabbedPane
The main tabbed pane in the volume view frame.

tabPanel

JPanel tabPanel
The main tab contrl panel.

targetList

JList targetList
Surface target list (tumors).

targetVolumeText

JTextField targetVolumeText
Label containing the volume of the current target surface.

targetXText

JTextField targetXText
X label for the center coordinate of the current target surface.

targetYText

JTextField targetYText
Y label for the center coordinate of the current target surface.

targetZText

JTextField targetZText
Z label for the center coordinate of the current target surface.

tipLengthCB

JComboBox tipLengthCB
Combo box for indicating the length of the probe tip. Currently used just by CoolTip probe.

toolBar

JToolBar toolBar
Tool bar.

totalVolumeLabel

JLabel totalVolumeLabel
Burning points total volume label.

totalVolumeText

JTextField totalVolumeText
Burning point total volume text.

traverseButton

JToggleButton traverseButton
Control the tri-planar default view nevigation mode.

treatmentVector

Vector<E> treatmentVector
List of treatment sets.

volumeLabel

JLabel volumeLabel
buring point volume label.

volumeText

JTextField volumeText
burning pont volume text box.

xBox

float xBox
Parent frame box value.

yBox

float yBox
Parent frame box value.

zBox

float zBox
Parent frame box value.

xLabel

JLabel xLabel
burning point X, Y, Z coordinate label.

yLabel

JLabel yLabel
burning point X, Y, Z coordinate label.

zLabel

JLabel zLabel
burning point X, Y, Z coordinate label.

xLabelEntry

JLabel xLabelEntry
entry point X, Y, Z coordinate label.

yLabelEntry

JLabel yLabelEntry
entry point X, Y, Z coordinate label.

zLabelEntry

JLabel zLabelEntry
entry point X, Y, Z coordinate label.

xRes

float xRes
The resolutions of the (possibly respampled) image (the one shown in the renderer).

yRes

float yRes
The resolutions of the (possibly respampled) image (the one shown in the renderer).

zRes

float zRes
The resolutions of the (possibly respampled) image (the one shown in the renderer).

xSliderS

JSlider xSliderS
slider that controls the probe moves along the x direction.

xText

JTextField xText
burning point X, Y, Z coordinate text box.

yText

JTextField yText
burning point X, Y, Z coordinate text box.

zText

JTextField zText
burning point X, Y, Z coordinate text box.

xTextEntry

JTextField xTextEntry
entry point X, Y, Z coordinate text box.

yTextEntry

JTextField yTextEntry
entry point X, Y, Z coordinate text box.

zTextEntry

JTextField zTextEntry
entry point X, Y, Z coordinate text box.

ySliderS

JSlider ySliderS
slider that controls the probe moves along the y direction.

zSliderS

JSlider zSliderS
slider that controls the probe moves along the z direction.

Class gov.nih.mipav.view.renderer.J3D.surfaceview.rfaview.JPanelProbe.DrawingPane extends JPanel implements Serializable

serialVersionUID: 199157917084746068L

Package gov.nih.mipav.view.renderer.J3D.volumeview

Class gov.nih.mipav.view.renderer.J3D.volumeview.JPanelRenderOptionsRayCast extends JPanelRendererJ3D implements Serializable

serialVersionUID: -6813615755994835860L

Serialized Fields

blurBox

JCheckBox blurBox
Blur image check box.

buttonPanel

JPanel buttonPanel
Button Panel.

colorButton

JButton colorButton
Color button for changing color.

colorButtonBackground

JButton colorButtonBackground
Color button for changing z color.

colorChooser

ViewJColorChooser colorChooser
Color chooser dialog.

diffuseButton

JButton diffuseButton
Diffuse color button for vertex material.

flag

boolean flag
Flag indicating if box is on or off.

m_kRadioGroupMaxRenExtent

ButtonGroup m_kRadioGroupMaxRenExtent
DOCUMENT ME!

m_kRadioMaxRenExtent_1024

JRadioButton m_kRadioMaxRenExtent_1024
DOCUMENT ME!

m_kRadioMaxRenExtent_128

JRadioButton m_kRadioMaxRenExtent_128
DOCUMENT ME!

m_kRadioMaxRenExtent_256

JRadioButton m_kRadioMaxRenExtent_256
DOCUMENT ME!

m_kRadioMaxRenExtent_512

JRadioButton m_kRadioMaxRenExtent_512
DOCUMENT ME!

m_kRadioMaxRenExtent_64

JRadioButton m_kRadioMaxRenExtent_64
Radio Button Group for the Render Image Target size of the raycast rendered image. Target sizes options are preset to be typical texture sizes:

myParent

VolumeRendererRayCast myParent
Volume rendering parent frame.

radioButtonGroupProjections

ButtonGroup radioButtonGroupProjections
Button group for projections.

radioButtonOrthographic

JRadioButton radioButtonOrthographic
Radio Button for Orthographic rendering.

radioButtonPerspective

JRadioButton radioButtonPerspective
Radio Button for Perspective rendering.

scroller

JScrollPane scroller
Scroll pane.

scrollPanel

gov.nih.mipav.view.renderer.J3D.volumeview.JPanelRenderOptionsRayCast.DrawingPanel scrollPanel
Scroll panel that holding the all the control components.

spaceText

JTextField spaceText
Text field of the ray trace space size.

specularButton

JButton specularButton
Specular color button for vertex material.

stepText

JTextField stepText
Text field of the ray trace step size.

Class gov.nih.mipav.view.renderer.J3D.volumeview.JPanelRenderOptionsShearWarp extends JPanelRendererJ3D implements Serializable

serialVersionUID: 4059526095627109190L

Serialized Fields

buttonPanel

JPanel buttonPanel
Button Panel.

colorButton

JButton colorButton
Color button for changing color.

colorButtonBackground

JButton colorButtonBackground
Color button for changing z color.

colorChooser

ViewJColorChooser colorChooser
Color chooser dialog.

myParent

VolumeRendererShearWarp myParent
Volume rendering parent frame.

radioButtonGroupProjections

ButtonGroup radioButtonGroupProjections
Button group for projections.

radioButtonOrthographic

JRadioButton radioButtonOrthographic
Radio Button for Orthographic rendering.

radioButtonPerspective

JRadioButton radioButtonPerspective
Radio Button for Perspective rendering.

scroller

JScrollPane scroller
Scroll pane.

scrollPanel

gov.nih.mipav.view.renderer.J3D.volumeview.JPanelRenderOptionsShearWarp.DrawingPanel scrollPanel
Scroll panel that holding the all the control components.

spaceText

JTextField spaceText
Text field of the ray trace space size.

stepText

JTextField stepText
Text field of the ray trace step size.

Class gov.nih.mipav.view.renderer.J3D.volumeview.VolumeRenderer extends RenderViewBase implements Serializable

serialVersionUID: -6617098263675852750L

Serialized Fields

componentImageXY

ViewJComponentRenderImage componentImageXY
Component holding the texture of the XY plane image.

extents

int[] extents
Extents of image A, same as xDim, yDim, etc.

imageA

ModelImage imageA
Current image A.

imageB

ModelImage imageB
Current image B.

lightControl

JPanelLights lightControl
light control panel.

maxRenExtent

int maxRenExtent
max Extent of X, Y dimensions.

optionsPanel

JPanelRendererBase optionsPanel
Dialog to turn bounding box of surface renderer on and off, and to change the color of the frame.

pBar

ViewJProgressBar pBar
Actual bar which fills with color as the percentage of completion increases.

pixBufferA_XY

int[] pixBufferA_XY
Buffer that holds image A pixel data for the XY plane, used to build displayable image.

pixBufferB_XY

int[] pixBufferB_XY
Buffer that holds image B pixel data for the XY plane, used to build displayable image.

sliderT

JSlider sliderT
Sliders for the image planes.

surfaceRender

SurfaceRender surfaceRender
Surface renderer reference.

textT

JTextField textT
Text fields that display the slice number next to the sliders.

tSlice

int tSlice
Which time slice is currently displayed.

xDim

int xDim
Dimensions of image A.

yDim

int yDim
Dimensions of image A.

zDim

int zDim
Dimensions of image A.

tDim

int tDim
Dimensions of image A.

zSlice

int zSlice
Which slice is currently displayed in the XY plane.

behavior

com.sun.j3d.utils.behaviors.mouse.MouseRotate behavior
Mouse rotate behavior.

behaviorTranslate

com.sun.j3d.utils.behaviors.mouse.MouseTranslate behaviorTranslate
Mouse translate behavior.

behaviorZoom

com.sun.j3d.utils.behaviors.mouse.MouseZoom behaviorZoom
Mouse zoom behavior.

boxSliceX

ViewJComponentBoxSlice boxSliceX
The frame around the x slice.

bufferFactor

int bufferFactor
Buffer factor, 1 usually, 4 for color images.

currentTransform

javax.media.j3d.Transform3D currentTransform
Current transform matrix.

currentTransType

int currentTransType
Current transform type.

isRotate

boolean isRotate
Flag indicating mouse rotation, avoid image disappearing problem.

kDefaultAppearance

javax.media.j3d.Appearance kDefaultAppearance
Original Appearance obj of the ImageComponent2D texture.

kShape

javax.media.j3d.Shape3D kShape
Shape object of the volume renderer.

m_bMouseListen

boolean m_bMouseListen
Flag to turn mouseListener on or off.

m_kImage

BufferedImage m_kImage
Buffer image for the volume renderer.

m_kImageComponent

javax.media.j3d.ImageComponent2D m_kImageComponent
Image component 2D to hold the volume renderer properties.

m_kSoftwareLightSet

SoftwareLightSet m_kSoftwareLightSet
Set of lights to use for software-based lighting.

m_kSoftwareMaterial

SoftwareMaterial m_kSoftwareMaterial
Material properties to use for software-based lighting.

m_kTextureXY

javax.media.j3d.Texture2D m_kTextureXY
2D texture of the volume renderer.

mouseReleased

boolean mouseReleased
Flag to indicate whether the mouseReleased event triggered or not.

objBoxSliceX

javax.media.j3d.BranchGroup objBoxSliceX
Parent of the x slice.

objTransSliceX

javax.media.j3d.TransformGroup objTransSliceX
Member variables used to display the rendered image on the texture-mapped polygon, stored so that they can be updated as the render target image size is changed by the user-interface:.

objTransXY

javax.media.j3d.TransformGroup objTransXY
Group dictating how the XY plane is translated.

objXYPlane

javax.media.j3d.BranchGroup objXYPlane
Parent of the XY plane image.

parallelRotation

boolean parallelRotation
Parallel rotation flag.

resols

float[] resols
Resolutions of image A.

shapeBG

javax.media.j3d.BranchGroup shapeBG
DOCUMENT ME!

shapeSliceBG

javax.media.j3d.BranchGroup shapeSliceBG
DOCUMENT ME!

units

int[] units
Units of measure of imageA.

updateWinlevel

boolean updateWinlevel
Update the window level flag, call by the plane renderer.

xBox

float xBox
Numbers dicatating the sizes of the planes based on the extents and resolutions of the image.

yBox

float yBox
Numbers dicatating the sizes of the planes based on the extents and resolutions of the image.

zBox

float zBox
Numbers dicatating the sizes of the planes based on the extents and resolutions of the image.

maxBox

float maxBox
Numbers dicatating the sizes of the planes based on the extents and resolutions of the image.

m_bTestFrameRate

boolean m_bTestFrameRate

m_dLastTime

double m_dLastTime
Framerate Performance parameters:

m_dAccumulatedTime

double m_dAccumulatedTime
Framerate Performance parameters:

m_dFrameRate

double m_dFrameRate
Framerate Performance parameters:

m_iFrameCount

int m_iFrameCount
Framerate Performance parameters:

m_iAccumulatedFrameCount

int m_iAccumulatedFrameCount
Framerate Performance parameters:

m_iTimer

int m_iTimer
Framerate Performance parameters:

m_iMaxTimer

int m_iMaxTimer
Framerate Performance parameters:

Class gov.nih.mipav.view.renderer.J3D.volumeview.VolumeRendererRayCast extends VolumeRenderer implements Serializable

serialVersionUID: 7864871507214707172L

Class gov.nih.mipav.view.renderer.J3D.volumeview.VolumeRendererShearWarp extends VolumeRenderer implements Serializable

serialVersionUID: -3304622158293691309L

Package gov.nih.mipav.view.renderer.WildMagic

Class gov.nih.mipav.view.renderer.WildMagic.VolumeTriPlanarDialog extends JInterfaceBase implements Serializable

serialVersionUID: -1966951185588087479L

Serialized Fields

RGBTA

ModelRGB RGBTA
Lookup table of the color imageA, B.

RGBTB

ModelRGB RGBTB
Lookup table of the color imageA, B.

extents

int[] extents
Original dimensions extents value array.

extXInput

JTextField extXInput
Original X, Y, Z dimension extents values.

extYInput

JTextField extYInput
Original X, Y, Z dimension extents values.

extZInput

JTextField extZInput
Original X, Y, Z dimension extents values.

extXOutput

JTextField extXOutput
Power of 2 X, Y, Z dimension extents values.

extYOutput

JTextField extYOutput
Power of 2 X, Y, Z dimension extents values.

extZOutput

JTextField extZOutput
Power of 2 X, Y, Z dimension extents values.

forcePadding

boolean forcePadding
Flag to force the padding of blank images to the end of images.

forceResample

boolean forceResample
Boolean flag to do resample images.

imageA

ModelImage imageA
Model images A and B.

imageB

ModelImage imageB
Model images A and B.

imageAOriginal

ModelImage imageAOriginal
The non-cloned image which we want to load into the renderer.

LUTa

ModelLUT LUTa
Lookup table of the imageA, B.

LUTb

ModelLUT LUTb
Lookup table of the imageA, B.

m_iFilter

int m_iFilter
Resample filter type, default: Trilinear Interpoloation.

m_kFilterType

JComboBox m_kFilterType
Resample filter selection box.

nDim

int nDim
Number of available dimension.

newRes

float[] newRes
Resample resolution corresponding to Power of 2.

padButton

JButton padButton
Pad button is used for inserting blank images to the end of the image. This approach creates the power of 2 image. Pad Button is only enabled when the power of 2 value is greater than the slices number.

res

float[] res
Original resolution array.

resampledImage

ModelImage resampledImage
Temp Model image.

startupCommand

String startupCommand
The action command to send to the volume renderer after we start it (can be used to open a tab). Used by RFAST to open up the RFA simulation immediately.

volExtents

int[] volExtents
Resampled dimension value in Power of 2.

volSize

int volSize
Volume size X*Y*Z.

m_kVolViewType

String m_kVolViewType
Type of ViewJFrameVolumeView object (using WildMagic or not)

Class gov.nih.mipav.view.renderer.WildMagic.VolumeTriPlanarInterface extends ViewJFrameBase implements Serializable

serialVersionUID: 1898957906984534260L

Serialized Fields

menuObj

ViewMenuBuilder menuObj
Menu items storage.

modelViewLabel

JLabel modelViewLabel
Labels for the current position in 3D ModelView coordinates.

modelViewLabelVals

JLabel[] modelViewLabelVals
Displayed values for the current position in 3D ModelView coordinates.

panelToolbar

JPanel panelToolbar
Panel that holds the toolbars.

patientSliceLabel

JLabel patientSliceLabel
Labels for the current position in PatientSlice coordinates.

patientSliceLabelVals

JLabel[] patientSliceLabelVals
Displayed values for the current position in PatientSlice coordinates.

RGBTA

ModelRGB RGBTA
Lookup table of the color imageA, B.

RGBTB

ModelRGB RGBTB
Lookup table of the color imageA, B.

serif12

Font serif12
Fonts, same as MipavUtil.font12 and MipavUtil.font12B.

serif12B

Font serif12B
Fonts, same as MipavUtil.font12 and MipavUtil.font12B.

m_kBrainsurfaceFlattenerPanel

JPanel m_kBrainsurfaceFlattenerPanel
Control panels for the Brain Surface Flattener:.

brainsurfaceFlattenerRender

CorticalAnalysisRender brainsurfaceFlattenerRender
Rendering the brainsurfaceFlattener objects.

m_kFlyThroughRender

FlyThroughRender m_kFlyThroughRender
Flythrough renderer:

m_kFlyThroughPanel

JPanel m_kFlyThroughPanel
Flythough setup user-interface container:

flythruControl

JPanelVirtualEndoscopySetup_WM flythruControl
Flythough setup panel:

flythruMovePanel

JPanel flythruMovePanel
Flythough Move container:

flythruMoveControl

JPanelFlythruMove flythruMoveControl
Flythough Move panel:

clipBox

JPanelClip_WM clipBox
Clipping user-interface panel:

sliceGUI

JPanelSlices_WM sliceGUI
3D Slice-view user-interface panel:

surfaceGUI

JPanelSurface_WM surfaceGUI
3D Surface user-interface panel:

displayGUI

JPanelDisplay_WM displayGUI
Display options panel:

geodesicGUI

JPanelGeodesic_WM geodesicGUI
Geodesic user-interface panel:

sculptGUI

JPanelSculptor_WM sculptGUI
Sculpting user-interface panel:

surfaceTextureGUI

JPanelSurfaceTexture_WM surfaceTextureGUI
Surface Texture user-interface panel:

rendererGUI

JPanelRenderMode_WM rendererGUI
Renderer mode user-interface panel

clipPanel

JPanel clipPanel
Clip user-interface container:

slicePanel

JPanel slicePanel
3D Slice panel container.

multiHistogramGUI

JPanelMultiHistogram multiHistogramGUI
Multihistogram panel:

multiHistogramPanel

JPanel multiHistogramPanel
Display panel container

surfaceTexturePanel

JPanel surfaceTexturePanel
Surface texture panel container

renderModePanel

JPanel renderModePanel
Render mode panel container

surfacePanel

JPanel surfacePanel
Surface user-interface panel container

clipButton

JButton clipButton
Button to invoke all the six clipping planes.

clipDisableButton

JButton clipDisableButton
Button to disable all the six clipping planes.

clipMaskButton

JButton clipMaskButton
Button to crop the clip volume.

clipMaskUndoButton

JButton clipMaskUndoButton
Button to undo crop the clip volume.

clipPlaneButton

JButton clipPlaneButton
Button to invoke clipping planes.

clipSaveButton

JButton clipSaveButton
Button to save clipped region.

displayPanel

JPanel displayPanel
Display panel container

histoLUTPanel

JPanel histoLUTPanel
Control panel for the surface renderer.

imageOrientation

int imageOrientation
Image orientation: coronal, sagittal, axial, unknown.

gpuPanel

JPanel gpuPanel
The image panel to hold one Canvas3D.

bf_flyPanel

JPanel bf_flyPanel
Panel to hold the BrainSurfaceFlattener or Flythrough views.

lightPanel

JPanel lightPanel
Light panel container

m_kLightsPanel

JPanelLights_WM m_kLightsPanel
Light panel

m_akPlaneRender

PlaneRender_WM[] m_akPlaneRender
The three slice views displayed as texture-mapped polygons:.

m_kGeodesicPanel

JPanel m_kGeodesicPanel
Control panel for drawing geodesic curves.

m_kSculptPanel

JPanel m_kSculptPanel
Control panel for volume sculpting.

maxPanelWidth

int maxPanelWidth
The max width of the control panels.

menuBar

JMenuBar menuBar
Menu bar.

opacityPanel

JPanel opacityPanel
Volume Opacity panel.

paddingImageA

ModelImage paddingImageA
Padding imageA with blank images feeding.

paddingImageB

ModelImage paddingImageB
Padding imageB with blank images feeding.

panelHistoLUT

JPanelHistoLUT panelHistoLUT
LUT control panel of the gray scale image.

panelHistoRGB

JPanelHistoRGB panelHistoRGB
RGB control panel of the color image.

radioSurrenderLIGHT

JRadioButton radioSurrenderLIGHT
Radio button of the surface render lighting mode.

raisedbevel

Border raisedbevel
Panel Border view.

loweredbevel

Border loweredbevel
Panel Border view.

compound

Border compound
Panel Border view.

redBorder

Border redBorder
Panel Border view.

etchedBorder

Border etchedBorder
Panel Border view.

pressedBorder

Border pressedBorder
Panel Border view.

m_kVolumeImageA

VolumeImage m_kVolumeImageA
VolumeImage contains data and textures for ModelImage A.

m_kVolumeImageB

VolumeImage m_kVolumeImageB
VolumeImage contains data and textures for ModelImage B.

m_kAnimator

com.sun.opengl.util.Animator m_kAnimator
Animator for GPU-based rendering with JOGL.

raycastRenderWM

VolumeTriPlanarRender raycastRenderWM
Volume/Slice/Surface renderer.

rfaButton

JButton rfaButton
Button for RFA.

rfaSeparator

JButton rfaSeparator
RFA separator.

rightPane

JSplitPane rightPane
The view pane that contains the image view and tri-planar view panels.

dualPane

JSplitPane dualPane
For displaying the BrainSurfaceFlattener or Flythrough renderers.

toolbarBuilder

ViewToolBarBuilder toolbarBuilder
Toolbar builder reference.

triImagePanel

JPanel triImagePanel
Tri image planar render panels.

viewToolBar

JToolBar viewToolBar
The top one render view switch toolbar.

m_kVolOpacityPanel

JPanelVolOpacityBase m_kVolOpacityPanel
Opacity panel.

m_kStereoIPD

JDialogStereoControls m_kStereoIPD
Stereo view IPD control.

panelAxial

JPanel panelAxial
Axial view panel.

panelSagittal

JPanel panelSagittal
Sagittal view panel.

panelCoronal

JPanel panelCoronal
Coronal view panel.

screenWidth

int screenWidth
Current frame width and height.

screenHeight

int screenHeight
Current frame width and height.

panelLabels

JPanel panelLabels
Panel containing the position labels:.

Package gov.nih.mipav.view.renderer.WildMagic.brainflattenerview_WM

Class gov.nih.mipav.view.renderer.WildMagic.brainflattenerview_WM.JPanelBrainSurfaceFlattener_WM extends JPanel implements Serializable

serialVersionUID: -2749305357977770854L

Serialized Fields

mainPanel

JPanel mainPanel
The main control.

serif12

Font serif12
Fonts, same as MipavUtil.font12 and MipavUtil.font12B.

serif12B

Font serif12B
Fonts, same as MipavUtil.font12 and MipavUtil.font12B.

OKButton

JButton OKButton
OK button is used on most dialogs. Defining it in the base allows default actions if the user presses return and the button is in focus.

cancelButton

JButton cancelButton
Cancel button is used on most dialogs. Defining it in the base allows default actions if the user presses return and the button is in focus.

m_bFileLoaded

boolean m_bFileLoaded
Set to true when a surface has been loaded

m_bFirstSurface

boolean m_bFirstSurface
Causes the surface LUT to be calculated for the first time.

m_iGridY

int m_iGridY
Keeps track of the user-interface position in the main panel.

m_kDisablePick

JRadioButton m_kDisablePick
Enable/disable correspondence picking

m_kDisplayButtonGroup

ButtonGroup m_kDisplayButtonGroup
ButtonGroup for the plane/surface display selection.

m_kDisplayPlane

JRadioButton m_kDisplayPlane
Toggle displaying the plane on/off

m_kDisplaySphere

JRadioButton m_kDisplaySphere
Toggle displaying the sphere on/off

m_kLatLonLines

JCheckBox m_kLatLonLines
Toggle display of latitude/longitude lines on/off.

m_kLUTa

ModelLUT m_kLUTa
Color LUT based on Volume Data

m_kLUTImageA

ModelImage m_kLUTImageA
Volume data for LUT

m_kNumLatText

JTextField m_kNumLatText
Text box for entering the number of latitude lines.

m_kNumLonText

JTextField m_kNumLonText
Text box for entering the number of longitude lines.

m_kPanelBrainsurfaceFlattenerLUT

JPanelHistoLUT m_kPanelBrainsurfaceFlattenerLUT
LUT Panel based on surface curvature.

m_kPickButtonGroup

ButtonGroup m_kPickButtonGroup
Picking button group -- switch between picking correspondence points and the puncture triangle.

m_kPickCorrespondence

JRadioButton m_kPickCorrespondence
Correspondence point picking.

m_kPickPuncture

JRadioButton m_kPickPuncture
Puncture triangle picking.

m_kTriangleMesh

WildMagic.LibGraphics.SceneGraph.TriMesh m_kTriangleMesh
Brain Surface TriMesh

m_kView

CorticalAnalysisRender m_kView
Brain Surface Renderer.

scroller

JScrollPane scroller
The scroll pane holding the panel content. Useful when the screen is small.

m_kInsidePanel

JPanel m_kInsidePanel
Panel container.

m_kVolumeViewer

VolumeTriPlanarInterface m_kVolumeViewer
Parent user-interface frame.

Package gov.nih.mipav.view.renderer.WildMagic.Decimate

Class gov.nih.mipav.view.renderer.WildMagic.Decimate.IDList extends Object implements Serializable

Serialized Fields

ID

int ID

next

IDList next

back

IDList back
Package gov.nih.mipav.view.renderer.WildMagic.DTI_FrameWork

Class gov.nih.mipav.view.renderer.WildMagic.DTI_FrameWork.JPanelDTIFiberTrack extends JInterfaceBase implements Serializable

serialVersionUID: -293668520247305166L

Serialized Fields

contentBox

Box contentBox
Box layout for control panel.

reconstructTracts

JCheckBox reconstructTracts

computeButton

JButton computeButton

parentFrame

VolumeTriPlanarInterfaceDTI parentFrame

Class gov.nih.mipav.view.renderer.WildMagic.DTI_FrameWork.JPanelDTILoad extends JInterfaceBase implements Serializable

serialVersionUID: 8011148684175711251L

Serialized Fields

contentBox

Box contentBox
Box layout for control panel.

openDTIimageButton

JButton openDTIimageButton

textDTIimage

JTextField textDTIimage

openDTIimageListFile

JButton openDTIimageListFile

openDTIMaskImage

JButton openDTIMaskImage

textDTIimageListFile

JTextField textDTIimageListFile

textDTIListFile

JTextField textDTIListFile

textDTIMaskImage

JTextField textDTIMaskImage

openDWIimageBT

JButton openDWIimageBT

reconstructTracts

JCheckBox reconstructTracts

computeButton

JButton computeButton

m_iDimX

int m_iDimX
X-dimensions for Diffusion Weighted Images.

m_iDimY

int m_iDimY
Y-dimensions for Diffusion Weighted Images.

m_kParentDir

String m_kParentDir
parent directory for the DTI output images.

m_kDTIImage

ModelImage m_kDTIImage
Diffusion Tensor image.

m_fResX

float m_fResX
Slice thickness read from .list file

m_fResY

float m_fResY
Slice thickness read from .list file

m_fResZ

float m_fResZ
Slice thickness read from .list file

m_bUseXRes

boolean m_bUseXRes
Set to true if the slice resolution is read from the .list file: (xRes)

m_bUseYRes

boolean m_bUseYRes
Set to true if the slice resolution is read from the .list file: (yRes)

m_bUseZRes

boolean m_bUseZRes
Set to true if the slice resolution is read from the .list file: (zRes)

m_fMeanNoise

float m_fMeanNoise
Mean noise vale read from the .list file

m_kRawFormat

String m_kRawFormat
raw image format read from the .list file:

m_iSlices

int m_iSlices
Number of slices in the Diffusion Weighted Images series.

m_iWeights

int m_iWeights
Number of weights in the Diffusion Weighted Images series.

m_kBMatrix

WildMagic.LibFoundation.Mathematics.GMatrixf m_kBMatrix
General matrix storing BMatrix values.

m_aakDWIList

String[][] m_aakDWIList
List of file names for the Diffusion Weighted Images, from the .path file.

m_aiMatrixEntries

int[] m_aiMatrixEntries
keeps track of unique entries in the BMatrix

m_iBOrig

int m_iBOrig
Number of different BMatrix rows:

m_kEigenVectorImage

ModelImage m_kEigenVectorImage
Eigenvector image

m_kAnisotropyImage

ModelImage m_kAnisotropyImage
Anisotropy image

parentFrame

VolumeTriPlanarInterfaceDTI parentFrame

alg

AlgorithmDTIColorDisplay alg
handle to the algorithm

resultImage

ModelImage resultImage
result image

m_kDWIMaskImage

ModelImage m_kDWIMaskImage
mask image

mainPanelGBC

GridBagConstraints mainPanelGBC

loadDataRadioGroup

ButtonGroup loadDataRadioGroup

listRadio

JRadioButton listRadio

dtiRadio

JRadioButton dtiRadio

dtiFileLabel

JLabel dtiFileLabel

maskImageLabel

JLabel maskImageLabel

listFileLabel

JLabel listFileLabel

tractCheckBox

JCheckBox tractCheckBox

kAlgorithm

AlgorithmDWI2DTI kAlgorithm

Class gov.nih.mipav.view.renderer.WildMagic.DTI_FrameWork.JPanelDTIParametersPanel extends JInterfaceBase implements Serializable

serialVersionUID: 2778749302064237729L

Serialized Fields

contentBox

Box contentBox
Box layout for control panel.

reconstructTracts

JCheckBox reconstructTracts

computeButton

JButton computeButton

m_kTractList

JList m_kTractList
The list box in the dialog for fiber bundle tracts.

m_kColorButton

JButton m_kColorButton
Color button for changing the color of the fiber bundles.

m_kColorButtonDefault

Color m_kColorButtonDefault
Color button detault color:

m_kUseVolumeColor

JCheckBox m_kUseVolumeColor
Checkbox for turning on/off volume color for the polylines.

m_kUseEllipsoids

JCheckBox m_kUseEllipsoids
Checkbox for switching between polylines and ellipsoids.

m_kAllEllipsoids

JCheckBox m_kAllEllipsoids
Checkbox for displaying all tensors as ellipsoids.

m_kUseCylinders

JCheckBox m_kUseCylinders
Checkbox for switching between polylines and ellipsoids and cylinders.

m_kTubes

JCheckBox m_kTubes
Checkbox for switching between polylines and ellipsoids and cylinders, Tubes

m_kAllCylinders

JCheckBox m_kAllCylinders
Checkbox for displaying all tensors as ellipsoids.

m_kDisplaySlider

JSlider m_kDisplaySlider
User-control over the number of ellipsoids displayed in GPUVolumeRender

parentFrame

VolumeTriPlanarInterfaceDTI parentFrame

m_kVolumeDisplay

VolumeTriPlanarRender m_kVolumeDisplay

m_kDTIImage

ModelImage m_kDTIImage

m_kTractFile

File m_kTractFile
Tract input file.

m_kTractsLimit

JTextField m_kTractsLimit
For TRACTS dialog: number of tracts to display.

m_kTractsMin

JTextField m_kTractsMin
For TRACTS dialog: minimum tract length to display.

m_kTractsMax

JTextField m_kTractsMax
For TRACTS dialog: maximum tract length to display.

m_kUseVOICheck

JCheckBox m_kUseVOICheck
When selected, only tracts that intersect the VOI are displayed.

m_kBundleList

Vector<E> m_kBundleList
Keeps track of the groups of polylines loaded.

m_iBundleCount

int m_iBundleCount
Number of currently loaded fiber bundle groups.

m_kImage

ModelImage m_kImage

m_kTractPath

JTextField m_kTractPath
Fiber bundle tract file input path name text box.

m_abVisited

boolean[] m_abVisited
Which tensor nodes are already on the fiber bundle tract

slicePickableCheckBox

JCheckBox slicePickableCheckBox
Check boxe enable the slice pickable or not

radioLines

JRadioButton radioLines

radioEllipzoids

JRadioButton radioEllipzoids

radioCylinders

JRadioButton radioCylinders

radioTubes

JRadioButton radioTubes

radioArrows

JRadioButton radioArrows

displayAllCheckBox

JCheckBox displayAllCheckBox

displayMode

int displayMode

displayAll

boolean displayAll

centerIndex

int centerIndex

loadingTrack

boolean loadingTrack

m_kColorChooser

ViewJColorChooser m_kColorChooser
Color chooser for when the user wants to change the color of the fiber bundle tracts.

Class gov.nih.mipav.view.renderer.WildMagic.DTI_FrameWork.VolumeTriPlanarInterfaceDTI extends VolumeTriPlanarInterface implements Serializable

serialVersionUID: 1898957906984534260L

Serialized Fields

DTIimageLoadPanel

JPanelDTILoad DTIimageLoadPanel

DTIFiberTrackPanel

JPanelDTIFiberTrack DTIFiberTrackPanel

DTIparamsPanel

JPanelDTIParametersPanel DTIparamsPanel

m_kEigenVectorImage

ModelImage m_kEigenVectorImage
Eigenvector image

m_kAnisotropyImage

ModelImage m_kAnisotropyImage
Anisotropy image

m_kDTIImage

ModelImage m_kDTIImage
Diffusion Tensor image.

m_kDTIColorImage

ModelImage m_kDTIColorImage
Diffusion Tensor image.

m_kParentDir

String m_kParentDir

DTIFiberPanel

JPanel DTIFiberPanel

DTIParametersPanel

JPanel DTIParametersPanel
Package gov.nih.mipav.view.renderer.WildMagic.flythroughview

Class gov.nih.mipav.view.renderer.WildMagic.flythroughview.JPanelVirtualEndoscopySetup_WM extends JPanelRendererBase implements Serializable

serialVersionUID: 5676430934584329807L

Serialized Fields

contentBox

Box contentBox
Box layout for control panel.

continueUpdate

boolean continueUpdate
Flag indicates to continue update the surface render and plane render or not.

endoscopyImage

ModelImage endoscopyImage
Loaded endoscopy image file.

fileName

String fileName
File name and directory.

directory

String directory
File name and directory.

flythruButtonLoadImage

JButton flythruButtonLoadImage
Load image button.

flythruLabelFileName

JLabel flythruLabelFileName
Image file name label.

kPanelButton

JPanel kPanelButton
Button panel.

m_bShowMeanCurvatures

boolean m_bShowMeanCurvatures
Flag indicates to show pseudo color or not.

m_kCheckBoxShowCurvatures

JCheckBox m_kCheckBoxShowCurvatures
Show curvature colors check box.

m_kContinueUpdate

JCheckBox m_kContinueUpdate
Continuous update check box.

m_kDecimalFormat

DecimalFormat m_kDecimalFormat
Used to create text representations of numbers.

m_kLabelBranch

JLabel m_kLabelBranch
Branch label.

m_kLabelDirection

JLabel m_kLabelDirection
View direction label.

m_kLabelDistance

JLabel m_kLabelDistance
Path distance label.

m_kLabelFileName

JLabel m_kLabelFileName
Automatically inserted by JBuilder Designer.

m_kLabelOrientation

JLabel m_kLabelOrientation
Orientation label.

m_kLabelPosition

JLabel m_kLabelPosition
Current path position label.

m_kLabelStepGaze

JLabel m_kLabelStepGaze
Step gaze label.

m_kOptions

FlyThroughRender.SetupOptions m_kOptions
Image option panel.

m_kTextBranch

JTextField m_kTextBranch
Current branch text box.

m_kTextDirection

JTextField m_kTextDirection
View direction text box.

m_kTextDistance

JTextField m_kTextDistance
Distance along path text box.

m_kTextMaxNumBranches

JTextField m_kTextMaxNumBranches
maximum number of branches created for the endoscopy view.

m_kTextMinBranchLength

JTextField m_kTextMinBranchLength
minimum branch length.

m_kTextOrientation

JTextField m_kTextOrientation
Orientation text box.

m_kTextPercentBSplineNumControlPoints

JTextField m_kTextPercentBSplineNumControlPoints
BSpline control points fraction of branch samples.

m_kTextPosition

JTextField m_kTextPosition
Position text box.

m_kTextStepGaze

JTextField m_kTextStepGaze
Step gaze text box.

m_kView

FlyThroughRender m_kView
Renderer for displaying the scene-graph.

scroller

JScrollPane scroller
Scroll pane.

scrollPanel

gov.nih.mipav.view.renderer.WildMagic.flythroughview.JPanelVirtualEndoscopySetup_WM.DrawingPanel scrollPanel
Scroll panel that holding all the control components.

updateButton

JButton updateButton
continue update button.

Package gov.nih.mipav.view.renderer.WildMagic.Interface

Class gov.nih.mipav.view.renderer.WildMagic.Interface.FileInfoSurfaceRefXML_WM extends FileInfoSurfaceRefXML implements Serializable

serialVersionUID: 819907577181061024L

Serialized Fields

m_kMaterial

WildMagic.LibGraphics.Rendering.MaterialState m_kMaterial
Material properties of the surface:.

Class gov.nih.mipav.view.renderer.WildMagic.Interface.JDialogDTIInput extends JInterfaceBase implements Serializable

serialVersionUID: 9207590841799033846L

Serialized Fields

m_kEigenVectorImage

ModelImage m_kEigenVectorImage
Eigenvector image

m_kAnisotropyImage

ModelImage m_kAnisotropyImage
Anisotropy image

m_kDTIImage

ModelImage m_kDTIImage
Diffusion Tensor image.

m_kDWIMaskImage

ModelImage m_kDWIMaskImage
Mask image for calculating the DTI image.

m_kLUTa

ModelLUT m_kLUTa
LUT of input image

m_kEigenVectorPath

JTextField m_kEigenVectorPath
EigenVector file input path name text box.

m_kAnisotropyPath

JTextField m_kAnisotropyPath
Anisotropy file input path name text box.

m_kDTIPath

JTextField m_kDTIPath
Diffusion Tensor file input path name text box.

m_kDWIPath

JTextField m_kDWIPath
Diffusion Weighted Images .list file input path name text box.

m_kDWIMaskPath

JTextField m_kDWIMaskPath
Diffusion Weighted Images Mask file input path name text box.

m_kTractPath

JTextField m_kTractPath
Fiber bundle tract file input path name text box.

m_kBMatrix

WildMagic.LibFoundation.Mathematics.GMatrixf m_kBMatrix
General matrix storing BMatrix values.

m_aakDWIList

String[][] m_aakDWIList
List of file names for the Diffusion Weighted Images, from the .path file.

m_iSlices

int m_iSlices
Number of slices in the Diffusion Weighted Images series.

m_iWeights

int m_iWeights
Number of weights in the Diffusion Weighted Images series.

m_iDimX

int m_iDimX
X-dimensions for Diffusion Weighted Images.

m_iDimY

int m_iDimY
Y-dimensions for Diffusion Weighted Images.

m_iType

int m_iType
Dialog type.

m_kImage

ModelImage m_kImage
Image displayed in the GPUVolumeRender and SurfaceRender

m_kReconstructTracts

JCheckBox m_kReconstructTracts
Checkbox for tract reconstruction.

m_kOpenB0

JCheckBox m_kOpenB0

m_kTractsLimit

JTextField m_kTractsLimit
For TRACTS dialog: number of tracts to display.

m_kTractsMin

JTextField m_kTractsMin
For TRACTS dialog: minimum tract length to display.

m_kTractsMax

JTextField m_kTractsMax
For TRACTS dialog: maximum tract length to display.

m_kTractFile

File m_kTractFile
Tract input file.

m_kUseVOICheck

JCheckBox m_kUseVOICheck
When selected, only tracts that intersect the VOI are displayed.

m_iBOrig

int m_iBOrig
Number of different BMatrix rows:

m_aiMatrixEntries

int[] m_aiMatrixEntries
keeps track of unique entries in the BMatrix

m_kTractList

JList m_kTractList
The list box in the dialog for fiber bundle tracts.

m_kColorButton

JButton m_kColorButton
Color button for changing the color of the fiber bundles.

m_kColorButtonDefault

Color m_kColorButtonDefault
Color button detault color:

m_kUseVolumeColor

JCheckBox m_kUseVolumeColor
Checkbox for turning on/off volume color for the polylines.

m_kUseEllipsoids

JCheckBox m_kUseEllipsoids
Checkbox for switching between polylines and ellipsoids.

m_kAllEllipsoids

JCheckBox m_kAllEllipsoids
Checkbox for displaying all tensors as ellipsoids.

m_kBundleList

Vector<E> m_kBundleList
Keeps track of the groups of polylines loaded.

m_iBundleCount

int m_iBundleCount
Number of currently loaded fiber bundle groups.

m_kParentDialog

JDialogDTIInput m_kParentDialog
DTI panel parent of load tract dialog

m_kDisplaySlider

JSlider m_kDisplaySlider
User-control over the number of ellipsoids displayed in GPUVolumeRender

m_fResX

float m_fResX
Slice thickness read from .list file

m_fResY

float m_fResY
Slice thickness read from .list file

m_fResZ

float m_fResZ
Slice thickness read from .list file

m_bUseXRes

boolean m_bUseXRes
Set to true if the slice resolution is read from the .list file: (xRes)

m_bUseYRes

boolean m_bUseYRes
Set to true if the slice resolution is read from the .list file: (yRes)

m_bUseZRes

boolean m_bUseZRes
Set to true if the slice resolution is read from the .list file: (zRes)

m_fMeanNoise

float m_fMeanNoise
Mean noise vale read from the .list file

m_kRawFormat

String m_kRawFormat
raw image format read from the .list file:

m_kParentDir

String m_kParentDir
parent directory for the DTI output images.

Class gov.nih.mipav.view.renderer.WildMagic.Interface.JDialogStereoControls extends JInterfaceBase implements Serializable

serialVersionUID: 844490628214011726L

Serialized Fields

mkCurrent

JLabel mkCurrent
Label that gives current value of slider.

m_fIPD

float m_fIPD
IPD number.

m_kIPDSlider

JSlider m_kIPDSlider
Opacity slider.

Class gov.nih.mipav.view.renderer.WildMagic.Interface.JFrameSurfaceMaterialProperties_WM extends JFrame implements Serializable

serialVersionUID: 3077827124095959620L

Serialized Fields

AFTER

int AFTER
Before/After index values for the two displayed spheres, canvases, and display panels:.

BEFORE

int BEFORE
Before/After index values for the two displayed spheres, canvases, and display panels:.

m_akMaterialPreset

WildMagic.LibGraphics.Rendering.MaterialState[] m_akMaterialPreset
Pre-defined materials

m_fShininess

float m_fShininess
specular coefficient

m_iNumPreset

int m_iNumPreset
Preset Material's examples:.

m_iSurfaceIndex

int m_iSurfaceIndex
the index of the surface that is being changed in the JPanelSurface

m_iWhichButton

int m_iWhichButton
Which button is pressed to activate the JColorChooser:.

m_kAmbient

WildMagic.LibFoundation.Mathematics.ColorRGB m_kAmbient
Current color values:.

m_kAmbientColorButton

JButton m_kAmbientColorButton
Material Properties color buttons:.

m_kColorChooser

JColorChooser m_kColorChooser
Color Chooser dialog:.

m_kDiffuse

WildMagic.LibFoundation.Mathematics.ColorRGB m_kDiffuse
diffuse color

m_kDiffuseColorButton

JButton m_kDiffuseColorButton
diffuse color button

m_kEmissive

WildMagic.LibFoundation.Mathematics.ColorRGB m_kEmissive
emissive color

m_kEmissiveColorButton

JButton m_kEmissiveColorButton
emissive color button

m_kImagePane

JSplitPane m_kImagePane
Split pane for displaying the canvases side-by-side:.

m_kImagePanel

JPanel[] m_kImagePanel
Canvas display panels:.

m_kMainPane

JSplitPane m_kMainPane
Split pane for displaying the rendered spheres above the interface:.

m_kMaterialNew

WildMagic.LibGraphics.Rendering.MaterialState m_kMaterialNew
Materials for new vales and backup:.

m_kMaterialPanel

JPanel m_kMaterialPanel
Window display panels: Material properties buttons/slider panel:.

m_kMaterialSave

WildMagic.LibGraphics.Rendering.MaterialState m_kMaterialSave
Saved Material for backup

m_kParent

JPanelSurface_WM m_kParent
Parent class:.

m_kShininessSlider

JSlider m_kShininessSlider
Shininess slider.

m_kSpecular

WildMagic.LibFoundation.Mathematics.ColorRGB m_kSpecular
Specular color component

m_kSpecularColorButton

JButton m_kSpecularColorButton
Specular color button

m_bColorApplied

boolean m_bColorApplied
keeps track of whether or not color has been applied to surface (for backup on cancel)

m_akSurfaceMaterial

SurfaceMaterialDisplay[] m_akSurfaceMaterial

m_kAnimator

com.sun.opengl.util.Animator m_kAnimator

Class gov.nih.mipav.view.renderer.WildMagic.Interface.JInterfaceBase extends JDialog implements Serializable

Serialized Fields

colorChooser

ViewJColorChooser colorChooser
Color chooser dialog.

mainPanel

JPanel mainPanel
The main control.

cancelButton

JButton cancelButton
Cancel button is used on most dialogs. Defining it in the base allows default actions if the user presses return and the button is in focus.

OKButton

JButton OKButton
OK button is used on most dialogs. Defining it in the base allows default actions if the user presses return and the button is in focus.

rayBasedRenderWM

VolumeTriPlanarRender rayBasedRenderWM
Raycast based renderer reference, raycast renderer or shear warp renderer.

m_kVolumeViewer

VolumeTriPlanarInterface m_kVolumeViewer
Render base.

Class gov.nih.mipav.view.renderer.WildMagic.Interface.JInterfaceBase.DrawingPanel extends JPanel implements Serializable

serialVersionUID: -6456589720445279985L

Class gov.nih.mipav.view.renderer.WildMagic.Interface.JPanelClip_WM extends JInterfaceBase implements Serializable

serialVersionUID: -3342110506544352170L

Serialized Fields

enables

boolean[] enables
Enable flags for the 6 ( X, Y, Z and inverse ) clipping planes.

enablesArbi

boolean[] enablesArbi
Enable flags for the arbitrary clipping planes.

enablesStatic

boolean[] enablesStatic
Enable flags for the static clipping planes.

aSlice

int aSlice
Which arbitray clipping slice is currently displayed.

boundingCheckA

JCheckBox boundingCheckA
Arbitrary and static clipping plane check box.

boundingCheckStatic

JCheckBox boundingCheckStatic
Arbitrary and static clipping plane check box.

boundingCheckStaticInv

JCheckBox boundingCheckStaticInv
Arbitrary and static clipping plane check box.

boundingCheckX

JCheckBox boundingCheckX
Check box to turn the clipping plane frame on and off.

boundingCheckY

JCheckBox boundingCheckY
Check box to turn the clipping plane frame on and off.

boundingCheckZ

JCheckBox boundingCheckZ
Check box to turn the clipping plane frame on and off.

boundingCheckXInv

JCheckBox boundingCheckXInv
X,Y,Z inverse clipping plane check box.

boundingCheckYInv

JCheckBox boundingCheckYInv
X,Y,Z inverse clipping plane check box.

boundingCheckZInv

JCheckBox boundingCheckZInv
X,Y,Z inverse clipping plane check box.

boxStatic

JCheckBox boxStatic
Static and static inverse, arbitrary clipping plane check box.

boxStaticInv

JCheckBox boxStaticInv
Static and static inverse, arbitrary clipping plane check box.

boxA

JCheckBox boxA
Static and static inverse, arbitrary clipping plane check box.

boxX

JCheckBox boxX
Check boxes that turn the image plane and the sliders on and off.

boxY

JCheckBox boxY
Check boxes that turn the image plane and the sliders on and off.

boxZ

JCheckBox boxZ
Check boxes that turn the image plane and the sliders on and off.

boxXInv

JCheckBox boxXInv
Check boxes that turn the image plane and the sliders on and off.

boxYInv

JCheckBox boxYInv
Check boxes that turn the image plane and the sliders on and off.

boxZInv

JCheckBox boxZInv
Check boxes that turn the image plane and the sliders on and off.

clipSliderStatic

JSlider clipSliderStatic
Static, static inverse and arbitrary clipping plane boundary box.

clipSliderStaticInv

JSlider clipSliderStaticInv
Static, static inverse and arbitrary clipping plane boundary box.

sliderA

JSlider sliderA
Static, static inverse and arbitrary clipping plane boundary box.

clipSliderX

JSlider clipSliderX
Sliders for the image planes.

clipSliderY

JSlider clipSliderY
Sliders for the image planes.

clipSliderZ

JSlider clipSliderZ
Sliders for the image planes.

sliderXInv

JSlider sliderXInv
Sliders for the image planes.

sliderYInv

JSlider sliderYInv
Sliders for the image planes.

sliderZInv

JSlider sliderZInv
Sliders for the image planes.

colorButtonA

JButton colorButtonA
Color button for the arbitrary clipping plane frame.

colorButtonStatic

JButton colorButtonStatic
Color button for the static clipping plane frame.

colorButtonStaticInv

JButton colorButtonStaticInv
Color button for the static clipping plane frame.

colorButtonX

JButton colorButtonX
Color button for X clipping plane frame.

colorButtonXInv

JButton colorButtonXInv
Color button for X clipping plane frame.

colorButtonY

JButton colorButtonY
Color button for Y clipping plane frame.

colorButtonYInv

JButton colorButtonYInv
Color button for Y clipping plane frame.

colorButtonZ

JButton colorButtonZ
Color button for Z clipping plane frame.

colorButtonZInv

JButton colorButtonZInv
Color button for Z clipping plane frame.

extractButtonA

JButton extractButtonA
Extract arbitrary clipping plane button.

extractButtonS

JButton extractButtonS
Extract static eye clipping plane button.

labelAStart

JLabel labelAStart
Arbitrary clipping slider labels.

labelAMid

JLabel labelAMid
Arbitrary clipping slider labels.

labelAEnd

JLabel labelAEnd
Arbitrary clipping slider labels.

labelStatic

JLabel labelStatic
Static clipping slider labels.

labelStaticInv

JLabel labelStaticInv
Static clipping slider labels.

labelA

JLabel labelA
Static clipping slider labels.

labelStaticInvStart

JLabel labelStaticInvStart
Static inverse clipping plane labels.

labelStaticInvMid

JLabel labelStaticInvMid
Static inverse clipping plane labels.

labelStaticInvEnd

JLabel labelStaticInvEnd
Static inverse clipping plane labels.

labelStaticStart

JLabel labelStaticStart
Static clipping plane labels.

labelStaticMid

JLabel labelStaticMid
Static clipping plane labels.

labelStaticEnd

JLabel labelStaticEnd
Static clipping plane labels.

labelX

JLabel labelX
Sliders labels.

labelY

JLabel labelY
Sliders labels.

labelZ

JLabel labelZ
Sliders labels.

labelXInv

JLabel labelXInv
Sliders labels.

labelYInv

JLabel labelYInv
Sliders labels.

labelZInv

JLabel labelZInv
Sliders labels.

labelXStart

JLabel labelXStart
Slider tick labels.

labelXMid

JLabel labelXMid
Slider tick labels.

labelXEnd

JLabel labelXEnd
Slider tick labels.

labelXStartInv

JLabel labelXStartInv
X clipping slider labels.

labelXMidInv

JLabel labelXMidInv
X clipping slider labels.

labelXEndInv

JLabel labelXEndInv
X clipping slider labels.

labelYStart

JLabel labelYStart
Y clipping slider labels.

labelYMid

JLabel labelYMid
Y clipping slider labels.

labelYEnd

JLabel labelYEnd
Y clipping slider labels.

labelYStartInv

JLabel labelYStartInv
Y inverse clipping slider labels.

labelYMidInv

JLabel labelYMidInv
Y inverse clipping slider labels.

labelYEndInv

JLabel labelYEndInv
Y inverse clipping slider labels.

labelZStart

JLabel labelZStart
Z clipping slider labels.

labelZMid

JLabel labelZMid
Z clipping slider labels.

labelZEnd

JLabel labelZEnd
Z clipping slider labels.

labelZStartInv

JLabel labelZStartInv
Z clipping slider labels.

labelZMidInv

JLabel labelZMidInv
Z clipping slider labels.

labelZEndInv

JLabel labelZEndInv
Z clipping slider labels.

panelA

JPanel panelA
Arbitrary and static control panels.

panelS

JPanel panelS
Arbitrary and static control panels.

panelSInv

JPanel panelSInv
Arbitrary and static control panels.

panelX

JPanel panelX
Declare each clipping plane control panel.

panelXInv

JPanel panelXInv
Declare each clipping plane control panel.

panelY

JPanel panelY
Declare each clipping plane control panel.

panelYInv

JPanel panelYInv
Declare each clipping plane control panel.

panelZ

JPanel panelZ
Declare each clipping plane control panel.

panelZInv

JPanel panelZInv
Declare each clipping plane control panel.

radicalRatio

float radicalRatio
Arbitrary clipping plane expanding ratio.

scroller

JScrollPane scroller
The scroll pane holding the panel content. Used when the screen is small.

scrollPanel

JPanel scrollPanel
Scroll panel that holding all the control components.

sSlice

int sSlice
Record the current static clipping slice number.

sSliceInv

int sSliceInv
Record the current static clipping slice number.

tabbedPane

JTabbedPane tabbedPane
Tabbed Panel that hold the each clipping planes control box.

textStatic

JTextField textStatic
Static and arbitrary text field.

textStaticInv

JTextField textStaticInv
Static and arbitrary text field.

textA

JTextField textA
Static and arbitrary text field.

textX

JTextField textX
Text fields that display the slice number when slider moves.

textY

JTextField textY
Text fields that display the slice number when slider moves.

textZ

JTextField textZ
Text fields that display the slice number when slider moves.

textXInv

JTextField textXInv
X, Y, Z inverse text field.

textYInv

JTextField textYInv
X, Y, Z inverse text field.

textZInv

JTextField textZInv
X, Y, Z inverse text field.

xDim

int xDim
Image X, Y, Z dimension.

yDim

int yDim
Image X, Y, Z dimension.

zDim

int zDim
Image X, Y, Z dimension.

xSlice

int xSlice
Which slice is currently displayed in the ZY plane.

xSliceInv

int xSliceInv
Which slice is currently displayed in the ZY plane.

ySlice

int ySlice
Which slice is currently displayed in the XZ plane.

ySliceInv

int ySliceInv
Which slice is currently displayed in the XZ plane.

zSlice

int zSlice
Which slice is currently displayed in the XY plane.

zSliceInv

int zSliceInv
Which slice is currently displayed in the XY plane.

Class gov.nih.mipav.view.renderer.WildMagic.Interface.JPanelDisplay_WM extends JInterfaceBase implements Serializable

serialVersionUID: 926266253314679850L

Serialized Fields

boundingCheck

JCheckBox boundingCheck
Check box for turning box on and off.

colorButton

JButton colorButton
Color button for changing color.

colorButtonBackground

JButton colorButtonBackground
Color button for changing z color.

cubePanel

JPanel cubePanel
Panel for the rotation cube.

cubicCheck

JCheckBox cubicCheck
Check box for cubic control.

radioButtonGroupProjections

ButtonGroup radioButtonGroupProjections
Button group for projections.

radioButtonOrthographic

JRadioButton radioButtonOrthographic
Radio Button for Orthographic rendering.

radioButtonPerspective

JRadioButton radioButtonPerspective
Radio Button for Perspective rendering.

viewAlignedButton

JRadioButton viewAlignedButton
Radio Button for Perspective rendering.

viewButton

JRadioButton viewButton
Radio Button for Orthographic rendering.

viewTextureButtonGroup

ButtonGroup viewTextureButtonGroup
Button group for projections.

serif12

Font serif12
Fonts, same as MipavUtil.font12 and MipavUtil.font12B.

serif12B

Font serif12B
Fonts, same as MipavUtil.font12 and MipavUtil.font12B.

flag

boolean flag
Flag indicating if the red bounding box is on or off.

scroller

JScrollPane scroller
The scroll pane holding the panel content. Useful when the screen is small.

scrollPanel

JInterfaceBase.DrawingPanel scrollPanel
Scroll panel that holding the all the control components.

saveButton

JButton saveButton
Save and Load camera and object parameters buttons.

loadButton

JButton loadButton
Save and Load camera and object parameters buttons.

cameraXLabel

JLabel cameraXLabel
Camera move parameter labels

cameraYLabel

JLabel cameraYLabel
Camera move parameter labels

cameraZLabel

JLabel cameraZLabel
Camera move parameter labels

xCameraMove

float xCameraMove
Camera move parameter values.

yCameraMove

float yCameraMove
Camera move parameter values.

zCameraMove

float zCameraMove
Camera move parameter values.

xCameraMoveText

JTextField xCameraMoveText
Camera move parameter text-field.

yCameraMoveText

JTextField yCameraMoveText
Camera move parameter text-field.

zCameraMoveText

JTextField zCameraMoveText
Camera move parameter text-field.

cameraXTurnLabel

JLabel cameraXTurnLabel
Camera turn parameter labels

cameraYTurnLabel

JLabel cameraYTurnLabel
Camera turn parameter labels

xCameraTurn

float xCameraTurn
Camera move parameter values

yCameraTurn

float yCameraTurn
Camera move parameter values

xCameraTurnText

JTextField xCameraTurnText
Camera move parameter text-field

yCameraTurnText

JTextField yCameraTurnText
Camera move parameter text-field

objectXRotLabel

JLabel objectXRotLabel
Object rotation parameter labels.

objectYRotLabel

JLabel objectYRotLabel
Object rotation parameter labels.

objectZRotLabel

JLabel objectZRotLabel
Object rotation parameter labels.

xObjectRotateText

JTextField xObjectRotateText
Object rotation parameter text-field.

yObjectRotateText

JTextField yObjectRotateText
Object rotation parameter text-field.

zObjectRotateText

JTextField zObjectRotateText
Object rotation parameter text-field.

xObjectRotate

float xObjectRotate
Object rotation angle parameter values.

yObjectRotate

float yObjectRotate
Object rotation angle parameter values.

zObjectRotate

float zObjectRotate
Object rotation angle parameter values.

Class gov.nih.mipav.view.renderer.WildMagic.Interface.JPanelGeodesic_WM extends JInterfaceBase implements Serializable

serialVersionUID: 4382184418236793404L

Serialized Fields

drawLabel

JLabel drawLabel
Geodesic line draw control label.

m_fDijkstraCurrent

float m_fDijkstraCurrent
Current Dijkstra path length.

m_fDijkstraPrevious

float m_fDijkstraPrevious
Previous Dijkstra path length.

m_fDijkstraTotal

float m_fDijkstraTotal
Total Dijkstra path length.

m_fEuclidianCurrent

float m_fEuclidianCurrent
Values for the current path length between the last two selected points:

m_fEuclidianPrevious

float m_fEuclidianPrevious
Values for the previous current path length between the last two selected points:

m_fEuclidianTotal

float m_fEuclidianTotal
Values for the total path lengths:.

m_fGeodesicSmoothCurrent

float m_fGeodesicSmoothCurrent
Current Geodesic path length

m_fGeodesicSmoothPrevious

float m_fGeodesicSmoothPrevious
Previous Geodesic path length

m_fGeodesicSmoothTotal

float m_fGeodesicSmoothTotal
Total Geodesic path length

m_kCheckLivewire

JCheckBox m_kCheckLivewire
Toggle between LiveWire Interaction and point & click interaction:.

m_kClearAllCutsButton

JButton m_kClearAllCutsButton
Clearsall cuts.

m_kClearAllGeodesicButton

JButton m_kClearAllGeodesicButton
Clearsall Geodesic components.

m_kClearLastCutButton

JButton m_kClearLastCutButton
Clear the last cut.

m_kClearLastGeodesicButton

JButton m_kClearLastGeodesicButton
Button for deleting the geodesic.

m_kCutGeodesicButton

JButton m_kCutGeodesicButton
Button for cutting the mesh along the geodesic:.

m_kDijkstraDistance

JLabel m_kDijkstraDistance
Label displaying the current Dijkstra path length.

m_kDijkstraDistanceValueLast

JLabel m_kDijkstraDistanceValueLast
Label displaying the previous Dijkstra path length.

m_kDijkstraDistanceValueTotal

JLabel m_kDijkstraDistanceValueTotal
Label displaying the total Dijkstra path length.

m_kDisplayButtonGroup

ButtonGroup m_kDisplayButtonGroup
ButtonGroup for the different path display options.

m_kDisplayDijkstra

JRadioButton m_kDisplayDijkstra
Display Dijkstra's path.

m_kDisplayEuclidian

JRadioButton m_kDisplayEuclidian
Display the Euclidian path.

m_kDisplayGeodesic

JRadioButton m_kDisplayGeodesic
Radio buttons for displaying the smoothed geodesic, dijkstra's path, or the euclidian path:.

m_kDrawGeodesicButton

JToggleButton m_kDrawGeodesicButton
Geodesic drawing interface Toggle button is down while points are added to the curve:.

m_kEuclidianDistance

JLabel m_kEuclidianDistance
Label displaying the current Euclidian path length.

m_kEuclidianDistanceValueLast

JLabel m_kEuclidianDistanceValueLast
Label displaying the previous Euclidian path length.

m_kEuclidianDistanceValueTotal

JLabel m_kEuclidianDistanceValueTotal
Label displaying the total Euclidian path length.

m_kFinishClosedGeodesicButton

JButton m_kFinishClosedGeodesicButton
Close and finish the Geodesic path.

m_kFinishOpenGeodesicButton

JButton m_kFinishOpenGeodesicButton
Finish the Geodesic path without closing.

m_kGeodesicSmoothDistance

JLabel m_kGeodesicSmoothDistance
Label displaying the current Geodesic path length.

m_kGeodesicSmoothDistanceValueLast

JLabel m_kGeodesicSmoothDistanceValueLast
Label displaying the previous Geodesic path length.

m_kGeodesicSmoothDistanceValueTotal

JLabel m_kGeodesicSmoothDistanceValueTotal
Label displaying the total Geodesic path length.

m_kGeodesicToggleWireframe

JToggleButton m_kGeodesicToggleWireframe
Toggle wireframe

scroller

JScrollPane scroller
The scroll pane holding the panel content. Useful when the screen is small.

scrollPanel

JInterfaceBase.DrawingPanel scrollPanel
Scroll panel that holding the all the control components.

surfaceGeodesic

Geodesic_WM surfaceGeodesic
Geodesic reference.

surPickLabel

JLabel surPickLabel
Label to indicate that enable Surface pickable before drawing geodesic line.

m_kSurfacePanel

JPanelSurface_WM m_kSurfacePanel
Surface panel.

Class gov.nih.mipav.view.renderer.WildMagic.Interface.JPanelLights_WM extends JInterfaceBase implements Serializable

serialVersionUID: 8549491288085975699L

Serialized Fields

ambientRadio

JRadioButton ambientRadio
Radio button for different light type.

colorButton

JButton colorButton
Color button, checkBox On/Off.

colorLabel

JLabel colorLabel
Color label.

controlPanel

JPanel controlPanel
Control panel.

controlPanelBox

Box controlPanelBox
Control panel box that hold the control panel.

directionalRadio

JRadioButton directionalRadio
Directional light radio botton.

drawPanel

JPanel drawPanel
Scroll panel reference.

intensitySlider

JSlider intensitySlider
Intensity slider.

iSelect

int iSelect
index of currently selected one.

labelIntensity

JLabel labelIntensity
Light intensity label.

labelIntensityBegin

JLabel labelIntensityBegin
Light intensity label begin.

labelIntensityEnd

JLabel labelIntensityEnd
Light intensity label end.

labelIntensityMid

JLabel labelIntensityMid
Light intensity label middle.

list

JList list
List of lights.

m_aiLightScale

int[] m_aiLightScale
Light scale factor array.

m_akLights

WildMagic.LibGraphics.Rendering.Light[] m_akLights
The structure for the light bulbs.

m_kLabelPosX

JLabel m_kLabelPosX
Label for slider X position.

m_kLabelPosY

JLabel m_kLabelPosY
Label for slider Y position.

m_kLabelPosZ

JLabel m_kLabelPosZ
Label for slider Z position.

m_kLabelTrgX

JLabel m_kLabelTrgX
Label for X light target position.

m_kLabelTrgY

JLabel m_kLabelTrgY
Label for Y light target position.

m_kLabelTrgZ

JLabel m_kLabelTrgZ
Label for Z light target position.

m_kSliderPosX

JSlider m_kSliderPosX
Light x position slider.

m_kSliderPosY

JSlider m_kSliderPosY
Light y position slider.

m_kSliderPosZ

JSlider m_kSliderPosZ
Light z position slider.

m_kSliderTrgX

JSlider m_kSliderTrgX
Light x target position slider.

m_kSliderTrgY

JSlider m_kSliderTrgY
Light y target position slider.

m_kSliderTrgZ

JSlider m_kSliderTrgZ
Light z target position slider.

m_kTextPosX

JTextField m_kTextPosX
X position text field.

m_kTextPosY

JTextField m_kTextPosY
Y position text field.

m_kTextPosZ

JTextField m_kTextPosZ
Z position text field.

m_kTextTrgX

JTextField m_kTextTrgX
X target position text field.

m_kTextTrgY

JTextField m_kTextTrgY
Y target position text field.

m_kTextTrgZ

JTextField m_kTextTrgZ
Z target position text field.

onOffCheckBox

JCheckBox onOffCheckBox
Light turn on/off check box.

onOffLabel

JLabel onOffLabel
Light turn on/off label.

pointRadio

JRadioButton pointRadio
Point light radio button.

scroller

JScrollPane scroller
Scroll pane.

scrollPanel

JPanel scrollPanel
Scroll the control panel when the frame changes size.

spotRadio

JRadioButton spotRadio
Spot light radio button.

textIntensity

JTextField textIntensity
Light intensity textfield.

xBox

float xBox
x, y, z box size.

yBox

float yBox
x, y, z box size.

zBox

float zBox
x, y, z box size.

maxBox

float maxBox
x, y, z box size.

Class gov.nih.mipav.view.renderer.WildMagic.Interface.JPanelMultiHistogram extends JInterfaceBase implements Serializable

serialVersionUID: 926266253314679850L

Serialized Fields

colorButton

JButton colorButton
Color button for changing color.

scroller

JScrollPane scroller
The scroll pane holding the panel content. Useful when the screen is small.

scrollPanel

JInterfaceBase.DrawingPanel scrollPanel
Scroll panel that holding the all the control components.

m_kAnimator

com.sun.opengl.util.Animator m_kAnimator

m_kMultiHistogram

VolumeImageHistogram m_kMultiHistogram

Class gov.nih.mipav.view.renderer.WildMagic.Interface.JPanelRenderMode_WM extends JInterfaceBase implements Serializable

Serialized Fields

scroller

JScrollPane scroller
The scroll pane holding the panel content. Useful when the screen is small.

m_kDisplayVolumeCheck

JCheckBox m_kDisplayVolumeCheck
Turn display volume on/off

m_kDisplaySlicesCheck

JCheckBox m_kDisplaySlicesCheck
Turn display 3D Slices on/off

m_kDisplaySurfaceCheck

JCheckBox m_kDisplaySurfaceCheck
Turn display 3D TriMesh Surface on/off

m_kStereoCheck

JCheckBox m_kStereoCheck
Turn display 3D Stereo on/off

radioCOMPOSITE

JRadioButton radioCOMPOSITE
Radio button of the COMPOSITE mode option.

radioMIP

JRadioButton radioMIP
Radio button of the MIP mode option.

radioSURFACE

JRadioButton radioSURFACE
Radio button of the SURFACE mode option.

radioSURFACEFAST

JRadioButton radioSURFACEFAST
Radio button of the SURFACE mode option.

radioSurrenderCOMPOSITE

JRadioButton radioSurrenderCOMPOSITE
Radio button of the surface render composite mode.

radioXRAY

JRadioButton radioXRAY
Radio button of the XRAY mode option.

serif12

Font serif12
Fonts, same as MipavUtil.font12 and MipavUtil.font12B.

serif12B

Font serif12B
Fonts, same as MipavUtil.font12 and MipavUtil.font12B.

kSelfShadow

JCheckBox kSelfShadow

m_kVolumeBlendSlider

JSlider m_kVolumeBlendSlider
Volume alpha-blending slider.

m_kExtractTriMesh

JButton m_kExtractTriMesh
Button for extracting a TriMesh surface based on the ray-cast volume rendered in Surface mode

m_kIntensityTF

JTextField m_kIntensityTF
Text box for setting the intensity level for extraction.

Class gov.nih.mipav.view.renderer.WildMagic.Interface.JPanelSculptor_WM extends JInterfaceBase implements Serializable

serialVersionUID: 4235930260988710821L

Serialized Fields

m_iSculptHeight

int m_iSculptHeight
Window width information for Sculpting.

m_iSculptWidth

int m_iSculptWidth
Window width information for Sculpting.

lineButton

JToggleButton lineButton
Line shape button.

m_kApplySculptButton

JButton m_kApplySculptButton
Button to apply sculpt region to the volume.

m_kClearDrawOutlineButton

JButton m_kClearDrawOutlineButton
Button for clearing the sculpt region.

m_kDrawOutlineButton

JToggleButton m_kDrawOutlineButton
Toggle button is down while the mouse is used to draw the sculpt outline.

m_kInvertOutlineButton

JButton m_kInvertOutlineButton
Button for inverting the sculpt region.

m_kSaveSculptButton

JButton m_kSaveSculptButton
Button to save the sculpt image.

m_kUndoSculptButton

JButton m_kUndoSculptButton
Button to undo the sculpt and restor the original volume.

rectButton

JToggleButton rectButton
Rectangle shape button.

scroller

JScrollPane scroller
The scroll pane holding the panel content. Useful when the screen is small.

scrollPanel

JInterfaceBase.DrawingPanel scrollPanel
Scroll panel that holding the all the control components.

toolbarBuilder

ViewToolBarBuilder toolbarBuilder
Toolbar builder reference.

Class gov.nih.mipav.view.renderer.WildMagic.Interface.JPanelSlices_WM extends JInterfaceBase implements Serializable

serialVersionUID: -8359831093707979536L

Serialized Fields

boxX

JCheckBox boxX
Check boxes that turn the image plane on and off.

boxY

JCheckBox boxY
Check boxes that turn the image plane on and off.

boxZ

JCheckBox boxZ
Check boxes that turn the image plane on and off.

sliderX

JSlider sliderX
Sliders for the image planes.

sliderY

JSlider sliderY
Sliders for the image planes.

sliderZ

JSlider sliderZ
Sliders for the image planes.

sliderT

JSlider sliderT
Sliders for the image planes.

tSlice

int tSlice
Which time slice is currently displayed.

xSlice

int xSlice
Which slice is currently displayed in the ZY plane.

sliceVisible

boolean[] sliceVisible
Flags indicating if the image slices are on or off.

ySlice

int ySlice
Which slice is currently displayed in the XZ plane.

zSlice

int zSlice
Which slice is currently displayed in the XY plane.

boundingBoxPanel

JPanel boundingBoxPanel
Bounding box control panel.

boundingCheck

JCheckBox[] boundingCheck
Check box for turning bounding boxes on and off.

colorButton

JButton[] colorButton
Color button for changing bounding box color.

controlPanel

JPanel controlPanel
Main panel for sliders.

labelX

JLabel labelX
Labels next to sliders.

labelY

JLabel labelY
Labels next to sliders.

labelZ

JLabel labelZ
Labels next to sliders.

labelT

JLabel labelT
Labels next to sliders.

labelX1

JLabel labelX1
Labels beneath sliders.

labelXMid

JLabel labelXMid
Labels beneath sliders.

labelXEnd

JLabel labelXEnd
Labels beneath sliders.

labelY1

JLabel labelY1
Labels beneath sliders.

labelYMid

JLabel labelYMid
Labels beneath sliders.

labelYEnd

JLabel labelYEnd
Labels beneath sliders.

labelZ1

JLabel labelZ1
Labels beneath sliders.

labelZMid

JLabel labelZMid
Labels beneath sliders.

labelZEnd

JLabel labelZEnd
Labels beneath sliders.

opacityControlPanel

JPanel opacityControlPanel
Opacity control panel.

opacityLabelX

JLabel opacityLabelX
The opacity slider label.

opacityLabelY

JLabel opacityLabelY
The opacity slider label.

opacityLabelZ

JLabel opacityLabelZ
The opacity slider label.

opacitySliderLabelsX

JLabel[] opacitySliderLabelsX
The labels below the opacity slider.

opacitySliderLabelsY

JLabel[] opacitySliderLabelsY
The labels below the opacity slider.

opacitySliderLabelsZ

JLabel[] opacitySliderLabelsZ
The labels below the opacity slider.

opacitySliderX

JSlider opacitySliderX
Opacity slider, not enabled yet.

opacitySliderY

JSlider opacitySliderY
Opacity slider, not enabled yet.

opacitySliderZ

JSlider opacitySliderZ
Opacity slider, not enabled yet.

scroller

JScrollPane scroller
The scroll pane holding the panel content. Useful when the screen is small.

scrollPanel

JInterfaceBase.DrawingPanel scrollPanel
Scroll panel that holding the all the control components.

textX

JTextField textX
Text fields that display the slice number next to the sliders.

textY

JTextField textY
Text fields that display the slice number next to the sliders.

textZ

JTextField textZ
Text fields that display the slice number next to the sliders.

textT

JTextField textT
Text fields that display the slice number next to the sliders.

xDim

int xDim
x, y, z and time dimension values.

yDim

int yDim
x, y, z and time dimension values.

zDim

int zDim
x, y, z and time dimension values.

tDim

int tDim
x, y, z and time dimension values.

xOpacitySlice

int xOpacitySlice
x, y, z opacity slider values.

yOpacitySlice

int yOpacitySlice
x, y, z opacity slider values.

zOpacitySlice

int zOpacitySlice
x, y, z opacity slider values.

xProbe

int xProbe
Probe x, y, z position.

yProbe

int yProbe
Probe x, y, z position.

zProbe

int zProbe
Probe x, y, z position.

Class gov.nih.mipav.view.renderer.WildMagic.Interface.JPanelSurface_WM extends JInterfaceBase implements Serializable

serialVersionUID: -4600563188022683359L

Serialized Fields

areaLabel

JLabel areaLabel
The area label.

areaText

JTextField areaText
Displays the area of triangle.

colorButton

JButton colorButton
The color button, which calls a color chooser.

colorLabel

JLabel colorLabel
The color button label.

comboLabel

JLabel comboLabel
The polygon mode combo box label.

decimateButton

JButton decimateButton
Decimate button.

detailLabel

JLabel detailLabel
The level of detail slider label.

detailSlider

JSlider detailSlider
Level of detail slider.

detailSliderLabels

JLabel[] detailSliderLabels
The labels below the detail slider.

levelSButton

JButton levelSButton
Save surface button.

levelVButton

JButton levelVButton
Save surface button.

levelWButton

JButton levelWButton
Save surface button.

levelXMLButton

JButton levelXMLButton
Save surface button.

levelSTLButton

JButton levelSTLButton
Save surface button.

levelPLYButton

JButton levelPLYButton
Save surface button.

m_kSurfacePaint

SurfacePaint_WM m_kSurfacePaint
Paint tool-bar (contained in the SurfacePaint class)

m_kAdvancedMaterialOptionsButton

JButton m_kAdvancedMaterialOptionsButton
The material options button, which launches the material editor window.

m_kSurfaceTextureButton

JButton m_kSurfaceTextureButton
Opens SurfaceTexture dialog:.

opacityLabel

JLabel opacityLabel
The opacity slider label.

opacitySlider

JSlider opacitySlider
Opacity slider, not enabled yet.

opacitySliderLabels

JLabel[] opacitySliderLabels
The labels below the opacity slider.

polygonModeCB

JComboBox polygonModeCB
The combo box for the polygon mode to display.

scroller

JScrollPane scroller
The scroll pane holding the panel content. Useful when the screen is small.

smooth1Button

JButton smooth1Button
Smooth button.

smooth2Button

JButton smooth2Button
Smooth button.

smooth3Button

JButton smooth3Button
Smooth button.

polylineList

JList polylineList
Polyline list box in the dialog for surfaces.

surfaceList

JList surfaceList
The list box in the dialog for surfaces.

surfacePickableCB

JCheckBox surfacePickableCB
Check Box for surface picking.

surfaceBackFaceCB

JCheckBox surfaceBackFaceCB
Check Box for surface back face culling.

surfaceClipCB

JCheckBox surfaceClipCB
Check Box for surface clpping of the volume render.

surfaceTransparencyCB

JCheckBox surfaceTransparencyCB
Check Box for surface transparency.

triangleLabel

JLabel triangleLabel
The number of triangles label.

triangleText

JTextField triangleText
Displays the number of triangles.

volumeLabel

JLabel volumeLabel
The volume label.

volumeText

JTextField volumeText
Displays the volume of triangle.

m_kMeshes

Vector<E> m_kMeshes
List of TriMeshes

polylineCounterList

DefaultListModel polylineCounterList
Polyline counter list

polylineCounter

int polylineCounter
constant polyline counter

decimationPercentage

double decimationPercentage
Decimation Percentage

tmesh

TriangleMesh[] tmesh
triangle mesh for decimation.

Class gov.nih.mipav.view.renderer.WildMagic.Interface.JPanelSurfaceTexture_WM extends JInterfaceBase implements Serializable

serialVersionUID: 7562070328632922435L

Serialized Fields

mHistoLUT

JPanelHistoLUT mHistoLUT
Display the independent LUT for Black/White images.

mHistoRGB

JPanelHistoRGB mHistoRGB
Display the independent RGB for Color Images.

mImageA

ModelImage mImageA
ModelImage used to generate the 3D texture:.

mImageALink

ModelImage mImageALink
Reference to ModelImage A for linking the texture to the imageA LUT.

mImageAsTextureCheck

JCheckBox mImageAsTextureCheck
RadioButton for turing on the surface image texture:.

mImageDirName

String mImageDirName
Stores the currently-loaded ModelImage directory name:.

mImageFileName

String mImageFileName
Stores the currently-loaded ModelImage file name:.

mImageFileNameLabel

JLabel mImageFileNameLabel
Display the currently-loaded ModelImage file name:.

mLoadImageButton

JButton mLoadImageButton
Load a new ModelImage:.

mModelImageRadioButton

JRadioButton mModelImageRadioButton
Use the ModelImage LUT.

mNewImageRadioButton

JRadioButton mNewImageRadioButton
Use a separate LUT.

mImageButtonGroup

ButtonGroup mImageButtonGroup
Grouping the radio buttons:.

mLUTImageA

ModelImage mLUTImageA
Independent ModelImage for independent LUT.

mLUTModel

ModelLUT mLUTModel
The LUT associated with the ModelImage imageA:.

mLUTSeparate

ModelLUT mLUTSeparate
The LUT associated with the independent texture LUT:.

mModelLUTRadioButton

JRadioButton mModelLUTRadioButton
Use the ModelImage LUT.

mNewLUTRadioButton

JRadioButton mNewLUTRadioButton
Use a separate LUT.

mLUTButtonGroup

ButtonGroup mLUTButtonGroup
Grouping the radio buttons:.

mRGBModel

ModelRGB mRGBModel
The RGB LUT associated with the ModelImage imageA:.

mRGBSeparate

ModelRGB mRGBSeparate
The RGB LUT associated with the independent texture LUT:.

m_kSurfacePanel

JPanelSurface_WM m_kSurfacePanel
Surface panel

Class gov.nih.mipav.view.renderer.WildMagic.Interface.SurfacePaint_WM extends JInterfaceBase implements Serializable

serialVersionUID: -3767599197318881261L

Serialized Fields

m_bEnabled

boolean m_bEnabled
Enables painting

mPaintToolBar

JToolBar mPaintToolBar
Paint user-interface ToolBar

mButtonGroup

ButtonGroup mButtonGroup
Button group for paint functions:

mPaintBrushButton

JToggleButton mPaintBrushButton
Paint brush button

mDropperButton

JToggleButton mDropperButton
Paint dropper button

mPaintCanButton

JToggleButton mPaintCanButton
Paint can button

mEraserButton

JToggleButton mEraserButton
Eraser paint button

mEraseAllButton

JButton mEraseAllButton
Erase all button

mBrushSizeText

JTextField mBrushSizeText
Paint brush size text field

mBrushSize

int mBrushSize
current paint brush size

mColorPaintButton

JButton mColorPaintButton
Color selection button

mPaintColor

WildMagic.LibFoundation.Mathematics.ColorRGBA mPaintColor
Current paint color

mOpacityPaintButton

JButton mOpacityPaintButton
Opacity paint button

mOpacity

float mOpacity
Current paint opacity

mColorChooser

JColorChooser mColorChooser
Color Chooser dialog.

mPaintGrowDialog

JDialogPaintGrow mPaintGrowDialog
Paint Grow Dialog.

m_kPanel

JPanelSurface_WM m_kPanel
Surface panel.

Package gov.nih.mipav.view.srb

Class gov.nih.mipav.view.srb.JargonFileChooser extends JComponent implements Serializable

serialVersionUID: 3089967755976324109L

Serialized Fields

approveButton

JButton approveButton
DOCUMENT ME!

approveButtonMnemonic

int approveButtonMnemonic
DOCUMENT ME!

approveButtonText

String approveButtonText
DOCUMENT ME!

approveButtonToolTipText

String approveButtonToolTipText
DOCUMENT ME!

defaultApproveButtonText

String defaultApproveButtonText
DOCUMENT ME!

dialog

JDialog dialog
DOCUMENT ME!

dialogTitle

String dialogTitle
DOCUMENT ME!

fileSelectionMode

int fileSelectionMode
DOCUMENT ME!

fileSystem

edu.sdsc.grid.io.srb.SRBFileSystem fileSystem
DOCUMENT ME!

jsrbTree

JSRBTree jsrbTree
DOCUMENT ME!

multiSelectionEnabled

boolean multiSelectionEnabled
DOCUMENT ME!

newFoldButton

JButton newFoldButton
DOCUMENT ME!

newFoldButtonMnemonic

int newFoldButtonMnemonic
DOCUMENT ME!

returnValue

int returnValue
DOCUMENT ME!

selectedFile

edu.sdsc.grid.io.srb.SRBFile selectedFile
The selected file.

selectedFileField

JTextField selectedFileField
DOCUMENT ME!

selectedFiles

edu.sdsc.grid.io.srb.SRBFile[] selectedFiles
The selected files(multi file selection is enabled).

srbConnectionTimeoutMonitor

TimeoutThread srbConnectionTimeoutMonitor
A thread which closes the srb connection if the user does not do anything for over 30 minutes (srb seems to have a shorter timeout anyway...).

title

String title
DOCUMENT ME!

Class gov.nih.mipav.view.srb.JDialogLoginSRB extends JDialog implements Serializable

serialVersionUID: 2797550808781412556L

Serialized Fields

authenticationComboBox

JComboBox authenticationComboBox
DOCUMENT ME!

authenticationLabel

JLabel authenticationLabel
the authentication schema that the srb server uses.

cancelButton

JButton cancelButton
DOCUMENT ME!

helpButton

JButton helpButton
DOCUMENT ME!

COLUMN_COUNT

int COLUMN_COUNT
DOCUMENT ME!

connectButton

JButton connectButton
DOCUMENT ME!

domainField

JTextField domainField
DOCUMENT ME!

domainLabel

JLabel domainLabel
domain name of the server.

hostField

JTextField hostField
DOCUMENT ME!

hostLabel

JLabel hostLabel
host name of the srb server.

nameField

JTextField nameField
DOCUMENT ME!

nameLabel

JLabel nameLabel
user name.

passwordField

JPasswordField passwordField
DOCUMENT ME!

passwordLabel

JLabel passwordLabel
the password that the user uses to login the server.

portField

JTextField portField
DOCUMENT ME!

portLabel

JLabel portLabel
the port number that the srb server listens.

srbLoginFailureCount

int srbLoginFailureCount
Keep track of the number of login failures to limit password guessing.

storageResourceField

JTextField storageResourceField
DOCUMENT ME!

storageResourceLabel

JLabel storageResourceLabel
The default storage resource that the user uses.

showPrivacyNotice

boolean showPrivacyNotice
Whether to show the NDAR Privacy notice after successful connection

Class gov.nih.mipav.view.srb.JDialogSetupPipeline extends JDialog implements Serializable

Serialized Fields

scriptFileNameLabel

JLabel scriptFileNameLabel
the authentication schema that the srb server uses.

scriptFileNameField

JTextField scriptFileNameField

scriptFileNameBrowseButton

JButton scriptFileNameBrowseButton

targetSRBDirField

JTextField targetSRBDirField
DOCUMENT ME!

targetSRBDirLabel

JLabel targetSRBDirLabel
the target srb directory

targetSRBDirBrowseButton

JButton targetSRBDirBrowseButton

okButton

JButton okButton
DOCUMENT ME!

cancelButton

JButton cancelButton
DOCUMENT ME!

helpButton

JButton helpButton
DOCUMENT ME!

COLUMN_COUNT

int COLUMN_COUNT
DOCUMENT ME!

cancelled

boolean cancelled

Class gov.nih.mipav.view.srb.JSRBTree extends JTree implements Serializable

serialVersionUID: 6486109552343342133L

Serialized Fields

conditions

edu.sdsc.grid.io.MetaDataCondition[] conditions
Only display files matching these conditions.

copyBuffer

edu.sdsc.grid.io.GeneralFile copyBuffer
Stores a selected abstract filepath. Presumably to be pasted somewhere else on the tree.

popup

JPopupMenu popup
The popupmenu.

See Also:
useDefaultPopupMenu( boolean )

popupListener

MouseListener popupListener
Watches for popup mouse click.

See Also:
useDefaultPopupMenu( boolean )

roots

edu.sdsc.grid.io.GeneralFile[] roots
The roots of the JTree, can have more then one root.

selects

edu.sdsc.grid.io.MetaDataSelect[] selects
Files will display these metadata values inline in the tree.

Class gov.nih.mipav.view.srb.SRBTreeCellRenderer extends JLabel implements Serializable

serialVersionUID: -8881545568255157801L

Serialized Fields

backgroundNonSelectionColor

Color backgroundNonSelectionColor
Color to use for the background when the node isn't selected.

backgroundSelectionColor

Color backgroundSelectionColor
Color to use for the background when a node is selected.

borderSelectionColor

Color borderSelectionColor
Color to use for the focus indicator when the node has focus.

hasFocus

boolean hasFocus
True if has focus.

selected

boolean selected
Is the value currently selected.

textNonSelectionColor

Color textNonSelectionColor
Color to use for the foreground for non-selected nodes.

textSelectionColor

Color textSelectionColor
Color to use for the foreground for selected nodes.

drawDashedFocusIndicator

boolean drawDashedFocusIndicator
If true, a dashed line is drawn as the focus indicator.

drawsFocusBorderAroundIcon

boolean drawsFocusBorderAroundIcon
True if draws focus border around icon as well.

focusBGColor

Color focusBGColor
Color to draw the focus indicator in, determined from the background. color.

tree

JTree tree
Last tree the renderer was painted in.

treeBGColor

Color treeBGColor
Background color of the tree.

Package gov.nih.mipav.view.xcede

Class gov.nih.mipav.view.xcede.JXCEDEExplorer extends JFrame implements Serializable

serialVersionUID: 205018093506676689L

Serialized Fields

document

Document document
DOCUMENT ME!

inforPane

JEditorPane inforPane
DOCUMENT ME!

leftScrollPane

JScrollPane leftScrollPane
DOCUMENT ME!

rightScrollPane

JScrollPane rightScrollPane
DOCUMENT ME!

splitPane

JSplitPane splitPane
DOCUMENT ME!

tree

JXCEDETree tree
DOCUMENT ME!

treeModel

XCEDEDOMToTreeModelAdapter treeModel
DOCUMENT ME!

userInterface

ViewUserInterface userInterface
DOCUMENT ME!

Class gov.nih.mipav.view.xcede.JXCEDETree extends JTree implements Serializable

Serialized Fields

popupMenu

JPopupMenu popupMenu

popupListener

MouseListener popupListener

Class gov.nih.mipav.view.xcede.JXCEDETreeCellRenderer extends DefaultTreeCellRenderer implements Serializable

Class gov.nih.mipav.view.xcede.MultiLineTableCellRenderer extends JTextArea implements Serializable

Serialized Fields

unselectedForeground

Color unselectedForeground

unselectedBackground

Color unselectedBackground

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