ModelImage (MIPAV API Documentation)

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gov.nih.mipav.model.structures
Class ModelImage

java.lang.Object
  gov.nih.mipav.model.structures.ModelSerialCloneable
      gov.nih.mipav.model.structures.ModelStorageBase
          gov.nih.mipav.model.structures.ModelImage

All Implemented Interfaces:: Serializable, Cloneable

public class ModelImage
extends ModelStorageBase
extends ModelStorageBase

This class extends the generic buffer class ModelStorageArray and is used to store n-dimensional images and buffer class that supports boolean, byte, short, int, long, float, double, etc. data types. After the buffer is created the minimum and maximum parameters are calculated. ModelImage is a specific buffer to addressing issues relating to images.

Version:: 1.0
Author:: Matthew J. McAuliffe Ph.D.
See Also:: Serialized Form

Field Summary
`static int`	`IMAGE_A` Used to indicate that this image object is Image A when two images are displayed in the same frame.
`static int`	`IMAGE_B` Used to indicate that this image object is Image B when two images are displayed in the same frame.

Fields inherited from class gov.nih.mipav.model.structures.ModelStorageBase
`ARGB, ARGB_FLOAT, ARGB_FLOAT_STRING, ARGB_STRING, ARGB_USHORT, ARGB_USHORT_STRING, BOOLEAN, BOOLEAN_STRING, bufferTypeStr, BYTE, BYTE_STRING, COMPLEX, COMPLEX_STRING, DCOMPLEX, DCOMPLEX_STRING, DOUBLE, DOUBLE_STRING, fileInfo, FLOAT, FLOAT_STRING, INTEGER, INTEGER_STRING, lastMax, lastMin, LINEAR, LONG, LONG_STRING, NEAREST, projectInfo, RW_LOCKED, SHORT, SHORT_STRING, TAYLOR, UBYTE, UBYTE_STRING, UINTEGER, UINTEGER_STRING, UNLOCKED, USHORT, USHORT_STRING, W_LOCKED`

Fields inherited from class gov.nih.mipav.model.structures.ModelStorageBase

ARGB, ARGB_FLOAT, ARGB_FLOAT_STRING, ARGB_STRING, ARGB_USHORT, ARGB_USHORT_STRING, BOOLEAN, BOOLEAN_STRING, bufferTypeStr, BYTE, BYTE_STRING, COMPLEX, COMPLEX_STRING, DCOMPLEX, DCOMPLEX_STRING, DOUBLE, DOUBLE_STRING, fileInfo, FLOAT, FLOAT_STRING, INTEGER, INTEGER_STRING, lastMax, lastMin, LINEAR, LONG, LONG_STRING, NEAREST, projectInfo, RW_LOCKED, SHORT, SHORT_STRING, TAYLOR, UBYTE, UBYTE_STRING, UINTEGER, UINTEGER_STRING, UNLOCKED, USHORT, USHORT_STRING, W_LOCKED

Constructor Summary
`ModelImage(int type, int[] dimExtents, String name)` Creates a new ModelImage object.
`ModelImage(int type, int[] dimExtents, String name, ViewUserInterface _UI)` Deprecated. DOCUMENT ME!

Method Summary
`void`	`addImageDisplayListener(ViewImageUpdateInterface obj)` Add a listener to this class so that notifyListener can be used to notify all listeners to update the display of the image.
`void`	`addVOIs(VOIVector VOIs)` adds VOI vector for with new VOIs.
`void`	`anonymize(boolean[] list, boolean doRename)` Anonymize the image by altering the sensitive data of each slice to something generic.
`void`	`calcMinMax()` Calculates the min and max values for the image array.
`void`	`changeExtents(int[] dimExtents)` Changes the image dimensionality or extents.
`void`	`clearMask()` Sets the entire mask object to false.
`Object`	`clone()` Copies the image and all data associated with the image (i.e.
`Object`	`clone(String newName)` Copies the image and all data associated with the image (i.e.
`void`	`copyFileTypeInfo(ModelImage fromImage)` Deep copies the file type info from the fromImage to the current image object.
`void`	`createMask(int length)` Creates mask and maskBU of new length.
`void`	`displayAboutInfo(JDialogBase dialog, int z, int t, boolean dicom, boolean xml)` Displays all information about an image.
`void`	`disposeLocal()` Unregisters image and disposes of image memory and associated objects.
`void`	`disposeLocal(boolean garbageCollect)` Unregisters image and disposes of image memory and associated objects.
`protected void`	`finalize()` Calls disposeLocal of this class to ensure this class nulls the references to global class variables so that memory will be recovered.
`ModelImage`	`generateBinaryImage()` Forms a solid (without holes) binary image from all VOIs in the image.
`ModelImage`	`generateBinaryImage(boolean XOR, boolean onlyActive)` Forms a binary image from VOIs.
`ModelImage`	`generateShortImage(int offset)` Generates a solid (no holes) short image of regions defined by VOIs.
`ModelImage`	`generateShortImage(int offset, boolean XOR, boolean onlyActive)` Exports a short mask of the VOI[index].
`ModelImage`	`generateUnsignedByteImage(int offset)` Generates a solid (no holes) unsigned byte image of regions defined by VOIs.
`ModelImage`	`generateUnsignedByteImage(int offset, boolean XOR, boolean onlyActive)` Exports an unsigned byte mask of the VOI[index].
`BitSet`	`generateVOIMask()` Generates a BitSet mask of all the VOIs and sets ImageModel mask.
`BitSet`	`generateVOIMask(boolean XOR)` Generates a BitSet mask of all the VOIs and sets ImageModel mask.
`BitSet`	`generateVOIMask(boolean XOR, boolean onlyActive)` Generates a BitSet mask of all the VOIs and sets ImageModel mask.
`short[]`	`generateVOIMask(short[] mask, int index)` Generates a mask of the type short - without XORing VOI contours.
`short[]`	`generateVOIMask(short[] mask, int index, boolean XOR)` Exports a short mask of the VOI[index].
`ViewJFrameAnimate`	`getAnimateFrame()` Method that returns the animate frame if it exists else returns null.
`ViewJFrameHistoLUT`	`getHistoLUTFrame()` Method that returns the HistoLUT frame if it exists else returns null.
`ViewJFrameHistoRGB`	`getHistoRGBFrame()` Method that returns the HistoRGB frame if it exists else returns null.
`WildMagic.LibFoundation.Mathematics.Vector3f`	`getImageCenter()` Calculates translation offset for transforming image about the center of the image.
`WildMagic.LibFoundation.Mathematics.Vector3f`	`getImageCentermm(boolean useScanner)` Calculates translation offset for transforming image about the center of the image in the resolution space.
`String`	`getImageDirectory()` Returns the directory where the image file is located.
`String`	`getImageFileName()` Returns the file name of the image.
`Vector<ViewImageUpdateInterface>`	`getImageFrameVector()` Accessor that returns.
`int`	`getImageModality()` Returns the type of image.
`String`	`getImageName()` Accessor that returns the name of the image.
`int`	`getImageOrder()` For multiple image viewers this indicates order of the image.
`ViewJFrameLightBox`	`getLightBoxFrame()` Method that returns the lightbox frame if it exists else returns null.
`BitSet`	`getMask()` Accessor that returns.
`BitSet`	`getMaskBU()` Accessor that returns.
`TransMatrix`	`getMatrix()` Accessor that returns transformation matrix.
`MatrixHolder`	`getMatrixHolder()` DOCUMENT ME!
`int`	`getPackedColor(int iIndex)` If no LUT or RGB color table is defined, this returns the packed int value for the color at iIndexs for the input ModelImage kImage:
`ViewJFrameImage`	`getParentFrame()` Returns the parent frame of this image.
`float[]`	`getPlane(WildMagic.LibFoundation.Mathematics.Vector3f topLeft, WildMagic.LibFoundation.Mathematics.Vector3f topRight, WildMagic.LibFoundation.Mathematics.Vector3f botLeft, WildMagic.LibFoundation.Mathematics.Vector3f botRight)` Extract an arbitrary slice plane from the image using tri-linear interpolation.
`ProvenanceHolder`	`getProvenanceHolder()`
`ViewJFrameRegistration`	`getRegistrationFrame()` Method that returns the registration frame if it exists else returns null.
`void`	`getScannerCoordLPS(int x, int y, int z, float[] scannerCoord)` Takes input x,y,z coordinate and returns that point transformed into the scanner's (DICOM) coordinate system.
`void`	`getScannerCoordRAS(int x, int y, int z, float[] scannerCoord)` Takes input x,y,z coordinate and returns that point transformed into the RAS coordinate system.
`TalairachTransformInfo`	`getTalairachTransformInfo()` Accessor that returns the talairach transform information.
`ViewJFrameTriImage`	`getTriImageFrame()` Method that returns the tri image frame if it exists else returns null.
`ViewUserInterface`	`getUserInterface()` Deprecated. DOCUMENT ME!
`VOIVector`	`getVOIs()` Accessor that returns.
`void`	`groupVOIs()` Forms a single VOI structure from all the VOIs presently loaded in the imageModel.
`void`	`groupVOIs(ViewVOIVector newVOIVector, int[] where, String name)` Forms a single VOI structure from all the VOIs presently loaded in the imageModel.
`boolean`	`is2DImage()`
`boolean`	`is3DImage()`
`boolean`	`isColorImage()` Accessor that returns whether or not the image is a color image.
`static boolean`	`isColorImage(int dataType)` Accessor that returns whether or not the given data type is a color data type.
`boolean`	`isComplexImage()` Accessor that returns whether or not the image is a COMPLEX or DCOMPLEX image.
`boolean`	`isDicomImage()` Accessor that returns whether or not the image is a DICOM image.
`boolean`	`isMincImage()` Accessor that returns whether or not the image is a MINC image.
`void`	`make2UnitsOfMeasureIdentical(int newUnitDim, int oldUnitDim)`
`void`	`makeUnitsOfMeasureIdentical()` Make all spatial units the same, all time units the same, and all frequency units the same
`void`	`notifyImageDisplayListeners_notTriFrame()` Used to notify all frames except the triImage frames that display this image model need to be updated.
`void`	`notifyImageDisplayListeners()` Used to notify all frames that display this image model need to be updated.
`void`	`notifyImageDisplayListeners(boolean forceShow, int alphaBlend, ModelRGB RGBT)` Used to notify all frames that display this image model need to be updated for RGB (color) images.
`void`	`notifyImageDisplayListeners(ModelLUT LUT, boolean forceShow)` Used to notify all frames that display this image model need to be updated.
`void`	`notifyImageDisplayListeners(ModelLUT LUT, boolean forceShow, int alphaBlend, int interpMode)` Used to notify all listeners that the image is to be redisplayed.
`void`	`notifyImageExtentsListeners()` Used to notify all frames that display this image model that this image's extents have changed.
`void`	`print()` Prints basic image parameters to the System.out.
`TransMatrix`	`readTransformMatrix(boolean composite)` Read matrix from a file.
`void`	`reallocate(int type)` Reallocates ModelImage with new type and all image data lost.
`void`	`registerVOI(VOI voi)` Method that register an VOI to this image.
`void`	`removeImageDisplayListener(ViewImageUpdateInterface obj)` Remove a listener from the class.
`void`	`resetVOIs()` Resets VOI vector for new VOIs.
`static void`	`saveImage(ModelImage kImage)` Save the gradient magnitude image into the MIPAV default dir.
`boolean`	`saveImage(String directory, String fileName, int fileType, boolean isActive)` Save the image to a file.
`void`	`saveTransformMatrix(String fileName, TransMatrix matrix)` Save the images transformation matrix in the working directory with the supplied fileName.
`void`	`saveTransformMatrix(TransMatrix matrix)` Saves the transformation matrix to file.
`void`	`setExtents(int[] dims)` Sets the dimExtents for this structure.
`void`	`setImageDirectory(String dir)` Sets the image directory.
`void`	`setImageModality(int type)` Sets the image type (MRI, CT, ...).
`void`	`setImageName(String name)` Accessor that sets the name of the image.
`void`	`setImageName(String name, boolean updateFileName)` Accessor that sets the name of the image.
`void`	`setImageNamePrivate(String name)` Accessor that sets the name of the image.
`void`	`setImageOrder(int order)` For multiple image viewers this indicates order of the image.
`void`	`setImageOrientation(int orient)` Sets the image orientation (sagittal, axial, ...).
`void`	`setMask(BitSet _mask)` Sets the mask which indicate which pixels/voxels to process.
`void`	`setMaskBU(BitSet mask)` Sets the mask which indicate which pixels/voxels to process.
`void`	`setMatrix(TransMatrix matrix)` Accessor that adds a matrix to the matrix holder.
`void`	`setSlice(int slice)` Sets the slice in all frames displaying this image.
`void`	`setTalairachTransformInfo(TalairachTransformInfo tal)` Accessor that sets the talairach transform information.
`void`	`setTimeSlice(int tSlice)` Sets the time slice in all frames displaying this image.
`void`	`setUserInterface(ViewUserInterface _UI)` Sets user interface.
`void`	`setVOIs(VOIVector VOIs)` Sets VOI vector for with new VOIs.
`String`	`toString()` Gives a readable representation of the ModelImage, including file name and extents.
`void`	`ungroupVOIs()` Forms separate VOIs from all the VOI structures presently loaded in the imageModel.
`void`	`unregisterAllVOIs()` Unregisters all VOIs from this image model.
`void`	`unRegisterImage()` Unregisters the image from the user interface.
`void`	`unregisterVOI(VOI voi)` Method that unregisters an VOI.
`void`	`updateFileName(String newImageName)` Give the image a new image name, updates frame (if not null), and file infos.
`void`	`updateImageOrigin(TransMatrix xfrm)` Updates the images origin.

Methods inherited from class gov.nih.mipav.model.structures.ModelStorageBase
addSurfaceMask, allocateData, calcAvgIntenStdDev, calcMinMaxMag, calcMinMaxNonZero, computeDataSize, construct, convertToFloat, export, export, exportComplexData, exportComplexSliceXY, exportData, exportData, exportData, exportData, exportData, exportData, exportData, exportData, exportData, exportData, exportDataNoLock, exportDataNoLock, exportDataNoLock, exportDataNoLock, exportDataNoLock, exportDataNoLock, exportDataNoLock, exportDataNoLock, exportDComplexData, exportDiagonal, exportDMagData, exportMagData, exportRGBData, exportRGBData, exportRGBData, exportRGBData, exportRGBDataNoLock, exportSliceXY, exportSliceXY, exportSliceXY, exportSliceXY, exportSliceXY, exportSliceXY, get, get, get, get, get, getAvgInten, getAvgIntenB, getAvgIntenG, getAvgIntenR, getAxisOrientation, getBiLinear, getBoolean, getBoolean, getBoolean, getBoolean, getBoolean, getBufferTypeStr, getByte, getByte, getByte, getByte, getByte, getByteBiLinear, getByteTriLinear, getC, getConvolve, getDouble, getDouble, getDouble, getDouble, getDouble, getDoubleBiLinear, getDoubleTriLinear, getExtents, getExtents, getFileInfo, getFileInfo, getFilterType, getFloat, getFloat, getFloat, getFloat, getFloat, getFloatBiLinear, getFloatC, getFloatC, getFloatC, getFloatTriLinear, getFloatTriLinearBounds, getFloatTriLinearBounds, getFreq1, getFreq2, getFreqU, getFreqV, getHaveWindowed, getHeight, getImage25D, getImageOrientation, getInt, getInt, getInt, getInt, getInt, getIntBiLinear, getIntTriLinear, getLockStatus, getLogMagDisplay, getLong, getLong, getLong, getLong, getLong, getLongBiLinear, getLongTriLinear, getMax, getMaxB, getMaxG, getMaxR, getMin, getMinB, getMinG, getMinR, getNDims, getNoLogMax, getNoLogMin, getNoLogMinNonZero, getNonZeroMax, getNonZeroMaxB, getNonZeroMaxG, getNonZeroMaxR, getNonZeroMin, getNonZeroMinB, getNonZeroMinG, getNonZeroMinR, getNumPixels, getOrigin, getOrigin, getOriginalButterworthOrder, getOriginalCropCheckbox, getOriginalDoCrop, getOriginalEnd, getOriginalExtents, getOriginalFilterConstruction, getOriginalKernelDimension, getOriginalMaximum, getOriginalMinimum, getOriginalStart, getProjectInfo, getRadiologicalView, getResolutions, getResolutions, getShort, getShort, getShort, getShort, getShort, getShortBiLinear, getShortTriLinear, getSigmaU, getSigmaV, getSize, getSliceSize, getSmallestMagnitudeNegative, getSmallestMagnitudeNegativeB, getSmallestMagnitudeNegativeG, getSmallestMagnitudeNegativeR, getSmallestMagnitudePositive, getSmallestMagnitudePositiveB, getSmallestMagnitudePositiveG, getSmallestMagnitudePositiveR, getStdDeviation, getStdDeviationB, getStdDeviationG, getStdDeviationR, getSumPixelInten, getSumPixelIntenB, getSumPixelIntenG, getSumPixelIntenR, getSurfaceMask, getSurfaceMaskColor, getTheta, getTriLinear, getType, getTypeMax, getTypeMin, getTypeString, getUByte, getUByte, getUByte, getUByte, getUByteBiLinear, getUByteTriLinear, getUInt, getUInt, getUInt, getUInt, getUInt, getUIntBiLinear, getUIntTriLinear, getUnequalDim, getUnitsOfMeasure, getUnitsOfMeasure, getUnitsOfMeasure, getUShort, getUShort, getUShort, getUShort, getUShort, getUShortBiLinear, getUShortTriLinear, getVolumeIterationFactors, getWidth, importComplexData, importData, importData, importData, importData, importData, importData, importData, importData, importData, importDComplexData, importRGBData, importUData, importUData, importUData, reallocate, reallocate, recomputeDataSize, releaseLock, removeSurfaceMask, removeSurfaceMasks, restoreSurfaceMasks, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, setAll, setAll, setAll, setAll, setAll, setAllUByte, setAllUShort, setC, setC, setC, setC, setC, setConvolve, setFileInfo, setFileInfo, setFilterType, setFreq1, setFreq2, setFreqU, setFreqV, setHaveWindowed, setImage25D, setLock, setLock, setLogMagDisplay, setMax, setMin, setOriginalButterworthOrder, setOriginalCropCheckbox, setOriginalDoCrop, setOriginalEnd, setOriginalExtents, setOriginalFilterConstruction, setOriginalKernelDimension, setOriginalMaximum, setOriginalMinimum, setOriginalStart, setProjectInfo, setRadiologicalView, setResolutions, setShort, setShort, setSigmaU, setSigmaV, setTheta, setType, setUByte, setUByte, setUByte, setUByte, setUByte, setUInt, setUInt, setUInt, setUInt, setUInt, setUnequalDim, setUShort, setUShort, setUShort, setUShort, setUShort

Methods inherited from class gov.nih.mipav.model.structures.ModelStorageBase

addSurfaceMask, allocateData, calcAvgIntenStdDev, calcMinMaxMag, calcMinMaxNonZero, computeDataSize, construct, convertToFloat, export, export, exportComplexData, exportComplexSliceXY, exportData, exportData, exportData, exportData, exportData, exportData, exportData, exportData, exportData, exportData, exportDataNoLock, exportDataNoLock, exportDataNoLock, exportDataNoLock, exportDataNoLock, exportDataNoLock, exportDataNoLock, exportDataNoLock, exportDComplexData, exportDiagonal, exportDMagData, exportMagData, exportRGBData, exportRGBData, exportRGBData, exportRGBData, exportRGBDataNoLock, exportSliceXY, exportSliceXY, exportSliceXY, exportSliceXY, exportSliceXY, exportSliceXY, get, get, get, get, get, getAvgInten, getAvgIntenB, getAvgIntenG, getAvgIntenR, getAxisOrientation, getBiLinear, getBoolean, getBoolean, getBoolean, getBoolean, getBoolean, getBufferTypeStr, getByte, getByte, getByte, getByte, getByte, getByteBiLinear, getByteTriLinear, getC, getConvolve, getDouble, getDouble, getDouble, getDouble, getDouble, getDoubleBiLinear, getDoubleTriLinear, getExtents, getExtents, getFileInfo, getFileInfo, getFilterType, getFloat, getFloat, getFloat, getFloat, getFloat, getFloatBiLinear, getFloatC, getFloatC, getFloatC, getFloatTriLinear, getFloatTriLinearBounds, getFloatTriLinearBounds, getFreq1, getFreq2, getFreqU, getFreqV, getHaveWindowed, getHeight, getImage25D, getImageOrientation, getInt, getInt, getInt, getInt, getInt, getIntBiLinear, getIntTriLinear, getLockStatus, getLogMagDisplay, getLong, getLong, getLong, getLong, getLong, getLongBiLinear, getLongTriLinear, getMax, getMaxB, getMaxG, getMaxR, getMin, getMinB, getMinG, getMinR, getNDims, getNoLogMax, getNoLogMin, getNoLogMinNonZero, getNonZeroMax, getNonZeroMaxB, getNonZeroMaxG, getNonZeroMaxR, getNonZeroMin, getNonZeroMinB, getNonZeroMinG, getNonZeroMinR, getNumPixels, getOrigin, getOrigin, getOriginalButterworthOrder, getOriginalCropCheckbox, getOriginalDoCrop, getOriginalEnd, getOriginalExtents, getOriginalFilterConstruction, getOriginalKernelDimension, getOriginalMaximum, getOriginalMinimum, getOriginalStart, getProjectInfo, getRadiologicalView, getResolutions, getResolutions, getShort, getShort, getShort, getShort, getShort, getShortBiLinear, getShortTriLinear, getSigmaU, getSigmaV, getSize, getSliceSize, getSmallestMagnitudeNegative, getSmallestMagnitudeNegativeB, getSmallestMagnitudeNegativeG, getSmallestMagnitudeNegativeR, getSmallestMagnitudePositive, getSmallestMagnitudePositiveB, getSmallestMagnitudePositiveG, getSmallestMagnitudePositiveR, getStdDeviation, getStdDeviationB, getStdDeviationG, getStdDeviationR, getSumPixelInten, getSumPixelIntenB, getSumPixelIntenG, getSumPixelIntenR, getSurfaceMask, getSurfaceMaskColor, getTheta, getTriLinear, getType, getTypeMax, getTypeMin, getTypeString, getUByte, getUByte, getUByte, getUByte, getUByteBiLinear, getUByteTriLinear, getUInt, getUInt, getUInt, getUInt, getUInt, getUIntBiLinear, getUIntTriLinear, getUnequalDim, getUnitsOfMeasure, getUnitsOfMeasure, getUnitsOfMeasure, getUShort, getUShort, getUShort, getUShort, getUShort, getUShortBiLinear, getUShortTriLinear, getVolumeIterationFactors, getWidth, importComplexData, importData, importData, importData, importData, importData, importData, importData, importData, importData, importDComplexData, importRGBData, importUData, importUData, importUData, reallocate, reallocate, recomputeDataSize, releaseLock, removeSurfaceMask, removeSurfaceMasks, restoreSurfaceMasks, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, set, setAll, setAll, setAll, setAll, setAll, setAllUByte, setAllUShort, setC, setC, setC, setC, setC, setConvolve, setFileInfo, setFileInfo, setFilterType, setFreq1, setFreq2, setFreqU, setFreqV, setHaveWindowed, setImage25D, setLock, setLock, setLogMagDisplay, setMax, setMin, setOriginalButterworthOrder, setOriginalCropCheckbox, setOriginalDoCrop, setOriginalEnd, setOriginalExtents, setOriginalFilterConstruction, setOriginalKernelDimension, setOriginalMaximum, setOriginalMinimum, setOriginalStart, setProjectInfo, setRadiologicalView, setResolutions, setShort, setShort, setSigmaU, setSigmaV, setTheta, setType, setUByte, setUByte, setUByte, setUByte, setUByte, setUInt, setUInt, setUInt, setUInt, setUInt, setUnequalDim, setUShort, setUShort, setUShort, setUShort, setUShort

Methods inherited from class java.lang.Object
`equals, getClass, hashCode, notify, notifyAll, wait, wait, wait`

Field Detail

IMAGE_A

public static final int IMAGE_A

Used to indicate that this image object is Image A when two images are displayed in the same frame. See also imageOrder in this class.

See Also:: Constant Field Values

IMAGE_B

public static final int IMAGE_B

Used to indicate that this image object is Image B when two images are displayed in the same frame. See also imageOrder in this class.

See Also:: Constant Field Values

Constructor Detail

ModelImage

public ModelImage(int type,
                  int[] dimExtents,
                  String name)

Creates a new ModelImage object.

Parameters:: type - indicates type of buffer(ie. boolean, byte ...); dimExtents - array indicating image extent in each dimension.; name - name of the image.

ModelImage

public ModelImage(int type,
                  int[] dimExtents,
                  String name,
                  ViewUserInterface _UI)

Deprecated. DOCUMENT ME!

Creates a new ModelImage object.

Parameters:: type - indicates type of buffer(ie. boolean, byte ...); dimExtents - DOCUMENT ME!; name - DOCUMENT ME!; _UI - DOCUMENT ME!

Method Detail

isColorImage

public static boolean isColorImage(int dataType)

Accessor that returns whether or not the given data type is a color data type.

Parameters:: dataType - The data type from a ModelImage to determine if it is of one of the three types of color images supported.
Returns:: true if color, false if not color.

addImageDisplayListener

public void addImageDisplayListener(ViewImageUpdateInterface obj)

Add a listener to this class so that notifyListener can be used to notify all listeners to update the display of the image.

Parameters:: obj - "object' to be added to the list

addVOIs

public void addVOIs(VOIVector VOIs)

adds VOI vector for with new VOIs.

Parameters:: VOIs - VOIs to add to image

anonymize

public void anonymize(boolean[] list,
                      boolean doRename)

Anonymize the image by altering the sensitive data of each slice to something generic.

See Also:: FileInfoDicom.anonymize(boolean[])

calcMinMax

public void calcMinMax()

Calculates the min and max values for the image array.

Overrides:: calcMinMax in class ModelStorageBase

setExtents

public void setExtents(int[] dims)

Description copied from class: ModelStorageBase

Sets the dimExtents for this structure.

Overrides:: setExtents in class ModelStorageBase

Parameters:: dims - new dimensions for image

changeExtents

public void changeExtents(int[] dimExtents)

Changes the image dimensionality or extents.

Parameters:: dimExtents - new dimensions for mask, maskBU, and fileInfo

clearMask

public void clearMask()

Sets the entire mask object to false.

clone

public Object clone()

Copies the image and all data associated with the image (i.e. VOIs). Invokes the clone(String newName) method with newName set to null;

Overrides:: clone in class ModelStorageBase

Returns:: the new copy of the image

clone

public Object clone(String newName)

Copies the image and all data associated with the image (i.e. VOIs). Sets the name of the new image to newName.

Parameters:: newName - String containing the name for the cloned image. If null then 'this' image name is appended with "_clone".
Returns:: the new copy of the image

copyFileTypeInfo

public void copyFileTypeInfo(ModelImage fromImage)

Deep copies the file type info from the fromImage to the current image object.

Parameters:: fromImage - image from which to copy file type info

createMask

public void createMask(int length)

Creates mask and maskBU of new length.

Parameters:: length - int

displayAboutInfo

public void displayAboutInfo(JDialogBase dialog,
                             int z,
                             int t,
                             boolean dicom,
                             boolean xml)

Displays all information about an image.

Parameters:: dialog - dialog object where image information is to be displayed; z - index of file information -- each image slice can have separate file information (i.e. like DICOM).; t - t slice of the fileinfo to display.; dicom - boolean indicating if this is a DICOM file; xml - boolean indicating if this is a XML file

disposeLocal

public void disposeLocal()

Unregisters image and disposes of image memory and associated objects.

Overrides:: disposeLocal in class ModelStorageBase

disposeLocal

public void disposeLocal(boolean garbageCollect)

Unregisters image and disposes of image memory and associated objects.

Parameters:: garbageCollect - boolean - A flag indicating whether or not garbage collection is invoked.

generateBinaryImage

public ModelImage generateBinaryImage()

Forms a solid (without holes) binary image from all VOIs in the image.

Returns:: image image of boolean type with VOI objects = 1 and background = 0

generateBinaryImage

public ModelImage generateBinaryImage(boolean XOR,
                                      boolean onlyActive)

Forms a binary image from VOIs.

Parameters:: XOR - indicates that nested VOI contours will be exclusive ORed with other contours of the VOI; onlyActive - Only mask regions that are active (i.e. selected VOIs)
Returns:: image image of boolean type with VOI objects = 1 and background = 0

generateShortImage

public ModelImage generateShortImage(int offset)

Generates a solid (no holes) short image of regions defined by VOIs.

Parameters:: offset - offset value added to ID - normally 1 used to label the masked regions
Returns:: ModelImage mask image of type short

generateShortImage

public ModelImage generateShortImage(int offset,
                                     boolean XOR,
                                     boolean onlyActive)

Exports a short mask of the VOI[index]. VOI[0] = 1 ... VOI[n] = n

Parameters:: offset - offset value added to ID - normally 1. ID is used to label the masked regions; XOR - indicates that nested VOI contours will be exclusive ORed with other contours of the VOI; onlyActive - Only mask regions that are active (i.e. selected VOIs)
Returns:: ModelImage mask image of type short

generateUnsignedByteImage

public ModelImage generateUnsignedByteImage(int offset)

Generates a solid (no holes) unsigned byte image of regions defined by VOIs.

Parameters:: offset - offset value added to ID - normally 1. ID is used to label the masked regions
Returns:: ModelImage mask image of type unsigned byte

generateUnsignedByteImage

public ModelImage generateUnsignedByteImage(int offset,
                                            boolean XOR,
                                            boolean onlyActive)

Exports an unsigned byte mask of the VOI[index]. VOI[0] = 1 ... VOI[n] = n

Parameters:: offset - offset value added to ID - normally 1. ID is used to label the masked regions; XOR - indicates that nested VOI contours will be exclusive ORed with other contours of the VOI; onlyActive - Only mask regions that are active (i.e. selected VOIs)
Returns:: ModelImage mask image of type unsigned byte

generateVOIMask

public BitSet generateVOIMask()

Generates a BitSet mask of all the VOIs and sets ImageModel mask.

Returns:: binary mask of all VOIs returned as a BitSet object

generateVOIMask

public BitSet generateVOIMask(boolean XOR)

Generates a BitSet mask of all the VOIs and sets ImageModel mask.

Parameters:: XOR - indicates that nested VOI contours will be exclusive ORed with other contours of the VOI
Returns:: binary mask of all VOIs returned as a BitSet object

generateVOIMask

public short[] generateVOIMask(short[] mask,
                               int index)

Generates a mask of the type short - without XORing VOI contours.

Parameters:: mask - mask of VOI of type short; index - indicates a specific VOI used to create the mask
Returns:: mask short mask of the VOI

generateVOIMask

public BitSet generateVOIMask(boolean XOR,
                              boolean onlyActive)

Generates a BitSet mask of all the VOIs and sets ImageModel mask.

Parameters:: XOR - indicates that nested VOI contours will be exclusive ORed with other contours of the VOI; onlyActive - Only mask regions that are active (i.e. selected )
Returns:: binary mask of all VOIs returned as a BitSet object

generateVOIMask

public short[] generateVOIMask(short[] mask,
                               int index,
                               boolean XOR)

Exports a short mask of the VOI[index].

Parameters:: mask - mask of VOI of type short; index - indicates a specific VOI used to create the mask; XOR - indicates that nested VOI contours will be exclusive ORed with other contours of the VOI
Returns:: mask short mask of the VOI

getAnimateFrame

public ViewJFrameAnimate getAnimateFrame()

Method that returns the animate frame if it exists else returns null.

Returns:: animate frame

getHistoLUTFrame

public ViewJFrameHistoLUT getHistoLUTFrame()

Method that returns the HistoLUT frame if it exists else returns null.

Returns:: histoLUTFrame

getHistoRGBFrame

public ViewJFrameHistoRGB getHistoRGBFrame()

Method that returns the HistoRGB frame if it exists else returns null.

Returns:: histoRGBFrame

getImageCenter

public WildMagic.LibFoundation.Mathematics.Vector3f getImageCenter()

Calculates translation offset for transforming image about the center of the image.

Returns:: Center of image in pixels.

getImageCentermm

public WildMagic.LibFoundation.Mathematics.Vector3f getImageCentermm(boolean useScanner)

Calculates translation offset for transforming image about the center of the image in the resolution space.

Parameters:: useScanner - DOCUMENT ME!
Returns:: Center of the image in millimeters (or other physical dimension).

getImageDirectory

public String getImageDirectory()

Returns the directory where the image file is located.

Returns:: The directory where the image file resides.

getImageFileName

public String getImageFileName()

Returns the file name of the image.

Returns:: the String that represents the filename (as stored in the fileinfo)

getImageFrameVector

public Vector<ViewImageUpdateInterface> getImageFrameVector()

Accessor that returns.

Returns:: image frame vector

getImageModality

public int getImageModality()

Returns the type of image.

Returns:: type of image (MRI, CT, ...)

getImageName

public String getImageName()

Accessor that returns the name of the image.

Returns:: the String representing the filename if DICOM image then ImageName is the patients' name else, imageName is the file name (see the contructor for more)

getImageOrder

public int getImageOrder()

For multiple image viewers this indicates order of the image.

Returns:: integer indicating image order

getLightBoxFrame

public ViewJFrameLightBox getLightBoxFrame()

Method that returns the lightbox frame if it exists else returns null.

Returns:: lightbox frame

getMask

public BitSet getMask()

Accessor that returns.

Returns:: mask that indicates which pixels/voxels will be processed.

getMaskBU

public BitSet getMaskBU()

Accessor that returns.

Returns:: a bakeup of mask that indicates which pixels/voxels will be processed.

getMatrix

public TransMatrix getMatrix()

Accessor that returns transformation matrix.

Returns:: transformation matrix

getMatrixHolder

public MatrixHolder getMatrixHolder()

DOCUMENT ME!

Returns:: DOCUMENT ME!

getProvenanceHolder

public ProvenanceHolder getProvenanceHolder()

getPackedColor

public final int getPackedColor(int iIndex)

If no LUT or RGB color table is defined, this returns the packed int value for the color at iIndexs for the input ModelImage kImage:

Parameters:: iIndex - pixel index
Returns:: RGB color value.

getParentFrame

public ViewJFrameImage getParentFrame()

Returns the parent frame of this image. Should always exist.

Returns:: The parent frame of this image.

getPlane

public final float[] getPlane(WildMagic.LibFoundation.Mathematics.Vector3f topLeft,
                              WildMagic.LibFoundation.Mathematics.Vector3f topRight,
                              WildMagic.LibFoundation.Mathematics.Vector3f botLeft,
                              WildMagic.LibFoundation.Mathematics.Vector3f botRight)

Extract an arbitrary slice plane from the image using tri-linear interpolation. Performs bounds checking and returns a full plane of the image (up to the slicesize * 2).

Parameters:: topLeft - the top left point of the plane; must be in the image coord system.; topRight - the top right point of the plane; must be in the image coord system.; botLeft - the bottom left point of the plane; must be in the image coord system.; botRight - the bottom right point of the plane; must be in the image coord system. not really used..
Returns:: a float buffer containing the extracted plane (size == image.getSliceSize() 2).

getRegistrationFrame

public ViewJFrameRegistration getRegistrationFrame()

Method that returns the registration frame if it exists else returns null.

Returns:: registration frame

getScannerCoordLPS

public void getScannerCoordLPS(int x,
                               int y,
                               int z,
                               float[] scannerCoord)

Takes input x,y,z coordinate and returns that point transformed into the scanner's (DICOM) coordinate system. L = Left - first axis is positive to the left P = Posterior - second axis is positive to the posterior S = Superior - third axis is positive to the superior

Parameters:: x - Absolute x value in slice.; y - Absolute y value in slice.; z - Absolute z value in slice.; scannerCoord - the point transformed into the scanner's (DICOM) coordinate system.

getScannerCoordRAS

public void getScannerCoordRAS(int x,
                               int y,
                               int z,
                               float[] scannerCoord)

Takes input x,y,z coordinate and returns that point transformed into the RAS coordinate system. R = Right - first axis is positive to the right A = Anterior - second axis is positive to the anterior S = Superior - third axis is positive to the superior

Parameters:: x - Absolute x value in slice.; y - Absolute y value in slice.; z - Absolute z value in slice.; scannerCoord - the point transformed into the scanner's (DICOM) coordinate system.

getTalairachTransformInfo

public TalairachTransformInfo getTalairachTransformInfo()

Accessor that returns the talairach transform information.

Returns:: TalairachTransformInfo talairach info

getTriImageFrame

public ViewJFrameTriImage getTriImageFrame()

Method that returns the tri image frame if it exists else returns null.

Returns:: tri image frame

getUserInterface

public ViewUserInterface getUserInterface()

Deprecated. DOCUMENT ME!

Returns the reference to the user interface.

Returns:: the reference to the user interface.

getVOIs

public VOIVector getVOIs()

Accessor that returns.

Returns:: VOI vector

groupVOIs

public void groupVOIs()

Forms a single VOI structure from all the VOIs presently loaded in the imageModel.

groupVOIs

public void groupVOIs(ViewVOIVector newVOIVector,
                      int[] where,
                      String name)

Forms a single VOI structure from all the VOIs presently loaded in the imageModel.

Parameters:: newVOIVector - a new ViewVOIVector to hold the grouped VOIs; where - int array telling where to sort; name - the name of the VOI

isColorImage

public boolean isColorImage()

Accessor that returns whether or not the image is a color image.

Returns:: true if color, false if not color.

is2DImage

public boolean is2DImage()

is3DImage

public boolean is3DImage()

isComplexImage

public boolean isComplexImage()

Accessor that returns whether or not the image is a COMPLEX or DCOMPLEX image.

Returns:: true if complex, false if not complex.

isDicomImage

public boolean isDicomImage()

Accessor that returns whether or not the image is a DICOM image.

Returns:: true if DICOM, false if not DICOM.

isMincImage

public boolean isMincImage()

Accessor that returns whether or not the image is a MINC image.

Returns:: true if MINC, false if not MINC.

notifyImageDisplayListeners

public void notifyImageDisplayListeners()

Used to notify all frames that display this image model need to be updated.

notifyImageDisplayListeners_notTriFrame

public void notifyImageDisplayListeners_notTriFrame()

Used to notify all frames except the triImage frames that display this image model need to be updated.

notifyImageDisplayListeners

public void notifyImageDisplayListeners(ModelLUT LUT,
                                        boolean forceShow)

Used to notify all frames that display this image model need to be updated.

Parameters:: LUT - new LUT used to display image (can be null);; forceShow - force the display method(s) to reload image data and display image slower but needed if image model changes.

notifyImageDisplayListeners

public void notifyImageDisplayListeners(boolean forceShow,
                                        int alphaBlend,
                                        ModelRGB RGBT)

Used to notify all frames that display this image model need to be updated for RGB (color) images.

Parameters:: forceShow - force the display method(s) to reload image data and display image slower but needed if image model changes.; alphaBlend - the amount to blend between two images displayed in the same frame.; RGBT - ModelRGB

notifyImageDisplayListeners

public void notifyImageDisplayListeners(ModelLUT LUT,
                                        boolean forceShow,
                                        int alphaBlend,
                                        int interpMode)

Used to notify all listeners that the image is to be redisplayed.

Parameters:: LUT - new LUT used to display image (can be null);; forceShow - force the display method(s) to reload image data and display image slower but needed if image model changes.; alphaBlend - indicates the amount of blending between two images (image 1's blending value) 1.0 - all of image 1; 0.5 - half image 1 and half image 2; interpMode - image interpolation method (Nearest or Smooth)

notifyImageExtentsListeners

public void notifyImageExtentsListeners()

Used to notify all frames that display this image model that this image's extents have changed. The display of this image may also need to be updated.

print

public void print()

Prints basic image parameters to the System.out.

readTransformMatrix

public TransMatrix readTransformMatrix(boolean composite)

Read matrix from a file.

Parameters:: composite - if true make a composite matrix of the by multipling this matrix with the one to be read from the file. If false replace this object matrix with a new matrix read from the file.
Returns:: DOCUMENT ME!

reallocate

public void reallocate(int type)

Reallocates ModelImage with new type and all image data lost.

Overrides:: reallocate in class ModelStorageBase

Parameters:: type - new type of image that is to be allocated

registerVOI

public void registerVOI(VOI voi)

Method that register an VOI to this image.

Parameters:: voi - Region of interest (VOI) to be registered with the image model

removeImageDisplayListener

public void removeImageDisplayListener(ViewImageUpdateInterface obj)

Remove a listener from the class.

Parameters:: obj - "object' to be added to the list

resetVOIs

public void resetVOIs()

Resets VOI vector for new VOIs.

saveImage

public boolean saveImage(String directory,
                         String fileName,
                         int fileType,
                         boolean isActive)

Save the image to a file. The file type the image is to be save in is passed into this method.

Parameters:: directory - location where the image is to stored.; fileName - the name of the file (without the extension).; fileType - The format of the image file (i.e. Analyze, XML, DICOM etc.); isActive - Whether saving is being done in a separate thread
Returns:: true if succeeded in saving.

saveTransformMatrix

public void saveTransformMatrix(TransMatrix matrix)

Saves the transformation matrix to file.

Parameters:: matrix - DOCUMENT ME!

saveImage

public static void saveImage(ModelImage kImage)

Save the gradient magnitude image into the MIPAV default dir.

Parameters:: gmImage - ModelImage gradient magnitude image to save

saveTransformMatrix

public void saveTransformMatrix(String fileName,
                                TransMatrix matrix)

Save the images transformation matrix in the working directory with the supplied fileName.

Parameters:: fileName - - fileName of transformation matrix; matrix - DOCUMENT ME!

setImageDirectory

public void setImageDirectory(String dir)

Sets the image directory.

Parameters:: dir - string representing the directory

setImageModality

public void setImageModality(int type)

Sets the image type (MRI, CT, ...).

Parameters:: type - integer representing the type

setImageName

public void setImageName(String name)

Accessor that sets the name of the image. This method also updates the file name in the fileInfos to match the new image name.

Parameters:: name - the String representing the filename

setImageName

public void setImageName(String name,
                         boolean updateFileName)

Accessor that sets the name of the image.

Parameters:: name - the String representing the filename; updateFileName - whether to update the file name stored in the image's fileInfos to match the new image name

setImageNamePrivate

public void setImageNamePrivate(String name)

Accessor that sets the name of the image. NOT TO BE USED BY ANYONE EXCEPT ViewUserInterface.registerImage. Use setImageName instead!!!

Parameters:: name - the String representing the filename

setImageOrder

public void setImageOrder(int order)

For multiple image viewers this indicates order of the image.

Parameters:: order - integer indicating image order

setImageOrientation

public void setImageOrientation(int orient)

Sets the image orientation (sagittal, axial, ...).

Parameters:: orient - integer representing the orientation

setMask

public void setMask(BitSet _mask)

Sets the mask which indicate which pixels/voxels to process.

Parameters:: _mask - mask in the form of a BitSet, 1 indicates pixel should be processed 0 indicates pixel should not be processed

setMaskBU

public void setMaskBU(BitSet mask)

Sets the mask which indicate which pixels/voxels to process.

Parameters:: mask - mask in the form of a BitSet, 1 indicates pixel should be processed 0 indicates pixel should not be processed

setMatrix

public void setMatrix(TransMatrix matrix)

Accessor that adds a matrix to the matrix holder.

Parameters:: matrix - transformation matrix structure.

setSlice

public void setSlice(int slice)

Sets the slice in all frames displaying this image.

Parameters:: slice - Indicates the z dim. slice that should be displayed.

setTalairachTransformInfo

public void setTalairachTransformInfo(TalairachTransformInfo tal)

Accessor that sets the talairach transform information.

Parameters:: tal - TalairachTransformInfo talairach info

setTimeSlice

public void setTimeSlice(int tSlice)

Sets the time slice in all frames displaying this image.

Parameters:: tSlice - Indicates the t (time) dim. slice that should be displayed.

setUserInterface

public void setUserInterface(ViewUserInterface _UI)

Sets user interface.

Parameters:: _UI - reference to user interface

setVOIs

public void setVOIs(VOIVector VOIs)

Sets VOI vector for with new VOIs.

Parameters:: VOIs - VOIs to image VOIs

toString

public String toString()

Gives a readable representation of the ModelImage, including file name and extents.

Overrides:: toString in class Object

Returns:: the string representation

ungroupVOIs

public void ungroupVOIs()

Forms separate VOIs from all the VOI structures presently loaded in the imageModel.

unregisterAllVOIs

public void unregisterAllVOIs()

Unregisters all VOIs from this image model.

unRegisterImage

public void unRegisterImage()

Unregisters the image from the user interface.

unregisterVOI

public void unregisterVOI(VOI voi)

Method that unregisters an VOI.

Parameters:: voi - Volume of interest (VOI) to be removed from the image model

updateFileName

public void updateFileName(String newImageName)

Give the image a new image name, updates frame (if not null), and file infos.

Parameters:: newImageName - The new name for the image

updateImageOrigin

public void updateImageOrigin(TransMatrix xfrm)

Updates the images origin.

Parameters:: xfrm - the transformation maxtrix used to transform the origin

makeUnitsOfMeasureIdentical

public void makeUnitsOfMeasureIdentical()

Make all spatial units the same, all time units the same, and all frequency units the same

make2UnitsOfMeasureIdentical

public void make2UnitsOfMeasureIdentical(int newUnitDim,
                                         int oldUnitDim)

Parameters:: newUnitDim -; oldUnitDim - dimension which will have unit of measure converted to unit of measure of dimension newUnitDim and will have the resolution correspondingly converted.

finalize

protected void finalize()
                 throws Throwable

Calls disposeLocal of this class to ensure this class nulls the references to global class variables so that memory will be recovered.

Overrides:: finalize in class ModelStorageBase

Throws:: Throwable - Throws an error if there is a problem with the finalization of this object.

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gov.nih.mipav.model.structures Class ModelImage

IMAGE_A

IMAGE_B

ModelImage

ModelImage

isColorImage

addImageDisplayListener

addVOIs

anonymize

calcMinMax

setExtents

changeExtents

clearMask

clone

clone

copyFileTypeInfo

createMask

displayAboutInfo

disposeLocal

disposeLocal

generateBinaryImage

generateBinaryImage

generateShortImage

generateShortImage

generateUnsignedByteImage

generateUnsignedByteImage

generateVOIMask

generateVOIMask

generateVOIMask

generateVOIMask

generateVOIMask

getAnimateFrame

getHistoLUTFrame

getHistoRGBFrame

getImageCenter

getImageCentermm

getImageDirectory

getImageFileName

getImageFrameVector

getImageModality

getImageName

getImageOrder

getLightBoxFrame

getMask

getMaskBU

getMatrix

getMatrixHolder

getProvenanceHolder

getPackedColor

getParentFrame

getPlane

getRegistrationFrame

getScannerCoordLPS

getScannerCoordRAS

getTalairachTransformInfo

getTriImageFrame

getUserInterface

getVOIs

groupVOIs

groupVOIs

isColorImage

is2DImage

is3DImage

isComplexImage

isDicomImage

isMincImage

notifyImageDisplayListeners

notifyImageDisplayListeners_notTriFrame

notifyImageDisplayListeners

notifyImageDisplayListeners

notifyImageDisplayListeners

notifyImageExtentsListeners

print

readTransformMatrix

reallocate

registerVOI

removeImageDisplayListener

resetVOIs

saveImage

saveTransformMatrix

gov.nih.mipav.model.structures
Class ModelImage