gov.nih.mipav.model.file
Class FileUtility

java.lang.Object
  gov.nih.mipav.model.file.FileUtility

public class FileUtility
extends Object

Constants and static methods which relate to file input, output or processing.

Field Summary

static int	AFNI AFNI file type. extension: .head, .brik
static int	ANALYZE Analyze format (Mayo). extension: .img, .hdr
static int	ANALYZE_MULTIFILE Multiple files of type analyze.
static int	AVI AVI file type.
static int	BFLOAT Extension: .hdr for header, .bfloat for data
static int	BIORAD Used by the Bio-Rad Pic format. extension: .pic && fileID(54L)==12345
static int	BMP extension: .bmp.
static int	BRUKER Bruker file format.
static int	CHESHIRE Cheshire file type (a kind of Analyze). extension: .imc Can also have .img extension
static int	CHESHIRE_OVERLAY Cheshire overlay file type.
static int	COR Used by FreeSurfer software. extension: -.info or -.info~ for header file -.nnn for slice data file where nnn is the slice number
static int	CUR extension: .cur.
static int	DIB extension: .dib.
static int	DICOM Digital Imaging and COmmunications in Medicine file type.
static int	DM3 Gatan's Digital Micrograph version 3 file format. extension: .dm3
static int	ERROR Ill defined file type.
static int	FITS FITS file type. extension: .fits
static int	GE_GENESIS GE Genesis 5X and LX. extension: .sig
static int	GE_GENESIS_MULTIFILE Multiple files of type GE_GENESIS
static int	GE_SIGNA4X GE Signa 4.x.
static int	GE_SIGNA4X_MULTIFILE Multiple files of type GE_SIGNA4X
static int	GIF extension: .gif.
static int	ICO extension: .ico.
static int	ICS Image Cytometry Standard. extension: .ics, .ids
static int	INTERFILE Interfile file format used in Nuclear Medicine. extension: .hdr
static int	JIMI Java Image Manangement Interface file type.
static int	JP2
static int	JPEG extension: .jpeg, .jpg.
static int	LIFF Do not confuse with Leica image file format .lif
static int	LSM Used by the Zeiss LSM 510 Dataserver. extension: .lsm
static int	LSM_MULTIFILE Used by the Zeiss LSM 510 Dataserver.
static int	MAGNETOM_VISION Siemens MAGNETOM VISION. extension: .ima
static int	MAGNETOM_VISION_MULTIFILE Multiple files of type MAGNETOM_VISION
static int	MAP Benes Trus special file type. extension: .map
static int	MEDIVISION extension: .bin.
static int	MGH MGH/MGZ volume format.
static int	MICRO_CAT Micro CT format for small animal imaging. extension: .log, .ct
static int	MINC MINC file type.
static int	MINC_HDF MINC 2.0 (HDF5)
static int	MIPAV Not presently implemented.
static int	MRC extension: .mrc.
static int	NIFTI NIFTI format. extension: .img, .hdr, .nii
static int	NIFTI_MULTIFILE NIFTI multi-file format.
static int	NRRD Nearly raw raster data.
static int	OSM Washington University OSM dataset structure. extension: .wu
static int	PARREC extension: "par","parv2","rec","frec".
static int	PCX extension: .pcx.
static int	PIC extension: .pic.
static int	PICT extension: .pict.
static int	PNG extension: .png.
static int	PROJECT MIPAV project format. project file format (.xml)
static int	PSD extension: .psd.
static int	QT Quicktime file type. extension: .mov, .qt
static int	RAW RAW image data, no header. extension: .raw
static int	RAW_MULTIFILE RAW MULTIFLE image data, no header.
static int	SPM SPM file format.
static int	STK MetaMorph Stack (STK) file type. extension: .stk
static int	SURFACE_XML MIPAV Surface XML file format. extension: .xml
static int	SURFACEREF_XML MIPAV Surface XML file format. extension: .xml
static int	TGA extension: .tga.
static int	TIFF TIFF file; tagged header. extension: .tif, .tiff
static int	TIFF_MULTIFILE Multiple files of TIFF images.
static int	TMG Optical coherence tomography. extension: .tmg
static int	UNDEFINED Undefined file type.
static int	VOI_FILE VOI file, used to read VOIs. extension: .voi
static int	XBM extension: .xbm.
static int	XML MIPAV XML file format. mipav xml image format. extension: .xml
static int	XML_MULTIFILE MIPAV XML file format.
static int	XPM extension: .xpm.

Constructor Summary

FileUtility()

Method Summary

static String[]	getCORFileList(String fileDir, String fileName, boolean quiet) Only for FreeSurfer COR volume files Looks in the image directory and returns all images with the same root up to the hyphen, sorted in lexicographical order.
static String	getCORSuffixFrom(String fn) Only used for COR volume files with hyphen in name Breaks the filename into basename and suffix, then returns the suffix.
static String	getExtension(String absolutePath) Returns the extension of the file name, if file name does not have extension, then return empty string.
static String	getFileDirectory(String fileName) Returns the path information from the file name with the path information.
static int	getFileIndex(String fName) Trims off the file extension and file name, but leaves the file index.
static String[]	getFileList(String fileDir, String fileName, boolean quiet) Looks in the image directory and returns all images with the same suffix as fileName, sorted in lexicographical order.
static String	getFileName(String absolutePath) Returns the file name without path information from file name with the path information.
static List<String>	getFileNameList(ModelImage image) Gets the file name list from which this ModelImage is opened.
static int	getFileType(String fileName, String fileDir, boolean quiet) Sets the FileBase.
static int	getFileType(String fileName, String fileDir, boolean doWrite, boolean quiet) Sets the FileBase.
static int	getFileTypeFromStr(String s) Returns the file type associated with a string.
static String	getFileTypeStr(int m) Return the string associated with a file type.
static int	isAnalyzeOrSPM(String fileName, String fileDir, boolean quiet) Tests if the unknown file is of type Analyze.
static int	isDicom_ver2(String fileName, String fileDir, boolean quiet) tests if unknown file is of type 2.0 dicom
static int	isDicom(String fileName, String fileDir, boolean quiet) Tests if the unknown file is of type Dicom.
static int	isGESigna4X(String fileName, String fileDir, boolean quiet) Tests if the unknown file is of type GE Signa 4X type.
static int	isGESigna5X(String fileName, String fileDir, boolean quiet) Tests if the unknown file is of type GE Signa 5X type.
static int	isInterfile(String fileName, String fileDir, boolean quiet) Tests if the unknown file is of type Interfile.
static int	isMagnetomVision(String fileName, String fileDir, boolean quiet) Tests if the unknown file is of type Siemens Magnetom Vision.
static int	isMinc(String fileName, String fileDir, boolean quiet) Tests if the unknown file is of type Minc.
static int	isMincHDF(String fileName, String fileDir, boolean quiet) Determines whether the file on disk is of type MINC 2.0
static int	isNIFTI(String fileName, String fileDir, boolean quiet) Tests if the unknown file is of type Nifti.
static int	isSPM(String fileName, String fileDir, boolean quiet) Tests if the unknown file is of type SPM.
static String	stripExtension(String fileName) Helper method to strip the image name of the extension, so when we save we don't have double extensions (like genormcor.img.tif).
static String	trimCOR(String fName) Trims the numbers or file extension from COR file names.
static String	trimNumbersAndSpecial(String fName) Trims the numbers and special character from the file name.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

ERROR

public static final int ERROR

Ill defined file type.

See Also:

Constant Field Values

UNDEFINED

public static final int UNDEFINED

Undefined file type.

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Constant Field Values

AFNI

public static final int AFNI

AFNI file type. extension: .head, .brik

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Constant Field Values

ANALYZE

public static final int ANALYZE

Analyze format (Mayo). extension: .img, .hdr

See Also:

Constant Field Values

ANALYZE_MULTIFILE

public static final int ANALYZE_MULTIFILE

Multiple files of type analyze.

See Also:

Constant Field Values

AVI

public static final int AVI

AVI file type. Windows Media. extension: .avi

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Constant Field Values

BIORAD

public static final int BIORAD

Used by the Bio-Rad Pic format. extension: .pic && fileID(54L)==12345

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Constant Field Values

BMP

public static final int BMP

extension: .bmp.

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Constant Field Values

BRUKER

public static final int BRUKER

Bruker file format. Reads a BRUKER file by first reading in the d3proc header file, second the reco header file, third the acqp file int the same directory or up one or two two parent directories, and finally the 2dseq binary file.

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Constant Field Values

CHESHIRE

public static final int CHESHIRE

Cheshire file type (a kind of Analyze). extension: .imc Can also have .img extension

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Constant Field Values

CHESHIRE_OVERLAY

public static final int CHESHIRE_OVERLAY

Cheshire overlay file type. Contains VOIs. extension: .oly

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Constant Field Values

COR

public static final int COR

Used by FreeSurfer software. extension: -.info or -.info~ for header file -.nnn for slice data file where nnn is the slice number

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Constant Field Values

CUR

public static final int CUR

extension: .cur.

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Constant Field Values

DIB

public static final int DIB

extension: .dib.

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Constant Field Values

DICOM

public static final int DICOM

Digital Imaging and COmmunications in Medicine file type. Fully implemented versions 2 & 3. extension: .dcm

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Constant Field Values

DM3

public static final int DM3

Gatan's Digital Micrograph version 3 file format. extension: .dm3

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Constant Field Values

FITS

public static final int FITS

FITS file type. extension: .fits

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Constant Field Values

GE_GENESIS

public static final int GE_GENESIS

GE Genesis 5X and LX. extension: .sig

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Constant Field Values

GE_GENESIS_MULTIFILE

public static final int GE_GENESIS_MULTIFILE

Multiple files of type GE_GENESIS

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Constant Field Values

GE_SIGNA4X

public static final int GE_SIGNA4X

GE Signa 4.x.

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Constant Field Values

GE_SIGNA4X_MULTIFILE

public static final int GE_SIGNA4X_MULTIFILE

Multiple files of type GE_SIGNA4X

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Constant Field Values

GIF

public static final int GIF

extension: .gif.

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Constant Field Values

ICO

public static final int ICO

extension: .ico.

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Constant Field Values

ICS

public static final int ICS

Image Cytometry Standard. extension: .ics, .ids

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Constant Field Values

INTERFILE

public static final int INTERFILE

Interfile file format used in Nuclear Medicine. extension: .hdr

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Constant Field Values

JIMI

public static final int JIMI

Java Image Manangement Interface file type.

See Also:

Constant Field Values

JPEG

public static final int JPEG

extension: .jpeg, .jpg.

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Constant Field Values

LSM

public static final int LSM

Used by the Zeiss LSM 510 Dataserver. extension: .lsm

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Constant Field Values

LSM_MULTIFILE

public static final int LSM_MULTIFILE

Used by the Zeiss LSM 510 Dataserver.

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Constant Field Values

MAGNETOM_VISION

public static final int MAGNETOM_VISION

Siemens MAGNETOM VISION. extension: .ima

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Constant Field Values

MAGNETOM_VISION_MULTIFILE

public static final int MAGNETOM_VISION_MULTIFILE

Multiple files of type MAGNETOM_VISION

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MAP

public static final int MAP

Benes Trus special file type. extension: .map

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Constant Field Values

MEDIVISION

public static final int MEDIVISION

extension: .bin.

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Constant Field Values

MGH

public static final int MGH

MGH/MGZ volume format.

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Constant Field Values

MICRO_CAT

public static final int MICRO_CAT

Micro CT format for small animal imaging. extension: .log, .ct

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Constant Field Values

MINC

public static final int MINC

MINC file type. MINC is a medical imaging oriented extension of the NetCDF file format. NetCDF stands for 'Network Common Data Form'. extension: .mnc

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Constant Field Values

MIPAV

public static final int MIPAV

Not presently implemented.

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MRC

public static final int MRC

extension: .mrc.

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Constant Field Values

NIFTI

public static final int NIFTI

NIFTI format. extension: .img, .hdr, .nii

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Constant Field Values

NIFTI_MULTIFILE

public static final int NIFTI_MULTIFILE

NIFTI multi-file format.

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Constant Field Values

NRRD

public static final int NRRD

Nearly raw raster data.

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Constant Field Values

OSM

public static final int OSM

Washington University OSM dataset structure. extension: .wu

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Constant Field Values

PCX

public static final int PCX

extension: .pcx.

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Constant Field Values

PIC

public static final int PIC

extension: .pic.

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Constant Field Values

PICT

public static final int PICT

extension: .pict.

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Constant Field Values

PNG

public static final int PNG

extension: .png.

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Constant Field Values

PROJECT

public static final int PROJECT

MIPAV project format. project file format (.xml)

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Constant Field Values

PSD

public static final int PSD

extension: .psd.

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Constant Field Values

QT

public static final int QT

Quicktime file type. extension: .mov, .qt

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RAW

public static final int RAW

RAW image data, no header. extension: .raw

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Constant Field Values

RAW_MULTIFILE

public static final int RAW_MULTIFILE

RAW MULTIFLE image data, no header.

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Constant Field Values

SPM

public static final int SPM

SPM file format. SPM99 and SPM2 are slight variants of analyze with the same .img, .hdr file extensions. The user could also change the extension .img to .spm to indicate SPM. The header extension would remain .hdr

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Constant Field Values

STK

public static final int STK

MetaMorph Stack (STK) file type. extension: .stk

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Constant Field Values

SURFACE_XML

public static final int SURFACE_XML

MIPAV Surface XML file format. extension: .xml

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TGA

public static final int TGA

extension: .tga.

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TIFF

public static final int TIFF

TIFF file; tagged header. extension: .tif, .tiff

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TIFF_MULTIFILE

public static final int TIFF_MULTIFILE

Multiple files of TIFF images.

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TMG

public static final int TMG

Optical coherence tomography. extension: .tmg

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Constant Field Values

VOI_FILE

public static final int VOI_FILE

VOI file, used to read VOIs. extension: .voi

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XBM

public static final int XBM

extension: .xbm.

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XML

public static final int XML

MIPAV XML file format. mipav xml image format. extension: .xml

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XML_MULTIFILE

public static final int XML_MULTIFILE

MIPAV XML file format.

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XPM

public static final int XPM

extension: .xpm.

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PARREC

public static final int PARREC

extension: "par","parv2","rec","frec".

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SURFACEREF_XML

public static final int SURFACEREF_XML

MIPAV Surface XML file format. extension: .xml

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MINC_HDF

public static final int MINC_HDF

MINC 2.0 (HDF5)

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LIFF

public static final int LIFF

Do not confuse with Leica image file format .lif

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BFLOAT

public static final int BFLOAT

Extension: .hdr for header, .bfloat for data

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JP2

public static final int JP2

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Constructor Detail

FileUtility

public FileUtility()

Method Detail

getFileTypeFromStr

public static int getFileTypeFromStr(String s)

Returns the file type associated with a string.

Parameters:

s - String to test

Returns:

axis orientation

getFileTypeStr

public static String getFileTypeStr(int m)

Return the string associated with a file type.

Parameters:

m - int representing the file type (see the above static definitions)

Returns:

String representing the string associated with the file type.

getCORFileList

public static final String[] getCORFileList(String fileDir,
                                            String fileName,
                                            boolean quiet)
                                     throws OutOfMemoryError

Only for FreeSurfer COR volume files Looks in the image directory and returns all images with the same root up to the hyphen, sorted in lexicographical order. Will set the number of images (nImages) for the calling program.

Parameters:

fileDir - Directory to look for images.

fileName - File name of the image.

quiet - Whether to avoid displaying errors using the GUI.

Returns:

An array of the image names to be read in or saved as.

Throws:

OutOfMemoryError - If there is a problem allocating required memory.

getCORSuffixFrom

public static final String getCORSuffixFrom(String fn)

Only used for COR volume files with hyphen in name Breaks the filename into basename and suffix, then returns the suffix.

Parameters:

fn - The filename.

Returns:

The suffix or file-extension. For example, -info. Note that suffix includes the separator '-'

getExtension

public static final String getExtension(String absolutePath)

Returns the extension of the file name, if file name does not have extension, then return empty string.

Parameters:

absolutePath - the file name.

Returns:

The file's extension.

getFileDirectory

public static final String getFileDirectory(String fileName)

Returns the path information from the file name with the path information.

Parameters:

fileName - the file name wiht the path information.

Returns:

The path information.

getFileIndex

public static final int getFileIndex(String fName)

Trims off the file extension and file name, but leaves the file index. An index might be 0001, or 140, for example.

Parameters:

fName - String file name to get index

Returns:

String (index string)

getFileList

public static final String[] getFileList(String fileDir,
                                         String fileName,
                                         boolean quiet)
                                  throws OutOfMemoryError

Looks in the image directory and returns all images with the same suffix as fileName, sorted in lexicographical order.

Parameters:

fileDir - Directory to look for images.

fileName - File name of the image.

quiet - Whether to avoid displaying errors using the GUI.

Returns:

An array of the image names to be read in or saved as.

Throws:

OutOfMemoryError - If there is a problem allocating required memory.

getFileName

public static final String getFileName(String absolutePath)

Returns the file name without path information from file name with the path information.

Parameters:

absolutePath - the file name with the path information.

Returns:

The file name without path information.

getFileType

public static final int getFileType(String fileName,
                                    String fileDir,
                                    boolean quiet)

Sets the FileBase.(filetype) based on the file extension of the given filename. Also sets file "suffix", if required.

Parameters:

fileName - Filename of the image to read in. Must include the file extension.

fileDir - Directory where fileName exists.

quiet - Whether to avoid any user interaction (ie, from error popups).

Returns:

Filetype from FileBase.

See Also:

FileBase

getFileType

public static final int getFileType(String fileName,
                                    String fileDir,
                                    boolean doWrite,
                                    boolean quiet)

Sets the FileBase.(filetype) based on the file extension of the given filename. Also sets file "suffix", if required.

Parameters:

fileName - Filename of the image to read in. Must include the file extension.

fileDir - Directory where fileName exists.

doWrite - If true about to write a file

quiet - Whether to avoid any user interaction (ie, from error popups).

Returns:

Filetype from FileBase.

See Also:

FileBase

isAnalyzeOrSPM

public static final int isAnalyzeOrSPM(String fileName,
                                       String fileDir,
                                       boolean quiet)
                                throws IOException

Tests if the unknown file is of type Analyze.

Parameters:

fileName - Name of the image file to read.

fileDir - Directory of the image file to read.

quiet - Whether to avoid any user interaction (ie, from error popups).

Returns:

FileUtility.ANALYZE if the file is a ANALYZE type, FileUtility.SPM if the file is a SPM type, and FileUtility.UNDEFINED otherwise

Throws:

IOException - If there is a problem determining the type of the given file.

isDicom

public static final int isDicom(String fileName,
                                String fileDir,
                                boolean quiet)
                         throws IOException

Tests if the unknown file is of type Dicom.

Parameters:

fileName - Name of the image file to read.

fileDir - Directory of the image file to read.

quiet - Whether to avoid any user interaction (ie, from error popups).

Returns:

FileUtility.DICOM if the file is a DICOM file, and FileUtility.UNDEFINED otherwise

Throws:

IOException - If there is a problem determining the type of the given file.

isDicom_ver2

public static final int isDicom_ver2(String fileName,
                                     String fileDir,
                                     boolean quiet)
                              throws IOException

tests if unknown file is of type 2.0 dicom

Parameters:

fileName -

fileDir -

quiet -

Returns:

Throws:

IOException

isGESigna4X

public static final int isGESigna4X(String fileName,
                                    String fileDir,
                                    boolean quiet)
                             throws IOException

Tests if the unknown file is of type GE Signa 4X type.

Parameters:

fileName - Name of the image file to read.

fileDir - Directory of the image file to read.

quiet - Whether to avoid any user interaction (ie, from error popups).

Returns:

FileUtility.GE_SIGNA4X if the file is a GE MR Signa 4.x file, and FileUtility.UNDEFINED otherwise

Throws:

IOException - If there is a problem determining the type of the given file.

isGESigna5X

public static final int isGESigna5X(String fileName,
                                    String fileDir,
                                    boolean quiet)
                             throws IOException

Tests if the unknown file is of type GE Signa 5X type.

Parameters:

fileName - Name of the image file to read.

fileDir - Directory of the image file to read.

quiet - Whether to avoid any user interaction (ie, from error popups).

Returns:

FileUtility.GE_GENESIS if the file is a GE MR Signa 5.x file, and FileUtility.UNDEFINED otherwise

Throws:

IOException - If there is a problem determining the type of the given file.

isInterfile

public static final int isInterfile(String fileName,
                                    String fileDir,
                                    boolean quiet)
                             throws IOException

Tests if the unknown file is of type Interfile.

Parameters:

fileName - Name of the image file to read.

fileDir - Directory of the image file to read.

quiet - Whether to avoid any user interaction (ie, from error popups).

Returns:

FileUtility.Interfile if the file is a Interfile type, and FileUtility.UNDEFINED otherwise

Throws:

IOException - If there is a problem determining the type of the given file.

isMagnetomVision

public static final int isMagnetomVision(String fileName,
                                         String fileDir,
                                         boolean quiet)
                                  throws IOException

Tests if the unknown file is of type Siemens Magnetom Vision.

Parameters:

fileName - Name of the image file to read.

fileDir - Directory of the image file to read.

quiet - Whether to avoid any user interaction (ie, from error popups).

Returns:

FileUtility.MAGNETOM_VISION if the file is a Siemens Magnetom Vision type, and FileUtility.UNDEFINED otherwise

Throws:

IOException - If there is a problem determining the type of the given file.

isMinc

public static final int isMinc(String fileName,
                               String fileDir,
                               boolean quiet)
                        throws IOException

Tests if the unknown file is of type Minc.

Parameters:

fileName - Name of the image file to read.

fileDir - Directory of the image file to read.

quiet - Whether to avoid any user interaction (ie, from error popups).

Returns:

FileUtility.MINC if the file is a MINC type, and FileUtility.UNDEFINED otherwise

Throws:

IOException - If there is a problem determining the type of the given file.

isMincHDF

public static final int isMincHDF(String fileName,
                                  String fileDir,
                                  boolean quiet)

Determines whether the file on disk is of type MINC 2.0

Parameters:

fileName - name of the file

fileDir - directory

quiet -

Returns:

whether the file is HDF5 type

isNIFTI

public static final int isNIFTI(String fileName,
                                String fileDir,
                                boolean quiet)
                         throws IOException

Tests if the unknown file is of type Nifti.

Parameters:

fileName - Name of the image file to read.

fileDir - Directory of the image file to read.

quiet - Whether to avoid any user interaction (ie, from error popups).

Returns:

FileUtility.NIFTI if the file is a NIFTI type, and FileUtility.UNDEFINED otherwise

Throws:

IOException - If there is a problem determining the type of the given file.

isSPM

public static final int isSPM(String fileName,
                              String fileDir,
                              boolean quiet)
                       throws IOException

Tests if the unknown file is of type SPM.

Parameters:

fileName - Name of the image file to read.

fileDir - Directory of the image file to read.

quiet - Whether to avoid any user interaction (ie, from error popups).

Returns:

FileUtility.SPM if the file is a SPM type, and FileUtility.UNDEFINED otherwise

Throws:

IOException - If there is a problem determining the type of the given file.

stripExtension

public static final String stripExtension(String fileName)

Helper method to strip the image name of the extension, so when we save we don't have double extensions (like genormcor.img.tif).

Parameters:

fileName - Original name.

Returns:

Name without extension, or original name if there was no extension.

trimCOR

public static final String trimCOR(String fName)

Trims the numbers or file extension from COR file names. Any numbers or .info or .info~ will be removed from after a hyphen in the given fname.

Parameters:

fName - File name where the last characters are alpha-numerics indicating the image number or .info or .info~

Returns:

File name without numbers on the end.

trimNumbersAndSpecial

public static final String trimNumbersAndSpecial(String fName)

Trims the numbers and special character from the file name. Numerics and some special characters [ - _ . are removed from the end of the file.

Parameters:

fName - File name where the last characters are alpha-numerics indicating the image number.

Returns:

File name without numbers on the end.

getFileNameList

public static final List<String> getFileNameList(ModelImage image)

Gets the file name list from which this ModelImage is opened.

Parameters:

image - the ModelImage object.

Returns:

the actual file name list.