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.

  See Also:

  Constant Field Values

• AFNI

  public static final int AFNI

  AFNI file type. extension: .head, .brik

  See Also:

  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

  See Also:

  Constant Field Values

• BIORAD

  public static final int BIORAD

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

  See Also:

  Constant Field Values

• BMP

  public static final int BMP

  extension: .bmp.

  See Also:

  Constant Field Values

• BMP_MULTIFILE

  public static final int BMP_MULTIFILE

  Bmp multifile

  See Also:

  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.

  See Also:

  Constant Field Values

• CHESHIRE

  public static final int CHESHIRE

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

  See Also:

  Constant Field Values

• CHESHIRE_OVERLAY

  public static final int CHESHIRE_OVERLAY

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

  See Also:

  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

  See Also:

  Constant Field Values

• CUR

  public static final int CUR

  extension: .cur.

  See Also:

  Constant Field Values

• DIB

  public static final int DIB

  extension: .dib.

  See Also:

  Constant Field Values

• DICOM

  public static final int DICOM

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

  See Also:

  Constant Field Values

• DM3

  public static final int DM3

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

  See Also:

  Constant Field Values

• FITS

  public static final int FITS

  FITS file type. extension: .fits

  See Also:

  Constant Field Values

• GE_GENESIS

  public static final int GE_GENESIS

  GE Genesis 5X and LX. extension: .sig

  See Also:

  Constant Field Values

• GE_GENESIS_MULTIFILE

  public static final int GE_GENESIS_MULTIFILE

  Multiple files of type GE_GENESIS

  See Also:

  Constant Field Values

• GE_SIGNA4X

  public static final int GE_SIGNA4X

  GE Signa 4.x.

  See Also:

  Constant Field Values

• GE_SIGNA4X_MULTIFILE

  public static final int GE_SIGNA4X_MULTIFILE

  Multiple files of type GE_SIGNA4X

  See Also:

  Constant Field Values

• GIF

  public static final int GIF

  extension: .gif.

  See Also:

  Constant Field Values

• ICO

  public static final int ICO

  extension: .ico.

  See Also:

  Constant Field Values

• ICS

  public static final int ICS

  Image Cytometry Standard. extension: .ics, .ids

  See Also:

  Constant Field Values

• INTERFILE

  public static final int INTERFILE

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

  See Also:

  Constant Field Values

• INTERFILE_MULTIFILE

  public static final int INTERFILE_MULTIFILE

  Multiple files of type INTERFILE

  See Also:

  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.

  See Also:

  Constant Field Values

• LSM

  public static final int LSM

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

  See Also:

  Constant Field Values

• LSM_MULTIFILE

  public static final int LSM_MULTIFILE

  Used by the Zeiss LSM 510 Dataserver.

  See Also:

  Constant Field Values

• MAGNETOM_VISION

  public static final int MAGNETOM_VISION

  Siemens MAGNETOM VISION. extension: .ima

  See Also:

  Constant Field Values

• MAGNETOM_VISION_MULTIFILE

  public static final int MAGNETOM_VISION_MULTIFILE

  Multiple files of type MAGNETOM_VISION

  See Also:

  Constant Field Values

• MAP

  public static final int MAP

  Benes Trus special file type. extension: .map

  See Also:

  Constant Field Values

• MEDIVISION

  public static final int MEDIVISION

  extension: .bin.

  See Also:

  Constant Field Values

• MGH

  public static final int MGH

  MGH/MGZ volume format.

  See Also:

  Constant Field Values

• MICRO_CAT

  public static final int MICRO_CAT

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

  See Also:

  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

  See Also:

  Constant Field Values

• MINC_MULTIFILE

  public static final int MINC_MULTIFILE

  Multiple files of type MINC.

  See Also:

  Constant Field Values

• MIPAV

  public static final int MIPAV

  Not presently implemented.

  See Also:

  Constant Field Values

• MRC

  public static final int MRC

  extension: .mrc.

  See Also:

  Constant Field Values

• NIFTI

  public static final int NIFTI

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

  See Also:

  Constant Field Values

• NIFTI_MULTIFILE

  public static final int NIFTI_MULTIFILE

  NIFTI multi-file format.

  See Also:

  Constant Field Values

• NRRD

  public static final int NRRD

  Nearly raw raster data.

  See Also:

  Constant Field Values

• NRRD_MULTIFILE

  public static final int NRRD_MULTIFILE

  Nearly raw raster data.

  See Also:

  Constant Field Values

• OSM

  public static final int OSM

  Washington University OSM dataset structure. extension: .wu

  See Also:

  Constant Field Values

• PCX

  public static final int PCX

  extension: .pcx.

  See Also:

  Constant Field Values

• PIC

  public static final int PIC

  extension: .pic.

  See Also:

  Constant Field Values

• PICT

  public static final int PICT

  extension: .pict.

  See Also:

  Constant Field Values

• PNG

  public static final int PNG

  extension: .png.

  See Also:

  Constant Field Values

• PSD

  public static final int PSD

  extension: .psd.

  See Also:

  Constant Field Values

• QT

  public static final int QT

  Quicktime file type. extension: .mov, .qt

  See Also:

  Constant Field Values

• RAW

  public static final int RAW

  RAW image data, no header. extension: .raw

  See Also:

  Constant Field Values

• RAW_MULTIFILE

  public static final int RAW_MULTIFILE

  RAW MULTIFLE image data, no header.

  See Also:

  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

  See Also:

  Constant Field Values

• STK

  public static final int STK

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

  See Also:

  Constant Field Values

• SURFACE_XML

  public static final int SURFACE_XML

  MIPAV Surface XML file format. extension: .xml

  See Also:

  Constant Field Values

• TGA

  public static final int TGA

  extension: .tga.

  See Also:

  Constant Field Values

• TIFF

  public static final int TIFF

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

  See Also:

  Constant Field Values

• TIFF_MULTIFILE

  public static final int TIFF_MULTIFILE

  Multiple files of TIFF images.

  See Also:

  Constant Field Values

• TMG

  public static final int TMG

  Optical coherence tomography. extension: .tmg

  See Also:

  Constant Field Values

• VOI_FILE

  public static final int VOI_FILE

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

  See Also:

  Constant Field Values

• XBM

  public static final int XBM

  extension: .xbm.

  See Also:

  Constant Field Values

• XML

  public static final int XML

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

  See Also:

  Constant Field Values

• XML_MULTIFILE

  public static final int XML_MULTIFILE

  MIPAV XML file format.

  See Also:

  Constant Field Values

• XPM

  public static final int XPM

  extension: .xpm.

  See Also:

  Constant Field Values

• PARREC

  public static final int PARREC

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

  See Also:

  Constant Field Values

• PARREC_MULTIFILE

  public static final int PARREC_MULTIFILE

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

  See Also:

  Constant Field Values

• SPAR

  public static final int SPAR

  SPAR file format for use with PARREC images

  See Also:

  Constant Field Values

• SURFACEREF_XML

  public static final int SURFACEREF_XML

  MIPAV Surface XML file format. extension: .xml

  See Also:

  Constant Field Values

• MINC_HDF

  public static final int MINC_HDF

  MINC 2.0 (HDF5)

  See Also:

  Constant Field Values

• LIFF

  public static final int LIFF

  Do not confuse with Leica image file format .lif

  See Also:

  Constant Field Values

• BFLOAT

  public static final int BFLOAT

  Extension: .hdr for header, .bfloat for data

  See Also:

  Constant Field Values

• SIEMENSTEXT

  public static final int SIEMENSTEXT

  Extension: .hdr for header, .img for data

  See Also:

  Constant Field Values

• ZVI

  public static final int ZVI

  Zeiss ZVI has extension .zvi

  See Also:

  Constant Field Values

• JP2

  public static final int JP2

  See Also:

  Constant Field Values

• MATLAB

  public static final int MATLAB

  extension .mat

  See Also:

  Constant Field Values

• VISTA

  public static final int VISTA

  Vista file extension .v

  See Also:

  Constant Field Values

• METAIMAGE

  public static final int METAIMAGE

  Metaimage files are either separate .mhd header and .raw image data files or combined .mha header and image data file

  See Also:

  Constant Field Values

• TRACKVIS

  public static final int TRACKVIS

  Extension: .trk, TrackVis track data

  See Also:

  Constant Field Values

• CZI

  public static final int CZI

  Zeiss ZISRAW (CZI) file format extension .czi

  See Also:

  Constant Field Values

• PGM

  public static final int PGM

  Portable Gray Map extension .pgm

  See Also:

  Constant Field Values

• PPM

  public static final int PPM

  Portable Pixmap Utilities .ppm

  See Also:

  Constant Field Values

• SVS

  public static final int SVS

  Aperio TIFF based .svs

  See Also:

  Constant Field Values

• JSON

  public static final int JSON

  extension .json

  See Also:

  Constant Field Values

• fileTypeStr

  private static final java.lang.String[] fileTypeStr

Constructor Detail

• FileUtility

  public FileUtility()

Method Detail

• getFileTypeFromStr

  public static int getFileTypeFromStr​(java.lang.String s)

  Returns the file type associated with a string.

  Parameters:

  s - String to test

  Returns:

  axis orientation

• getFileTypeStr

  public static java.lang.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 java.lang.String[] getCORFileList​(java.lang.String fileDir,
                                                        java.lang.String fileName,
                                                        boolean quiet)
                                                 throws java.lang.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:

  java.lang.OutOfMemoryError - If there is a problem allocating required memory.

• getCORSuffixFrom

  public static final java.lang.String getCORSuffixFrom​(java.lang.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 java.lang.String getExtension​(java.lang.String absolutePath)

  Returns the extension of the file name (including the dot), 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 java.lang.String getFileDirectory​(java.lang.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​(java.lang.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 java.lang.String[] getFileList​(java.lang.String fileDir,
                                                     java.lang.String fileName,
                                                     boolean quiet)
                                              throws java.lang.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:

  java.lang.OutOfMemoryError - If there is a problem allocating required memory.

• getFileName

  public static final java.lang.String getFileName​(java.lang.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​(java.lang.String fileName,
                                      java.lang.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​(java.lang.String fileName,
                                      java.lang.String fileDir,
                                      boolean doWrite,
                                      boolean quiet,
                                      boolean[] zerofunused)

  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).

  zerofunused - If true, zero funused fields in an analyze write

  Returns:

  Filetype from FileBase.

  See Also:

  FileBase

• isAnalyzeOrSPM

  public static final int isAnalyzeOrSPM​(java.lang.String fileName,
                                         java.lang.String fileDir,
                                         boolean quiet)
                                  throws java.io.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:

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

• isDicom

  public static final int isDicom​(java.lang.String fileName,
                                  java.lang.String fileDir,
                                  boolean quiet)
                           throws java.io.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:

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

• isDicom_ver2

  public static final int isDicom_ver2​(java.lang.String fileName,
                                       java.lang.String fileDir,
                                       boolean quiet)
                                throws java.io.IOException

  tests if unknown file is of type 2.0 dicom

  Parameters:

  fileName -

  fileDir -

  quiet -

  Returns:

  Throws:

  java.io.IOException

• isGESigna4X

  public static final int isGESigna4X​(java.lang.String fileName,
                                      java.lang.String fileDir,
                                      boolean quiet)
                               throws java.io.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:

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

• isGESigna5X

  public static final int isGESigna5X​(java.lang.String fileName,
                                      java.lang.String fileDir,
                                      boolean quiet)
                               throws java.io.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:

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

• isInterfile

  public static final int isInterfile​(java.lang.String fileName,
                                      java.lang.String fileDir,
                                      boolean quiet)
                               throws java.io.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:

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

• isMagnetomVision

  public static final int isMagnetomVision​(java.lang.String fileName,
                                           java.lang.String fileDir,
                                           boolean quiet)
                                    throws java.io.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:

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

• isMinc

  public static final int isMinc​(java.lang.String fileName,
                                 java.lang.String fileDir,
                                 boolean quiet)
                          throws java.io.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:

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

• isMincHDF

  public static final int isMincHDF​(java.lang.String fileName,
                                    java.lang.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​(java.lang.String fileName,
                                  java.lang.String fileDir,
                                  boolean quiet)
                           throws java.io.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:

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

• isSPM

  public static final int isSPM​(java.lang.String fileName,
                                java.lang.String fileDir,
                                boolean quiet)
                         throws java.io.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:

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

• stripExtension

  public static final java.lang.String stripExtension​(java.lang.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 java.lang.String trimCOR​(java.lang.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 java.lang.String trimNumbersAndSpecial​(java.lang.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 java.util.List<java.lang.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.

• getFileNameList

  public static final java.util.List<java.lang.String> getFileNameList​(FileInfoBase[] fileInfoList)

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

  Parameters:

  image - the ModelImage object.

  Returns:

  the actual file name list.