java.lang.Object
- gov.nih.mipav.model.file.FileIO

```
public class FileIO
extends java.lang.Object
```
This class controls the file input/output of most formats that MIPAV supports, including tiff, raw, analyze, DICOM, and Medvision. It switches based on file type and calls the file constructors, readers, and writers for the specific file type. However, note the FileAvi and FileQT are called directly from ViewJFrameBase for file writes.

Version:

0.1 Sept 5, 1997

Author:

Matthew J. McAuliffe, Ph.D., Neva Cherniavsky

See Also:

FileAnalyze, FileDicom, FileMedVision, FileRaw, FileTiff

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description
`private static class`	`FileIO.LinkedComparator`
`(package private) static class`	`FileIO.LinkedNum`
`class`	`FileIO.OrientStatus`	Orientation information held by orientation.

Field Summary

Fields
Modifier and Type	Field	Description
`private java.lang.String[]`	`dataFileName`	For multi file formats where data is saved in a set of files
`private boolean`	`displayRangeOfSlicesDialog`
`private boolean`	`doTIFFOrientation`
`private DTIParameters`	`dtiparams`
`static java.lang.String`	`FILE_READ`	DOCUMENT ME!
`static java.lang.String`	`FILE_WRITE`	DOCUMENT ME!
`private java.lang.String`	`fileDir`	Directory where the image file can be found.
`private ModelImage`	`imageA`
`private boolean`	`isDTISort`
`private ModelLUT`	`LUT`	If a LUT is to be saved with the image it is stored here.
`private ModelRGB`	`modelRGB`	DOCUMENT ME!
`private ViewJProgressBar`	`progressBar`	DOCUMENT ME!
`private boolean`	`quiet`	Refers to whether or not the FileIO reports progress or errors.
`private RawImageInfo`	`rawInfo`	DOCUMENT ME!
`private boolean`	`saveAsEncapJP2`
`private int`	`secondImage`	Address of second image in file.
`private boolean`	`suppressProgressBar`
`private ViewUserInterface`	`UI`	Reference to the user interface.
`private JDialogUnknownIO`	`unknownIODialog`	Dialog to prompt the user to determine the correct file type.

Constructor Summary

Constructors
Constructor	Description
`FileIO()`	Creates the FileIO and displays Choose File Type unknown file dialog.
`FileIO(ModelLUT _LUT)`	Creates the FileIO and displays Choose File Type unknown file dialog.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private int`	`absBiggest(double zero, double one, double two)`	Helper method for finding biggest (absolute value) of three numbers.
`private boolean`	`callDialog(int[] extents, int dataType, FileWriteOptions options)`	Calls GUI dialogs based on what type of image this is and the number of dimensions.
`static int`	`chkMultiFile(int fileType, boolean multiFile)`	Sets specific types to be multifile based on the input argument.
`private java.lang.String`	`convertNumbersToStr(java.lang.String dicomNumberString)`
`static ModelImage`	`convertToARGB(ModelImage modelImage)`	DOCUMENT ME!
`private ModelImage`	`convertToMultifile(ModelImage existingMultifileImage, ModelImage origImage, int[] extents, int pos)`
`static ModelImage`	`convertToUBYTE(ModelImage modelImageResult)`	DOCUMENT ME!
`private static void`	`copyResolutions(ModelImage modelImageSrc, ModelImage modelImageResult, int sliceNum)`	DOCUMENT ME!
`private ModelImage`	`createMultifile(FileInfoBase myFileInfo, ModelImage origImage, java.lang.String fileDir, java.lang.String fileName, boolean quiet)`
`private void`	`createProgressBar(FileBase fBase, java.lang.String fName, java.lang.String message)`	Creates the progress bar and links (if not null) the progress bar to a FileBase for reading/writing if the progress bar should not be updated within the FileBase's readImage/writeImage, pass in null to the fBase and update within FileIO's read[ImageType] or write[ImageType] methods.
`protected boolean`	`dataConversion(FileInfoBase sourceInfo, FileInfoBase destInfo)`	Provides a method of conversion from `FileInfoDicom` to `FileInfoImageXML`, by filling the `FileInfoImageXML` with sets of chosen image information (from the DICOM tags).
`void`	`dispose()`
`private static java.lang.String`	`generateGEID(FileDicomTagTable tagTable)`
`byte[]`	`getByteImageData(ModelImage image, int start, int length)`
`protected java.util.Hashtable<FileDicomKey,FileDicomTag>`	`getDicomSaveList(FileInfoDicom sourceInfo, boolean isXML)`	Returns a list of tags that are a subset of the DICOM dictionary.
`private double`	`getDoubleValOrAsciiVal(java.lang.String value)`
`int`	`getFileType()`	Presents a dialog for a user-entered definition of the image type.
`private java.lang.String`	`getModality(FileDicom imageFile)`	Gets the value of the Dicom modality tag, 0008,0060.
`ModelLUT`	`getModelLUT()`	Returns LUT associated with the image file.
`ModelRGB`	`getModelRGB()`	Gets the model RGB.
`private java.awt.image.BufferedImage`	`getRenderedImage(java.awt.Image in)`
`int`	`getSecondImage()`	Returns address of TIFF header of second image if present in CZ-Private Tag of LSM 510 file Returns zero if not present.
`private void`	`insertEnhancedSequence(FileInfoDicom myFileInfo, FileInfoDicom[][] infoAr, int dataType)`
`private boolean`	`isDiffusionSeries(FileInfoDicom dicomInfo)`
`boolean`	`isQuiet()`	Refers to whether or not the FileIO will send alerts to the user about progress or errors.
`protected void`	`LSMDataConversion(FileInfoLSM sourceInfo, FileInfoImageXML destInfo)`	Provides a method of conversion from `FileInfoLSM` to `FileInfoImageXML`, by filling the `FileInfoImageXML` with sets of chosen image information.
`private ModelImage`	`readAfni(java.lang.String fileName, java.lang.String fileDir, boolean loadB)`	Reads an AFNI file by calling the read method of the file.
`private ModelImage`	`readAnalyze(java.lang.String fileName, java.lang.String fileDir, boolean one)`	Reads an analyze file by calling the read method of the file.
`private ModelImage`	`readAnalyzeMulti(java.lang.String fileName, java.lang.String fileDir)`	Reads a multi Analyze file.
`private ModelImage`	`readAvi(java.lang.String fileName, java.lang.String fileDir, boolean one, boolean readQT)`	Reads an AVI file by calling the read method of the file.
`private ModelImage`	`readBFLOAT(java.lang.String fileName, java.lang.String fileDir, boolean one)`	Reads a BFLOAT file by calling the read method of the file.
`private ModelImage`	`readBioRad(java.lang.String fileName, java.lang.String fileDir, boolean one)`	Reads a BioRad PIC file by calling the read method of the file.
`private ModelImage`	`readBMP(java.lang.String fileName, java.lang.String fileDir, boolean one)`	Reads a BMP file by calling the read method of the file.
`private ModelImage`	`readBMPMulti(java.lang.String fileName, java.lang.String fileDir, boolean one)`
`private ModelImage`	`readBRUKER(java.lang.String fileName, java.lang.String fileDir, boolean one)`	Reads a BRUKER file by first reading in the d3proc header file, second the reco header file, third the acqp file, and finally the 2dseq binary file.
`private ModelImage`	`readCheshire(java.lang.String fileName, java.lang.String fileDir)`	Reads a Cheshire file by calling the read method of the file.
`private ModelImage`	`readCOR(java.lang.String fileName, java.lang.String fileDir)`	Reads a COR file by first reading the header file then reading in each separate slice file.
`private ModelImage`	`readCZI(java.lang.String fileName, java.lang.String fileDir, boolean one)`	Reads a Zeiss ZISRAW (CZI) file by calling the read method of the file.
`ModelImage`	`readDicom(java.lang.String selectedFileName, java.lang.String[] fileList, boolean performSort)`	Reads a list of DICOM files.
`private ModelImage`	`readDM3(java.lang.String fileName, java.lang.String fileDir, boolean one)`	Reads a Dm3 file by calling the read method of the file.
`private int`	`readFileType(boolean niftiCompressed, boolean multiFile, java.lang.String fileName, java.lang.String fDir)`
`private ModelImage`	`readFits(java.lang.String fileName, java.lang.String fileDir, boolean one)`	Reads a FITS file by calling the read method of the file.
`ModelImage`	`readGEGenesis5X(java.lang.String fileName, java.lang.String fileDir)`	Reads in a single GE Genesis type file.
`ModelImage`	`readGEGenesis5XMulti(java.lang.String fileName, java.lang.String fileDir)`	Reads in multiple GE Genesis 5x type files.
`ModelImage`	`readGESigna4X(java.lang.String fileName, java.lang.String fileDir)`	Reads in a single GE Signa 4x type file.
`private ModelImage`	`readGESigna4XMulti(java.lang.String fileName, java.lang.String fileDir)`	Reads in multiple GE Signa 4x type files.
`FileInfoBase`	`readHeader(java.lang.String absoluteFilename)`	Reads generic file from an absolute filename.
`FileInfoBase`	`readHeader(java.lang.String absoluteFilename, boolean multiFile)`	Reads generic file from an absolute filename.
`FileInfoBase`	`readHeader(java.lang.String fileName, java.lang.String fileDir)`	Reads file, determines file type, and calls a read function specific to the file.
`FileInfoBase`	`readHeader(java.lang.String fileName, java.lang.String fileDir, boolean multiFile)`	Reads file, determines file type, and calls a read function specific to the file.
`private ModelImage`	`readICS(java.lang.String fileName, java.lang.String fileDir)`	Reads an ICS file by calling the read method of the file.
`ModelImage`	`readImage(java.lang.String absoluteFilename)`	Reads generic file from an absolute filename.
`ModelImage`	`readImage(java.lang.String fileName, java.lang.String fileDir)`	Reads file, determines file type, and calls a read function specific to the file.
`ModelImage`	`readImage(java.lang.String fileName, java.lang.String fileDir, boolean multiFile, FileInfoBase fileInfo)`	Reads file, determines file type, and calls a read function specific to the file.
`ModelImage`	`readImage(java.lang.String fileName, java.lang.String fileDir, boolean multiFile, FileInfoBase fileInfo, boolean loadB)`	Reads file, determines file type, and calls a read function specific to the file.
`ModelImage`	`readImage(java.lang.String fileName, java.lang.String fileDir, boolean multiFile, FileInfoBase fileInfo, int secondAddress)`	Reads file, determines file type, and calls a read function specific to the file.
`ModelImage`	`readImage(java.lang.String fileName, java.lang.String fileDir, boolean multiFile, FileInfoBase fileInfo, int secondAddress, boolean loadB, boolean one)`	Reads file, determines file type, and calls a read function specific to the file.
`private ModelImage`	`readInterfile(java.lang.String fileName, java.lang.String fileDir, boolean one)`	Reads an Interfile file by calling the read method of the file.
`private ModelImage`	`readInterfileMulti(java.lang.String fileName, java.lang.String fileDir)`	Reads a multi Interfile file.
`ModelImage`	`readJimi(java.lang.String fileName, java.lang.String fileDir, boolean multifile)`	Reads a JIMI file by calling the read method of the file.
`private ModelImage`	`readJpeg2000(java.lang.String fileName, java.lang.String fileDir, boolean one)`	Reads a JPEG2000 file by calling the read method of the file.
`private ModelImage`	`readLIFF(java.lang.String fileName, java.lang.String fileDir, boolean one)`	Reads a Improvision OpenLab LIFF file by calling the read method of the file.
`private ModelImage`	`readLSM(java.lang.String fileName, java.lang.String fileDir, int secondAddress, boolean one)`	Reads a LSM file by calling the read method of the file.
`private ModelImage`	`readLSMMulti(java.lang.String fileName, java.lang.String fileDir)`	Reads a multi LSM file by first reading the headers then reading in each separate file.
`private ModelImage`	`readMagnetomVision(java.lang.String fileName, java.lang.String fileDir)`	Reads a Magnetom Vision file by calling the read method of the file.
`private ModelImage`	`readMagnetomVisionMulti(java.lang.String fileName, java.lang.String fileDir)`	Reads multiple Magnetom Vision files by calling the read method of the file.
`private ModelImage`	`readMap(java.lang.String fileName, java.lang.String fileDir)`	Reads a Map file by calling the read method of the file.
`private ModelImage`	`readMATLAB(java.lang.String fileName, java.lang.String fileDir, boolean one)`	Reads a NATLAB file by calling the read method of the file.
`private ModelImage`	`readMedVision(java.lang.String fileName, java.lang.String fileDir)`	Reads a MedVision file by calling the read method of the file.
`private ModelImage`	`readMetaImage(java.lang.String fileName, java.lang.String fileDir, boolean one)`	Reads a MetaImage file by calling the read method of the file. if so, calls that method instead.
`private ModelImage`	`readMGH(java.lang.String fileName, java.lang.String fileDir, boolean one)`	Reads a MGH file by calling the read method of the file. if so, calls that method instead.
`private ModelImage`	`readMicroCat(java.lang.String fileName, java.lang.String fileDir, boolean one)`	Reads an Micro Cat file by calling the read method of the file.
`private ModelImage`	`readMinc(java.lang.String fileName, java.lang.String fileDir, boolean one)`	Reads a MINC file by calling the read method of the file.
`private ModelImage`	`readMincHDF(java.lang.String fileName, java.lang.String fileDir, boolean one)`
`private ModelImage`	`readMincMulti(java.lang.String fileName, java.lang.String fileDir)`	Reads a multi Minc file.
`private ModelImage`	`readMRC(java.lang.String fileName, java.lang.String fileDir)`	Reads a MRC file by calling the read method of the file.
`ModelImage`	`readNIFTI(java.lang.String fileName, java.lang.String fileDir, boolean one, boolean niftiCompressed, boolean noImportData, boolean noReadPrivateTags)`	Reads a NIFTI file by calling the read method of the file. if so, calls that method instead.
`private ModelImage`	`readNIFTIMulti(java.lang.String fileName, java.lang.String fileDir)`	Reads a multi NIFTI file.
`private ModelImage`	`readNRRD(java.lang.String fileName, java.lang.String fileDir, boolean one)`	Reads a NRRD file by calling the read method of the file. if so, calls that method instead.
`private ModelImage`	`readNRRDMulti(java.lang.String fileName, java.lang.String fileDir)`	Reads a multi NRRD file.
`ModelImage`	`readOneImage(java.lang.String fileName, java.lang.String fileDir)`	Reads file, determines file type, and calls a read function specific to the file.
`ModelImage`	`readOrderedARGB(java.io.File[] fileList, int numChannels, int[] channelMap, boolean showOrderedProgressBar, java.awt.Dimension subsampleDimension, boolean forceUBYTE)`	This method examines parameter fileList and loads TIFF files according to the order in the list.
`ModelImage`	`readOrderedGrayscale(java.io.File[] fileList, boolean showLocalProgressBar, java.awt.Dimension subsampleDimension, boolean forceUBYTE)`	This method will load a group of files in the order of fileList.
`ModelImage`	`readOrderedGrayscale(java.io.File[] fileList, boolean showLocalProgressBar, java.awt.Dimension subsampleDimension, boolean forceUBYTE, int numSlices, int numTimePoints)`	This method will load a group of files in the order of fileList.
`ModelImage`	`readOrderedGrayscale2(java.io.File[] fileList, boolean showLocalProgressBar, java.awt.Dimension subsampleDimension, boolean forceUBYTE, int numSlices, int numTimePoints)`
`private ModelImage`	`readPARREC(java.lang.String fileName, java.lang.String fileDir, boolean one)`	Reads a PARREC file by calling the read method of the file.
`private ModelImage`	`readPARRECMulti(java.lang.String fileName, java.lang.String fileDir)`	Reads a multi PARREC file.
`private ModelImage`	`readPGM(java.lang.String fileName, java.lang.String fileDir)`	Reads a PGM file by calling the read method of the file.
`private ModelImage`	`readPPM(java.lang.String fileName, java.lang.String fileDir)`	Reads a PPM file by calling the read method of the file.
`private ModelImage`	`readQT(java.lang.String fileName, java.lang.String fileDir)`	Reads a QT file by calling the read method of the file.
`private ModelImage`	`readRaw(java.lang.String fileName, java.lang.String fileDir, FileInfoBase fileInfo)`	Reads a RAW file by calling the read method of the file.
`private ModelImage`	`readRawMulti(java.lang.String fileName, java.lang.String fileDir, FileInfoBase fileInfo)`	Reads a RAW file by calling the read method of the file.
`private ModelImage`	`readSiemensText(java.lang.String fileName, java.lang.String fileDir, boolean one)`	Reads an siemenstext file by calling the read method of the file.
`private ModelImage`	`readSpar(FileInfoBase fileInfo, java.lang.String fileName, java.lang.String fileDir, boolean one)`	Reads a Spar file by calling the read method of the file.
`private ModelImage`	`readSPM(java.lang.String fileName, java.lang.String fileDir, boolean one)`	Reads an SPM file by calling the read method of the file.
`private ModelImage`	`readSTK(java.lang.String fileName, java.lang.String fileDir, boolean one)`	Reads a STK file by calling the read method of the file.
`private ModelImage`	`readSVS(java.lang.String fileName, java.lang.String fileDir, boolean one)`	Reads a SVS file by calling the read method of the file.
`ModelImage`	`readTiff(java.lang.String fileName, java.lang.String fileDir, boolean one)`	Reads a TIFF file by calling the read method of the file.
`private ModelImage`	`readTiffMulti(java.lang.String fileName, java.lang.String fileDir)`	Reads a multi TIFF file by first reading the headers then reading in each separate file.
`private ModelImage`	`readTMG(java.lang.String fileName, java.lang.String fileDir)`	Reads a TMG file by calling the read method of the file.
`private ModelImage`	`readTrackVis(java.lang.String fileName, java.lang.String fileDir)`	Reads in a single TrackVis file.
`private ModelImage`	`readVista(java.lang.String fileName, java.lang.String fileDir, boolean one)`
`ModelImage`	`readXML(java.lang.String fileName, java.lang.String fileDir, boolean one, boolean bDisplayProgress)`	Reads an XML file by calling the read method of the file.
`private ModelImage`	`readXMLMulti(java.lang.String fileName, java.lang.String fileDir)`	Reads a multi XML file.
`FileImageXML`	`readXMLThumbnail(java.lang.String name, java.lang.String directory)`	Reads a thumbnail image from an XML file. if thumbnail is empty, will returned FileImageXML will be null.
`private ModelImage`	`readZVI(java.lang.String fileName, java.lang.String fileDir, boolean one)`	Reads a Zeiss ZVI file by calling the read method of the file.
`(package private) java.lang.String`	`reduceStringLengthTo16(java.lang.String str)`
`private void`	`removeEnhancedDicomInfo(FileInfoDicom myFileInfo, FileInfoBase[] fileInfoBases)`
`private java.lang.String[]`	`removeFromImageList(java.lang.String selectedFileName, java.lang.String[] fileList)`
`private static float[]`	`resample255(float[] buffer, float min, float max)`	The purpose of this method is to take a buffer of float and resample the values to proper UBYTE values.
`void`	`setDisplayRangeOfSlicesDialog(boolean displayRangeOfSlicesDialog)`
`void`	`setFileDir(java.lang.String dir)`	Sets the directory where the file will be saved or opened.
`void`	`setImageA(ModelImage imageA)`
`void`	`setModelLUT(ModelLUT lut)`	Sets the LUT.
`void`	`setModelRGB(ModelRGB rgb)`	Sets the RGB.
`void`	`setPBar(ProgressBarInterface pBar)`	Sets the progress bar (either panel or frame) to be used in image opening to update status.
`void`	`setQuiet(boolean q)`	Refers to whether or not the FileIO will send alerts to the user about progress or errors.
`void`	`setRawImageInfo(RawImageInfo rawInfo)`	DOCUMENT ME!
`void`	`setSuppressProgressBar(boolean suppressProgressBar)`
`void`	`setTIFFOrientation(boolean doTIFFOrientation)`
`void`	`setUserDefinedFileTypes_textFieldPref(java.lang.String udefSuffix)`	This method sets the userDefinedFileTypes_textField preference.
`void`	`setUserDefinedFileTypesPref(java.lang.String udefSuffix)`	This method sets the userDefinedFileTypes preference.
`private static boolean`	`sort(float[] A, int[] B, int size)`	Sorts an array of floats (using Arrays.sort), turns into array of ints used to sort images by A; thus, the final value of B[i] is for the ith image read in, put that image at location B[i] in the image buffer.
`private static boolean`	`sort(int[] A, int[] B, int size)`	Sorts an array of ints (using insertion sort), turns into array of ints used to sort images by image number; thus, the final value of B[i] is for the ith image read in, put that image at location B[i] in the image buffer.
`private int`	`sortDtiDicomData(java.lang.String studyDescription, java.lang.String seriesDescription, java.lang.String scannerType, FileDicomTagTable tagTable, FileInfoDicom[] savedFileInfos, int[] indices, int instanceNumsLength, int[] zInst)`
`static ModelImage`	`subsample(ModelImage modelImage, java.awt.Dimension subsampleDimension)`	The purpose of this method is to subsample a ModelImage to the dimensions specified by the subsampleDimension parameter.
`private int[]`	`tryPartitionByMediaUID(FileInfoDicom[] savedFileInfos)`	partition into image subsets using media instance uids
`private boolean`	`writeAfni(ModelImage image, FileWriteOptions options)`	Writes an AFNI file to store the image.
`private boolean`	`writeAnalyze(ModelImage image, FileWriteOptions options, boolean zerofunused)`	Writes an analyze file to store the image.
`private boolean`	`writeAvi(ModelImage image, FileWriteOptions options)`	Writes an AVI file to store the image.
`private boolean`	`writeCOR(ModelImage image, FileWriteOptions options)`	Writes a Freesurfer COR file to store the image.
`private boolean`	`writeDicom(ModelImage image, FileWriteOptions options)`	Writes a DICOM file to store the image.
`private boolean`	`writeDicomSlice(ModelImage image, int sliceNumber, FileWriteOptions options, FileInfoDicom fileDicom, FileInfoBase originalFileInfo, int originalImageDataType, TransMatrix originalImageMatrix, double originalImageMin, double originalImageMax, boolean originalIsDicom, boolean originalIsColor)`	Writes a DICOM file on a slice basis.
`private boolean`	`writeFits(ModelImage image, FileWriteOptions options)`	Writes a Fits file to store the image.
`private boolean`	`writeGEGenesis5X(ModelImage image, FileWriteOptions options)`	Writes a GESigna5X file to store the image.
`private boolean`	`writeGESigna4X(ModelImage image, FileWriteOptions options)`	Writes a GESigna4X file to store the image.
`private boolean`	`writeICS(ModelImage image, FileWriteOptions options)`	Writes an ICS file to store the image.
`void`	`writeImage(ModelImage image, FileWriteOptions options)`	Determines file type from the file name and calls different write functions based on the file type.
`void`	`writeImage(ModelImage image, FileWriteOptions options, boolean bDisplayProgress, boolean allowScriptRecording)`	Determines file type from the file name and calls different write functions based on the file type.
`private boolean`	`writeInterfile(ModelImage image, FileWriteOptions options)`	Writes an Interfile file to store the image.
`private boolean`	`writeJimi(ModelImage image, FileWriteOptions options)`	Writes a JIMI file to store the image.
`private boolean`	`writeJpeg2000(ModelImage image, FileWriteOptions options)`	Writes a JPEG2000 file to store the image.
`private boolean`	`writeMATLAB(ModelImage image, FileWriteOptions options)`	Writes a MATLAB file to store the image.
`private boolean`	`writeMetaImage(ModelImage image, FileWriteOptions options)`	Writes a MetaImage file to store the image.
`private boolean`	`writeMGH(ModelImage image, FileWriteOptions options)`	Writes a MGH or MGZ file to store the image.
`private boolean`	`writeMinc(ModelImage image, FileWriteOptions options)`	Writes a Minc file to store the image.
`private boolean`	`writeMincHDF(ModelImage image, FileWriteOptions options)`	Writes out a MINC 2.0 HDF5 formatted file
`private boolean`	`writeMRC(ModelImage image, FileWriteOptions options)`	Writes a MRC file to store the image.
`private boolean`	`writeNIFTI(ModelImage image, FileWriteOptions options)`	Writes a NIFTI file to store the image.
`private boolean`	`writeNRRD(ModelImage image, FileWriteOptions options)`	Writes a NRRD file to store the image.
`private boolean`	`writePARREC(ModelImage image, FileWriteOptions options)`	Writes a PAR/REC file to store the image.
`private boolean`	`writeRaw(ModelImage image, FileWriteOptions options)`	Writes a raw file to store the image.
`private boolean`	`writeSPM(ModelImage image, FileWriteOptions options)`	Writes a SPM file to store the image.
`private boolean`	`writeSTK(ModelImage image, FileWriteOptions options)`	Writes a STK file to store the image.
`private boolean`	`writeTiff(ModelImage image, FileWriteOptions options)`	Writes a TIFF file to store the image.
`private boolean`	`writeVista(ModelImage image, FileWriteOptions options)`	writes Vista format files
`private boolean`	`writeXML(ModelImage image, FileWriteOptions options, boolean bDisplayProgress)`	Writes the image in our MIPAV XML format.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - FILE_READ
```
public static final java.lang.String FILE_READ
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - FILE_WRITE
```
public static final java.lang.String FILE_WRITE
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - fileDir
```
private java.lang.String fileDir
```
    Directory where the image file can be found.
  - LUT
```
private ModelLUT LUT
```
    If a LUT is to be saved with the image it is stored here.
  - modelRGB
```
private ModelRGB modelRGB
```
    DOCUMENT ME!
  - progressBar
```
private ViewJProgressBar progressBar
```
    DOCUMENT ME!
  - quiet
```
private boolean quiet
```
    Refers to whether or not the FileIO reports progress or errors.
  - rawInfo
```
private RawImageInfo rawInfo
```
    DOCUMENT ME!
  - secondImage
```
private int secondImage
```
    Address of second image in file.
  - UI
```
private final ViewUserInterface UI
```
    Reference to the user interface.
  - unknownIODialog
```
private JDialogUnknownIO unknownIODialog
```
    Dialog to prompt the user to determine the correct file type. If the type of file to read is unknown (ie., the suffix doesn't match one of the known types, build and display the unknown file dialog so the user can try to identify the image type so the correct reader can be used
  - saveAsEncapJP2
```
private boolean saveAsEncapJP2
```
  - displayRangeOfSlicesDialog
```
private boolean displayRangeOfSlicesDialog
```
  - dataFileName
```
private java.lang.String[] dataFileName
```
    For multi file formats where data is saved in a set of files
  - dtiparams
```
private DTIParameters dtiparams
```
  - isDTISort
```
private boolean isDTISort
```
  - doTIFFOrientation
```
private boolean doTIFFOrientation
```
  - imageA
```
private ModelImage imageA
```
  - suppressProgressBar
```
private boolean suppressProgressBar
```
- Constructor Detail
  - FileIO
```
public FileIO()
```
    Creates the FileIO and displays Choose File Type unknown file dialog. Constructs a new FileIO object, sets the user interface, and initializes the unknown file dialog. Also gets the userDefinedFileTypeAssociations preferences
  - FileIO
```
public FileIO(ModelLUT _LUT)
```
    Creates the FileIO and displays Choose File Type unknown file dialog. Constructs a new FileIO object, sets the user interface, sets the LUT, and initializes the unknown file dialog. Also gets the userDefinedFileTypeAssociations preferences
    
    Parameters:
    
    _LUT - Passes LUT into file IO object so that LUT can be store with image (i.e. TIFF).
- Method Detail
  - dispose
```
public void dispose()
```
  - chkMultiFile
```
public static final int chkMultiFile(int fileType,
                                     boolean multiFile)
```
    Sets specific types to be multifile based on the input argument. Not all file types are supported to handle multifiles. Those that do support building a 3D image out of a series of 2D images are defined to have that input capability here.
    
    Parameters:
    
    fileType - Input file type. File types which MIPAV does not allow multifile images get the file type returned as sent.
    
    multiFile - If true, returns a new filetype corresponding to the input filetype + MULTIFILE. If false, returns the given filetype.
    
    Returns:
    
    The new or old fileType.
  - setImageA
```
public void setImageA(ModelImage imageA)
```
  - setSuppressProgressBar
```
public void setSuppressProgressBar(boolean suppressProgressBar)
```
    Parameters:
    
    suppressProgressBar -
  - convertToARGB
```
public static final ModelImage convertToARGB(ModelImage modelImage)
```
    DOCUMENT ME!
    
    Parameters:
    
    modelImage - ModelImage - the image to resample to UBYTE
    
    Returns:
    
    ModelImage
  - convertToUBYTE
```
public static final ModelImage convertToUBYTE(ModelImage modelImageResult)
```
    DOCUMENT ME!
    
    Parameters:
    
    modelImageResult - ModelImage - the image to resample to UBYTE
    
    Returns:
    
    ModelImage
  - subsample
```
public static final ModelImage subsample(ModelImage modelImage,
                                         java.awt.Dimension subsampleDimension)
```
    The purpose of this method is to subsample a ModelImage to the dimensions specified by the subsampleDimension parameter.
    
    Parameters:
    
    modelImage - ModelImage - the image to be subsampled. This image will be destroyed in the course of the algorithm
    
    subsampleDimension - Dimension - the dimensions to subsample to.
    
    Returns:
    
    ModelImage - the subsampled image
  - getFileType
```
public int getFileType()
```
    Presents a dialog for a user-entered definition of the image type.
    
    Returns:
    
    The image file type entered by the user, or FileUtility.ERROR if FileIO is quiet or the dialog is cancelled. see FileUtility.ERROR see isQuiet()
    
    See Also:
    
    JDialogUnknownIO
  - getModelLUT
```
public ModelLUT getModelLUT()
```
    Returns LUT associated with the image file.
    
    Returns:
    
    The LUT associated with the image although it may be null.
  - getModelRGB
```
public ModelRGB getModelRGB()
```
    Gets the model RGB.
    
    Returns:
    
    ModelRGB
  - getSecondImage
```
public int getSecondImage()
```
    Returns address of TIFF header of second image if present in CZ-Private Tag of LSM 510 file Returns zero if not present.
    
    Returns:
    
    secondImage
  - isQuiet
```
public boolean isQuiet()
```
    Refers to whether or not the FileIO will send alerts to the user about progress or errors.
    
    Returns:
    
    Whether to suppress GUI elements which would require user interaction (ie, error dialogs).
  - readDicom
```
public ModelImage readDicom(java.lang.String selectedFileName,
                            java.lang.String[] fileList,
                            boolean performSort)
```
    Reads a list of DICOM files. DICOM images have all their slices in separate files (except multi-frame), with different information in each header. The position of the slice in the image is determined by information found in the header so all the headers must be read before the images can be read. That's why this method goes through all the images twice.
    
    Parameters:
    
    selectedFileName - Name of the image file selected to be readin this#fileDir to read. Used to ID study and series number
    
    fileList - List of all the files to be read in.
    
    performSort - true if this method is to sort the files in the list, or, false will apply the images in each file in the order they appear as the order to use in the ModelImage.
    
    Returns:
    
    The image that was read in, or null if failure.
  - isDiffusionSeries
```
private boolean isDiffusionSeries(FileInfoDicom dicomInfo)
```
  - sortDtiDicomData
```
private int sortDtiDicomData(java.lang.String studyDescription,
                             java.lang.String seriesDescription,
                             java.lang.String scannerType,
                             FileDicomTagTable tagTable,
                             FileInfoDicom[] savedFileInfos,
                             int[] indices,
                             int instanceNumsLength,
                             int[] zInst)
```
  - generateGEID
```
private static java.lang.String generateGEID(FileDicomTagTable tagTable)
```
  - tryPartitionByMediaUID
```
private int[] tryPartitionByMediaUID(FileInfoDicom[] savedFileInfos)
```
    partition into image subsets using media instance uids
  - removeFromImageList
```
private java.lang.String[] removeFromImageList(java.lang.String selectedFileName,
                                               java.lang.String[] fileList)
```
  - getModality
```
private java.lang.String getModality(FileDicom imageFile)
```
    Gets the value of the Dicom modality tag, 0008,0060. SR tags indicate a structured report file.
    
    Parameters:
    
    imageFile -
    
    Returns:
  - readHeader
```
public FileInfoBase readHeader(java.lang.String absoluteFilename)
```
    Reads generic file from an absolute filename.
    
    Parameters:
    
    absoluteFilename - String - the absolute filename, including the path
    
    Returns:
    
    ModelImage
  - readHeader
```
public FileInfoBase readHeader(java.lang.String absoluteFilename,
                               boolean multiFile)
```
    Reads generic file from an absolute filename.
    
    Parameters:
    
    absoluteFilename - String - the absolute filename, including the path
    
    multiFile - Flag indicating multi file.
    
    Returns:
    
    ModelImage
  - readHeader
```
public FileInfoBase readHeader(java.lang.String fileName,
                               java.lang.String fileDir)
```
    Reads file, determines file type, and calls a read function specific to the file. That read function returns an image and this function stores it in ModelImage. File is not multi file, file info is not previously known, there's no "second address" for AFNI, and this is not an image B.
    
    Parameters:
    
    fileName - File name where image is located.
    
    fileDir - File directory where image is located.
    
    Returns:
    
    The image that was read in from the file.
  - readHeader
```
public FileInfoBase readHeader(java.lang.String fileName,
                               java.lang.String fileDir,
                               boolean multiFile)
```
    Reads file, determines file type, and calls a read function specific to the file. That read function returns an image and this function stores it in ModelImage.
    
    Parameters:
    
    fileName - File name where image is located.
    
    fileDir - File directory where image is located.
    
    multiFile - Flag indicating multi file.
    
    Returns:
    
    The image that was read in from the file.
  - readImage
```
public ModelImage readImage(java.lang.String absoluteFilename)
```
    Reads generic file from an absolute filename.
    
    Parameters:
    
    absoluteFilename - String - the absolute filename, including the path
    
    Returns:
    
    ModelImage
  - readImage
```
public ModelImage readImage(java.lang.String fileName,
                            java.lang.String fileDir)
```
    Reads file, determines file type, and calls a read function specific to the file. That read function returns an image and this function stores it in ModelImage. File is not multi file, file info is not previously known, there's no "second address" for AFNI, and this is not an image B.
    
    Parameters:
    
    fileName - File name where image is located.
    
    fileDir - File directory where image is located.
    
    Returns:
    
    The image that was read in from the file.
  - readImage
```
public ModelImage readImage(java.lang.String fileName,
                            java.lang.String fileDir,
                            boolean multiFile,
                            FileInfoBase fileInfo)
```
    Reads file, determines file type, and calls a read function specific to the file. That read function returns an image and this function stores it in ModelImage.
    
    Parameters:
    
    fileName - File name where image is located.
    
    fileDir - File directory where image is located.
    
    multiFile - Flag indicating multi file.
    
    fileInfo - File info already known; will usually be null, but valid if called from script parser.
    
    Returns:
    
    The image that was read in from the file.
  - readImage
```
public ModelImage readImage(java.lang.String fileName,
                            java.lang.String fileDir,
                            boolean multiFile,
                            FileInfoBase fileInfo,
                            boolean loadB)
```
    Reads file, determines file type, and calls a read function specific to the file. That read function returns an image and this function stores it in ModelImage.
    
    Parameters:
    
    fileName - File name where image is located.
    
    fileDir - File directory where image is located.
    
    multiFile - Flag indicating multi file.
    
    fileInfo - File info already known; will usually be null, but valid if called from script parser.
    
    loadB - Flag indicating if this is an image B.
    
    Returns:
    
    The image that was read in from the file.
  - readImage
```
public ModelImage readImage(java.lang.String fileName,
                            java.lang.String fileDir,
                            boolean multiFile,
                            FileInfoBase fileInfo,
                            int secondAddress)
```
    Reads file, determines file type, and calls a read function specific to the file. That read function returns an image and this function stores it in ModelImage.
    
    Parameters:
    
    fileName - File name where image is located.
    
    fileDir - File directory where image is located.
    
    multiFile - Flag indicating multi file.
    
    fileInfo - File info already known; will usually be null, but valid if called from script parser.
    
    secondAddress - Address of second TIFF header
    
    Returns:
    
    The image that was read in from the file.
  - readImage
```
public ModelImage readImage(java.lang.String fileName,
                            java.lang.String fileDir,
                            boolean multiFile,
                            FileInfoBase fileInfo,
                            int secondAddress,
                            boolean loadB,
                            boolean one)
```
    Reads file, determines file type, and calls a read function specific to the file. That read function returns an image and this function stores it in ModelImage.
    
    Parameters:
    
    fileName - File name where image is located.
    
    fileDir - File directory where image is located.
    
    multiFile - Flag indicating multi file loading of images from directory. true is load images of this filetype to be loaded as a set (when this feature is supported).
    
    fileInfo - File info already known; will usually be null, but valid if called from script parser.
    
    secondAddress - Address of second TIFF header
    
    loadB - Flag indicating if this is an image B.
    
    one - A load-single flag. true indicates that the method is to load only the file that is defined by the fileName, rather than a multiple file load of a 3d Image.
    
    Returns:
    
    The image that was read in from the file.
  - readFileType
```
private int readFileType(boolean niftiCompressed,
                         boolean multiFile,
                         java.lang.String fileName,
                         java.lang.String fDir)
```
  - readOneImage
```
public ModelImage readOneImage(java.lang.String fileName,
                               java.lang.String fileDir)
```
    Reads file, determines file type, and calls a read function specific to the file. That read function returns an image and this function stores it in ModelImage. File is not multi file, file info is not previously known, there's no "second address" for AFNI, and this is not an image B. This is just one image regardless of how many slices there are; the middle slice of a 3D dataset will be displayed.
    
    Parameters:
    
    fileName - File name where image is located.
    
    fileDir - File directory where image is located.
    
    Returns:
    
    The image that was read in from the file.
  - readOrderedARGB
```
public ModelImage readOrderedARGB(java.io.File[] fileList,
                                  int numChannels,
                                  int[] channelMap,
                                  boolean showOrderedProgressBar,
                                  java.awt.Dimension subsampleDimension,
                                  boolean forceUBYTE)
```
    This method examines parameter fileList and loads TIFF files according to the order in the list. It can load 2, 3, or 4 channel images. The method will examine channelMap to determine in which order the ARGB channels should be interleaved.
    
    Parameters:
    
    fileList - File[] - the list of File objects, preordered
    
    numChannels - int - the number of channels the result image is to have
    
    channelMap - int[] - a mapping of channels (ARGB) to positions. For example, a channelMap parameter of {2, 1, 0, 3} means the first channel will be G, the second will be R, the third will be A and the last will be B.
    
    showOrderedProgressBar - boolean - This parameter is used to control whether the local progress bar is shown. Note this is different than FileIO's global progress bar. The reason for the difference is because this method uses FileIO's readOneImage() method. That method uses the global progress bar. Its useless to have two progress bars, and FileIO isn't set up in a way that allows this method to directly control the global progress bar, hence the need for its own local one.
    
    subsampleDimension - - the dimensions of the result image if subsampling is desired. To skip subsampling, this parameter should be null
    
    forceUBYTE - boolean - force the image to be constructed with an unsigned byte data type
    
    Returns:
    
    ModelImage
  - readOrderedGrayscale
```
public ModelImage readOrderedGrayscale(java.io.File[] fileList,
                                       boolean showLocalProgressBar,
                                       java.awt.Dimension subsampleDimension,
                                       boolean forceUBYTE)
```
    This method will load a group of files in the order of fileList. The result will be a grayscale ModelImage.
    
    Parameters:
    
    fileList - File[] - list of File objects, preordered
    
    showLocalProgressBar - boolean - This parameter is used to control whether the local progress bar is shown. Note this is different than FileIO's global progress bar. The reason for the difference is because this method uses FileIO's readOneImage() method. That method uses the global progress bar. Its useless to have two progress bars, and FileIO isn't set up in a way that allows this method to directly control the global progress bar, hence the need for its own local one.
    
    subsampleDimension - - the dimensions of the result image if subsampling is desired. To skip subsampling, this parameter should be null
    
    forceUBYTE - boolean - force the image to be constructed with an unsigned byte data type
    
    Returns:
    
    ModelImage
  - readOrderedGrayscale
```
public ModelImage readOrderedGrayscale(java.io.File[] fileList,
                                       boolean showLocalProgressBar,
                                       java.awt.Dimension subsampleDimension,
                                       boolean forceUBYTE,
                                       int numSlices,
                                       int numTimePoints)
```
    This method will load a group of files in the order of fileList. The result will be a grayscale ModelImage.
    
    Parameters:
    
    fileList - File[] - list of File objects, preordered
    
    showLocalProgressBar - boolean - This parameter is used to control whether the local progress bar is shown. Note this is different than FileIO's global progress bar. The reason for the difference is because this method uses FileIO's readOneImage() method. That method uses the global progress bar. Its useless to have two progress bars, and FileIO isn't set up in a way that allows this method to directly control the global progress bar, hence the need for its own local one.
    
    subsampleDimension - - the dimensions of the result image if subsampling is desired. To skip subsampling, this parameter should be null
    
    forceUBYTE - boolean - force the image to be constructed with an unsigned byte data type
    
    Returns:
    
    ModelImage
  - readOrderedGrayscale2
```
public ModelImage readOrderedGrayscale2(java.io.File[] fileList,
                                        boolean showLocalProgressBar,
                                        java.awt.Dimension subsampleDimension,
                                        boolean forceUBYTE,
                                        int numSlices,
                                        int numTimePoints)
```
  - readXMLThumbnail
```
public FileImageXML readXMLThumbnail(java.lang.String name,
                                     java.lang.String directory)
```
    Reads a thumbnail image from an XML file. if thumbnail is empty, will returned FileImageXML will be null.
    
    Parameters:
    
    name - filename
    
    directory - file's directory
    
    Returns:
    
    FileImageXML containing thumbnail or null
  - setFileDir
```
public void setFileDir(java.lang.String dir)
```
    Sets the directory where the file will be saved or opened.
    
    Parameters:
    
    dir - String directory
  - setModelLUT
```
public void setModelLUT(ModelLUT lut)
```
    Sets the LUT.
    
    Parameters:
    
    lut - the lookup table.
  - setModelRGB
```
public void setModelRGB(ModelRGB rgb)
```
    Sets the RGB.
    
    Parameters:
    
    rgb - lut the lookup table.
  - setPBar
```
public void setPBar(ProgressBarInterface pBar)
```
    Sets the progress bar (either panel or frame) to be used in image opening to update status.
    
    Parameters:
    
    pBar - ProgressBarInterface
  - setQuiet
```
public void setQuiet(boolean q)
```
    Refers to whether or not the FileIO will send alerts to the user about progress or errors.
    
    Parameters:
    
    q - Indicates if the output from the methods in this object are to display dialogs interrupting flow in a locally-defined manner. true indicates that the process is to NOT inform the user and therefore be quiet.
  - setRawImageInfo
```
public void setRawImageInfo(RawImageInfo rawInfo)
```
    DOCUMENT ME!
    
    Parameters:
    
    rawInfo - DOCUMENT ME!
  - setUserDefinedFileTypes_textFieldPref
```
public void setUserDefinedFileTypes_textFieldPref(java.lang.String udefSuffix)
```
    This method sets the userDefinedFileTypes_textField preference.
    
    Parameters:
    
    udefSuffix - the user defined suffix
  - setUserDefinedFileTypesPref
```
public void setUserDefinedFileTypesPref(java.lang.String udefSuffix)
```
    This method sets the userDefinedFileTypes preference.
    
    Parameters:
    
    udefSuffix - the user defined suffix
  - writeImage
```
public void writeImage(ModelImage image,
                       FileWriteOptions options)
```
    Determines file type from the file name and calls different write functions based on the file type. Stores file in the specified file name and directory given by the options. Calls appropriate dialogs if necessary. Supports files of type raw, analyze, and DICOM.
    
    Parameters:
    
    image - Image to write.
    
    options - Needed info to write this image.
  - writeImage
```
public void writeImage(ModelImage image,
                       FileWriteOptions options,
                       boolean bDisplayProgress,
                       boolean allowScriptRecording)
```
    Determines file type from the file name and calls different write functions based on the file type. Stores file in the specified file name and directory given by the options. Calls appropriate dialogs if necessary. Supports files of type raw, analyze, and DICOM.
    
    Parameters:
    
    image - Image to write.
    
    options - Needed info to write this image.
    
    bDisplayProgress - when true display the progress bar for writing.
  - getByteImageData
```
public byte[] getByteImageData(ModelImage image,
                               int start,
                               int length)
```
  - dataConversion
```
protected boolean dataConversion(FileInfoBase sourceInfo,
                                 FileInfoBase destInfo)
```
    Provides a method of conversion from FileInfoDicom to FileInfoImageXML, by filling the FileInfoImageXML with sets of chosen image information (from the DICOM tags).
    The XML format suggests that each DICOM tag become a seperate set, and any multiple values stored in the DICOM tag, becomes parameter data. The set name is the DICOM tag name. Each value of the tag is stored as a separate parameter in the set, and its description is stored as the DICOM key (group and element number, as displayed in the file, "dicom.dictionary") along with its position in the value multiplicity. All values stored are stored as value-type "string", and neither date nor time are set. Order of entries is not guaranteed, as order is not meaningful in XML.
    
    Be sure to see the image.xsd file for more information.
    
    Parameters:
    
    sourceInfo - The FileInfoDicom which is the source for user-selectable tags
    
    destInfo - The FileInfoBase that holds the image information to be stored in XML (or MincHDF)format.
    
    See Also:
    
    #getDicomSaveList(FileInfoDicom), JDialogDicom2XMLSelection
  - getDicomSaveList
```
protected java.util.Hashtable<FileDicomKey,FileDicomTag> getDicomSaveList(FileInfoDicom sourceInfo,
                                                                                boolean isXML)
```
    Returns a list of tags that are a subset of the DICOM dictionary. This method chooses the tags to be saved by presenting a dialog for the user to select a list of tags or by reading the dicomsave.dictionary file.
    
    Parameters:
    
    sourceInfo - Source of DICOM information.
    
    Returns:
    
    The Hashtable filled as an XML
  - LSMDataConversion
```
protected void LSMDataConversion(FileInfoLSM sourceInfo,
                                 FileInfoImageXML destInfo)
```
    Provides a method of conversion from FileInfoLSM to FileInfoImageXML, by filling the FileInfoImageXML with sets of chosen image information.
    
    Parameters:
    
    sourceInfo - the LSM-formatted Source information
    
    destInfo - the XML-format file information that is the output.
  - copyResolutions
```
private static void copyResolutions(ModelImage modelImageSrc,
                                    ModelImage modelImageResult,
                                    int sliceNum)
```
    DOCUMENT ME!
    
    Parameters:
    
    modelImageSrc - DOCUMENT ME!
    
    modelImageResult - DOCUMENT ME!
    
    sliceNum - DOCUMENT ME!
  - resample255
```
private static float[] resample255(float[] buffer,
                                   float min,
                                   float max)
```
    The purpose of this method is to take a buffer of float and resample the values to proper UBYTE values.
    
    Parameters:
    
    buffer - float[] - the buffer to be sampled
    
    min - - the image's minimum pixel value
    
    max - - the image's maximum pixel value
    
    Returns:
    
    float[] - the resampled buffer with min and max values in the range 0 - 255
  - sort
```
private static boolean sort(float[] A,
                            int[] B,
                            int size)
```
    Sorts an array of floats (using Arrays.sort), turns into array of ints used to sort images by A; thus, the final value of B[i] is for the ith image read in, put that image at location B[i] in the image buffer. This is necessary for images labeled dicom1, dicom2, etc because dicom11, dicom12, ... will come before dicom2. Also our only indication of the "true" ordering is slice location.
    
    Parameters:
    
    A - Array to be sorted.
    
    B - Array it goes into.
    
    size - Size of the array (both arrays are the same size).
    
    Returns:
    
    false only if any of the numbers in the array are equal.
  - sort
```
private static boolean sort(int[] A,
                            int[] B,
                            int size)
```
    Sorts an array of ints (using insertion sort), turns into array of ints used to sort images by image number; thus, the final value of B[i] is for the ith image read in, put that image at location B[i] in the image buffer. This is necessary for images labeled dicom1, dicom2, etc because dicom11, dicom12, ... will come before dicom2. Also our only indication of the "true" ordering is image number.
    
    Parameters:
    
    A - Array to be sorted.
    
    B - Array it goes into.
    
    size - Size of the array (both arrays are the same size).
    
    Returns:
    
    false only if any of the numbers in the array are equal.
  - absBiggest
```
private int absBiggest(double zero,
                       double one,
                       double two)
```
    Helper method for finding biggest (absolute value) of three numbers.
    
    Parameters:
    
    zero - First value
    
    one - Second value
    
    two - Third value
    
    Returns:
    
    Index of argument that is the biggest. That is, if zero is the largest of the three numbers, the value 0 is returned; alternatively, if the second argument is the largest of the three numbers, the value 1 is returned; and so on.
  - callDialog
```
private boolean callDialog(int[] extents,
                           int dataType,
                           FileWriteOptions options)
```
    Calls GUI dialogs based on what type of image this is and the number of dimensions.
    
    Parameters:
    
    extents - Extents of the image, used to determine what type of dialog to call and initialize variables.
    
    isTiff - Flag indicating if this is a TIFF file; TIFF files require more options.
    
    options - Options to get from the dialog and save.
    
    Returns:
    
    DOCUMENT ME!
  - createProgressBar
```
private void createProgressBar(FileBase fBase,
                               java.lang.String fName,
                               java.lang.String message)
```
    Creates the progress bar and links (if not null) the progress bar to a FileBase for reading/writing if the progress bar should not be updated within the FileBase's readImage/writeImage, pass in null to the fBase and update within FileIO's read[ImageType] or write[ImageType] methods.
    
    Parameters:
    
    fBase - the FileBase that will add the Progress Bar as a listener (for fireProgressStateChanged())
    
    fName - the filename (will be displayed in the title and part of the message)
    
    message - this message should FILE_READ, FILE_OPEN
  - readAfni
```
private ModelImage readAfni(java.lang.String fileName,
                            java.lang.String fileDir,
                            boolean loadB)
```
    Reads an AFNI file by calling the read method of the file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    loadB - true if loading imageB
    
    Returns:
    
    The image that was read in, or null if failure.
  - readAnalyze
```
private ModelImage readAnalyze(java.lang.String fileName,
                               java.lang.String fileDir,
                               boolean one)
```
    Reads an analyze file by calling the read method of the file. Also checks if it's a Cheshire and if so, calls that method instead. This method contains special code to not display the progress bar should the image be splash.img.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    one - Indicates that only the named file should be read, as opposed to reading the matching files in the directory, as defined by the filetype. true if only want to read one image from 3D dataset.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readSiemensText
```
private ModelImage readSiemensText(java.lang.String fileName,
                                   java.lang.String fileDir,
                                   boolean one)
```
    Reads an siemenstext file by calling the read method of the file. Also checks if it's a Cheshire and if so, calls that method instead. This method contains special code to not display the progress bar should the image be splash.img.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    one - Indicates that only the named file should be read, as opposed to reading the matching files in the directory, as defined by the filetype. true if only want to read one image from 3D dataset.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readAnalyzeMulti
```
private ModelImage readAnalyzeMulti(java.lang.String fileName,
                                    java.lang.String fileDir)
```
    Reads a multi Analyze file. Gets a list of the images from the file directory and reads them each in.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readAvi
```
private ModelImage readAvi(java.lang.String fileName,
                           java.lang.String fileDir,
                           boolean one,
                           boolean readQT)
```
    Reads an AVI file by calling the read method of the file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    one - Indicates that only the named file should be read, as opposed to reading the matching files in the directory, as defined by the filetype. true if only want to read one image from 3D dataset.
    
    readQT - Indicates that a QuickTime movie file is being read. true if this file represents QuickTime.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readBioRad
```
private ModelImage readBioRad(java.lang.String fileName,
                              java.lang.String fileDir,
                              boolean one)
```
    Reads a BioRad PIC file by calling the read method of the file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    one - Indicates that only the named file should be read, as opposed to reading the matching files in the directory, as defined by the filetype. true if only want to read one image from 3D dataset.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readBRUKER
```
private ModelImage readBRUKER(java.lang.String fileName,
                              java.lang.String fileDir,
                              boolean one)
```
    Reads a BRUKER file by first reading in the d3proc header file, second the reco header file, third the acqp file, and finally the 2dseq binary file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    one - Indicates that only the named file should be read, as opposed to reading the matching files in the directory, as defined by the filetype. true if only want to read one image from 3D dataset.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readCheshire
```
private ModelImage readCheshire(java.lang.String fileName,
                                java.lang.String fileDir)
```
    Reads a Cheshire file by calling the read method of the file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readCOR
```
private ModelImage readCOR(java.lang.String fileName,
                           java.lang.String fileDir)
```
    Reads a COR file by first reading the header file then reading in each separate slice file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readDM3
```
private ModelImage readDM3(java.lang.String fileName,
                           java.lang.String fileDir,
                           boolean one)
```
    Reads a Dm3 file by calling the read method of the file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    one - Indicates that only the named file should be read, as opposed to reading the matching files in the directory, as defined by the filetype. true if only want to read one image from 3D dataset.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readFits
```
private ModelImage readFits(java.lang.String fileName,
                            java.lang.String fileDir,
                            boolean one)
```
    Reads a FITS file by calling the read method of the file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    one - Indicates that only the named file should be read, as opposed to reading the matching files in the directory, as defined by the filetype. true if only want to read one image from 3D dataset.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readGEGenesis5XMulti
```
public ModelImage readGEGenesis5XMulti(java.lang.String fileName,
                                       java.lang.String fileDir)
```
    Reads in multiple GE Genesis 5x type files.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readGESigna4XMulti
```
private ModelImage readGESigna4XMulti(java.lang.String fileName,
                                      java.lang.String fileDir)
```
    Reads in multiple GE Signa 4x type files.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readICS
```
private ModelImage readICS(java.lang.String fileName,
                           java.lang.String fileDir)
```
    Reads an ICS file by calling the read method of the file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readInterfile
```
private ModelImage readInterfile(java.lang.String fileName,
                                 java.lang.String fileDir,
                                 boolean one)
```
    Reads an Interfile file by calling the read method of the file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    one - Indicates that only the named file should be read, as opposed to reading the matching files in the directory, as defined by the filetype. true if only want to read one image from 3D dataset.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readInterfileMulti
```
private ModelImage readInterfileMulti(java.lang.String fileName,
                                      java.lang.String fileDir)
```
    Reads a multi Interfile file. Gets a list of the images from the file directory and reads them each in.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readJimi
```
public ModelImage readJimi(java.lang.String fileName,
                           java.lang.String fileDir,
                           boolean multifile)
```
    Reads a JIMI file by calling the read method of the file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    multifile - Indication whether this file is be read alone, or if the reader is to read all matching filenames as a part of the dataset. true if want to read all matching files to form an image into a 3D dataset.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readLSM
```
private ModelImage readLSM(java.lang.String fileName,
                           java.lang.String fileDir,
                           int secondAddress,
                           boolean one)
```
    Reads a LSM file by calling the read method of the file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    secondAddress - DOCUMENT ME!
    
    one - Indicates that only the named file should be read, as opposed to reading the matching files in the directory, as defined by the filetype. true if only want to read one image from 3D dataset.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readLSMMulti
```
private ModelImage readLSMMulti(java.lang.String fileName,
                                java.lang.String fileDir)
```
    Reads a multi LSM file by first reading the headers then reading in each separate file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readMagnetomVisionMulti
```
private ModelImage readMagnetomVisionMulti(java.lang.String fileName,
                                           java.lang.String fileDir)
```
    Reads multiple Magnetom Vision files by calling the read method of the file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readMap
```
private ModelImage readMap(java.lang.String fileName,
                           java.lang.String fileDir)
```
    Reads a Map file by calling the read method of the file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readMedVision
```
private ModelImage readMedVision(java.lang.String fileName,
                                 java.lang.String fileDir)
```
    Reads a MedVision file by calling the read method of the file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readMGH
```
private ModelImage readMGH(java.lang.String fileName,
                           java.lang.String fileDir,
                           boolean one)
```
    Reads a MGH file by calling the read method of the file. if so, calls that method instead.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    one - Indicates that only the named file should be read, as opposed to reading the matching files in the directory, as defined by the filetype. true if only want to read one image from 3D dataset.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readMicroCat
```
private ModelImage readMicroCat(java.lang.String fileName,
                                java.lang.String fileDir,
                                boolean one)
```
    Reads an Micro Cat file by calling the read method of the file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    one - Indicates that only the named file should be read, as opposed to reading the matching files in the directory, as defined by the filetype. true if only want to read one image from 3D dataset.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readMinc
```
private ModelImage readMinc(java.lang.String fileName,
                            java.lang.String fileDir,
                            boolean one)
```
    Reads a MINC file by calling the read method of the file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    one - Indicates that only the named file should be read, as opposed to reading the matching files in the directory, as defined by the filetype. true if only want to read one image from 3D dataset.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readMincMulti
```
private ModelImage readMincMulti(java.lang.String fileName,
                                 java.lang.String fileDir)
```
    Reads a multi Minc file. Gets a list of the images from the file directory and reads them each in.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readMincHDF
```
private ModelImage readMincHDF(java.lang.String fileName,
                               java.lang.String fileDir,
                               boolean one)
```
  - readMRC
```
private ModelImage readMRC(java.lang.String fileName,
                           java.lang.String fileDir)
```
    Reads a MRC file by calling the read method of the file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readBFLOAT
```
private ModelImage readBFLOAT(java.lang.String fileName,
                              java.lang.String fileDir,
                              boolean one)
```
    Reads a BFLOAT file by calling the read method of the file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    one - If true, read in only one middle slice
    
    Returns:
    
    The image that was read in, or null if failure.
  - readNIFTI
```
public ModelImage readNIFTI(java.lang.String fileName,
                            java.lang.String fileDir,
                            boolean one,
                            boolean niftiCompressed,
                            boolean noImportData,
                            boolean noReadPrivateTags)
```
    Reads a NIFTI file by calling the read method of the file. if so, calls that method instead.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    one - Indicates that only the named file should be read, as opposed to reading the matching files in the directory, as defined by the filetype. true if only want to read one image from 3D dataset.
    
    niftiCompressed -
    
    noImportData -
    
    Returns:
    
    The image that was read in, or null if failure.
  - readMetaImage
```
private ModelImage readMetaImage(java.lang.String fileName,
                                 java.lang.String fileDir,
                                 boolean one)
```
    Reads a MetaImage file by calling the read method of the file. if so, calls that method instead.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    one - Indicates that only the named file should be read, as opposed to reading the matching files in the directory, as defined by the filetype. true if only want to read one image from 3D dataset.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readNIFTIMulti
```
private ModelImage readNIFTIMulti(java.lang.String fileName,
                                  java.lang.String fileDir)
```
    Reads a multi NIFTI file. Gets a list of the images from the file directory and reads them each in.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readNRRD
```
private ModelImage readNRRD(java.lang.String fileName,
                            java.lang.String fileDir,
                            boolean one)
```
    Reads a NRRD file by calling the read method of the file. if so, calls that method instead.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    one - Indicates that only the named file should be read, as opposed to reading the matching files in the directory, as defined by the filetype. true if only want to read one image from 3D dataset.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readNRRDMulti
```
private ModelImage readNRRDMulti(java.lang.String fileName,
                                 java.lang.String fileDir)
```
    Reads a multi NRRD file. Gets a list of the images from the file directory and reads them each in.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readGEGenesis5X
```
public ModelImage readGEGenesis5X(java.lang.String fileName,
                                  java.lang.String fileDir)
```
    Reads in a single GE Genesis type file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readGESigna4X
```
public ModelImage readGESigna4X(java.lang.String fileName,
                                java.lang.String fileDir)
```
    Reads in a single GE Signa 4x type file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readMagnetomVision
```
private ModelImage readMagnetomVision(java.lang.String fileName,
                                      java.lang.String fileDir)
```
    Reads a Magnetom Vision file by calling the read method of the file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readVista
```
private ModelImage readVista(java.lang.String fileName,
                             java.lang.String fileDir,
                             boolean one)
```
  - readPARREC
```
private ModelImage readPARREC(java.lang.String fileName,
                              java.lang.String fileDir,
                              boolean one)
```
    Reads a PARREC file by calling the read method of the file. This method contains special code to not display the progress bar should the image be splash.img.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    one - Indicates that only the named file should be read, as opposed to reading the matching files in the directory, as defined by the filetype. true if only want to read one image from 3D dataset.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readPARRECMulti
```
private ModelImage readPARRECMulti(java.lang.String fileName,
                                   java.lang.String fileDir)
```
    Reads a multi PARREC file. Gets a list of the images from the file directory and reads them each in.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readPGM
```
private ModelImage readPGM(java.lang.String fileName,
                           java.lang.String fileDir)
```
    Reads a PGM file by calling the read method of the file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readPPM
```
private ModelImage readPPM(java.lang.String fileName,
                           java.lang.String fileDir)
```
    Reads a PPM file by calling the read method of the file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readQT
```
private ModelImage readQT(java.lang.String fileName,
                          java.lang.String fileDir)
```
    Reads a QT file by calling the read method of the file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readRaw
```
private ModelImage readRaw(java.lang.String fileName,
                           java.lang.String fileDir,
                           FileInfoBase fileInfo)
```
    Reads a RAW file by calling the read method of the file. Gets the necessary information from a dialog, if the fileInfo parameter is null, and otherwise relies on the information stored in fileInfo to properly read in the file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    fileInfo - File info of the image file; usually null, but if defined no dialog appears.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readRawMulti
```
private ModelImage readRawMulti(java.lang.String fileName,
                                java.lang.String fileDir,
                                FileInfoBase fileInfo)
```
    Reads a RAW file by calling the read method of the file. Gets the necessary information from a dialog, if the fileInfo parameter is null, and otherwise relies on the information stored in fileInfo to properly read in the file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    fileInfo - File info of the image file; usually null, but if defined no dialog appears.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readSpar
```
private ModelImage readSpar(FileInfoBase fileInfo,
                            java.lang.String fileName,
                            java.lang.String fileDir,
                            boolean one)
```
    Reads a Spar file by calling the read method of the file.
    
    Parameters:
    
    fileInfo -
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    one - Indicates that only the named file should be read, as opposed to reading the matching files in the directory, as defined by the filetype. true if only want to read one image from 3D dataset.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readSPM
```
private ModelImage readSPM(java.lang.String fileName,
                           java.lang.String fileDir,
                           boolean one)
```
    Reads an SPM file by calling the read method of the file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    one - Indicates that only the named file should be read, as opposed to reading the matching files in the directory, as defined by the filetype. true if only want to read one image from 3D dataset.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readSTK
```
private ModelImage readSTK(java.lang.String fileName,
                           java.lang.String fileDir,
                           boolean one)
```
    Reads a STK file by calling the read method of the file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    one - Indicates that only the named file should be read, as opposed to reading the matching files in the directory, as defined by the filetype. true if only want to read one image from 3D dataset.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readTrackVis
```
private ModelImage readTrackVis(java.lang.String fileName,
                                java.lang.String fileDir)
```
    Reads in a single TrackVis file.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readCZI
```
private ModelImage readCZI(java.lang.String fileName,
                           java.lang.String fileDir,
                           boolean one)
```
    Reads a Zeiss ZISRAW (CZI) file by calling the read method of the file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    one - Indicates that only the named file should be read, as opposed to reading the matching files in the directory, as defined by the filetype. true if only want to read one image from 3D dataset.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readLIFF
```
private ModelImage readLIFF(java.lang.String fileName,
                            java.lang.String fileDir,
                            boolean one)
```
    Reads a Improvision OpenLab LIFF file by calling the read method of the file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    one - Indicates that only the named file should be read, as opposed to reading the matching files in the directory, as defined by the filetype. true if only want to read one image from 3D dataset.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readBMP
```
private ModelImage readBMP(java.lang.String fileName,
                           java.lang.String fileDir,
                           boolean one)
```
    Reads a BMP file by calling the read method of the file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    one - Indicates that only the named file should be read, as opposed to reading the matching files in the directory, as defined by the filetype. true if only want to read one image from 3D dataset.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readBMPMulti
```
private ModelImage readBMPMulti(java.lang.String fileName,
                                java.lang.String fileDir,
                                boolean one)
```
  - createMultifile
```
private ModelImage createMultifile(FileInfoBase myFileInfo,
                                   ModelImage origImage,
                                   java.lang.String fileDir,
                                   java.lang.String fileName,
                                   boolean quiet)
```
  - convertToMultifile
```
private ModelImage convertToMultifile(ModelImage existingMultifileImage,
                                      ModelImage origImage,
                                      int[] extents,
                                      int pos)
```
  - readMATLAB
```
private ModelImage readMATLAB(java.lang.String fileName,
                              java.lang.String fileDir,
                              boolean one)
```
    Reads a NATLAB file by calling the read method of the file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    one - Indicates that only the named file should be read, as opposed to reading the matching files in the directory, as defined by the filetype. true if only want to read one image from 3D dataset.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readZVI
```
private ModelImage readZVI(java.lang.String fileName,
                           java.lang.String fileDir,
                           boolean one)
```
    Reads a Zeiss ZVI file by calling the read method of the file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    one - Indicates that only the named file should be read, as opposed to reading the matching files in the directory, as defined by the filetype. true if only want to read one image from 3D dataset.
    
    Returns:
    
    The image that was read in, or null if failure.
  - setTIFFOrientation
```
public void setTIFFOrientation(boolean doTIFFOrientation)
```
  - readTiff
```
public ModelImage readTiff(java.lang.String fileName,
                           java.lang.String fileDir,
                           boolean one)
```
    Reads a TIFF file by calling the read method of the file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    one - Indicates that only the named file should be read, as opposed to reading the matching files in the directory, as defined by the filetype. true if only want to read one image from 3D dataset.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readTiffMulti
```
private ModelImage readTiffMulti(java.lang.String fileName,
                                 java.lang.String fileDir)
```
    Reads a multi TIFF file by first reading the headers then reading in each separate file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readSVS
```
private ModelImage readSVS(java.lang.String fileName,
                           java.lang.String fileDir,
                           boolean one)
```
    Reads a SVS file by calling the read method of the file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    one - Indicates that only the named file should be read, as opposed to reading the matching files in the directory, as defined by the filetype. true if only want to read one image from 3D dataset.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readTMG
```
private ModelImage readTMG(java.lang.String fileName,
                           java.lang.String fileDir)
```
    Reads a TMG file by calling the read method of the file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readXML
```
public ModelImage readXML(java.lang.String fileName,
                          java.lang.String fileDir,
                          boolean one,
                          boolean bDisplayProgress)
```
    Reads an XML file by calling the read method of the file. This method contains special code to not display the progress bar should it load splash.xml.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    one - Indicates that only the named file should be read, as opposed to reading the matching files in the directory, as defined by the filetype. true if only want to read one image from 3D dataset.
    
    Returns:
    
    The image that was read in, or null if failure.
  - readXMLMulti
```
private ModelImage readXMLMulti(java.lang.String fileName,
                                java.lang.String fileDir)
```
    Reads a multi XML file. Gets a list of the images from the file directory and reads them each in.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    Returns:
    
    The image that was read in, or null if failure.
  - writeAfni
```
private boolean writeAfni(ModelImage image,
                          FileWriteOptions options)
```
    Writes an AFNI file to store the image.
    
    Parameters:
    
    image - The image to write.
    
    options - The options to use to write the image.
    
    Returns:
    
    Flag indicating that this was a successful write.
  - writeAnalyze
```
private boolean writeAnalyze(ModelImage image,
                             FileWriteOptions options,
                             boolean zerofunused)
```
    Writes an analyze file to store the image.
    
    Parameters:
    
    image - The image to write.
    
    options - The options to use to write the image.
    
    zerofunused - If true, zero funused fields
    
    Returns:
    
    Flag indicating that this was a successful write.
  - writeAvi
```
private boolean writeAvi(ModelImage image,
                         FileWriteOptions options)
```
    Writes an AVI file to store the image.
    
    Parameters:
    
    image - The image to write.
    
    options - The options to use to write the image.
    
    Returns:
    
    Flag indicating that this was a successful write.
  - writeCOR
```
private boolean writeCOR(ModelImage image,
                         FileWriteOptions options)
```
    Writes a Freesurfer COR file to store the image.
    
    Parameters:
    
    image - The image to write.
    
    options - The options to use to write the image.
    
    Returns:
    
    Flag indicating that this was a successful write.
  - writeDicomSlice
```
private boolean writeDicomSlice(ModelImage image,
                                int sliceNumber,
                                FileWriteOptions options,
                                FileInfoDicom fileDicom,
                                FileInfoBase originalFileInfo,
                                int originalImageDataType,
                                TransMatrix originalImageMatrix,
                                double originalImageMin,
                                double originalImageMax,
                                boolean originalIsDicom,
                                boolean originalIsColor)
```
    Writes a DICOM file on a slice basis. This method is specifically used in very large 3d datasets where memory becomes an issue DICOM images are each written to a separate file with a different header.
    
    Parameters:
    
    image - The 2D image to write.
    
    options - The options to use to write the image.
    
    Returns:
    
    Flag indicating that this was a successful write.
  - writeDicom
```
private boolean writeDicom(ModelImage image,
                           FileWriteOptions options)
```
    Writes a DICOM file to store the image. Calls a dialog if the source isn't a DICOM image. DICOM images are each written to a separate file with a different header.
    
    Parameters:
    
    image - The image to write.
    
    options - The options to use to write the image.
    
    Returns:
    
    Flag indicating that this was a successful write.
  - reduceStringLengthTo16
```
java.lang.String reduceStringLengthTo16(java.lang.String str)
```
  - removeEnhancedDicomInfo
```
private void removeEnhancedDicomInfo(FileInfoDicom myFileInfo,
                                     FileInfoBase[] fileInfoBases)
```
  - insertEnhancedSequence
```
private void insertEnhancedSequence(FileInfoDicom myFileInfo,
                                    FileInfoDicom[][] infoAr,
                                    int dataType)
```
  - writeFits
```
private boolean writeFits(ModelImage image,
                          FileWriteOptions options)
```
    Writes a Fits file to store the image.
    
    Parameters:
    
    image - The image to write.
    
    options - The options to use to write the image.
    
    Returns:
    
    Flag indicating that this was a successful write.
  - writeGESigna4X
```
private boolean writeGESigna4X(ModelImage image,
                               FileWriteOptions options)
```
    Writes a GESigna4X file to store the image.
    
    Parameters:
    
    image - The image to write.
    
    options - The options to use to write the image.
    
    Returns:
    
    Flag indicating that this was a successful write.
  - writeGEGenesis5X
```
private boolean writeGEGenesis5X(ModelImage image,
                                 FileWriteOptions options)
```
    Writes a GESigna5X file to store the image.
    
    Parameters:
    
    image - The image to write.
    
    options - The options to use to write the image.
    
    Returns:
    
    Flag indicating that this was a successful write.
  - writeICS
```
private boolean writeICS(ModelImage image,
                         FileWriteOptions options)
```
    Writes an ICS file to store the image.
    
    Parameters:
    
    image - The image to write.
    
    options - The options to use to write the image.
    
    Returns:
    
    Flag indicating that this was a successful write.
  - writeInterfile
```
private boolean writeInterfile(ModelImage image,
                               FileWriteOptions options)
```
    Writes an Interfile file to store the image.
    
    Parameters:
    
    image - The image to write.
    
    options - The options to use to write the image.
    
    Returns:
    
    Flag indicating that this was a successful write.
  - writeJimi
```
private boolean writeJimi(ModelImage image,
                          FileWriteOptions options)
```
    Writes a JIMI file to store the image.
    
    Parameters:
    
    image - The image to write.
    
    options - The options to use to write the image.
    
    Returns:
    
    Flag indicating that this was a successful write.
  - getRenderedImage
```
private final java.awt.image.BufferedImage getRenderedImage(java.awt.Image in)
```
  - writeMGH
```
private boolean writeMGH(ModelImage image,
                         FileWriteOptions options)
```
    Writes a MGH or MGZ file to store the image.
    
    Parameters:
    
    image - The image to write.
    
    options - The options to use to write the image.
    
    Returns:
    
    Flag indicating that this was a successful write.
  - writeMinc
```
private boolean writeMinc(ModelImage image,
                          FileWriteOptions options)
```
    Writes a Minc file to store the image.
    
    Parameters:
    
    image - The image to write.
    
    options - The options to use to write the image.
    
    Returns:
    
    Flag indicating that this was a successful write.
  - writeMincHDF
```
private boolean writeMincHDF(ModelImage image,
                             FileWriteOptions options)
```
    Writes out a MINC 2.0 HDF5 formatted file
    
    Parameters:
    
    image -
    
    options -
    
    Returns:
  - writeMRC
```
private boolean writeMRC(ModelImage image,
                         FileWriteOptions options)
```
    Writes a MRC file to store the image.
    
    Parameters:
    
    image - The image to write.
    
    options - The options to use to write the image.
    
    Returns:
    
    Flag indicating that this was a successful write.
  - writeMATLAB
```
private boolean writeMATLAB(ModelImage image,
                            FileWriteOptions options)
```
    Writes a MATLAB file to store the image.
    
    Parameters:
    
    image - The image to write.
    
    options - The options to use to write the image.
    
    Returns:
    
    Flag indicating that this was a successful write.
  - writeNIFTI
```
private boolean writeNIFTI(ModelImage image,
                           FileWriteOptions options)
```
    Writes a NIFTI file to store the image.
    
    Parameters:
    
    image - The image to write.
    
    options - The options to use to write the image.
    
    Returns:
    
    Flag indicating that this was a successful write.
  - writeMetaImage
```
private boolean writeMetaImage(ModelImage image,
                               FileWriteOptions options)
```
    Writes a MetaImage file to store the image.
    
    Parameters:
    
    image - The image to write.
    
    options - The options to use to write the image.
    
    Returns:
    
    Flag indicating that this was a successful write.
  - writeRaw
```
private boolean writeRaw(ModelImage image,
                         FileWriteOptions options)
```
    Writes a raw file to store the image.
    
    Parameters:
    
    image - The image to write.
    
    options - The options to use to write the image.
    
    Returns:
    
    Flag indicating that this was a successful write.
  - writeSPM
```
private boolean writeSPM(ModelImage image,
                         FileWriteOptions options)
```
    Writes a SPM file to store the image.
    
    Parameters:
    
    image - The image to write.
    
    options - The options to use to write the image.
    
    Returns:
    
    Flag indicating that this was a successful write.
  - writeTiff
```
private boolean writeTiff(ModelImage image,
                          FileWriteOptions options)
```
    Writes a TIFF file to store the image.
    
    Parameters:
    
    image - The image to write.
    
    options - The options to use to write the image.
    
    Returns:
    
    Flag indicating that this was a successful write.
  - writeSTK
```
private boolean writeSTK(ModelImage image,
                         FileWriteOptions options)
```
    Writes a STK file to store the image.
    
    Parameters:
    
    image - The image to write.
    
    options - The options to use to write the image.
    
    Returns:
    
    Flag indicating that this was a successful write.
  - writeXML
```
private boolean writeXML(ModelImage image,
                         FileWriteOptions options,
                         boolean bDisplayProgress)
```
    Writes the image in our MIPAV XML format.
    
    Parameters:
    
    image - The image to be saved to the file.
    
    options - Write options that control aspects of writing the image.
    
    Returns:
    
    True if the file was successfully saved to a file.
  - writeVista
```
private boolean writeVista(ModelImage image,
                           FileWriteOptions options)
```
    writes Vista format files
    
    Parameters:
    
    image -
    
    options -
    
    Returns:
  - writePARREC
```
private boolean writePARREC(ModelImage image,
                            FileWriteOptions options)
```
    Writes a PAR/REC file to store the image.
    
    Parameters:
    
    image - The image to write.
    
    options - The options to use to write the image.
    
    Returns:
    
    Flag indicating that this was a successful write.
  - writeNRRD
```
private boolean writeNRRD(ModelImage image,
                          FileWriteOptions options)
```
    Writes a NRRD file to store the image.
    
    Parameters:
    
    image - The image to write.
    
    options - The options to use to write the image.
    
    Returns:
    
    Flag indicating that this was a successful write.
  - readJpeg2000
```
private ModelImage readJpeg2000(java.lang.String fileName,
                                java.lang.String fileDir,
                                boolean one)
```
    Reads a JPEG2000 file by calling the read method of the file.
    
    Parameters:
    
    fileName - Name of the image file to read.
    
    fileDir - Directory of the image file to read.
    
    one - Indicates that only the named file should be read, as opposed to reading the matching files in the directory, as defined by the filetype. true if only want to read one image from 3D dataset.
    
    Returns:
    
    The image that was read in, or null if failure.
  - writeJpeg2000
```
private boolean writeJpeg2000(ModelImage image,
                              FileWriteOptions options)
```
    Writes a JPEG2000 file to store the image.
    
    Parameters:
    
    image - The image to write.
    
    options - The options to use to write the image.
    
    Returns:
    
    Flag indicating that this was a successful write.
  - setDisplayRangeOfSlicesDialog
```
public void setDisplayRangeOfSlicesDialog(boolean displayRangeOfSlicesDialog)
```
  - getDoubleValOrAsciiVal
```
private double getDoubleValOrAsciiVal(java.lang.String value)
```
  - convertNumbersToStr
```
private java.lang.String convertNumbersToStr(java.lang.String dicomNumberString)
```

Class FileIO

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

FILE_READ

FILE_WRITE

fileDir

LUT

modelRGB

progressBar

quiet

rawInfo

secondImage

UI

unknownIODialog

saveAsEncapJP2

displayRangeOfSlicesDialog

dataFileName

dtiparams

isDTISort

doTIFFOrientation

imageA

suppressProgressBar

Constructor Detail

FileIO

FileIO

Method Detail

dispose

chkMultiFile

setImageA

setSuppressProgressBar

convertToARGB

convertToUBYTE

subsample

getFileType

getModelLUT

getModelRGB

getSecondImage

isQuiet

readDicom

isDiffusionSeries

sortDtiDicomData

generateGEID

tryPartitionByMediaUID

removeFromImageList

getModality

readHeader

readHeader

readHeader

readHeader

readImage

readImage

readImage

readImage

readImage

readImage

readFileType

readOneImage

readOrderedARGB

readOrderedGrayscale

readOrderedGrayscale

readOrderedGrayscale2

readXMLThumbnail

setFileDir

setModelLUT

setModelRGB

setPBar

setQuiet

setRawImageInfo

setUserDefinedFileTypes_textFieldPref

setUserDefinedFileTypesPref

writeImage

writeImage

getByteImageData

dataConversion

getDicomSaveList

LSMDataConversion