Package gov.nih.mipav.model.file

Class FileWriteOptions

java.lang.Object
gov.nih.mipav.model.file.FileWriteOptions
public class FileWriteOptions extends Object
This structure contains information to direct file writing.
Version:
0.1 June 21, 2001
Author:
Neva Cherniavsky
See Also:

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    private float
    alphaBlend
    DOCUMENT ME!
    private int
    AVICompression
    DOCUMENT ME!
    private int[]
    axisOrientation
    DOCUMENT ME!
    private int
    beginSlice
    3D options.
    private int
    beginTimePeriod
    4D options.
    private int
    blue
    DOCUMENT ME!
    private boolean
    defaults
    DOCUMENT ME!
    private boolean
    doEnhanced
    Whether dicom files are saved in enhanced format.
    private boolean
    doStamp
    Used for stamping DICOM images with MIPAV reference.
    private int
    endSlice
    DOCUMENT ME!
    private int
    endTimePeriod
    DOCUMENT ME!
    private int
    fileDigitNumber
    DOCUMENT ME!
    private String
    fileDirectory
    DOCUMENT ME!
    private String
    fileName
    All file options.
    private int
    fileStartNumber
    DOCUMENT ME!
    private int
    fileType
    A FileUtility.Type
    private boolean
    floatToShort
     
    private int
    green
    DOCUMENT ME!
    private ModelImage
    imageB
    DOCUMENT ME!
    private boolean
    isAVI
    AVI option.
    private boolean
    isBz2zip
     
    private boolean
    isGzip
     
    private boolean
    isScript
    For Scripts.
    private boolean
    isZip
     
    private ModelLUT
    LUTa
    DOCUMENT ME!
    private ModelLUT
    LUTb
    DOCUMENT ME!
    private int
    microSecPerFrame
    DOCUMENT ME!
    private float
    mjpegQuality
    DOCUMENT ME!
    private boolean
    multiFile
    DOCUMENT ME!
    private NDARWriteData
    ndarData
     
    private String
    niftiExtension
     
    private float
    opacity
    DOCUMENT ME!
    private boolean
    optionsSet
    DOCUMENT ME!
    private boolean
    packBitEnable
    DOCUMENT ME!
    private BitSet
    paintBitmap
    DOCUMENT ME!
    private HashMap<?,?>
    pSetsHashMap
     
    private boolean
    putInQuicklist
    Tells FileIO whether or not to insert the saved image into the Quicklist (recently used image list) after successful saving
    private boolean
    recalculateInstanceNumber
    recalculate the Instance Number (0020,0013).
    private int
    red
    DOCUMENT ME!
    private ModelRGB
    RGBTa
    DOCUMENT ME!
    private ModelRGB
    RGBTb
    DOCUMENT ME!
    private boolean
    runningInSeparateThread
    DOCUMENT ME!
    private boolean
    saveAs
    DOCUMENT ME!
    private boolean
    saveInSubdirectory
    To save the image file in a subdirectory of image-name (without extension) when true.
    private int
    timeSlice
    DOCUMENT ME!
    private float
    tSpace
    DOCUMENT ME!
    private float
    tStart
    DOCUMENT ME!
    private boolean
    writeHeaderOnly
    Tells the FileBase (FileImageXML only now) to write only the header (.xml) if true
    private boolean
    writePackBit
    TIFF options.
    private String
    xmlLinkedFilename
    XML option.
    private float
    xSpace
    DOCUMENT ME!
    private float
    xStart
    DOCUMENT ME!
    private float
    ySpace
    DOCUMENT ME!
    private float
    yStart
    DOCUMENT ME!
    private float
    zSpace
    DOCUMENT ME!
    private float
    zStart
    DOCUMENT ME!

  • Constructor Summary

    Constructors
    Constructor
    Description
    FileWriteOptions(boolean saveAs)
    Constructs an options structure with the given saveAs value.
    FileWriteOptions(String fileName, String directory, boolean saveAs)
    Constructs an options structure with the given file name, directory, and saveAs values.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    disposeLocal()
    DOCUMENT ME!
    boolean
    doEnhanced()
    Whether to save dicom files in enhanced format.
    void
    doEnhanced(boolean doSaveEnhancedDicom)
    Sets the flag for saving dicom files in enhanced format.
    boolean
    doPutInQuicklist()
    Whether or not to put the file into the recently used image list after saving
    void
    doPutInQuicklist(boolean doPut)
    Sets the flag for putting the image into the recently used image list
    boolean
    doStamp()
    Whether or not to stamp DICOM images.
    void
    doStamp(boolean doStamp)
    Sets the flag for stamping DICOM images with a reference to MIPAV as a secondary processor.
    float
    getAlphaBlend()
    DOCUMENT ME!
    int
    getAVICompression()
    Gets the AVI compression.
    int[]
    getAxisOrientation()
    Returns the orientations of the 3 axes.
    int
    getBeginSlice()
    Accessor that returns the slice to begin saving at.
    int
    getBeginTime()
    Accessor that returns the time slice to begin saving at.
    int
    getBlue()
    DOCUMENT ME!
    int
    getDigitNumber()
    Accessor that returns the number of digits to use when appending to the multi file save (i.e., if you want test00.tif to be the first file, 0 is the start number and 2 is the digit number).
    int
    getEndSlice()
    Accessor that returns the slice to stop saving at.
    int
    getEndTime()
    Accessor that returns the time slice to stop saving at.
    String
    getFileDirectory()
    Accessor that returns the directory to be written to.
    String
    getFileName()
    Accessor that returns the file name to be written to.
    int
    getFileType()
    Accessor to get what type of file this is, such as analyze, raw, DICOM, etc.
    boolean
    getFloatToShort()
     
    int
    getGreen()
    DOCUMENT ME!
    ModelImage
    getImageB()
    DOCUMENT ME!
    ModelLUT
    getLUTa()
    DOCUMENT ME!
    ModelLUT
    getLUTb()
    DOCUMENT ME!
    int
    getMicroSecPerFrame()
    DOCUMENT ME!
    float
    getMJPEGQuality()
    DOCUMENT ME!
    NDARWriteData
    getNDARData()
    Retrieves the NDAR data for use in populating XML fields
    String
    getNIFTIExtension()
     
    float
    getOpacity()
    DOCUMENT ME!
    BitSet
    getPaintBitmap()
    DOCUMENT ME!
    HashMap<?,?>
    getPSetsHashMap()
    gets the psets hashmap
    int
    getRed()
    DOCUMENT ME!
    ModelRGB
    getRGBTa()
    DOCUMENT ME!
    ModelRGB
    getRGBTb()
    DOCUMENT ME!
    int
    getStartNumber()
    Accessor that returns the number to append to the multi file save (i.e., if you want test00.tif to be the first file, 0 is the start number and 2 is the digit number).
    int
    getTimeSlice()
    Accessor that returns the time slice to save at; for TIFF, because TIFF only saves to 3D.
    float
    getTSpace()
    Accessor that returns value of T Space text field.
    float
    getTStart()
    Accessor that returns value of T Start text field.
    String
    getXMLLinkedFilename()
    Gets the filename for the linked file for the XML header.
    float
    getXSpace()
    Accessor that returns value of X Space text field.
    float
    getXStart()
    Accessor that returns value of X Start text field.
    float
    getYSpace()
    Accessor that returns value of Y Space text field.
    float
    getYStart()
    Accessor that returns value of Y Start text field.
    float
    getZSpace()
    Accessor that returns value of Z Space text field.
    float
    getZStart()
    Accessor that returns value of Z Start text field.
    boolean
    isAVI()
    DOCUMENT ME!
    boolean
    isBz2zip()
     
    boolean
    isDefault()
    Accessor that returns whether or not this is the default save.
    boolean
    isGzip()
     
    boolean
    isInstanceNumberRecalculated()
    Accessor that returns whether or not the Instance Number (0020,0013) should be recalculated before saving.
    boolean
    isMultiFile()
    Accessor that returns whether or not this is an image to be stored as multiple files.
    boolean
    isPackBitEnabled()
    Accessor that returns whether or not it is possible to write with packed bits compression (only possible with TIFF byte images).
    boolean
    isRunningInSeparateThread()
    DOCUMENT ME!
    boolean
    isSaveAs()
    Accessor that returns whether or not this is a Save or SaveAs operation.
    boolean
    isSaveInSubdirectory()
    Accessor that returns whether or not the save should be into a subdirectory of imagename (without extension).
    boolean
    isScript()
    Checks to see if this is being run from a script.
    boolean
    isSet()
    Accessor that returns whether all of the options have been previously set (usually by the script parser).
    boolean
    isWritePackBit()
    Accessor that returns whether or not to write with packed bits compression (only possible with TIFF byte images).
    boolean
    isZip()
     
    void
    setAlphaBlend(float alphaBlend)
    DOCUMENT ME!
    void
    setAVICompression(int AVICompression)
    Accessor that sets the AVI compression.
    void
    setAxisOrientation(int[] ori)
    Accessor that sets the orientations of the 3 axes.
    void
    setBeginSlice(int slice)
    Accessor that sets the slice to begin writing at (3D).
    void
    setBeginTime(int slice)
    Accessor that sets the time slice to begin writing at (4D).
    void
    setBlue(int blue)
    DOCUMENT ME!
    void
    setBz2zip(boolean isBz2zip)
     
    void
    setDefault(boolean flag)
    Accessor that sets the "default" flag.
    void
    setDigitNumber(int digit)
    /** Accessor that sets the number of digits to use when appending to the multi file save (i.e., if you want test00.tif to be the first file, 0 is the start number and 2 is the digit number).
    void
    setEndSlice(int slice)
    Accessor that sets the slice to stop writing at (3D).
    void
    setEndTime(int slice)
    Accessor that sets the time slice to stop writing at (4D).
    void
    setFileDirectory(String dir)
    Accessor that sets the file directory.
    void
    setFileName(String name)
    Accessor that sets the file name to write out.
    void
    setFileType(int type)
    Accessor that sets the file type (analyze, raw, TIFF, DICOM, etc.).
    void
    setFloatToShort(boolean floatToShort)
     
    void
    setGreen(int green)
    DOCUMENT ME!
    void
    setGzip(boolean isGzip)
     
    void
    setImageB(ModelImage imageB)
    DOCUMENT ME!
    void
    setIsAVI(boolean isAVI)
    DOCUMENT ME!
    void
    setIsScript(boolean isScript)
    Accessor that sets the options to be run in a script.
    void
    setLUTa(ModelLUT LUTa)
    DOCUMENT ME!
    void
    setLUTb(ModelLUT LUTb)
    DOCUMENT ME!
    void
    setMicroSecPerFrame(int microSec)
    DOCUMENT ME!
    void
    setMJPEGQuality(float mjpegQuality)
    DOCUMENT ME!
    void
    setMultiFile(boolean flag)
    Accessor that sets whether or not to write the image as multiple files, one 2D slice per file.
    void
    setNDARData(NDARWriteData data)
    Sets the NDAR Data that will be used to populate XML header fields
    void
    setNIFTIExtension(String niftiExtension)
    Accessor that sets whether or not nifti should be written as a combined .nii file or as separate .hdr and .img files.
    void
    setOpacity(float opacity)
    DOCUMENT ME!
    void
    setOptionsSet(boolean set)
    Accessor that sets whether all of the options have been previously set (usually by the script parser).
    void
    setPackBitEnabled(boolean flag)
    Accessor that sets whether it is possible to write with packed bits compression.
    void
    setPaintBitmap(BitSet paintBitmap)
    DOCUMENT ME!
    void
    setPSetsHashMap(HashMap<?,?> setsHashMap)
    sets the pset hasmap
    void
    setRecalculateInstanceNumber(boolean flag)
    Accessor that sets whether or not the Instance Number (0020,0013) should be recalculated before saving.
    void
    setRed(int red)
    DOCUMENT ME!
    void
    setRGBTa(ModelRGB RGBTa)
    DOCUMENT ME!
    void
    setRGBTb(ModelRGB RGBTb)
    DOCUMENT ME!
    void
    setRunningInSeparateThread(boolean isActive)
    DOCUMENT ME!
    void
    setSaveAs(boolean flag)
    Accessor that sets the "save as" flag.
    void
    setSaveInSubdirectory(boolean flag)
    Accessor that sets the "save as" flag.
    void
    setStartNumber(int num)
    Accessor that sets the number to append to the multi file save (i.e., if you want test00.tif to be the first file, 0 is the start number and 2 is the digit number).
    void
    setTimeSlice(int slice)
    Accessor that sets the time slice to record (4D TIFF).
    void
    setTSpace(float value)
    Accessor that sets t space (used for MINC images).
    void
    setTStart(float value)
    Accessor that sets t start (used for MINC images).
    void
    setWriteHeaderOnly(boolean headerOnly)
    Sets the options to write only the .xml header if true
    void
    setWritePackBit(boolean flag)
    Accessor that sets whether to write with packed bits compression.
    void
    setXMLLinkedFilename(String xmlfilename)
    Accessor that sets the xml linked filename (for XML files).
    void
    setXSpace(float value)
    Accessor that sets x space (used for MINC images).
    void
    setXStart(float value)
    Accessor that sets x start (used for MINC images).
    void
    setYSpace(float value)
    Accessor that sets y space (used for MINC images).
    void
    setYStart(float value)
    Accessor that sets y start (used for MINC images).
    void
    setZip(boolean isZip)
     
    void
    setZSpace(float value)
    Accessor that sets z space (used for MINC images).
    void
    setZStart(float value)
    Accessor that sets z start (used for MINC images).
    String
    toString()
    Shows these options as a string, useful for debugging.
    boolean
    writeHeaderOnly()
    Determines whether to write only the header (for now, .xml files) and no raw file...for NDAR SRB transfer

    Methods inherited from class java.lang.Object

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

  • Field Details

    • runningInSeparateThread

      private boolean runningInSeparateThread
      DOCUMENT ME!

    • alphaBlend

      private float alphaBlend
      DOCUMENT ME!

    • AVICompression

      private int AVICompression
      DOCUMENT ME!

    • axisOrientation

      private int[] axisOrientation
      DOCUMENT ME!

    • beginSlice

      private int beginSlice
      3D options.

    • beginTimePeriod

      private int beginTimePeriod
      4D options.

    • blue

      private int blue
      DOCUMENT ME!

    • defaults

      private boolean defaults
      DOCUMENT ME!

    • endSlice

      private int endSlice
      DOCUMENT ME!

    • endTimePeriod

      private int endTimePeriod
      DOCUMENT ME!

    • fileDigitNumber

      private int fileDigitNumber
      DOCUMENT ME!

    • fileDirectory

      private String fileDirectory
      DOCUMENT ME!

    • fileName

      private String fileName
      All file options.

    • fileStartNumber

      private int fileStartNumber
      DOCUMENT ME!

    • fileType

      private int fileType
      A FileUtility.Type

    • green

      private int green
      DOCUMENT ME!

    • imageB

      private ModelImage imageB
      DOCUMENT ME!

    • isAVI

      private boolean isAVI
      AVI option.

    • isScript

      private boolean isScript
      For Scripts.

    • LUTa

      private ModelLUT LUTa
      DOCUMENT ME!

    • LUTb

      private ModelLUT LUTb
      DOCUMENT ME!

    • microSecPerFrame

      private int microSecPerFrame
      DOCUMENT ME!

    • mjpegQuality

      private float mjpegQuality
      DOCUMENT ME!

    • multiFile

      private boolean multiFile
      DOCUMENT ME!

    • doStamp

      private boolean doStamp
      Used for stamping DICOM images with MIPAV reference.

    • doEnhanced

      private boolean doEnhanced
      Whether dicom files are saved in enhanced format.

    • niftiExtension

      private String niftiExtension

    • opacity

      private float opacity
      DOCUMENT ME!

    • optionsSet

      private boolean optionsSet
      DOCUMENT ME!

    • packBitEnable

      private boolean packBitEnable
      DOCUMENT ME!

    • paintBitmap

      private BitSet paintBitmap
      DOCUMENT ME!

    • recalculateInstanceNumber

      private boolean recalculateInstanceNumber
      recalculate the Instance Number (0020,0013). Default true

    • red

      private int red
      DOCUMENT ME!

    • RGBTa

      private ModelRGB RGBTa
      DOCUMENT ME!

    • RGBTb

      private ModelRGB RGBTb
      DOCUMENT ME!

    • saveAs

      private boolean saveAs
      DOCUMENT ME!

    • saveInSubdirectory

      private boolean saveInSubdirectory
      To save the image file in a subdirectory of image-name (without extension) when true. Implementation elsewhere, obviously.

    • timeSlice

      private int timeSlice
      DOCUMENT ME!

    • writePackBit

      private boolean writePackBit
      TIFF options.

    • xmlLinkedFilename

      private String xmlLinkedFilename
      XML option.

    • xSpace

      private float xSpace
      DOCUMENT ME!

    • xStart

      private float xStart
      DOCUMENT ME!

    • ySpace

      private float ySpace
      DOCUMENT ME!

    • yStart

      private float yStart
      DOCUMENT ME!

    • zSpace

      private float zSpace
      DOCUMENT ME!

    • zStart

      private float zStart
      DOCUMENT ME!

    • tSpace

      private float tSpace
      DOCUMENT ME!

    • tStart

      private float tStart
      DOCUMENT ME!

    • putInQuicklist

      private boolean putInQuicklist
      Tells FileIO whether or not to insert the saved image into the Quicklist (recently used image list) after successful saving

    • writeHeaderOnly

      private boolean writeHeaderOnly
      Tells the FileBase (FileImageXML only now) to write only the header (.xml) if true

    • ndarData

      private NDARWriteData ndarData

    • pSetsHashMap

      private HashMap<?,?> pSetsHashMap

    • isGzip

      private boolean isGzip

    • isZip

      private boolean isZip

    • isBz2zip

      private boolean isBz2zip

    • floatToShort

      private boolean floatToShort

  • Constructor Details

    • FileWriteOptions

      public FileWriteOptions(boolean saveAs)
      Constructs an options structure with the given saveAs value. The file name and directory will need to be set later.
      Parameters:
      saveAs - true indicates this is a file with a new file name.

    • FileWriteOptions

      public FileWriteOptions(String fileName, String directory, boolean saveAs)
      Constructs an options structure with the given file name, directory, and saveAs values. The image is written to this file name and directory, under the preference of saveAs.
      Parameters:
      fileName - File name to save the image at.
      directory - Directory to save the image at.
      saveAs - true indicates this is a file with a new file name.

  • Method Details

    • disposeLocal

      public void disposeLocal()
      DOCUMENT ME!

    • doPutInQuicklist

      public boolean doPutInQuicklist()
      Whether or not to put the file into the recently used image list after saving
      Returns:
      if the image should be put into the quicklist

    • doPutInQuicklist

      public void doPutInQuicklist(boolean doPut)
      Sets the flag for putting the image into the recently used image list
      Parameters:
      doPut - true = do put into quicklist

    • doEnhanced

      public boolean doEnhanced()
      Whether to save dicom files in enhanced format.
      Returns:

    • doStamp

      public boolean doStamp()
      Whether or not to stamp DICOM images.
      Returns:

    • doEnhanced

      public void doEnhanced(boolean doSaveEnhancedDicom)
      Sets the flag for saving dicom files in enhanced format.
      Parameters:
      doSaveEnhancedDicom -

    • doStamp

      public void doStamp(boolean doStamp)
      Sets the flag for stamping DICOM images with a reference to MIPAV as a secondary processor.
      Parameters:
      doStamp -

    • writeHeaderOnly

      public boolean writeHeaderOnly()
      Determines whether to write only the header (for now, .xml files) and no raw file...for NDAR SRB transfer
      Returns:
      write header only

    • setWriteHeaderOnly

      public void setWriteHeaderOnly(boolean headerOnly)
      Sets the options to write only the .xml header if true
      Parameters:
      headerOnly - write header only flag

    • getPSetsHashMap

      public HashMap<?,?> getPSetsHashMap()
      gets the psets hashmap
      Returns:

    • setPSetsHashMap

      public void setPSetsHashMap(HashMap<?,?> setsHashMap)
      sets the pset hasmap
      Parameters:
      setsHashMap -

    • setNDARData

      public void setNDARData(NDARWriteData data)
      Sets the NDAR Data that will be used to populate XML header fields
      Parameters:
      data - NDAR data generated from JDialogNDAR

    • getNDARData

      public NDARWriteData getNDARData()
      Retrieves the NDAR data for use in populating XML fields
      Returns:
      the ndar data

    • getAlphaBlend

      public float getAlphaBlend()
      DOCUMENT ME!
      Returns:
      DOCUMENT ME!

    • getAVICompression

      public int getAVICompression()
      Gets the AVI compression.
      Returns:
      AVICompression

    • getAxisOrientation

      public int[] getAxisOrientation()
      Returns the orientations of the 3 axes.
      Returns:
      DOCUMENT ME!

    • getBeginSlice

      public int getBeginSlice()
      Accessor that returns the slice to begin saving at.
      Returns:
      The first slice to save at.

    • getBeginTime

      public int getBeginTime()
      Accessor that returns the time slice to begin saving at.
      Returns:
      The first time slice to save at.

    • getBlue

      public int getBlue()
      DOCUMENT ME!
      Returns:
      DOCUMENT ME!

    • getDigitNumber

      public int getDigitNumber()
      Accessor that returns the number of digits to use when appending to the multi file save (i.e., if you want test00.tif to be the first file, 0 is the start number and 2 is the digit number).
      Returns:
      The number of digits to append to the multi file save.

    • getEndSlice

      public int getEndSlice()
      Accessor that returns the slice to stop saving at.
      Returns:
      The last slice to save at.

    • getEndTime

      public int getEndTime()
      Accessor that returns the time slice to stop saving at.
      Returns:
      The last time slice to save at.

    • getFileDirectory

      public String getFileDirectory()
      Accessor that returns the directory to be written to.
      Returns:
      The directory to write this image to.

    • getFileName

      public String getFileName()
      Accessor that returns the file name to be written to.
      Returns:
      The file name to write this image to.

    • getFileType

      public int getFileType()
      Accessor to get what type of file this is, such as analyze, raw, DICOM, etc.
      Returns:
      The file type of this image.
      See Also:

    • getGreen

      public int getGreen()
      DOCUMENT ME!
      Returns:
      DOCUMENT ME!

    • getImageB

      public ModelImage getImageB()
      DOCUMENT ME!
      Returns:
      DOCUMENT ME!

    • getLUTa

      public ModelLUT getLUTa()
      DOCUMENT ME!
      Returns:
      DOCUMENT ME!

    • getLUTb

      public ModelLUT getLUTb()
      DOCUMENT ME!
      Returns:
      DOCUMENT ME!

    • getMicroSecPerFrame

      public int getMicroSecPerFrame()
      DOCUMENT ME!
      Returns:
      DOCUMENT ME!

    • getMJPEGQuality

      public float getMJPEGQuality()
      DOCUMENT ME!
      Returns:
      DOCUMENT ME!

    • getNIFTIExtension

      public String getNIFTIExtension()

    • getOpacity

      public float getOpacity()
      DOCUMENT ME!
      Returns:
      DOCUMENT ME!

    • getPaintBitmap

      public BitSet getPaintBitmap()
      DOCUMENT ME!
      Returns:
      DOCUMENT ME!

    • getRed

      public int getRed()
      DOCUMENT ME!
      Returns:
      DOCUMENT ME!

    • getRGBTa

      public ModelRGB getRGBTa()
      DOCUMENT ME!
      Returns:
      DOCUMENT ME!

    • getRGBTb

      public ModelRGB getRGBTb()
      DOCUMENT ME!
      Returns:
      DOCUMENT ME!

    • getStartNumber

      public int getStartNumber()
      Accessor that returns the number to append to the multi file save (i.e., if you want test00.tif to be the first file, 0 is the start number and 2 is the digit number).
      Returns:
      The number to append to the multi file save.

    • getTimeSlice

      public int getTimeSlice()
      Accessor that returns the time slice to save at; for TIFF, because TIFF only saves to 3D.
      Returns:
      The time slice to save at.

    • getXMLLinkedFilename

      public String getXMLLinkedFilename()
      Gets the filename for the linked file for the XML header.
      Returns:
      xml linked filename

    • getXSpace

      public float getXSpace()
      Accessor that returns value of X Space text field.
      Returns:
      Value typed in field.

    • getXStart

      public float getXStart()
      Accessor that returns value of X Start text field.
      Returns:
      Value typed in field.

    • getYSpace

      public float getYSpace()
      Accessor that returns value of Y Space text field.
      Returns:
      Value typed in field.

    • getYStart

      public float getYStart()
      Accessor that returns value of Y Start text field.
      Returns:
      Value typed in field.

    • getZSpace

      public float getZSpace()
      Accessor that returns value of Z Space text field.
      Returns:
      Value typed in field.

    • getZStart

      public float getZStart()
      Accessor that returns value of Z Start text field.
      Returns:
      Value typed in field.

    • getTSpace

      public float getTSpace()
      Accessor that returns value of T Space text field.
      Returns:
      Value typed in field.

    • getTStart

      public float getTStart()
      Accessor that returns value of T Start text field.
      Returns:
      Value typed in field.

    • isRunningInSeparateThread

      public boolean isRunningInSeparateThread()
      DOCUMENT ME!
      Returns:
      DOCUMENT ME!

    • isAVI

      public boolean isAVI()
      DOCUMENT ME!
      Returns:
      DOCUMENT ME!

    • isDefault

      public boolean isDefault()
      Accessor that returns whether or not this is the default save. So if a user just hits the "OK" button in the dialog without changing anything, it is default. However, if something needs to be recorded, all necessary information is recorded.
      Returns:
      true indicates default, false otherwise.

    • isInstanceNumberRecalculated

      public boolean isInstanceNumberRecalculated()
      Accessor that returns whether or not the Instance Number (0020,0013) should be recalculated before saving.
      Returns:
      true indicates recalculate the Instance number, false don't modify the Instance Number.

    • isMultiFile

      public boolean isMultiFile()
      Accessor that returns whether or not this is an image to be stored as multiple files. (Used primarily for TIFF images).
      Returns:
      true indicates multiple file save, false otherwise.

    • isPackBitEnabled

      public boolean isPackBitEnabled()
      Accessor that returns whether or not it is possible to write with packed bits compression (only possible with TIFF byte images).
      Returns:
      true indicates possible, false otherwise.

    • isSaveAs

      public boolean isSaveAs()
      Accessor that returns whether or not this is a Save or SaveAs operation.
      Returns:
      true indicates save as, false save.

    • isSaveInSubdirectory

      public boolean isSaveInSubdirectory()
      Accessor that returns whether or not the save should be into a subdirectory of imagename (without extension).
      Returns:
      true indicates save should be into a subdirectory as, false save.

    • isScript

      public boolean isScript()
      Checks to see if this is being run from a script.
      Returns:
      is it a script?

    • isSet

      public boolean isSet()
      Accessor that returns whether all of the options have been previously set (usually by the script parser).
      Returns:
      true indicates the options are already set, false otherwise.

    • isWritePackBit

      public boolean isWritePackBit()
      Accessor that returns whether or not to write with packed bits compression (only possible with TIFF byte images).
      Returns:
      true indicates w/compression, false otherwise.

    • setRunningInSeparateThread

      public void setRunningInSeparateThread(boolean isActive)
      DOCUMENT ME!
      Parameters:
      isActive - DOCUMENT ME!

    • setAlphaBlend

      public void setAlphaBlend(float alphaBlend)
      DOCUMENT ME!
      Parameters:
      alphaBlend - DOCUMENT ME!

    • setAVICompression

      public void setAVICompression(int AVICompression)
      Accessor that sets the AVI compression.
      Parameters:
      AVICompression - DOCUMENT ME!

    • setAxisOrientation

      public void setAxisOrientation(int[] ori)
      Accessor that sets the orientations of the 3 axes.
      Parameters:
      ori - DOCUMENT ME!

    • setBeginSlice

      public void setBeginSlice(int slice)
      Accessor that sets the slice to begin writing at (3D).
      Parameters:
      slice - First slice to begin writing at.

    • setBeginTime

      public void setBeginTime(int slice)
      Accessor that sets the time slice to begin writing at (4D).
      Parameters:
      slice - Time slice to begin writing at.

    • setBlue

      public void setBlue(int blue)
      DOCUMENT ME!
      Parameters:
      blue - DOCUMENT ME!

    • setDefault

      public void setDefault(boolean flag)
      Accessor that sets the "default" flag.
      Parameters:
      flag - true indicates default options, false otherwise.

    • setDigitNumber

      public void setDigitNumber(int digit)
      /** Accessor that sets the number of digits to use when appending to the multi file save (i.e., if you want test00.tif to be the first file, 0 is the start number and 2 is the digit number).
      Parameters:
      digit - Number of digits to write out.

    • setEndSlice

      public void setEndSlice(int slice)
      Accessor that sets the slice to stop writing at (3D).
      Parameters:
      slice - Last slice to stop writing at.

    • setEndTime

      public void setEndTime(int slice)
      Accessor that sets the time slice to stop writing at (4D).
      Parameters:
      slice - Time slice to stop writing at.

    • setFileDirectory

      public void setFileDirectory(String dir)
      Accessor that sets the file directory.
      Parameters:
      dir - File directory to write to.

    • setFileName

      public void setFileName(String name)
      Accessor that sets the file name to write out.
      Parameters:
      name - File name to write to.

    • setFileType

      public void setFileType(int type)
      Accessor that sets the file type (analyze, raw, TIFF, DICOM, etc.).
      Parameters:
      type - File type to set to.

    • setGreen

      public void setGreen(int green)
      DOCUMENT ME!
      Parameters:
      green - DOCUMENT ME!

    • setImageB

      public void setImageB(ModelImage imageB)
      DOCUMENT ME!
      Parameters:
      imageB - DOCUMENT ME!

    • setIsAVI

      public void setIsAVI(boolean isAVI)
      DOCUMENT ME!
      Parameters:
      isAVI - DOCUMENT ME!

    • setIsScript

      public void setIsScript(boolean isScript)
      Accessor that sets the options to be run in a script.
      Parameters:
      isScript - whether the options are being used as part of a script

    • setLUTa

      public void setLUTa(ModelLUT LUTa)
      DOCUMENT ME!
      Parameters:
      LUTa - DOCUMENT ME!

    • setLUTb

      public void setLUTb(ModelLUT LUTb)
      DOCUMENT ME!
      Parameters:
      LUTb - DOCUMENT ME!

    • setMicroSecPerFrame

      public void setMicroSecPerFrame(int microSec)
      DOCUMENT ME!
      Parameters:
      microSec - DOCUMENT ME!

    • setMJPEGQuality

      public void setMJPEGQuality(float mjpegQuality)
      DOCUMENT ME!
      Parameters:
      mjpegQuality - DOCUMENT ME!

    • setMultiFile

      public void setMultiFile(boolean flag)
      Accessor that sets whether or not to write the image as multiple files, one 2D slice per file. Used primarily for TIFF images.
      Parameters:
      flag - true indicates write this as multiple files, false otherwise.

    • setNIFTIExtension

      public void setNIFTIExtension(String niftiExtension)
      Accessor that sets whether or not nifti should be written as a combined .nii file or as separate .hdr and .img files.
      Parameters:
      niftiExtension -

    • setOpacity

      public void setOpacity(float opacity)
      DOCUMENT ME!
      Parameters:
      opacity - DOCUMENT ME!

    • setOptionsSet

      public void setOptionsSet(boolean set)
      Accessor that sets whether all of the options have been previously set (usually by the script parser).
      Parameters:
      set - true indicates the options are already set, false otherwise.

    • setPackBitEnabled

      public void setPackBitEnabled(boolean flag)
      Accessor that sets whether it is possible to write with packed bits compression. It is only an options for TIFF files that are byte images.
      Parameters:
      flag - true indicates it is possible to write with packed bits compression, false otherwise.

    • setPaintBitmap

      public void setPaintBitmap(BitSet paintBitmap)
      DOCUMENT ME!
      Parameters:
      paintBitmap - DOCUMENT ME!

    • setRecalculateInstanceNumber

      public void setRecalculateInstanceNumber(boolean flag)
      Accessor that sets whether or not the Instance Number (0020,0013) should be recalculated before saving.
      Parameters:
      flag - DOCUMENT ME!

    • setRed

      public void setRed(int red)
      DOCUMENT ME!
      Parameters:
      red - DOCUMENT ME!

    • setRGBTa

      public void setRGBTa(ModelRGB RGBTa)
      DOCUMENT ME!
      Parameters:
      RGBTa - DOCUMENT ME!

    • setRGBTb

      public void setRGBTb(ModelRGB RGBTb)
      DOCUMENT ME!
      Parameters:
      RGBTb - DOCUMENT ME!

    • setSaveAs

      public void setSaveAs(boolean flag)
      Accessor that sets the "save as" flag.
      Parameters:
      flag - true indicates save as, false indicates regular save.

    • setSaveInSubdirectory

      public void setSaveInSubdirectory(boolean flag)
      Accessor that sets the "save as" flag.
      Parameters:
      flag - true indicates image should be saved in a subdirectory (imagename without extension) false indicates regular save.

    • setStartNumber

      public void setStartNumber(int num)
      Accessor that sets the number to append to the multi file save (i.e., if you want test00.tif to be the first file, 0 is the start number and 2 is the digit number).
      Parameters:
      num - Start number to write out.

    • setTimeSlice

      public void setTimeSlice(int slice)
      Accessor that sets the time slice to record (4D TIFF). This would have the same functionality as setting the begin time slice and end time slice to the same number. With TIFF images, we do not allow the user to specify a range of time slices, so we will save a 4D image to a 3D TIFF but not to a 4D TIFF.
      Parameters:
      slice - Time slice to write.

    • setWritePackBit

      public void setWritePackBit(boolean flag)
      Accessor that sets whether to write with packed bits compression. Only possible for TIFF files that are byte images.
      Parameters:
      flag - true indicates write with packed bits compression, false otherwise.

    • setXMLLinkedFilename

      public void setXMLLinkedFilename(String xmlfilename)
      Accessor that sets the xml linked filename (for XML files).
      Parameters:
      xmlfilename - the linked xml filename

    • setXSpace

      public void setXSpace(float value)
      Accessor that sets x space (used for MINC images).
      Parameters:
      value - Value to set the x space to.
      See Also:

    • setXStart

      public void setXStart(float value)
      Accessor that sets x start (used for MINC images).
      Parameters:
      value - Value to set the x start to.
      See Also:

    • setYSpace

      public void setYSpace(float value)
      Accessor that sets y space (used for MINC images).
      Parameters:
      value - Value to set the y space to.
      See Also:

    • setYStart

      public void setYStart(float value)
      Accessor that sets y start (used for MINC images).
      Parameters:
      value - Value to set the y start to.
      See Also:

    • setZSpace

      public void setZSpace(float value)
      Accessor that sets z space (used for MINC images).
      Parameters:
      value - Value to set the z space to.
      See Also:

    • setZStart

      public void setZStart(float value)
      Accessor that sets z start (used for MINC images).
      Parameters:
      value - Value to set the z start to.
      See Also:

    • setTSpace

      public void setTSpace(float value)
      Accessor that sets t space (used for MINC images).
      Parameters:
      value - Value to set the t space to.
      See Also:

    • setTStart

      public void setTStart(float value)
      Accessor that sets t start (used for MINC images).
      Parameters:
      value - Value to set the t start to.
      See Also:

    • isGzip

      public boolean isGzip()

    • setGzip

      public void setGzip(boolean isGzip)

    • isZip

      public boolean isZip()

    • setZip

      public void setZip(boolean isZip)

    • isBz2zip

      public boolean isBz2zip()

    • setBz2zip

      public void setBz2zip(boolean isBz2zip)

    • setFloatToShort

      public void setFloatToShort(boolean floatToShort)

    • getFloatToShort

      public boolean getFloatToShort()

    • toString

      public String toString()
      Shows these options as a string, useful for debugging.
      Overrides:
      toString in class Object
      Returns:
      A string containing the saved file write options.