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

```
public class FileWriteOptions
extends java.lang.Object
```
This structure contains information to direct file writing.

Version:

0.1 June 21, 2001

Author:

Neva Cherniavsky

See Also:

FileIO

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 java.lang.String`	`fileDirectory`	DOCUMENT ME!
`private java.lang.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 java.lang.String`	`niftiExtension`
`private float`	`opacity`	DOCUMENT ME!
`private boolean`	`optionsSet`	DOCUMENT ME!
`private boolean`	`packBitEnable`	DOCUMENT ME!
`private java.util.BitSet`	`paintBitmap`	DOCUMENT ME!
`private java.util.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 java.lang.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(java.lang.String fileName, java.lang.String directory, boolean saveAs)`	Constructs an options structure with the given file name, directory, and saveAs values.

Method Summary

All Methods Instance Methods Concrete Methods
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.
`java.lang.String`	`getFileDirectory()`	Accessor that returns the directory to be written to.
`java.lang.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
`java.lang.String`	`getNIFTIExtension()`
`float`	`getOpacity()`	DOCUMENT ME!
`java.util.BitSet`	`getPaintBitmap()`	DOCUMENT ME!
`java.util.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.
`java.lang.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(java.lang.String dir)`	Accessor that sets the file directory.
`void`	`setFileName(java.lang.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(java.lang.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(java.util.BitSet paintBitmap)`	DOCUMENT ME!
`void`	`setPSetsHashMap(java.util.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(java.lang.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).
`java.lang.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 Detail
  - 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 java.lang.String fileDirectory
```
    DOCUMENT ME!
  - fileName
```
private java.lang.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 java.lang.String niftiExtension
```
  - opacity
```
private float opacity
```
    DOCUMENT ME!
  - optionsSet
```
private boolean optionsSet
```
    DOCUMENT ME!
  - packBitEnable
```
private boolean packBitEnable
```
    DOCUMENT ME!
  - paintBitmap
```
private java.util.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 java.lang.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 java.util.HashMap<?,?> pSetsHashMap
```
  - isGzip
```
private boolean isGzip
```
  - isZip
```
private boolean isZip
```
  - isBz2zip
```
private boolean isBz2zip
```
  - floatToShort
```
private boolean floatToShort
```
- Constructor Detail
  - 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(java.lang.String fileName,
                        java.lang.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 Detail
  - 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 java.util.HashMap<?,?> getPSetsHashMap()
```
    gets the psets hashmap
    
    Returns:
  - setPSetsHashMap
```
public void setPSetsHashMap(java.util.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 java.lang.String getFileDirectory()
```
    Accessor that returns the directory to be written to.
    
    Returns:
    
    The directory to write this image to.
  - getFileName
```
public java.lang.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:
    
    FileBase
  - 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 java.lang.String getNIFTIExtension()
```
  - getOpacity
```
public float getOpacity()
```
    DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - getPaintBitmap
```
public java.util.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 java.lang.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(java.lang.String dir)
```
    Accessor that sets the file directory.
    
    Parameters:
    
    dir - File directory to write to.
  - setFileName
```
public void setFileName(java.lang.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(java.lang.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(java.util.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(java.lang.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:
    
    JDialogSaveMinc
  - 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:
    
    JDialogSaveMinc
  - 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:
    
    JDialogSaveMinc
  - 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:
    
    JDialogSaveMinc
  - 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:
    
    JDialogSaveMinc
  - 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:
    
    JDialogSaveMinc
  - 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:
    
    JDialogSaveMinc
  - 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:
    
    JDialogSaveMinc
  - 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 java.lang.String toString()
```
    Shows these options as a string, useful for debugging.
    
    Overrides:
    
    toString in class java.lang.Object
    
    Returns:
    
    A string containing the saved file write options.

Class FileWriteOptions

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

runningInSeparateThread

alphaBlend

AVICompression

axisOrientation

beginSlice

beginTimePeriod

blue

defaults

endSlice

endTimePeriod

fileDigitNumber

fileDirectory

fileName

fileStartNumber

fileType

green

imageB

isAVI

isScript

LUTa

LUTb

microSecPerFrame

mjpegQuality

multiFile

doStamp

doEnhanced

niftiExtension

opacity

optionsSet

packBitEnable

paintBitmap

recalculateInstanceNumber

red

RGBTa

RGBTb

saveAs

saveInSubdirectory

timeSlice

writePackBit

xmlLinkedFilename

xSpace

xStart

ySpace

yStart

zSpace

zStart

tSpace

tStart

putInQuicklist

writeHeaderOnly

ndarData

pSetsHashMap

isGzip

isZip

isBz2zip

floatToShort

Constructor Detail

FileWriteOptions

FileWriteOptions

Method Detail

disposeLocal

doPutInQuicklist

doPutInQuicklist

doEnhanced

doStamp

doEnhanced

doStamp

writeHeaderOnly

setWriteHeaderOnly

getPSetsHashMap

setPSetsHashMap

setNDARData

getNDARData

getAlphaBlend