java.lang.Object
- gov.nih.mipav.model.file.FileBase
- - gov.nih.mipav.model.file.FileInterfile

public class FileInterfile
extends FileBase

Author:: William Gandler
See Also:: FileIO

Field Summary

Fields
Modifier and Type	Field	Description
`private static int`	`ASCII`	DOCUMENT ME!
`private static int`	`BIT`	DOCUMENT ME!
`private int`	`bufferSize`	DOCUMENT ME!
`private int`	`bytesPerPixel`	DOCUMENT ME!
`private long`	`dataByteOffset`	DOCUMENT ME!
`private java.io.File`	`dataFile`	DOCUMENT ME!
`private java.lang.String`	`dataFileName`	DOCUMENT ME!
`private int`	`dataStartingBlock`	DOCUMENT ME!
`private boolean`	`endianess`	DOCUMENT ME!
`private java.io.File`	`file`	DOCUMENT ME!
`private java.lang.String`	`fileDir`	DOCUMENT ME!
`private FileInfoInterfile`	`fileInfo`	DOCUMENT ME!
`private FileInfoInterfile`	`fileInfoCopy`
`private long`	`fileLength`	DOCUMENT ME!
`private java.lang.String`	`fileName`	DOCUMENT ME!
`private FileRawChunk`	`fileRW`	DOCUMENT ME!
`private boolean`	`foundEOF`	DOCUMENT ME!
`private boolean`	`haveBytesPerPixel`	DOCUMENT ME!
`private boolean`	`haveDataByteOffset`	DOCUMENT ME!
`private boolean`	`haveDataStartingBlock`	DOCUMENT ME!
`private boolean`	`haveDecayCorrected`	DOCUMENT ME!
`private boolean`	`haveDetectorHeadNumber`	DOCUMENT ME!
`private boolean`	`haveEndianess`	DOCUMENT ME!
`private boolean`	`haveEnergyWindowsNumber`	DOCUMENT ME!
`private boolean`	`haveFileName`	DOCUMENT ME!
`private boolean`	`haveFloodCorrected`	DOCUMENT ME!
`private boolean`	`haveImagesPerEWindow`	DOCUMENT ME!
`private boolean`	`haveNumberFormat`	DOCUMENT ME!
`private boolean`	`haveOrientation`	DOCUMENT ME!
`private boolean`	`haveReconstructed`	DOCUMENT ME!
`private boolean`	`haveReferenceFrameNumber`	DOCUMENT ME!
`private boolean`	`haveResolsT`	DOCUMENT ME!
`private boolean`	`haveResolsX`	DOCUMENT ME!
`private boolean`	`haveResolsY`	DOCUMENT ME!
`private boolean`	`haveResolsZ`	DOCUMENT ME!
`private boolean`	`haveSliceThickness`	DOCUMENT ME!
`private boolean`	`haveStaticStudy`
`private boolean`	`haveTDim`
`private boolean`	`haveTomographic`	DOCUMENT ME!
`private boolean`	`haveTotalImageNumber`	DOCUMENT ME!
`private boolean`	`haveXDim`	DOCUMENT ME!
`private boolean`	`haveYDim`	DOCUMENT ME!
`private boolean`	`haveZDim`	DOCUMENT ME!
`private java.lang.String`	`headerFileName`
`private ModelImage`	`image`	DOCUMENT ME!
`private int`	`imageOrientation`	DOCUMENT ME!
`private float[]`	`imgBuffer`	DOCUMENT ME!
`private double[]`	`imgDBuffer`	DOCUMENT ME!
`private int[]`	`imgExtents`	DOCUMENT ME!
`private long[]`	`imgLBuffer`	DOCUMENT ME!
`private float[]`	`imgResols`	DOCUMENT ME!
`private java.lang.String`	`isotopeNumber`	DOCUMENT ME!
`private static int`	`LONG_FLOAT`	DOCUMENT ME!
`private ModelLUT`	`LUT`	DOCUMENT ME!
`private int`	`numberFormat`	DOCUMENT ME!
`private int`	`numberSlices`	DOCUMENT ME!
`private int`	`orientation`	DOCUMENT ME!
`private java.lang.String`	`originalFileName`	DOCUMENT ME!
`private int`	`resXUnit`	DOCUMENT ME!
`private int`	`resYUnit`	DOCUMENT ME!
`private int`	`resZUnit`	DOCUMENT ME!
`private float`	`scalingFactor1`	DOCUMENT ME!
`private float`	`scalingFactor2`	DOCUMENT ME!
`private float`	`scalingFactor3`	DOCUMENT ME!
`private float`	`scalingFactor4`	DOCUMENT ME!
`private static int`	`SHORT_FLOAT`	DOCUMENT ME!
`private static int`	`SIGNED_INTEGER`	DOCUMENT ME!
`private int`	`tDim`	DOCUMENT ME!
`private java.lang.String`	`timeFrame`	DOCUMENT ME!
`private int`	`totalImageNumber`	DOCUMENT ME!
`private int`	`type`	DOCUMENT ME!
`private static int`	`UNSIGNED_INTEGER`	DOCUMENT ME!
`private java.lang.String`	`windowNumber`	DOCUMENT ME!
`private int`	`xDim`	DOCUMENT ME!
`private float`	`xResol`	DOCUMENT ME!
`private int`	`yDim`	DOCUMENT ME!
`private float`	`yResol`	DOCUMENT ME!
`private int`	`zDim`	DOCUMENT ME!
`private float`	`zResol`	DOCUMENT ME!

Fields inherited from class gov.nih.mipav.model.file.FileBase
BIG_ENDIAN, bitsPerPixel, fileNames, LITTLE_ENDIAN, pBarVisible, raFile, READ, READ_WRITE

Constructor Summary

Constructors
Constructor Description

FileInterfile(java.lang.String originalFileName, java.lang.String fileDir)
Interfile reader/writer constructor.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`finalize()`	Prepares this class for cleanup.
`FileInfoInterfile`	`getFileInfo()`	Returns the file info.
`float[]`	`getImageBuffer()`	Returns the image buffer.
`ModelLUT`	`getModelLUT()`	Returns LUT if defined.
`static java.lang.String`	`isInterfile(java.lang.String fName, java.lang.String fDir)`	Method to test to determine if the image format is Cheshire, so appropriate read method may be called.
`private void`	`readBBuffer(int slice, float[] buffer)`	DOCUMENT ME!
`private void`	`readBuffer(int slice, float[] buffer)`	Reads a slice of data at a time and stores the results in the buffer.
`private void`	`readDBuffer(int slice, double[] buffer)`	Reads a slice of data at a time and stores the results in the buffer.
`ModelImage`	`readImage(boolean one, boolean readData)`	Reads the image.
`private void`	`readLBuffer(int slice, long[] buffer)`	Reads a slice of data at a time and stores the results in the buffer.
`private java.lang.String`	`readLine()`	Reads lines of the file and strips comments indicated by the ; symbol until a nonnull String results or the end of the file is reached.
`private static java.lang.String`	`removeChars(java.lang.String inString)`	Removes white space and exclamation marks.
`private static java.lang.String`	`returnKey(java.lang.String inString)`	Returns the key found in the string.
`private java.lang.String`	`returnValue(java.lang.String inString)`	Returns the value found in the string.
`void`	`setFileName(java.lang.String fName)`	Sets the file name (used when reading TIFF multiFile).
`void`	`writeImage(ModelImage image, FileWriteOptions options)`	Writes an Interfile format type image.

Methods inherited from class gov.nih.mipav.model.file.FileBase
addProgressChangeListener, bytesToDouble, bytesToFloat, bytesToInt, bytesToShort, doubleToBytes, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, floatToBytes, getBufferDouble, getBufferFloat, getBufferInt, getBufferLong, getBufferShort, getBufferUShort, getDataType, getDouble, getFloat, getInt, getLong, getProgressChangeListeners, getRaFile, getSignedShort, getString, getUInt, getUnsignedByte, getUnsignedShort, intToBytes, isBigEndian, isProgressBarVisible, linkProgress, longToBytes, readDouble, readFloat, readInt, readLong, readShort, readString, readUnsignedShort, removeProgressChangeListener, setBigEndian, setBufferFloat, setBufferInt, setBufferLong, setBufferShort, setBufferString, setDataType, setEndianess, shortToBytes, writeBytes, writeDouble, writeFloat, writeInt, writeLong, writeShort

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

- Field Detail
  - SIGNED_INTEGER
```
private static final int SIGNED_INTEGER
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - UNSIGNED_INTEGER
```
private static final int UNSIGNED_INTEGER
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - LONG_FLOAT
```
private static final int LONG_FLOAT
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - SHORT_FLOAT
```
private static final int SHORT_FLOAT
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - BIT
```
private static final int BIT
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - ASCII
```
private static final int ASCII
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - bufferSize
```
private int bufferSize
```
    DOCUMENT ME!
  - bytesPerPixel
```
private int bytesPerPixel
```
    DOCUMENT ME!
  - dataByteOffset
```
private long dataByteOffset
```
    DOCUMENT ME!
  - dataFile
```
private java.io.File dataFile
```
    DOCUMENT ME!
  - dataFileName
```
private java.lang.String dataFileName
```
    DOCUMENT ME!
  - headerFileName
```
private java.lang.String headerFileName
```
  - dataStartingBlock
```
private int dataStartingBlock
```
    DOCUMENT ME!
  - endianess
```
private boolean endianess
```
    DOCUMENT ME!
  - file
```
private java.io.File file
```
    DOCUMENT ME!
  - fileDir
```
private java.lang.String fileDir
```
    DOCUMENT ME!
  - fileInfo
```
private FileInfoInterfile fileInfo
```
    DOCUMENT ME!
  - fileInfoCopy
```
private FileInfoInterfile fileInfoCopy
```
  - fileLength
```
private long fileLength
```
    DOCUMENT ME!
  - fileName
```
private java.lang.String fileName
```
    DOCUMENT ME!
  - fileRW
```
private FileRawChunk fileRW
```
    DOCUMENT ME!
  - foundEOF
```
private boolean foundEOF
```
    DOCUMENT ME!
  - haveBytesPerPixel
```
private boolean haveBytesPerPixel
```
    DOCUMENT ME!
  - haveDataByteOffset
```
private boolean haveDataByteOffset
```
    DOCUMENT ME!
  - haveDataStartingBlock
```
private boolean haveDataStartingBlock
```
    DOCUMENT ME!
  - haveDecayCorrected
```
private boolean haveDecayCorrected
```
    DOCUMENT ME!
  - haveDetectorHeadNumber
```
private boolean haveDetectorHeadNumber
```
    DOCUMENT ME!
  - haveEndianess
```
private boolean haveEndianess
```
    DOCUMENT ME!
  - haveEnergyWindowsNumber
```
private boolean haveEnergyWindowsNumber
```
    DOCUMENT ME!
  - haveFileName
```
private boolean haveFileName
```
    DOCUMENT ME!
  - haveFloodCorrected
```
private boolean haveFloodCorrected
```
    DOCUMENT ME!
  - haveImagesPerEWindow
```
private boolean haveImagesPerEWindow
```
    DOCUMENT ME!
  - haveNumberFormat
```
private boolean haveNumberFormat
```
    DOCUMENT ME!
  - haveOrientation
```
private boolean haveOrientation
```
    DOCUMENT ME!
  - haveReconstructed
```
private boolean haveReconstructed
```
    DOCUMENT ME!
  - haveReferenceFrameNumber
```
private boolean haveReferenceFrameNumber
```
    DOCUMENT ME!
  - haveResolsT
```
private boolean haveResolsT
```
    DOCUMENT ME!
  - haveResolsX
```
private boolean haveResolsX
```
    DOCUMENT ME!
  - haveResolsY
```
private boolean haveResolsY
```
    DOCUMENT ME!
  - haveResolsZ
```
private boolean haveResolsZ
```
    DOCUMENT ME!
  - haveSliceThickness
```
private boolean haveSliceThickness
```
    DOCUMENT ME!
  - haveTDim
```
private boolean haveTDim
```
  - haveTomographic
```
private boolean haveTomographic
```
    DOCUMENT ME!
  - haveTotalImageNumber
```
private boolean haveTotalImageNumber
```
    DOCUMENT ME!
  - haveXDim
```
private boolean haveXDim
```
    DOCUMENT ME!
  - haveYDim
```
private boolean haveYDim
```
    DOCUMENT ME!
  - haveZDim
```
private boolean haveZDim
```
    DOCUMENT ME!
  - image
```
private ModelImage image
```
    DOCUMENT ME!
  - imageOrientation
```
private int imageOrientation
```
    DOCUMENT ME!
  - imgBuffer
```
private float[] imgBuffer
```
    DOCUMENT ME!
  - imgDBuffer
```
private double[] imgDBuffer
```
    DOCUMENT ME!
  - imgExtents
```
private int[] imgExtents
```
    DOCUMENT ME!
  - imgLBuffer
```
private long[] imgLBuffer
```
    DOCUMENT ME!
  - imgResols
```
private float[] imgResols
```
    DOCUMENT ME!
  - isotopeNumber
```
private java.lang.String isotopeNumber
```
    DOCUMENT ME!
  - LUT
```
private ModelLUT LUT
```
    DOCUMENT ME!
  - numberFormat
```
private int numberFormat
```
    DOCUMENT ME!
  - numberSlices
```
private int numberSlices
```
    DOCUMENT ME!
  - orientation
```
private int orientation
```
    DOCUMENT ME!
  - originalFileName
```
private java.lang.String originalFileName
```
    DOCUMENT ME!
  - resXUnit
```
private int resXUnit
```
    DOCUMENT ME!
  - resYUnit
```
private int resYUnit
```
    DOCUMENT ME!
  - resZUnit
```
private int resZUnit
```
    DOCUMENT ME!
  - scalingFactor1
```
private float scalingFactor1
```
    DOCUMENT ME!
  - scalingFactor2
```
private float scalingFactor2
```
    DOCUMENT ME!
  - scalingFactor3
```
private float scalingFactor3
```
    DOCUMENT ME!
  - scalingFactor4
```
private float scalingFactor4
```
    DOCUMENT ME!
  - tDim
```
private int tDim
```
    DOCUMENT ME!
  - timeFrame
```
private java.lang.String timeFrame
```
    DOCUMENT ME!
  - totalImageNumber
```
private int totalImageNumber
```
    DOCUMENT ME!
  - type
```
private int type
```
    DOCUMENT ME!
  - windowNumber
```
private java.lang.String windowNumber
```
    DOCUMENT ME!
  - xDim
```
private int xDim
```
    DOCUMENT ME!
  - xResol
```
private float xResol
```
    DOCUMENT ME!
  - yResol
```
private float yResol
```
    DOCUMENT ME!
  - zResol
```
private float zResol
```
    DOCUMENT ME!
  - yDim
```
private int yDim
```
    DOCUMENT ME!
  - zDim
```
private int zDim
```
    DOCUMENT ME!
  - haveStaticStudy
```
private boolean haveStaticStudy
```
- Constructor Detail
  - FileInterfile
```
public FileInterfile(java.lang.String originalFileName,
                     java.lang.String fileDir)
              throws java.io.IOException
```
    Interfile reader/writer constructor.
    
    Parameters:
    
    originalFileName - file name
    
    fileDir - file directory
    
    Throws:
    
    java.io.IOException - if there is an error making the file
- Method Detail
  - finalize
```
public void finalize()
```
    Prepares this class for cleanup. Calls the finalize method for existing elements, closes any open files and sets other elements to null.
    
    Overrides:
    
    finalize in class FileBase
  - isInterfile
```
public static java.lang.String isInterfile(java.lang.String fName,
                                           java.lang.String fDir)
```
    Method to test to determine if the image format is Cheshire, so appropriate read method may be called.
    
    Parameters:
    
    fName - File name of image.
    
    fDir - Directory.
    
    Returns:
    
    true if Cheshire file, false otherwise.
  - getFileInfo
```
public FileInfoInterfile getFileInfo()
```
    Returns the file info.
    
    Returns:
    
    FileInfoBase containing the file info
  - getImageBuffer
```
public float[] getImageBuffer()
```
    Returns the image buffer.
    
    Returns:
    
    buffer of image.
  - getModelLUT
```
public ModelLUT getModelLUT()
```
    Returns LUT if defined.
    
    Returns:
    
    the LUT if defined else it is null
  - readImage
```
public ModelImage readImage(boolean one,
                            boolean readData)
                     throws java.io.IOException
```
    Reads the image.
    
    Parameters:
    
    one - Flag for only reading one image of dataset.
    
    readData -
    
    Returns:
    
    returns the image
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - setFileName
```
public void setFileName(java.lang.String fName)
```
    Sets the file name (used when reading TIFF multiFile).
    
    Parameters:
    
    fName - file name of image to read.
  - writeImage
```
public void writeImage(ModelImage image,
                       FileWriteOptions options)
                throws java.io.IOException
```
    Writes an Interfile format type image.
    
    Parameters:
    
    image - Image model of data to write.
    
    options - options such as starting and ending slices and times
    
    Throws:
    
    java.io.IOException - if there is an error writing the file
  - removeChars
```
private static java.lang.String removeChars(java.lang.String inString)
```
    Removes white space and exclamation marks.
    
    Parameters:
    
    inString - String to remove characters from.
    
    Returns:
    
    new String with removed white space.
  - returnKey
```
private static java.lang.String returnKey(java.lang.String inString)
```
    Returns the key found in the string.
    
    Parameters:
    
    inString - String to search for key in.
    
    Returns:
    
    Key, or null if not found
  - readBBuffer
```
private void readBBuffer(int slice,
                         float[] buffer)
                  throws java.io.IOException
```
    DOCUMENT ME!
    
    Parameters:
    
    slice - DOCUMENT ME!
    
    buffer - DOCUMENT ME!
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!
  - readBuffer
```
private void readBuffer(int slice,
                        float[] buffer)
                 throws java.io.IOException
```
    Reads a slice of data at a time and stores the results in the buffer.
    
    Parameters:
    
    slice - offset into the file stored in the dataOffset array
    
    buffer - buffer where the info is stored
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - readDBuffer
```
private void readDBuffer(int slice,
                         double[] buffer)
                  throws java.io.IOException
```
    Reads a slice of data at a time and stores the results in the buffer.
    
    Parameters:
    
    slice - offset into the file stored in the dataOffset array
    
    buffer - buffer where the info is stored
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - readLBuffer
```
private void readLBuffer(int slice,
                         long[] buffer)
                  throws java.io.IOException
```
    Reads a slice of data at a time and stores the results in the buffer.
    
    Parameters:
    
    slice - offset into the file stored in the dataOffset array
    
    buffer - buffer where the info is stored
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - readLine
```
private java.lang.String readLine()
                           throws java.io.IOException
```
    Reads lines of the file and strips comments indicated by the ; symbol until a nonnull String results or the end of the file is reached.
    
    Returns:
    
    the line read in
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - returnValue
```
private java.lang.String returnValue(java.lang.String inString)
```
    Returns the value found in the string.
    
    Parameters:
    
    inString - String to search for value in.
    
    Returns:
    
    Value, or null if not found

Class FileInterfile

Field Summary

Fields inherited from class gov.nih.mipav.model.file.FileBase

Constructor Summary

Method Summary

Methods inherited from class gov.nih.mipav.model.file.FileBase

Methods inherited from class java.lang.Object

Field Detail

SIGNED_INTEGER

UNSIGNED_INTEGER

LONG_FLOAT

SHORT_FLOAT

BIT

ASCII

bufferSize

bytesPerPixel

dataByteOffset

dataFile

dataFileName

headerFileName

dataStartingBlock

endianess

file

fileDir

fileInfo

fileInfoCopy

fileLength

fileName

fileRW

foundEOF

haveBytesPerPixel

haveDataByteOffset

haveDataStartingBlock

haveDecayCorrected

haveDetectorHeadNumber

haveEndianess

haveEnergyWindowsNumber

haveFileName

haveFloodCorrected

haveImagesPerEWindow

haveNumberFormat

haveOrientation

haveReconstructed

haveReferenceFrameNumber

haveResolsT

haveResolsX

haveResolsY

haveResolsZ

haveSliceThickness

haveTDim

haveTomographic

haveTotalImageNumber

haveXDim

haveYDim

haveZDim

image

imageOrientation

imgBuffer

imgDBuffer

imgExtents

imgLBuffer

imgResols

isotopeNumber

LUT

numberFormat

numberSlices

orientation

originalFileName

resXUnit

resYUnit

resZUnit

scalingFactor1

scalingFactor2

scalingFactor3

scalingFactor4

tDim

timeFrame

totalImageNumber

type

windowNumber