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

public class FileMATLAB
extends FileBase

Field Summary

Fields
Modifier and Type	Field	Description
`(package private) int[]`	`extentsf`
`(package private) int[]`	`extentsv`
`(package private) java.util.Vector<java.lang.Integer>`	`f`
`private java.io.File`	`file`	DOCUMENT ME!
`private java.lang.String`	`fileDir`	DOCUMENT ME!
`private FileInfoMATLAB`	`fileInfo`	DOCUMENT ME!
`private FileInfoMATLAB`	`fileInfo2`
`private java.lang.String`	`fileName`	DOCUMENT ME!
`private long`	`filePointer`
`private boolean`	`haveImported`
`private boolean`	`haveNumericArrayCharacter`
`private ModelImage`	`image`	DOCUMENT ME!
`private ModelImage`	`image2`
`private int[]`	`imageExtents`	DOCUMENT ME!
`private float[]`	`imgBuffer`	DOCUMENT ME!
`private float[]`	`imgResols`	DOCUMENT ME!
`private ModelLUT`	`LUT`	DOCUMENT ME!
`private FileInfoMATLAB`	`maskFileInfo`
`private FileInfoMATLAB`	`maskFileInfo2`
`private ModelImage`	`maskImage`
`private ModelImage`	`maskImage2`
`private int`	`maximumNonZeroElements`
`private static int`	`miCOMPRESSED`	Compressed Data
`private static int`	`miDOUBLE`	IEEE 754 double format
`private static int`	`miINT16`	16-bit, signed
`private static int`	`miINT32`	32-bit signed
`private static int`	`miINT64`	64-bit, signed
`private static int`	`miINT8`	8 bit, signed
`private static int`	`miMATRIX`	MATLAB ARRAY
`private static int`	`miSINGLE`	IEEE 754 single format
`private static int`	`miUINT16`	16-bit, unsigned
`private static int`	`miUINT32`	32-bit, unsigned
`private static int`	`miUINT64`	64-bit, unsigned
`private static int`	`miUINT8`	8 bit, unsigned
`private static int`	`miUTF16`	Unicode UTF-16 Encoded Character Data
`private static int`	`miUTF32`	Unicode UTF-32 Encoded Character Data
`private static int`	`miUTF8`	Unicode UTF-8 Encoded Character Data
`private static byte`	`mxCELL_CLASS`	Cell array
`private static byte`	`mxCHAR_CLASS`	Character array
`private static byte`	`mxDOUBLE_CLASS`	Double precision array
`private static byte`	`mxINT16_CLASS`	16-bit, signed integer
`private static byte`	`mxINT32_CLASS`	32-bit, signed integer
`private static byte`	`mxINT64_CLASS`	64-bit, signed integer
`private static byte`	`mxINT8_CLASS`	8-bit, signed integer
`private static byte`	`mxOBJECT_CLASS`	Object
`private static byte`	`mxSINGLE_CLASS`	Single precision array
`private static byte`	`mxSPARSE_CLASS`	Sparse array
`private static byte`	`mxSTRUCT_CLASS`	Structure
`private static byte`	`mxUINT16_CLASS`	16-bit, unsigned integer
`private static byte`	`mxUINT32_CLASS`	32-bit, unsigned integer
`private static byte`	`mxUINT64_CLASS`	64-bit, unsigned integer
`private static byte`	`mxUINT8_CLASS`	8-bit, unsigned integer
`private int`	`numberCharacterClasses`
`(package private) boolean`	`readf`
`(package private) boolean`	`readv`
`(package private) java.util.Vector<java.lang.Double>`	`v`
`private ViewJFrameImage`	`vFrame2`
`private ViewJFrameImage`	`vmFrame`
`private ViewJFrameImage`	`vmFrame2`
`private java.util.zip.Inflater`	`zlibDecompresser`

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

FileMATLAB(java.lang.String fileName, java.lang.String fileDir)
LIFF reader/writer constructor.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`finalize()`	Prepares this class for cleanup.
`FileInfoBase`	`getFileInfo()`	Accessor that returns the file info.
`float[]`	`getImageBuffer()`	Accessor that returns the image buffer.
`ModelLUT`	`getModelLUT()`	Rreturns LUT if defined.
`private java.lang.String`	`readCString()`
`ModelImage`	`readImage(boolean multiFile, boolean one)`	Reads the MATLAB header.
`void`	`setFileName(java.lang.String fName)`	Accessor to set the file name (used for reading COR multiFile).
`void`	`setfv(java.util.Vector<java.lang.Integer> f, java.util.Vector<java.lang.Double> v, int[] extentsf, int[] extentsv)`
`void`	`writeImage(ModelImage image, FileWriteOptions options)`	Writes a MATLAB 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
  - miINT8
```
private static final int miINT8
```
    8 bit, signed
    
    See Also:
    
    Constant Field Values
  - miUINT8
```
private static final int miUINT8
```
    8 bit, unsigned
    
    See Also:
    
    Constant Field Values
  - miINT16
```
private static final int miINT16
```
    16-bit, signed
    
    See Also:
    
    Constant Field Values
  - miUINT16
```
private static final int miUINT16
```
    16-bit, unsigned
    
    See Also:
    
    Constant Field Values
  - miINT32
```
private static final int miINT32
```
    32-bit signed
    
    See Also:
    
    Constant Field Values
  - miUINT32
```
private static final int miUINT32
```
    32-bit, unsigned
    
    See Also:
    
    Constant Field Values
  - miSINGLE
```
private static final int miSINGLE
```
    IEEE 754 single format
    
    See Also:
    
    Constant Field Values
  - miDOUBLE
```
private static final int miDOUBLE
```
    IEEE 754 double format
    
    See Also:
    
    Constant Field Values
  - miINT64
```
private static final int miINT64
```
    64-bit, signed
    
    See Also:
    
    Constant Field Values
  - miUINT64
```
private static final int miUINT64
```
    64-bit, unsigned
    
    See Also:
    
    Constant Field Values
  - miMATRIX
```
private static final int miMATRIX
```
    MATLAB ARRAY
    
    See Also:
    
    Constant Field Values
  - miCOMPRESSED
```
private static final int miCOMPRESSED
```
    Compressed Data
    
    See Also:
    
    Constant Field Values
  - miUTF8
```
private static final int miUTF8
```
    Unicode UTF-8 Encoded Character Data
    
    See Also:
    
    Constant Field Values
  - miUTF16
```
private static final int miUTF16
```
    Unicode UTF-16 Encoded Character Data
    
    See Also:
    
    Constant Field Values
  - miUTF32
```
private static final int miUTF32
```
    Unicode UTF-32 Encoded Character Data
    
    See Also:
    
    Constant Field Values
  - mxCELL_CLASS
```
private static final byte mxCELL_CLASS
```
    Cell array
    
    See Also:
    
    Constant Field Values
  - mxSTRUCT_CLASS
```
private static final byte mxSTRUCT_CLASS
```
    Structure
    
    See Also:
    
    Constant Field Values
  - mxOBJECT_CLASS
```
private static final byte mxOBJECT_CLASS
```
    Object
    
    See Also:
    
    Constant Field Values
  - mxCHAR_CLASS
```
private static final byte mxCHAR_CLASS
```
    Character array
    
    See Also:
    
    Constant Field Values
  - mxSPARSE_CLASS
```
private static final byte mxSPARSE_CLASS
```
    Sparse array
    
    See Also:
    
    Constant Field Values
  - mxDOUBLE_CLASS
```
private static final byte mxDOUBLE_CLASS
```
    Double precision array
    
    See Also:
    
    Constant Field Values
  - mxSINGLE_CLASS
```
private static final byte mxSINGLE_CLASS
```
    Single precision array
    
    See Also:
    
    Constant Field Values
  - mxINT8_CLASS
```
private static final byte mxINT8_CLASS
```
    8-bit, signed integer
    
    See Also:
    
    Constant Field Values
  - mxUINT8_CLASS
```
private static final byte mxUINT8_CLASS
```
    8-bit, unsigned integer
    
    See Also:
    
    Constant Field Values
  - mxINT16_CLASS
```
private static final byte mxINT16_CLASS
```
    16-bit, signed integer
    
    See Also:
    
    Constant Field Values
  - mxUINT16_CLASS
```
private static final byte mxUINT16_CLASS
```
    16-bit, unsigned integer
    
    See Also:
    
    Constant Field Values
  - mxINT32_CLASS
```
private static final byte mxINT32_CLASS
```
    32-bit, signed integer
    
    See Also:
    
    Constant Field Values
  - mxUINT32_CLASS
```
private static final byte mxUINT32_CLASS
```
    32-bit, unsigned integer
    
    See Also:
    
    Constant Field Values
  - mxINT64_CLASS
```
private static final byte mxINT64_CLASS
```
    64-bit, signed integer
    
    See Also:
    
    Constant Field Values
  - mxUINT64_CLASS
```
private static final byte mxUINT64_CLASS
```
    64-bit, unsigned integer
    
    See Also:
    
    Constant Field Values
  - file
```
private java.io.File file
```
    DOCUMENT ME!
  - fileDir
```
private java.lang.String fileDir
```
    DOCUMENT ME!
  - fileInfo
```
private FileInfoMATLAB fileInfo
```
    DOCUMENT ME!
  - fileInfo2
```
private FileInfoMATLAB fileInfo2
```
  - maskFileInfo
```
private FileInfoMATLAB maskFileInfo
```
  - maskFileInfo2
```
private FileInfoMATLAB maskFileInfo2
```
  - fileName
```
private java.lang.String fileName
```
    DOCUMENT ME!
  - image
```
private ModelImage image
```
    DOCUMENT ME!
  - imageExtents
```
private int[] imageExtents
```
    DOCUMENT ME!
  - imgBuffer
```
private float[] imgBuffer
```
    DOCUMENT ME!
  - imgResols
```
private float[] imgResols
```
    DOCUMENT ME!
  - LUT
```
private ModelLUT LUT
```
    DOCUMENT ME!
  - zlibDecompresser
```
private java.util.zip.Inflater zlibDecompresser
```
  - image2
```
private ModelImage image2
```
  - vFrame2
```
private ViewJFrameImage vFrame2
```
  - maskImage
```
private ModelImage maskImage
```
  - vmFrame
```
private ViewJFrameImage vmFrame
```
  - maskImage2
```
private ModelImage maskImage2
```
  - vmFrame2
```
private ViewJFrameImage vmFrame2
```
  - filePointer
```
private long filePointer
```
  - maximumNonZeroElements
```
private int maximumNonZeroElements
```
  - haveNumericArrayCharacter
```
private boolean haveNumericArrayCharacter
```
  - numberCharacterClasses
```
private int numberCharacterClasses
```
  - haveImported
```
private boolean haveImported
```
  - f
```
java.util.Vector<java.lang.Integer> f
```
  - v
```
java.util.Vector<java.lang.Double> v
```
  - extentsf
```
int[] extentsf
```
  - extentsv
```
int[] extentsv
```
  - readf
```
boolean readf
```
  - readv
```
boolean readv
```
- Constructor Detail
  - FileMATLAB
```
public FileMATLAB(java.lang.String fileName,
                  java.lang.String fileDir)
           throws java.io.IOException
```
    LIFF reader/writer constructor.
    
    Parameters:
    
    fileName - 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
  - getFileInfo
```
public FileInfoBase getFileInfo()
```
    Accessor that returns the file info.
    
    Returns:
    
    FileInfoBase containing the file info
  - getImageBuffer
```
public float[] getImageBuffer()
```
    Accessor that returns the image buffer.
    
    Returns:
    
    buffer of image.
  - getModelLUT
```
public ModelLUT getModelLUT()
```
    Rreturns LUT if defined.
    
    Returns:
    
    the LUT if defined else it is null
  - setfv
```
public void setfv(java.util.Vector<java.lang.Integer> f,
                  java.util.Vector<java.lang.Double> v,
                  int[] extentsf,
                  int[] extentsv)
```
  - readImage
```
public ModelImage readImage(boolean multiFile,
                            boolean one)
                     throws java.io.IOException
```
    Reads the MATLAB header.
    
    Parameters:
    
    multiFile - true if a set of files each containing a separate 2D image is present false if one file with either a 2D image or a stack of 2D images
    
    one - true if only want to read in one image of the 3D set
    
    Returns:
    
    returns the image
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - readCString
```
private java.lang.String readCString()
                              throws java.io.IOException
```
    Throws:
    
    java.io.IOException
  - setFileName
```
public void setFileName(java.lang.String fName)
```
    Accessor to set the file name (used for reading COR multiFile).
    
    Parameters:
    
    fName - file name of image to read.
  - writeImage
```
public void writeImage(ModelImage image,
                       FileWriteOptions options)
                throws java.io.IOException
```
    Writes a MATLAB 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

Class FileMATLAB

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

miINT8

miUINT8

miINT16

miUINT16

miINT32

miUINT32

miSINGLE

miDOUBLE

miINT64

miUINT64

miMATRIX

miCOMPRESSED

miUTF8

miUTF16

miUTF32

mxCELL_CLASS

mxSTRUCT_CLASS

mxOBJECT_CLASS

mxCHAR_CLASS

mxSPARSE_CLASS

mxDOUBLE_CLASS

mxSINGLE_CLASS

mxINT8_CLASS

mxUINT8_CLASS

mxINT16_CLASS

mxUINT16_CLASS

mxINT32_CLASS

mxUINT32_CLASS

mxINT64_CLASS

mxUINT64_CLASS

file

fileDir

fileInfo

fileInfo2

maskFileInfo

maskFileInfo2

fileName

image

imageExtents

imgBuffer

imgResols

LUT

zlibDecompresser

image2

vFrame2

maskImage

vmFrame

maskImage2

vmFrame2

filePointer

maximumNonZeroElements

haveNumericArrayCharacter

numberCharacterClasses

haveImported

f

v

extentsf

extentsv

readf

readv

Constructor Detail

FileMATLAB

Method Detail

finalize

getFileInfo

getImageBuffer

getModelLUT

setfv

readImage

readCString

setFileName

writeImage