Package gov.nih.mipav.model.file

Class FileDM3

java.lang.Object

gov.nih.mipav.model.file.FileBase

gov.nih.mipav.model.file.FileDM3

public class FileDM3
extends FileBase

Some of this code is derived from DM3_Reader.java in ImageJ.

ImageJ disclaimer:

ImageJ is being developed at the National Institutes of Health by an employee of the Federal Government in the course of his official duties. Pursuant to Title 17, Section 105 of the United States Code, this software is not subject to copyright protection and is in the public domain. ImageJ is an experimental system. NIH assumes no responsibility whatsoever for its use by other parties, and makes no guarantees, expressed or implied, about its quality, reliability, or any other characteristic.

Field Summary

Fields

Modifier and Type	Field	Description
private static final int	ARRAY	DOCUMENT ME!
private long[]	arrayLocationArray	DOCUMENT ME!
private int[]	arraySizeArray	DOCUMENT ME!
private static final int	BOOLEAN	DOCUMENT ME!
private int	byteOrder	DOCUMENT ME!
private static final int	CHAR	DOCUMENT ME!
private boolean	dataEndianess	DOCUMENT ME!
private int[]	dataTypeArray	DOCUMENT ME!
private int	desiredArraySize	DOCUMENT ME!
private int	desiredImageNumber	DOCUMENT ME!
private String[]	desiredPixelUnitsArray	DOCUMENT ME!
private int[][]	dimArray	DOCUMENT ME!
private static final int	DOUBLE	DOCUMENT ME!
private boolean	endianess	DOCUMENT ME!
private File	file	DOCUMENT ME!
private int	fileBytes	DOCUMENT ME!
private String	fileDir	DOCUMENT ME!
private FileInfoDM3	fileInfo	DOCUMENT ME!
private FileInfoDM3	fileInfoCopy
private String	fileName	DOCUMENT ME!
private int	fileVersion	DOCUMENT ME!
private static final int	FLOAT	DOCUMENT ME!
private int	identicalDesiredArraySize	DOCUMENT ME!
private ModelImage	image	DOCUMENT ME!
private int	imageNum	DOCUMENT ME!
private int[]	imgExtents	DOCUMENT ME!
private boolean	isCalibrations	DOCUMENT ME!
private boolean	isData	DOCUMENT ME!
private boolean	isDataType	DOCUMENT ME!
private boolean	isDimension	DOCUMENT ME!
private boolean	isDimensions	DOCUMENT ME!
private boolean	isImageData	DOCUMENT ME!
private boolean	isScale	DOCUMENT ME!
private boolean	isUnits	DOCUMENT ME!
private static final int	LONG	DOCUMENT ME!
private ModelLUT	LUT	DOCUMENT ME!
private int	nDimensions	DOCUMENT ME!
private int	numberSlices	DOCUMENT ME!
private int[]	numDimArray	DOCUMENT ME!
private static final int	OCTET	DOCUMENT ME!
private float[][]	pixelScaleArray	DOCUMENT ME!
private String[][]	pixelUnitsArray	DOCUMENT ME!
private int[]	pixelUnitsNumber	DOCUMENT ME!
private ViewJProgressBar	progressBar	DOCUMENT ME!
private int	routineTagEntry	DOCUMENT ME!
private int	routineTagGroup	DOCUMENT ME!
private int	scaleIndex	DOCUMENT ME!
private static final int	SHORT	Different encoded data types used in DM3 files.
private int	sourceType	DOCUMENT ME!
private static final int	STRING	DOCUMENT ME!
private static final int	STRUCT	DOCUMENT ME!
private static final int	ULONG	DOCUMENT ME!
private int	unitsIndex	DOCUMENT ME!
private static final int	USHORT	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
FileDM3(String fileName, String fileDir)	DM3 reader constructor.

Method Summary

Modifier and Type	Method	Description
void	finalize()	Prepares this class for cleanup.
ModelLUT	getModelLUT()	returns LUT if defined.
private void	readArray()	DOCUMENT ME!
private int[]	readArrayTypes()	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	readComplexBuffer(int slice, float[] bufferR, float[] bufferI)	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.
private void	readDComplexBuffer(int slice, double[] bufferR, double[] bufferI)	Reads a slice of data at a time and stores the results in the buffer.
ModelImage	readImage(boolean one)	reads the DM3 file header and data.
private void	readLBuffer(int slice, long[] buffer)	Reads a slice of data at a time and stores the results in the buffer.
private void	readSimpleData(int index, int encodedType)	DOCUMENT ME!
private void	readString()	DOCUMENT ME!
private void	readStruct()	DOCUMENT ME!
private int[]	readStructTypes()	DOCUMENT ME!
private void	readTagEntry(int index)	DOCUMENT ME!
private void	readTagGroup()	DOCUMENT ME!
private void	readTagType(int index)	DOCUMENT ME!

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 Details

SHORT

private static final int SHORT

Different encoded data types used in DM3 files.

See Also:

• Constant Field Values

LONG

private static final int LONG

DOCUMENT ME!

See Also:

• Constant Field Values

USHORT

private static final int USHORT

DOCUMENT ME!

See Also:

• Constant Field Values

ULONG

private static final int ULONG

DOCUMENT ME!

See Also:

• Constant Field Values

FLOAT

private static final int FLOAT

DOCUMENT ME!

See Also:

• Constant Field Values

DOUBLE

private static final int DOUBLE

DOCUMENT ME!

See Also:

• Constant Field Values

BOOLEAN

private static final int BOOLEAN

DOCUMENT ME!

See Also:

• Constant Field Values

CHAR

private static final int CHAR

DOCUMENT ME!

See Also:

• Constant Field Values

OCTET

private static final int OCTET

DOCUMENT ME!

See Also:

• Constant Field Values

STRUCT

private static final int STRUCT

DOCUMENT ME!

See Also:

• Constant Field Values

STRING

private static final int STRING

DOCUMENT ME!

See Also:

• Constant Field Values

ARRAY

private static final int ARRAY

DOCUMENT ME!

See Also:

• Constant Field Values

arrayLocationArray

private long[] arrayLocationArray

DOCUMENT ME!

arraySizeArray

private int[] arraySizeArray

DOCUMENT ME!

byteOrder

private int byteOrder

DOCUMENT ME!

dataEndianess

private boolean dataEndianess

DOCUMENT ME!

dataTypeArray

private int[] dataTypeArray

DOCUMENT ME!

desiredArraySize

private int desiredArraySize

DOCUMENT ME!

desiredImageNumber

private int desiredImageNumber

DOCUMENT ME!

desiredPixelUnitsArray

private String[] desiredPixelUnitsArray

DOCUMENT ME!

dimArray

private int[][] dimArray

DOCUMENT ME!

endianess

private boolean endianess

DOCUMENT ME!

file

private File file

DOCUMENT ME!

fileBytes

private int fileBytes

DOCUMENT ME!

fileDir

private String fileDir

DOCUMENT ME!

fileInfo

private FileInfoDM3 fileInfo

DOCUMENT ME!

fileInfoCopy

private FileInfoDM3 fileInfoCopy

fileName

private String fileName

DOCUMENT ME!

fileVersion

private int fileVersion

DOCUMENT ME!

identicalDesiredArraySize

private int identicalDesiredArraySize

DOCUMENT ME!

image

private ModelImage image

DOCUMENT ME!

imageNum

private int imageNum

DOCUMENT ME!

imgExtents

private int[] imgExtents

DOCUMENT ME!

isCalibrations

private boolean isCalibrations

DOCUMENT ME!

isData

private boolean isData

DOCUMENT ME!

isDataType

private boolean isDataType

DOCUMENT ME!

isDimension

private boolean isDimension

DOCUMENT ME!

isDimensions

private boolean isDimensions

DOCUMENT ME!

isImageData

private boolean isImageData

DOCUMENT ME!

isScale

private boolean isScale

DOCUMENT ME!

isUnits

private boolean isUnits

DOCUMENT ME!

LUT

private ModelLUT LUT

DOCUMENT ME!

nDimensions

private int nDimensions

DOCUMENT ME!

numberSlices

private int numberSlices

DOCUMENT ME!

numDimArray

private int[] numDimArray

DOCUMENT ME!

pixelScaleArray

private float[][] pixelScaleArray

DOCUMENT ME!

pixelUnitsArray

private String[][] pixelUnitsArray

DOCUMENT ME!

pixelUnitsNumber

private int[] pixelUnitsNumber

DOCUMENT ME!

progressBar

private ViewJProgressBar progressBar

DOCUMENT ME!

routineTagEntry

private int routineTagEntry

DOCUMENT ME!

routineTagGroup

private int routineTagGroup

DOCUMENT ME!

scaleIndex

private int scaleIndex

DOCUMENT ME!

sourceType

private int sourceType

DOCUMENT ME!

unitsIndex

private int unitsIndex

DOCUMENT ME!

Constructor Details

FileDM3

public FileDM3(String fileName,
 String fileDir)
        throws IOException

DM3 reader constructor.

Parameters:

fileName - file name

fileDir - file directory

Throws:

IOException - if there is an error making the file

Method Details

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

getModelLUT

public ModelLUT getModelLUT()

returns LUT if defined.

Returns:

the LUT if defined else it is null

readImage

public ModelImage readImage(boolean one)
                     throws IOException

reads the DM3 file header and data.

Parameters:

one - DOCUMENT ME!

Returns:

DOCUMENT ME!

Throws:

IOException - if there is an error reading the file

readArray

private void readArray()
                throws IOException

DOCUMENT ME!

Throws:

IOException - DOCUMENT ME!

readArrayTypes

private int[] readArrayTypes()
                      throws IOException

DOCUMENT ME!

Returns:

DOCUMENT ME!

Throws:

IOException - DOCUMENT ME!

readBuffer

private void readBuffer(int slice,
 float[] buffer)
                 throws 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:

IOException - if there is an error reading the file

readComplexBuffer

private void readComplexBuffer(int slice,
 float[] bufferR,
 float[] bufferI)
                        throws 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

bufferR - buffer where the real info is stored

bufferI - buffer where the imaginary info is stored

Throws:

IOException - if there is an error reading the file

readDBuffer

private void readDBuffer(int slice,
 double[] buffer)
                  throws 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:

IOException - if there is an error reading the file

readDComplexBuffer

private void readDComplexBuffer(int slice,
 double[] bufferR,
 double[] bufferI)
                         throws 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

bufferR - buffer where the real info is stored

bufferI - buffer where the imaginary info is stored

Throws:

IOException - if there is an error reading the file

readLBuffer

private void readLBuffer(int slice,
 long[] buffer)
                  throws 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:

IOException - if there is an error reading the file

readSimpleData

private void readSimpleData(int index,
 int encodedType)
                     throws IOException

DOCUMENT ME!

Parameters:

index - DOCUMENT ME!

encodedType - DOCUMENT ME!

Throws:

IOException - DOCUMENT ME!

readString

private void readString()
                 throws IOException

DOCUMENT ME!

Throws:

IOException - DOCUMENT ME!

readStruct

private void readStruct()
                 throws IOException

DOCUMENT ME!

Throws:

IOException - DOCUMENT ME!

readStructTypes

private int[] readStructTypes()
                       throws IOException

DOCUMENT ME!

Returns:

DOCUMENT ME!

Throws:

IOException - DOCUMENT ME!

readTagEntry

private void readTagEntry(int index)
                   throws IOException

DOCUMENT ME!

Parameters:

index - DOCUMENT ME!

Throws:

IOException - DOCUMENT ME!

readTagGroup

private void readTagGroup()
                   throws IOException

DOCUMENT ME!

Throws:

IOException - DOCUMENT ME!

readTagType

private void readTagType(int index)
                  throws IOException

DOCUMENT ME!

Parameters:

index - DOCUMENT ME!

Throws:

IOException - DOCUMENT ME!