Package gov.nih.mipav.model.file

Class FileSTK

java.lang.Object

gov.nih.mipav.model.file.FileBase

gov.nih.mipav.model.file.FileSTK

public class FileSTK
extends FileBase

The MetaMorph Stack (STK) file format is derived from the TIFF format. Note that the IMAGE_DESCRIPTION and STRIP_OFFSETS tags are handled differently in STK file format than in TIFF file format. Also note that the UIC1Tag, UIC2Tag, UIC3Tag, and UIC4Tag are found in STK but not in TIFF. While TIFF files can be either big-endian or little-endian, STK files must be little endian. Only packed bit compression is supported at this time. Note that although EchoTech has a tResolution field, there is no provision for 4D in TIFF.

See Also:

• FileIO
• FileInfoTiff
• FileRaw

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
private class	FileSTK.Index	Simple class to store image offsets and bytes located at the offset.

Field Summary

Fields

Modifier and Type	Field	Description
static final int	ASCII	DOCUMENT ME!
static final int	BITS_PER_SAMPLE	DOCUMENT ME!
static final int	BYTE	TIFF Types.
private byte[]	byteBuffer	DOCUMENT ME!
private boolean	chunky	DOCUMENT ME!
static final int	COLOR_MAP	DOCUMENT ME!
static final int	COMPRESSION	DOCUMENT ME!
private Vector<FileSTK.Index>[]	dataOffsets
static final int	DATE_TIME	DOCUMENT ME!
private byte[]	dateTime	DOCUMENT ME!
private boolean	doTile	DOCUMENT ME!
static final int	DOUBLE	DOCUMENT ME!
private boolean	endianess	DOCUMENT ME!
private File	file	DOCUMENT ME!
private String	fileDir	DOCUMENT ME!
private FileInfoSTK	fileInfo	DOCUMENT ME!
private String	fileName	DOCUMENT ME!
private FilePackBit	filePB	DOCUMENT ME!
private FileRawChunk	fileRW	DOCUMENT ME!
static final int	FLOAT	DOCUMENT ME!
private int[]	IFDoffsets	DOCUMENT ME!
private ModelImage	image	DOCUMENT ME!
static final int	IMAGE_DESCRIPTION	DOCUMENT ME!
static final int	IMAGE_LENGTH	DOCUMENT ME!
static final int	IMAGE_WIDTH	DOCUMENT ME!
private byte[]	imageDescription	DOCUMENT ME!
private int	imageSlice	DOCUMENT ME!
private float[]	imgBuffer	DOCUMENT ME!
private float[]	imgResols	DOCUMENT ME!
static final int	LONG	DOCUMENT ME!
private ModelLUT	LUT	DOCUMENT ME!
private int	LUTOffset	DOCUMENT ME!
static final int	MAX_SAMPLE_VALUE	DOCUMENT ME!
static final int	MIN_SAMPLE_VALUE	DOCUMENT ME!
private short	nDirEntries	DOCUMENT ME!
static final int	NEW_SUBFILE_TYPE	TIFF Tags.
private int	numberImages	DOCUMENT ME!
private int	offsetConstant	DOCUMENT ME!
private boolean	packBit	DOCUMENT ME!
static final int	PHOTO_INTERP	DOCUMENT ME!
static final int	PLANAR_CONFIG	DOCUMENT ME!
private int	planeOffset	DOCUMENT ME!
static final int	PREDICTOR	DOCUMENT ME!
static final int	RATIONAL	DOCUMENT ME!
static final int	RESOLUTION_UNIT	DOCUMENT ME!
static final int	ROWS_PER_STRIP	DOCUMENT ME!
static final int	SAMPLE_FORMAT	DOCUMENT ME!
static final int	SAMPLES_PER_PIXEL	DOCUMENT ME!
private int	samplesPerPixel	DOCUMENT ME!
static final int	SBYTE	DOCUMENT ME!
static final int	SHORT	DOCUMENT ME!
static final int	SLONG	DOCUMENT ME!
private byte[]	software	DOCUMENT ME!
static final int	SOFTWARE	DOCUMENT ME!
static final int	SRATIONAL	DOCUMENT ME!
static final int	SSHORT	DOCUMENT ME!
private String	str	DOCUMENT ME!
static final int	STRIP_BYTE_COUNTS	DOCUMENT ME!
static final int	STRIP_OFFSETS	DOCUMENT ME!
static final int	TILE_BYTE_COUNTS	DOCUMENT ME!
static final int	TILE_LENGTH	DOCUMENT ME!
static final int	TILE_OFFSETS	DOCUMENT ME!
static final int	TILE_WIDTH	DOCUMENT ME!
private int[]	tileByteCounts	DOCUMENT ME!
private int	tileByteNumber	DOCUMENT ME!
private int	tileLength	DOCUMENT ME!
private int	tileOffsetNumber	DOCUMENT ME!
private int[]	tileOffsets	DOCUMENT ME!
private int	tilesAcross	DOCUMENT ME!
private int	tilesDown	DOCUMENT ME!
private int	tilesPerImage	DOCUMENT ME!
private int	tilesPerSlice	DOCUMENT ME!
private int[]	tileTemp	DOCUMENT ME!
private int	tileWidth	DOCUMENT ME!
private double	tRes	DOCUMENT ME!
static final int	TRESOLUTION	DOCUMENT ME!
static final int	UIC1Tag	DOCUMENT ME!
static final int	UIC2Tag	DOCUMENT ME!
static final int	UIC3Tag	DOCUMENT ME!
static final int	UIC4Tag	DOCUMENT ME!
static final int	UNDEFINED	DOCUMENT ME!
private int	xDim	DOCUMENT ME!
static final int	XRESOLUTION	DOCUMENT ME!
private int	yDim	DOCUMENT ME!
static final int	YRESOLUTION	DOCUMENT ME!
private double	zRes	DOCUMENT ME!
static final int	ZRESOLUTION	EchoTech Tiff TAGS.

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
FileSTK(String fileName, String fileDir)	STK reader/writer constructor.

Method Summary

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 boolean	openIFD(FileInfoSTK fileInfo)	Reads and decodes IFDs (Image File Directory).
private void	readBuffer(int slice, float[] buffer)	Reads a slice of data at a time and stores the results in the buffer.
ModelImage	readImage(boolean multiFile, boolean one)	Reads the Tiff header which indicates endianess, the TIFF magic number, and the offset in bytes of the first IFD.
private void	readTileBuffer(int slice, float[] buffer)	Reads a slice of data at a time and stores the results in the buffer.
void	setFileName(String fName)	Accessor to set the file name (used when reading TIFF multiFile).
private void	writeColorMap(int location)	Writes color map to the TIFF file.
private void	writeHeader()	Writes TIFF starting file header.
private void	writeIFD(int tag, int type, int count, int value, int value2)	Writes one 12 byte IFD entry.
private void	writeIFDs(int imageOffset, int nextIFD, int index, int theStripCount, boolean writePackBit)	Writes one IFD (Image File Directory).
void	writeImage(ModelImage image, ModelLUT LUT, FileWriteOptions options)	This method writes a STK image file.

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

BYTE

public static final int BYTE

TIFF Types.

See Also:

• Constant Field Values

ASCII

public static final int ASCII

DOCUMENT ME!

See Also:

• Constant Field Values

SHORT

public static final int SHORT

DOCUMENT ME!

See Also:

• Constant Field Values

LONG

public static final int LONG

DOCUMENT ME!

See Also:

• Constant Field Values

RATIONAL

public static final int RATIONAL

DOCUMENT ME!

See Also:

• Constant Field Values

SBYTE

public static final int SBYTE

DOCUMENT ME!

See Also:

• Constant Field Values

UNDEFINED

public static final int UNDEFINED

DOCUMENT ME!

See Also:

• Constant Field Values

SSHORT

public static final int SSHORT

DOCUMENT ME!

See Also:

• Constant Field Values

SLONG

public static final int SLONG

DOCUMENT ME!

See Also:

• Constant Field Values

SRATIONAL

public static final int SRATIONAL

DOCUMENT ME!

See Also:

• Constant Field Values

FLOAT

public static final int FLOAT

DOCUMENT ME!

See Also:

• Constant Field Values

DOUBLE

public static final int DOUBLE

DOCUMENT ME!

See Also:

• Constant Field Values

NEW_SUBFILE_TYPE

public static final int NEW_SUBFILE_TYPE

TIFF Tags.

See Also:

• Constant Field Values

IMAGE_WIDTH

public static final int IMAGE_WIDTH

DOCUMENT ME!

See Also:

• Constant Field Values

IMAGE_LENGTH

public static final int IMAGE_LENGTH

DOCUMENT ME!

See Also:

• Constant Field Values

BITS_PER_SAMPLE

public static final int BITS_PER_SAMPLE

DOCUMENT ME!

See Also:

• Constant Field Values

COMPRESSION

public static final int COMPRESSION

DOCUMENT ME!

See Also:

• Constant Field Values

PHOTO_INTERP

public static final int PHOTO_INTERP

DOCUMENT ME!

See Also:

• Constant Field Values

IMAGE_DESCRIPTION

public static final int IMAGE_DESCRIPTION

DOCUMENT ME!

See Also:

• Constant Field Values

STRIP_OFFSETS

public static final int STRIP_OFFSETS

DOCUMENT ME!

See Also:

• Constant Field Values

SAMPLES_PER_PIXEL

public static final int SAMPLES_PER_PIXEL

DOCUMENT ME!

See Also:

• Constant Field Values

ROWS_PER_STRIP

public static final int ROWS_PER_STRIP

DOCUMENT ME!

See Also:

• Constant Field Values

STRIP_BYTE_COUNTS

public static final int STRIP_BYTE_COUNTS

DOCUMENT ME!

See Also:

• Constant Field Values

MIN_SAMPLE_VALUE

public static final int MIN_SAMPLE_VALUE

DOCUMENT ME!

See Also:

• Constant Field Values

MAX_SAMPLE_VALUE

public static final int MAX_SAMPLE_VALUE

DOCUMENT ME!

See Also:

• Constant Field Values

XRESOLUTION

public static final int XRESOLUTION

DOCUMENT ME!

See Also:

• Constant Field Values

YRESOLUTION

public static final int YRESOLUTION

DOCUMENT ME!

See Also:

• Constant Field Values

PLANAR_CONFIG

public static final int PLANAR_CONFIG

DOCUMENT ME!

See Also:

• Constant Field Values

RESOLUTION_UNIT

public static final int RESOLUTION_UNIT

DOCUMENT ME!

See Also:

• Constant Field Values

SOFTWARE

public static final int SOFTWARE

DOCUMENT ME!

See Also:

• Constant Field Values

DATE_TIME

public static final int DATE_TIME

DOCUMENT ME!

See Also:

• Constant Field Values

PREDICTOR

public static final int PREDICTOR

DOCUMENT ME!

See Also:

• Constant Field Values

COLOR_MAP

public static final int COLOR_MAP

DOCUMENT ME!

See Also:

• Constant Field Values

TILE_WIDTH

public static final int TILE_WIDTH

DOCUMENT ME!

See Also:

• Constant Field Values

TILE_LENGTH

public static final int TILE_LENGTH

DOCUMENT ME!

See Also:

• Constant Field Values

TILE_OFFSETS

public static final int TILE_OFFSETS

DOCUMENT ME!

See Also:

• Constant Field Values

TILE_BYTE_COUNTS

public static final int TILE_BYTE_COUNTS

DOCUMENT ME!

See Also:

• Constant Field Values

SAMPLE_FORMAT

public static final int SAMPLE_FORMAT

DOCUMENT ME!

See Also:

• Constant Field Values

UIC1Tag

public static final int UIC1Tag

DOCUMENT ME!

See Also:

• Constant Field Values

UIC2Tag

public static final int UIC2Tag

DOCUMENT ME!

See Also:

• Constant Field Values

UIC3Tag

public static final int UIC3Tag

DOCUMENT ME!

See Also:

• Constant Field Values

UIC4Tag

public static final int UIC4Tag

DOCUMENT ME!

See Also:

• Constant Field Values

ZRESOLUTION

public static final int ZRESOLUTION

EchoTech Tiff TAGS.

See Also:

• Constant Field Values

TRESOLUTION

public static final int TRESOLUTION

DOCUMENT ME!

See Also:

• Constant Field Values

byteBuffer

private byte[] byteBuffer

DOCUMENT ME!

chunky

private boolean chunky

DOCUMENT ME!

dataOffsets

private Vector<FileSTK.Index>[] dataOffsets

dateTime

private byte[] dateTime

DOCUMENT ME!

doTile

private boolean doTile

DOCUMENT ME!

endianess

private boolean endianess

DOCUMENT ME!

file

private File file

DOCUMENT ME!

fileDir

private String fileDir

DOCUMENT ME!

fileInfo

private FileInfoSTK fileInfo

DOCUMENT ME!

fileName

private String fileName

DOCUMENT ME!

filePB

private FilePackBit filePB

DOCUMENT ME!

fileRW

private FileRawChunk fileRW

DOCUMENT ME!

IFDoffsets

private int[] IFDoffsets

DOCUMENT ME!

image

private ModelImage image

DOCUMENT ME!

imageDescription

private byte[] imageDescription

DOCUMENT ME!

imageSlice

private int imageSlice

DOCUMENT ME!

imgBuffer

private float[] imgBuffer

DOCUMENT ME!

imgResols

private float[] imgResols

DOCUMENT ME!

LUT

private ModelLUT LUT

DOCUMENT ME!

LUTOffset

private int LUTOffset

DOCUMENT ME!

nDirEntries

private short nDirEntries

DOCUMENT ME!

numberImages

private int numberImages

DOCUMENT ME!

offsetConstant

private int offsetConstant

DOCUMENT ME!

packBit

private boolean packBit

DOCUMENT ME!

planeOffset

private int planeOffset

DOCUMENT ME!

samplesPerPixel

private int samplesPerPixel

DOCUMENT ME!

software

private byte[] software

DOCUMENT ME!

str

private String str

DOCUMENT ME!

tileByteCounts

private int[] tileByteCounts

DOCUMENT ME!

tileByteNumber

private int tileByteNumber

DOCUMENT ME!

tileLength

private int tileLength

DOCUMENT ME!

tileOffsetNumber

private int tileOffsetNumber

DOCUMENT ME!

tileOffsets

private int[] tileOffsets

DOCUMENT ME!

tilesAcross

private int tilesAcross

DOCUMENT ME!

tilesDown

private int tilesDown

DOCUMENT ME!

tilesPerImage

private int tilesPerImage

DOCUMENT ME!

tilesPerSlice

private int tilesPerSlice

DOCUMENT ME!

tileTemp

private int[] tileTemp

DOCUMENT ME!

tileWidth

private int tileWidth

DOCUMENT ME!

tRes

private double tRes

DOCUMENT ME!

xDim

private int xDim

DOCUMENT ME!

yDim

private int yDim

DOCUMENT ME!

zRes

private double zRes

DOCUMENT ME!

Constructor Details

FileSTK

public FileSTK(String fileName,
 String fileDir)
        throws IOException

STK reader/writer 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

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

readImage

public ModelImage readImage(boolean multiFile,
 boolean one)
                     throws IOException

Reads the Tiff header which indicates endianess, the TIFF magic number, and the offset in bytes of the first IFD. It then reads all the IFDs. This method then opens a Model of an image and imports the the images one slice at a time. Image slices are separated by an IFD.

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 - DOCUMENT ME!

Returns:

returns the image

Throws:

IOException - if there is an error reading the file

setFileName

public void setFileName(String fName)

Accessor to set the file name (used when reading TIFF multiFile).

Parameters:

fName - file name of image to read.

writeImage

public void writeImage(ModelImage image,
 ModelLUT LUT,
 FileWriteOptions options)
                throws IOException

This method writes a STK image file.

Parameters:

image - image model where the data is stored.

LUT - LUT to be saved with image if not null.

options - DOCUMENT ME!

Throws:

IOException - if there is an error writing the file.

openIFD

private boolean openIFD(FileInfoSTK fileInfo)
                 throws IOException

Reads and decodes IFDs (Image File Directory).

Parameters:

fileInfo - DOCUMENT ME!

Returns:

DOCUMENT ME!

Throws:

IOException - if there is an error reading the file

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

readTileBuffer

private void readTileBuffer(int slice,
 float[] buffer)
                     throws IOException

Reads a slice of data at a time and stores the results in the buffer.

Parameters:

slice - image slice

buffer - buffer where the info is stored

Throws:

IOException - if there is an error reading the file

writeColorMap

private void writeColorMap(int location)
                    throws IOException

Writes color map to the TIFF file.

Parameters:

location - Location to write at.

Throws:

IOException - DOCUMENT ME!

writeHeader

private void writeHeader()
                  throws IOException

Writes TIFF starting file header.

Throws:

IOException - DOCUMENT ME!

writeIFD

private void writeIFD(int tag,
 int type,
 int count,
 int value,
 int value2)
               throws IOException

Writes one 12 byte IFD entry.

Parameters:

tag - DOCUMENT ME!

type - DOCUMENT ME!

count - DOCUMENT ME!

value - DOCUMENT ME!

value2 - DOCUMENT ME!

Throws:

IOException - DOCUMENT ME!

writeIFDs

private void writeIFDs(int imageOffset,
 int nextIFD,
 int index,
 int theStripCount,
 boolean writePackBit)
                throws IOException

Writes one IFD (Image File Directory). One IFD per image

Parameters:

imageOffset - offset to next IFD. If equal to zero then end of images

nextIFD - DOCUMENT ME!

index - image index for file information.

theStripCount - DOCUMENT ME!

writePackBit - DOCUMENT ME!

Throws:

IOException - DOCUMENT ME!