Package gov.nih.mipav.model.file

Class FileBioRad

java.lang.Object

gov.nih.mipav.model.file.FileBase

gov.nih.mipav.model.file.FileBioRad

public class FileBioRad
extends FileBase

Reads BioRaD pic file format.

Field Summary

Fields

Modifier and Type	Field	Description
private int	bufferSize	DOCUMENT ME!
private byte[]	byteBuffer	DOCUMENT ME!
private short	byteFormat	if 1 data is UBYTE, otherwise data is SHORT.
private int	color1	LUT1 color status.
private int	color2	LUT2 color status.
private int	dataType	DOCUMENT ME!
private short	edited	not used in disk files.
private File	file	DOCUMENT ME!
private String	fileDir	DOCUMENT ME!
private int	fileID	always set to 12345 in BioRad pic files.
private FileInfoBioRad	fileInfo	DOCUMENT ME!
private FileInfoBioRad	fileInfoCopy
private String	fileName	DOCUMENT ME!
private String	fName	DOCUMENT ME!
private ModelImage	image	DOCUMENT ME!
private float[]	imgBuffer	DOCUMENT ME!
private int[]	imgExtents	DOCUMENT ME!
private short	lens	Integer part of the lens magnification.
private float	magFactor	magnification factor.
private short	merged	merged format.
private byte[]	name	DOCUMENT ME!
private int	notes	if 0 no notes are present if nonzero 96 byte notes follow after the image data at the end of the file.
private short	ramp1Max
private short	ramp1Min
private short	ramp2Max	LUT2 ramp max.
private short	ramp2Min	LUT2 ramp min.
private boolean	readAgain	DOCUMENT ME!
private int	xDim	DOCUMENT ME!
private int	yDim	DOCUMENT ME!
private int	zDim	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
FileBioRad(String fileName, String fileDir)	reader/writer constructor.

Method Summary

Modifier and Type	Method	Description
void	finalize()	Prepares this class for cleanup.
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 one)	reads the BioRad pic file header and data.

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

bufferSize

private int bufferSize

DOCUMENT ME!

byteBuffer

private byte[] byteBuffer

DOCUMENT ME!

byteFormat

private short byteFormat

if 1 data is UBYTE, otherwise data is SHORT.

color1

private int color1

LUT1 color status.

color2

private int color2

LUT2 color status.

dataType

private int dataType

DOCUMENT ME!

edited

private short edited

not used in disk files.

file

private File file

DOCUMENT ME!

fileDir

private String fileDir

DOCUMENT ME!

fileID

private int fileID

always set to 12345 in BioRad pic files.

fileInfo

private FileInfoBioRad fileInfo

DOCUMENT ME!

fileInfoCopy

private FileInfoBioRad fileInfoCopy

fileName

private String fileName

DOCUMENT ME!

fName

private String fName

DOCUMENT ME!

image

private ModelImage image

DOCUMENT ME!

imgBuffer

private float[] imgBuffer

DOCUMENT ME!

imgExtents

private int[] imgExtents

DOCUMENT ME!

lens

private short lens

Integer part of the lens magnification.

magFactor

private float magFactor

magnification factor.

merged

private short merged

merged format.

name

private byte[] name

DOCUMENT ME!

notes

private int notes

if 0 no notes are present if nonzero 96 byte notes follow after the image data at the end of the file.

ramp1Max

private short ramp1Max

ramp1Min

private short ramp1Min

ramp2Max

private short ramp2Max

LUT2 ramp max.

ramp2Min

private short ramp2Min

LUT2 ramp min.

readAgain

private boolean readAgain

DOCUMENT ME!

xDim

private int xDim

DOCUMENT ME!

yDim

private int yDim

DOCUMENT ME!

zDim

private int zDim

DOCUMENT ME!

Constructor Details

FileBioRad

public FileBioRad(String fileName,
 String fileDir)
           throws IOException

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

readImage

public ModelImage readImage(boolean one)
                     throws IOException

reads the BioRad pic file header and data.

Parameters:

one - DOCUMENT ME!

Returns:

returns a black and white image

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 - into the file

buffer - buffer where the info is stored

Throws:

IOException - if there is an error reading the file