Package gov.nih.mipav.model.file

Class FileICS

java.lang.Object

gov.nih.mipav.model.file.FileBase

gov.nih.mipav.model.file.FileICS

public class FileICS
extends FileBase

Reference: 1. Proposed Standard for Image Cytometry Data Files by Philip Dean, Laura Mascio, David Ow, Damir Sudar, and James Mullikin, Cytometry, 11, pp. 561- 569, 1990.

2. libics v.1.3 Online Documentation, copyright 2000-2002 by Cris Luengo. http://www.ph.tn.tudelft.nl/~cris/libics

Author:

William Gandler

See Also:

• FileIO

Field Summary

Fields

Modifier and Type	Field	Description
private String[]	actualHistory	DOCUMENT ME!
private int	bufferSize	DOCUMENT ME!
private String	captureVersion	DOCUMENT ME!
private String	category	DOCUMENT ME!
private String[]	channels	DOCUMENT ME!
private int	colorSpacing	DOCUMENT ME!
private String	compression	DOCUMENT ME!
private String	dataFileName	DOCUMENT ME!
private long	dataOffset	DOCUMENT ME!
private String	dataSetFileName	DOCUMENT ME!
private int	dataType	DOCUMENT ME!
private int	endBytes	DOCUMENT ME!
private int	endFloats	DOCUMENT ME!
private boolean	endianess	DOCUMENT ME!
private int	endShorts	DOCUMENT ME!
private boolean	exchangeXY	DOCUMENT ME!
private String[]	exPhotonCnt	DOCUMENT ME!
private byte	fieldSeparator	DOCUMENT ME!
private File	file	DOCUMENT ME!
private String	fileDir	DOCUMENT ME!
private FileInfoICS	fileInfo	DOCUMENT ME!
private FileInfoICS	fileInfoCopy
private String	fileName	DOCUMENT ME!
private String	filterExposureTimeX	DOCUMENT ME!
private String[]	filterFluorophoreX	DOCUMENT ME!
private String	format	DOCUMENT ME!
private boolean	hasRGB
private String	headerFileName	DOCUMENT ME!
private String[]	history	DOCUMENT ME!
private int	historyNumber	DOCUMENT ME!
private ModelImage	image	DOCUMENT ME!
private float[]	imgBuffer	DOCUMENT ME!
private float[]	imgBuffer2	DOCUMENT ME!
private float[]	imgBufferI	DOCUMENT ME!
private float[]	imgBufferI2	DOCUMENT ME!
private double[]	imgDBuffer	DOCUMENT ME!
private double[]	imgDBuffer2	DOCUMENT ME!
private double[]	imgDBufferI	DOCUMENT ME!
private double[]	imgDBufferI2	DOCUMENT ME!
private int[]	imgExtents	DOCUMENT ME!
private long[]	imgLBuffer	DOCUMENT ME!
private long[]	imgLBuffer2	DOCUMENT ME!
private float[]	imgResols	DOCUMENT ME!
private boolean	invertY	DOCUMENT ME!
private String[]	labels	DOCUMENT ME!
private String[]	lambdaEm	DOCUMENT ME!
private String[]	lambdaEx	DOCUMENT ME!
private ModelLUT	LUT	DOCUMENT ME!
private String[]	mapchannel	DOCUMENT ME!
private int	nDims	DOCUMENT ME!
private String[]	numAperture	DOCUMENT ME!
private int	numberSlices	DOCUMENT ME!
private int	numberSpaceSlices	DOCUMENT ME!
private int	numColors	DOCUMENT ME!
private int	numValues	DOCUMENT ME!
private String[]	order	DOCUMENT ME!
private float[]	origin	DOCUMENT ME!
private int	parameters	DOCUMENT ME!
private String[]	pinholeRadius	DOCUMENT ME!
private String	plateChamberID	DOCUMENT ME!
private String	plateVesselID	DOCUMENT ME!
private String[]	probe	DOCUMENT ME!
private String[]	refrInxLensMedium	DOCUMENT ME!
private String[]	refrInxMedium	DOCUMENT ME!
private static final int	RGB_BETWEEN_SPACEANDTIME	DOCUMENT ME!
private static final int	RGB_FIRST	DOCUMENT ME!
private static final int	RGB_LAST	DOCUMENT ME!
private int	rgbPos	DOCUMENT ME!
private float[]	scale	DOCUMENT ME!
private String	scilType	DOCUMENT ME!
private String	sensorModel	DOCUMENT ME!
private String	sensorType	DOCUMENT ME!
private String	sign	DOCUMENT ME!
private int	significant_bits
private int[]	sizes	DOCUMENT ME!
private String[]	specimen	DOCUMENT ME!
private String[]	specimenSpecies	DOCUMENT ME!
private float[]	startLocations	DOCUMENT ME!
private String	subcategory	DOCUMENT ME!
private int	tPos	DOCUMENT ME!
private String[]	units	DOCUMENT ME!
private int[]	unitsOfMeasure	DOCUMENT ME!
private String[]	unitsStr	DOCUMENT ME!
private boolean	useGZIP	DOCUMENT ME!
private String[]	values	DOCUMENT ME!
private String	version	DOCUMENT ME!
private int	xPos	DOCUMENT ME!
private int	yPos	DOCUMENT ME!
private int	zPos	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
FileICS(String fileName, String fileDir)	ICS reader constructor.

Method Summary

Modifier and Type	Method	Description
void	finalize()	Prepares this class for cleanup.
FileInfoBase	getFileInfo()	getFileInfo - accessor that returns the file info.
float[]	getImageBuffer()	getImageBuffer - accessor that returns the image buffer.
ModelLUT	getModelLUT()	getModelLUT - returns LUT if defined.
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.
boolean	readHeader()	Reads the image header.
ModelImage	readImage()	readImage.
private void	readLBuffer(int slice, long[] buffer)	Reads a slice of data at a time and stores the results in the buffer.
private void	readLine()	readLine() - reads a line of the file header separate into category, subcategory, and values.
void	writeImage(ModelImage image, FileWriteOptions options)	Writes an ICS 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 Details

RGB_FIRST

private static final int RGB_FIRST

DOCUMENT ME!

See Also:

• Constant Field Values

RGB_BETWEEN_SPACEANDTIME

private static final int RGB_BETWEEN_SPACEANDTIME

DOCUMENT ME!

See Also:

• Constant Field Values

RGB_LAST

private static final int RGB_LAST

DOCUMENT ME!

See Also:

• Constant Field Values

actualHistory

private String[] actualHistory

DOCUMENT ME!

bufferSize

private int bufferSize

DOCUMENT ME!

captureVersion

private String captureVersion

DOCUMENT ME!

category

private String category

DOCUMENT ME!

channels

private String[] channels

DOCUMENT ME!

colorSpacing

private int colorSpacing

DOCUMENT ME!

compression

private String compression

DOCUMENT ME!

dataFileName

private String dataFileName

DOCUMENT ME!

dataOffset

private long dataOffset

DOCUMENT ME!

dataSetFileName

private String dataSetFileName

DOCUMENT ME!

dataType

private int dataType

DOCUMENT ME!

endBytes

private int endBytes

DOCUMENT ME!

endFloats

private int endFloats

DOCUMENT ME!

endianess

private boolean endianess

DOCUMENT ME!

endShorts

private int endShorts

DOCUMENT ME!

exchangeXY

private boolean exchangeXY

DOCUMENT ME!

exPhotonCnt

private String[] exPhotonCnt

DOCUMENT ME!

fieldSeparator

private byte fieldSeparator

DOCUMENT ME!

file

private File file

DOCUMENT ME!

fileDir

private String fileDir

DOCUMENT ME!

fileInfo

private FileInfoICS fileInfo

DOCUMENT ME!

fileInfoCopy

private FileInfoICS fileInfoCopy

fileName

private String fileName

DOCUMENT ME!

filterExposureTimeX

private String filterExposureTimeX

DOCUMENT ME!

filterFluorophoreX

private String[] filterFluorophoreX

DOCUMENT ME!

format

private String format

DOCUMENT ME!

headerFileName

private String headerFileName

DOCUMENT ME!

history

private String[] history

DOCUMENT ME!

historyNumber

private int historyNumber

DOCUMENT ME!

image

private ModelImage image

DOCUMENT ME!

imgBuffer

private float[] imgBuffer

DOCUMENT ME!

imgBuffer2

private float[] imgBuffer2

DOCUMENT ME!

imgBufferI

private float[] imgBufferI

DOCUMENT ME!

imgBufferI2

private float[] imgBufferI2

DOCUMENT ME!

imgDBuffer

private double[] imgDBuffer

DOCUMENT ME!

imgDBuffer2

private double[] imgDBuffer2

DOCUMENT ME!

imgDBufferI

private double[] imgDBufferI

DOCUMENT ME!

imgDBufferI2

private double[] imgDBufferI2

DOCUMENT ME!

imgExtents

private int[] imgExtents

DOCUMENT ME!

imgLBuffer

private long[] imgLBuffer

DOCUMENT ME!

imgLBuffer2

private long[] imgLBuffer2

DOCUMENT ME!

imgResols

private float[] imgResols

DOCUMENT ME!

invertY

private boolean invertY

DOCUMENT ME!

labels

private String[] labels

DOCUMENT ME!

lambdaEm

private String[] lambdaEm

DOCUMENT ME!

lambdaEx

private String[] lambdaEx

DOCUMENT ME!

LUT

private ModelLUT LUT

DOCUMENT ME!

mapchannel

private String[] mapchannel

DOCUMENT ME!

nDims

private int nDims

DOCUMENT ME!

numAperture

private String[] numAperture

DOCUMENT ME!

numberSlices

private int numberSlices

DOCUMENT ME!

numberSpaceSlices

private int numberSpaceSlices

DOCUMENT ME!

numColors

private int numColors

DOCUMENT ME!

numValues

private int numValues

DOCUMENT ME!

order

private String[] order

DOCUMENT ME!

origin

private float[] origin

DOCUMENT ME!

parameters

private int parameters

DOCUMENT ME!

pinholeRadius

private String[] pinholeRadius

DOCUMENT ME!

plateChamberID

private String plateChamberID

DOCUMENT ME!

plateVesselID

private String plateVesselID

DOCUMENT ME!

probe

private String[] probe

DOCUMENT ME!

refrInxLensMedium

private String[] refrInxLensMedium

DOCUMENT ME!

refrInxMedium

private String[] refrInxMedium

DOCUMENT ME!

rgbPos

private int rgbPos

DOCUMENT ME!

scale

private float[] scale

DOCUMENT ME!

scilType

private String scilType

DOCUMENT ME!

sensorModel

private String sensorModel

DOCUMENT ME!

sensorType

private String sensorType

DOCUMENT ME!

sign

private String sign

DOCUMENT ME!

significant_bits

private int significant_bits

sizes

private int[] sizes

DOCUMENT ME!

specimen

private String[] specimen

DOCUMENT ME!

specimenSpecies

private String[] specimenSpecies

DOCUMENT ME!

startLocations

private float[] startLocations

DOCUMENT ME!

subcategory

private String subcategory

DOCUMENT ME!

tPos

private int tPos

DOCUMENT ME!

units

private String[] units

DOCUMENT ME!

unitsOfMeasure

private int[] unitsOfMeasure

DOCUMENT ME!

unitsStr

private String[] unitsStr

DOCUMENT ME!

useGZIP

private boolean useGZIP

DOCUMENT ME!

values

private String[] values

DOCUMENT ME!

version

private String version

DOCUMENT ME!

xPos

private int xPos

DOCUMENT ME!

yPos

private int yPos

DOCUMENT ME!

zPos

private int zPos

DOCUMENT ME!

hasRGB

private boolean hasRGB

Constructor Details

FileICS

public FileICS(String fileName,
 String fileDir)
        throws IOException

ICS 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

getFileInfo

public FileInfoBase getFileInfo()

getFileInfo - accessor that returns the file info.

Returns:

FileInfoBase containing the file info

getImageBuffer

public float[] getImageBuffer()

getImageBuffer - accessor that returns the image buffer.

Returns:

buffer of image.

getModelLUT

public ModelLUT getModelLUT()

getModelLUT - returns LUT if defined.

Returns:

the LUT if defined else it is null

readImage

public ModelImage readImage()
                     throws IOException

readImage.

Returns:

returns the image

Throws:

IOException - if there is an error reading the file

writeImage

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

Writes an ICS format type image.

Parameters:

image - Image model of data to write.

options - options such as starting and ending slices and times

Throws:

IOException - if there is an error writing 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

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

readHeader

public boolean readHeader()
                   throws IOException

Reads the image header.

Throws:

IOException - DOCUMENT ME!

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

readLine

private void readLine()
               throws IOException

readLine() - reads a line of the file header separate into category, subcategory, and values.

Throws:

IOException - if there is an error reading the file