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 java.lang.String[]`	`actualHistory`	DOCUMENT ME!
`private int`	`bufferSize`	DOCUMENT ME!
`private java.lang.String`	`captureVersion`	DOCUMENT ME!
`private java.lang.String`	`category`	DOCUMENT ME!
`private java.lang.String[]`	`channels`	DOCUMENT ME!
`private int`	`colorSpacing`	DOCUMENT ME!
`private java.lang.String`	`compression`	DOCUMENT ME!
`private java.lang.String`	`dataFileName`	DOCUMENT ME!
`private long`	`dataOffset`	DOCUMENT ME!
`private java.lang.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 java.lang.String[]`	`exPhotonCnt`	DOCUMENT ME!
`private byte`	`fieldSeparator`	DOCUMENT ME!
`private java.io.File`	`file`	DOCUMENT ME!
`private java.lang.String`	`fileDir`	DOCUMENT ME!
`private FileInfoICS`	`fileInfo`	DOCUMENT ME!
`private FileInfoICS`	`fileInfoCopy`
`private java.lang.String`	`fileName`	DOCUMENT ME!
`private java.lang.String`	`filterExposureTimeX`	DOCUMENT ME!
`private java.lang.String[]`	`filterFluorophoreX`	DOCUMENT ME!
`private java.lang.String`	`format`	DOCUMENT ME!
`private boolean`	`hasRGB`
`private java.lang.String`	`headerFileName`	DOCUMENT ME!
`private java.lang.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 java.lang.String[]`	`labels`	DOCUMENT ME!
`private java.lang.String[]`	`lambdaEm`	DOCUMENT ME!
`private java.lang.String[]`	`lambdaEx`	DOCUMENT ME!
`private ModelLUT`	`LUT`	DOCUMENT ME!
`private java.lang.String[]`	`mapchannel`	DOCUMENT ME!
`private int`	`nDims`	DOCUMENT ME!
`private java.lang.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 java.lang.String[]`	`order`	DOCUMENT ME!
`private float[]`	`origin`	DOCUMENT ME!
`private int`	`parameters`	DOCUMENT ME!
`private java.lang.String[]`	`pinholeRadius`	DOCUMENT ME!
`private java.lang.String`	`plateChamberID`	DOCUMENT ME!
`private java.lang.String`	`plateVesselID`	DOCUMENT ME!
`private java.lang.String[]`	`probe`	DOCUMENT ME!
`private java.lang.String[]`	`refrInxLensMedium`	DOCUMENT ME!
`private java.lang.String[]`	`refrInxMedium`	DOCUMENT ME!
`private static int`	`RGB_BETWEEN_SPACEANDTIME`	DOCUMENT ME!
`private static int`	`RGB_FIRST`	DOCUMENT ME!
`private static int`	`RGB_LAST`	DOCUMENT ME!
`private int`	`rgbPos`	DOCUMENT ME!
`private float[]`	`scale`	DOCUMENT ME!
`private java.lang.String`	`scilType`	DOCUMENT ME!
`private java.lang.String`	`sensorModel`	DOCUMENT ME!
`private java.lang.String`	`sensorType`	DOCUMENT ME!
`private java.lang.String`	`sign`	DOCUMENT ME!
`private int`	`significant_bits`
`private int[]`	`sizes`	DOCUMENT ME!
`private java.lang.String[]`	`specimen`	DOCUMENT ME!
`private java.lang.String[]`	`specimenSpecies`	DOCUMENT ME!
`private float[]`	`startLocations`	DOCUMENT ME!
`private java.lang.String`	`subcategory`	DOCUMENT ME!
`private int`	`tPos`	DOCUMENT ME!
`private java.lang.String[]`	`units`	DOCUMENT ME!
`private int[]`	`unitsOfMeasure`	DOCUMENT ME!
`private java.lang.String[]`	`unitsStr`	DOCUMENT ME!
`private boolean`	`useGZIP`	DOCUMENT ME!
`private java.lang.String[]`	`values`	DOCUMENT ME!
`private java.lang.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(java.lang.String fileName, java.lang.String fileDir)
ICS reader constructor.

Method Summary

All Methods Instance Methods Concrete Methods
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 Detail
  - 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 java.lang.String[] actualHistory
```
    DOCUMENT ME!
  - bufferSize
```
private int bufferSize
```
    DOCUMENT ME!
  - captureVersion
```
private java.lang.String captureVersion
```
    DOCUMENT ME!
  - category
```
private java.lang.String category
```
    DOCUMENT ME!
  - channels
```
private java.lang.String[] channels
```
    DOCUMENT ME!
  - colorSpacing
```
private int colorSpacing
```
    DOCUMENT ME!
  - compression
```
private java.lang.String compression
```
    DOCUMENT ME!
  - dataFileName
```
private java.lang.String dataFileName
```
    DOCUMENT ME!
  - dataOffset
```
private long dataOffset
```
    DOCUMENT ME!
  - dataSetFileName
```
private java.lang.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 java.lang.String[] exPhotonCnt
```
    DOCUMENT ME!
  - fieldSeparator
```
private byte fieldSeparator
```
    DOCUMENT ME!
  - file
```
private java.io.File file
```
    DOCUMENT ME!
  - fileDir
```
private java.lang.String fileDir
```
    DOCUMENT ME!
  - fileInfo
```
private FileInfoICS fileInfo
```
    DOCUMENT ME!
  - fileInfoCopy
```
private FileInfoICS fileInfoCopy
```
  - fileName
```
private java.lang.String fileName
```
    DOCUMENT ME!
  - filterExposureTimeX
```
private java.lang.String filterExposureTimeX
```
    DOCUMENT ME!
  - filterFluorophoreX
```
private java.lang.String[] filterFluorophoreX
```
    DOCUMENT ME!
  - format
```
private java.lang.String format
```
    DOCUMENT ME!
  - headerFileName
```
private java.lang.String headerFileName
```
    DOCUMENT ME!
  - history
```
private java.lang.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 java.lang.String[] labels
```
    DOCUMENT ME!
  - lambdaEm
```
private java.lang.String[] lambdaEm
```
    DOCUMENT ME!
  - lambdaEx
```
private java.lang.String[] lambdaEx
```
    DOCUMENT ME!
  - LUT
```
private ModelLUT LUT
```
    DOCUMENT ME!
  - mapchannel
```
private java.lang.String[] mapchannel
```
    DOCUMENT ME!
  - nDims
```
private int nDims
```
    DOCUMENT ME!
  - numAperture
```
private java.lang.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 java.lang.String[] order
```
    DOCUMENT ME!
  - origin
```
private float[] origin
```
    DOCUMENT ME!
  - parameters
```
private int parameters
```
    DOCUMENT ME!
  - pinholeRadius
```
private java.lang.String[] pinholeRadius
```
    DOCUMENT ME!
  - plateChamberID
```
private java.lang.String plateChamberID
```
    DOCUMENT ME!
  - plateVesselID
```
private java.lang.String plateVesselID
```
    DOCUMENT ME!
  - probe
```
private java.lang.String[] probe
```
    DOCUMENT ME!
  - refrInxLensMedium
```
private java.lang.String[] refrInxLensMedium
```
    DOCUMENT ME!
  - refrInxMedium
```
private java.lang.String[] refrInxMedium
```
    DOCUMENT ME!
  - rgbPos
```
private int rgbPos
```
    DOCUMENT ME!
  - scale
```
private float[] scale
```
    DOCUMENT ME!
  - scilType
```
private java.lang.String scilType
```
    DOCUMENT ME!
  - sensorModel
```
private java.lang.String sensorModel
```
    DOCUMENT ME!
  - sensorType
```
private java.lang.String sensorType
```
    DOCUMENT ME!
  - sign
```
private java.lang.String sign
```
    DOCUMENT ME!
  - significant_bits
```
private int significant_bits
```
  - sizes
```
private int[] sizes
```
    DOCUMENT ME!
  - specimen
```
private java.lang.String[] specimen
```
    DOCUMENT ME!
  - specimenSpecies
```
private java.lang.String[] specimenSpecies
```
    DOCUMENT ME!
  - startLocations
```
private float[] startLocations
```
    DOCUMENT ME!
  - subcategory
```
private java.lang.String subcategory
```
    DOCUMENT ME!
  - tPos
```
private int tPos
```
    DOCUMENT ME!
  - units
```
private java.lang.String[] units
```
    DOCUMENT ME!
  - unitsOfMeasure
```
private int[] unitsOfMeasure
```
    DOCUMENT ME!
  - unitsStr
```
private java.lang.String[] unitsStr
```
    DOCUMENT ME!
  - useGZIP
```
private boolean useGZIP
```
    DOCUMENT ME!
  - values
```
private java.lang.String[] values
```
    DOCUMENT ME!
  - version
```
private java.lang.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 Detail
  - FileICS
```
public FileICS(java.lang.String fileName,
               java.lang.String fileDir)
        throws java.io.IOException
```
    ICS reader 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()
```
    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 java.io.IOException
```
    readImage.
    
    Returns:
    
    returns the image
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - writeImage
```
public void writeImage(ModelImage image,
                       FileWriteOptions options)
                throws java.io.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:
    
    java.io.IOException - if there is an error writing the file
  - readBuffer
```
private void readBuffer(int slice,
                        float[] buffer)
                 throws java.io.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:
    
    java.io.IOException - if there is an error reading the file
  - readComplexBuffer
```
private void readComplexBuffer(int slice,
                               float[] bufferR,
                               float[] bufferI)
                        throws java.io.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:
    
    java.io.IOException - if there is an error reading the file
  - readDBuffer
```
private void readDBuffer(int slice,
                         double[] buffer)
                  throws java.io.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:
    
    java.io.IOException - if there is an error reading the file
  - readDComplexBuffer
```
private void readDComplexBuffer(int slice,
                                double[] bufferR,
                                double[] bufferI)
                         throws java.io.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:
    
    java.io.IOException - if there is an error reading the file
  - readHeader
```
public boolean readHeader()
                   throws java.io.IOException
```
    Reads the image header.
    
    Throws:
    
    java.io.IOException - DOCUMENT ME!
  - readLBuffer
```
private void readLBuffer(int slice,
                         long[] buffer)
                  throws java.io.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:
    
    java.io.IOException - if there is an error reading the file
  - readLine
```
private void readLine()
               throws java.io.IOException
```
    readLine() - reads a line of the file header separate into category, subcategory, and values.
    
    Throws:
    
    java.io.IOException - if there is an error reading the file

Class FileICS

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

RGB_FIRST

RGB_BETWEEN_SPACEANDTIME

RGB_LAST

actualHistory

bufferSize

captureVersion

category

channels

colorSpacing

compression

dataFileName

dataOffset

dataSetFileName

dataType

endBytes

endFloats

endianess

endShorts

exchangeXY

exPhotonCnt

fieldSeparator

file

fileDir

fileInfo

fileInfoCopy

fileName

filterExposureTimeX

filterFluorophoreX

format

headerFileName

history

historyNumber

image

imgBuffer

imgBuffer2

imgBufferI

imgBufferI2

imgDBuffer

imgDBuffer2

imgDBufferI

imgDBufferI2

imgExtents

imgLBuffer

imgLBuffer2

imgResols

invertY

labels

lambdaEm

lambdaEx

LUT

mapchannel

nDims

numAperture

numberSlices

numberSpaceSlices

numColors

numValues

order

origin

parameters

pinholeRadius

plateChamberID

plateVesselID

probe

refrInxLensMedium

refrInxMedium

rgbPos

scale

scilType

sensorModel

sensorType

sign