loci.formats
Class ICSReader

java.lang.Object
  loci.formats.FormatHandler
      loci.formats.FormatReader
          loci.formats.ICSReader

public class ICSReader

extends FormatReader

ICSReader is the file format reader for ICS (Image Cytometry Standard) files. More information on ICS can be found at http://libics.sourceforge.net

Field Summary

protected String	currentIcsId Current filename.
protected String	currentIdsId
protected int[]	dimensions Dimensions in the following order: 1) bits per pixel 2) width 3) height 4) z 5) channels 6) timepoints
protected File	icsIn
protected RandomAccessFile	idsIn Current file.
protected boolean	littleEndian Flag indicating whether current file is little endian.
protected int	numImages Number of images.

Fields inherited from class loci.formats.FormatReader

DEBUG, DEBUG_LEVEL, metadata, ome

Fields inherited from class loci.formats.FormatHandler

chooser, currentId, filters, format, suffixes

Constructor Summary

ICSReader()
Constructs a new ICSReader.

Method Summary

void	close() Closes any open files.
int	getImageCount(String id) Determines the number of images in the given ICS file.
protected void	initFile(String id) Initializes the given IPLab file.
boolean	isThisType(byte[] block) Checks if the given block is a valid header for an ICS file.
static void	main(String[] args)
BufferedImage	open(String id, int no) Obtains the specified image from the given ICS file.
byte[]	openBytes(String id, int no) Obtains the bytes for the specified image from the given ICS file.

Methods inherited from class loci.formats.FormatReader

createFilters, getMetadata, getMetadataValue, getOMENode, open, testRead

Methods inherited from class loci.formats.FormatHandler

getFileChooser, getFileFilters, getFormat, getSuffixes, isThisType

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

currentIcsId

protected String currentIcsId

Current filename.

currentIdsId

protected String currentIdsId

idsIn

protected RandomAccessFile idsIn

Current file.

icsIn

protected File icsIn

littleEndian

protected boolean littleEndian

Flag indicating whether current file is little endian.

numImages

protected int numImages

Number of images.

dimensions

protected int[] dimensions

Dimensions in the following order: 1) bits per pixel 2) width 3) height 4) z 5) channels 6) timepoints

Constructor Detail

ICSReader

public ICSReader()

Constructs a new ICSReader.

Method Detail

isThisType

public boolean isThisType(byte[] block)

Checks if the given block is a valid header for an ICS file.

Specified by:

isThisType in class FormatReader

getImageCount

public int getImageCount(String id)
                  throws FormatException,
                         IOException

Determines the number of images in the given ICS file.

Specified by:

getImageCount in class FormatReader

Throws:

FormatException

IOException

openBytes

public byte[] openBytes(String id,
                        int no)
                 throws FormatException,
                        IOException

Obtains the bytes for the specified image from the given ICS file. Note : this method will be added to the FormatReader API.

Throws:

FormatException

IOException

open

public BufferedImage open(String id,
                          int no)
                   throws FormatException,
                          IOException

Obtains the specified image from the given ICS file.

Specified by:

open in class FormatReader

Throws:

FormatException

IOException

close

public void close()
           throws FormatException,
                  IOException

Closes any open files.

Specified by:

close in class FormatReader

Throws:

FormatException

IOException

initFile

protected void initFile(String id)
                 throws FormatException,
                        IOException

Initializes the given IPLab file.

Overrides:

initFile in class FormatReader

Throws:

FormatException

IOException

main

public static void main(String[] args)
                 throws FormatException,
                        IOException

Throws:

FormatException

IOException