loci.formats.in
Class ICSReader

java.lang.Object
  extended by loci.formats.FormatHandler
      extended by loci.formats.FormatReader
          extended by loci.formats.in.ICSReader
All Implemented Interfaces:
IFormatHandler, IFormatReader, StatusReporter

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

Source code:
Trac, SVN

Author:
Melissa Linkert linkert at wisc.edu

Field Summary
protected  int bitsPerPixel
          Number of bits per pixel.
protected  String currentIcsId
          Current filename.
protected  String currentIdsId
           
protected  byte[] data
          Image data.
protected  Location icsIn
          Current ICS file.
protected  boolean versionTwo
          Flag indicating whether current file is v2.0.
 
Fields inherited from class loci.formats.FormatReader
collectMetadata, core, filterMetadata, group, in, metadata, metadataStore, normalizeData, saveOriginalMetadata, series, THUMBNAIL_DIMENSION
 
Fields inherited from class loci.formats.FormatHandler
currentId, debug, debugLevel, format, statusListeners, suffixes
 
Fields inherited from interface loci.formats.IFormatReader
CAN_GROUP, CANNOT_GROUP, MUST_GROUP
 
Constructor Summary
ICSReader()
          Constructs a new ICSReader.
 
Method Summary
 void close()
          Closes currently open file(s) and frees allocated memory.
 int fileGroupOption(String id)
          Returns an int indicating that we cannot, must, or might group the files in a given dataset.
 String[] getUsedFiles()
          Returns an array of filenames needed to open this dataset.
protected  void initFile(String id)
          Initializes the given file (parsing header information, etc.).
 boolean isThisType(byte[] block)
          Checks if the given block is a valid header for this file format.
 byte[] openBytes(int no, byte[] buf)
          Obtains the specified image from the current file into a pre-allocated byte array of (sizeX * sizeY * bytesPerPixel).
 
Methods inherited from class loci.formats.FormatReader
addMeta, checkBytes, close, get16BitLookupTable, get8BitLookupTable, getChannelDimLengths, getChannelDimLengths, getChannelDimTypes, getChannelDimTypes, getCoreMetadata, getCoreMetadata, getCurrentFile, getDimensionOrder, getDimensionOrder, getEffectiveSizeC, getEffectiveSizeC, getImageCount, getImageCount, getIndex, getIndex, getMeta, getMetadata, getMetadata, getMetadataStore, getMetadataStore, getMetadataStoreRoot, getMetadataStoreRoot, getMetadataValue, getMetadataValue, getPixelType, getPixelType, getRGBChannelCount, getRGBChannelCount, getSeries, getSeries, getSeriesCount, getSeriesCount, getSizeC, getSizeC, getSizeT, getSizeT, getSizeX, getSizeX, getSizeY, getSizeY, getSizeZ, getSizeZ, getThumbSizeX, getThumbSizeX, getThumbSizeY, getThumbSizeY, getUsedFiles, getZCTCoords, getZCTCoords, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isInterleaved, isInterleaved, isLittleEndian, isLittleEndian, isMetadataCollected, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOrderCertain, isOriginalMetadataPopulated, isRGB, isRGB, isUsedFile, openBytes, openBytes, openBytes, openImage, openImage, openThumbBytes, openThumbBytes, openThumbImage, openThumbImage, setGroupFiles, setId, setMetadataCollected, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setSeries, setSeries
 
Methods inherited from class loci.formats.FormatHandler
addStatusListener, debug, getFormat, getStatusListeners, getSuffixes, isThisType, isThisType, removeStatusListener, setDebug, setDebugLevel, setId, status, status, status, trace, trace
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 
Methods inherited from interface loci.formats.IFormatHandler
getFormat, getSuffixes, isThisType, isThisType, setId
 
Methods inherited from interface loci.formats.StatusReporter
addStatusListener, getStatusListeners, removeStatusListener
 

Field Detail

currentIcsId

protected String currentIcsId
Current filename.


currentIdsId

protected String currentIdsId

icsIn

protected Location icsIn
Current ICS file.


bitsPerPixel

protected int bitsPerPixel
Number of bits per pixel.


versionTwo

protected boolean versionTwo
Flag indicating whether current file is v2.0.


data

protected byte[] data
Image data.

Constructor Detail

ICSReader

public ICSReader()
Constructs a new ICSReader.

Method Detail

isThisType

public boolean isThisType(byte[] block)
Description copied from interface: IFormatReader
Checks if the given block is a valid header for this file format.


fileGroupOption

public int fileGroupOption(String id)
                    throws FormatException,
                           IOException
Description copied from interface: IFormatReader
Returns an int indicating that we cannot, must, or might group the files in a given dataset.

Specified by:
fileGroupOption in interface IFormatReader
Overrides:
fileGroupOption in class FormatReader
Throws:
FormatException
IOException

openBytes

public byte[] openBytes(int no,
                        byte[] buf)
                 throws FormatException,
                        IOException
Description copied from interface: IFormatReader
Obtains the specified image from the current file into a pre-allocated byte array of (sizeX * sizeY * bytesPerPixel).

Parameters:
no - the image index within the file.
buf - a pre-allocated buffer.
Returns:
the pre-allocated buffer buf for convenience.
Throws:
FormatException - if there was a problem parsing the metadata of the file.
IOException - if there was a problem reading the file.

getUsedFiles

public String[] getUsedFiles()
Description copied from interface: IFormatReader
Returns an array of filenames needed to open this dataset.

Specified by:
getUsedFiles in interface IFormatReader
Overrides:
getUsedFiles in class FormatReader

close

public void close()
           throws IOException
Description copied from interface: IFormatHandler
Closes currently open file(s) and frees allocated memory.

Specified by:
close in interface IFormatHandler
Overrides:
close in class FormatReader
Throws:
IOException

initFile

protected void initFile(String id)
                 throws FormatException,
                        IOException
Description copied from class: FormatReader
Initializes the given file (parsing header information, etc.). Most subclasses should override this method to perform initialization operations such as parsing metadata.

Overrides:
initFile in class FormatReader
Throws:
FormatException
IOException