loci.formats.in
Class LeicaReader

java.lang.Object
  loci.formats.FormatHandler
      loci.formats.FormatReader
          loci.formats.in.LeicaReader

All Implemented Interfaces:

loci.formats.IFormatHandler, loci.formats.IFormatReader, loci.formats.StatusReporter

public class LeicaReader
extends loci.formats.FormatReader

LeicaReader is the file format reader for Leica files.

Source code:

Trac, SVN

Author:

Melissa Linkert linkert at wisc.edu

Field Summary

protected Vector[]	files Array of image file names.
protected Hashtable[]	headerIFDs Array of IFD-like structures containing metadata.
protected Hashtable[]	ifds
protected TiffReader[][]	tiff Helper readers.

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

LeicaReader()
Constructs a new Leica reader.

Method Summary

void	close()
void	close(boolean fileOnly)
int	fileGroupOption(String id)
short[][]	get16BitLookupTable()
byte[][]	get8BitLookupTable()
String[]	getUsedFiles()
protected void	initFile(String id)
protected void	initMetadata()
boolean	isThisType(byte[] block)
boolean	isThisType(String name, boolean open)
byte[]	openBytes(int no, byte[] buf)

Methods inherited from class loci.formats.FormatReader

addMeta, checkBytes, 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, 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, setId

Methods inherited from interface loci.formats.StatusReporter

addStatusListener, getStatusListeners, removeStatusListener

Field Detail

ifds

protected Hashtable[] ifds

headerIFDs

protected Hashtable[] headerIFDs

Array of IFD-like structures containing metadata.

tiff

protected TiffReader[][] tiff

Helper readers.

files

protected Vector[] files

Array of image file names.

Constructor Detail

LeicaReader

public LeicaReader()

Constructs a new Leica reader.

Method Detail

isThisType

public boolean isThisType(byte[] block)

get8BitLookupTable

public byte[][] get8BitLookupTable()
                            throws loci.formats.FormatException,
                                   IOException

Specified by:

get8BitLookupTable in interface loci.formats.IFormatReader

Overrides:

get8BitLookupTable in class loci.formats.FormatReader

Throws:

loci.formats.FormatException

IOException

get16BitLookupTable

public short[][] get16BitLookupTable()
                              throws loci.formats.FormatException,
                                     IOException

Specified by:

get16BitLookupTable in interface loci.formats.IFormatReader

Overrides:

get16BitLookupTable in class loci.formats.FormatReader

Throws:

loci.formats.FormatException

IOException

fileGroupOption

public int fileGroupOption(String id)
                    throws loci.formats.FormatException,
                           IOException

Specified by:

fileGroupOption in interface loci.formats.IFormatReader

Overrides:

fileGroupOption in class loci.formats.FormatReader

Throws:

loci.formats.FormatException

IOException

openBytes

public byte[] openBytes(int no,
                        byte[] buf)
                 throws loci.formats.FormatException,
                        IOException

Throws:

loci.formats.FormatException

IOException

getUsedFiles

public String[] getUsedFiles()

Specified by:

getUsedFiles in interface loci.formats.IFormatReader

Overrides:

getUsedFiles in class loci.formats.FormatReader

close

public void close(boolean fileOnly)
           throws IOException

Specified by:

close in interface loci.formats.IFormatReader

Overrides:

close in class loci.formats.FormatReader

Throws:

IOException

isThisType

public boolean isThisType(String name,
                          boolean open)

Specified by:

isThisType in interface loci.formats.IFormatHandler

Overrides:

isThisType in class loci.formats.FormatHandler

close

public void close()
           throws IOException

Specified by:

close in interface loci.formats.IFormatHandler

Overrides:

close in class loci.formats.FormatReader

Throws:

IOException

initFile

protected void initFile(String id)
                 throws loci.formats.FormatException,
                        IOException

Overrides:

initFile in class loci.formats.FormatReader

Throws:

loci.formats.FormatException

IOException

initMetadata

protected void initMetadata()
                     throws loci.formats.FormatException,
                            IOException

Throws:

loci.formats.FormatException

IOException