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

Fields

Modifier and Type	Field and Description
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

Constructors

Constructor and Description
LeicaReader() Constructs a new Leica reader.

Method Summary

Methods

Modifier and Type	Method and Description
void	close() Closes currently open file(s) and frees allocated memory.
void	close(boolean fileOnly) Closes the currently open file.
int	fileGroupOption(String id) Returns an int indicating that we cannot, must, or might group the files in a given dataset.
short[][]	get16BitLookupTable() Gets the 16-bit color lookup table associated with the most recently opened image.
byte[][]	get8BitLookupTable() Gets the 8-bit color lookup table associated with the most recently opened image.
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.).
protected void	initMetadata()
boolean	isThisType(byte[] block) Checks if the given block is a valid header for this file format.
boolean	isThisType(String name, boolean open) Checks if a file matches the type of this format handler.
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, 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)

Description copied from interface: loci.formats.IFormatReader

Checks if the given block is a valid header for this file format.

get8BitLookupTable

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

Description copied from interface: loci.formats.IFormatReader

Gets the 8-bit color lookup table associated with the most recently opened image. If no images have been opened, or if isIndexed() returns false, then this returns null. Also, if getPixelType() returns anything other than INT8 or UINT8, this method will return null.

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

Description copied from interface: loci.formats.IFormatReader

Gets the 16-bit color lookup table associated with the most recently opened image. If no images have been opened, or if isIndexed() returns false, then this returns null. Also, if getPixelType() returns anything other than INT16 or UINT16, this method will return null.

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

Description copied from interface: loci.formats.IFormatReader

Returns an int indicating that we cannot, must, or might group the files in a given dataset.

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

Description copied from interface: loci.formats.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:

loci.formats.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: loci.formats.IFormatReader

Returns an array of filenames needed to open this dataset.

Specified by:

getUsedFiles in interface loci.formats.IFormatReader

Overrides:

getUsedFiles in class loci.formats.FormatReader

close

public void close(boolean fileOnly)
           throws IOException

Description copied from interface: loci.formats.IFormatReader

Closes the currently open file. If the flag is set, this is all that happens; if unset, it is equivalent to calling IFormatHandler.close().

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)

Description copied from class: loci.formats.FormatHandler

Checks if a file matches the type of this format handler. The default implementation checks filename suffixes against those known for this format (the open parameter does nothing).

Specified by:

isThisType in interface loci.formats.IFormatHandler

Overrides:

isThisType in class loci.formats.FormatHandler

open - If true, and the file extension is insufficient to determine the file type, the (existing) file is opened for further analysis. Does nothing in the default implementation.

close

public void close()
           throws IOException

Description copied from interface: loci.formats.IFormatHandler

Closes currently open file(s) and frees allocated memory.

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

Description copied from class: loci.formats.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 loci.formats.FormatReader

Throws:

loci.formats.FormatException

IOException

initMetadata

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

Throws:

loci.formats.FormatException

IOException