Package loci.formats.in

Class LeicaReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.LeicaReader

All Implemented Interfaces:

Closeable, AutoCloseable, ICompressedTileReader, IFormatHandler, IFormatReader, IMetadataConfigurable, IPyramidHandler

public class LeicaReader
extends FormatReader

LeicaReader is the file format reader for Leica files.

Author:

Melissa Linkert melissa at glencoesoftware.com

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
(package private) class	LeicaReader.Detector

Field Summary

Fields

Modifier and Type	Field	Description
private List<Integer>	activeChannelIndices
private static final Integer	CHANDESC
private ome.xml.model.primitives.Color[][]	channelColor
private List[]	channelNames
private boolean[][]	cutInPopulated
private boolean[][]	cutOutPopulated
private static final String	DATE_FORMAT	Format for dates.
private List<LeicaReader.Detector>	detectors
private static final Integer	DIMDESCR
private static final com.google.common.collect.ImmutableMap<Integer,String>	DIMENSION_NAMES
private List[]	emWaves
private static final Integer	EXPERIMENT
private double[]	exposureTime
private List[]	exWaves
private int	fileLength	Length of each file name.
protected List<String>[]	files	Array of image file names.
private boolean[][]	filterRefPopulated
private static final Integer	FILTERSET
protected IFDList	headerIFDs	Array of IFD-like structures containing metadata.
protected IFDList	ifds
private static final Integer	IMAGES
private int	lastPlane
static final String[]	LEI_SUFFIX
private static final int	LEICA_MAGIC_TAG	All Leica TIFFs have this tag.
private String	leiFilename	Name of current LEI file
private static final org.slf4j.Logger	LOGGER
private static final Integer	LUTDESC
private int	nameLength
private int	nextChannel
private int	nextDetector
private int	numSeries	Number of series in the file.
private double[][]	physicalSizes
private double[]	pinhole
private static final Integer	SCANNERSET
private static final Integer	SEQ_FILTERSET
private static final int	SEQ_FILTERSET_END
private static final Integer	SEQ_SCANNERSET
private static final int	SEQ_SCANNERSET_END
private boolean	sequential
private static final Integer	SEQUENTIALSET
private static final Integer	SERIES	IFD tags.
private List<String>	seriesDescriptions
private List<String>	seriesNames
protected MinimalTiffReader	tiff	Helper readers.
private int[]	tileHeight
private int[]	tileWidth
private static final Integer	TIMEINFO
private String[][]	timestamps
private boolean[]	valid

Fields inherited from class loci.formats.FormatReader

core, coreIndex, datasetDescription, domains, fillColor, filterMetadata, flattenedResolutions, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataStore, normalizeData, resolution, saveOriginalMetadata, series, suffixNecessary, suffixSufficient, THUMBNAIL_DIMENSION

Fields inherited from class loci.formats.FormatHandler

COMPRESSION_SUFFIXES, currentId, format, metadataOptions, suffixes

Fields inherited from interface loci.formats.IFormatReader

CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors

Constructor	Description
LeicaReader()	Constructs a new Leica reader.

Method Summary

Modifier and Type	Method	Description
void	close(boolean fileOnly)	Closes the currently open file.
int	fileGroupOption(String id)	Returns an indication of whether the files in a multi-file dataset can be handled individually.
private String	findLEIFile(String baseFile)	Find the .lei file that belongs to the same dataset as the given file.
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.
int	getOptimalTileHeight()	Returns the optimal sub-image height for use with openBytes.
int	getOptimalTileWidth()	Returns the optimal sub-image width for use with openBytes.
String[]	getSeriesUsedFiles(boolean noPixels)	Returns an array of filenames needed to open the current series.
private String	getString(boolean doubleLength)
private String	getString(int len)
private String[]	getTIFFList()
protected void	initFile(String id)	Initializes the given file (parsing header information, etc.).
boolean	isSingleFile(String id)	Returns true if the named file is expected to be the only file in the dataset.
boolean	isThisType(String name, boolean open)	Checks if a file matches the type of this format reader.
boolean	isThisType(loci.common.RandomAccessInputStream stream)	Checks if the given stream is a valid stream for this file format.
private static com.google.common.collect.ImmutableMap<Integer,String>	makeDimensionTable()
byte[]	openBytes(int no, byte[] buf, int x, int y, int w, int h)	Obtains a sub-image of the specified image plane into a pre-allocated byte array.
private void	parseChannelTag()
private void	parseDimensionTag(int seriesIndex)
private void	parseExperimentTag()
private void	parseFilenames(int seriesIndex)
private void	parseImageTag(int seriesIndex)
private void	parseInstrumentData(MetadataStore store, int blockNum)
private void	parseLUT(int seriesIndex)
private void	parseSeriesTag()
private void	parseTimeTag(int seriesIndex)
private boolean	usedFile(String s)

Methods inherited from class loci.formats.FormatReader

addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMetaList, addMeta, addMetaList, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMetaList, close, coreIndexToSeries, flattenHashtables, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getAvailableOptions, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCoreIndex, getCoreMetadataList, getCorrection, getCurrentCore, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, getEffectiveSizeC, getExperimentType, getFilamentType, getFillColor, getFillRule, getFilterType, getFontFamily, getFontStyle, getGlobalMeta, getGlobalMetadata, getIlluminationType, getImageCount, getImmersion, getIndex, getIndex, getLaserMedium, getLaserType, getMarker, getMedium, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getMicrobeamManipulationType, getMicroscopeType, getModuloC, getModuloT, getModuloZ, getNamingConvention, getPixelType, getPixelType, getPossibleDomains, getPulse, getRequiredDirectories, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getThumbSizeX, getThumbSizeY, getTileColumns, getTileRows, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, readPlane, reopenFile, seriesToCoreIndex, setCoreIndex, setFillColor, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries, updateMetadataLists

Methods inherited from class loci.formats.FormatHandler

checkSuffix, checkSuffix, getFormat, getMetadataOptions, getNativeDataType, getSuffixes, getSupportedMetadataLevels, setMetadataOptions

Methods inherited from class java.lang.Object

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

Methods inherited from interface loci.formats.ICompressedTileReader

getTileCodec, getTileCodecOptions, openCompressedBytes, openCompressedBytes

Methods inherited from interface loci.formats.IFormatHandler

getFormat, getNativeDataType, getSuffixes

Methods inherited from interface loci.formats.IMetadataConfigurable

getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

Field Details

LOGGER

private static final org.slf4j.Logger LOGGER

LEI_SUFFIX

public static final String[] LEI_SUFFIX

LEICA_MAGIC_TAG

private static final int LEICA_MAGIC_TAG

All Leica TIFFs have this tag.

See Also:

• Constant Field Values

DATE_FORMAT

private static final String DATE_FORMAT

Format for dates.

See Also:

• Constant Field Values

SERIES

private static final Integer SERIES

IFD tags.

IMAGES

private static final Integer IMAGES

DIMDESCR

private static final Integer DIMDESCR

FILTERSET

private static final Integer FILTERSET

TIMEINFO

private static final Integer TIMEINFO

SCANNERSET

private static final Integer SCANNERSET

EXPERIMENT

private static final Integer EXPERIMENT

LUTDESC

private static final Integer LUTDESC

CHANDESC

private static final Integer CHANDESC

SEQUENTIALSET

private static final Integer SEQUENTIALSET

SEQ_SCANNERSET

private static final Integer SEQ_SCANNERSET

SEQ_FILTERSET

private static final Integer SEQ_FILTERSET

SEQ_SCANNERSET_END

private static final int SEQ_SCANNERSET_END

See Also:

• Constant Field Values

SEQ_FILTERSET_END

private static final int SEQ_FILTERSET_END

See Also:

• Constant Field Values

DIMENSION_NAMES

private static final com.google.common.collect.ImmutableMap<Integer,String> DIMENSION_NAMES

ifds

protected IFDList ifds

headerIFDs

protected IFDList headerIFDs

Array of IFD-like structures containing metadata.

tiff

protected MinimalTiffReader tiff

Helper readers.

files

protected List<String>[] files

Array of image file names.

numSeries

private int numSeries

Number of series in the file.

leiFilename

private String leiFilename

Name of current LEI file

fileLength

private int fileLength

Length of each file name.

valid

private boolean[] valid

timestamps

private String[][] timestamps

seriesNames

private List<String> seriesNames

seriesDescriptions

private List<String> seriesDescriptions

lastPlane

private int lastPlane

nameLength

private int nameLength

physicalSizes

private double[][] physicalSizes

pinhole

private double[] pinhole

exposureTime

private double[] exposureTime

nextDetector

private int nextDetector

nextChannel

private int nextChannel

activeChannelIndices

private List<Integer> activeChannelIndices

sequential

private boolean sequential

channelNames

private List[] channelNames

emWaves

private List[] emWaves

exWaves

private List[] exWaves

cutInPopulated

private boolean[][] cutInPopulated

cutOutPopulated

private boolean[][] cutOutPopulated

filterRefPopulated

private boolean[][] filterRefPopulated

detectors

private List<LeicaReader.Detector> detectors

tileWidth

private int[] tileWidth

tileHeight

private int[] tileHeight

channelColor

private ome.xml.model.primitives.Color[][] channelColor

Constructor Details

LeicaReader

public LeicaReader()

Constructs a new Leica reader.

Method Details

isSingleFile

public boolean isSingleFile(String id)
                     throws FormatException,
IOException

Description copied from interface: IFormatReader

Returns true if the named file is expected to be the only file in the dataset. For single-file formats, always returns true.

Specified by:

isSingleFile in interface IFormatReader

Overrides:

isSingleFile in class FormatReader

Throws:

FormatException

IOException

isThisType

public boolean isThisType(String name,
 boolean open)

Description copied from class: FormatReader

Checks if a file matches the type of this format reader. Checks filename suffixes against those known for this format. If the suffix check is inconclusive and the open parameter is true, the file is opened and tested with FormatReader.isThisType(RandomAccessInputStream).

Specified by:

isThisType in interface IFormatReader

Overrides:

isThisType in class FormatReader

Parameters:

open - If true, and the file extension is insufficient to determine the file type, the (existing) file is opened for further analysis.

isThisType

public boolean isThisType(loci.common.RandomAccessInputStream stream)
                   throws IOException

Description copied from interface: IFormatReader

Checks if the given stream is a valid stream for this file format. The number of bytes read is format-dependent.

Specified by:

isThisType in interface IFormatReader

Overrides:

isThisType in class FormatReader

Parameters:

stream - A RandomAccessInputStream representing the file to check. The first byte in the stream is assumed to be the first byte in the file.

Returns:

true if the file represented by the stream can be read by this reader; false otherwise.

Throws:

IOException

get8BitLookupTable

public byte[][] get8BitLookupTable()
                            throws FormatException,
IOException

Description copied from interface: IFormatReader

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

Specified by:

get8BitLookupTable in interface IFormatReader

Overrides:

get8BitLookupTable in class FormatReader

Throws:

FormatException

IOException

get16BitLookupTable

public short[][] get16BitLookupTable()
                              throws FormatException,
IOException

Description copied from interface: IFormatReader

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

Specified by:

get16BitLookupTable in interface IFormatReader

Overrides:

get16BitLookupTable in class FormatReader

Throws:

FormatException

IOException

fileGroupOption

public int fileGroupOption(String id)
                    throws FormatException,
IOException

Description copied from interface: IFormatReader

Returns an indication of whether the files in a multi-file dataset can be handled individually. This method is only useful for formats and datasets which contain multiple files.

Specified by:

fileGroupOption in interface IFormatReader

Overrides:

fileGroupOption in class FormatReader

Parameters:

id - a file in the multi-file dataset

Returns:

an int indicating that we cannot, must, or might group the files. A return value of FormatTools.MUST_GROUP indicates that the files cannot be handled separately; the reader will always detect and read all files in the dataset. FormatTools.CAN_GROUP indicates that the files may be handled separately, but file grouping must then be disabled via IFormatReader.setGroupFiles(boolean). FormatTools.CANNOT_GROUP indicates that the files must be handled separately; the reader will not attempt to read all files in the dataset (this is rare).

Throws:

FormatException

IOException

See Also:

• FormatTools.MUST_GROUP
• FormatTools.CAN_GROUP
• FormatTools.CANNOT_GROUP

openBytes

public byte[] openBytes(int no,
 byte[] buf,
 int x,
 int y,
 int w,
 int h)
                 throws FormatException,
IOException

Description copied from interface: IFormatReader

Obtains a sub-image of the specified image plane into a pre-allocated byte array.

Specified by:

openBytes in interface IFormatReader

Specified by:

openBytes in class FormatReader

Parameters:

no - the plane index within the current series.

buf - a pre-allocated buffer.

x - X coordinate of the upper-left corner of the sub-image

y - Y coordinate of the upper-left corner of the sub-image

w - width of the sub-image

h - height of the sub-image

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.

See Also:

• IFormatReader.openBytes(int, byte[], int, int, int, int)

getSeriesUsedFiles

public String[] getSeriesUsedFiles(boolean noPixels)

Description copied from interface: IFormatReader

Returns an array of filenames needed to open the current series. If the 'noPixels' flag is set, then only files that do not contain pixel data will be returned. The first element in the array is expected to be the path passed to IFormatHandler.setId(String), if appropriate based upon 'noPixels'. The remaining elements are expected to be in a consistent order; if a directory listing is necessary to build the list then it should be sorted first.

Specified by:

getSeriesUsedFiles in interface IFormatReader

Overrides:

getSeriesUsedFiles in class FormatReader

close

public void close(boolean fileOnly)
           throws IOException

Description copied from interface: IFormatReader

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

Specified by:

close in interface IFormatReader

Overrides:

close in class FormatReader

Throws:

IOException

getOptimalTileWidth

public int getOptimalTileWidth()

Description copied from interface: IFormatReader

Returns the optimal sub-image width for use with openBytes.

Specified by:

getOptimalTileWidth in interface IFormatReader

Overrides:

getOptimalTileWidth in class FormatReader

getOptimalTileHeight

public int getOptimalTileHeight()

Description copied from interface: IFormatReader

Returns the optimal sub-image height for use with openBytes.

Specified by:

getOptimalTileHeight in interface IFormatReader

Overrides:

getOptimalTileHeight in class FormatReader

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 - if a parsing error occurs processing the file.

IOException - if an I/O error occurs processing the file

findLEIFile

private String findLEIFile(String baseFile)
                    throws FormatException,
IOException

Find the .lei file that belongs to the same dataset as the given file.

Throws:

FormatException

IOException

getTIFFList

private String[] getTIFFList()

parseFilenames

private void parseFilenames(int seriesIndex)
                     throws IOException

Throws:

IOException

parseSeriesTag

private void parseSeriesTag()
                     throws IOException

Throws:

IOException

parseImageTag

private void parseImageTag(int seriesIndex)
                    throws IOException

Throws:

IOException

parseDimensionTag

private void parseDimensionTag(int seriesIndex)
                        throws FormatException,
IOException

Throws:

FormatException

IOException

parseTimeTag

private void parseTimeTag(int seriesIndex)
                   throws IOException

Throws:

IOException

parseExperimentTag

private void parseExperimentTag()
                         throws IOException

Throws:

IOException

parseLUT

private void parseLUT(int seriesIndex)
               throws IOException

Throws:

IOException

parseChannelTag

private void parseChannelTag()
                      throws IOException

Throws:

IOException

parseInstrumentData

private void parseInstrumentData(MetadataStore store,
 int blockNum)
                          throws FormatException,
IOException

Throws:

FormatException

IOException

usedFile

private boolean usedFile(String s)

getString

private String getString(int len)
                  throws IOException

Throws:

IOException

getString

private String getString(boolean doubleLength)
                  throws IOException

Throws:

IOException

makeDimensionTable

private static com.google.common.collect.ImmutableMap<Integer,String> makeDimensionTable()