LeicaReader (Bio-Formats API)

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

All Implemented Interfaces:

Closeable, AutoCloseable, IFormatHandler, IFormatReader, IMetadataConfigurable
```
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 and Description

(package private) class LeicaReader.Detector

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

Field Summary

Fields
Modifier and Type	Field and Description
`private List<Integer>`	`activeChannelIndices`
`private static Integer`	`CHANDESC`
`private ome.xml.model.primitives.Color[][]`	`channelColor`
`private List[]`	`channelNames`
`private boolean[][]`	`cutInPopulated`
`private boolean[][]`	`cutOutPopulated`
`private static String`	`DATE_FORMAT` Format for dates.
`private List<LeicaReader.Detector>`	`detectors`
`private static Integer`	`DIMDESCR`
`private static com.google.common.collect.ImmutableMap<Integer,String>`	`DIMENSION_NAMES`
`private List[]`	`emWaves`
`private static 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 Integer`	`FILTERSET`
`protected IFDList`	`headerIFDs` Array of IFD-like structures containing metadata.
`protected IFDList`	`ifds`
`private static Integer`	`IMAGES`
`private int`	`lastPlane`
`static String[]`	`LEI_SUFFIX`
`private static int`	`LEICA_MAGIC_TAG` All Leica TIFFs have this tag.
`private String`	`leiFilename` Name of current LEI file
`private static org.slf4j.Logger`	`LOGGER`
`private static 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 Integer`	`SCANNERSET`
`private static Integer`	`SEQ_FILTERSET`
`private static int`	`SEQ_FILTERSET_END`
`private static Integer`	`SEQ_SCANNERSET`
`private static int`	`SEQ_SCANNERSET_END`
`private boolean`	`sequential`
`private static Integer`	`SEQUENTIALSET`
`private static 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 Integer`	`TIMEINFO`
`private String[][]`	`timestamps`
`private boolean[]`	`valid`

Fields inherited from class loci.formats.FormatReader
core, coreIndex, datasetDescription, domains, 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 and Description

LeicaReader()
Constructs a new Leica reader.

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

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`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.
`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 this is a single-file format.
`boolean`	`isThisType(loci.common.RandomAccessInputStream stream)` Checks if the given stream is a valid stream for this file format.
`boolean`	`isThisType(String name, boolean open)` Checks if a file matches the type of this format reader.
`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, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCoreIndex, getCoreMetadataList, getCorrection, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, getEffectiveSizeC, getExperimentType, getFilamentType, 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, 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, reopenFile, seriesToCoreIndex, setCoreIndex, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries

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.IFormatHandler
getFormat, getNativeDataType, getSuffixes

Methods inherited from interface loci.formats.IMetadataConfigurable
getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

- Field Detail
  - 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 Detail
  - LeicaReader
```
public LeicaReader()
```
    Constructs a new Leica reader.
- Method Detail
  - isSingleFile
```
public boolean isSingleFile(String id)
                     throws FormatException,
                            IOException
```
    Description copied from interface: IFormatReader
    
    Returns true if this is a single-file format.
    
    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
    
    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.
    
    Specified by:
    
    isThisType in interface IFormatReader
    
    Overrides:
    
    isThisType in class FormatReader
    
    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 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,
                        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 image index within the file.
    
    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.
    
    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()
```

Class LeicaReader

Nested Class Summary

Field Summary

Fields inherited from class loci.formats.FormatReader

Fields inherited from class loci.formats.FormatHandler

Fields inherited from interface loci.formats.IFormatReader

Constructor Summary

Method Summary

Methods inherited from class loci.formats.FormatReader

Methods inherited from class loci.formats.FormatHandler

Methods inherited from class java.lang.Object

Methods inherited from interface loci.formats.IFormatHandler

Methods inherited from interface loci.formats.IMetadataConfigurable

Field Detail

LOGGER

LEI_SUFFIX

LEICA_MAGIC_TAG

DATE_FORMAT

SERIES

IMAGES

DIMDESCR

FILTERSET

TIMEINFO

SCANNERSET

EXPERIMENT

LUTDESC

CHANDESC

SEQUENTIALSET

SEQ_SCANNERSET

SEQ_FILTERSET

SEQ_SCANNERSET_END

SEQ_FILTERSET_END

DIMENSION_NAMES

ifds

headerIFDs

tiff

files

numSeries

leiFilename

fileLength

valid

timestamps

seriesNames

seriesDescriptions

lastPlane

nameLength

physicalSizes

pinhole

exposureTime

nextDetector

nextChannel

activeChannelIndices

sequential

channelNames

emWaves

exWaves

cutInPopulated

cutOutPopulated

filterRefPopulated

detectors

tileWidth

tileHeight

channelColor

Constructor Detail

LeicaReader

Method Detail

isSingleFile

isThisType

isThisType

get8BitLookupTable

get16BitLookupTable

fileGroupOption

openBytes

getSeriesUsedFiles

close

getOptimalTileWidth

getOptimalTileHeight

initFile

findLEIFile

getTIFFList