Package loci.formats.in

Class ZeissLSMReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.ZeissLSMReader

All Implemented Interfaces:

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

public class ZeissLSMReader
extends FormatReader

ZeissLSMReader is the file format reader for Zeiss LSM files.

Field Summary

Fields

Modifier and Type	Field	Description
static final String[]	MDB_SUFFIX

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, LOGGER, metadataOptions, suffixes

Fields inherited from interface loci.formats.IFormatReader

CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors

Constructor	Description
ZeissLSMReader()	Constructs a new Zeiss LSM reader.

Method Summary

Modifier and Type	Method	Description
void	close(boolean fileOnly)
int	fileGroupOption(String id)
short[][]	get16BitLookupTable()
byte[][]	get8BitLookupTable()
int	getOptimalTileHeight()
int	getOptimalWidth()
String[]	getSeriesUsedFiles(boolean noPixels)
protected void	initFile(String id)
protected void	initMetadata(int series)
boolean	isSingleFile(String id)
boolean	isThisType(RandomAccessInputStream stream)
byte[]	openBytes(int no, byte[] buf, int x, int y, int w, int h)
protected void	parseOverlays(int series, long data, String suffix, MetadataStore store)	Parses overlay-related fields.
protected void	populateMetadataStore(loci.formats.in.ZeissLSMReader.SubBlock block, MetadataStore store, int series)
void	setCoreIndex(int coreIndex)
void	setSeries(int series)

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, getOptimalTileWidth, 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, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, readPlane, reopenFile, seriesToCoreIndex, setFillColor, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, 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

MDB_SUFFIX

public static final String[] MDB_SUFFIX

Constructor Details

ZeissLSMReader

public ZeissLSMReader()

Constructs a new Zeiss LSM reader.

Method Details

getOptimalWidth

public int getOptimalWidth()

getOptimalTileHeight

public int getOptimalTileHeight()

Specified by:

getOptimalTileHeight in interface IFormatReader

Overrides:

getOptimalTileHeight in class FormatReader

isSingleFile

public boolean isSingleFile(String id)
                     throws FormatException,
IOException

Specified by:

isSingleFile in interface IFormatReader

Overrides:

isSingleFile in class FormatReader

Throws:

FormatException

IOException

close

public void close(boolean fileOnly)
           throws IOException

Specified by:

close in interface IFormatReader

Overrides:

close in class FormatReader

Throws:

IOException

isThisType

public boolean isThisType(RandomAccessInputStream stream)
                   throws IOException

Specified by:

isThisType in interface IFormatReader

Overrides:

isThisType in class FormatReader

Throws:

IOException

fileGroupOption

public int fileGroupOption(String id)
                    throws FormatException,
IOException

Specified by:

fileGroupOption in interface IFormatReader

Overrides:

fileGroupOption in class FormatReader

Throws:

FormatException

IOException

getSeriesUsedFiles

public String[] getSeriesUsedFiles(boolean noPixels)

Specified by:

getSeriesUsedFiles in interface IFormatReader

Overrides:

getSeriesUsedFiles in class FormatReader

get8BitLookupTable

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

Specified by:

get8BitLookupTable in interface IFormatReader

Overrides:

get8BitLookupTable in class FormatReader

Throws:

FormatException

IOException

get16BitLookupTable

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

Specified by:

get16BitLookupTable in interface IFormatReader

Overrides:

get16BitLookupTable in class FormatReader

Throws:

FormatException

IOException

setCoreIndex

public void setCoreIndex(int coreIndex)

Specified by:

setCoreIndex in interface IFormatReader

Overrides:

setCoreIndex in class FormatReader

setSeries

public void setSeries(int series)

Specified by:

setSeries in interface IFormatReader

Overrides:

setSeries in class FormatReader

openBytes

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

Specified by:

openBytes in interface IFormatReader

Specified by:

openBytes in class FormatReader

Throws:

FormatException

IOException

See Also:

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

initFile

protected void initFile(String id)
                 throws FormatException,
IOException

Overrides:

initFile in class FormatReader

Throws:

FormatException

IOException

initMetadata

protected void initMetadata(int series)
                     throws FormatException,
IOException

Throws:

FormatException

IOException

populateMetadataStore

protected void populateMetadataStore(loci.formats.in.ZeissLSMReader.SubBlock block,
 MetadataStore store,
 int series)
                              throws FormatException

Throws:

FormatException

parseOverlays

protected void parseOverlays(int series,
 long data,
 String suffix,
 MetadataStore store)
                      throws IOException

Parses overlay-related fields.

Throws:

IOException