loci.formats.in

Class ZeissLSMReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.ZeissLSMReader

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable, IFormatHandler, IFormatReader, IMetadataConfigurable

public class ZeissLSMReader
extends FormatReader

ZeissLSMReader is the file format reader for Zeiss LSM files.

Source code:

Trac, Gitweb

Author:

Eric Kjellman egkjellman at wisc.edu, Melissa Linkert melissa at glencoesoftware.com, Curtis Rueden ctrueden at wisc.edu

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String[]	MDB_SUFFIX

Fields inherited from class loci.formats.FormatReader

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

Fields inherited from class loci.formats.FormatHandler

COMPRESSION_SUFFIXES, currentId, format, LOGGER, suffixes

Fields inherited from interface loci.formats.IFormatReader

CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
void	close(boolean fileOnly) Closes the currently open file.
int	fileGroupOption(java.lang.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.
int	getOptimalTileHeight() Returns the optimal sub-image height for use with openBytes.
int	getOptimalWidth()
java.lang.String[]	getSeriesUsedFiles(boolean noPixels) Returns an array of filenames needed to open the current series.
protected void	initFile(java.lang.String id) Initializes the given file (parsing header information, etc.).
protected void	initMetadata(int series)
boolean	isSingleFile(java.lang.String id) Returns true if this is a single-file format.
boolean	isThisType(RandomAccessInputStream stream) Checks if the given stream is a valid stream for this file format.
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.
protected void	parseOverlays(int series, long data, java.lang.String suffix, MetadataStore store) Parses overlay-related fields.
protected void	populateMetadataStore(loci.formats.in.ZeissLSMReader.SubBlock block, MetadataStore store, int series)
void	setSeries(int series) Activates the specified series.

Methods inherited from class loci.formats.FormatReader

addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMetaList, addMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMetaList, close, coreIndexToSeries, flattenHashtables, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getBinning, getBitsPerPixel, getChannelDimLengths, getChannelDimTypes, getCompression, getContrastMethod, getCoreIndex, getCoreMetadata, getCoreMetadataList, getCorrection, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, getEffectiveSizeC, getExperimentType, getFilamentType, getFillRule, getFilterType, getFontFamily, getFontStyle, getGlobalMeta, getGlobalMetadata, getIlluminationType, getImageCount, getImmersion, getIndex, getLaserMedium, getLaserType, getLineCap, getMarker, getMedium, getMetadataOptions, 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, getSupportedMetadataLevels, getThumbSizeX, getThumbSizeY, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, 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, seriesToCoreIndex, setCoreIndex, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataOptions, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution

Methods inherited from class loci.formats.FormatHandler

checkSuffix, checkSuffix, getFormat, getNativeDataType, getSuffixes

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

Field Detail

MDB_SUFFIX

public static final java.lang.String[] MDB_SUFFIX

Constructor Detail

ZeissLSMReader

public ZeissLSMReader()

Constructs a new Zeiss LSM reader.

Method Detail

getOptimalWidth

public int getOptimalWidth()

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

isSingleFile

public boolean isSingleFile(java.lang.String id)
                     throws FormatException,
                            java.io.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

java.io.IOException

close

public void close(boolean fileOnly)
           throws java.io.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:

java.io.IOException

isThisType

public boolean isThisType(RandomAccessInputStream stream)
                   throws java.io.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:

java.io.IOException

fileGroupOption

public int fileGroupOption(java.lang.String id)
                    throws FormatException,
                           java.io.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

java.io.IOException

getSeriesUsedFiles

public java.lang.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

get8BitLookupTable

public byte[][] get8BitLookupTable()
                            throws FormatException,
                                   java.io.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

java.io.IOException

get16BitLookupTable

public short[][] get16BitLookupTable()
                              throws FormatException,
                                     java.io.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

java.io.IOException

setSeries

public void setSeries(int series)

Description copied from interface: IFormatReader

Activates the specified series. This also resets the resolution to 0.

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,
                        java.io.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.

java.io.IOException - if there was a problem reading the file.

See Also:

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

initFile

protected void initFile(java.lang.String id)
                 throws FormatException,
                        java.io.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.

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

initMetadata

protected void initMetadata(int series)
                     throws FormatException,
                            java.io.IOException

Throws:

FormatException

java.io.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,
                 java.lang.String suffix,
                 MetadataStore store)
                      throws java.io.IOException

Parses overlay-related fields.

Throws:

java.io.IOException