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.

Author:

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

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
(package private) class	ZeissLSMReader.BeamSplitter
(package private) class	ZeissLSMReader.DataChannel
(package private) class	ZeissLSMReader.DetectionChannel
(package private) class	ZeissLSMReader.IlluminationChannel
(package private) class	ZeissLSMReader.Laser
(package private) class	ZeissLSMReader.Marker
(package private) class	ZeissLSMReader.Recording
(package private) class	ZeissLSMReader.SubBlock
(package private) class	ZeissLSMReader.Timer
(package private) class	ZeissLSMReader.Track

Field Summary

Fields

Modifier and Type	Field	Description
private Map<Integer,String>	acquiredDate
private static final int	ANGLE
private static final int	BEAM_SPLITTER_FILTER
private static final int	BEAM_SPLITTER_FILTER_SET
private static final int	BEZIER_WITH_ARROW
private String	binning
private static final int	CHANNEL_ACQUIRE
private static final int	CHANNEL_AMPLIFIER_GAIN
private static final int	CHANNEL_DETECTOR_GAIN
private static final int	CHANNEL_FILTER
private static final int	CHANNEL_FILTER_SET
private static final int	CHANNEL_NAME
private static final int	CHANNEL_PINHOLE_DIAMETER
private ome.xml.model.primitives.Color[]	channelColor
private String[][]	channelNames
private static final int	CIRCLE
private static final int	CIRCLE_3POINT
private static final int	CLOSED_ARROW
private static final int	CLOSED_BEZIER
private static final int	CLOSED_POLYLINE
private static final int	DATA_CHANNEL_ACQUIRE
private static final int	DATA_CHANNEL_NAME
private int	dimensionM
private int	dimensionP
private static final int	ELLIPSE
private List<IFDList>	ifdsList
private static final int	ILLUM_CHANNEL_ACQUIRE
private static final int	ILLUM_CHANNEL_ATTENUATION
private static final int	ILLUM_CHANNEL_NAME
private static final int	ILLUM_CHANNEL_WAVELENGTH
private int	illuminations
private List<String>	imageNames
private boolean	isSIM
private static final int	LASER_ACQUIRE
private static final int	LASER_NAME
private static final int	LASER_POWER
private static final int	LINE
private String[]	lsmFilenames
private byte[][][]	lut
static final String[]	MDB_SUFFIX
private static final com.google.common.collect.ImmutableMap<Integer,String>	METADATA_KEYS
private int	nextDetectChannel
private int	nextDetector
private int	nextDichroic
private int	nextDichroicChannel
private int	nextFilter
private int	nextIllumChannel
private int	nextLaser
private static final int	OPEN_ARROW
private static final int	OPEN_BEZIER
private static final int	OPEN_POLYLINE
private double	originX
private double	originY
private double	originZ
private static final int	PALETTE
private int	phases
private double	pixelSizeX
private double	pixelSizeY
private double	pixelSizeZ
private static final int	POLYLINE_ARROW
private byte[]	prevBuf
private int	prevChannel
private int	prevPlane
private loci.common.Region	prevRegion
private static final int	RECORDING_CAMERA_BINNING
private static final int	RECORDING_DESCRIPTION
private static final int	RECORDING_NAME	Data types.
private static final int	RECORDING_OBJECTIVE
private static final int	RECORDING_SAMPLE_0TIME
private static final int	RECORDING_ZOOM
private static final int	RECTANGLE
private int	rotations
private static final int	SCALE_BAR
private Map<String,Integer>	seriesCounts
private boolean	splitPlanes
private static final int	START_TIME
private static final int	SUBBLOCK_BEAM_SPLITTER
private static final int	SUBBLOCK_DATA_CHANNEL
private static final int	SUBBLOCK_DETECTION_CHANNEL
private static final int	SUBBLOCK_END
private static final int	SUBBLOCK_ILLUMINATION_CHANNEL
private static final int	SUBBLOCK_LASER
private static final int	SUBBLOCK_MARKER
private static final int	SUBBLOCK_RECORDING	Subblock types.
private static final int	SUBBLOCK_TIMER
private static final int	SUBBLOCK_TRACK
private static final int	TEXT	Drawing element types.
private TiffParser	tiffParser
private List<Double>	timestamps
private int	totalROIs
private static final int	TRACK_ACQUIRE
private static final int	TRACK_TIME_BETWEEN_STACKS
private static final int	TYPE_ASCII
private static final int	TYPE_BOOLEAN
private static final int	TYPE_DATE
private static final int	TYPE_LONG
private static final int	TYPE_RATIONAL
private static final int	TYPE_SUBBLOCK	Data types.
private String	userName
private List<Double>	xCoordinates
private List<Double>	yCoordinates
private List<Double>	zCoordinates
private static final int	ZEISS_ID	Tag identifying a Zeiss LSM file.
private double	zoom

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)	Closes the currently open file.
private static com.google.common.collect.ImmutableMap<Integer,String>	createKeys()
int	fileGroupOption(String id)	Returns an indication of whether the files in a multi-file dataset can be handled individually.
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.
private loci.common.RandomAccessInputStream	getCZTag(IFD ifd)
private int	getEffectiveSeries(int currentSeries)
private int	getExtraSeries(String file)
private String	getLSMFileFromSeries(int currentSeries)
private String	getMDBFile(String id)
int	getOptimalTileHeight()	Returns the optimal sub-image height for use with openBytes.
int	getOptimalWidth()
private int	getPosition(int currentSeries)
String[]	getSeriesUsedFiles(boolean noPixels)	Returns an array of filenames needed to open the current series.
protected void	initFile(String id)	Initializes the given file (parsing header information, etc.).
protected void	initMetadata(int series)
boolean	isSingleFile(String id)	Returns true if the named file is expected to be the only file in the dataset.
boolean	isThisType(loci.common.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.
private void	parseApplicationTags()
private String[]	parseMDB(String mdbFile)	Parse a .mdb file and return a list of referenced .lsm files.
protected void	parseOverlays(int series, long data, String suffix, MetadataStore store)	Parses overlay-related fields.
protected void	populateMetadataStore(ZeissLSMReader.SubBlock block, MetadataStore store, int series)
private Integer	readEntry()
private Object	readValue()
void	setCoreIndex(int coreIndex)	Set the current resolution/series (ignores subresolutions).
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, 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

ZEISS_ID

private static final int ZEISS_ID

Tag identifying a Zeiss LSM file.

See Also:

• Constant Field Values

TYPE_SUBBLOCK

private static final int TYPE_SUBBLOCK

Data types.

See Also:

• Constant Field Values

TYPE_ASCII

private static final int TYPE_ASCII

See Also:

• Constant Field Values

TYPE_LONG

private static final int TYPE_LONG

See Also:

• Constant Field Values

TYPE_RATIONAL

private static final int TYPE_RATIONAL

See Also:

• Constant Field Values

TYPE_DATE

private static final int TYPE_DATE

See Also:

• Constant Field Values

TYPE_BOOLEAN

private static final int TYPE_BOOLEAN

See Also:

• Constant Field Values

SUBBLOCK_RECORDING

private static final int SUBBLOCK_RECORDING

Subblock types.

See Also:

• Constant Field Values

SUBBLOCK_LASER

private static final int SUBBLOCK_LASER

See Also:

• Constant Field Values

SUBBLOCK_TRACK

private static final int SUBBLOCK_TRACK

See Also:

• Constant Field Values

SUBBLOCK_DETECTION_CHANNEL

private static final int SUBBLOCK_DETECTION_CHANNEL

See Also:

• Constant Field Values

SUBBLOCK_ILLUMINATION_CHANNEL

private static final int SUBBLOCK_ILLUMINATION_CHANNEL

See Also:

• Constant Field Values

SUBBLOCK_BEAM_SPLITTER

private static final int SUBBLOCK_BEAM_SPLITTER

See Also:

• Constant Field Values

SUBBLOCK_DATA_CHANNEL

private static final int SUBBLOCK_DATA_CHANNEL

See Also:

• Constant Field Values

SUBBLOCK_TIMER

private static final int SUBBLOCK_TIMER

See Also:

• Constant Field Values

SUBBLOCK_MARKER

private static final int SUBBLOCK_MARKER

See Also:

• Constant Field Values

SUBBLOCK_END

private static final int SUBBLOCK_END

See Also:

• Constant Field Values

RECORDING_NAME

private static final int RECORDING_NAME

Data types.

See Also:

• Constant Field Values

RECORDING_DESCRIPTION

private static final int RECORDING_DESCRIPTION

See Also:

• Constant Field Values

RECORDING_OBJECTIVE

private static final int RECORDING_OBJECTIVE

See Also:

• Constant Field Values

RECORDING_ZOOM

private static final int RECORDING_ZOOM

See Also:

• Constant Field Values

RECORDING_SAMPLE_0TIME

private static final int RECORDING_SAMPLE_0TIME

See Also:

• Constant Field Values

RECORDING_CAMERA_BINNING

private static final int RECORDING_CAMERA_BINNING

See Also:

• Constant Field Values

TRACK_ACQUIRE

private static final int TRACK_ACQUIRE

See Also:

• Constant Field Values

TRACK_TIME_BETWEEN_STACKS

private static final int TRACK_TIME_BETWEEN_STACKS

See Also:

• Constant Field Values

LASER_NAME

private static final int LASER_NAME

See Also:

• Constant Field Values

LASER_ACQUIRE

private static final int LASER_ACQUIRE

See Also:

• Constant Field Values

LASER_POWER

private static final int LASER_POWER

See Also:

• Constant Field Values

CHANNEL_DETECTOR_GAIN

private static final int CHANNEL_DETECTOR_GAIN

See Also:

• Constant Field Values

CHANNEL_PINHOLE_DIAMETER

private static final int CHANNEL_PINHOLE_DIAMETER

See Also:

• Constant Field Values

CHANNEL_AMPLIFIER_GAIN

private static final int CHANNEL_AMPLIFIER_GAIN

See Also:

• Constant Field Values

CHANNEL_FILTER_SET

private static final int CHANNEL_FILTER_SET

See Also:

• Constant Field Values

CHANNEL_FILTER

private static final int CHANNEL_FILTER

See Also:

• Constant Field Values

CHANNEL_ACQUIRE

private static final int CHANNEL_ACQUIRE

See Also:

• Constant Field Values

CHANNEL_NAME

private static final int CHANNEL_NAME

See Also:

• Constant Field Values

ILLUM_CHANNEL_NAME

private static final int ILLUM_CHANNEL_NAME

See Also:

• Constant Field Values

ILLUM_CHANNEL_ATTENUATION

private static final int ILLUM_CHANNEL_ATTENUATION

See Also:

• Constant Field Values

ILLUM_CHANNEL_WAVELENGTH

private static final int ILLUM_CHANNEL_WAVELENGTH

See Also:

• Constant Field Values

ILLUM_CHANNEL_ACQUIRE

private static final int ILLUM_CHANNEL_ACQUIRE

See Also:

• Constant Field Values

START_TIME

private static final int START_TIME

See Also:

• Constant Field Values

DATA_CHANNEL_NAME

private static final int DATA_CHANNEL_NAME

See Also:

• Constant Field Values

DATA_CHANNEL_ACQUIRE

private static final int DATA_CHANNEL_ACQUIRE

See Also:

• Constant Field Values

BEAM_SPLITTER_FILTER

private static final int BEAM_SPLITTER_FILTER

See Also:

• Constant Field Values

BEAM_SPLITTER_FILTER_SET

private static final int BEAM_SPLITTER_FILTER_SET

See Also:

• Constant Field Values

TEXT

private static final int TEXT

Drawing element types.

See Also:

• Constant Field Values

LINE

private static final int LINE

See Also:

• Constant Field Values

SCALE_BAR

private static final int SCALE_BAR

See Also:

• Constant Field Values

OPEN_ARROW

private static final int OPEN_ARROW

See Also:

• Constant Field Values

CLOSED_ARROW

private static final int CLOSED_ARROW

See Also:

• Constant Field Values

RECTANGLE

private static final int RECTANGLE

See Also:

• Constant Field Values

ELLIPSE

private static final int ELLIPSE

See Also:

• Constant Field Values

CLOSED_POLYLINE

private static final int CLOSED_POLYLINE

See Also:

• Constant Field Values

OPEN_POLYLINE

private static final int OPEN_POLYLINE

See Also:

• Constant Field Values

CLOSED_BEZIER

private static final int CLOSED_BEZIER

See Also:

• Constant Field Values

OPEN_BEZIER

private static final int OPEN_BEZIER

See Also:

• Constant Field Values

CIRCLE

private static final int CIRCLE

See Also:

• Constant Field Values

PALETTE

private static final int PALETTE

See Also:

• Constant Field Values

POLYLINE_ARROW

private static final int POLYLINE_ARROW

See Also:

• Constant Field Values

BEZIER_WITH_ARROW

private static final int BEZIER_WITH_ARROW

See Also:

• Constant Field Values

ANGLE

private static final int ANGLE

See Also:

• Constant Field Values

CIRCLE_3POINT

private static final int CIRCLE_3POINT

See Also:

• Constant Field Values

METADATA_KEYS

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

pixelSizeX

private double pixelSizeX

pixelSizeY

private double pixelSizeY

pixelSizeZ

private double pixelSizeZ

lut

private byte[][][] lut

timestamps

private List<Double> timestamps

lsmFilenames

private String[] lsmFilenames

ifdsList

private List<IFDList> ifdsList

tiffParser

private transient TiffParser tiffParser

nextLaser

private int nextLaser

nextDetector

private int nextDetector

nextFilter

private int nextFilter

nextDichroicChannel

private int nextDichroicChannel

nextDichroic

private int nextDichroic

nextIllumChannel

private int nextIllumChannel

nextDetectChannel

private int nextDetectChannel

splitPlanes

private boolean splitPlanes

zoom

private double zoom

imageNames

private List<String> imageNames

binning

private String binning

xCoordinates

private List<Double> xCoordinates

yCoordinates

private List<Double> yCoordinates

zCoordinates

private List<Double> zCoordinates

dimensionM

private int dimensionM

dimensionP

private int dimensionP

rotations

private int rotations

phases

private int phases

illuminations

private int illuminations

seriesCounts

private Map<String,Integer> seriesCounts

userName

private String userName

channelNames

private String[][] channelNames

originX

private double originX

originY

private double originY

originZ

private double originZ

totalROIs

private int totalROIs

prevPlane

private int prevPlane

prevChannel

private int prevChannel

prevBuf

private byte[] prevBuf

prevRegion

private loci.common.Region prevRegion

acquiredDate

private Map<Integer,String> acquiredDate

channelColor

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

isSIM

private transient boolean isSIM

Constructor Details

ZeissLSMReader

public ZeissLSMReader()

Constructs a new Zeiss LSM reader.

Method Details

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(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

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

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

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

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

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

setCoreIndex

public void setCoreIndex(int coreIndex)

Description copied from interface: IFormatReader

Set the current resolution/series (ignores subresolutions). Equivalent to setSeries, but with flattened resolutions always set to false.

Specified by:

setCoreIndex in interface IFormatReader

Overrides:

setCoreIndex in class FormatReader

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,
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)

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

getMDBFile

private String getMDBFile(String id)
                   throws FormatException,
IOException

Throws:

FormatException

IOException

getEffectiveSeries

private int getEffectiveSeries(int currentSeries)

getLSMFileFromSeries

private String getLSMFileFromSeries(int currentSeries)

getExtraSeries

private int getExtraSeries(String file)
                    throws FormatException,
IOException

Throws:

FormatException

IOException

getPosition

private int getPosition(int currentSeries)

getCZTag

private loci.common.RandomAccessInputStream getCZTag(IFD ifd)
                                              throws FormatException,
IOException

Throws:

FormatException

IOException

initMetadata

protected void initMetadata(int series)
                     throws FormatException,
IOException

Throws:

FormatException

IOException

populateMetadataStore

protected void populateMetadataStore(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

parseMDB

private String[] parseMDB(String mdbFile)
                   throws FormatException,
IOException

Parse a .mdb file and return a list of referenced .lsm files.

Throws:

FormatException

IOException

createKeys

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

readEntry

private Integer readEntry()
                   throws IOException

Throws:

IOException

readValue

private Object readValue()
                  throws IOException

Throws:

IOException

parseApplicationTags

private void parseApplicationTags()
                           throws IOException

Throws:

IOException