ZeissLSMReader (Bio-Formats API)

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

All Implemented Interfaces:

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

ZeissLSMReader()
Constructs a new Zeiss LSM reader.

Constructors
Constructor and Description
`ZeissLSMReader()` Constructs a new Zeiss LSM 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.
`private static com.google.common.collect.ImmutableMap<java.lang.Integer,java.lang.String>`	`createKeys()`
`int`	`fileGroupOption(java.lang.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(java.lang.String file)`
`private java.lang.String`	`getLSMFileFromSeries(int currentSeries)`
`private java.lang.String`	`getMDBFile(java.lang.String id)`
`int`	`getOptimalTileHeight()` Returns the optimal sub-image height for use with openBytes.
`int`	`getOptimalWidth()`
`private int`	`getPosition(int currentSeries)`
`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 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 java.lang.String[]`	`parseMDB(java.lang.String mdbFile)` Parse a .mdb file and return a list of referenced .lsm files.
`protected void`	`parseOverlays(int series, long data, java.lang.String suffix, MetadataStore store)` Parses overlay-related fields.
`protected void`	`populateMetadataStore(ZeissLSMReader.SubBlock block, MetadataStore store, int series)`
`private java.lang.Integer`	`readEntry()`
`private java.lang.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.IFormatHandler
getFormat, getNativeDataType, getSuffixes

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

Methods inherited from interface loci.formats.ICompressedTileReader
getTileCodec, getTileCodecOptions, openCompressedBytes, openCompressedBytes

- Field Detail
  - MDB_SUFFIX
```
public static final java.lang.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<java.lang.Integer,java.lang.String> METADATA_KEYS
```
  - pixelSizeX
```
private double pixelSizeX
```
  - pixelSizeY
```
private double pixelSizeY
```
  - pixelSizeZ
```
private double pixelSizeZ
```
  - lut
```
private byte[][][] lut
```
  - timestamps
```
private java.util.List<java.lang.Double> timestamps
```
  - lsmFilenames
```
private java.lang.String[] lsmFilenames
```
  - ifdsList
```
private java.util.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 java.util.List<java.lang.String> imageNames
```
  - binning
```
private java.lang.String binning
```
  - xCoordinates
```
private java.util.List<java.lang.Double> xCoordinates
```
  - yCoordinates
```
private java.util.List<java.lang.Double> yCoordinates
```
  - zCoordinates
```
private java.util.List<java.lang.Double> zCoordinates
```
  - dimensionM
```
private int dimensionM
```
  - dimensionP
```
private int dimensionP
```
  - rotations
```
private int rotations
```
  - phases
```
private int phases
```
  - illuminations
```
private int illuminations
```
  - seriesCounts
```
private java.util.Map<java.lang.String,java.lang.Integer> seriesCounts
```
  - userName
```
private java.lang.String userName
```
  - channelNames
```
private java.lang.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 java.util.Map<java.lang.Integer,java.lang.String> acquiredDate
```
  - channelColor
```
private ome.xml.model.primitives.Color[] channelColor
```
  - isSIM
```
private transient boolean isSIM
```
- 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 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
    
    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(loci.common.RandomAccessInputStream stream)
                   throws java.io.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:
    
    java.io.IOException
  - fileGroupOption
```
public int fileGroupOption(java.lang.String id)
                    throws FormatException,
                           java.io.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
    
    java.io.IOException
    
    See Also:
    
    FormatTools.MUST_GROUP, FormatTools.CAN_GROUP, FormatTools.CANNOT_GROUP
  - 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. 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,
                                   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
  - 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,
                        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 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.
    
    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
  - getMDBFile
```
private java.lang.String getMDBFile(java.lang.String id)
                             throws FormatException,
                                    java.io.IOException
```
    Throws:
    
    FormatException
    
    java.io.IOException
  - getEffectiveSeries
```
private int getEffectiveSeries(int currentSeries)
```
  - getLSMFileFromSeries
```
private java.lang.String getLSMFileFromSeries(int currentSeries)
```
  - getExtraSeries
```
private int getExtraSeries(java.lang.String file)
                    throws FormatException,
                           java.io.IOException
```
    Throws:
    
    FormatException
    
    java.io.IOException
  - getPosition
```
private int getPosition(int currentSeries)
```
  - getCZTag
```
private loci.common.RandomAccessInputStream getCZTag(IFD ifd)
                                              throws FormatException,
                                                     java.io.IOException
```
    Throws:
    
    FormatException
    
    java.io.IOException
  - initMetadata
```
protected void initMetadata(int series)
                     throws FormatException,
                            java.io.IOException
```
    Throws:
    
    FormatException
    
    java.io.IOException
  - populateMetadataStore
```
protected void populateMetadataStore(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
  - parseMDB
```
private java.lang.String[] parseMDB(java.lang.String mdbFile)
                             throws FormatException,
                                    java.io.IOException
```
    Parse a .mdb file and return a list of referenced .lsm files.
    
    Throws:
    
    FormatException
    
    java.io.IOException
  - createKeys
```
private static com.google.common.collect.ImmutableMap<java.lang.Integer,java.lang.String> createKeys()
```
  - readEntry
```
private java.lang.Integer readEntry()
                             throws java.io.IOException
```
    Throws:
    
    java.io.IOException
  - readValue
```
private java.lang.Object readValue()
                            throws java.io.IOException
```
    Throws:
    
    java.io.IOException
  - parseApplicationTags
```
private void parseApplicationTags()
                           throws java.io.IOException
```
    Throws:
    
    java.io.IOException

Class ZeissLSMReader

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

Methods inherited from interface loci.formats.ICompressedTileReader

Field Detail

MDB_SUFFIX

ZEISS_ID

TYPE_SUBBLOCK

TYPE_ASCII

TYPE_LONG

TYPE_RATIONAL

TYPE_DATE

TYPE_BOOLEAN

SUBBLOCK_RECORDING

SUBBLOCK_LASER

SUBBLOCK_TRACK

SUBBLOCK_DETECTION_CHANNEL

SUBBLOCK_ILLUMINATION_CHANNEL

SUBBLOCK_BEAM_SPLITTER

SUBBLOCK_DATA_CHANNEL

SUBBLOCK_TIMER

SUBBLOCK_MARKER

SUBBLOCK_END

RECORDING_NAME

RECORDING_DESCRIPTION

RECORDING_OBJECTIVE

RECORDING_ZOOM

RECORDING_SAMPLE_0TIME

RECORDING_CAMERA_BINNING

TRACK_ACQUIRE

TRACK_TIME_BETWEEN_STACKS

LASER_NAME

LASER_ACQUIRE

LASER_POWER

CHANNEL_DETECTOR_GAIN

CHANNEL_PINHOLE_DIAMETER

CHANNEL_AMPLIFIER_GAIN

CHANNEL_FILTER_SET

CHANNEL_FILTER

CHANNEL_ACQUIRE

CHANNEL_NAME

ILLUM_CHANNEL_NAME

ILLUM_CHANNEL_ATTENUATION

ILLUM_CHANNEL_WAVELENGTH

ILLUM_CHANNEL_ACQUIRE

START_TIME

DATA_CHANNEL_NAME

DATA_CHANNEL_ACQUIRE

BEAM_SPLITTER_FILTER

BEAM_SPLITTER_FILTER_SET

TEXT

LINE

SCALE_BAR

OPEN_ARROW

CLOSED_ARROW

RECTANGLE

ELLIPSE

CLOSED_POLYLINE

OPEN_POLYLINE

CLOSED_BEZIER

OPEN_BEZIER

CIRCLE

PALETTE

POLYLINE_ARROW

BEZIER_WITH_ARROW

ANGLE

CIRCLE_3POINT

METADATA_KEYS

pixelSizeX

pixelSizeY