loci.formats.in
Class ZeissLSMReader

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

All Implemented Interfaces:

loci.formats.IFormatHandler, loci.formats.IFormatReader, loci.formats.StatusReporter

public class ZeissLSMReader
extends BaseTiffReader

ZeissLSMReader is the file format reader for Zeiss LSM files.

Source code:

Trac, SVN

Author:

Eric Kjellman egkjellman at wisc.edu, Melissa Linkert linkert at wisc.edu, Curtis Rueden ctrueden at wisc.edu

Field Summary

Fields inherited from class loci.formats.in.BaseTiffReader

ifds

Fields inherited from class loci.formats.FormatReader

collectMetadata, core, filterMetadata, group, in, metadata, metadataStore, normalizeData, saveOriginalMetadata, series, THUMBNAIL_DIMENSION

Fields inherited from class loci.formats.FormatHandler

currentId, debug, debugLevel, format, statusListeners, suffixes

Fields inherited from interface loci.formats.IFormatReader

CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

ZeissLSMReader()
Constructs a new Zeiss LSM reader.

Method Summary

protected void	initFile(String id)
protected void	initMetadata() Populates the metadata hashtable and metadata store.
boolean	isThisType(byte[] block)
byte[]	openBytes(int no, byte[] buf)
BufferedImage	openThumbImage(int no)
protected void	parseOverlays(long data, String suffix, boolean little) Parses overlay-related fields.
protected void	parseSubBlocks(long data, String suffix, boolean little) Parses subblock-related fields.

Methods inherited from class loci.formats.in.BaseTiffReader

get16BitLookupTable, get8BitLookupTable, getImageCreationDate, getImageDescription, getImageName, getMetadataValue, getTiffDimensions, initMetadataStore, initStandardMetadata, put, put, put, put, put, put, put, put, put, put, putInt, swapIfRequired

Methods inherited from class loci.formats.FormatReader

addMeta, checkBytes, close, close, fileGroupOption, getChannelDimLengths, getChannelDimLengths, getChannelDimTypes, getChannelDimTypes, getCoreMetadata, getCoreMetadata, getCurrentFile, getDimensionOrder, getDimensionOrder, getEffectiveSizeC, getEffectiveSizeC, getImageCount, getImageCount, getIndex, getIndex, getMeta, getMetadata, getMetadata, getMetadataStore, getMetadataStore, getMetadataStoreRoot, getMetadataStoreRoot, getMetadataValue, getPixelType, getPixelType, getRGBChannelCount, getRGBChannelCount, getSeries, getSeries, getSeriesCount, getSeriesCount, getSizeC, getSizeC, getSizeT, getSizeT, getSizeX, getSizeX, getSizeY, getSizeY, getSizeZ, getSizeZ, getThumbSizeX, getThumbSizeX, getThumbSizeY, getThumbSizeY, getUsedFiles, getUsedFiles, getZCTCoords, getZCTCoords, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isInterleaved, isInterleaved, isLittleEndian, isLittleEndian, isMetadataCollected, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOrderCertain, isOriginalMetadataPopulated, isRGB, isRGB, isUsedFile, openBytes, openBytes, openBytes, openImage, openImage, openThumbBytes, openThumbBytes, openThumbImage, setGroupFiles, setId, setMetadataCollected, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setSeries, setSeries

Methods inherited from class loci.formats.FormatHandler

addStatusListener, debug, getFormat, getStatusListeners, getSuffixes, isThisType, isThisType, removeStatusListener, setDebug, setDebugLevel, setId, status, status, status, trace, trace

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, getSuffixes, isThisType, isThisType, setId

Methods inherited from interface loci.formats.StatusReporter

addStatusListener, getStatusListeners, removeStatusListener

Constructor Detail

ZeissLSMReader

public ZeissLSMReader()

Constructs a new Zeiss LSM reader.

Method Detail

isThisType

public boolean isThisType(byte[] block)

Specified by:

isThisType in interface loci.formats.IFormatReader

Overrides:

isThisType in class BaseTiffReader

openBytes

public byte[] openBytes(int no,
                        byte[] buf)
                 throws loci.formats.FormatException,
                        IOException

Specified by:

openBytes in interface loci.formats.IFormatReader

Overrides:

openBytes in class BaseTiffReader

Throws:

loci.formats.FormatException

IOException

openThumbImage

public BufferedImage openThumbImage(int no)
                             throws loci.formats.FormatException,
                                    IOException

Specified by:

openThumbImage in interface loci.formats.IFormatReader

Overrides:

openThumbImage in class loci.formats.FormatReader

Throws:

loci.formats.FormatException

IOException

initMetadata

protected void initMetadata()

Description copied from class: BaseTiffReader

Populates the metadata hashtable and metadata store.

Overrides:

initMetadata in class BaseTiffReader

initFile

protected void initFile(String id)
                 throws loci.formats.FormatException,
                        IOException

Overrides:

initFile in class BaseTiffReader

Throws:

loci.formats.FormatException

IOException

parseOverlays

protected void parseOverlays(long data,
                             String suffix,
                             boolean little)
                      throws IOException

Parses overlay-related fields.

Throws:

IOException

parseSubBlocks

protected void parseSubBlocks(long data,
                              String suffix,
                              boolean little)
                       throws IOException,
                              loci.formats.FormatException

Parses subblock-related fields.

Throws:

IOException

loci.formats.FormatException