loci.formats.in
Class ZeissLSMReader

java.lang.Object
  extended by loci.formats.FormatHandler
      extended by loci.formats.FormatReader
          extended by loci.formats.in.BaseTiffReader
              extended by 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