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:
IFormatHandler, IFormatReader, 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)
          Initializes the given file (parsing header information, etc.).
protected  void initMetadata()
          Populates the metadata hashtable and metadata store.
 boolean isThisType(byte[] block)
          Checks if the given block is a valid header for this file format.
 byte[] openBytes(int no, byte[] buf)
          Obtains the specified image from the current file into a pre-allocated byte array of (sizeX * sizeY * bytesPerPixel).
 BufferedImage openThumbImage(int no)
          Obtains a thumbnail for the specified image from the current file.
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)
Description copied from interface: IFormatReader
Checks if the given block is a valid header for this file format.

Specified by:
isThisType in interface IFormatReader
Overrides:
isThisType in class BaseTiffReader

openBytes

public byte[] openBytes(int no,
                        byte[] buf)
                 throws FormatException,
                        IOException
Description copied from interface: IFormatReader
Obtains the specified image from the current file into a pre-allocated byte array of (sizeX * sizeY * bytesPerPixel).

Specified by:
openBytes in interface IFormatReader
Overrides:
openBytes in class BaseTiffReader
Parameters:
no - the image index within the file.
buf - a pre-allocated buffer.
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.

openThumbImage

public BufferedImage openThumbImage(int no)
                             throws FormatException,
                                    IOException
Description copied from interface: IFormatReader
Obtains a thumbnail for the specified image from the current file.

Specified by:
openThumbImage in interface IFormatReader
Overrides:
openThumbImage in class FormatReader
Throws:
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 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 BaseTiffReader
Throws:
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,
                              FormatException
Parses subblock-related fields.

Throws:
IOException
FormatException