loci.formats.in
Class DeltavisionReader

java.lang.Object
  extended by loci.formats.FormatHandler
      extended by loci.formats.FormatReader
          extended by loci.formats.in.DeltavisionReader
All Implemented Interfaces:
IFormatHandler, IFormatReader, StatusReporter

public class DeltavisionReader
extends FormatReader

DeltavisionReader is the file format reader for Deltavision files.

Source code:
Trac, SVN

Author:
Melissa Linkert linkert at wisc.edu

Field Summary
protected  loci.formats.in.DeltavisionReader.DVExtHdrFields[][][] extHdrFields
          Initialize an array of Extended Header Field structures.
protected  int numFloatsPerSection
           
protected  int numIntsPerSection
          The number of ints in each extended header section.
protected  int tSize
          Size of one time element in the extended header.
protected  int wSize
          Size of one wave in the extended header.
protected  int zSize
          Size of one z section in the extended header.
 
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
DeltavisionReader()
          Constructs a new Deltavision reader.
 
Method Summary
 int getPlaneNumber(int currentZ, int currentW, int currentT)
          This method returns the a plane number from when given a Z, W and T offsets.
 int getTotalOffset(int currentZ, int currentW, int currentT)
          Given any specific Z, W, and T of a plane, determine the totalOffset from the start of the extended header.
protected  void initFile(String id)
          Initializes the given file (parsing header information, etc.).
 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).
 
Methods inherited from class loci.formats.FormatReader
addMeta, checkBytes, close, close, fileGroupOption, get16BitLookupTable, get8BitLookupTable, getChannelDimLengths, getChannelDimLengths, getChannelDimTypes, getChannelDimTypes, getCoreMetadata, getCoreMetadata, getCurrentFile, getDimensionOrder, getDimensionOrder, getEffectiveSizeC, getEffectiveSizeC, getImageCount, getImageCount, getIndex, getIndex, getMeta, getMetadata, getMetadata, getMetadataStore, getMetadataStore, getMetadataStoreRoot, getMetadataStoreRoot, getMetadataValue, 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, 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
 

Field Detail

wSize

protected int wSize
Size of one wave in the extended header.


zSize

protected int zSize
Size of one z section in the extended header.


tSize

protected int tSize
Size of one time element in the extended header.


numIntsPerSection

protected int numIntsPerSection
The number of ints in each extended header section. These fields appear to be all blank but need to be skipped to get to the floats afterwards


numFloatsPerSection

protected int numFloatsPerSection

extHdrFields

protected loci.formats.in.DeltavisionReader.DVExtHdrFields[][][] extHdrFields
Initialize an array of Extended Header Field structures.

Constructor Detail

DeltavisionReader

public DeltavisionReader()
Constructs a new Deltavision 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.


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).

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.

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
IOException

getTotalOffset

public int getTotalOffset(int currentZ,
                          int currentW,
                          int currentT)
Given any specific Z, W, and T of a plane, determine the totalOffset from the start of the extended header.

Parameters:
currentZ -
currentW -
currentT -

getPlaneNumber

public int getPlaneNumber(int currentZ,
                          int currentW,
                          int currentT)
This method returns the a plane number from when given a Z, W and T offsets.

Parameters:
currentZ -
currentW -
currentT -