loci.formats.in
Class DeltavisionReader

java.lang.Object
  loci.formats.FormatHandler
      loci.formats.FormatReader
          loci.formats.in.DeltavisionReader

All Implemented Interfaces:

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

public class DeltavisionReader
extends loci.formats.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)
boolean	isThisType(byte[] block)
byte[]	openBytes(int no, byte[] buf)

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)

openBytes

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

Throws:

loci.formats.FormatException

IOException

initFile

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

Overrides:

initFile in class loci.formats.FormatReader

Throws:

loci.formats.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 -