Package loci.formats.in

Class DeltavisionReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.DeltavisionReader

All Implemented Interfaces:

Closeable, AutoCloseable, ICompressedTileReader, IFormatHandler, IFormatReader, IMetadataConfigurable, IPyramidHandler

Direct Known Subclasses:

RCPNLReader

public class DeltavisionReader
extends FormatReader

DeltavisionReader is the file format reader for Deltavision files.

Field Summary

Fields

Modifier and Type	Field	Description
static final String	DATE_FORMAT	Deprecated. Use DATE_FORMATS instead
static final String[]	DATE_FORMATS
static final int	DV_MAGIC_BYTES_1
static final int	DV_MAGIC_BYTES_2
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	panelSize
protected boolean	positionInT
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

core, coreIndex, datasetDescription, domains, fillColor, filterMetadata, flattenedResolutions, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataStore, normalizeData, resolution, saveOriginalMetadata, series, suffixNecessary, suffixSufficient, THUMBNAIL_DIMENSION

Fields inherited from class loci.formats.FormatHandler

COMPRESSION_SUFFIXES, currentId, format, LOGGER, metadataOptions, suffixes

Fields inherited from interface loci.formats.IFormatReader

CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors

Constructor	Description
DeltavisionReader()	Constructs a new Deltavision reader.

Method Summary

Modifier and Type	Method	Description
void	close(boolean fileOnly)
long	getPlaneByteOffset(int currentZ, int currentW, int currentT)	Given any specific Z, W, and T of a plane, determine the absolute byte offset of the plane in the file.
String[]	getSeriesUsedFiles(boolean noPixels)
protected void	initExtraMetadata()
protected void	initFile(String id)
protected void	initPixels()
boolean	isSingleFile(String id)
boolean	isThisType(String name, boolean open)
boolean	isThisType(RandomAccessInputStream stream)
byte[]	openBytes(int no, byte[] buf, int x, int y, int w, int h)
protected void	populateObjective(MetadataStore store, int lensID)	Populate an Objective based upon the lens ID.
void	setTruncatedFileFlag(boolean truncatedFileFlag)	This flag indicates if the file is known to be truncated.

Methods inherited from class loci.formats.FormatReader

addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMetaList, addMeta, addMetaList, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMetaList, close, coreIndexToSeries, fileGroupOption, flattenHashtables, get16BitLookupTable, get8BitLookupTable, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getAvailableOptions, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCoreIndex, getCoreMetadataList, getCorrection, getCurrentCore, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, getEffectiveSizeC, getExperimentType, getFilamentType, getFillColor, getFillRule, getFilterType, getFontFamily, getFontStyle, getGlobalMeta, getGlobalMetadata, getIlluminationType, getImageCount, getImmersion, getIndex, getIndex, getLaserMedium, getLaserType, getMarker, getMedium, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getMicrobeamManipulationType, getMicroscopeType, getModuloC, getModuloT, getModuloZ, getNamingConvention, getOptimalTileHeight, getOptimalTileWidth, getPixelType, getPixelType, getPossibleDomains, getPulse, getRequiredDirectories, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getThumbSizeX, getThumbSizeY, getTileColumns, getTileRows, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, readPlane, reopenFile, seriesToCoreIndex, setCoreIndex, setFillColor, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries, updateMetadataLists

Methods inherited from class loci.formats.FormatHandler

checkSuffix, checkSuffix, getFormat, getMetadataOptions, getNativeDataType, getSuffixes, getSupportedMetadataLevels, setMetadataOptions

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface loci.formats.ICompressedTileReader

getTileCodec, getTileCodecOptions, openCompressedBytes, openCompressedBytes

Methods inherited from interface loci.formats.IFormatHandler

getFormat, getNativeDataType, getSuffixes

Methods inherited from interface loci.formats.IMetadataConfigurable

getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

Field Details

DV_MAGIC_BYTES_1

public static final int DV_MAGIC_BYTES_1

See Also:

• Constant Field Values

DV_MAGIC_BYTES_2

public static final int DV_MAGIC_BYTES_2

See Also:

• Constant Field Values

DATE_FORMAT

@Deprecated
public static final String DATE_FORMAT

Deprecated.

Use DATE_FORMATS instead

See Also:

• Constant Field Values

DATE_FORMATS

public static final String[] DATE_FORMATS

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.

panelSize

protected int panelSize

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.

positionInT

protected boolean positionInT

Constructor Details

DeltavisionReader

public DeltavisionReader()

Constructs a new Deltavision reader.

Method Details

isSingleFile

public boolean isSingleFile(String id)
                     throws FormatException,
IOException

Specified by:

isSingleFile in interface IFormatReader

Overrides:

isSingleFile in class FormatReader

Throws:

FormatException

IOException

isThisType

public boolean isThisType(String name,
 boolean open)

Specified by:

isThisType in interface IFormatReader

Overrides:

isThisType in class FormatReader

isThisType

public boolean isThisType(RandomAccessInputStream stream)
                   throws IOException

Specified by:

isThisType in interface IFormatReader

Overrides:

isThisType in class FormatReader

Throws:

IOException

getSeriesUsedFiles

public String[] getSeriesUsedFiles(boolean noPixels)

Specified by:

getSeriesUsedFiles in interface IFormatReader

Overrides:

getSeriesUsedFiles in class FormatReader

openBytes

public byte[] openBytes(int no,
 byte[] buf,
 int x,
 int y,
 int w,
 int h)
                 throws FormatException,
IOException

Specified by:

openBytes in interface IFormatReader

Specified by:

openBytes in class FormatReader

Throws:

FormatException

IOException

See Also:

• IFormatReader.openBytes(int, byte[], int, int, int, int)

close

public void close(boolean fileOnly)
           throws IOException

Specified by:

close in interface IFormatReader

Overrides:

close in class FormatReader

Throws:

IOException

setTruncatedFileFlag

public void setTruncatedFileFlag(boolean truncatedFileFlag)

This flag indicates if the file is known to be truncated. If true, the dimension size information is kept as it is specified in the file header, otherwise the length of the file is used to override size information. This flag must be set before FormatReader.setId(String) is called. Default is false.

initFile

protected void initFile(String id)
                 throws FormatException,
IOException

Overrides:

initFile in class FormatReader

Throws:

FormatException

IOException

initPixels

protected void initPixels()
                   throws FormatException,
IOException

Throws:

FormatException

IOException

initExtraMetadata

protected void initExtraMetadata()
                          throws FormatException,
IOException

Throws:

FormatException

IOException

getPlaneByteOffset

public long getPlaneByteOffset(int currentZ,
 int currentW,
 int currentT)

Given any specific Z, W, and T of a plane, determine the absolute byte offset of the plane in the file.

Parameters:

currentZ -

currentW -

currentT -

populateObjective

protected void populateObjective(MetadataStore store,
 int lensID)
                          throws FormatException

Populate an Objective based upon the lens ID. This is based upon information received from Applied Precision.

Throws:

FormatException