loci.formats.in

Class DeltavisionReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.DeltavisionReader

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable, IFormatHandler, IFormatReader, IMetadataConfigurable

public class DeltavisionReader
extends FormatReader

DeltavisionReader is the file format reader for Deltavision files.

Source code:

Trac, Gitweb

Author:

Melissa Linkert melissa at glencoesoftware.com

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	DATE_FORMAT
static int	DV_MAGIC_BYTES_1
static 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	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, filterMetadata, flattenedResolutions, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataOptions, metadataStore, normalizeData, resolution, saveOriginalMetadata, series, suffixNecessary, suffixSufficient, THUMBNAIL_DIMENSION

Fields inherited from class loci.formats.FormatHandler

COMPRESSION_SUFFIXES, currentId, format, LOGGER, suffixes

Fields inherited from interface loci.formats.IFormatReader

CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors

Constructor and Description
DeltavisionReader() Constructs a new Deltavision reader.

Method Summary

Methods

Modifier and Type	Method and Description
void	close(boolean fileOnly) Closes the currently open file.
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.
java.lang.String[]	getSeriesUsedFiles(boolean noPixels) Returns an array of filenames needed to open the current series.
protected void	initExtraMetadata()
protected void	initFile(java.lang.String id) Initializes the given file (parsing header information, etc.).
protected void	initPixels()
boolean	isSingleFile(java.lang.String id) Returns true if this is a single-file format.
boolean	isThisType(RandomAccessInputStream stream) Checks if the given stream is a valid stream for this file format.
boolean	isThisType(java.lang.String name, boolean open) Checks if a file matches the type of this format reader.
byte[]	openBytes(int no, byte[] buf, int x, int y, int w, int h) Obtains a sub-image of the specified image plane into a pre-allocated byte array.
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, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMetaList, close, coreIndexToSeries, fileGroupOption, flattenHashtables, get16BitLookupTable, get8BitLookupTable, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getBinning, getBitsPerPixel, getChannelDimLengths, getChannelDimTypes, getCompression, getContrastMethod, getCoreIndex, getCoreMetadata, getCoreMetadataList, getCorrection, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, getEffectiveSizeC, getExperimentType, getFilamentType, getFillRule, getFilterType, getFontFamily, getFontStyle, getGlobalMeta, getGlobalMetadata, getIlluminationType, getImageCount, getImmersion, getIndex, getLaserMedium, getLaserType, getLineCap, getMarker, getMedium, getMetadataOptions, 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, getSupportedMetadataLevels, getThumbSizeX, getThumbSizeY, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, 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, seriesToCoreIndex, setCoreIndex, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataOptions, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries

Methods inherited from class loci.formats.FormatHandler

checkSuffix, checkSuffix, getFormat, getNativeDataType, getSuffixes

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, getNativeDataType, getSuffixes

Field Detail

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

public static final java.lang.String DATE_FORMAT

See Also:

Constant Field Values

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

isSingleFile

public boolean isSingleFile(java.lang.String id)
                     throws FormatException,
                            java.io.IOException

Description copied from interface: IFormatReader

Returns true if this is a single-file format.

Specified by:

isSingleFile in interface IFormatReader

Overrides:

isSingleFile in class FormatReader

Throws:

FormatException

java.io.IOException

isThisType

public boolean isThisType(java.lang.String name,
                 boolean open)

Description copied from class: FormatReader

Checks if a file matches the type of this format reader. Checks filename suffixes against those known for this format. If the suffix check is inconclusive and the open parameter is true, the file is opened and tested with FormatReader.isThisType(RandomAccessInputStream).

Specified by:

isThisType in interface IFormatReader

Overrides:

isThisType in class FormatReader

open - If true, and the file extension is insufficient to determine the file type, the (existing) file is opened for further analysis.

isThisType

public boolean isThisType(RandomAccessInputStream stream)
                   throws java.io.IOException

Description copied from interface: IFormatReader

Checks if the given stream is a valid stream for this file format.

Specified by:

isThisType in interface IFormatReader

Overrides:

isThisType in class FormatReader

Throws:

java.io.IOException

getSeriesUsedFiles

public java.lang.String[] getSeriesUsedFiles(boolean noPixels)

Description copied from interface: IFormatReader

Returns an array of filenames needed to open the current series. If the 'noPixels' flag is set, then only files that do not contain pixel data will be returned.

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,
                        java.io.IOException

Description copied from interface: IFormatReader

Obtains a sub-image of the specified image plane into a pre-allocated byte array.

Specified by:

openBytes in interface IFormatReader

Specified by:

openBytes in class FormatReader

Parameters:

no - the image index within the file.

buf - a pre-allocated buffer.

x - X coordinate of the upper-left corner of the sub-image

y - Y coordinate of the upper-left corner of the sub-image

w - width of the sub-image

h - height of the sub-image

Returns:

the pre-allocated buffer buf for convenience.

Throws:

FormatException - if there was a problem parsing the metadata of the file.

java.io.IOException - if there was a problem reading the file.

See Also:

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

close

public void close(boolean fileOnly)
           throws java.io.IOException

Description copied from interface: IFormatReader

Closes the currently open file. If the flag is set, this is all that happens; if unset, it is equivalent to calling Closeable.close().

Specified by:

close in interface IFormatReader

Overrides:

close in class FormatReader

Throws:

java.io.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(java.lang.String id)
                 throws FormatException,
                        java.io.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 - if a parsing error occurs processing the file.

java.io.IOException - if an I/O error occurs processing the file

initPixels

protected void initPixels()
                   throws FormatException,
                          java.io.IOException

Throws:

FormatException

java.io.IOException

initExtraMetadata

protected void initExtraMetadata()
                          throws FormatException,
                                 java.io.IOException

Throws:

FormatException

java.io.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 -