Package loci.formats.in

Class SDTReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.SDTReader

All Implemented Interfaces:

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

public class SDTReader
extends FormatReader

SDTReader is the file format reader for Becker & Hickl SPC-Image SDT files.

Field Summary

Fields

Modifier and Type	Field	Description
protected int	blockLength	No of timeBins pre-loaded as a block
protected int	channels	Number of spectral channels.
protected int	currentBlock	Block of time bins currently stored for faster loading.
protected byte[]	dataStore
protected SDTInfo	info	Object containing SDT header information.
protected boolean	intensity	Whether to combine lifetime bins into single intensity image planes.
protected boolean	preLoad	Whether to pre-load all lifetime bins for faster loading.
protected int	storedChannel
protected int	storedSeries
protected int	timeBins	Number of time bins in lifetime histogram.

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
SDTReader()	Constructs a new SDT reader.

Method Summary

Modifier and Type	Method	Description
void	close(boolean fileOnly)
int	getChannelCount()	Gets the number of spectral channels.
SDTInfo	getInfo()	Gets object containing SDT header information.
int	getTimeBinCount()	Gets the number of bins in the lifetime histogram.
protected void	initFile(String id)
boolean	isIntensity()	Gets whether the reader is combining each lifetime histogram into a summed intensity image plane.
boolean	isInterleaved(int subC)
byte[]	openBytes(int no, byte[] buf, int x, int y, int w, int h)
void	setIntensity(boolean intensity)	Toggles whether the reader should return intensity data only (the sum of each lifetime histogram).
void	setPreLoad(boolean preLoad)	Toggles whether the reader should pre-load data for increased performance.

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, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getThumbSizeX, getThumbSizeY, getTileColumns, getTileRows, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, isThisType, isThisType, 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

info

protected SDTInfo info

Object containing SDT header information.

timeBins

protected int timeBins

Number of time bins in lifetime histogram.

channels

protected int channels

Number of spectral channels.

intensity

protected boolean intensity

Whether to combine lifetime bins into single intensity image planes.

preLoad

protected boolean preLoad

Whether to pre-load all lifetime bins for faster loading.

storedChannel

protected int storedChannel

storedSeries

protected int storedSeries

dataStore

protected byte[] dataStore

currentBlock

protected int currentBlock

Block of time bins currently stored for faster loading.

blockLength

protected int blockLength

No of timeBins pre-loaded as a block

Constructor Details

SDTReader

public SDTReader()

Constructs a new SDT reader.

Method Details

setIntensity

public void setIntensity(boolean intensity)

Toggles whether the reader should return intensity data only (the sum of each lifetime histogram).

setPreLoad

public void setPreLoad(boolean preLoad)

Toggles whether the reader should pre-load data for increased performance.

isIntensity

public boolean isIntensity()

Gets whether the reader is combining each lifetime histogram into a summed intensity image plane.

getTimeBinCount

public int getTimeBinCount()

Gets the number of bins in the lifetime histogram.

getChannelCount

public int getChannelCount()

Gets the number of spectral channels.

getInfo

public SDTInfo getInfo()

Gets object containing SDT header information.

isInterleaved

public boolean isInterleaved(int subC)

Specified by:

isInterleaved in interface IFormatReader

Overrides:

isInterleaved 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

initFile

protected void initFile(String id)
                 throws FormatException,
IOException

Overrides:

initFile in class FormatReader

Throws:

FormatException

IOException