loci.formats.in

Class SDTReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.SDTReader

All Implemented Interfaces:

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

public class SDTReader
extends FormatReader

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

Author:

Curtis Rueden ctrueden at wisc.edu Please Note: This format holds FLIM data arranged so that each decay is stored contiguously. Therefore, as in other FLIM format readers e.g. SDTReader.java, on the first call to openBytes the whole data cube (x, y, t) (NB actually t, not real-time T) is loaded from the file and buffered. On further calls to openBytes the appropriate 2D (x, y) plane (timebin) is returned from this buffer. This is in the interest of significantly improved performance when all the planes are requested one after another. There will be a performance cost if a single plane is requested but this is highly unlikely for FLIM data. In order to limit the size of the buffer, beyond a certain size threshold only a subset of planes (a Block) are retained in the buffer.

Field Summary

Fields

Modifier and Type	Field and 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 and Description
SDTReader() Constructs a new SDT reader.

Method Summary

Modifier and Type	Method and Description
void	close(boolean fileOnly) Closes the currently open file.
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(java.lang.String id) Initializes the given file (parsing header information, etc.).
boolean	isIntensity() Gets whether the reader is combining each lifetime histogram into a summed intensity image plane.
boolean	isInterleaved(int subC) Gets whether or not the given sub-channel is interleaved.
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.
private void	readPixels(byte[] rowBuf, loci.common.RandomAccessInputStream in, java.util.zip.ZipInputStream codec, long skip)
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.IFormatHandler

getFormat, getNativeDataType, getSuffixes

Methods inherited from interface loci.formats.IMetadataConfigurable

getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

Methods inherited from interface loci.formats.ICompressedTileReader

getTileCodec, getTileCodecOptions, openCompressedBytes, openCompressedBytes

Field Detail

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 Detail

SDTReader

public SDTReader()

Constructs a new SDT reader.

Method Detail

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)

Description copied from interface: IFormatReader

Gets whether or not the given sub-channel is interleaved. This method exists because some data with multiple rasterized sub-dimensions within C have one sub-dimension interleaved, and the other not—e.g., SDTReader handles spectral-lifetime data with interleaved lifetime bins and non-interleaved spectral channels.

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,
                        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 plane index within the current series.

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

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

readPixels

private void readPixels(byte[] rowBuf,
                        loci.common.RandomAccessInputStream in,
                        java.util.zip.ZipInputStream codec,
                        long skip)
                 throws java.io.IOException

Throws:

java.io.IOException