loci.formats.in

Class SDTReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.SDTReader

All Implemented Interfaces:

Closeable, AutoCloseable, IFormatHandler, IFormatReader, IMetadataConfigurable

public class SDTReader
extends FormatReader

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

Source code:

Trac, Gitweb

Author:

Curtis Rueden ctrueden at wisc.edu

Field Summary

Fields

Modifier and Type	Field and Description
protected int	channels Number of spectral channels.
protected SDTInfo	info Object containing SDT header information.
protected boolean	intensity Whether to combine lifetime bins into single intensity image planes.
protected int	off Offset to binary data.
protected int	timeBins Number of time bins in lifetime histogram.

Fields inherited from class loci.formats.FormatReader

core, 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
SDTReader() Constructs a new SDT reader.

Method Summary

Methods

Modifier and Type	Method and Description
void	close(boolean fileOnly) Closes the currently open file.
int	getChannelCount() Gets the number of spectral channels.
int[]	getChannelDimLengths() Gets the lengths of each subdimension of C, in fastest-to-slowest rasterization order.
String[]	getChannelDimTypes() Gets the name of each subdimension of C, in fastest-to-slowest rasterization order.
SDTInfo	getInfo() Gets object containing SDT header information.
int	getTimeBinCount() Gets the number of bins in the lifetime histogram.
protected void	initFile(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.
void	setIntensity(boolean intensity) Toggles whether the reader should return intensity data only (the sum of each lifetime histogram).

Methods inherited from class loci.formats.FormatReader

addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, close, coreIndexToSeries, fileGroupOption, get16BitLookupTable, get8BitLookupTable, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCoreIndex, getCoreMetadata, 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, getMetadata, getMetadataOptions, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getMicrobeamManipulationType, getMicroscopeType, getNamingConvention, getOptimalTileHeight, getOptimalTileWidth, getPixelType, getPixelType, getPossibleDomains, getPulse, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getSupportedMetadataLevels, getThumbSizeX, getThumbSizeY, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isLittleEndian, isMetadataCollected, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, isThisType, isThisType, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, seriesToCoreIndex, setFlattenedResolutions, setGroupFiles, setId, setMetadataCollected, 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

info

protected SDTInfo info

Object containing SDT header information.

off

protected int off

Offset to binary data.

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.

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).

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.

getChannelDimLengths

public int[] getChannelDimLengths()

Description copied from interface: IFormatReader

Gets the lengths of each subdimension of C, in fastest-to-slowest rasterization order.

Specified by:

getChannelDimLengths in interface IFormatReader

Overrides:

getChannelDimLengths in class FormatReader

getChannelDimTypes

public String[] getChannelDimTypes()

Description copied from interface: IFormatReader

Gets the name of each subdimension of C, in fastest-to-slowest rasterization order. Common subdimensional types are enumerated in FormatTools.

Specified by:

getChannelDimTypes in interface IFormatReader

Overrides:

getChannelDimTypes in class FormatReader

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,
                        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.

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 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:

IOException

initFile

protected void initFile(String id)
                 throws FormatException,
                        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.

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