loci.formats.in

Class SDTReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.SDTReader

All Implemented Interfaces:

loci.formats.IFormatHandler, loci.formats.IFormatReader, loci.formats.StatusReporter

public class SDTReader
extends loci.formats.FormatReader

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

Source code:

Trac, SVN

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

collectMetadata, core, filterMetadata, group, in, metadata, metadataStore, normalizeData, saveOriginalMetadata, series, THUMBNAIL_DIMENSION

Fields inherited from class loci.formats.FormatHandler

currentId, debug, debugLevel, format, statusListeners, 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
int	getChannelCount() Gets the number of spectral channels.
int	getChannelCount(String id) Deprecated. Replaced by getChannelCount()
int[]	getChannelDimLengths() Gets the lengths of each subdimension of C, in fastest-to-sloweset 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.
SDTInfo	getInfo(String id) Deprecated. Replaced by getInfo()
int	getTimeBinCount() Gets the number of bins in the lifetime histogram.
int	getTimeBinCount(String id) Deprecated. Replaced by getTimeBinCount()
protected void	initFile(String id) Initializes the given SDT file.
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.
boolean	isThisType(byte[] block) Checks if the given block is a valid header for this file format.
byte[]	openBytes(int no, byte[] buf) Obtains the specified image from the current file into a pre-allocated byte array of (sizeX * sizeY * bytesPerPixel).
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

addMeta, checkBytes, close, close, fileGroupOption, get16BitLookupTable, get8BitLookupTable, getChannelDimLengths, getChannelDimTypes, getCoreMetadata, getCoreMetadata, getCurrentFile, getDimensionOrder, getDimensionOrder, getEffectiveSizeC, getEffectiveSizeC, getImageCount, getImageCount, getIndex, getIndex, getMeta, getMetadata, getMetadata, getMetadataStore, getMetadataStore, getMetadataStoreRoot, getMetadataStoreRoot, getMetadataValue, getMetadataValue, getPixelType, getPixelType, getRGBChannelCount, getRGBChannelCount, getSeries, getSeries, getSeriesCount, getSeriesCount, getSizeC, getSizeC, getSizeT, getSizeT, getSizeX, getSizeX, getSizeY, getSizeY, getSizeZ, getSizeZ, getThumbSizeX, getThumbSizeX, getThumbSizeY, getThumbSizeY, getUsedFiles, getUsedFiles, getZCTCoords, getZCTCoords, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isInterleaved, isLittleEndian, isLittleEndian, isMetadataCollected, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOrderCertain, isOriginalMetadataPopulated, isRGB, isRGB, isUsedFile, openBytes, openBytes, openBytes, openImage, openImage, openThumbBytes, openThumbBytes, openThumbImage, openThumbImage, setGroupFiles, setId, setMetadataCollected, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setSeries, setSeries

Methods inherited from class loci.formats.FormatHandler

addStatusListener, debug, getFormat, getStatusListeners, getSuffixes, isThisType, isThisType, removeStatusListener, setDebug, setDebugLevel, setId, status, status, status, trace, trace

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, getSuffixes, isThisType, isThisType, setId

Methods inherited from interface loci.formats.StatusReporter

addStatusListener, getStatusListeners, removeStatusListener

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.

isThisType

public boolean isThisType(byte[] block)

Description copied from interface: loci.formats.IFormatReader

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

getChannelDimLengths

public int[] getChannelDimLengths()

Description copied from interface: loci.formats.IFormatReader

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

Specified by:

getChannelDimLengths in interface loci.formats.IFormatReader

Overrides:

getChannelDimLengths in class loci.formats.FormatReader

getChannelDimTypes

public String[] getChannelDimTypes()

Description copied from interface: loci.formats.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 loci.formats.IFormatReader

Overrides:

getChannelDimTypes in class loci.formats.FormatReader

isInterleaved

public boolean isInterleaved(int subC)

Description copied from interface: loci.formats.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 the interleaved lifetime bins and non-interleaved spectral channels.

Specified by:

isInterleaved in interface loci.formats.IFormatReader

Overrides:

isInterleaved in class loci.formats.FormatReader

openBytes

public byte[] openBytes(int no,
               byte[] buf)
                 throws loci.formats.FormatException,
                        IOException

Description copied from interface: loci.formats.IFormatReader

Obtains the specified image from the current file into a pre-allocated byte array of (sizeX * sizeY * bytesPerPixel).

Parameters:

no - the image index within the file.

buf - a pre-allocated buffer.

Returns:

the pre-allocated buffer buf for convenience.

Throws:

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

IOException - if there was a problem reading the file.

initFile

protected void initFile(String id)
                 throws loci.formats.FormatException,
                        IOException

Initializes the given SDT file.

Overrides:

initFile in class loci.formats.FormatReader

Throws:

loci.formats.FormatException

IOException

getTimeBinCount

public int getTimeBinCount(String id)
                    throws loci.formats.FormatException,
                           IOException

Deprecated. Replaced by getTimeBinCount()

Throws:

loci.formats.FormatException

IOException

getChannelCount

public int getChannelCount(String id)
                    throws loci.formats.FormatException,
                           IOException

Deprecated. Replaced by getChannelCount()

Throws:

loci.formats.FormatException

IOException

getInfo

public SDTInfo getInfo(String id)
                throws loci.formats.FormatException,
                       IOException

Deprecated. Replaced by getInfo()

Throws:

loci.formats.FormatException

IOException