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java.lang.Objectloci.formats.FormatHandler
loci.formats.FormatReader
loci.formats.in.SDTReader
public class SDTReader
SDTReader is the file format reader for Becker & Hickl SPC-Image SDT files.
Field Summary | |
---|---|
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 |
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collectMetadata, core, filterMetadata, group, in, metadata, metadataStore, normalizeData, saveOriginalMetadata, series, THUMBNAIL_DIMENSION |
Fields inherited from class loci.formats.FormatHandler |
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currentId, debug, debugLevel, format, statusListeners, suffixes |
Fields inherited from interface loci.formats.IFormatReader |
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CAN_GROUP, CANNOT_GROUP, MUST_GROUP |
Constructor Summary | |
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SDTReader()
Constructs a new SDT reader. |
Method Summary | |
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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.FormatHandler |
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addStatusListener, debug, getFormat, getStatusListeners, getSuffixes, isThisType, isThisType, removeStatusListener, setDebug, setDebugLevel, setId, status, status, status, trace, trace |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface loci.formats.IFormatHandler |
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getFormat, getSuffixes, isThisType, isThisType, setId |
Methods inherited from interface loci.formats.StatusReporter |
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addStatusListener, getStatusListeners, removeStatusListener |
Field Detail |
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protected SDTInfo info
protected int off
protected int timeBins
protected int channels
protected boolean intensity
Constructor Detail |
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public SDTReader()
Method Detail |
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public void setIntensity(boolean intensity)
public boolean isIntensity()
public int getTimeBinCount()
public int getChannelCount()
public SDTInfo getInfo()
public boolean isThisType(byte[] block)
IFormatReader
public int[] getChannelDimLengths()
IFormatReader
getChannelDimLengths
in interface IFormatReader
getChannelDimLengths
in class FormatReader
public String[] getChannelDimTypes()
IFormatReader
FormatTools
.
getChannelDimTypes
in interface IFormatReader
getChannelDimTypes
in class FormatReader
public boolean isInterleaved(int subC)
IFormatReader
SDTReader
handles spectral-lifetime data with
the interleaved lifetime bins and non-interleaved spectral channels.
isInterleaved
in interface IFormatReader
isInterleaved
in class FormatReader
public byte[] openBytes(int no, byte[] buf) throws FormatException, IOException
IFormatReader
no
- the image index within the file.buf
- a pre-allocated buffer.
buf
for convenience.
FormatException
- if there was a problem parsing the metadata of the
file.
IOException
- if there was a problem reading the file.protected void initFile(String id) throws FormatException, IOException
initFile
in class FormatReader
FormatException
IOException
public int getTimeBinCount(String id) throws FormatException, IOException
getTimeBinCount()
FormatException
IOException
public int getChannelCount(String id) throws FormatException, IOException
getChannelCount()
FormatException
IOException
public SDTInfo getInfo(String id) throws FormatException, IOException
getInfo()
FormatException
IOException
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