public class SDTReader extends FormatReader
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.
|
core, coreIndex, datasetDescription, domains, filterMetadata, flattenedResolutions, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataStore, normalizeData, resolution, saveOriginalMetadata, series, suffixNecessary, suffixSufficient, THUMBNAIL_DIMENSION
COMPRESSION_SUFFIXES, currentId, format, LOGGER, metadataOptions, suffixes
CAN_GROUP, CANNOT_GROUP, MUST_GROUP
Constructor and Description |
---|
SDTReader()
Constructs a new SDT reader.
|
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.
|
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, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCoreIndex, getCoreMetadataList, getCorrection, getCurrentCore, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, getEffectiveSizeC, getExperimentType, getFilamentType, 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, 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, reopenFile, seriesToCoreIndex, setCoreIndex, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries, updateMetadataLists
checkSuffix, checkSuffix, getFormat, getMetadataOptions, getNativeDataType, getSuffixes, getSupportedMetadataLevels, setMetadataOptions
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
getFormat, getNativeDataType, getSuffixes
getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions
protected SDTInfo info
protected int timeBins
protected int channels
protected boolean intensity
protected boolean preLoad
protected int storedChannel
protected int storedSeries
protected byte[] dataStore
protected int currentBlock
protected int blockLength
public void setIntensity(boolean intensity)
public void setPreLoad(boolean preLoad)
public boolean isIntensity()
public int getTimeBinCount()
public int getChannelCount()
public SDTInfo getInfo()
public boolean isInterleaved(int subC)
IFormatReader
SDTReader
handles spectral-lifetime data with
interleaved lifetime bins and non-interleaved spectral channels.isInterleaved
in interface IFormatReader
isInterleaved
in class FormatReader
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h) throws FormatException, java.io.IOException
IFormatReader
openBytes
in interface IFormatReader
openBytes
in class FormatReader
no
- the image index within the file.buf
- a pre-allocated buffer.x
- X coordinate of the upper-left corner of the sub-imagey
- Y coordinate of the upper-left corner of the sub-imagew
- width of the sub-imageh
- height of the sub-imagebuf
for convenience.FormatException
- if there was a problem parsing the metadata of the
file.java.io.IOException
- if there was a problem reading the file.IFormatReader.openBytes(int, byte[], int, int, int, int)
public void close(boolean fileOnly) throws java.io.IOException
IFormatReader
Closeable.close()
.close
in interface IFormatReader
close
in class FormatReader
java.io.IOException
protected void initFile(java.lang.String id) throws FormatException, java.io.IOException
FormatReader
initFile
in class FormatReader
FormatException
- if a parsing error occurs processing the file.java.io.IOException
- if an I/O error occurs processing the fileprivate void readPixels(byte[] rowBuf, loci.common.RandomAccessInputStream in, java.util.zip.ZipInputStream codec, long skip) throws java.io.IOException
java.io.IOException
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