public class SISReader extends BaseTiffReader
Modifier and Type | Field and Description |
---|---|
private java.lang.String |
acquisitionDate |
private java.lang.String |
cameraName |
private java.lang.String |
channelName |
private java.lang.String |
imageName |
private double |
magnification |
private double |
physicalSizeX |
private double |
physicalSizeY |
private static int |
SIS_INI_TAG |
private static int |
SIS_TAG |
private static int |
SIS_TAG_2 |
DATE_FORMATS, LOGGER
canSeparateSeries, equalStrips, ifds, lastPlane, mergeSubIFDs, noSubresolutions, seriesToIFD, subResolutionIFDs, thumbnailIFDs, tiffParser, use64Bit
core
coreIndex, datasetDescription, domains, filterMetadata, flattenedResolutions, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataStore, normalizeData, resolution, saveOriginalMetadata, series, suffixNecessary, suffixSufficient, THUMBNAIL_DIMENSION
COMPRESSION_SUFFIXES, currentId, format, metadataOptions, suffixes
CAN_GROUP, CANNOT_GROUP, MUST_GROUP
Constructor and Description |
---|
SISReader() |
Modifier and Type | Method and Description |
---|---|
void |
close(boolean fileOnly)
Closes the currently open file.
|
protected void |
initMetadataStore()
Populates the metadata store using the data parsed in
BaseTiffReader.initStandardMetadata() along with some further parsing done in
the method itself. |
protected void |
initStandardMetadata()
Parses standard metadata.
|
boolean |
isThisType(loci.common.RandomAccessInputStream stream)
Checks if the given stream is a valid stream for this file format.
|
getExifTagName, getImageCreationDate, initFile, initMetadata, put, put, put, put, put, put, put, put, put, put, putDouble, putInt, putString
get16BitLookupTable, get8BitLookupTable, getIFDs, getOptimalTileHeight, getOptimalTileWidth, getThumbnailIFDs, getThumbSizeX, getThumbSizeY, initTiffParser, openBytes, openThumbBytes, reopenFile, setResolutionLevel
coreIndexToSeries, flattenHashtables, getCoreIndex, getCoreMetadataList, getCurrentCore, getResolution, getResolutionCount, getSeries, getSeriesCount, seriesToCoreIndex, setCoreIndex, setResolution, setSeries
addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMetaList, addMeta, addMetaList, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMetaList, close, fileGroupOption, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCorrection, 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, getPixelType, getPixelType, getPossibleDomains, getPulse, getRequiredDirectories, getRGBChannelCount, getRotationTransform, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, isThisType, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, readPlane, readPlane, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, 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
private static final int SIS_TAG
private static final int SIS_INI_TAG
private static final int SIS_TAG_2
private java.lang.String imageName
private double magnification
private java.lang.String channelName
private java.lang.String cameraName
private double physicalSizeX
private double physicalSizeY
private java.lang.String acquisitionDate
public boolean isThisType(loci.common.RandomAccessInputStream stream) throws java.io.IOException
IFormatReader
isThisType
in interface IFormatReader
isThisType
in class MinimalTiffReader
stream
- A RandomAccessInputStream representing the file to check.
The first byte in the stream is assumed to be the first byte
in the file.java.io.IOException
public void close(boolean fileOnly) throws java.io.IOException
IFormatReader
Closeable.close()
.close
in interface IFormatReader
close
in class MinimalTiffReader
java.io.IOException
protected void initStandardMetadata() throws FormatException, java.io.IOException
BaseTiffReader
initStandardMetadata
in class BaseTiffReader
FormatException
java.io.IOException
protected void initMetadataStore() throws FormatException
BaseTiffReader
BaseTiffReader.initStandardMetadata()
along with some further parsing done in
the method itself.
All calls to the active MetadataStore
should be made in this
method and only in this method. This is especially important for
sub-classes that override the getters for pixel set array size, etc.initMetadataStore
in class BaseTiffReader
FormatException
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