public class JPKReader extends BaseTiffReader
DATE_FORMATS, LOGGERcanSeparateSeries, equalStrips, ifds, lastPlane, mergeSubIFDs, noSubresolutions, seriesToIFD, subResolutionIFDs, thumbnailIFDs, tiffParser, use64BitcorecoreIndex, datasetDescription, domains, filterMetadata, flattenedResolutions, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataStore, normalizeData, resolution, saveOriginalMetadata, series, suffixNecessary, suffixSufficient, THUMBNAIL_DIMENSIONCOMPRESSION_SUFFIXES, currentId, format, metadataOptions, suffixesCAN_GROUP, CANNOT_GROUP, MUST_GROUP| Constructor and Description |
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JPKReader()
Constructs a new JPK reader.
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| Modifier and Type | Method and Description |
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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.
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boolean |
isThisType(java.lang.String name,
boolean open)
Checks if a file matches the type of this format reader.
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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.
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getExifTagName, getImageCreationDate, initFile, initMetadata, put, put, put, put, put, put, put, put, put, put, putDouble, putInt, putStringclose, get16BitLookupTable, get8BitLookupTable, getIFDs, getOptimalTileHeight, getOptimalTileWidth, getThumbnailIFDs, getThumbSizeX, getThumbSizeY, initTiffParser, isThisType, openThumbBytes, reopenFile, setResolutionLevelcoreIndexToSeries, flattenHashtables, getCoreIndex, getCoreMetadataList, getCurrentCore, getResolution, getResolutionCount, getSeries, getSeriesCount, seriesToCoreIndex, setCoreIndex, setResolution, setSeriesaddGlobalMeta, 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, getAvailableOptions, 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, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, readPlane, readPlane, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, updateMetadataListscheckSuffix, checkSuffix, getFormat, getMetadataOptions, getNativeDataType, getSuffixes, getSupportedMetadataLevels, setMetadataOptionsclone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitgetFormat, getNativeDataType, getSuffixesgetMetadataOptions, getSupportedMetadataLevels, setMetadataOptionspublic boolean isThisType(java.lang.String name,
boolean open)
FormatReaderFormatReader.isThisType(RandomAccessInputStream).isThisType in interface IFormatReaderisThisType in class FormatReaderopen - If true, and the file extension is insufficient to determine
the file type, the (existing) file is opened for further analysis.public byte[] openBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h)
throws FormatException,
java.io.IOException
IFormatReaderopenBytes in interface IFormatReaderopenBytes in class MinimalTiffReaderno - the plane index within the current series.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)protected void initStandardMetadata()
throws FormatException,
java.io.IOException
BaseTiffReaderinitStandardMetadata in class BaseTiffReaderFormatExceptionjava.io.IOExceptionprotected void initMetadataStore()
throws FormatException
BaseTiffReaderBaseTiffReader.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 BaseTiffReaderFormatExceptionCopyright © 2020 Open Microscopy Environment