public class PyramidTiffReader extends BaseTiffReader
| Modifier and Type | Field and Description |
|---|---|
private static org.slf4j.Logger |
LOGGER
Logger for this class.
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DATE_FORMATSequalStrips, ifds, lastPlane, noSubresolutions, seriesToIFD, subResolutionIFDs, thumbnailIFDs, tiffParser, use64Bitcore, coreIndex, 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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PyramidTiffReader()
Constructs a new pyramid TIFF reader.
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| Modifier and Type | Method and Description |
|---|---|
int |
getOptimalTileHeight()
Returns the optimal sub-image height for use with openBytes.
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int |
getOptimalTileWidth()
Returns the optimal sub-image width for use with openBytes.
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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(loci.common.RandomAccessInputStream stream)
Checks if the given stream is a valid stream for this file format.
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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, putInt, putStringclose, get16BitLookupTable, get8BitLookupTable, getIFDs, getThumbnailIFDs, getThumbSizeX, getThumbSizeY, initTiffParser, openThumbBytes, reopenFile, setResolutionLeveladdGlobalMeta, 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, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCoreIndex, getCoreMetadataList, 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, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, 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, seriesToCoreIndex, setCoreIndex, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeriescheckSuffix, checkSuffix, getFormat, getMetadataOptions, getNativeDataType, getSuffixes, getSupportedMetadataLevels, setMetadataOptionsclone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitgetFormat, getNativeDataType, getSuffixesgetMetadataOptions, getSupportedMetadataLevels, setMetadataOptionspublic PyramidTiffReader()
public boolean isThisType(loci.common.RandomAccessInputStream stream)
throws java.io.IOException
IFormatReaderisThisType in interface IFormatReaderisThisType in class MinimalTiffReaderjava.io.IOExceptionpublic 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 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 int getOptimalTileWidth()
IFormatReadergetOptimalTileWidth in interface IFormatReadergetOptimalTileWidth in class MinimalTiffReaderpublic int getOptimalTileHeight()
IFormatReadergetOptimalTileHeight in interface IFormatReadergetOptimalTileHeight in class MinimalTiffReaderprotected 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 © 2017 Open Microscopy Environment