Package loci.formats.in

Class OMETiffReader

java.lang.Object
loci.formats.FormatHandler
loci.formats.FormatReader
loci.formats.SubResolutionFormatReader
loci.formats.in.OMETiffReader
All Implemented Interfaces:
Closeable, AutoCloseable, loci.formats.ICompressedTileReader, loci.formats.IFormatHandler, loci.formats.IFormatReader, loci.formats.IMetadataConfigurable, loci.formats.IPyramidHandler
public class OMETiffReader extends loci.formats.SubResolutionFormatReader
OMETiffReader is the file format reader for OME-TIFF files.

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final boolean
    FAIL_ON_MISSING_DEFAULT
     
    static final String
    FAIL_ON_MISSING_KEY
     
    protected loci.formats.in.OMETiffReader.OMETiffPlane[][]
    info
    Mapping from series and plane numbers to files and IFD entries.
    static final String[]
    OME_TIFF_SUFFIXES
     
    protected String[]
    used
    List of used files.

    Fields inherited from class loci.formats.SubResolutionFormatReader

    core

    Fields inherited from class loci.formats.FormatReader

    coreIndex, datasetDescription, domains, fillColor, filterMetadata, flattenedResolutions, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataStore, normalizeData, resolution, saveOriginalMetadata, series, suffixNecessary, suffixSufficient, THUMBNAIL_DIMENSION

    Fields inherited from class loci.formats.FormatHandler

    COMPRESSION_SUFFIXES, currentId, format, LOGGER, metadataOptions, suffixes

    Fields inherited from interface loci.formats.IFormatReader

    CAN_GROUP, CANNOT_GROUP, MUST_GROUP

  • Constructor Summary

    Constructors
    Constructor
    Description
    OMETiffReader()
    Constructs a new OME-TIFF reader.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    close(boolean fileOnly)
     
    boolean
    failOnMissingTIFF()
     
    int
    fileGroupOption(String id)
     
    short[][]
    get16BitLookupTable()
     
    byte[][]
    get8BitLookupTable()
     
    protected ArrayList<String>
    getAvailableOptions()
     
    String[]
    getDomains()
     
    loci.formats.meta.MetadataStore
    getMetadataStoreForConversion()
    Deprecated.
    Use the general FormatReader.getMetadataStore() method.
    loci.formats.meta.MetadataStore
    getMetadataStoreForDisplay()
    Deprecated.
    Use the general FormatReader.getMetadataStore() method.
    int
    getOptimalTileHeight()
     
    int
    getOptimalTileWidth()
     
    int
    getRequiredDirectories(String[] files)
     
    String[]
    getSeriesUsedFiles(boolean noPixels)
     
    protected void
    initFile(String id)
     
    boolean
    isSingleFile(String id)
     
    boolean
    isThisType(String name, boolean open)
     
    boolean
    isThisType(RandomAccessInputStream stream)
     
    byte[]
    openBytes(int no, byte[] buf, int x, int y, int w, int h)
     
    void
    reopenFile()
     
    void
    setSeries(int series)
     

    Methods inherited from class loci.formats.SubResolutionFormatReader

    coreIndexToSeries, flattenHashtables, getCoreIndex, getCoreMetadataList, getCurrentCore, getResolution, getResolutionCount, getSeries, getSeriesCount, seriesToCoreIndex, setCoreIndex, setResolution

    Methods inherited from class loci.formats.FormatReader

    addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMetaList, addMeta, addMetaList, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMetaList, close, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCorrection, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getEffectiveSizeC, getExperimentType, getFilamentType, getFillColor, 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, getRGBChannelCount, getRotationTransform, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getThumbSizeX, getThumbSizeY, getTileColumns, getTileRows, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, readPlane, setFillColor, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, updateMetadataLists

    Methods inherited from class loci.formats.FormatHandler

    checkSuffix, checkSuffix, getFormat, getMetadataOptions, getNativeDataType, getSuffixes, getSupportedMetadataLevels, setMetadataOptions

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    Methods inherited from interface loci.formats.ICompressedTileReader

    getTileCodec, getTileCodecOptions, openCompressedBytes, openCompressedBytes

    Methods inherited from interface loci.formats.IFormatHandler

    getFormat, getNativeDataType, getSuffixes

    Methods inherited from interface loci.formats.IMetadataConfigurable

    getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions