Package loci.formats.in

Class FilePatternReader

java.lang.Object
loci.formats.FormatHandler
loci.formats.FormatReader
loci.formats.WrappedReader
loci.formats.in.FilePatternReader
All Implemented Interfaces:
Closeable, AutoCloseable, loci.formats.ICompressedTileReader, loci.formats.IFormatHandler, loci.formats.IFormatReader, loci.formats.IMetadataConfigurable, loci.formats.IPyramidHandler
public class FilePatternReader extends loci.formats.WrappedReader

  • Field Summary

    Fields inherited from class loci.formats.FormatReader

    core, 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
    FilePatternReader()
    Constructs a new pattern reader.

  • Method Summary

    Modifier and Type
    Method
    Description
    short[][]
    get16BitLookupTable()
     
    byte[][]
    get8BitLookupTable()
     
    List<loci.formats.CoreMetadata>
    getCoreMetadataList()
     
    protected loci.formats.ReaderWrapper
    getHelper()
     
    loci.formats.meta.MetadataStore
    getMetadataStore()
     
    String[]
    getSeriesUsedFiles(boolean noPixels)
     
    String[]
    getUsedFiles(boolean noPixels)
     
    boolean
    hasCompanionFiles()
     
    boolean
    hasFlattenedResolutions()
     
    protected void
    initFile(String id)
     
    boolean
    isGroupFiles()
     
    boolean
    isMetadataFiltered()
     
    boolean
    isNormalized()
     
    boolean
    isOriginalMetadataPopulated()
     
    boolean
    isSingleFile(String id)
     
    void
    setFlattenedResolutions(boolean flattened)
     
    void
    setGroupFiles(boolean group)
     
    void
    setMetadataFiltered(boolean filter)
     
    void
    setMetadataStore(loci.formats.meta.MetadataStore store)
     
    void
    setNormalized(boolean normalize)
     
    void
    setOriginalMetadataPopulated(boolean populate)
     

    Methods inherited from class loci.formats.WrappedReader

    callDeferredSetters, close, close, coreIndexToSeries, getBitsPerPixel, getCoreIndex, getDatasetStructureDescription, getDimensionOrder, getDomains, getEffectiveSizeC, getGlobalMetadata, getImageCount, getIndex, getMetadataStoreRoot, getMetadataValue, getModuloC, getModuloT, getModuloZ, getNativeDataType, getOptimalTileHeight, getOptimalTileWidth, getPixelType, getPossibleDomains, getResolution, getResolutionCount, getRGBChannelCount, getSeries, getSeriesCount, getSeriesMetadata, getSeriesMetadataValue, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getThumbSizeX, getThumbSizeY, getUnderlyingReaders, getZCTCoords, isFalseColor, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isOrderCertain, isRGB, isThumbnailSeries, openBytes, openBytes, openBytes, openBytes, openPlane, openThumbBytes, reopenFile, seriesToCoreIndex, setCoreIndex, setResolution, setSeries

    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, fileGroupOption, flattenHashtables, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getAvailableOptions, getBinning, getCompression, getContrastMethod, getCorrection, getCurrentCore, getCurrentFile, getDetectorType, getDimensionOrder, getExperimentType, getFilamentType, getFillColor, getFillRule, getFilterType, getFontFamily, getFontStyle, getGlobalMeta, getIlluminationType, getImmersion, getIndex, getLaserMedium, getLaserType, getMarker, getMedium, getMicrobeamManipulationType, getMicroscopeType, getNamingConvention, getPixelType, getPulse, getRequiredDirectories, getRotationTransform, getSeriesMeta, getSeriesUsedFiles, getTileColumns, getTileRows, getUsedFiles, getZCTModuloCoords, isThisType, isThisType, isThisType, isThisType, isUsedFile, makeFilterMetadata, readPlane, readPlane, readPlane, setFillColor, setId, updateMetadataLists

    Methods inherited from class loci.formats.FormatHandler

    checkSuffix, checkSuffix, getFormat, getMetadataOptions, 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, getSuffixes

    Methods inherited from interface loci.formats.IMetadataConfigurable

    getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions