Package loci.formats

Class ChannelFiller

java.lang.Object
loci.formats.ReaderWrapper
loci.formats.ChannelFiller
All Implemented Interfaces:
Closeable, AutoCloseable, loci.formats.ICompressedTileReader, loci.formats.IFormatHandler, loci.formats.IFormatReader, loci.formats.IMetadataConfigurable, loci.formats.IPyramidHandler
public class ChannelFiller extends loci.formats.ReaderWrapper
For indexed color data representing true color, factors out the indices, replacing them with the color table values directly. For all other data (either non-indexed, or indexed with "false color" tables), does nothing.

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    protected Boolean
    filled
    Whether to fill in the indices.
    protected int
    lutLength
    Number of LUT components.

    Fields inherited from class loci.formats.ReaderWrapper

    reader

    Fields inherited from interface loci.formats.IFormatReader

    CAN_GROUP, CANNOT_GROUP, MUST_GROUP

  • Constructor Summary

    Constructors
    Constructor
    Description
    ChannelFiller()
    Constructs a ChannelFiller around a new image reader.
    ChannelFiller(loci.formats.IFormatReader r)
    Constructs a ChannelFiller with a given reader.

  • Method Summary

    Modifier and Type
    Method
    Description
    short[][]
    get16BitLookupTable()
     
    byte[][]
    get8BitLookupTable()
     
    int
    getBitsPerPixel()
     
    Class<?>
    getNativeDataType()
     
    int
    getSizeC()
     
    loci.formats.codec.Codec
    getTileCodec(int no)
     
    loci.formats.codec.CodecOptions
    getTileCodecOptions(int no, int x, int y)
     
    boolean
    isFilled()
    Returns true if the indices are being factored out.
    boolean
    isIndexed()
     
    boolean
    isRGB()
     
    static ChannelFiller
    makeChannelFiller(loci.formats.IFormatReader r)
    Converts the given reader into a ChannelFiller, wrapping if needed.
    byte[]
    openBytes(int no)
     
    byte[]
    openBytes(int no, byte[] buf)
     
    byte[]
    openBytes(int no, byte[] buf, int x, int y, int w, int h)
     
    byte[]
    openBytes(int no, int x, int y, int w, int h)
     
    byte[]
    openCompressedBytes(int no, byte[] buf, int x, int y)
     
    byte[]
    openCompressedBytes(int no, int x, int y)
     
    void
    setFilled(boolean filled)
    Toggles whether the indices should be factored out.
    void
    setId(String id)
     

    Methods inherited from class loci.formats.ReaderWrapper

    close, close, coreIndexToSeries, duplicate, fileGroupOption, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getCoreIndex, getCoreMetadataList, getCurrentFile, getDatasetStructureDescription, getDimensionOrder, getDomains, getEffectiveSizeC, getFillColor, getFormat, getGlobalMetadata, getImageCount, getIndex, getIndex, getMetadataOptions, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getModuloC, getModuloT, getModuloZ, getOptimalTileHeight, getOptimalTileWidth, getPixelType, getPossibleDomains, getReader, getRequiredDirectories, getResolution, getResolutionCount, getRGBChannelCount, getSeries, getSeriesCount, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSizeT, getSizeX, getSizeY, getSizeZ, getSuffixes, getSupportedMetadataLevels, getThumbSizeX, getThumbSizeY, getTileColumns, getTileRows, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isSingleFile, isThisType, isThisType, isThisType, isThisType, isThumbnailSeries, openPlane, openThumbBytes, reopenFile, seriesToCoreIndex, setCoreIndex, setFillColor, setFlattenedResolutions, setGroupFiles, setMetadataFiltered, setMetadataOptions, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries, unwrap, unwrap, unwrap

    Methods inherited from class java.lang.Object

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