Package loci.formats

Class DimensionSwapper

java.lang.Object
loci.formats.ReaderWrapper
loci.formats.DimensionSwapper
All Implemented Interfaces:
Closeable, AutoCloseable, loci.formats.ICompressedTileReader, loci.formats.IFormatHandler, loci.formats.IFormatReader, loci.formats.IMetadataConfigurable, loci.formats.IPyramidHandler
public class DimensionSwapper extends loci.formats.ReaderWrapper
Handles swapping the dimension order of an image series. This class is useful for both reassigning ZCT sizes (the input dimension order), and shuffling around the resultant planar order (the output dimension order).

  • Field Summary

    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
    DimensionSwapper()
    Constructs a DimensionSwapper around a new image reader.
    DimensionSwapper(loci.formats.IFormatReader r)
    Constructs a DimensionSwapper with the given reader.

  • Method Summary

    Modifier and Type
    Method
    Description
    List<loci.formats.CoreMetadata>
    getCoreMetadataList()
     
    String
    getDimensionOrder()
     
    int
    getIndex(int z, int c, int t)
     
    int
    getIndex(int z, int c, int t, int moduloZ, int moduloC, int moduloT)
     
    String
    getInputOrder()
     
    int
    getSizeC()
     
    int
    getSizeT()
     
    int
    getSizeX()
     
    int
    getSizeY()
     
    int
    getSizeZ()
     
    loci.formats.codec.Codec
    getTileCodec(int no)
     
    loci.formats.codec.CodecOptions
    getTileCodecOptions(int no, int x, int y)
     
    int[]
    getZCTCoords(int no)
     
    int[]
    getZCTModuloCoords(int index)
     
    static DimensionSwapper
    makeDimensionSwapper(loci.formats.IFormatReader r)
    Converts the given reader into a DimensionSwapper, 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)
     
    byte[]
    openThumbBytes(int no)
     
    protected int
    reorder(int no)
     
    void
    setId(String id)
     
    void
    setOutputOrder(String outputOrder)
    Sets the output dimension order according to the given string (e.g., "XYZCT").
    void
    swapDimensions(String order)
    Sets the input dimension order according to the given string (e.g., "XYZCT").

    Methods inherited from class loci.formats.ReaderWrapper

    close, close, coreIndexToSeries, duplicate, fileGroupOption, get16BitLookupTable, get8BitLookupTable, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getBitsPerPixel, getCoreIndex, getCurrentFile, getDatasetStructureDescription, getDomains, getEffectiveSizeC, getFillColor, getFormat, getGlobalMetadata, getImageCount, getMetadataOptions, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getModuloC, getModuloT, getModuloZ, getNativeDataType, getOptimalTileHeight, getOptimalTileWidth, getPixelType, getPossibleDomains, getReader, getRequiredDirectories, getResolution, getResolutionCount, getRGBChannelCount, getSeries, getSeriesCount, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSuffixes, getSupportedMetadataLevels, getThumbSizeX, getThumbSizeY, getTileColumns, getTileRows, getUnderlyingReaders, getUsedFiles, getUsedFiles, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, isThisType, isThisType, isThisType, isThisType, isThumbnailSeries, openPlane, 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