Package loci.formats.in

Class MinimalTiffReader

java.lang.Object
loci.formats.FormatHandler
loci.formats.FormatReader
loci.formats.SubResolutionFormatReader
loci.formats.in.MinimalTiffReader
All Implemented Interfaces:
Closeable, AutoCloseable, loci.formats.ICompressedTileReader, loci.formats.IFormatHandler, loci.formats.IFormatReader, loci.formats.IMetadataConfigurable, loci.formats.IPyramidHandler
Direct Known Subclasses:
BaseTiffReader
public class MinimalTiffReader extends loci.formats.SubResolutionFormatReader
MinimalTiffReader is the superclass for file format readers compatible with or derived from the TIFF 6.0 file format.

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    protected boolean
    canSeparateSeries
    Whether or not IFDs with different dimensions can be split into separate series.
    protected boolean
    equalStrips
     
    protected IFDList
    ifds
    List of IFDs for the current TIFF.
    protected int
    lastPlane
     
    protected boolean
    mergeSubIFDs
    Merge SubIFDs into the main IFD list.
    protected boolean
    noSubresolutions
     
    protected boolean
    seriesToIFD
     
    protected List<IFDList>
    subResolutionIFDs
    List of sub-resolution IFDs for each IFD in the current TIFF with the same order as ifds.
    protected IFDList
    thumbnailIFDs
    List of thumbnail IFDs for the current TIFF.
    protected TiffParser
    tiffParser
     
    protected boolean
    use64Bit
     

    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, metadataOptions, suffixes

    Fields inherited from interface loci.formats.IFormatReader

    CAN_GROUP, CANNOT_GROUP, MUST_GROUP

  • Constructor Summary

    Constructors
    Constructor
    Description
    MinimalTiffReader()
    Constructs a new MinimalTiffReader.
    MinimalTiffReader(String name, String suffix)
    Constructs a new MinimalTiffReader.
    MinimalTiffReader(String name, String[] suffixes)
    Constructs a new MinimalTiffReader.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    close(boolean fileOnly)
     
    protected byte[]
    copyTile(IFD ifd, byte[] buf, int x, int y)
     
    short[][]
    get16BitLookupTable()
     
    byte[][]
    get8BitLookupTable()
     
    protected long
    getCompressedByteCount(IFD ifd, int x, int y)
     
    IFDList
    getIFDs()
    Gets the list of IFDs associated with the current TIFF's image planes.
    int
    getOptimalTileHeight()
     
    int
    getOptimalTileWidth()
     
    IFDList
    getThumbnailIFDs()
    Gets the list of IFDs associated with the current TIFF's thumbnails.
    int
    getThumbSizeX()
     
    int
    getThumbSizeY()
     
    protected int
    getTileIndex(IFD ifd, int x, int y)
    Get the index of the tile corresponding to given IFD (plane) and tile XY indexes.
    protected void
    initFile(String id)
     
    protected void
    initTiffParser()
    Reinitialize the underlying TiffParser.
    boolean
    isThisType(RandomAccessInputStream stream)
     
    byte[]
    openBytes(int no, byte[] buf, int x, int y, int w, int h)
     
    byte[]
    openThumbBytes(int no)
     
    void
    reopenFile()
     
    protected void
    setResolutionLevel(IFD ifd)
    Sets the resolution level when we have JPEG 2000 compressed data.

    Methods inherited from class loci.formats.SubResolutionFormatReader

    coreIndexToSeries, flattenHashtables, getCoreIndex, getCoreMetadataList, getCurrentCore, getResolution, getResolutionCount, getSeries, getSeriesCount, 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, close, fileGroupOption, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getAvailableOptions, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCorrection, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, 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, getRequiredDirectories, getRGBChannelCount, getRotationTransform, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getTileColumns, getTileRows, 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, 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