Package loci.formats.in

Class BIFormatReader

java.lang.Object
loci.formats.FormatHandler
loci.formats.FormatReader
loci.formats.in.BIFormatReader
All Implemented Interfaces:
Closeable, AutoCloseable, loci.formats.ICompressedTileReader, loci.formats.IFormatHandler, loci.formats.IFormatReader, loci.formats.IMetadataConfigurable, loci.formats.IPyramidHandler
Direct Known Subclasses:
ImageIOReader, MNGReader, TiffJAIReader
public abstract class BIFormatReader extends loci.formats.FormatReader
BIFormatReader is the superclass for file format readers that use java.awt.image.BufferedImage as the native data type.

  • 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
    BIFormatReader(String name, String suffix)
    Constructs a new BIFormatReader.
    BIFormatReader(String name, String[] suffixes)
    Constructs a new BIFormatReader.

  • Method Summary

    Modifier and Type
    Method
    Description
    Class<?>
    getNativeDataType()
     
    byte[]
    openBytes(int no, byte[] buf, int x, int y, int w, int h)
     

    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, close, coreIndexToSeries, fileGroupOption, flattenHashtables, get16BitLookupTable, get8BitLookupTable, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getAvailableOptions, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCoreIndex, getCoreMetadataList, getCorrection, getCurrentCore, 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, getOptimalTileHeight, getOptimalTileWidth, getPixelType, getPixelType, getPossibleDomains, getPulse, getRequiredDirectories, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getThumbSizeX, getThumbSizeY, getTileColumns, getTileRows, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, initFile, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, isThisType, isThisType, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, readPlane, reopenFile, seriesToCoreIndex, setCoreIndex, setFillColor, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries, 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