Package loci.formats.in

Class DicomReader

java.lang.Object
loci.formats.FormatHandler
loci.formats.FormatReader
loci.formats.SubResolutionFormatReader
loci.formats.in.DicomReader
All Implemented Interfaces:
Closeable, AutoCloseable, loci.formats.ICompressedTileReader, loci.formats.IFormatHandler, loci.formats.IFormatReader, loci.formats.IMetadataConfigurable, loci.formats.IPyramidHandler
public class DicomReader extends loci.formats.SubResolutionFormatReader
DicomReader is the file format reader for DICOM files.

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final String
    DICOM_MAGIC_STRING
     
    static final int
    HEADER_LENGTH
     

    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, LOGGER, metadataOptions, suffixes

    Fields inherited from interface loci.formats.IFormatReader

    CAN_GROUP, CANNOT_GROUP, MUST_GROUP

  • Constructor Summary

    Constructors
    Constructor
    Description
    DicomReader()
    Constructs a new DICOM reader.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    close(boolean fileOnly)
     
    int
    fileGroupOption(String id)
     
    short[][]
    get16BitLookupTable()
     
    byte[][]
    get8BitLookupTable()
     
    List<String>
    getChannelNames()
     
    int
    getConcatenationIndex()
     
    String
    getImageType()
     
    int
    getOptimalTileHeight()
     
    int
    getOptimalTileWidth()
     
    Length
    getPixelSizeX()
     
    Length
    getPixelSizeY()
     
    Length
    getPixelSizeZ()
     
    List<Double>
    getPositionX()
     
    List<Double>
    getPositionY()
     
    List<Double>
    getPositionZ()
     
    int
    getRequiredDirectories(String[] files)
     
    String[]
    getSeriesUsedFiles(boolean noPixels)
     
    List<DicomTag>
    getTags()
    Provide the complete hierarchy of DICOM tags.
    List<DicomTile>
    getTiles()
     
    Timestamp
    getTimestamp()
     
    List<Double>
    getZOffsets()
     
    protected void
    initFile(String id)
     
    boolean
    isExtendedDepthOfField()
     
    boolean
    isThisType(String name, boolean open)
     
    boolean
    isThisType(RandomAccessInputStream stream)
     
    byte[]
    openBytes(int no, byte[] buf, int x, int y, int w, int h)
     

    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, 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, getRGBChannelCount, getRotationTransform, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getThumbSizeX, getThumbSizeY, getTileColumns, getTileRows, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, readPlane, reopenFile, 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