Package loci.formats.in

Class FakeReader

java.lang.Object
loci.formats.FormatHandler
loci.formats.FormatReader
loci.formats.in.FakeReader
All Implemented Interfaces:
Closeable, AutoCloseable, loci.formats.ICompressedTileReader, loci.formats.IFormatHandler, loci.formats.IFormatReader, loci.formats.IMetadataConfigurable, loci.formats.IPyramidHandler
public class FakeReader extends loci.formats.FormatReader
FakeReader is the file format reader for faking input data. It is mainly useful for testing.

Examples:

  • showinf 'multi-series&series=11&sizeZ=3&sizeC=5&sizeT=7&sizeY=50.fake' -series 9
  • showinf '8bit-signed&pixelType=int8&sizeZ=3&sizeC=5&sizeT=7&sizeY=50.fake'
  • showinf '8bit-unsigned&pixelType=uint8&sizeZ=3&sizeC=5&sizeT=7&sizeY=50.fake'
  • showinf '16bit-signed&pixelType=int16&sizeZ=3&sizeC=5&sizeT=7&sizeY=50.fake'
  • showinf '16bit-unsigned&pixelType=uint16&sizeZ=3&sizeC=5&sizeT=7&sizeY=50.fake'
  • showinf '32bit-signed&pixelType=int32&sizeZ=3&sizeC=5&sizeT=7&sizeY=50.fake'
  • showinf '32bit-unsigned&pixelType=uint32&sizeZ=3&sizeC=5&sizeT=7&sizeY=50.fake'
  • showinf '32bit-floating&pixelType=float&sizeZ=3&sizeC=5&sizeT=7&sizeY=50.fake'
  • showinf '64bit-floating&pixelType=double&sizeZ=3&sizeC=5&sizeT=7&sizeY=50.fake'
  • showinf 'SPW&plates=2&plateRows=3&plateCols=3&fields=8&plateAcqs=5.fake'
  • showinf 'SPW&screens=2&plates=1&plateRows=3&plateCols=3&fields=1&plateAcqs=1.fake'
  • showinf 'Plate&screens=0&plates=1&plateRows=3&plateCols=3&fields=8&plateAcqs=5.fake'
  • showinf 'regions&points=10&ellipses=5&rectangles=10.fake'
  • showinf 'pyramid&sizeX=10000&sizeY=10000&resolutions=5&resolutionScale=2.fake' -noflat -resolution 4

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final int
    BOX_SIZE
     
    static final String
    DEFAULT_DIMENSION_ORDER
     
    static final int
    DEFAULT_PIXEL_TYPE
     
    static final int
    DEFAULT_RESOLUTION_SCALE
     
    static final int
    DEFAULT_RGB_CHANNEL_COUNT
     
    static final String
    DEFAULT_RGB_DIMENSION_ORDER
     
    static final int
    DEFAULT_SIZE_C
     
    static final int
    DEFAULT_SIZE_T
     
    static final int
    DEFAULT_SIZE_X
     
    static final int
    DEFAULT_SIZE_Y
     
    static final int
    DEFAULT_SIZE_Z
     

    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
    FakeReader()
    Constructs a new fake reader.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    close(boolean fileOnly)
     
    short[][]
    get16BitLookupTable()
     
    byte[][]
    get8BitLookupTable()
     
    loci.formats.ome.OMEXMLMetadata
    getOmeXmlMetadata()
     
    loci.formats.services.OMEXMLService
    getOmeXmlService()
     
    String[]
    getSeriesUsedFiles(boolean noPixels)
     
    protected void
    initFile(String id)
     
    boolean
    isSingleFile(String id)
     
    boolean
    isThisType(String name, boolean open)
     
    byte[]
    openBytes(int no, byte[] buf, int x, int y, int w, int h)
     
    static int[]
    readSpecialPixels(byte[] plane)
    Read byte-encoded metadata from the given plane.
    static int[]
    readSpecialPixels(byte[] plane, int pixelType, boolean little)
    Read byte-encoded metadata from the given plane.
    static int[]
    readSpecialPixels(byte[] plane, int pixelType, boolean little, int rgb, boolean interleaved)
    Read byte-encoded metadata from the given plane.
    void
    reopenFile()
     

    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, coreIndexToSeries, fileGroupOption, flattenHashtables, 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, 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, isThisType, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, readPlane, seriesToCoreIndex, setCoreIndex, setFillColor, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries, 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