Package ome.io.bioformats

Class OmeroPixelsPyramidReader

  • All Implemented Interfaces:
    java.io.Closeable, java.lang.AutoCloseable, loci.formats.ICompressedTileReader, loci.formats.IFormatHandler, loci.formats.IFormatReader, loci.formats.IMetadataConfigurable, loci.formats.IPyramidHandler
    public class OmeroPixelsPyramidReader
extends loci.formats.in.MinimalTiffReader
    File format reader for OMERO pixels pyramid files.
    Since:
    Beta4.3

    • Field Summary

      • Fields inherited from class loci.formats.in.MinimalTiffReader

        canSeparateSeries, equalStrips, ifds, lastPlane, mergeSubIFDs, noSubresolutions, seriesToIFD, subResolutionIFDs, thumbnailIFDs, tiffParser, 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

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void close()  
      boolean isThisType​(java.lang.String name, boolean open)  
      void setId​(java.lang.String id)  
      protected void setResolutionLevel​(loci.formats.tiff.IFD ifd)  

      • Methods inherited from class loci.formats.in.MinimalTiffReader

        close, copyTile, get16BitLookupTable, get8BitLookupTable, getCompressedByteCount, getIFDs, getOptimalTileHeight, getOptimalTileWidth, getThumbnailIFDs, getThumbSizeX, getThumbSizeY, getTileIndex, initFile, initTiffParser, isThisType, openBytes, openThumbBytes, reopenFile

      • 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, 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, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, readPlane, readPlane, readPlane, setFillColor, setFlattenedResolutions, setGroupFiles, 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

    • Constructor Detail

      • OmeroPixelsPyramidReader

        public OmeroPixelsPyramidReader()

    • Method Detail

      • isThisType

        public boolean isThisType​(java.lang.String name,
                          boolean open)
        Specified by:
        isThisType in interface loci.formats.IFormatReader
        Overrides:
        isThisType in class loci.formats.FormatReader

      • setId

        public void setId​(java.lang.String id)
           throws loci.formats.FormatException,
                  java.io.IOException
        Specified by:
        setId in interface loci.formats.IFormatHandler
        Overrides:
        setId in class loci.formats.FormatReader
        Throws:
        loci.formats.FormatException
        java.io.IOException

      • close

        public void close()
           throws java.io.IOException
        Specified by:
        close in interface java.lang.AutoCloseable
        Specified by:
        close in interface java.io.Closeable
        Overrides:
        close in class loci.formats.FormatReader
        Throws:
        java.io.IOException

      • setResolutionLevel

        protected void setResolutionLevel​(loci.formats.tiff.IFD ifd)
        Overrides:
        setResolutionLevel in class loci.formats.in.MinimalTiffReader