Package ome.formats.importer

Class OMEROWrapper

  • 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 OMEROWrapper
extends loci.formats.MinMaxCalculator

    • Field Summary

      Fields 
      Modifier and Type Field Description
      java.lang.Boolean minMaxSet  

      • Fields inherited from class loci.formats.MinMaxCalculator

        chanMax, chanMin, minMaxDone, minMaxStore, planeMax, planeMin

      • Fields inherited from class loci.formats.ReaderWrapper

        reader

      • 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()  
      ImportConfig getConfig()  
      loci.formats.ImageReader getImageReader()
      Return the base image reader
      loci.formats.in.MetadataOptions getMetadataOptions()  
      java.util.Set<loci.formats.in.MetadataLevel> getSupportedMetadataLevels()  
      boolean isLeicaReader()  
      boolean isMinMaxSet()  
      boolean isSPWReader()  
      ome.util.PixelData openPlane2D​(java.lang.String id, int planeNumber, byte[] buf)
      Obtains an object which represents a given sub-image of a plane within the file.
      ome.util.PixelData openPlane2D​(java.lang.String id, int planeNumber, byte[] buf, int x, int y, int w, int h)
      Obtains an object which represents a given sub-image of a plane within the file.
      void setMetadataOptions​(loci.formats.in.MetadataOptions options)  
      protected void updateMinMax​(int no, byte[] buf, int len)  

      • Methods inherited from class loci.formats.MinMaxCalculator

        close, getChannelGlobalMaximum, getChannelGlobalMinimum, getChannelKnownMaximum, getChannelKnownMinimum, getMinMaxStore, getNativeDataType, getPlaneMaximum, getPlaneMinimum, initMinMax, isMinMaxPopulated, makeMinMaxCalculator, openBytes, openBytes, openBytes, openBytes, setMinMaxStore

      • Methods inherited from class loci.formats.ReaderWrapper

        coreIndexToSeries, duplicate, fileGroupOption, get16BitLookupTable, get8BitLookupTable, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getBitsPerPixel, getCoreIndex, getCoreMetadataList, getCurrentFile, getDatasetStructureDescription, getDimensionOrder, getDomains, getEffectiveSizeC, getFillColor, getFormat, getGlobalMetadata, getImageCount, getIndex, getIndex, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getModuloC, getModuloT, getModuloZ, getOptimalTileHeight, getOptimalTileWidth, getPixelType, getPossibleDomains, getReader, getRequiredDirectories, getResolution, getResolutionCount, getRGBChannelCount, getSeries, getSeriesCount, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getSuffixes, getThumbSizeX, getThumbSizeY, getTileCodec, getTileCodecOptions, 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, isThisType, isThumbnailSeries, openCompressedBytes, openCompressedBytes, openPlane, openThumbBytes, reopenFile, seriesToCoreIndex, setCoreIndex, setFillColor, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries, unwrap, unwrap, unwrap

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Field Detail

      • minMaxSet

        public java.lang.Boolean minMaxSet

    • Constructor Detail

      • OMEROWrapper

        public OMEROWrapper​(ImportConfig config)
        Wrapper for bio-formats
        Parameters:
        config - - ImportConfit

      • OMEROWrapper

        @Deprecated
public OMEROWrapper​(ImportConfig config,
                    long elapsedTime,
                    java.io.File cacheDirectory)
        Deprecated.

      • OMEROWrapper

        public OMEROWrapper​(ImportConfig config,
                    long elapsedTime,
                    java.io.File cacheDirectory,
                    ome.io.nio.ReaderSecurityCheck readerSecurityCheck)

    • Method Detail

      • openPlane2D

        public ome.util.PixelData openPlane2D​(java.lang.String id,
                                      int planeNumber,
                                      byte[] buf)
                               throws loci.formats.FormatException,
                                      java.io.IOException
        Obtains an object which represents a given sub-image of a plane within the file.
        Parameters:
        id - The path to the file.
        planeNumber - The plane or section within the file to obtain.
        buf - Pre-allocated buffer which has a length that can fit the entire plane.
        Returns:
        an object which represents the plane.
        Throws:
        loci.formats.FormatException - If there is an error parsing the file.
        java.io.IOException - If there is an error reading from the file or acquiring permissions to read the file.

      • openPlane2D

        public ome.util.PixelData openPlane2D​(java.lang.String id,
                                      int planeNumber,
                                      byte[] buf,
                                      int x,
                                      int y,
                                      int w,
                                      int h)
                               throws loci.formats.FormatException,
                                      java.io.IOException
        Obtains an object which represents a given sub-image of a plane within the file.
        Parameters:
        id - The path to the file.
        planeNumber - The plane or section within the file to obtain.
        buf - Pre-allocated buffer which has a length that can fit the byte count of the sub-image.
        x - X coordinate of the upper-left corner of the sub-image
        y - Y coordinate of the upper-left corner of the sub-image
        w - width of the sub-image
        h - height of the sub-image
        Returns:
        an object which represents the sub-image of the plane.
        Throws:
        loci.formats.FormatException - If there is an error parsing the file.
        java.io.IOException - If there is an error reading from the file or acquiring permissions to read the file.

      • isLeicaReader

        public boolean isLeicaReader()
        Returns:
        true if reader being used is LeicaReader

      • isMinMaxSet

        public boolean isMinMaxSet()
                    throws loci.formats.FormatException,
                           java.io.IOException
        Returns:
        true if min-max is set
        Throws:
        loci.formats.FormatException
        java.io.IOException

      • updateMinMax

        protected void updateMinMax​(int no,
                            byte[] buf,
                            int len)
                     throws loci.formats.FormatException,
                            java.io.IOException
        Overrides:
        updateMinMax in class loci.formats.MinMaxCalculator
        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.ReaderWrapper
        Throws:
        java.io.IOException

      • getImageReader

        public loci.formats.ImageReader getImageReader()
        Return the base image reader
        Returns:
        See above.

      • isSPWReader

        public boolean isSPWReader()
        Returns:
        true if using SPW reader

      • getMetadataOptions

        public loci.formats.in.MetadataOptions getMetadataOptions()
        Specified by:
        getMetadataOptions in interface loci.formats.IMetadataConfigurable
        Overrides:
        getMetadataOptions in class loci.formats.ReaderWrapper

      • setMetadataOptions

        public void setMetadataOptions​(loci.formats.in.MetadataOptions options)
        Specified by:
        setMetadataOptions in interface loci.formats.IMetadataConfigurable
        Overrides:
        setMetadataOptions in class loci.formats.ReaderWrapper

      • getSupportedMetadataLevels

        public java.util.Set<loci.formats.in.MetadataLevel> getSupportedMetadataLevels()
        Specified by:
        getSupportedMetadataLevels in interface loci.formats.IMetadataConfigurable
        Overrides:
        getSupportedMetadataLevels in class loci.formats.ReaderWrapper