Package ome.io.bioformats

Class OmeroPixelsPyramidWriter

  • All Implemented Interfaces:
    java.io.Closeable, java.lang.AutoCloseable, loci.formats.ICompressedTileWriter, loci.formats.IFormatHandler, loci.formats.IFormatWriter, loci.formats.IMetadataConfigurable, loci.formats.IPyramidHandler
    public class OmeroPixelsPyramidWriter
extends loci.formats.out.TiffWriter
    File format writer for OMERO pixels pyramid files.
    Since:
    Beta4.3

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static int IFD_TAG_PLANE_NUMBER
      TIFF tag we're using to store the Bio-Formats plane number.
      static int IFD_TAG_SERIES
      TIFF tag we're using to store the Bio-Formats series.
      static java.lang.String IMAGE_DESCRIPTION
      Current TIFF image comment for OMERO pixels pyramid TIFFs.

      • Fields inherited from class loci.formats.out.TiffWriter

        canDetectBigTiff, checkParams, COMPRESSION_J2K, COMPRESSION_J2K_LOSSY, COMPRESSION_JPEG, COMPRESSION_LZW, COMPRESSION_UNCOMPRESSED, COMPRESSION_ZLIB, in, isBigTiff, tiffSaver, tileSizeX, tileSizeY

      • Fields inherited from class loci.formats.FormatWriter

        cm, compression, compressionTypes, fps, initialized, interleaved, metadataRetrieve, options, out, resolution, resolutionData, sequential, series, validBits

      • Fields inherited from class loci.formats.FormatHandler

        COMPRESSION_SUFFIXES, currentId, format, LOGGER, metadataOptions, suffixes

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void close()  
      protected void postProcess()
      Performs re-compression post processing on the pixel pyramid.
      protected void recompressSeries​(loci.formats.in.TiffReader source, int series)
      Re-compresses a source series, that is JPEG 2000 compressed, via its resolution level.
      void setId​(java.lang.String id)  

      • Methods inherited from class loci.formats.out.TiffWriter

        canDoStacks, createInputStream, createTiffSaver, getCodec, getPixelTypes, getPlaneCount, getTileSizeX, getTileSizeY, makeIFD, prepareToWriteImage, saveBytes, saveBytes, saveBytes, saveCompressedBytes, setBigTiff, setCanDetectBigTiff, setTileSizeX, setTileSizeY, setupTiffSaver

      • Methods inherited from class loci.formats.FormatWriter

        changeOutputFile, checkParams, createOutputStream, getCodecOptions, getColorModel, getCompression, getCompressionTypes, getFramesPerSecond, getMetadataRetrieve, getPixelTypes, getPlaneCount, getResolution, getResolutionCount, getResolutions, getSamplesPerPixel, getSamplesPerPixel, getSeries, getSizeX, getSizeY, hasResolutions, isFullPlane, isInterleaved, isSupportedType, saveBytes, saveBytes, savePlane, savePlane, savePlane, seekToPlaneOffset, setCodecOptions, setColorModel, setCompression, setFramesPerSecond, setInterleaved, setMetadataRetrieve, setResolution, setResolutions, setSeries, setValidBitsPerPixel, setWriteSequentially

      • Methods inherited from class loci.formats.FormatHandler

        checkSuffix, checkSuffix, getFormat, getMetadataOptions, getNativeDataType, getSuffixes, getSupportedMetadataLevels, isThisType, 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.IFormatHandler

        getFormat, getNativeDataType, getSuffixes, isThisType

      • Methods inherited from interface loci.formats.IMetadataConfigurable

        getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

    • Field Detail

      • IMAGE_DESCRIPTION

        public static final java.lang.String IMAGE_DESCRIPTION
        Current TIFF image comment for OMERO pixels pyramid TIFFs.
        See Also:
        Constant Field Values

      • IFD_TAG_SERIES

        public static final int IFD_TAG_SERIES
        TIFF tag we're using to store the Bio-Formats series.
        See Also:
        Constant Field Values

      • IFD_TAG_PLANE_NUMBER

        public static final int IFD_TAG_PLANE_NUMBER
        TIFF tag we're using to store the Bio-Formats plane number.
        See Also:
        Constant Field Values

    • Constructor Detail

      • OmeroPixelsPyramidWriter

        public OmeroPixelsPyramidWriter()

    • Method Detail

      • 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.out.TiffWriter
        Throws:
        java.io.IOException

      • 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.out.TiffWriter
        Throws:
        loci.formats.FormatException
        java.io.IOException

      • postProcess

        protected void postProcess()
                    throws java.io.IOException,
                           loci.formats.FormatException
        Performs re-compression post processing on the pixel pyramid.
        Throws:
        java.io.IOException
        loci.formats.FormatException

      • recompressSeries

        protected void recompressSeries​(loci.formats.in.TiffReader source,
                                int series)
                         throws loci.formats.FormatException,
                                java.io.IOException
        Re-compresses a source series, that is JPEG 2000 compressed, via its resolution level.
        Parameters:
        source - Reader created of ourselves.
        series - Target series for the re-compressed data which is the inverse of the source resolution level.
        Throws:
        loci.formats.FormatException
        java.io.IOException