Package loci.formats

Interface IFormatWriter

All Superinterfaces:
AutoCloseable, Closeable, ICompressedTileWriter, IFormatHandler, IMetadataConfigurable, IPyramidHandler
All Known Implementing Classes:
APNGWriter, AVIWriter, BufferedImageWriter, CellH5Writer, DicomWriter, EPSWriter, FormatWriter, ICSWriter, ImageIOWriter, ImageWriter, JavaWriter, JPEG2000Writer, JPEGWriter, OMETiffWriter, OMEXMLWriter, PyramidOMETiffWriter, QTWriter, TiffWriter, V3DrawWriter, WriterWrapper
public interface IFormatWriter extends IFormatHandler, IPyramidHandler, ICompressedTileWriter
Interface for all biological file format writers.

  • Method Details

    • saveBytes

      void saveBytes(int no, byte[] buf) throws FormatException, IOException
      Saves the given image to the current series in the current file.
      Parameters:
      no - the plane index within the series.
      buf - the byte array that represents the image.
      Throws:
      FormatException - if one of the parameters is invalid.
      IOException - if there was a problem writing to the file.

    • saveBytes

      void saveBytes(int no, byte[] buf, int x, int y, int w, int h) throws FormatException, IOException
      Saves the given image tile to the current series in the current file.
      Parameters:
      no - the plane index within the series.
      buf - the byte array that represents the image tile.
      x - the X coordinate of the upper-left corner of the image tile.
      y - the Y coordinate of the upper-left corner of the image tile.
      w - the width (in pixels) of the image tile.
      h - the height (in pixels) of the image tile.
      Throws:
      FormatException - if one of the parameters is invalid.
      IOException - if there was a problem writing to the file.

    • saveBytes

      void saveBytes(int no, byte[] buf, loci.common.Region tile) throws FormatException, IOException
      Saves the given image tile to the current series in the current file.
      Parameters:
      no - the plane index within the series.
      buf - the byte array that represents the image tile.
      tile - the Region representing the image tile to be read.
      Throws:
      FormatException - if one of the parameters is invalid.
      IOException - if there was a problem writing to the file.

    • savePlane

      void savePlane(int no, Object plane) throws FormatException, IOException
      Saves the given image plane to the current series in the current file.
      Parameters:
      no - the plane index within the series.
      plane - the image plane.
      Throws:
      FormatException - if one of the parameters is invalid.
      IOException - if there was a problem writing to the file.

    • savePlane

      void savePlane(int no, Object plane, int x, int y, int w, int h) throws FormatException, IOException
      Saves the given image plane to the current series in the current file.
      Parameters:
      no - the plane index within the series.
      plane - the image plane.
      x - the X coordinate of the upper-left corner of the image tile.
      y - the Y coordinate of the upper-left corner of the image tile.
      w - the width (in pixels) of the image tile.
      h - the height (in pixels) of the image tile.
      Throws:
      FormatException - if one of the parameters is invalid.
      IOException - if there was a problem writing to the file.

    • savePlane

      void savePlane(int no, Object plane, loci.common.Region tile) throws FormatException, IOException
      Saves the given image plane to the current series in the current file.
      Parameters:
      no - the plane index within the series.
      plane - the image plane.
      tile - the Region representing the image tile to be read.
      Throws:
      FormatException - if one of the parameters is invalid.
      IOException - if there was a problem writing to the file.

    • setSeries

      void setSeries(int series) throws FormatException
      Sets the current series.
      Parameters:
      series - the series index, starting from 0.
      Throws:
      FormatException - if the specified series is invalid.

    • getSeries

      int getSeries()
      Returns the current series.

    • setInterleaved

      void setInterleaved(boolean interleaved)
      Sets whether or not the channels in an image are interleaved.

    • setValidBitsPerPixel

      void setValidBitsPerPixel(int bits)
      Sets the number of valid bits per pixel.

    • isInterleaved

      boolean isInterleaved()
      Gets whether or not the channels in an image are interleaved.

    • canDoStacks

      boolean canDoStacks()
      Reports whether the writer can save multiple images to a single file.

    • setMetadataRetrieve

      void setMetadataRetrieve(MetadataRetrieve r)
      Sets the metadata retrieval object from which to retrieve standardized metadata.

    • getMetadataRetrieve

      MetadataRetrieve getMetadataRetrieve()
      Retrieves the current metadata retrieval object for this writer. You can be assured that this method will never return a null metadata retrieval object.
      Returns:
      A metadata retrieval object.

    • setColorModel

      void setColorModel(ColorModel cm)
      Sets the color model.

    • getColorModel

      ColorModel getColorModel()
      Gets the color model.

    • setFramesPerSecond

      void setFramesPerSecond(int rate)
      Sets the frames per second to use when writing.

    • getFramesPerSecond

      int getFramesPerSecond()
      Gets the frames per second to use when writing.

    • getCompressionTypes

      String[] getCompressionTypes()
      Gets the available compression types.

    • getPixelTypes

      int[] getPixelTypes()
      Gets the supported pixel types.

    • getPixelTypes

      int[] getPixelTypes(String codec)
      Gets the supported pixel types for the given codec.

    • isSupportedType

      boolean isSupportedType(int type)
      Checks if the given pixel type is supported.

    • setCompression

      void setCompression(String compress) throws FormatException
      Sets the current compression type.
      Throws:
      FormatException

    • setCodecOptions

      void setCodecOptions(CodecOptions options)
      Sets the codec options.
      Parameters:
      options - The options to set.

    • getCompression

      String getCompression()
      Gets the current compression type.

    • changeOutputFile

      void changeOutputFile(String id) throws FormatException, IOException
      Switch the output file for the current dataset.
      Throws:
      FormatException
      IOException

    • setWriteSequentially

      void setWriteSequentially(boolean sequential)
      Sets whether or not we know that planes will be written sequentially. If planes are written sequentially and this flag is set, then performance will be slightly improved.

    • getTileSizeX

      int getTileSizeX() throws FormatException
      Retrieves the current tile width Defaults to 0 if not supported
      Returns:
      The current tile width being used
      Throws:
      FormatException - Image metadata including Pixels Size X must be set prior to calling getTileSizeX()

    • setTileSizeX

      int setTileSizeX(int tileSize) throws FormatException
      Will attempt to set the tile width to the desired value and return the actual value which will be used
      Parameters:
      tileSize - The tile width you wish to use. Setting to 0 will disable tiling
      Returns:
      The tile width which will actually be used, this may differ from the value requested. If the requested value is not supported the writer will return and use the closest appropriate value.
      Throws:
      FormatException - Tile size must be greater than or equal to 0 and less than the image width

    • getTileSizeY

      int getTileSizeY() throws FormatException
      Retrieves the current tile height Defaults to 0 if not supported
      Returns:
      The current tile height being used
      Throws:
      FormatException - Image metadata including Pixels Size Y must be set prior to calling getTileSizeY()

    • setTileSizeY

      int setTileSizeY(int tileSize) throws FormatException
      Will attempt to set the tile height to the desired value and return the actual value which will be used
      Parameters:
      tileSize - The tile height you wish to use. Setting to 0 will disable tiling
      Returns:
      The tile height which will actually be used, this may differ from the value requested. If the requested value is not supported the writer will return and use the closest appropriate value.
      Throws:
      FormatException - Tile size must be greater than or equal to 0 and less than the image height

    • setResolutions

      void setResolutions(List<Resolution> resolutions)
      Specify a list of resolution objects for the current series. If resolutions are specified using this method, then any resolution data supplied via the MetadataRetrieve will be ignored.

    • getResolutions

      List<Resolution> getResolutions()
      Get a list of resolution objects for the current series.