Package loci.formats

Class FormatWriter

java.lang.Object
loci.formats.FormatHandler
loci.formats.FormatWriter
All Implemented Interfaces:
Closeable, AutoCloseable, ICompressedTileWriter, IFormatHandler, IFormatWriter, IMetadataConfigurable, IPyramidHandler
Direct Known Subclasses:
APNGWriter, AVIWriter, CellH5Writer, DicomWriter, EPSWriter, ICSWriter, ImageIOWriter, JavaWriter, JPEG2000Writer, OMEXMLWriter, QTWriter, TiffWriter, V3DrawWriter
public abstract class FormatWriter extends FormatHandler implements IFormatWriter
Abstract superclass of all biological file format writers.

  • Field Details

    • fps

      protected int fps
      Frame rate to use when writing in frames per second, if applicable.

    • cm

      protected ColorModel cm
      Default color model.

    • compressionTypes

      protected String[] compressionTypes
      Available compression types.

    • compression

      protected String compression
      Current compression type.

    • options

      protected CodecOptions options
      The options if required.

    • initialized

      protected boolean[][] initialized
      Whether each plane in each series of the current file has been prepped for writing.

    • interleaved

      protected boolean interleaved
      Whether the channels in an RGB image are interleaved.

    • validBits

      protected int validBits
      The number of valid bits per pixel.

    • series

      protected int series
      Current series.

    • sequential

      protected boolean sequential
      Whether or not we are writing planes sequentially.

    • metadataRetrieve

      protected MetadataRetrieve metadataRetrieve
      Current metadata retrieval object. Should never be accessed directly as the semantics of getMetadataRetrieve() prevent "null" access.

    • out

      protected loci.common.RandomAccessOutputStream out
      Current file.

    • resolution

      protected int resolution
      Current pyramid resolution.

    • resolutionData

      protected List<List<Resolution>> resolutionData

  • Constructor Details

    • FormatWriter

      public FormatWriter(String format, String suffix)
      Constructs a format writer with the given name and default suffix.

    • FormatWriter

      public FormatWriter(String format, String[] suffixes)
      Constructs a format writer with the given name and default suffixes.

  • Method Details

    • changeOutputFile

      public void changeOutputFile(String id) throws FormatException, IOException
      Description copied from interface: IFormatWriter
      Switch the output file for the current dataset.
      Specified by:
      changeOutputFile in interface IFormatWriter
      Throws:
      FormatException
      IOException

    • saveBytes

      public void saveBytes(int no, byte[] buf) throws FormatException, IOException
      Description copied from interface: IFormatWriter
      Saves the given image to the current series in the current file.
      Specified by:
      saveBytes in interface IFormatWriter
      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

      public void saveBytes(int no, byte[] buf, loci.common.Region tile) throws FormatException, IOException
      Description copied from interface: IFormatWriter
      Saves the given image tile to the current series in the current file.
      Specified by:
      saveBytes in interface IFormatWriter
      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

      public void savePlane(int no, Object plane) throws FormatException, IOException
      Description copied from interface: IFormatWriter
      Saves the given image plane to the current series in the current file.
      Specified by:
      savePlane in interface IFormatWriter
      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

      public void savePlane(int no, Object plane, int x, int y, int w, int h) throws FormatException, IOException
      Description copied from interface: IFormatWriter
      Saves the given image plane to the current series in the current file.
      Specified by:
      savePlane in interface IFormatWriter
      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

      public void savePlane(int no, Object plane, loci.common.Region tile) throws FormatException, IOException
      Description copied from interface: IFormatWriter
      Saves the given image plane to the current series in the current file.
      Specified by:
      savePlane in interface IFormatWriter
      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

      public void setSeries(int series) throws FormatException
      Description copied from interface: IFormatWriter
      Sets the current series.
      Specified by:
      setSeries in interface IFormatWriter
      Parameters:
      series - the series index, starting from 0.
      Throws:
      FormatException - if the specified series is invalid.

    • getSeries

      public int getSeries()
      Description copied from interface: IFormatWriter
      Returns the current series.
      Specified by:
      getSeries in interface IFormatWriter

    • setInterleaved

      public void setInterleaved(boolean interleaved)
      Description copied from interface: IFormatWriter
      Sets whether or not the channels in an image are interleaved.
      Specified by:
      setInterleaved in interface IFormatWriter

    • isInterleaved

      public boolean isInterleaved()
      Description copied from interface: IFormatWriter
      Gets whether or not the channels in an image are interleaved.
      Specified by:
      isInterleaved in interface IFormatWriter

    • setValidBitsPerPixel

      public void setValidBitsPerPixel(int bits)
      Description copied from interface: IFormatWriter
      Sets the number of valid bits per pixel.
      Specified by:
      setValidBitsPerPixel in interface IFormatWriter

    • canDoStacks

      public boolean canDoStacks()
      Description copied from interface: IFormatWriter
      Reports whether the writer can save multiple images to a single file.
      Specified by:
      canDoStacks in interface IFormatWriter

    • setMetadataRetrieve

      public void setMetadataRetrieve(MetadataRetrieve retrieve)
      Description copied from interface: IFormatWriter
      Sets the metadata retrieval object from which to retrieve standardized metadata.
      Specified by:
      setMetadataRetrieve in interface IFormatWriter

    • getMetadataRetrieve

      public MetadataRetrieve getMetadataRetrieve()
      Description copied from interface: IFormatWriter
      Retrieves the current metadata retrieval object for this writer. You can be assured that this method will never return a null metadata retrieval object.
      Specified by:
      getMetadataRetrieve in interface IFormatWriter
      Returns:
      A metadata retrieval object.

    • setColorModel

      public void setColorModel(ColorModel model)
      Description copied from interface: IFormatWriter
      Sets the color model.
      Specified by:
      setColorModel in interface IFormatWriter

    • getColorModel

      public ColorModel getColorModel()
      Description copied from interface: IFormatWriter
      Gets the color model.
      Specified by:
      getColorModel in interface IFormatWriter

    • setFramesPerSecond

      public void setFramesPerSecond(int rate)
      Description copied from interface: IFormatWriter
      Sets the frames per second to use when writing.
      Specified by:
      setFramesPerSecond in interface IFormatWriter

    • getFramesPerSecond

      public int getFramesPerSecond()
      Description copied from interface: IFormatWriter
      Gets the frames per second to use when writing.
      Specified by:
      getFramesPerSecond in interface IFormatWriter

    • getCompressionTypes

      public String[] getCompressionTypes()
      Description copied from interface: IFormatWriter
      Gets the available compression types.
      Specified by:
      getCompressionTypes in interface IFormatWriter

    • setCompression

      public void setCompression(String compress) throws FormatException
      Description copied from interface: IFormatWriter
      Sets the current compression type.
      Specified by:
      setCompression in interface IFormatWriter
      Throws:
      FormatException

    • setCodecOptions

      public void setCodecOptions(CodecOptions options)
      Description copied from interface: IFormatWriter
      Sets the codec options.
      Specified by:
      setCodecOptions in interface IFormatWriter
      Parameters:
      options - The options to set.

    • getCodecOptions

      public CodecOptions getCodecOptions()
      Specified by:
      getCodecOptions in interface ICompressedTileWriter
      Returns:
      the codec options that can be used to compress tiles

    • getCompression

      public String getCompression()
      Description copied from interface: IFormatWriter
      Gets the current compression type.
      Specified by:
      getCompression in interface IFormatWriter

    • getPixelTypes

      public int[] getPixelTypes()
      Description copied from interface: IFormatWriter
      Gets the supported pixel types.
      Specified by:
      getPixelTypes in interface IFormatWriter

    • getPixelTypes

      public int[] getPixelTypes(String codec)
      Description copied from interface: IFormatWriter
      Gets the supported pixel types for the given codec.
      Specified by:
      getPixelTypes in interface IFormatWriter

    • isSupportedType

      public boolean isSupportedType(int type)
      Description copied from interface: IFormatWriter
      Checks if the given pixel type is supported.
      Specified by:
      isSupportedType in interface IFormatWriter

    • setWriteSequentially

      public void setWriteSequentially(boolean sequential)
      Description copied from interface: IFormatWriter
      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.
      Specified by:
      setWriteSequentially in interface IFormatWriter

    • getTileSizeX

      public int getTileSizeX() throws FormatException
      Description copied from interface: IFormatWriter
      Retrieves the current tile width Defaults to 0 if not supported
      Specified by:
      getTileSizeX in interface IFormatWriter
      Returns:
      The current tile width being used
      Throws:
      FormatException - Image metadata including Pixels Size X must be set prior to calling getTileSizeX()

    • setTileSizeX

      public int setTileSizeX(int tileSize) throws FormatException
      Description copied from interface: IFormatWriter
      Will attempt to set the tile width to the desired value and return the actual value which will be used
      Specified by:
      setTileSizeX in interface IFormatWriter
      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

      public int getTileSizeY() throws FormatException
      Description copied from interface: IFormatWriter
      Retrieves the current tile height Defaults to 0 if not supported
      Specified by:
      getTileSizeY in interface IFormatWriter
      Returns:
      The current tile height being used
      Throws:
      FormatException - Image metadata including Pixels Size Y must be set prior to calling getTileSizeY()

    • setTileSizeY

      public int setTileSizeY(int tileSize) throws FormatException
      Description copied from interface: IFormatWriter
      Will attempt to set the tile height to the desired value and return the actual value which will be used
      Specified by:
      setTileSizeY in interface IFormatWriter
      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

      public void setResolutions(List<Resolution> resolutions)
      Description copied from interface: IFormatWriter
      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.
      Specified by:
      setResolutions in interface IFormatWriter

    • getResolutions

      public List<Resolution> getResolutions()
      Description copied from interface: IFormatWriter
      Get a list of resolution objects for the current series.
      Specified by:
      getResolutions in interface IFormatWriter

    • getResolutionCount

      public int getResolutionCount()
      Description copied from interface: IPyramidHandler
      Return the number of resolutions for the current series. Resolutions are stored in descending order, so the largest resolution is first and the smallest resolution is last.
      Specified by:
      getResolutionCount in interface IPyramidHandler

    • getResolution

      public int getResolution()
      Description copied from interface: IPyramidHandler
      Get the current resolution level.
      Specified by:
      getResolution in interface IPyramidHandler
      See Also:

    • setResolution

      public void setResolution(int resolution)
      Description copied from interface: IPyramidHandler
      Set the resolution level.
      Specified by:
      setResolution in interface IPyramidHandler
      See Also:

    • setId

      public void setId(String id) throws FormatException, IOException
      Initializes a writer from the input file name. Initializes a RandomAccessOutputStream for the output file and initializes the metadata for all the series using setSeries(int).
      Specified by:
      setId in interface IFormatHandler
      Parameters:
      id - a String specifying the path to the file
      Throws:
      FormatException
      IOException

    • close

      public void close() throws IOException
      Specified by:
      close in interface AutoCloseable
      Specified by:
      close in interface Closeable
      Throws:
      IOException

    • checkParams

      protected void checkParams(int no, byte[] buf, int x, int y, int w, int h) throws FormatException
      Ensure that the arguments that are being passed to saveBytes(...) are valid.
      Throws:
      FormatException - if any of the arguments is invalid.

    • seekToPlaneOffset

      protected void seekToPlaneOffset(long baseOffset, int x, int y) throws IOException
      Seek to the given (x, y) coordinate of the image that starts at the given offset.
      Throws:
      IOException

    • isFullPlane

      protected boolean isFullPlane(int x, int y, int w, int h) throws FormatException
      Returns true if the given rectangle coordinates correspond to a full image in the given series.
      Throws:
      FormatException

    • getSamplesPerPixel

      protected int getSamplesPerPixel()
      Retrieve the number of samples per pixel for the current series.

    • getSamplesPerPixel

      protected int getSamplesPerPixel(int series)
      Retrieve the number of samples per pixel for given series.

    • getPlaneCount

      protected int getPlaneCount()
      Retrieve the total number of planes in the current series.

    • getPlaneCount

      protected int getPlaneCount(int series)
      Retrieve the total number of planes in given series.

    • createOutputStream

      protected loci.common.RandomAccessOutputStream createOutputStream() throws IOException
      Create an output stream for the current file path. If the file path's parent directory does not exist, it will be created.
      Returns:
      an open RandomAccessOuputStream for the current file
      Throws:
      IOException - if the directory or output stream creation fails

    • getSizeX

      protected int getSizeX() throws FormatException
      Throws:
      FormatException

    • getSizeY

      protected int getSizeY() throws FormatException
      Throws:
      FormatException

    • hasResolutions

      protected boolean hasResolutions()