Package loci.formats.out

Class DicomWriter

java.lang.Object
loci.formats.FormatHandler
loci.formats.FormatWriter
loci.formats.out.DicomWriter
All Implemented Interfaces:
Closeable, AutoCloseable, ICompressedTileWriter, IFormatHandler, IFormatWriter, IMetadataConfigurable, IPyramidHandler, IExtraMetadataWriter
public class DicomWriter extends FormatWriter implements IExtraMetadataWriter
DicomWriter is the file format writer for DICOM files. This is designed for whole slide images, and may not produce schema-compliant files for other modalities.

  • Field Details

    • UID_ROOT_KEY

      public static final String UID_ROOT_KEY
      Option for setting the organization root for UIDs.
      See Also:

    • UID_DEFAULT_ROOT

      public static final String UID_DEFAULT_ROOT
      See Also:

    • TIFF_KEY

      public static final String TIFF_KEY
      Option for turning off TIFF metadata.
      See Also:

    • SOP_CLASS_UID_VALUE

      private static final String SOP_CLASS_UID_VALUE
      See Also:

    • pixelDataLengthPointer

      private long[] pixelDataLengthPointer

    • pixelDataSize

      private int[] pixelDataSize

    • transferSyntaxPointer

      private long[] transferSyntaxPointer

    • compressionMethodPointer

      private long[] compressionMethodPointer

    • nextIFDPointer

      private long[] nextIFDPointer

    • ifds

      private IFD[][] ifds

    • fileMetaLengthPointer

      private long fileMetaLengthPointer

    • baseTileWidth

      private int baseTileWidth

    • baseTileHeight

      private int baseTileHeight

    • tileWidth

      private int[] tileWidth

    • tileHeight

      private int[] tileHeight

    • tileWidthPointer

      private long[] tileWidthPointer

    • tileHeightPointer

      private long[] tileHeightPointer

    • tileCountPointer

      private long[] tileCountPointer

    • planeOffsets

      private DicomWriter.PlaneOffset[][] planeOffsets

    • currentPlane

      private Integer currentPlane

    • uids

      private DicomWriter.UIDCreator uids

    • instanceUIDValue

      private String instanceUIDValue

    • implementationUID

      private String implementationUID

    • tagProviders

      private ArrayList<ITagProvider> tagProviders

    • bigTiff

      private boolean bigTiff

    • tiffSaver

      private TiffSaver tiffSaver

    • validPixelCount

      private Boolean validPixelCount

  • Constructor Details

    • DicomWriter

      public DicomWriter()

  • Method Details

    • setExtraMetadata

      public void setExtraMetadata(String tagSource)
      Description copied from interface: IExtraMetadataWriter
      Provide additional metadata that should be written as part of this dataset. Primarily intended for DicomWriter. Calling this method is optional. Multiple calls are allowed, e.g. if tags come from multiple external sources. If multiple calls to this method are made then the order matters, with earlier calls implying higher priority when resolving duplicate or conflicting tags. All calls to this method must occur before setId is called.
      Specified by:
      setExtraMetadata in interface IExtraMetadataWriter

    • setBigTiff

      public void setBigTiff(boolean bigTiff)
      Sets whether or not BigTIFF files should be written. This flag is not reset when close() is called.

    • writeDualPersonality

      public boolean writeDualPersonality()
      Checks the writer's associated MetadataOptions to see if dual personality writing has been explicitly enabled or disabled. If the option is not set, the default is to return true, enabling dual personality writing.

    • setSeries

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

    • setResolution

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

    • getCodec

      public Codec getCodec()
      Specified by:
      getCodec in interface ICompressedTileWriter
      Returns:
      the codec that can be used to compress tiles

    • saveCompressedBytes

      public void saveCompressedBytes(int no, byte[] buf, int x, int y, int w, int h) throws FormatException, IOException
      Description copied from interface: ICompressedTileWriter
      Save a compressed tile to the current output file. The compression type of the tile should match the compression type set in the writer.
      Specified by:
      saveCompressedBytes in interface ICompressedTileWriter
      Parameters:
      no - plane index
      buf - compressed tile bytes
      x - pixel X coordinate of the upper-left corner of the tile
      y - pixel Y coordinate of the upper-left corner of the tile
      w - width in pixels of the compressed tile
      h - height in pixels of the compressed tile
      Throws:
      FormatException
      IOException

    • saveBytes

      public void saveBytes(int no, byte[] buf, int x, int y, int w, int h) 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.
      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.
      See Also:

    • 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
      Overrides:
      canDoStacks in class FormatWriter

    • 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
      Overrides:
      getPixelTypes in class FormatWriter

    • setId

      public void setId(String id) throws FormatException, IOException
      Description copied from class: FormatWriter
      Initializes a writer from the input file name. Initializes a RandomAccessOutputStream for the output file and initializes the metadata for all the series using FormatWriter.setSeries(int).
      Specified by:
      setId in interface IFormatHandler
      Overrides:
      setId in class FormatWriter
      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
      Overrides:
      close in class FormatWriter
      Throws:
      IOException

    • 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
      Overrides:
      setTileSizeX in class FormatWriter
      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

    • getTileSizeX

      public int getTileSizeX()
      Description copied from interface: IFormatWriter
      Retrieves the current tile width Defaults to 0 if not supported
      Specified by:
      getTileSizeX in interface IFormatWriter
      Overrides:
      getTileSizeX in class FormatWriter
      Returns:
      The current tile width being used

    • 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
      Overrides:
      setTileSizeY in class FormatWriter
      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

    • getTileSizeY

      public int getTileSizeY()
      Description copied from interface: IFormatWriter
      Retrieves the current tile height Defaults to 0 if not supported
      Specified by:
      getTileSizeY in interface IFormatWriter
      Overrides:
      getTileSizeY in class FormatWriter
      Returns:
      The current tile height being used

    • getUIDRoot

      public String getUIDRoot()

    • getStoredLength

      private int getStoredLength(DicomTag tag)

    • writeTag

      private void writeTag(DicomTag tag) throws IOException
      Throws:
      IOException

    • writeTag

      private void writeTag(DicomTag tag, loci.common.RandomAccessOutputStream output) throws IOException
      Throws:
      IOException

    • padString

      private String padString(String value)
      Pad the given string so that the length is a multiple of 2. If the input is null, an empty string is returned. Otherwise, a space is appended if necessary. This should not be used for UID values.
      Parameters:
      value - original string
      Returns:
      padded string whose length is a multiple of 2

    • padUID

      private String padUID(String value)
      Pad the given string so that the length is a multiple of 2. If the input is null, an empty string is returned. Otherwise, a null character is appended if necessary. This should not be used for non-UID values.
      Parameters:
      value - original string
      Returns:
      padded string whose length is a multiple of 2

    • padString

      private String padString(String value, String append)

    • padString

      private String padString(String value, String append, int length)

    • getTransferSyntax

      private String getTransferSyntax()
      Returns:
      transfer syntax UID corresponding to the current compression type

    • getCompressionMethod

      private String getCompressionMethod()
      Returns:
      compression method corresponding to the current compression type

    • openFile

      private void openFile(int pyramid, int res) throws IOException
      Throws:
      IOException

    • writeHeader

      private void writeHeader() throws IOException
      Write the preamble, prefix, and file meta elements. See http://dicom.nema.org/medical/dicom/current/output/html/part10.html#sect_7.1
      Throws:
      IOException

    • getFilename

      private String getFilename(int pyramid, int res)

    • getIndex

      private int getIndex(int pyramid, int res)

    • getZCTCoords

      private int[] getZCTCoords(int no)

    • isReallySequential

      private boolean isReallySequential()

    • getImageType

      private String getImageType(String pyramidName, int res, boolean hasPyramid, int resolutionCount)

    • writeIFDs

      private void writeIFDs(int resIndex) throws IOException
      Throws:
      IOException

    • getTIFFCompression

      private TiffCompression getTIFFCompression()

    • makeItem

      private DicomTag makeItem()
      Returns:
      item tag with an undefined length

    • makeItemDelimitation

      private DicomTag makeItemDelimitation()
      Returns:
      item delimitation tag with 0 length

    • lookupTag

      private DicomTag lookupTag(List<DicomTag> tags, DicomTag compare)

    • padTagValues

      private void padTagValues(DicomTag t)

    • makeShortArray

      private short[] makeShortArray(int v)

    • fixUnits

      private ome.units.quantity.Length fixUnits(ome.units.quantity.Length size)
      Check if the unit for the given Length is "pixel" or "referenceframe". These two units cannot be assigned to proper physical units (e.g. mm), so need to be handled specially.

    • getPhysicalSize

      private TiffRational getPhysicalSize(ome.units.quantity.Length size)

    • checkPrecompressedSupport

      private void checkPrecompressedSupport()
      Check if pre-compressed tiles are supported with the current options. TODO: maybe this should be a higher-level API method?
      Throws:
      UnsupportedOperationException - if pre-compressed tiles are not supported

    • checkPixelCount

      private void checkPixelCount(boolean warn) throws FormatException
      Throws:
      FormatException

    • getScientificNotationPattern

      private static String getScientificNotationPattern(int intDigits, int signBytes, int width)

    • formatFixedWidth

      public static String formatFixedWidth(double v, int width)
      Format the given double as a string with no more than width characters.

    • stopWatch

      protected org.perf4j.slf4j.Slf4JStopWatch stopWatch()