Beispiel #1
0
  /**
   * Return the closest compatible {@link IcyColorModel} supported by writer from the specified
   * image description.<br>
   * That means the writer is able to save the data described by the returned {@link IcyColorModel}
   * without any loss or conversion.<br>
   *
   * @param writer IFormatWriter we want to test compatibility
   * @param numChannel number of channel of the image
   * @param dataType image data type
   */
  public static IcyColorModel getCompatibleColorModel(
      IFormatWriter writer, int numChannel, DataType dataType) {
    final DataType outDataType;
    final int outNumChannel;

    if (writer instanceof OMETiffWriter) {
      // TIFF supports all formats
      outDataType = dataType;
      outNumChannel = numChannel;
    } else if (writer instanceof APNGWriter) {
      // PNG only supports byte and short data type
      if (dataType.getSize() > 2) outDataType = DataType.USHORT;
      else outDataType = dataType;

      // PNG supports a maximum of 4 channels
      outNumChannel = Math.min(numChannel, 4);
    } else {
      // JPG, AVI, default only supports byte data type
      if (dataType.getSize() > 1) outDataType = DataType.UBYTE;
      else outDataType = dataType;

      // 3 channels at max
      if (numChannel > 3) outNumChannel = 3;
      else {
        // special case of 2 channels
        if (numChannel == 2)
          // convert to RGB
          outNumChannel = 3;
        else outNumChannel = numChannel;
      }
    }

    return IcyColorModel.createInstance(outNumChannel, outDataType);
  }
Beispiel #2
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 /** @deprecated use {@link OMEUtil#generateMetaData(int, int, int, DataType, boolean)} instead */
 @Deprecated
 public static OMEXMLMetadata generateMetaData(
     int sizeX, int sizeY, int sizeC, int dataType, boolean signedDataType)
     throws ServiceException {
   return OMEUtil.generateMetaData(
       sizeX, sizeY, sizeC, DataType.getDataType(dataType, signedDataType), false);
 }
Beispiel #3
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 /** @deprecated Use {@link #saveImage(byte[], int, int, int, DataType, File, boolean)} instead */
 @Deprecated
 public static void saveImage(
     byte[] data,
     int width,
     int height,
     int numChannel,
     int dataType,
     boolean signedDataType,
     File file,
     boolean force)
     throws FormatException, IOException {
   saveImage(
       data,
       width,
       height,
       numChannel,
       DataType.getDataType(dataType, signedDataType),
       file,
       force);
 }
Beispiel #4
0
  /** Save a single image from bytes buffer to the specified file. */
  private static void saveImage(
      IFormatWriter formatWriter,
      byte[] data,
      int width,
      int height,
      int numChannel,
      boolean separateChannel,
      DataType dataType,
      File file,
      boolean force)
      throws FormatException, IOException {
    final String filePath = FileUtil.cleanPath(FileUtil.getGenericPath(file.getAbsolutePath()));

    if (FileUtil.exists(filePath)) {
      // forced ? first delete the file else LOCI won't save it
      if (force) FileUtil.delete(filePath, true);
      else throw new IOException("File already exists");
    }
    // ensure parent directory exist
    FileUtil.ensureParentDirExist(filePath);

    final IFormatWriter writer;
    final boolean separateCh;

    if (formatWriter == null) {
      // get the writer
      writer = getWriter(FileUtil.getFileExtension(filePath, false), ImageFileFormat.TIFF);

      // prepare the metadata
      try {
        separateCh = getSeparateChannelFlag(writer, numChannel, dataType);
        writer.setMetadataRetrieve(
            MetaDataUtil.generateMetaData(width, height, numChannel, dataType, separateCh));
      } catch (ServiceException e) {
        System.err.println("Saver.saveImage(...) error :");
        IcyExceptionHandler.showErrorMessage(e, true);
      }
    } else {
      // ready to use writer (metadata already prepared)
      writer = formatWriter;
      separateCh = separateChannel;
    }

    // we never interleaved data even if some image viewer need it to correctly read image (win XP
    // viewer)
    writer.setInterleaved(false);
    writer.setId(filePath);
    writer.setSeries(0);
    // usually give better save performance
    writer.setWriteSequentially(true);

    try {
      // separated channel data
      if (separateChannel) {
        final int pitch = width * height * dataType.getSize();
        final byte[] dataChannel = new byte[pitch];
        int offset = 0;

        for (int c = 0; c < numChannel; c++) {
          System.arraycopy(data, offset, dataChannel, 0, pitch);
          writer.saveBytes(c, dataChannel);
          offset += pitch;
        }
      } else
        // save all data at once
        writer.saveBytes(0, data);
    } catch (Exception e) {
      System.err.println("Saver.saveImage(...) error :");
      IcyExceptionHandler.showErrorMessage(e, true);
    }

    writer.close();
  }