Пример #1
0
  private IFD writeYCbCrImage(
      ImageOutputStream out, BufferedImage image, int comp, TIFFImageWriteParam param)
      throws IOException {
    image = convert(image, BufferedImage.TYPE_INT_RGB);
    try {
      int width = image.getWidth();
      int height = image.getHeight();

      IFD ifd = new IFD(); // entries need to be in tag order !

      int ss = (param == null) ? 0x22 : param.getSubSampling();

      int ssh = (ss >> 4) & 0x0F;
      int ssv = ss & 0x0F;

      if (ssh
          < ssv) { // YCbCrSubsampleVert shall always be less than or equal to YCbCrSubsampleHoriz.
        throw new IOException(
            "Internal error: YCbCrSubsampleVert is not less than YCbCrSubsampleHoriz.");
      }

      //      int ww=((width +ssh-1)/ssh)*ssh;                                   // [1] p.92
      //      int hh=((height+ssv-1)/ssv)*ssv;
      int ww = width;
      int hh = height;

      ifd.add(new DEFactory.NewSubfileTypeDE(2)); // 254 single page of multipage file
      ifd.add(new DEFactory.ImageWidthDE(ww)); // 256
      ifd.add(new DEFactory.ImageLengthDE(hh)); // 257

      DEFactory.BitsPerSampleDE bpss = new DEFactory.BitsPerSampleDE(3);
      bpss.setBitsPerSample(0, 8); // Y
      bpss.setBitsPerSample(1, 8); // Cb
      bpss.setBitsPerSample(2, 8); // Cr
      ifd.add(bpss); // 258

      ifd.add(new DEFactory.CompressionDE(comp)); // 259
      ifd.add(new DEFactory.PhotometricInterpretationDE(YCbCr)); // 262

      int maxrps, maxstripes; // max RowsPerStrip
      if ((1 << 13) <= width) {
        maxrps = 1;
        maxstripes = height; // one row per strip
      } else {
        maxrps = (1 << 13) / width;
        maxstripes = (height + maxrps - 1) / maxrps;
      }
      if (comp == JPEG) {
        maxrps = ((maxrps + 8 * ssv - 1) / (8 * ssv)) * (8 * ssv);
        maxstripes = (height + maxrps - 1) / maxrps;
      }

      DEFactory.StripOffsetsDE offsets = new DEFactory.StripOffsetsDE(maxstripes);
      ifd.add(offsets); // 273
      ifd.add(new DEFactory.SamplesPerPixelDE(3)); // 277
      ifd.add(new DEFactory.RowsPerStripDE(maxrps)); // 278
      DEFactory.StripByteCountsDE counts = new DEFactory.StripByteCountsDE(maxstripes);
      ifd.add(counts); // 279

      if (param == null) {
        ifd.add(new DEFactory.XResolutionDE(72.0)); // 282
        ifd.add(new DEFactory.YResolutionDE(72.0)); // 283
      } else {
        ifd.add(new DEFactory.XResolutionDE(param.getXResolution())); // 282
        ifd.add(new DEFactory.YResolutionDE(param.getYResolution())); // 283
      }
      ifd.add(new DEFactory.ResolutionUnitDE(Inch)); // 296

      ByteArrayOutputStream baos = new ByteArrayOutputStream();
      OutputStream os = baos;
      JPEGOutputStream jpegos = null;

      if (comp == JPEG) {
        jpegos = new JPEGOutputStream(baos);

        int quality = (param == null) ? 50 : (int) (param.getCompressionQuality() * 100);

        jpegos.setZZQuantizationTable(0, JPEGConstants.LQT, quality);
        jpegos.setZZQuantizationTable(1, JPEGConstants.CQT, quality);

        jpegos.setRawDCHuffmanTable(0, JPEGConstants.HLDCTable);
        jpegos.setRawACHuffmanTable(0, JPEGConstants.HLACTable);
        jpegos.setRawDCHuffmanTable(1, JPEGConstants.HCDCTable);
        jpegos.setRawACHuffmanTable(1, JPEGConstants.HCACTable);

        jpegos.defineQuantizationTables();
        jpegos.defineHuffmanTables();
        jpegos.close();

        DEFactory.JPEGTablesDE jpegtables = new DEFactory.JPEGTablesDE(baos.toByteArray());
        ifd.add(jpegtables); // 347

        baos.reset();

        os = jpegos;
      }

      //      CCIR Recommendation 601-1  LumaRed=299/1000 LumaGreen=587/1000 LumeBlue=114/1000
      //      Y  = ( LumaRed * R + LumaGreen * G + LumaBlue * B )
      //      Cb = ( B - Y ) / ( 2 - 2 * LumaBlue )
      //      Cr = ( R - Y ) / ( 2 - 2 * LumaRed )

      double LumaRed = 299.0 / 1000.0;
      double LumaGreen = 587.0 / 1000.0;
      double LumaBlue = 114.0 / 1000.0;

      DEFactory.YCbCrCoefficientsDE YCbCrCoeff = new DEFactory.YCbCrCoefficientsDE();
      YCbCrCoeff.setLumaRed(LumaRed); // Y
      YCbCrCoeff.setLumaGreen(LumaGreen); // Cb
      YCbCrCoeff.setLumaBlue(LumaBlue); // Cr
      ifd.add(YCbCrCoeff); // 529

      DEFactory.YCbCrSubSamplingDE YCbCrSubSampling = new DEFactory.YCbCrSubSamplingDE();
      YCbCrSubSampling.setHoriz(ssh);
      YCbCrSubSampling.setVert(ssv);
      ifd.add(YCbCrSubSampling); // 530

      double RfBY = 0;
      double RfWY = 255;
      double RfBCb = 128;
      double RfWCb = 255;
      double RfBCr = 128;
      double RfWCr = 255;

      DEFactory.ReferenceBlackWhiteDE ReferenceBlackWhite = new DEFactory.ReferenceBlackWhiteDE();
      ReferenceBlackWhite.setY(RfBY, RfWY);
      ReferenceBlackWhite.setCb(RfBCb, RfWCb);
      ReferenceBlackWhite.setCr(RfBCr, RfWCr);
      ifd.add(ReferenceBlackWhite); // 532

      TIFFYCbCrOutputStream ycbcros;
      if (jpegos == null) {
        ycbcros = new TIFFYCbCrOutputStream(os, width, ssv, ssh);
        os = new TIFFSubSamplingOutputStream(ycbcros, width, ssv, ssh);
      } else {
        ycbcros = new TIFFYCbCrOutputStream(os, width, 1, 1); // jpeg does own subsampling
        os = ycbcros;
      }

      ycbcros.setPositioning(1);
      ycbcros.setColourCoefficients(LumaRed, LumaGreen, LumaBlue);
      ycbcros.setRfBWY(RfBY, RfWY);
      ycbcros.setRfBWCb(RfBCb, RfWCb);
      ycbcros.setRfBWCr(RfBCr, RfWCr);

      WritableRaster raster = image.getRaster();
      DataBufferInt buffer = (DataBufferInt) raster.getDataBuffer();
      int[] imgdata = (int[]) buffer.getData();

      int c = 0, index = 0;
      for (int y = 0; y < height; y += maxrps) {

        if ((height - y) < maxrps) {
          maxrps = height - y;
        }

        if (jpegos != null) {
          jpegos.startOfImage();
          int[] hv = {(ssh << 4) | ssv, 0x11, 0x11}; // (Hi<<4)|Vi
          int[] q = {0, 1, 1}; // quantization table Y=0, Cb=Cr=1
          //          jpegos.startOfFrame(((maxrps+ssv-1)/ssv)*ssv,ww,hv,q);
          jpegos.startOfFrame(maxrps, ww, hv, q);
          int[] sel = {0, 1, 1}; // DC,AC code table Y=0, Cb=Cr=1
          jpegos.startOfScan(sel);
        }

        for (int i = 0; i < maxrps; i++) {
          int x = 0;
          while (x < width) {
            c = imgdata[x + (y + i) * width];
            //            c = image.getRGB(x,y+i);
            os.write((c >> 16) & 0x000000FF);
            os.write((c >> 8) & 0x000000FF);
            os.write(c & 0x000000FF);
            x++;
          }
          while (x < ww) {
            os.write((c >> 16) & 0x000000FF);
            os.write((c >> 8) & 0x000000FF);
            os.write(c & 0x000000FF);
            x++;
          }
        }
        os.close();

        byte[] data = baos.toByteArray();
        counts.setCount(index, data.length); // update ifd strip counter array
        offsets.setOffset(index, out.getStreamPosition()); // update ifd image data offset array
        out.write(data); // write to image stream
        baos.reset();
        index++;
      }
      return ifd;
    } catch (Exception e) {
      e.printStackTrace();
      throw new IOException(getClass().getName() + ".writeYCbCrImage:\n\t" + e.getMessage());
    }
  }
Пример #2
0
  private IFD writeCMYKImage(ImageOutputStream out, BufferedImage image, TIFFImageWriteParam param)
      throws IOException {
    try {
      int width = image.getWidth();
      int height = image.getHeight();

      IFD ifd = new IFD(); // entries need to be in tag order !

      ifd.add(new DEFactory.NewSubfileTypeDE(2)); // 254 single page of multipage file
      ifd.add(new DEFactory.ImageWidthDE(width)); // 256
      ifd.add(new DEFactory.ImageLengthDE(height)); // 257

      DEFactory.BitsPerSampleDE bpss = new DEFactory.BitsPerSampleDE(4);
      bpss.setBitsPerSample(0, 8); // cyan
      bpss.setBitsPerSample(1, 8); // magneta
      bpss.setBitsPerSample(2, 8); // yellow
      bpss.setBitsPerSample(3, 8); // key (black)
      ifd.add(bpss); // 258

      ifd.add(new DEFactory.CompressionDE(NOCOMPRESSION)); // 259
      ifd.add(new DEFactory.PhotometricInterpretationDE(CMYK)); // 262

      int maxrps, maxstripes; // max RowsPerStrip
      if ((1 << 13) <= width) {
        maxrps = 1;
        maxstripes = height; // one row per strip
      } else {
        maxrps = (1 << 13) / width;
        maxstripes = (height + maxrps - 1) / maxrps;
      }

      DEFactory.StripOffsetsDE offsets = new DEFactory.StripOffsetsDE(maxstripes);
      ifd.add(offsets); // 273
      ifd.add(new DEFactory.SamplesPerPixelDE(4)); // 277
      ifd.add(new DEFactory.RowsPerStripDE(maxrps)); // 278
      DEFactory.StripByteCountsDE counts = new DEFactory.StripByteCountsDE(maxstripes);
      ifd.add(counts); // 279

      if (param == null) {
        ifd.add(new DEFactory.XResolutionDE(72.0)); // 282
        ifd.add(new DEFactory.YResolutionDE(72.0)); // 283
      } else {
        ifd.add(new DEFactory.XResolutionDE(param.getXResolution())); // 282
        ifd.add(new DEFactory.YResolutionDE(param.getYResolution())); // 283
      }
      ifd.add(new DEFactory.ResolutionUnitDE(Inch)); // 296

      int index = 0;
      for (int y = 0; y < height; y += maxrps) {
        /*
        Assume rgb image.

        Each strip: evaluate c m y k colour
                    save in byte array
                    write to image file
        */

        ByteArrayOutputStream baos = new ByteArrayOutputStream();

        for (int i = 0; i < maxrps; i++) {
          if ((y + i) == height) {
            break;
          } // last strip might have less rows
          for (int x = 0; x < width; x++) {
            int c = image.getRGB(x, y + i);

            int R = (c >> 16) & 0x00FF;
            int G = (c >> 8) & 0x00FF;
            int B = (c) & 0x00FF;

            if ((R == 255) && (G == 255) && (B == 255)) {
              baos.write(0);
              baos.write(0);
              baos.write(0);
              baos.write(0);
            } else {
              double C = 1.0 - R / 255.0;
              double M = 1.0 - G / 255.0;
              double Y = 1.0 - B / 255.0;

              double K = C;
              if (M < K) {
                K = M;
              }
              if (Y < K) {
                K = Y;
              }

              C = ((C - K) / (1.0 - K)) * 255.0;
              M = ((M - K) / (1.0 - K)) * 255.0;
              Y = ((Y - K) / (1.0 - K)) * 255.0;
              K *= 255.0;

              baos.write((int) C);
              baos.write((int) M);
              baos.write((int) Y);
              baos.write((int) K);
            }
          }
        }
        baos.close();

        byte[] data = baos.toByteArray();
        counts.setCount(index, data.length); // update ifd strip counter array
        offsets.setOffset(index, out.getStreamPosition()); // update ifd image data offset array
        out.write(data); // write to image stream

        index++;
      }
      return ifd;
    } catch (Exception e) {
      e.printStackTrace();
      throw new IOException(getClass().getName() + ".writeCMYKImage:\n\t" + e.getMessage());
    }
  }
Пример #3
0
  private IFD writeBModHufImage(
      ImageOutputStream out, BufferedImage image, TIFFImageWriteParam param) throws IOException {
    try {
      int width = image.getWidth();
      int height = image.getHeight();

      IFD ifd = new IFD(); // entries need to be in tag order !

      ifd.add(new DEFactory.NewSubfileTypeDE(2)); // 254 single page of multipage file
      ifd.add(new DEFactory.ImageWidthDE(width)); // 256
      ifd.add(new DEFactory.ImageLengthDE(height)); // 257
      ifd.add(new DEFactory.CompressionDE(CCITTGROUP3MODHUFFMAN)); // 259
      ifd.add(new DEFactory.PhotometricInterpretationDE(WhiteIsZero)); // 262

      int maxrps, maxstripes; // max RowsPerStrip
      if ((1 << 13) <= width) {
        maxrps = 1;
        maxstripes = height; // one row per stripe
      } else {
        maxrps = (1 << 13) / width;
        maxstripes = (height + maxrps - 1) / maxrps;
      }

      DEFactory.StripOffsetsDE offsets = new DEFactory.StripOffsetsDE(maxstripes);
      ifd.add(offsets); // 273
      ifd.add(new DEFactory.RowsPerStripDE(maxrps)); // 278
      DEFactory.StripByteCountsDE counts = new DEFactory.StripByteCountsDE(maxstripes);
      ifd.add(counts); // 279

      if (param == null) {
        ifd.add(new DEFactory.XResolutionDE(72.0)); // 282
        ifd.add(new DEFactory.YResolutionDE(72.0)); // 283
      } else {
        ifd.add(new DEFactory.XResolutionDE(param.getXResolution())); // 282
        ifd.add(new DEFactory.YResolutionDE(param.getYResolution())); // 283
      }
      ifd.add(new DEFactory.ResolutionUnitDE(Inch)); // 296

      int index = 0;
      for (int y = 0; y < height; y += maxrps) {
        /*
        Assume bilevel image (black/white[=-1])

        Each strip: count run length
                    encode into modified hufman codes
                    swap bits
                    save in byte array
                    write to image file
        */

        ByteArrayOutputStream baos = new ByteArrayOutputStream();
        BitSwapOutputStream bsos = new BitSwapOutputStream(baos);
        ModHuffmanOutputStream mhos = new ModHuffmanOutputStream(bsos);

        RLEOutputStream rlos =
            new RLEOutputStream(mhos, 3); // rgb = 3 bytes per sample code word (not needed here)

        for (int i = 0; i < maxrps; i++) {
          if ((y + i) == height) {
            break;
          } // last strip might have less rows
          rlos.setStartCodeWord(-1); // white run first
          for (int x = 0; x < width; x++) {
            rlos.write(image.getRGB(x, y + i));
          }
          rlos.flush(); // write padding after ever image row
        }
        rlos.close();

        byte[] data = baos.toByteArray();
        counts.setCount(index, data.length); // update ifd strip counter array
        offsets.setOffset(index, out.getStreamPosition()); // update ifd image data offset array
        out.write(data); // write to image stream

        index++;
      }
      return ifd;
    } catch (Exception e) {
      e.printStackTrace();
      throw new IOException(getClass().getName() + ".writeBModHufImage:\n\t" + e.getMessage());
    }
  }
Пример #4
0
  private IFD writeRGBImage(
      ImageOutputStream out, BufferedImage image, int comp, TIFFImageWriteParam param)
      throws IOException {
    image = convert(image, BufferedImage.TYPE_INT_RGB);
    try {
      int width = image.getWidth();
      int height = image.getHeight();

      IFD ifd = new IFD(); // entries need to be in tag order !

      ifd.add(new DEFactory.NewSubfileTypeDE(2)); // 254 single page of multipage file
      ifd.add(new DEFactory.ImageWidthDE(width)); // 256
      ifd.add(new DEFactory.ImageLengthDE(height)); // 257

      DEFactory.BitsPerSampleDE bpss = new DEFactory.BitsPerSampleDE(3);
      bpss.setBitsPerSample(0, 8); // red
      bpss.setBitsPerSample(1, 8); // green
      bpss.setBitsPerSample(2, 8); // blue
      ifd.add(bpss); // 258

      ifd.add(new DEFactory.CompressionDE(comp)); // 259
      ifd.add(new DEFactory.PhotometricInterpretationDE(RGB)); // 262

      int maxrps, maxstripes; // max RowsPerStrip
      if ((1 << 13) <= width) {
        maxrps = 1;
        maxstripes = height; // one row per strip
      } else {
        maxrps = (1 << 13) / width;
        maxstripes = (height + maxrps - 1) / maxrps;
      }
      if (comp == JPEG) {
        maxrps = ((maxrps + 8 - 1) / 8) * 8;
        maxstripes = (height + maxrps - 1) / maxrps;
      }
      DEFactory.StripOffsetsDE offsets = new DEFactory.StripOffsetsDE(maxstripes);
      ifd.add(offsets); // 273
      ifd.add(new DEFactory.SamplesPerPixelDE(3)); // 277
      ifd.add(new DEFactory.RowsPerStripDE(maxrps)); // 278
      DEFactory.StripByteCountsDE counts = new DEFactory.StripByteCountsDE(maxstripes);
      ifd.add(counts); // 279
      if (param == null) {
        ifd.add(new DEFactory.XResolutionDE(72.0)); // 282
        ifd.add(new DEFactory.YResolutionDE(72.0)); // 283
      } else {
        ifd.add(new DEFactory.XResolutionDE(param.getXResolution())); // 282
        ifd.add(new DEFactory.YResolutionDE(param.getYResolution())); // 283
      }
      ifd.add(new DEFactory.ResolutionUnitDE(Inch)); // 296

      ByteArrayOutputStream baos = new ByteArrayOutputStream();
      OutputStream os = baos;
      JPEGOutputStream jpegos = null;

      if (comp == JPEG) { // add JPEGTables tag
        jpegos = new JPEGOutputStream(baos);

        int quality = (param == null) ? 50 : (int) (param.getCompressionQuality() * 100);

        jpegos.setZZQuantizationTable(0, JPEGConstants.LQT, quality);
        jpegos.setRawDCHuffmanTable(0, JPEGConstants.HLDCTable);
        jpegos.setRawACHuffmanTable(0, JPEGConstants.HLACTable);

        jpegos.defineQuantizationTables();
        jpegos.defineHuffmanTables();
        jpegos.close();

        DEFactory.JPEGTablesDE jpegtables = new DEFactory.JPEGTablesDE(baos.toByteArray());
        ifd.add(jpegtables); // 347

        baos.reset();

        os = jpegos;
      }

      WritableRaster raster = image.getRaster();
      DataBufferInt buffer = (DataBufferInt) raster.getDataBuffer();
      int[] imgdata = (int[]) buffer.getData();

      int index = 0;
      for (int y = 0; y < height; y += maxrps) {
        /*
        Assume rgb image.

        Each strip: evaluate r g b colour
                    save in byte array
                    write to image file
        */

        if ((height - y) < maxrps) {
          maxrps = height - y;
        }

        if (jpegos != null) { // jpeg: SOI,SOF,SOS marker
          jpegos.startOfImage();
          int[] hv = {0x11, 0x11, 0x11}; // (Hi<<4)|Vi
          int[] q = {0, 0, 0}; // quantization table 0
          jpegos.startOfFrame(maxrps, width, hv, q);
          int[] sel = {0, 0, 0}; // DC,AC code table 0
          jpegos.startOfScan(sel);
        }

        for (int i = 0; i < maxrps; i++) { // write RGB data
          for (int x = 0; x < width; x++) {
            int c = imgdata[x + (y + i) * width];
            os.write((c >> 16) & 0x000000FF);
            os.write((c >> 8) & 0x000000FF);
            os.write(c & 0x000000FF);
          }
        }
        os.close(); // jpeg: EOI marker

        byte[] data = baos.toByteArray();
        counts.setCount(index, data.length); // update ifd strip counter array
        offsets.setOffset(index, out.getStreamPosition()); // update ifd image data offset array
        out.write(data); // write to image stream
        baos.reset();
        index++;
      }
      return ifd;
    } catch (Exception e) {
      e.printStackTrace();
      throw new IOException(getClass().getName() + ".writeRGBImage:\n\t" + e.getMessage());
    }
  }
Пример #5
0
  /**
   * Convert an image to RGB.
   *
   * @param inFile the file to convert.
   * @param outFile the output file, which may be same as inFile.
   * @return the static status result
   */
  public static AnonymizerStatus convert(File inFile, File outFile) {

    long fileLength = inFile.length();
    logger.debug("Entering DICOMPaletteImageConverter.convert");
    logger.debug("File length       = " + fileLength);

    BufferedInputStream in = null;
    BufferedOutputStream out = null;
    File tempFile = null;
    byte[] buffer = new byte[4096];
    try {
      // Check that this is a known format.
      in = new BufferedInputStream(new FileInputStream(inFile));
      DcmParser parser = pFact.newDcmParser(in);
      FileFormat fileFormat = parser.detectFileFormat();
      if (fileFormat == null) {
        throw new IOException("Unrecognized file format: " + inFile);
      }

      // Get the dataset (excluding pixels) and leave the input stream open
      Dataset dataset = oFact.newDataset();
      parser.setDcmHandler(dataset.getDcmHandler());
      parser.parseDcmFile(fileFormat, Tags.PixelData);

      // Make sure this is an image
      if (parser.getReadTag() != Tags.PixelData) {
        close(in);
        return AnonymizerStatus.SKIP(inFile, "Not an image");
      }

      // Get the required parameters and make sure they are okay
      int numberOfFrames = getInt(dataset, Tags.NumberOfFrames, 1);
      int rows = getInt(dataset, Tags.Rows, 0);
      int columns = getInt(dataset, Tags.Columns, 0);
      String photometricInterpretation = getString(dataset, Tags.PhotometricInterpretation, "");
      if ((rows == 0) || (columns == 0)) {
        close(in);
        return AnonymizerStatus.SKIP(inFile, "Unable to get the rows and columns");
      }
      if (!photometricInterpretation.equals("PALETTE COLOR")) {
        close(in);
        return AnonymizerStatus.SKIP(
            inFile, "Unsupported PhotometricInterpretation: " + photometricInterpretation);
      }
      if (parser.getReadTag() != Tags.PixelData) {
        close(in);
        return AnonymizerStatus.SKIP(inFile, "No pixels");
      }

      // Get the encoding and set the parameters
      DcmDecodeParam fileParam = parser.getDcmDecodeParam();
      String fileEncodingUID = UIDs.ImplicitVRLittleEndian;
      FileMetaInfo fmi = dataset.getFileMetaInfo();
      if (fmi != null) fileEncodingUID = fmi.getTransferSyntaxUID();
      boolean isBigEndian = fileEncodingUID.equals(UIDs.ExplicitVRBigEndian);
      String encodingUID = UIDs.ExplicitVRLittleEndian;
      DcmEncodeParam encoding = (DcmEncodeParam) DcmDecodeParam.valueOf(encodingUID);
      boolean swap = (fileParam.byteOrder != encoding.byteOrder);

      if (encoding.encapsulated) {
        logger.debug("Encapsulated pixel data found");
        close(in);
        return AnonymizerStatus.SKIP(inFile, "Encapsulated pixel data not supported");
      }

      // Get the LUTs
      LUT red =
          new LUT(
              dataset.getInts(Tags.RedPaletteColorLUTDescriptor),
              dataset.getInts(Tags.RedPaletteColorLUTData));
      LUT green =
          new LUT(
              dataset.getInts(Tags.GreenPaletteColorLUTDescriptor),
              dataset.getInts(Tags.GreenPaletteColorLUTData));
      LUT blue =
          new LUT(
              dataset.getInts(Tags.BluePaletteColorLUTDescriptor),
              dataset.getInts(Tags.BluePaletteColorLUTData));

      // Set the PlanarConfiguration to 0
      dataset.putUS(Tags.PlanarConfiguration, 0);

      // Set the PhotometricInterpretation to RGB
      dataset.putCS(Tags.PhotometricInterpretation, "RGB");

      // Set the pixel parameters
      dataset.putUS(Tags.SamplesPerPixel, 3);
      dataset.putUS(Tags.BitsAllocated, 8);
      dataset.putUS(Tags.BitsStored, 8);
      dataset.putUS(Tags.HighBit, 7);

      // Remove the lookup tables and their descriptors
      dataset.remove(Tags.RedPaletteColorLUTDescriptor);
      dataset.remove(Tags.GreenPaletteColorLUTDescriptor);
      dataset.remove(Tags.BluePaletteColorLUTDescriptor);
      dataset.remove(Tags.RedPaletteColorLUTData);
      dataset.remove(Tags.GreenPaletteColorLUTData);
      dataset.remove(Tags.BluePaletteColorLUTData);

      // Save the dataset to a temporary file, and rename at the end.
      File tempDir = outFile.getParentFile();
      tempFile = File.createTempFile("DCMtemp-", ".anon", tempDir);
      out = new BufferedOutputStream(new FileOutputStream(tempFile));

      // Create and write the metainfo for the encoding we are using
      fmi = oFact.newFileMetaInfo(dataset, encodingUID);
      dataset.setFileMetaInfo(fmi);
      fmi.write(out);

      // Write the dataset as far as was parsed
      dataset.writeDataset(out, encoding);

      // Process the pixels
      int nPixels = numberOfFrames * rows * columns;
      int nPixelBytes = nPixels * 3 /*samplesPerPixel*/;
      int pad = nPixelBytes & 1;
      dataset.writeHeader(out, encoding, parser.getReadTag(), VRs.OB, nPixelBytes + pad);

      int pd;
      int b1, b2;
      int bytesPerFrame = rows * columns * 2;
      byte[] frameBytes = new byte[bytesPerFrame];
      for (int frame = 0; frame < numberOfFrames; frame++) {
        if (in.read(frameBytes, 0, frameBytes.length) != bytesPerFrame)
          throw new Exception("End of File");
        for (int p = 0; p < bytesPerFrame; ) {
          b1 = frameBytes[p++];
          b2 = frameBytes[p++];
          if (!swap) {
            pd = ((b2 & 0xff) << 8) | (b1 & 0xff);
          } else {
            pd = ((b1 & 0xff) << 8) | (b2 & 0xff);
          }
          out.write(red.get(pd));
          out.write(green.get(pd));
          out.write(blue.get(pd));
        }
      }
      if (pad != 0) out.write(0);
      logger.debug("Finished writing the pixels");

      // Skip everything after the pixels
      out.flush();
      out.close();
      in.close();
      outFile.delete();
      tempFile.renameTo(outFile);
      return AnonymizerStatus.OK(outFile, "");
    } catch (Exception e) {
      logger.debug("Exception while processing image.", e);

      // Close the input stream if it actually got opened.
      close(in);

      // Close the output stream if it actually got opened,
      // and delete the tempFile in case it is still there.
      try {
        if (out != null) {
          out.close();
          tempFile.delete();
        }
      } catch (Exception ex) {
        logger.warn("Unable to close the output stream.");
      }

      // Quarantine the object
      return AnonymizerStatus.QUARANTINE(inFile, e.getMessage());
    }
  }