Esempio n. 1
0
  /**
   * Save the specified sequence in the specified file.<br>
   * When the sequence contains severals image the multipleFile flag is used to indicate<br>
   * if images are saved as separate files (file then specify a directory) or not.<br>
   * zMin - zMax and tMin - tMax define the Z and T images range to save.<br>
   *
   * @param formatWriter writer used to save sequence (define the image format)
   * @param sequence sequence to save
   * @param filePath file name where we want to save sequence
   * @param zMin start Z position to save
   * @param zMax end Z position to save
   * @param tMin start T position to save
   * @param tMax end T position to save
   * @param fps frame rate for AVI sequence save
   * @param saveFrame progress frame for save operation (can be null)
   * @throws ServiceException
   * @throws IOException
   * @throws FormatException
   */
  private static void save(
      IFormatWriter formatWriter,
      Sequence sequence,
      String filePath,
      int zMin,
      int zMax,
      int tMin,
      int tMax,
      int fps,
      FileFrame saveFrame)
      throws ServiceException, FormatException, IOException {
    final File file = new File(filePath);
    final IFormatWriter writer;

    if (formatWriter == null) writer = getWriter(file, ImageFileFormat.TIFF);
    else writer = formatWriter;

    // TODO: temporary fix for the "incorrect close operation" bug in Bio-Formats
    // with OME TIF writer, remove it when fixed.
    // {
    // try
    // {
    // writer = formatWriter.getClass().newInstance();
    // }
    // catch (Exception e)
    // {
    // throw new ServiceException("Can't create new writer instance: " + e);
    // }
    // }

    if (writer == null)
      throw new UnknownFormatException(
          "Can't find a valid image writer for the specified file: " + filePath);

    // first delete the file else LOCI won't save it correctly
    if (file.exists()) file.delete();
    // ensure parent directory exist
    FileUtil.ensureParentDirExist(file);

    final int sizeC = sequence.getSizeC();
    final boolean separateChannel = getSeparateChannelFlag(writer, sequence.getColorModel());

    // set settings
    writer.setFramesPerSecond(fps);
    // generate metadata
    writer.setMetadataRetrieve(
        MetaDataUtil.generateMetaData(
            sequence, (zMax - zMin) + 1, (tMax - tMin) + 1, separateChannel));
    // no interleave (XP default viewer want interleaved channel to correctly read image)
    writer.setInterleaved(false);
    // set id
    writer.setId(filePath);
    // init
    writer.setSeries(0);
    // usually give better save performance
    writer.setWriteSequentially(true);

    // get endianess
    final boolean littleEndian =
        !writer.getMetadataRetrieve().getPixelsBinDataBigEndian(0, 0).booleanValue();
    byte[] data = null;

    try {
      int imageIndex = 0;
      // XYCZT order is important here (see metadata)
      for (int t = tMin; t <= tMax; t++) {
        for (int z = zMin; z <= zMax; z++) {
          if ((saveFrame != null) && saveFrame.isCancelRequested()) return;

          final IcyBufferedImage image = sequence.getImage(t, z);

          // separated channel data
          if (separateChannel) {
            for (int c = 0; c < sizeC; c++) {
              if (image != null) {
                // avoid multiple allocation
                data = image.getRawData(c, data, 0, littleEndian);
                writer.saveBytes(imageIndex, data);
              }

              imageIndex++;
            }
          } else {
            if (image != null) {
              // avoid multiple allocation
              data = image.getRawData(data, 0, littleEndian);
              writer.saveBytes(imageIndex, data);
            }

            imageIndex++;
          }

          if (saveFrame != null) saveFrame.incPosition();
        }
      }
    } finally {
      // always close writer after a file has been saved
      writer.close();
    }
  }
Esempio n. 2
0
  /**
   * Save the specified sequence in the specified file.<br>
   * When the sequence contains severals image the multipleFile flag is used to indicate if images
   * are saved as separate files (file then specify a directory) or not.<br>
   * <code>zMin</code> - <code>zMax</code> and <code>tMin</code> - <code>tMax</code> define the Z
   * and T images range to save.<br>
   *
   * @param formatWriter writer used to save sequence (define the image format).<br>
   *     If set to <code>null</code> then writer is determined from the file extension.<br>
   *     If destination file does not have a valid extension (for folder for instance) then you have
   *     to specify a valid Writer to write the image file (see {@link #getWriter(ImageFileFormat)})
   * @param sequence sequence to save
   * @param file file where we want to save sequence.<br>
   *     Depending the <code>formatWriter</code> the file extension may be modified.<br>
   *     That is preferred as saving an image with a wrong extension may result in error on future
   *     read (wrong reader detection).
   * @param zMin start Z position to save
   * @param zMax end Z position to save
   * @param tMin start T position to save
   * @param tMax end T position to save
   * @param fps frame rate for AVI sequence save
   * @param multipleFile flag to indicate if images are saved in separate file
   * @param showProgress show progress bar
   * @param addToRecent add the saved sequence to recent opened sequence list
   */
  public static void save(
      IFormatWriter formatWriter,
      Sequence sequence,
      File file,
      int zMin,
      int zMax,
      int tMin,
      int tMax,
      int fps,
      boolean multipleFile,
      boolean showProgress,
      boolean addToRecent) {
    final String filePath = FileUtil.cleanPath(FileUtil.getGenericPath(file.getAbsolutePath()));
    final int sizeT = (tMax - tMin) + 1;
    final int sizeZ = (zMax - zMin) + 1;
    final int numImages = sizeT * sizeZ;
    final FileFrame saveFrame;
    final ApplicationMenu mainMenu;

    if (addToRecent) mainMenu = Icy.getMainInterface().getApplicationMenu();
    else mainMenu = null;
    if (showProgress && !Icy.getMainInterface().isHeadLess())
      saveFrame = new FileFrame("Saving", filePath);
    else saveFrame = null;
    try {
      if (saveFrame != null) {
        saveFrame.setLength(numImages);
        saveFrame.setPosition(0);
      }

      // need multiple files ?
      if ((numImages > 1) && multipleFile) {
        final IFormatWriter writer;

        // so we won't create it for each image
        if (formatWriter == null) writer = getWriter(file, ImageFileFormat.TIFF);
        else writer = formatWriter;

        if (writer == null)
          throw new UnknownFormatException(
              "Can't find a valid image writer for the specified file: " + file);

        // save as severals images
        final DecimalFormat decimalFormat = new DecimalFormat("0000");
        final String fileName = FileUtil.getFileName(filePath, false);
        String fileExt = FileUtil.getFileExtension(filePath, true);

        String fileBaseDirectory = FileUtil.getDirectory(filePath);
        if (fileBaseDirectory.endsWith("/"))
          fileBaseDirectory = fileBaseDirectory.substring(0, fileBaseDirectory.length() - 1);

        // no extension (directory) ?
        if (StringUtil.isEmpty(fileExt)) {
          // filename is part of directory
          fileBaseDirectory += FileUtil.separator + fileName;
          // use the default file extension for the specified writer
          fileExt = "." + getImageFileFormat(writer, ImageFileFormat.TIFF).getExtensions()[0];
        }

        final String filePathWithoutExt = fileBaseDirectory + FileUtil.separator + fileName;

        // create output directory
        FileUtil.createDir(fileBaseDirectory);

        // default name used --> use filename
        if (sequence.isDefaultName()) sequence.setName(fileName);
        sequence.setFilename(fileBaseDirectory);

        for (int t = tMin; t <= tMax; t++) {
          for (int z = zMin; z <= zMax; z++) {
            String filename = filePathWithoutExt;

            if ((tMax - tMin) > 0) filename += "_t" + decimalFormat.format(t);
            if ((zMax - zMin) > 0) filename += "_z" + decimalFormat.format(z);
            filename += fileExt;

            // save as single image file
            save(writer, sequence, filename, z, z, t, t, fps, saveFrame);
          }
        }

        // add as one item to recent file list
        if (mainMenu != null) mainMenu.addRecentFile(fileBaseDirectory);
      } else {
        final String fileExt = FileUtil.getFileExtension(filePath, false);
        final ImageFileFormat iff;

        if (formatWriter != null) iff = getImageFileFormat(formatWriter, ImageFileFormat.TIFF);
        else iff = ImageFileFormat.getWriteFormat(fileExt, ImageFileFormat.TIFF);

        // force to set correct file extension
        final String fixedFilePath;

        if (iff.matches(fileExt)) fixedFilePath = filePath;
        else fixedFilePath = filePath + "." + iff.getExtensions()[0];

        // default name used --> use filename
        if (sequence.isDefaultName()) sequence.setName(FileUtil.getFileName(fixedFilePath, false));
        sequence.setFilename(fixedFilePath);

        // save into a single file
        save(formatWriter, sequence, fixedFilePath, zMin, zMax, tMin, tMax, fps, saveFrame);

        // add as one item to recent file list
        if (mainMenu != null) mainMenu.addRecentFile(fixedFilePath);
      }

      // Sequence persistence enabled --> save XML
      if (GeneralPreferences.getSequencePersistence()) sequence.saveXMLData();
    } catch (Exception e) {
      IcyExceptionHandler.showErrorMessage(e, true);
      if (showProgress && !Icy.getMainInterface().isHeadLess())
        new FailedAnnounceFrame("Failed to save image(s) (see output console for details)", 15);
      return;
    } finally {
      if (saveFrame != null) saveFrame.close();
    }
  }