Beispiel #1
0
  /**
   * Save a single image to the specified file
   *
   * @param image
   * @throws IOException
   * @throws FormatException
   */
  public static void saveImage(IcyBufferedImage image, File file, boolean force)
      throws FormatException, IOException {
    final IFormatWriter writer = getWriter(file, ImageFileFormat.TIFF);

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

    final boolean separateChannel = getSeparateChannelFlag(writer, image.getIcyColorModel());

    try {
      writer.setMetadataRetrieve(MetaDataUtil.generateMetaData(image, separateChannel));
    } catch (ServiceException e) {
      System.err.println("Saver.saveImage(...) error :");
      IcyExceptionHandler.showErrorMessage(e, true);
    }

    // get byte order
    final boolean littleEndian =
        !writer.getMetadataRetrieve().getPixelsBinDataBigEndian(0, 0).booleanValue();
    // then save the image
    saveImage(
        writer,
        image.getRawData(littleEndian),
        image.getSizeX(),
        image.getSizeY(),
        image.getSizeC(),
        separateChannel,
        image.getDataType_(),
        file,
        force);
  }
Beispiel #2
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();
  }
Beispiel #3
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();
    }
  }