Ejemplo n.º 1
0
  private <T extends RealType<T>> void populatePlane(
      IFormatReader r, int no, byte[] plane, LocalizablePlaneCursor<T> cursor) {
    final int sizeX = r.getSizeX();
    final int pixelType = r.getPixelType();
    final boolean little = r.isLittleEndian();

    final int[] dimLengths = getDimLengths(r);
    final int[] pos = new int[dimLengths.length];

    final int planeX = 0;
    final int planeY = 1;

    getPosition(r, no, pos);
    cursor.reset(planeX, planeY, pos);

    while (cursor.hasNext()) {
      cursor.fwd();
      final int index = cursor.getPosition(planeX) + cursor.getPosition(planeY) * sizeX;
      final double value = decodeWord(plane, index, pixelType, little);
      cursor.getType().setReal(value);
    }
  }
Ejemplo n.º 2
0
  /**
   * Reads in an imglib {@link Image} from the given initialized {@link IFormatReader}, using the
   * given {@link ImageFactory}.
   */
  public <T extends RealType<T>> Image<T> openImage(IFormatReader r, ImageFactory<T> imageFactory)
      throws FormatException, IOException {
    final String[] dimTypes = getDimTypes(r);
    final int[] dimLengths = getDimLengths(r);

    // TEMP - make suffix out of dimension types, until imglib supports them
    final String id = r.getCurrentFile();
    final File idFile = new File(id);
    String name = idFile.exists() ? idFile.getName() : id;
    name = encodeName(name, dimTypes);

    // create image object
    final Image<T> img = imageFactory.createImage(dimLengths, name);

    // set calibration of the image
    img.setCalibration(getCalibration(r, dimLengths));

    // TODO - create better container types; either:
    // 1) an array container type using one byte array per plane
    // 2) as #1, but with an IFormatReader reference reading planes on demand
    // 3) as PlanarContainer, but with an IFormatReader reference
    //    reading planes on demand

    // PlanarContainer is useful for efficient access to pixels in ImageJ
    // (e.g., getPixels)
    // #1 is useful for efficient Bio-Formats import, and useful for tools
    //   needing byte arrays (e.g., BufferedImage Java3D texturing by reference)
    // #2 is useful for efficient memory use for tools wanting matching
    //   primitive arrays (e.g., virtual stacks in ImageJ)
    // #3 is useful for efficient memory use

    // get container
    final PlanarAccess<?> planarAccess = getPlanarAccess(img);
    final T inputType = makeType(r.getPixelType());
    final T outputType = imageFactory.createType();
    final boolean compatibleTypes = outputType.getClass().isAssignableFrom(inputType.getClass());

    final long startTime = System.currentTimeMillis();

    // populate planes
    final int planeCount = r.getImageCount();
    if (planarAccess == null || !compatibleTypes) {
      // use cursor to populate planes

      // NB: This solution is general and works regardless of container,
      // but at the expense of performance both now and later.

      final LocalizablePlaneCursor<T> cursor = img.createLocalizablePlaneCursor();
      byte[] plane = null;
      for (int no = 0; no < planeCount; no++) {
        notifyListeners(
            new StatusEvent(no, planeCount, "Reading plane " + (no + 1) + "/" + planeCount));
        if (plane == null) plane = r.openBytes(no);
        else r.openBytes(no, plane);
        populatePlane(r, no, plane, cursor);
      }
      cursor.close();
    } else {
      // populate the values directly using PlanarAccess interface;
      // e.g., to a PlanarContainer

      byte[] plane = null;
      for (int no = 0; no < planeCount; no++) {
        notifyListeners(
            new StatusEvent(no, planeCount, "Reading plane " + (no + 1) + "/" + planeCount));
        if (plane == null) plane = r.openBytes(no);
        else r.openBytes(no, plane);
        populatePlane(r, no, plane, planarAccess);
      }
    }
    r.close();

    final long endTime = System.currentTimeMillis();
    final float time = (endTime - startTime) / 1000f;
    notifyListeners(
        new StatusEvent(
            planeCount, planeCount, id + ": read " + planeCount + " planes in " + time + "s"));

    return img;
  }