@Override
  public void run(final String arg0) {
    final GenericDialogPlus dialog = new GenericDialogPlus("Inverse Compositional Image Alignment");
    dialog.addImageChoice("template", null);
    dialog.addImageChoice("image to align", null);
    dialog.addNumericField("max iterations", 50, 0);
    dialog.addNumericField("min parameter change", 0.001, 4);
    dialog.showDialog();
    if (dialog.wasCanceled()) return;

    ImagePlus impTemplate = dialog.getNextImage();
    ImagePlus impImage = dialog.getNextImage();
    int maxIterations = (int) dialog.getNextNumber();
    double minParameterChange = dialog.getNextNumber();

    if (impTemplate == null || impImage == null) {
      IJ.showMessage("Please select two images.");
      return;
    }

    RandomAccessibleInterval<FloatType> template = ImageJFunctions.convertFloat(impTemplate);
    RandomAccessibleInterval<FloatType> image = ImageJFunctions.convertFloat(impImage);
    if (image == null || template == null) {
      IJ.showMessage("Image type not supported.");
      return;
    }

    Align<FloatType> align = new Align<>(template, new ArrayImgFactory<>());
    AffineTransform transform = align.align(image, maxIterations, minParameterChange);

    // TODO:
    // 1.) Use ImageJFunctions.wrapRGBA(), wrapByte(), etc. to get a Img<T> wrapping impImage
    //     with T according to the type of the ImagePlus.
    // 2.) Show the transformed Img<T>. Maybe put this functionality into a generic method to
    //     avoid having to re-implement each case.
    switch (impTemplate.getType()) {
      case ImagePlus.GRAY8:
        // TODO
        break;
      case ImagePlus.GRAY16:
        // TODO
        break;
      case ImagePlus.GRAY32:
        // TODO
        break;
      case ImagePlus.COLOR_RGB:
        // TODO
        break;
      default:
        IJ.showMessage("Image type not supported.");
    }
  }
  public <T extends RealType<T>> void process(Img<T> img) {
    // compute the gradient on the image
    Img<FloatType> gradient = gradient(img);

    // show the new Img that contains the gradient
    ImageJFunctions.show(gradient);
  }
Ejemplo n.º 3
0
  public Example1c() {
    // create the ImgFactory based on cells (cellsize = 5x5x5...x5) that will
    // instantiate the Img
    final ImgFactory<FloatType> imgFactory = new CellImgFactory<FloatType>(5);

    // create an 3d-Img with dimensions 20x30x40 (here cellsize is 5x5x5)Ø
    final Img<FloatType> img1 = imgFactory.create(new long[] {20, 30, 40}, new FloatType());

    // create another image with the same size
    // note that the input provides the size for the new image as it implements
    // the Interval interface
    final Img<FloatType> img2 = imgFactory.create(img1, img1.firstElement());

    // display both (but they are empty)
    ImageJFunctions.show(img1);
    ImageJFunctions.show(img2);
  }
Ejemplo n.º 4
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  public Example6a1() throws ImgIOException {
    // open with ImgOpener as a FloatType
    Img<FloatType> image = new ImgOpener().openImg("DrosophilaWing.tif", new FloatType());

    // perform gaussian convolution with float precision
    double[] sigma = new double[image.numDimensions()];

    for (int d = 0; d < image.numDimensions(); ++d) sigma[d] = 8;

    // convolve & display
    ImageJFunctions.show(Gauss.toFloat(sigma, image));
  }
  public void run(String arg0) {
    // get the current ImageJ ImagePlus
    ImagePlus imp = WindowManager.getCurrentImage();

    // test if an image is open
    if (imp == null) {
      IJ.log("No image open");
      return;
    }

    // wrap it into an ImgLib2 Img (no copying)
    Img<RealType> img = ImageJFunctions.wrapReal(imp);

    // test if it could be wrapped
    if (img == null) {
      IJ.log("Cannot wrap image");
      return;
    }

    // process wrapped image with ImgLib2
    process(img);
  }
Ejemplo n.º 6
0
  public static void main(final String[] args) {

    final int N_BLOBS = 20;
    final double RADIUS = 5; // µm
    final Random RAN = new Random();
    final double WIDTH = 100; // µm
    final double HEIGHT = 100; // µm
    final double DEPTH = 50; // µm
    final double[] CALIBRATION = new double[] {0.5f, 0.5f, 1};
    final AxisType[] AXES = new AxisType[] {Axes.X, Axes.Y, Axes.Z};

    // Create 3D image
    final Img<UnsignedByteType> source =
        new ArrayImgFactory<UnsignedByteType>()
            .create(
                new int[] {
                  (int) (WIDTH / CALIBRATION[0]),
                  (int) (HEIGHT / CALIBRATION[1]),
                  (int) (DEPTH / CALIBRATION[2])
                },
                new UnsignedByteType());
    final ImgPlus<UnsignedByteType> img =
        new ImgPlus<UnsignedByteType>(source, "Test", AXES, CALIBRATION);

    // Random blobs
    final double[] radiuses = new double[N_BLOBS];
    final ArrayList<double[]> centers = new ArrayList<double[]>(N_BLOBS);
    final int[] intensities = new int[N_BLOBS];
    double x, y, z;
    for (int i = 0; i < N_BLOBS; i++) {
      radiuses[i] = RADIUS + RAN.nextGaussian();
      x = WIDTH * RAN.nextFloat();
      y = HEIGHT * RAN.nextFloat();
      z = DEPTH * RAN.nextFloat();
      centers.add(i, new double[] {x, y, z});
      intensities[i] = RAN.nextInt(100) + 100;
    }

    // Put the blobs in the image
    for (int i = 0; i < N_BLOBS; i++) {
      final Spot tmpSpot =
          new Spot(centers.get(i)[0], centers.get(i)[1], centers.get(i)[2], radiuses[i], -1d);
      tmpSpot.putFeature(Spot.RADIUS, radiuses[i]);
      final SpotNeighborhood<UnsignedByteType> sphere =
          new SpotNeighborhood<UnsignedByteType>(tmpSpot, img);
      for (final UnsignedByteType pixel : sphere) {
        pixel.set(intensities[i]);
      }
    }

    // Instantiate detector
    final LogDetector<UnsignedByteType> detector =
        new LogDetector<UnsignedByteType>(
            img, img, TMUtils.getSpatialCalibration(img), RADIUS, 0, true, false);

    // Segment
    final long start = System.currentTimeMillis();
    if (!detector.checkInput() || !detector.process()) {
      System.out.println(detector.getErrorMessage());
      return;
    }
    final Collection<Spot> spots = detector.getResult();
    final long end = System.currentTimeMillis();

    // Display image
    ImageJFunctions.show(img);

    // Display results
    final int spot_found = spots.size();
    System.out.println("Segmentation took " + (end - start) + " ms.");
    System.out.println("Found " + spot_found + " blobs.\n");

    Point3d p1, p2;
    double dist, min_dist;
    int best_index = 0;
    double[] best_match;
    final ArrayList<Spot> spot_list = new ArrayList<Spot>(spots);
    Spot best_spot = null;
    final double[] coords = new double[3];
    final String[] posFeats = Spot.POSITION_FEATURES;

    while (!spot_list.isEmpty() && !centers.isEmpty()) {

      min_dist = Float.POSITIVE_INFINITY;
      for (final Spot s : spot_list) {

        int index = 0;
        for (final String pf : posFeats) {
          coords[index++] = s.getFeature(pf).doubleValue();
        }
        p1 = new Point3d(coords);

        for (int j = 0; j < centers.size(); j++) {
          p2 = new Point3d(centers.get(j));
          dist = p1.distance(p2);
          if (dist < min_dist) {
            min_dist = dist;
            best_index = j;
            best_spot = s;
          }
        }
      }

      spot_list.remove(best_spot);
      best_match = centers.remove(best_index);
      int index = 0;
      for (final String pf : posFeats) {
        coords[index++] = best_spot.getFeature(pf).doubleValue();
      }
      System.out.println("Blob coordinates: " + Util.printCoordinates(coords));
      System.out.println(
          String.format(
              "  Best matching center at distance %.1f with coords: "
                  + Util.printCoordinates(best_match),
              min_dist));
    }
    System.out.println();
    System.out.println("Unmatched centers:");
    for (int i = 0; i < centers.size(); i++)
      System.out.println("Center " + i + " at position: " + Util.printCoordinates(centers.get(i)));
  }
Ejemplo n.º 7
0
  public static void main(final String[] args) {

    // TEST 2D case

    // Parameters
    final int size_x = 200;
    final int size_y = 200;

    final long a = 10;
    final long b = 5;
    final double phi_r = Math.toRadians(30);

    final long max_radius = Math.max(a, b);
    final double[] calibration = new double[] {1, 1};

    // Create blank image
    final Img<UnsignedByteType> img =
        new ArrayImgFactory<UnsignedByteType>()
            .create(new int[] {200, 200}, new UnsignedByteType());
    final ImgPlus<UnsignedByteType> imgplus = new ImgPlus<UnsignedByteType>(img);
    for (int d = 0; d < imgplus.numDimensions(); d++) {
      imgplus.setAxis(new DefaultLinearAxis(imgplus.axis(d).type(), calibration[d]), d);
    }
    final byte on = (byte) 255;

    // Create an ellipse
    long start = System.currentTimeMillis();
    System.out.println(String.format("Creating an ellipse with a = %d, b = %d", a, b));
    System.out.println(String.format("phi = %.1f", Math.toDegrees(phi_r)));
    final long[] center = new long[] {size_x / 2, size_y / 2};
    final long[] radiuses = new long[] {max_radius, max_radius};

    final EllipseNeighborhood<UnsignedByteType> disc =
        new EllipseNeighborhood<UnsignedByteType>(img, center, radiuses);
    final EllipseCursor<UnsignedByteType> sc = disc.cursor();

    double r2, phi, term;
    double cosphi, sinphi;
    while (sc.hasNext()) {
      sc.fwd();
      r2 = sc.getDistanceSquared();
      phi = sc.getPhi();
      cosphi = Math.cos(phi - phi_r);
      sinphi = Math.sin(phi - phi_r);
      term = r2 * cosphi * cosphi / a / a + r2 * sinphi * sinphi / b / b;
      if (term <= 1) sc.get().set(on);
    }
    final long end = System.currentTimeMillis();
    System.out.println("Ellipse creation done in " + (end - start) + " ms.");
    System.out.println();

    ij.ImageJ.main(args);
    ImageJFunctions.show(imgplus);

    start = System.currentTimeMillis();
    final Spot spot = new Spot(center[0], center[1], 0d, max_radius, -1d);

    final SpotMorphologyAnalyzer<UnsignedByteType> bm =
        new SpotMorphologyAnalyzer<UnsignedByteType>(imgplus, null);
    bm.process(spot);

    System.out.println("Blob morphology analyzed in " + (end - start) + " ms.");
    double phiv, thetav, lv;
    for (int j = 0; j < 2; j++) {
      lv = spot.getFeature(featurelist_sa[j]);
      phiv = spot.getFeature(featurelist_phi[j]);
      thetav = spot.getFeature(featurelist_theta[j]);
      System.out.println(
          String.format(
              "For axis of semi-length %.1f, orientation is phi = %.1f°, theta = %.1f°",
              lv, Math.toDegrees(phiv), Math.toDegrees(thetav)));
    }
    System.out.println(spot.echo());

    // TEST 3D case
    /*
     *
     * // Parameters int size_x = 200; int size_y = 200; int size_z = 200;
     *
     * double a = 5.5f; double b = 4.9f; double c = 5; double theta_r =
     * (double) Math.toRadians(0); // I am unable to have it working for
     * theta_r != 0 double phi_r = (double) Math.toRadians(45);
     *
     * double max_radius = Math.max(a, Math.max(b, c)); double[] calibration
     * = new double[] {1, 1, 1};
     *
     * // Create blank image Image<UnsignedByteType> img = new
     * ImageFactory<UnsignedByteType>( new UnsignedByteType(), new
     * ArrayContainerFactory() ).createImage(new int[] {200, 200, 200});
     * final byte on = (byte) 255;
     *
     * // Create an ellipse long start = System.currentTimeMillis();
     * System.out.println(String.format(
     * "Creating an ellipse with a = %.1f, b = %.1f, c = %.1f", a, b, c));
     * System.out.println(String.format("phi = %.1f and theta = %.1f",
     * Math.toDegrees(phi_r), Math.toDegrees(theta_r))); double[] center =
     * new double[] { size_x/2, size_y/2, size_z/2 };
     * SphereCursor<UnsignedByteType> sc = new
     * SphereCursor<UnsignedByteType>(img, center, max_radius, calibration);
     * double r2, theta, phi, term; double cosphi, sinphi, costheta,
     * sintheta; while (sc.hasNext()) { sc.fwd(); r2 =
     * sc.getDistanceSquared(); phi = sc.getPhi(); theta = sc.getTheta();
     * cosphi = Math.cos(phi-phi_r); sinphi = Math.sin(phi-phi_r); costheta
     * = Math.cos(theta-theta_r); sintheta = Math.sin(theta-theta_r); term =
     * r2*cosphi*cosphi*sintheta*sintheta/a/a +
     * r2*sinphi*sinphi*sintheta*sintheta/b/b + r2*costheta*costheta/c/c; if
     * (term <= 1) sc.getType().set(on); } sc.close(); long end =
     * System.currentTimeMillis();
     * System.out.println("Ellipse creation done in " + (end-start) +
     * " ms."); System.out.println();
     *
     * ij.ImageJ.main(args); img.getDisplay().setMinMax();
     * ImageJFunctions.copyToImagePlus(img).show();
     *
     * start = System.currentTimeMillis(); BlobMorphology<UnsignedByteType>
     * bm = new BlobMorphology<UnsignedByteType>(img, calibration); SpotImp
     * spot = new SpotImp(center); spot.putFeature(Feature.RADIUS,
     * max_radius); bm.process(spot); end = System.currentTimeMillis();
     * System.out.println("Blob morphology analyzed in " + (end-start) +
     * " ms."); double phiv, thetav, lv; for (int j = 0; j < 3; j++) { lv =
     * spot.getFeature(featurelist_sa[j]); phiv =
     * spot.getFeature(featurelist_phi[j]); thetav =
     * spot.getFeature(featurelist_theta[j]);
     * System.out.println(String.format(
     * "For axis of semi-length %.1f, orientation is phi = %.1f°, theta = %.1f°"
     * , lv, Math.toDegrees(phiv), Math.toDegrees(thetav))); }
     * System.out.println(spot.echo());
     */
  }
  /**
   * Fuses one stack, i.e. all angles/illuminations for one timepoint and channel
   *
   * @param timepoint
   * @param channel
   * @return
   */
  public boolean fuseStacksAndGetPSFs(
      final TimePoint timepoint,
      final Channel channel,
      final ImgFactory<FloatType> imgFactory,
      final int osemIndex,
      double osemspeedup,
      WeightType weightType,
      final HashMap<Channel, ChannelPSF> extractPSFLabels,
      final long[] psfSize,
      final HashMap<Channel, ArrayList<Pair<Pair<Angle, Illumination>, String>>> psfFiles,
      final boolean transformLoadedPSFs) {
    // TODO: get rid of this hack
    if (files != null) {
      weightType = WeightType.LOAD_WEIGHTS;
      IOFunctions.println("WARNING: LOADING WEIGHTS FROM IMAGES, files.length()=" + files.length);
    }

    // get all views that are fused for this timepoint & channel
    this.viewDescriptions =
        FusionHelper.assembleInputData(spimData, timepoint, channel, viewIdsToProcess);

    if (this.viewDescriptions.size() == 0) return false;

    this.imgs = new HashMap<ViewId, RandomAccessibleInterval<FloatType>>();
    this.weights = new HashMap<ViewId, RandomAccessibleInterval<FloatType>>();

    final Img<FloatType> overlapImg;

    if (weightType == WeightType.WEIGHTS_ONLY)
      overlapImg = imgFactory.create(bb.getDimensions(), new FloatType());
    else overlapImg = null;

    final boolean extractPSFs =
        (extractPSFLabels != null) && (extractPSFLabels.get(channel).getLabel() != null);
    final boolean loadPSFs = (psfFiles != null);

    if (extractPSFs) ePSF = new ExtractPSF<FloatType>();
    else if (loadPSFs) ePSF = loadPSFs(channel, viewDescriptions, psfFiles, transformLoadedPSFs);
    else {
      ePSF = assignOtherChannel(channel, extractPSFLabels);
    }

    if (ePSF == null) return false;

    // remember the extracted or loaded PSFs
    extractPSFLabels.get(channel).setExtractPSFInstance(ePSF);

    // we will need to run some batches until all is fused
    for (int i = 0; i < viewDescriptions.size(); ++i) {
      final ViewDescription vd = viewDescriptions.get(i);

      IOFunctions.println(
          "Transforming view "
              + i
              + " of "
              + (viewDescriptions.size() - 1)
              + " (viewsetup="
              + vd.getViewSetupId()
              + ", tp="
              + vd.getTimePointId()
              + ")");
      IOFunctions.println(
          "("
              + new Date(System.currentTimeMillis())
              + "): Reserving memory for transformed & weight image.");

      // creating the output
      RandomAccessibleInterval<FloatType> transformedImg; // might be null if WEIGHTS_ONLY
      final RandomAccessibleInterval<FloatType>
          weightImg; // never null (except LOAD_WEIGHTS which is not implemented yet)

      if (weightType == WeightType.WEIGHTS_ONLY) transformedImg = overlapImg;
      else transformedImg = imgFactory.create(bb.getDimensions(), new FloatType());

      IOFunctions.println(
          "("
              + new Date(System.currentTimeMillis())
              + "): Transformed image factory: "
              + imgFactory.getClass().getSimpleName());

      // loading the input if necessary
      final RandomAccessibleInterval<FloatType> img;

      if (weightType == WeightType.WEIGHTS_ONLY && !extractPSFs) {
        img = null;
      } else {
        IOFunctions.println("(" + new Date(System.currentTimeMillis()) + "): Loading image.");
        img = ProcessFusion.getImage(new FloatType(), spimData, vd, true);

        if (Img.class.isInstance(img))
          IOFunctions.println(
              "("
                  + new Date(System.currentTimeMillis())
                  + "): Input image factory: "
                  + ((Img<FloatType>) img).factory().getClass().getSimpleName());
      }

      // initializing weights
      IOFunctions.println(
          "("
              + new Date(System.currentTimeMillis())
              + "): Initializing transformation & weights: "
              + weightType.name());

      spimData.getViewRegistrations().getViewRegistration(vd).updateModel();
      final AffineTransform3D transform =
          spimData.getViewRegistrations().getViewRegistration(vd).getModel();
      final long[] offset = new long[] {bb.min(0), bb.min(1), bb.min(2)};

      if (weightType == WeightType.PRECOMPUTED_WEIGHTS || weightType == WeightType.WEIGHTS_ONLY)
        weightImg = imgFactory.create(bb.getDimensions(), new FloatType());
      else if (weightType == WeightType.NO_WEIGHTS)
        weightImg =
            Views.interval(
                new ConstantRandomAccessible<FloatType>(
                    new FloatType(1), transformedImg.numDimensions()),
                transformedImg);
      else if (weightType == WeightType.VIRTUAL_WEIGHTS) {
        final Blending blending = getBlending(img, blendingBorder, blendingRange, vd);

        weightImg =
            new TransformedRealRandomAccessibleInterval<FloatType>(
                blending, new FloatType(), transformedImg, transform, offset);
      } else // if ( processType == ProcessType.LOAD_WEIGHTS )
      {
        IOFunctions.println("WARNING: LOADING WEIGHTS FROM: '" + new File(files[i]) + "'");
        ImagePlus imp = StackImgLoaderIJ.open(new File(files[i]));
        weightImg = imgFactory.create(bb.getDimensions(), new FloatType());
        StackImgLoaderIJ.imagePlus2ImgLib2Img(imp, (Img<FloatType>) weightImg, false);
        imp.close();
        if (debugImport) {
          imp = ImageJFunctions.show(weightImg);
          imp.setTitle("ViewSetup " + vd.getViewSetupId() + " Timepoint " + vd.getTimePointId());
        }
      }

      // split up into many parts for multithreading
      final Vector<ImagePortion> portions =
          FusionHelper.divideIntoPortions(
              Views.iterable(transformedImg).size(), Threads.numThreads() * 4);

      // set up executor service
      final ExecutorService taskExecutor = Executors.newFixedThreadPool(Threads.numThreads());
      final ArrayList<Callable<String>> tasks = new ArrayList<Callable<String>>();

      IOFunctions.println(
          "("
              + new Date(System.currentTimeMillis())
              + "): Transforming image & computing weights.");

      for (final ImagePortion portion : portions) {
        if (weightType == WeightType.WEIGHTS_ONLY) {
          final Interval imgInterval =
              new FinalInterval(
                  ViewSetupUtils.getSizeOrLoad(
                      vd.getViewSetup(),
                      vd.getTimePoint(),
                      spimData.getSequenceDescription().getImgLoader()));
          final Blending blending = getBlending(imgInterval, blendingBorder, blendingRange, vd);

          tasks.add(
              new TransformWeights(
                  portion, imgInterval, blending, transform, overlapImg, weightImg, offset));
        } else if (weightType == WeightType.PRECOMPUTED_WEIGHTS) {
          final Blending blending = getBlending(img, blendingBorder, blendingRange, vd);

          tasks.add(
              new TransformInputAndWeights(
                  portion, img, blending, transform, transformedImg, weightImg, offset));
        } else if (weightType == WeightType.NO_WEIGHTS
            || weightType == WeightType.VIRTUAL_WEIGHTS
            || weightType == WeightType.LOAD_WEIGHTS) {
          tasks.add(new TransformInput(portion, img, transform, transformedImg, offset));
        } else {
          throw new RuntimeException(weightType.name() + " not implemented yet.");
        }
      }

      try {
        // invokeAll() returns when all tasks are complete
        taskExecutor.invokeAll(tasks);
      } catch (final InterruptedException e) {
        IOFunctions.println("Failed to compute fusion: " + e);
        e.printStackTrace();
        return false;
      }

      taskExecutor.shutdown();

      // extract PSFs if wanted
      if (extractPSFs) {
        final ArrayList<double[]> llist =
            getLocationsOfCorrespondingBeads(
                timepoint, vd, extractPSFLabels.get(channel).getLabel());

        IOFunctions.println(
            "("
                + new Date(System.currentTimeMillis())
                + "): Extracting PSF for viewsetup "
                + vd.getViewSetupId()
                + " using label '"
                + extractPSFLabels.get(channel).getLabel()
                + "'"
                + " ("
                + llist.size()
                + " corresponding detections available)");

        ePSF.extractNextImg(img, vd, transform, llist, psfSize);
      }

      if (weightType != WeightType.WEIGHTS_ONLY) imgs.put(vd, transformedImg);
      weights.put(vd, weightImg);
    }

    // normalize the weights
    final ArrayList<RandomAccessibleInterval<FloatType>> weightsSorted =
        new ArrayList<RandomAccessibleInterval<FloatType>>();

    for (final ViewDescription vd : viewDescriptions) weightsSorted.add(weights.get(vd));

    IOFunctions.println(
        "("
            + new Date(System.currentTimeMillis())
            + "): Computing weight normalization for deconvolution.");

    final WeightNormalizer wn;

    if (weightType == WeightType.WEIGHTS_ONLY
        || weightType == WeightType.PRECOMPUTED_WEIGHTS
        || weightType == WeightType.LOAD_WEIGHTS) wn = new WeightNormalizer(weightsSorted);
    else if (weightType == WeightType.VIRTUAL_WEIGHTS)
      wn = new WeightNormalizer(weightsSorted, imgFactory);
    else // if ( processType == ProcessType.NO_WEIGHTS )
    wn = null;

    if (wn != null && !wn.process()) return false;

    // put the potentially modified weights back
    for (int i = 0; i < viewDescriptions.size(); ++i)
      weights.put(viewDescriptions.get(i), weightsSorted.get(i));

    this.minOverlappingViews = wn.getMinOverlappingViews();
    this.avgOverlappingViews = wn.getAvgOverlappingViews();

    IOFunctions.println(
        "("
            + new Date(System.currentTimeMillis())
            + "): Minimal number of overlapping views: "
            + getMinOverlappingViews()
            + ", using "
            + (this.minOverlappingViews = Math.max(1, this.minOverlappingViews)));
    IOFunctions.println(
        "("
            + new Date(System.currentTimeMillis())
            + "): Average number of overlapping views: "
            + getAvgOverlappingViews()
            + ", using "
            + (this.avgOverlappingViews = Math.max(1, this.avgOverlappingViews)));

    if (osemIndex == 1) osemspeedup = getMinOverlappingViews();
    else if (osemIndex == 2) osemspeedup = getAvgOverlappingViews();

    IOFunctions.println(
        "("
            + new Date(System.currentTimeMillis())
            + "): Adjusting for OSEM speedup = "
            + osemspeedup);

    if (weightType == WeightType.WEIGHTS_ONLY)
      displayWeights(osemspeedup, weightsSorted, overlapImg, imgFactory);
    else adjustForOSEM(weights, weightType, osemspeedup);

    IOFunctions.println(
        "("
            + new Date(System.currentTimeMillis())
            + "): Finished precomputations for deconvolution.");

    return true;
  }
Ejemplo n.º 9
0
 /** Saves image using imageJ */
 public void saveImage(final String file) {
   ImagePlus ips = ImageJFunctions.show(getImage());
   FileSaver fs = new FileSaver(ips);
   fs.saveAsTiff(file);
 }
Ejemplo n.º 10
0
 /** Shows image using fiji */
 public void showImage(final String title) {
   ImageJFunctions.show(getImage()).setTitle(title);
 }