Examples with AffineModel3D mpicbg.trakem2.transform.AffineModel3D used on opensource projects

Example 1 with AffineModel3D

use of mpicbg.trakem2.transform.AffineModel3D in project TrakEM2 by trakem2.

the class Display method insertStack.

/**
 * @param stack_patch is just a Patch of a series of Patch that make a stack of Patches.
 */
private boolean insertStack(final ProjectThing target_landmarks, final Project source, final ProjectThing source_landmarks, final Patch stack_patch) {
    final List<Ball> l1 = new ArrayList<Ball>();
    final List<Ball> l2 = new ArrayList<Ball>();
    // source is the one that has the stack_patch
    final Collection<ProjectThing> b1s = source_landmarks.findChildrenOfType("ball");
    // target is this
    final Collection<ProjectThing> b2s = target_landmarks.findChildrenOfType("ball");
    final HashSet<String> seen = new HashSet<String>();
    for (final ProjectThing b1 : b1s) {
        final Ball ball1 = (Ball) b1.getObject();
        if (null == ball1) {
            Utils.log("ERROR: there's an empty 'ball' node in target project" + project.toString());
            return false;
        }
        final String title1 = ball1.getTitle();
        for (final ProjectThing b2 : b2s) {
            final Ball ball2 = (Ball) b2.getObject();
            if (null == ball2) {
                Utils.log("ERROR: there's an empty 'ball' node in source project" + source.toString());
                return false;
            }
            if (title1.equals(ball2.getTitle())) {
                if (seen.contains(title1))
                    continue;
                seen.add(title1);
                l1.add(ball1);
                l2.add(ball2);
            }
        }
    }
    if (l1.size() < 4) {
        Utils.log("ERROR: found only " + l1.size() + " common landmarks: needs at least 4!");
        return false;
    }
    // Extract coordinates of source project landmarks, in patch stack coordinate space
    final List<double[]> c1 = new ArrayList<double[]>();
    for (final Ball ball1 : l1) {
        final Map<Layer, double[]> m = ball1.getRawBalls();
        if (1 != m.size()) {
            Utils.log("ERROR: ball object " + ball1 + " from target project " + project + " has " + m.size() + " balls instead of just 1.");
            return false;
        }
        final Map.Entry<Layer, double[]> e = m.entrySet().iterator().next();
        final Layer layer = e.getKey();
        final double[] xyr = e.getValue();
        final double[] fin = new double[] { xyr[0], xyr[1] };
        final AffineTransform affine = ball1.getAffineTransformCopy();
        try {
            affine.preConcatenate(stack_patch.getAffineTransform().createInverse());
        } catch (final Exception nite) {
            IJError.print(nite);
            return false;
        }
        final double[] fout = new double[2];
        affine.transform(fin, 0, fout, 0, 1);
        c1.add(new double[] { fout[0], fout[1], layer.getParent().indexOf(layer) });
    }
    // Extract coordinates of target (this) project landmarks, in calibrated world space
    final List<double[]> c2 = new ArrayList<double[]>();
    for (final Ball ball2 : l2) {
        final double[][] b = ball2.getBalls();
        if (1 != b.length) {
            Utils.log("ERROR: ball object " + ball2 + " from source project " + source + " has " + b.length + " balls instead of just 1.");
            return false;
        }
        final double[] fin = new double[] { b[0][0], b[0][1] };
        final AffineTransform affine = ball2.getAffineTransformCopy();
        final double[] fout = new double[2];
        affine.transform(fin, 0, fout, 0, 1);
        c2.add(new double[] { fout[0], fout[1], b[0][2] });
    }
    // Print landmarks:
    Utils.log("Landmarks:");
    for (Iterator<double[]> it1 = c1.iterator(), it2 = c2.iterator(); it1.hasNext(); ) {
        Utils.log(Utils.toString(it1.next()) + " <--> " + Utils.toString(it2.next()));
    }
    // Create point matches
    final List<PointMatch> pm = new ArrayList<PointMatch>();
    for (Iterator<double[]> it1 = c1.iterator(), it2 = c2.iterator(); it1.hasNext(); ) {
        pm.add(new mpicbg.models.PointMatch(new mpicbg.models.Point(it1.next()), new mpicbg.models.Point(it2.next())));
    }
    // Estimate AffineModel3D
    final AffineModel3D aff3d = new AffineModel3D();
    try {
        aff3d.fit(pm);
    } catch (final Exception e) {
        IJError.print(e);
        return false;
    }
    // Create and add the Stack
    final String path = stack_patch.getImageFilePath();
    final Stack st = new Stack(project, new File(path).getName(), 0, 0, getLayerSet().getLayers().get(0), path);
    st.setInvertibleCoordinateTransform(aff3d);
    getLayerSet().add(st);
    return true;
}

Example 2 with AffineModel3D

use of mpicbg.trakem2.transform.AffineModel3D in project TrakEM2 by trakem2.

the class Stack method fetchFutureImage.

private final Future<Image> fetchFutureImage(final Long imageId, final double magnification, final Layer active_layer, final boolean trigger_repaint_event) {
    synchronized (futureImages) {
        Future<Image> fu = futureImages.get(imageId);
        if (null == fu) {
            fu = project.getLoader().doLater(new Callable<Image>() {

                @Override
                public Image call() {
                    final InvertibleCoordinateTransformList<mpicbg.models.InvertibleCoordinateTransform> ictl = new InvertibleCoordinateTransformList<mpicbg.models.InvertibleCoordinateTransform>();
                    if (ict != null) {
                        // Utils.log2( "ictScale of " + getTitle() + " is " + ictScale );
                        ictl.add(ict);
                        /* Remove boundingBox shift ict ... */
                        final TranslationModel3D unShiftBounds = new TranslationModel3D();
                        unShiftBounds.set(-boundsMin[0], -boundsMin[1], 0);
                        ictl.add(unShiftBounds);
                        if (ictScale != 1.0) {
                            final AffineModel3D unScaleXY = new AffineModel3D();
                            unScaleXY.set(1.0 / ictScale, 0, 0, 0, 0, 1.0 / ictScale, 0, 0, 0, 0, 1.0, 0);
                            ictl.add(unScaleXY);
                        }
                    }
                    /* TODO remove that scale from ict and put it into atp */
                    final ImagePlus imp = project.getLoader().fetchImagePlus(Stack.this);
                    final ImageProcessor ip = imp.getStack().getProcessor(1).createProcessor((int) Math.ceil((boundsMax[0] - boundsMin[0]) / ictScale), (int) Math.ceil((boundsMax[1] - boundsMin[1]) / ictScale));
                    // Utils.log2( "ictScale is " + ictScale );
                    // Utils.log2( "rendering an image of " + ip.getWidth() + " x " + ip.getHeight() + " px" );
                    final double currentZ = active_layer.getZ();
                    final TranslationModel3D sliceShift = new TranslationModel3D();
                    sliceShift.set(0, 0, -currentZ);
                    ictl.add(sliceShift);
                    /* optimization: if ict is affine, reduce ictl into a single affine */
                    final InverseTransformMapping<mpicbg.models.InvertibleCoordinateTransform> mapping;
                    if (AffineModel3D.class.isInstance(ict)) {
                        final AffineModel3D ictAffine = new AffineModel3D();
                        boolean isAffine = true;
                        for (final mpicbg.models.InvertibleCoordinateTransform t : ictl.getList(null)) {
                            if (AffineModel3D.class.isInstance(t))
                                ictAffine.preConcatenate((AffineModel3D) t);
                            else if (TranslationModel3D.class.isInstance(t))
                                ictAffine.preConcatenate((TranslationModel3D) t);
                            else {
                                isAffine = false;
                                break;
                            }
                        }
                        if (isAffine)
                            mapping = new InverseTransformMapping<mpicbg.models.InvertibleCoordinateTransform>(ictAffine);
                        else
                            mapping = new InverseTransformMapping<mpicbg.models.InvertibleCoordinateTransform>(ictl);
                    } else
                        mapping = new InverseTransformMapping<mpicbg.models.InvertibleCoordinateTransform>(ictl);
                    mapping.mapInterpolated(imp.getStack(), ip);
                    // wast: atp
                    final double s = estimateAffineScale(new AffineTransform(at));
                    final double smoothMag = magnification * s * ictScale;
                    if (smoothMag < 1.0f) {
                        Filter.smoothForScale(ip, smoothMag, 0.5f, 0.5f);
                    }
                    final Image image = ip.createImage();
                    if (null == image) {
                        Utils.log2("Stack.paint: null image, returning");
                        // TEMPORARY from lazy
                        return null;
                    // repaints after closing a
                    // Project
                    }
                    project.getLoader().cacheAWT(imageId, image);
                    synchronized (futureImages) {
                        futureImages.remove(imageId);
                    }
                    if (trigger_repaint_event) {
                        // Display.repaint( active_layer, Stack.this );
                        Display.repaint(active_layer);
                    }
                    return image;
                }
            });
        }
        // else {
        // Utils.log2( "fu is not null" );
        // // We don't do anything: we wait for itself to launch a
        // repaint event
        // }
        futureImages.put(imageId, fu);
        return fu;
    }
}