Examples with Align mpicbg.trakem2.align.Align used on opensource projects

Example 6 with Align

use of mpicbg.trakem2.align.Align in project TrakEM2 by trakem2.

the class Align method alignTileCollections.

/**
 * Align two collections of tiles
 * @param p
 * @param a
 * @param b
 */
public static final void alignTileCollections(final Param p, final Collection<AbstractAffineTile2D<?>> a, final Collection<AbstractAffineTile2D<?>> b) {
    final ArrayList<Patch> pa = new ArrayList<Patch>();
    final ArrayList<Patch> pb = new ArrayList<Patch>();
    for (final AbstractAffineTile2D<?> t : a) pa.add(t.getPatch());
    for (final AbstractAffineTile2D<?> t : b) pb.add(t.getPatch());
    final Layer la = pa.iterator().next().getLayer();
    final Layer lb = pb.iterator().next().getLayer();
    final Rectangle boxA = Displayable.getBoundingBox(pa, null);
    final Rectangle boxB = Displayable.getBoundingBox(pb, null);
    final double scale = Math.min(1.0, Math.min(Math.min((double) p.sift.maxOctaveSize / boxA.width, (double) p.sift.maxOctaveSize / boxA.height), Math.min((double) p.sift.maxOctaveSize / boxB.width, (double) p.sift.maxOctaveSize / boxB.height)));
    final Param pp = p.clone();
    pp.maxEpsilon *= scale;
    final FloatArray2DSIFT sift = new FloatArray2DSIFT(pp.sift);
    final SIFT ijSIFT = new SIFT(sift);
    final Collection<Feature> featuresA = new ArrayList<Feature>();
    final Collection<Feature> featuresB = new ArrayList<Feature>();
    final List<PointMatch> candidates = new ArrayList<PointMatch>();
    final List<PointMatch> inliers = new ArrayList<PointMatch>();
    long s = System.currentTimeMillis();
    ijSIFT.extractFeatures(la.getProject().getLoader().getFlatImage(la, boxA, scale, 0xffffffff, ImagePlus.GRAY8, null, pa, true, Color.GRAY).getProcessor(), featuresA);
    Utils.log(featuresA.size() + " features extracted in graph A in layer \"" + la.getTitle() + "\" (took " + (System.currentTimeMillis() - s) + " ms).");
    s = System.currentTimeMillis();
    ijSIFT.extractFeatures(lb.getProject().getLoader().getFlatImage(lb, boxB, scale, 0xffffffff, ImagePlus.GRAY8, null, pb, true, Color.GRAY).getProcessor(), featuresB);
    Utils.log(featuresB.size() + " features extracted in graph B in layer \"" + lb.getTitle() + "\" (took " + (System.currentTimeMillis() - s) + " ms).");
    if (featuresA.size() > 0 && featuresB.size() > 0) {
        s = System.currentTimeMillis();
        FeatureTransform.matchFeatures(featuresA, featuresB, candidates, pp.rod);
        final AbstractAffineModel2D<?> model;
        switch(p.expectedModelIndex) {
            case 0:
                model = new TranslationModel2D();
                break;
            case 1:
                model = new RigidModel2D();
                break;
            case 2:
                model = new SimilarityModel2D();
                break;
            case 3:
                model = new AffineModel2D();
                break;
            default:
                return;
        }
        boolean modelFound;
        boolean again = false;
        try {
            do {
                again = false;
                modelFound = model.filterRansac(candidates, inliers, 1000, p.maxEpsilon, p.minInlierRatio, p.minNumInliers, 3);
                if (modelFound && p.rejectIdentity) {
                    final ArrayList<Point> points = new ArrayList<Point>();
                    PointMatch.sourcePoints(inliers, points);
                    if (Transforms.isIdentity(model, points, p.identityTolerance)) {
                        Utils.log("Identity transform for " + inliers.size() + " matches rejected.");
                        candidates.removeAll(inliers);
                        inliers.clear();
                        again = true;
                    }
                }
            } while (again);
        } catch (final NotEnoughDataPointsException e) {
            modelFound = false;
        }
        if (modelFound) {
            Utils.log("Model found for graph A and B in layers \"" + la.getTitle() + "\" and \"" + lb.getTitle() + "\":\n  correspondences  " + inliers.size() + " of " + candidates.size() + "\n  average residual error  " + (model.getCost() / scale) + " px\n  took " + (System.currentTimeMillis() - s) + " ms");
            final AffineTransform at = new AffineTransform();
            at.translate(boxA.x, boxA.y);
            at.scale(1.0f / scale, 1.0f / scale);
            at.concatenate(model.createAffine());
            at.scale(scale, scale);
            at.translate(-boxB.x, -boxB.y);
            for (final Patch t : pa) t.preTransform(at, false);
            Display.repaint(la);
        } else
            Utils.log("No model found for graph A and B in layers \"" + la.getTitle() + "\" and \"" + lb.getTitle() + "\":\n  correspondence candidates  " + candidates.size() + "\n  took " + (System.currentTimeMillis() - s) + " ms");
    }
}