Examples with PointMatch mpicbg.models.PointMatch used on opensource projects

Example 21 with PointMatch

use of mpicbg.models.PointMatch in project TrakEM2 by trakem2.

the class TransformMesh method applyInverseInPlace.

/**
 * Catch non-invertible locations outside of the meshes boundaries and
 * transfer them with the affine defined by the `closest' affine (the affine
 * whose summed up control points distances to location are smallest).
 */
@Override
public void applyInverseInPlace(final double[] location) throws NoninvertibleModelException {
    assert location.length == 2 : "2d transform meshs can be applied to 2d points only.";
    final Set<AffineModel2D> s = av.keySet();
    for (final AffineModel2D ai : s) {
        final ArrayList<PointMatch> pm = av.get(ai);
        if (isInConvexTargetPolygon(pm, location)) {
            ai.applyInverseInPlace(location);
            return;
        }
    }
    /* not in the mesh, find the closest affine */
    double dMin = Double.MAX_VALUE;
    AffineModel2D closestAffine = new AffineModel2D();
    final double x = location[0];
    final double y = location[1];
    for (final AffineModel2D ai : s) {
        final ArrayList<PointMatch> pm = av.get(ai);
        double d = 0;
        for (final PointMatch p : pm) {
            final double[] w = p.getP2().getW();
            final double dx = w[0] - x;
            final double dy = w[1] - y;
            d += Math.sqrt(dx * dx + dy * dy);
        }
        if (d < dMin) {
            dMin = d;
            closestAffine = ai;
        }
    }
    closestAffine.applyInverseInPlace(location);
    throw new NoninvertibleModelException("Mesh external location ( " + x + ", " + y + " ) transferred to ( " + location[0] + ", " + location[1] + " ) by closest affine.");
}

Example 22 with PointMatch

use of mpicbg.models.PointMatch in project TrakEM2 by trakem2.

the class MovingLeastSquaresTransform method applyInPlace.

@Override
public final void applyInPlace(final double[] location) {
    final Collection<PointMatch> weightedMatches = new ArrayList<PointMatch>();
    for (final PointMatch m : matches) {
        final double[] l = m.getP1().getL();
        double s = 0;
        for (int i = 0; i < location.length; ++i) {
            final double dx = l[i] - location[i];
            s += dx * dx;
        }
        if (s <= 0) {
            final double[] w = m.getP2().getW();
            for (int i = 0; i < location.length; ++i) location[i] = w[i];
            return;
        }
        final double weight = m.getWeight() * weigh(s);
        final PointMatch mw = new PointMatch(m.getP1(), m.getP2(), weight);
        weightedMatches.add(mw);
    }
    try {
        synchronized (model) {
            model.fit(weightedMatches);
            model.applyInPlace(location);
        }
    } catch (final IllDefinedDataPointsException e) {
    } catch (final NotEnoughDataPointsException e) {
    }
}

Example 23 with PointMatch

use of mpicbg.models.PointMatch in project TrakEM2 by trakem2.

the class MovingLeastSquaresTransform method init.

@Override
public final void init(final String data) throws NumberFormatException {
    matches.clear();
    final String[] fields = data.split("\\s+");
    if (fields.length > 3) {
        final int d = Integer.parseInt(fields[1]);
        if ((fields.length - 3) % (2 * d + 1) == 0) {
            if (d == 2) {
                if (fields[0].equals("translation"))
                    model = new TranslationModel2D();
                else if (fields[0].equals("rigid"))
                    model = new RigidModel2D();
                else if (fields[0].equals("similarity"))
                    model = new SimilarityModel2D();
                else if (fields[0].equals("affine"))
                    model = new AffineModel2D();
                else
                    throw new NumberFormatException("Inappropriate parameters for " + this.getClass().getCanonicalName());
            } else if (d == 3) {
                if (fields[0].equals("affine"))
                    model = new AffineModel3D();
                else
                    throw new NumberFormatException("Inappropriate parameters for " + this.getClass().getCanonicalName());
            } else
                throw new NumberFormatException("Inappropriate parameters for " + this.getClass().getCanonicalName());
            alpha = Double.parseDouble(fields[2]);
            int i = 2;
            while (i < fields.length - 1) {
                final double[] p1 = new double[d];
                for (int k = 0; k < d; ++k) p1[k] = Double.parseDouble(fields[++i]);
                final double[] p2 = new double[d];
                for (int k = 0; k < d; ++k) p2[k] = Double.parseDouble(fields[++i]);
                final double weight = Double.parseDouble(fields[++i]);
                final PointMatch m = new PointMatch(new Point(p1), new Point(p2), weight);
                matches.add(m);
            }
        } else
            throw new NumberFormatException("Inappropriate parameters for " + this.getClass().getCanonicalName());
    } else
        throw new NumberFormatException("Inappropriate parameters for " + this.getClass().getCanonicalName());
}

Example 24 with PointMatch

use of mpicbg.models.PointMatch in project TrakEM2 by trakem2.

the class StitchingTEM method addMatches.

/**
 * dx, dy is the position of t2 relative to the 0,0 of t1.
 */
private static final void addMatches(final AbstractAffineTile2D<?> t1, final AbstractAffineTile2D<?> t2, final double dx, final double dy) {
    final Point p1 = new Point(new double[] { 0, 0 });
    final Point p2 = new Point(new double[] { dx, dy });
    t1.addMatch(new PointMatch(p2, p1, 1.0f));
    t2.addMatch(new PointMatch(p1, p2, 1.0f));
    t1.addConnectedTile(t2);
    t2.addConnectedTile(t1);
}

Example 25 with PointMatch

use of mpicbg.models.PointMatch in project TrakEM2 by trakem2.

the class Distortion_Correction method extractSIFTPointsThreaded.

protected static void extractSIFTPointsThreaded(final int index, final List<Feature>[] siftFeatures, final List<PointMatch>[] inliers, final AbstractAffineModel2D<?>[] models) {
    // save all matching candidates
    final List<PointMatch>[] candidates = new List[siftFeatures.length - 1];
    final Thread[] threads = MultiThreading.newThreads();
    // start at second
    final AtomicInteger ai = new AtomicInteger(0);
    for (int ithread = 0; ithread < threads.length; ++ithread) {
        threads[ithread] = new Thread() {

            @Override
            public void run() {
                setPriority(Thread.NORM_PRIORITY);
                for (int j = ai.getAndIncrement(); j < candidates.length; j = ai.getAndIncrement()) {
                    final int i = (j < index ? j : j + 1);
                    candidates[j] = FloatArray2DSIFT.createMatches(siftFeatures[index], siftFeatures[i], 1.5f, null, Float.MAX_VALUE, 0.5f);
                }
            }
        };
    }
    MultiThreading.startAndJoin(threads);
    // get rid of the outliers and save the rigid transformations to match
    // the inliers
    final AtomicInteger ai2 = new AtomicInteger(0);
    for (int ithread = 0; ithread < threads.length; ++ithread) {
        threads[ithread] = new Thread() {

            @Override
            public void run() {
                setPriority(Thread.NORM_PRIORITY);
                for (int i = ai2.getAndIncrement(); i < candidates.length; i = ai2.getAndIncrement()) {
                    final List<PointMatch> tmpInliers = new ArrayList<PointMatch>();
                    // RigidModel2D m =
                    // RigidModel2D.estimateBestModel(candidates.get(i),
                    // tmpInliers, sp.min_epsilon, sp.max_epsilon,
                    // sp.min_inlier_ratio);
                    final AbstractAffineModel2D<?> m;
                    switch(sp.expectedModelIndex) {
                        case 0:
                            m = new TranslationModel2D();
                            break;
                        case 1:
                            m = new RigidModel2D();
                            break;
                        case 2:
                            m = new SimilarityModel2D();
                            break;
                        case 3:
                            m = new AffineModel2D();
                            break;
                        default:
                            return;
                    }
                    boolean modelFound = false;
                    try {
                        modelFound = m.filterRansac(candidates[i], tmpInliers, 1000, sp.maxEpsilon, sp.minInlierRatio, 10);
                    } catch (final NotEnoughDataPointsException e) {
                        modelFound = false;
                    }
                    if (modelFound)
                        IJ.log("Model found:\n  " + candidates[i].size() + " candidates\n  " + tmpInliers.size() + " inliers\n  " + String.format("%.2f", m.getCost()) + "px average displacement");
                    else
                        IJ.log("No Model found.");
                    inliers[index * (sp.numberOfImages - 1) + i] = tmpInliers;
                    models[index * (sp.numberOfImages - 1) + i] = m;
                // System.out.println("**** MODEL ADDED: " +
                // (index*(sp.numberOfImages-1)+i));
                }
            }
        };
    }
    MultiThreading.startAndJoin(threads);
}