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

Example 6 with PointMatch

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

the class Align method serializePointMatches.

/**
 * Save a {@link Collection} of {@link PointMatch PointMatches} two-sided.
 * Creates two serialization files which is desperately required to clean
 * up properly invalid serializations on change of a {@link Patch}.
 *
 * @param p
 * @param t1
 * @param t2
 * @param m
 * @return
 */
protected static final boolean serializePointMatches(final Param p, final AbstractAffineTile2D<?> t1, final AbstractAffineTile2D<?> t2, final Collection<PointMatch> m) {
    final ArrayList<PointMatch> list = new ArrayList<PointMatch>();
    list.addAll(m);
    final ArrayList<PointMatch> tsil = new ArrayList<PointMatch>();
    PointMatch.flip(m, tsil);
    final Patch p1 = t1.getPatch();
    final Patch p2 = t2.getPatch();
    final Loader loader = p1.getProject().getLoader();
    return loader.serialize(new PointMatches(p, list), new StringBuilder(loader.getUNUIdFolder()).append("pointmatches.ser/").append(FSLoader.createIdPath(Long.toString(p1.getId()) + "_" + Long.toString(p2.getId()), "pointmatches", ".ser")).toString()) && loader.serialize(new PointMatches(p, tsil), new StringBuilder(loader.getUNUIdFolder()).append("pointmatches.ser/").append(FSLoader.createIdPath(Long.toString(p2.getId()) + "_" + Long.toString(p1.getId()), "pointmatches", ".ser")).toString());
}

Example 7 with PointMatch

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

the class Align method fetchPointMatches.

/**
 * Fetch a {@link Collection} of corresponding
 * {@link Feature SIFT-features}.  Both {@link Feature SIFT-features} and
 * {@linkplain PointMatch corresponding points} are cached to disk.
 *
 * @param p
 * @param t1
 * @param t2
 * @return
 *   <dl>
 *     <dt>null</dt><dd>if matching failed for some reasons</dd>
 *     <dt>empty {@link Collection}</dt><dd>if there was no consistent set
 *       of {@link PointMatch matches}</dd>
 *     <dt>{@link Collection} of {@link PointMatch PointMatches}</dt>
 *       <dd>if there was a consistent set of {@link PointMatch
 *         PointMatches}</dd>
 *   </dl>
 */
protected static final Collection<PointMatch> fetchPointMatches(final Param p, final AbstractAffineTile2D<?> t1, final AbstractAffineTile2D<?> t2) {
    final Collection<PointMatch> pointMatches = deserializePointMatches(p, t1, t2);
    if (pointMatches == null) {
        final List<PointMatch> candidates = new ArrayList<PointMatch>();
        final List<PointMatch> inliers = new ArrayList<PointMatch>();
        final long s = System.currentTimeMillis();
        FeatureTransform.matchFeatures(fetchFeatures(p, t1), fetchFeatures(p, t2), candidates, p.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 null;
        }
        final boolean modelFound = findModel(model, candidates, inliers, p.maxEpsilon, p.minInlierRatio, p.minNumInliers, p.rejectIdentity, p.identityTolerance);
        if (modelFound)
            Utils.log("Model found for tiles \"" + t1.getPatch() + "\" and \"" + t2.getPatch() + "\":\n  correspondences  " + inliers.size() + " of " + candidates.size() + "\n  average residual error  " + model.getCost() + " px\n  took " + (System.currentTimeMillis() - s) + " ms");
        else
            Utils.log("No model found for tiles \"" + t1.getPatch() + "\" and \"" + t2.getPatch() + "\":\n  correspondence candidates  " + candidates.size() + "\n  took " + (System.currentTimeMillis() - s) + " ms");
        if (!serializePointMatches(p, t1, t2, pointMatches))
            Utils.log("Saving point matches failed for tile \"" + t1.getPatch() + "\" and tile \"" + t2.getPatch() + "\"");
    }
    return pointMatches;
}

Example 8 with PointMatch

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

the class AlignLayersTask method alignLayersNonLinearlyJob.

public static final void alignLayersNonLinearlyJob(final LayerSet layerSet, final int first, final int last, final boolean propagateTransform, final Rectangle fov, final Filter<Patch> filter) {
    // will reverse order if necessary
    final List<Layer> layerRange = layerSet.getLayers(first, last);
    final Align.Param p = Align.param.clone();
    // Remove all empty layers
    for (final Iterator<Layer> it = layerRange.iterator(); it.hasNext(); ) {
        if (!it.next().contains(Patch.class, true)) {
            it.remove();
        }
    }
    if (0 == layerRange.size()) {
        Utils.log("No layers in range show any images!");
        return;
    }
    /* do not work if there is only one layer selected */
    if (layerRange.size() < 2)
        return;
    final List<Patch> all = new ArrayList<Patch>();
    for (final Layer la : layerRange) {
        for (final Patch patch : la.getAll(Patch.class)) {
            if (null != filter && !filter.accept(patch))
                continue;
            all.add(patch);
        }
    }
    AlignTask.transformPatchesAndVectorData(all, new Runnable() {

        @Override
        public void run() {
            // ///
            final Loader loader = layerSet.getProject().getLoader();
            // Not concurrent safe! So two copies, one per layer and Thread:
            final SIFT ijSIFT1 = new SIFT(new FloatArray2DSIFT(p.sift));
            final SIFT ijSIFT2 = new SIFT(new FloatArray2DSIFT(p.sift));
            final Collection<Feature> features1 = new ArrayList<Feature>();
            final Collection<Feature> features2 = new ArrayList<Feature>();
            final List<PointMatch> candidates = new ArrayList<PointMatch>();
            final List<PointMatch> inliers = new ArrayList<PointMatch>();
            final int n_proc = Runtime.getRuntime().availableProcessors() > 1 ? 2 : 1;
            final ExecutorService exec = Utils.newFixedThreadPool(n_proc, "alignLayersNonLinearly");
            List<Patch> previousPatches = null;
            int s = 0;
            for (int i = 1; i < layerRange.size(); ++i) {
                if (Thread.currentThread().isInterrupted())
                    break;
                final Layer layer1 = layerRange.get(i - 1);
                final Layer layer2 = layerRange.get(i);
                final long t0 = System.currentTimeMillis();
                features1.clear();
                features2.clear();
                final Rectangle box1 = null == fov ? layer1.getMinimalBoundingBox(Patch.class, true) : fov;
                final Rectangle box2 = null == fov ? layer2.getMinimalBoundingBox(Patch.class, true) : fov;
                /* calculate the common scale factor for both flat images */
                final double scale = Math.min(1.0f, (double) p.sift.maxOctaveSize / (double) Math.max(box1.width, Math.max(box1.height, Math.max(box2.width, box2.height))));
                final List<Patch> patches1;
                if (null == previousPatches) {
                    patches1 = layer1.getAll(Patch.class);
                    if (null != filter) {
                        for (final Iterator<Patch> it = patches1.iterator(); it.hasNext(); ) {
                            if (!filter.accept(it.next()))
                                it.remove();
                        }
                    }
                } else {
                    patches1 = previousPatches;
                }
                final List<Patch> patches2 = layer2.getAll(Patch.class);
                if (null != filter) {
                    for (final Iterator<Patch> it = patches2.iterator(); it.hasNext(); ) {
                        if (!filter.accept(it.next()))
                            it.remove();
                    }
                }
                final Future<ImageProcessor> fu1 = exec.submit(new Callable<ImageProcessor>() {

                    @Override
                    public ImageProcessor call() {
                        final ImageProcessor ip1 = loader.getFlatImage(layer1, box1, scale, 0xffffffff, ImagePlus.GRAY8, Patch.class, patches1, true).getProcessor();
                        ijSIFT1.extractFeatures(ip1, features1);
                        Utils.log(features1.size() + " features extracted in layer \"" + layer1.getTitle() + "\" (took " + (System.currentTimeMillis() - t0) + " ms).");
                        return ip1;
                    }
                });
                final Future<ImageProcessor> fu2 = exec.submit(new Callable<ImageProcessor>() {

                    @Override
                    public ImageProcessor call() {
                        final ImageProcessor ip2 = loader.getFlatImage(layer2, box2, scale, 0xffffffff, ImagePlus.GRAY8, Patch.class, patches2, true).getProcessor();
                        ijSIFT2.extractFeatures(ip2, features2);
                        Utils.log(features2.size() + " features extracted in layer \"" + layer2.getTitle() + "\" (took " + (System.currentTimeMillis() - t0) + " ms).");
                        return ip2;
                    }
                });
                final ImageProcessor ip1, ip2;
                try {
                    ip1 = fu1.get();
                    ip2 = fu2.get();
                } catch (final Exception e) {
                    IJError.print(e);
                    return;
                }
                if (features1.size() > 0 && features2.size() > 0) {
                    final long t1 = System.currentTimeMillis();
                    candidates.clear();
                    FeatureTransform.matchFeatures(features2, features1, candidates, p.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)) {
                                    IJ.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) {
                        IJ.log("Model found for layer \"" + layer2.getTitle() + "\" and its predecessor:\n  correspondences  " + inliers.size() + " of " + candidates.size() + "\n  average residual error  " + (model.getCost() / scale) + " px\n  took " + (System.currentTimeMillis() - t1) + " ms");
                        final ImagePlus imp1 = new ImagePlus("target", ip1);
                        final ImagePlus imp2 = new ImagePlus("source", ip2);
                        final List<Point> sourcePoints = new ArrayList<Point>();
                        final List<Point> targetPoints = new ArrayList<Point>();
                        PointMatch.sourcePoints(inliers, sourcePoints);
                        PointMatch.targetPoints(inliers, targetPoints);
                        imp2.setRoi(Util.pointsToPointRoi(sourcePoints));
                        imp1.setRoi(Util.pointsToPointRoi(targetPoints));
                        final ImageProcessor mask1 = ip1.duplicate();
                        mask1.threshold(1);
                        final ImageProcessor mask2 = ip2.duplicate();
                        mask2.threshold(1);
                        final Transformation warp = bUnwarpJ_.computeTransformationBatch(imp2, imp1, mask2, mask1, elasticParam);
                        final CubicBSplineTransform transf = new CubicBSplineTransform();
                        transf.set(warp.getIntervals(), warp.getDirectDeformationCoefficientsX(), warp.getDirectDeformationCoefficientsY(), imp2.getWidth(), imp2.getHeight());
                        final ArrayList<Future<?>> fus = new ArrayList<Future<?>>();
                        // Transform desired patches only
                        for (final Patch patch : patches2) {
                            try {
                                final Rectangle pbox = patch.getCoordinateTransformBoundingBox();
                                final AffineTransform at = patch.getAffineTransform();
                                final AffineTransform pat = new AffineTransform();
                                pat.scale(scale, scale);
                                pat.translate(-box2.x, -box2.y);
                                pat.concatenate(at);
                                pat.translate(-pbox.x, -pbox.y);
                                final mpicbg.trakem2.transform.AffineModel2D toWorld = new mpicbg.trakem2.transform.AffineModel2D();
                                toWorld.set(pat);
                                final CoordinateTransformList<CoordinateTransform> ctl = new CoordinateTransformList<CoordinateTransform>();
                                // move the patch into the global space where bUnwarpJ calculated the transformation
                                ctl.add(toWorld);
                                // Apply non-linear transformation
                                ctl.add(transf);
                                // move it back
                                ctl.add(toWorld.createInverse());
                                patch.appendCoordinateTransform(ctl);
                                fus.add(patch.updateMipMaps());
                                // Compensate for offset between boxes
                                final AffineTransform offset = new AffineTransform();
                                offset.translate(box1.x - box2.x, box1.y - box2.y);
                                offset.concatenate(at);
                                patch.setAffineTransform(offset);
                            } catch (final Exception e) {
                                e.printStackTrace();
                            }
                        }
                        // await regeneration of all mipmaps
                        Utils.wait(fus);
                        Display.repaint(layer2);
                    } else
                        IJ.log("No model found for layer \"" + layer2.getTitle() + "\" and its predecessor:\n  correspondence candidates  " + candidates.size() + "\n  took " + (System.currentTimeMillis() - s) + " ms");
                }
                IJ.showProgress(++s, layerRange.size());
                // for next iteration
                previousPatches = patches2;
            }
            exec.shutdown();
            if (propagateTransform)
                Utils.log("Propagation not implemented yet for non-linear layer alignment.");
        /* // CANNOT be done (at least not trivially:
		 * //an appropriate "scale" cannot be computed, and the box2 is part of the spline computation.
		if ( propagateTransform && null != lastTransform )
		{
			for (final Layer la : l.getParent().getLayers(last > first ? last +1 : first -1, last > first ? l.getParent().size() -1 : 0)) {
				// Transform visible patches only
				final Rectangle box2 = la.getMinimalBoundingBox( Patch.class, true );
				for ( final Displayable disp : la.getDisplayables( Patch.class, true ) )
				{
					// ...
				}
			}
		}
		*/
        }
    });
// end of transformPatchesAndVectorData
}

Example 9 with PointMatch

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

the class Util method serializePointMatches.

/**
 * Save a {@link Collection} of {@link PointMatch PointMatches} two-sided.
 * Creates two serialization files which is desperately required to clean
 * up properly invalid serializations on change of a {@link Patch}.
 *
 * @param project
 * @param key
 * @param prefix
 * @param id1
 * @param id2
 * @param m
 * @return
 */
public static final boolean serializePointMatches(final Project project, final Object key, final String prefix, final long id1, final long id2, final Collection<PointMatch> m) {
    final ArrayList<PointMatch> list = new ArrayList<PointMatch>();
    list.addAll(m);
    final ArrayList<PointMatch> tsil = new ArrayList<PointMatch>();
    PointMatch.flip(m, tsil);
    final String name = prefix == null ? "pointmatches" : prefix + ".pointmatches";
    final Loader loader = project.getLoader();
    return loader.serialize(new PointMatches(key, list), new StringBuilder(loader.getUNUIdFolder()).append("pointmatches.ser/").append(FSLoader.createIdPath(Long.toString(id1) + "_" + Long.toString(id2), name, ".ser")).toString()) && loader.serialize(new PointMatches(key, tsil), new StringBuilder(loader.getUNUIdFolder()).append("pointmatches.ser/").append(FSLoader.createIdPath(Long.toString(id2) + "_" + Long.toString(id1), name, ".ser")).toString());
}

Example 10 with PointMatch

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

the class MatchIntensities method identityConnect.

protected static final void identityConnect(final Tile<?> t1, final Tile<?> t2, final double weight) {
    final ArrayList<PointMatch> matches = new ArrayList<PointMatch>();
    matches.add(new PointMatch(new Point(new double[] { 0 }), new Point(new double[] { 0 })));
    matches.add(new PointMatch(new Point(new double[] { 1 }), new Point(new double[] { 1 })));
    t1.connect(t2, matches);
}