Examples with FloatArray2DSIFT mpicbg.imagefeatures.FloatArray2DSIFT used on opensource projects

Example 6 with FloatArray2DSIFT

use of mpicbg.imagefeatures.FloatArray2DSIFT 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");
    }
}

Example 7 with FloatArray2DSIFT

use of mpicbg.imagefeatures.FloatArray2DSIFT in project TrakEM2 by trakem2.

the class AlignLayersTask method alignLayersLinearlyJob.

public static final void alignLayersLinearlyJob(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();
    // find the first non-empty layer, and remove all empty layers
    Rectangle box = fov;
    for (final Iterator<Layer> it = layerRange.iterator(); it.hasNext(); ) {
        final Layer la = it.next();
        if (!la.contains(Patch.class, true)) {
            it.remove();
            continue;
        }
        if (null == box) {
            // The first layer:
            // Only for visible patches
            box = la.getMinimalBoundingBox(Patch.class, true);
        }
    }
    if (0 == layerRange.size()) {
        Utils.log("All layers in range are empty!");
        return;
    }
    /* do not work if there is only one layer selected */
    if (layerRange.size() < 2)
        return;
    final double scale = Math.min(1.0, Math.min((double) p.sift.maxOctaveSize / (double) box.width, (double) p.sift.maxOctaveSize / (double) box.height));
    p.maxEpsilon *= scale;
    p.identityTolerance *= scale;
    // Utils.log2("scale: " + scale + "  maxOctaveSize: " + p.sift.maxOctaveSize + "  box: " + box.width + "," + box.height);
    final FloatArray2DSIFT sift = new FloatArray2DSIFT(p.sift);
    final SIFT ijSIFT = new SIFT(sift);
    Rectangle box1 = fov;
    Rectangle box2 = fov;
    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 AffineTransform a = new AffineTransform();
    int s = 0;
    for (final Layer layer : layerRange) {
        if (Thread.currentThread().isInterrupted())
            return;
        final long t0 = System.currentTimeMillis();
        features1.clear();
        features1.addAll(features2);
        features2.clear();
        final Rectangle box3 = layer.getMinimalBoundingBox(Patch.class, true);
        // skipping empty layer
        if (box3 == null || (box3.width == 0 && box3.height == 0))
            continue;
        box1 = null == fov ? box2 : fov;
        box2 = null == fov ? box3 : fov;
        final List<Patch> patches = layer.getAll(Patch.class);
        if (null != filter) {
            for (final Iterator<Patch> it = patches.iterator(); it.hasNext(); ) {
                if (!filter.accept(it.next()))
                    it.remove();
            }
        }
        final ImageProcessor flatImage = layer.getProject().getLoader().getFlatImage(layer, box2, scale, 0xffffffff, ImagePlus.GRAY8, Patch.class, patches, true).getProcessor();
        ijSIFT.extractFeatures(flatImage, features2);
        IJ.log(features2.size() + " features extracted in layer \"" + layer.getTitle() + "\" (took " + (System.currentTimeMillis() - t0) + " ms).");
        if (features1.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;
            }
            final AbstractAffineModel2D<?> desiredModel;
            switch(p.desiredModelIndex) {
                case 0:
                    desiredModel = new TranslationModel2D();
                    break;
                case 1:
                    desiredModel = new RigidModel2D();
                    break;
                case 2:
                    desiredModel = new SimilarityModel2D();
                    break;
                case 3:
                    desiredModel = 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);
                if (modelFound)
                    desiredModel.fit(inliers);
            } catch (final NotEnoughDataPointsException e) {
                modelFound = false;
            } catch (final IllDefinedDataPointsException e) {
                modelFound = false;
            }
            if (Thread.currentThread().isInterrupted())
                return;
            if (modelFound) {
                IJ.log("Model found for layer \"" + layer.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 AffineTransform b = new AffineTransform();
                b.translate(box1.x, box1.y);
                b.scale(1.0f / scale, 1.0f / scale);
                b.concatenate(desiredModel.createAffine());
                b.scale(scale, scale);
                b.translate(-box2.x, -box2.y);
                a.concatenate(b);
                AlignTask.transformPatchesAndVectorData(patches, a);
                Display.repaint(layer);
            } else {
                IJ.log("No model found for layer \"" + layer.getTitle() + "\" and its predecessor:\n  correspondence candidates  " + candidates.size() + "\n  took " + (System.currentTimeMillis() - s) + " ms");
                a.setToIdentity();
            }
        }
        IJ.showProgress(++s, layerRange.size());
    }
    if (Thread.currentThread().isInterrupted())
        return;
    if (propagateTransform) {
        if (last > first && last < layerSet.size() - 2)
            for (final Layer la : layerSet.getLayers(last + 1, layerSet.size() - 1)) {
                if (Thread.currentThread().isInterrupted())
                    return;
                AlignTask.transformPatchesAndVectorData(la, a);
            }
        else if (first > last && last > 0)
            for (final Layer la : layerSet.getLayers(0, last - 1)) {
                if (Thread.currentThread().isInterrupted())
                    return;
                AlignTask.transformPatchesAndVectorData(la, a);
            }
    }
}

Example 8 with FloatArray2DSIFT

use of mpicbg.imagefeatures.FloatArray2DSIFT in project TrakEM2 by trakem2.

the class ElasticMontage method extractAndSaveFeatures.

/**
 * Extract SIFT features and save them into the project folder.
 *
 * @param tiles
 * @param siftParam
 * @param clearCache
 * @throws Exception
 */
protected static final void extractAndSaveFeatures(final List<AbstractAffineTile2D<?>> tiles, final FloatArray2DSIFT.Param siftParam, final boolean clearCache) throws Exception {
    final ExecutorService exec = Executors.newFixedThreadPool(p.maxNumThreads);
    /* extract features for all slices and store them to disk */
    final AtomicInteger counter = new AtomicInteger(0);
    final ArrayList<Future<ArrayList<Feature>>> siftTasks = new ArrayList<Future<ArrayList<Feature>>>();
    for (int i = 0; i < tiles.size(); ++i) {
        final int tileIndex = i;
        siftTasks.add(exec.submit(new Callable<ArrayList<Feature>>() {

            @Override
            public ArrayList<Feature> call() {
                final AbstractAffineTile2D<?> tile = tiles.get(tileIndex);
                final String patchName = patchName(tile.getPatch());
                IJ.showProgress(counter.getAndIncrement(), tiles.size() - 1);
                ArrayList<Feature> fs = null;
                if (!clearCache)
                    fs = mpicbg.trakem2.align.Util.deserializeFeatures(tile.getPatch().getProject(), siftParam, null, tile.getPatch().getId());
                if (null == fs) {
                    final FloatArray2DSIFT sift = new FloatArray2DSIFT(siftParam);
                    final SIFT ijSIFT = new SIFT(sift);
                    fs = new ArrayList<Feature>();
                    final ByteProcessor ip = tile.createMaskedByteImage();
                    ijSIFT.extractFeatures(ip, fs);
                    Utils.log(fs.size() + " features extracted for " + patchName);
                    if (!mpicbg.trakem2.align.Util.serializeFeatures(tile.getPatch().getProject(), siftParam, null, tile.getPatch().getId(), fs))
                        Utils.log("FAILED to store serialized features for " + patchName);
                } else
                    Utils.log(fs.size() + " features loaded for " + patchName);
                return fs;
            }
        }));
    }
    /* join */
    for (final Future<ArrayList<Feature>> fu : siftTasks) fu.get();
    siftTasks.clear();
    exec.shutdown();
}