Examples with AbstractAffineModel2D mpicbg.models.AbstractAffineModel2D used on opensource projects

Example 6 with AbstractAffineModel2D

use of mpicbg.models.AbstractAffineModel2D in project TrakEM2 by trakem2.

the class ManualAlignMode method apply.

@Override
public boolean apply() {
    // Check there's more than one layer
    if (m.size() < 2) {
        Utils.showMessage("Need more than one layer to align!");
        return false;
    }
    // Check that the current layer is one of the layers with landmarks.
    // Will be used as reference
    final Layer ref_layer = display.getLayer();
    if (null == m.get(ref_layer)) {
        Utils.showMessage("Please scroll to a layer with landmarks,\nto be used as reference.");
        return false;
    }
    // Check that all layers have the same number of landmarks
    int n_landmarks = -1;
    for (final Map.Entry<Layer, Landmarks> e : m.entrySet()) {
        final Landmarks lm = e.getValue();
        if (-1 == n_landmarks) {
            n_landmarks = lm.points.size();
            continue;
        }
        if (n_landmarks != lm.points.size()) {
            Utils.showMessage("Can't apply: there are different amounts of landmarks per layer.\nSee the log window.");
            for (final Map.Entry<Layer, Landmarks> ee : m.entrySet()) {
                Utils.log(ee.getValue().points.size() + " landmarks in layer " + ee.getKey());
            }
            return false;
        }
    }
    // Sort Layers by Z
    final TreeMap<Layer, Landmarks> sorted = new TreeMap<Layer, Landmarks>(new Comparator<Layer>() {

        @Override
        public boolean equals(final Object ob) {
            return this == ob;
        }

        @Override
        public int compare(final Layer l1, final Layer l2) {
            // Ascending order
            final double dz = l1.getZ() - l2.getZ();
            if (dz < 0)
                return -1;
            else if (dz > 0)
                return 1;
            else
                return 0;
        }
    });
    sorted.putAll(m);
    int iref = 0;
    for (final Layer la : sorted.keySet()) {
        if (la != ref_layer)
            iref++;
        else
            break;
    }
    // Ok, now ask for a model
    final GenericDialog gd = new GenericDialog("Model");
    gd.addChoice("Model:", Align.Param.modelStrings, Align.Param.modelStrings[1]);
    gd.addCheckbox("Propagate to first layer", 0 != iref);
    ((Component) gd.getCheckboxes().get(0)).setEnabled(0 != iref);
    gd.addCheckbox("Propagate to last layer", sorted.size() - 1 != iref);
    ((Component) gd.getCheckboxes().get(1)).setEnabled(sorted.size() - 1 != iref);
    gd.showDialog();
    if (gd.wasCanceled())
        return false;
    final int model_index = gd.getNextChoiceIndex();
    final boolean propagate_to_first = gd.getNextBoolean();
    final boolean propagate_to_last = gd.getNextBoolean();
    int min;
    // Create a model as desired
    final AbstractAffineModel2D<?> model;
    switch(model_index) {
        case 0:
            min = 1;
            model = new TranslationModel2D();
            break;
        case 1:
            min = 2;
            model = new RigidModel2D();
            break;
        case 2:
            min = 2;
            model = new SimilarityModel2D();
            break;
        case 3:
            min = 3;
            model = new AffineModel2D();
            break;
        default:
            Utils.log("Unknown model index!");
            return false;
    }
    if (n_landmarks < min) {
        Utils.showMessage("Need at least " + min + " landmarks for a " + Align.Param.modelStrings[model_index] + " model");
        return false;
    }
    Bureaucrat.createAndStart(new Worker.Task("Aligning layers with landmarks") {

        @Override
        public void exec() {
            // Find layers with landmarks, in increasing Z.
            // Match in pairs.
            // So, get two submaps: from ref_layer to first, and from ref_layer to last
            // strictly lower Z than ref_layer
            final SortedMap<Layer, Landmarks> first_chunk_ = new TreeMap<Layer, Landmarks>(sorted.headMap(ref_layer));
            // .. so add ref_layer
            first_chunk_.put(ref_layer, m.get(ref_layer));
            // equal or larger Z than ref_layer
            final SortedMap<Layer, Landmarks> second_chunk = sorted.tailMap(ref_layer);
            final SortedMap<Layer, Landmarks> first_chunk;
            // Reverse order of first_chunk
            if (first_chunk_.size() > 1) {
                final SortedMap<Layer, Landmarks> fc = new TreeMap<Layer, Landmarks>(new Comparator<Layer>() {

                    @Override
                    public boolean equals(final Object ob) {
                        return this == ob;
                    }

                    @Override
                    public int compare(final Layer l1, final Layer l2) {
                        // Descending order
                        final double dz = l2.getZ() - l1.getZ();
                        if (dz < 0)
                            return -1;
                        else if (dz > 0)
                            return 1;
                        else
                            return 0;
                    }
                });
                fc.putAll(first_chunk_);
                first_chunk = fc;
            } else {
                first_chunk = first_chunk_;
            }
            final LayerSet ls = ref_layer.getParent();
            final Collection<Layer> affected_layers = new HashSet<Layer>(m.keySet());
            // Gather all Patch instances that will be affected
            final ArrayList<Patch> patches = new ArrayList<Patch>();
            for (final Layer la : m.keySet()) patches.addAll(la.getAll(Patch.class));
            if (propagate_to_first && first_chunk.size() > 1) {
                final Collection<Layer> affected = ls.getLayers().subList(0, ls.indexOf(first_chunk.lastKey()));
                for (final Layer la : affected) {
                    patches.addAll(la.getAll(Patch.class));
                }
                affected_layers.addAll(affected);
            }
            if (propagate_to_last && second_chunk.size() > 1) {
                final Collection<Layer> affected = ls.getLayers().subList(ls.indexOf(second_chunk.lastKey()) + 1, ls.size());
                for (final Layer la : affected) {
                    patches.addAll(la.getAll(Patch.class));
                }
            }
            // Transform segmentations along with patches
            AlignTask.transformPatchesAndVectorData(patches, new Runnable() {

                @Override
                public void run() {
                    // Apply!
                    // TODO: when adding non-linear transforms, use this single line for undo instead of all below:
                    // (these transforms may be non-linear as well, which alter mipmaps.)
                    // ls.addTransformStepWithData(affected_layers);
                    // Setup undo:
                    // Find all images in the range of affected layers,
                    // plus all Displayable of those layers (but Patch instances in a separate DoTransforms step,
                    // to avoid adding a "data" undo for them, which would recreate mipmaps when undone).
                    // plus all ZDisplayable that paint in those layers
                    final HashSet<Displayable> ds = new HashSet<Displayable>();
                    final ArrayList<Displayable> patches = new ArrayList<Displayable>();
                    for (final Layer layer : affected_layers) {
                        for (final Displayable d : layer.getDisplayables()) {
                            if (d.getClass() == Patch.class) {
                                patches.add(d);
                            } else {
                                ds.add(d);
                            }
                        }
                    }
                    for (final ZDisplayable zd : ls.getZDisplayables()) {
                        for (final Layer layer : affected_layers) {
                            if (zd.paintsAt(layer)) {
                                ds.add((Displayable) zd);
                                break;
                            }
                        }
                    }
                    if (ds.size() > 0) {
                        final Displayable.DoEdits step = ls.addTransformStepWithData(ds);
                        if (patches.size() > 0) {
                            final ArrayList<DoStep> a = new ArrayList<DoStep>();
                            a.add(new Displayable.DoTransforms().addAll(patches));
                            step.addDependents(a);
                        }
                    }
                    if (first_chunk.size() > 1) {
                        final AffineTransform aff = align(first_chunk, model);
                        if (propagate_to_first) {
                            for (final Layer la : ls.getLayers().subList(0, ls.indexOf(first_chunk.lastKey()))) {
                                // exclusive last
                                la.apply(Patch.class, aff);
                            }
                        }
                    }
                    if (second_chunk.size() > 1) {
                        final AffineTransform aff = align(second_chunk, model);
                        if (propagate_to_last) {
                            for (final Layer la : ls.getLayers().subList(ls.indexOf(second_chunk.lastKey()) + 1, ls.size())) {
                                // exclusive last
                                la.apply(Patch.class, aff);
                            }
                        }
                    }
                    Display.repaint();
                    // Store current state
                    if (ds.size() > 0) {
                        final Displayable.DoEdits step2 = ls.addTransformStepWithData(ds);
                        if (patches.size() > 0) {
                            final ArrayList<DoStep> a2 = new ArrayList<DoStep>();
                            a2.add(new Displayable.DoTransforms().addAll(patches));
                            step2.addDependents(a2);
                        }
                    }
                }
            });
        }
    }, display.getProject());
    return true;
}

Example 7 with AbstractAffineModel2D

use of mpicbg.models.AbstractAffineModel2D in project TrakEM2 by trakem2.

the class NonLinearTransformMode method createCT.

private CoordinateTransform createCT() throws Exception {
    final Collection<PointMatch> pm = new ArrayList<PointMatch>();
    for (final Point p : points) {
        pm.add(new PointMatch(new Point(p.getL()), new Point(p.getW())));
    }
    /*
		 * TODO replace this with the desired parameters of the transformation
		 */
    final MovingLeastSquaresTransform2 mlst = new MovingLeastSquaresTransform2();
    mlst.setAlpha(1.0f);
    Class<? extends AbstractAffineModel2D<?>> c = AffineModel2D.class;
    switch(points.size()) {
        case 1:
            c = TranslationModel2D.class;
            break;
        case 2:
            c = SimilarityModel2D.class;
            break;
        default:
            break;
    }
    mlst.setModel(c);
    mlst.setMatches(pm);
    return mlst;
}

Example 8 with AbstractAffineModel2D

use of mpicbg.models.AbstractAffineModel2D 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);
}

Example 9 with AbstractAffineModel2D

use of mpicbg.models.AbstractAffineModel2D in project TrakEM2 by trakem2.

the class Distortion_Correction method extractSIFTPoints.

protected void extractSIFTPoints(final int index, final List<Feature>[] siftFeatures, final List<List<PointMatch>> inliers, final List<AbstractAffineModel2D<?>> models) {
    // save all matching candidates
    final List<List<PointMatch>> candidates = new ArrayList<List<PointMatch>>();
    for (int j = 0; j < siftFeatures.length; j++) {
        if (index == j)
            continue;
        candidates.add(FloatArray2DSIFT.createMatches(siftFeatures[index], siftFeatures[j], 1.5f, null, Float.MAX_VALUE, 0.5f));
    }
    // get rid of the outliers and save the transformations to match the inliers
    for (int i = 0; i < candidates.size(); ++i) {
        final List<PointMatch> tmpInliers = new ArrayList<PointMatch>();
        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;
        }
        try {
            m.filterRansac(candidates.get(i), tmpInliers, 1000, sp.maxEpsilon, sp.minInlierRatio, 10);
        } catch (final NotEnoughDataPointsException e) {
            e.printStackTrace();
        }
        inliers.add(tmpInliers);
        models.add(m);
    }
}

Example 10 with AbstractAffineModel2D

use of mpicbg.models.AbstractAffineModel2D in project TrakEM2 by trakem2.

the class Align method alignLayersLinearly.

/**
 * Align a range of layers by accumulating pairwise alignments of contiguous layers.
 *
 * @param layers The range of layers to align pairwise.
 * @param numThreads The number of threads to use.
 * @param filter The {@link Filter} to decide which {@link Patch} instances to use in each {@link Layer}. Can be null.
 */
public static final void alignLayersLinearly(final List<Layer> layers, final int numThreads, final Filter<Patch> filter) {
    param.sift.maxOctaveSize = 1600;
    if (!param.setup("Align layers linearly"))
        return;
    final Rectangle box = layers.get(0).getParent().getMinimalBoundingBox(Patch.class);
    final double scale = Math.min(1.0, Math.min((double) param.sift.maxOctaveSize / box.width, (double) param.sift.maxOctaveSize / box.height));
    final Param p = param.clone();
    p.maxEpsilon *= scale;
    final FloatArray2DSIFT sift = new FloatArray2DSIFT(p.sift);
    final SIFT ijSIFT = new SIFT(sift);
    Rectangle box1 = null;
    Rectangle box2 = null;
    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 i = 0;
    for (final Layer l : layers) {
        long s = System.currentTimeMillis();
        features1.clear();
        features1.addAll(features2);
        features2.clear();
        final Rectangle box3 = l.getMinimalBoundingBox(Patch.class);
        if (box3 == null)
            continue;
        box1 = box2;
        box2 = box3;
        final List<Patch> patches = l.getAll(Patch.class);
        if (null != filter) {
            for (final Iterator<Patch> it = patches.iterator(); it.hasNext(); ) {
                if (!filter.accept(it.next()))
                    it.remove();
            }
        }
        ijSIFT.extractFeatures(l.getProject().getLoader().getFlatImage(l, box2, scale, 0xffffffff, ImagePlus.GRAY8, Patch.class, patches, true).getProcessor(), features2);
        Utils.log(features2.size() + " features extracted in layer \"" + l.getTitle() + "\" (took " + (System.currentTimeMillis() - s) + " ms).");
        if (features1.size() > 0) {
            s = 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)) {
                            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 layer \"" + l.getTitle() + "\" and its predecessor:\n  correspondences  " + inliers.size() + " of " + candidates.size() + "\n  average residual error  " + (model.getCost() / scale) + " px\n  took " + (System.currentTimeMillis() - s) + " ms");
                final AffineTransform b = new AffineTransform();
                b.translate(box1.x, box1.y);
                b.scale(1.0f / scale, 1.0f / scale);
                b.concatenate(model.createAffine());
                b.scale(scale, scale);
                b.translate(-box2.x, -box2.y);
                a.concatenate(b);
                l.apply(Displayable.class, a);
                Display.repaint(l);
            } else {
                Utils.log("No model found for layer \"" + l.getTitle() + "\" and its predecessor:\n  correspondence candidates  " + candidates.size() + "\n  took " + (System.currentTimeMillis() - s) + " ms");
                a.setToIdentity();
            }
        }
        IJ.showProgress(++i, layers.size());
    }
}