Examples with Project ini.trakem2.Project used on opensource projects

Example 16 with Project

use of ini.trakem2.Project in project TrakEM2 by trakem2.

the class AlignTask method transformPatchesAndVectorData.

/**
 * For registering within the same project instance.
 */
public static final void transformPatchesAndVectorData(final Collection<Patch> patches, final Runnable alignment) {
    if (patches.isEmpty()) {
        Utils.log("No patches to align!");
        return;
    }
    // 1 - Collect all VectorData to transform
    final ArrayList<Displayable> vdata = new ArrayList<Displayable>();
    final LayerSet ls = patches.iterator().next().getLayerSet();
    for (final Layer layer : ls.getLayers()) {
        vdata.addAll(layer.getDisplayables(VectorData.class, false, true));
    }
    vdata.addAll(ls.getZDisplayables(VectorData.class, true));
    // Perhaps none:
    if (vdata.isEmpty()) {
        alignment.run();
        return;
    }
    // 2 - Store current transformation of each Patch under any VectorData
    final HashSet<Long> lids = new HashSet<Long>();
    for (final Patch p : patches) lids.add(p.getLayer().getId());
    final ReferenceData rd = createTransformPropertiesTable(vdata, null, lids);
    // 3 - Align:
    alignment.run();
    // 4 - Transform VectorData instances to match the position of the Patch instances over which they were defined
    if (null != rd && !vdata.isEmpty())
        transformVectorData(rd, vdata, ls);
}

Example 17 with Project

use of ini.trakem2.Project in project TrakEM2 by trakem2.

the class ElasticLayerAlignment method exec.

/**
 * Stateful.  Changing the parameters of this instance.  Do not use in parallel.
 *
 * @param layerRange
 * @param fixedLayers
 * @param propagateTransformBefore
 * @param propagateTransformAfter
 * @param fov
 * @param filter
 * @throws Exception
 */
public final void exec(final Project project, final List<Layer> layerRange, final Set<Layer> fixedLayers, final boolean propagateTransformBefore, final boolean propagateTransformAfter, final Rectangle fov, final Filter<Patch> filter) throws Exception {
    Rectangle box = null;
    final HashSet<Layer> emptyLayers = new HashSet<Layer>();
    for (final Iterator<Layer> it = layerRange.iterator(); it.hasNext(); ) {
        /* remove empty layers */
        final Layer la = it.next();
        if (!la.contains(Patch.class, true)) {
            emptyLayers.add(la);
        // it.remove();
        } else {
            /* accumulate boxes */
            if (// The first layer:
            null == box)
                box = la.getMinimalBoundingBox(Patch.class, true);
            else
                box = box.union(la.getMinimalBoundingBox(Patch.class, true));
        }
    }
    if (box == null)
        box = new Rectangle();
    if (fov != null)
        box = box.intersection(fov);
    if (box.width <= 0 || box.height <= 0) {
        Utils.log("Bounding box empty.");
        return;
    }
    if (layerRange.size() == emptyLayers.size()) {
        Utils.log("All layers in range are empty!");
        return;
    }
    /* do not work if there is only one layer selected */
    if (layerRange.size() - emptyLayers.size() < 2) {
        Utils.log("All except one layer in range are empty!");
        return;
    }
    if (!p.setup(box))
        return;
    exec(p.clone(), project, layerRange, fixedLayers, emptyLayers, box, propagateTransformBefore, propagateTransformAfter, filter);
}

Example 18 with Project

use of ini.trakem2.Project in project TrakEM2 by trakem2.

the class ElasticLayerAlignment method exec.

/**
 * @param param
 * @param layerRange
 * @param fixedLayers
 * @param emptyLayers
 * @param box
 * @param filter
 * @param useTps true if using TPS transforms, otherwise MLS
 * @throws Exception
 */
@SuppressWarnings("deprecation")
public final void exec(final Param param, final Project project, final List<Layer> layerRange, final Set<Layer> fixedLayers, final Set<Layer> emptyLayers, final Rectangle box, final boolean propagateTransformBefore, final boolean propagateTransformAfter, final Filter<Patch> filter) throws Exception {
    final ExecutorService service = ExecutorProvider.getExecutorService(1.0f);
    /* create tiles and models for all layers */
    final ArrayList<Tile<?>> tiles = new ArrayList<Tile<?>>();
    for (int i = 0; i < layerRange.size(); ++i) {
        switch(param.desiredModelIndex) {
            case 0:
                tiles.add(new Tile<TranslationModel2D>(new TranslationModel2D()));
                break;
            case 1:
                tiles.add(new Tile<RigidModel2D>(new RigidModel2D()));
                break;
            case 2:
                tiles.add(new Tile<SimilarityModel2D>(new SimilarityModel2D()));
                break;
            case 3:
                tiles.add(new Tile<AffineModel2D>(new AffineModel2D()));
                break;
            case 4:
                tiles.add(new Tile<HomographyModel2D>(new HomographyModel2D()));
                break;
            default:
                return;
        }
    }
    /* collect all pairs of slices for which a model could be found */
    final ArrayList<Triple<Integer, Integer, AbstractModel<?>>> pairs = new ArrayList<Triple<Integer, Integer, AbstractModel<?>>>();
    if (!param.isAligned) {
        preAlignStack(param, project, layerRange, box, filter, pairs);
    } else {
        for (int i = 0; i < layerRange.size(); ++i) {
            final int range = Math.min(layerRange.size(), i + param.maxNumNeighbors + 1);
            for (int j = i + 1; j < range; ++j) {
                pairs.add(new Triple<Integer, Integer, AbstractModel<?>>(i, j, new TranslationModel2D()));
            }
        }
    }
    /* Elastic alignment */
    /* Initialization */
    final TileConfiguration initMeshes = new TileConfiguration();
    final int meshWidth = (int) Math.ceil(box.width * param.layerScale);
    final int meshHeight = (int) Math.ceil(box.height * param.layerScale);
    final ArrayList<SpringMesh> meshes = new ArrayList<SpringMesh>(layerRange.size());
    for (int i = 0; i < layerRange.size(); ++i) {
        meshes.add(new SpringMesh(param.resolutionSpringMesh, meshWidth, meshHeight, param.stiffnessSpringMesh, param.maxStretchSpringMesh * param.layerScale, param.dampSpringMesh));
    }
    // final int blockRadius = Math.max( 32, meshWidth / p.resolutionSpringMesh / 2 );
    final int blockRadius = Math.max(16, mpicbg.util.Util.roundPos(param.layerScale * param.blockRadius));
    Utils.log("effective block radius = " + blockRadius);
    final ArrayList<Future<BlockMatchPairCallable.BlockMatchResults>> futures = new ArrayList<Future<BlockMatchPairCallable.BlockMatchResults>>(pairs.size());
    for (final Triple<Integer, Integer, AbstractModel<?>> pair : pairs) {
        /* free memory */
        project.getLoader().releaseAll();
        final SpringMesh m1 = meshes.get(pair.a);
        final SpringMesh m2 = meshes.get(pair.b);
        final ArrayList<Vertex> v1 = m1.getVertices();
        final ArrayList<Vertex> v2 = m2.getVertices();
        final Layer layer1 = layerRange.get(pair.a);
        final Layer layer2 = layerRange.get(pair.b);
        final boolean layer1Fixed = fixedLayers.contains(layer1);
        final boolean layer2Fixed = fixedLayers.contains(layer2);
        if (!(layer1Fixed && layer2Fixed)) {
            final BlockMatchPairCallable bmpc = new BlockMatchPairCallable(pair, layerRange, layer1Fixed, layer2Fixed, filter, param, v1, v2, box);
            futures.add(service.submit(bmpc));
        }
    }
    for (final Future<BlockMatchPairCallable.BlockMatchResults> future : futures) {
        final BlockMatchPairCallable.BlockMatchResults results = future.get();
        final Collection<PointMatch> pm12 = results.pm12, pm21 = results.pm21;
        final Triple<Integer, Integer, AbstractModel<?>> pair = results.pair;
        final Tile<?> t1 = tiles.get(pair.a);
        final Tile<?> t2 = tiles.get(pair.b);
        final SpringMesh m1 = meshes.get(pair.a);
        final SpringMesh m2 = meshes.get(pair.b);
        final double springConstant = 1.0 / (pair.b - pair.a);
        final boolean layer1Fixed = results.layer1Fixed;
        final boolean layer2Fixed = results.layer2Fixed;
        if (layer1Fixed) {
            initMeshes.fixTile(t1);
        } else {
            if (param.useLocalSmoothnessFilter) {
                Utils.log(pair.a + " > " + pair.b + ": " + pm12.size() + " candidates passed local smoothness filter.");
            } else {
                Utils.log(pair.a + " > " + pair.b + ": found " + pm12.size() + " correspondences.");
            }
            for (final PointMatch pm : pm12) {
                final Vertex p1 = (Vertex) pm.getP1();
                final Vertex p2 = new Vertex(pm.getP2());
                p1.addSpring(p2, new Spring(0, springConstant));
                m2.addPassiveVertex(p2);
            }
            /*
                * adding Tiles to the initialing TileConfiguration, adding a Tile
                * multiple times does not harm because the TileConfiguration is
                * backed by a Set.
                */
            if (pm12.size() > pair.c.getMinNumMatches()) {
                initMeshes.addTile(t1);
                initMeshes.addTile(t2);
                t1.connect(t2, pm12);
            }
        }
        if (layer2Fixed)
            initMeshes.fixTile(t2);
        else {
            if (param.useLocalSmoothnessFilter) {
                Utils.log(pair.a + " < " + pair.b + ": " + pm21.size() + " candidates passed local smoothness filter.");
            } else {
                Utils.log(pair.a + " < " + pair.b + ": found " + pm21.size() + " correspondences.");
            }
            for (final PointMatch pm : pm21) {
                final Vertex p1 = (Vertex) pm.getP1();
                final Vertex p2 = new Vertex(pm.getP2());
                p1.addSpring(p2, new Spring(0, springConstant));
                m1.addPassiveVertex(p2);
            }
            /*
                * adding Tiles to the initialing TileConfiguration, adding a Tile
                * multiple times does not harm because the TileConfiguration is
                * backed by a Set.
                */
            if (pm21.size() > pair.c.getMinNumMatches()) {
                initMeshes.addTile(t1);
                initMeshes.addTile(t2);
                t2.connect(t1, pm21);
            }
        }
        Utils.log(pair.a + " <> " + pair.b + " spring constant = " + springConstant);
    }
    /* pre-align by optimizing a piecewise linear model */
    initMeshes.optimize(param.maxEpsilon * param.layerScale, param.maxIterationsSpringMesh, param.maxPlateauwidthSpringMesh);
    for (int i = 0; i < layerRange.size(); ++i) meshes.get(i).init(tiles.get(i).getModel());
    /* optimize the meshes */
    try {
        final long t0 = System.currentTimeMillis();
        Utils.log("Optimizing spring meshes...");
        if (param.useLegacyOptimizer) {
            Utils.log("  ...using legacy optimizer...");
            SpringMesh.optimizeMeshes2(meshes, param.maxEpsilon * param.layerScale, param.maxIterationsSpringMesh, param.maxPlateauwidthSpringMesh, param.visualize);
        } else {
            SpringMesh.optimizeMeshes(meshes, param.maxEpsilon * param.layerScale, param.maxIterationsSpringMesh, param.maxPlateauwidthSpringMesh, param.visualize);
        }
        Utils.log("Done optimizing spring meshes. Took " + (System.currentTimeMillis() - t0) + " ms");
    } catch (final NotEnoughDataPointsException e) {
        Utils.log("There were not enough data points to get the spring mesh optimizing.");
        e.printStackTrace();
        return;
    }
    /* translate relative to bounding box */
    for (final SpringMesh mesh : meshes) {
        for (final PointMatch pm : mesh.getVA().keySet()) {
            final Point p1 = pm.getP1();
            final Point p2 = pm.getP2();
            final double[] l = p1.getL();
            final double[] w = p2.getW();
            l[0] = l[0] / param.layerScale + box.x;
            l[1] = l[1] / param.layerScale + box.y;
            w[0] = w[0] / param.layerScale + box.x;
            w[1] = w[1] / param.layerScale + box.y;
        }
    }
    /* free memory */
    project.getLoader().releaseAll();
    final Layer first = layerRange.get(0);
    final List<Layer> layers = first.getParent().getLayers();
    final LayerSet ls = first.getParent();
    final Area infArea = AreaUtils.infiniteArea();
    final List<VectorData> vectorData = new ArrayList<VectorData>();
    for (final Layer layer : ls.getLayers()) {
        vectorData.addAll(Utils.castCollection(layer.getDisplayables(VectorData.class, false, true), VectorData.class, true));
    }
    vectorData.addAll(Utils.castCollection(ls.getZDisplayables(VectorData.class, true), VectorData.class, true));
    /* transfer layer transform into patch transforms and append to patches */
    if (propagateTransformBefore || propagateTransformAfter) {
        if (propagateTransformBefore) {
            final ThinPlateSplineTransform tps = makeTPS(meshes.get(0).getVA().keySet());
            final int firstLayerIndex = first.getParent().getLayerIndex(first.getId());
            for (int i = 0; i < firstLayerIndex; ++i) {
                applyTransformToLayer(layers.get(i), tps, filter);
                for (final VectorData vd : vectorData) {
                    vd.apply(layers.get(i), infArea, tps);
                }
            }
        }
        if (propagateTransformAfter) {
            final Layer last = layerRange.get(layerRange.size() - 1);
            final CoordinateTransform ct;
            if (param.useTps)
                ct = makeTPS(meshes.get(meshes.size() - 1).getVA().keySet());
            else {
                final MovingLeastSquaresTransform2 mls = new MovingLeastSquaresTransform2();
                mls.setMatches(meshes.get(meshes.size() - 1).getVA().keySet());
                ct = mls;
            }
            final int lastLayerIndex = last.getParent().getLayerIndex(last.getId());
            for (int i = lastLayerIndex + 1; i < layers.size(); ++i) {
                applyTransformToLayer(layers.get(i), ct, filter);
                for (final VectorData vd : vectorData) {
                    vd.apply(layers.get(i), infArea, ct);
                }
            }
        }
    }
    for (int l = 0; l < layerRange.size(); ++l) {
        IJ.showStatus("Applying transformation to patches ...");
        IJ.showProgress(0, layerRange.size());
        final Layer layer = layerRange.get(l);
        final ThinPlateSplineTransform tps = makeTPS(meshes.get(l).getVA().keySet());
        applyTransformToLayer(layer, tps, filter);
        for (final VectorData vd : vectorData) {
            vd.apply(layer, infArea, tps);
        }
        if (Thread.interrupted()) {
            Utils.log("Interrupted during applying transformations to patches.  No all patches have been updated.  Re-generate mipmaps manually.");
        }
        IJ.showProgress(l + 1, layerRange.size());
    }
    /* update patch mipmaps */
    final int firstLayerIndex;
    final int lastLayerIndex;
    if (propagateTransformBefore)
        firstLayerIndex = 0;
    else {
        firstLayerIndex = first.getParent().getLayerIndex(first.getId());
    }
    if (propagateTransformAfter)
        lastLayerIndex = layers.size() - 1;
    else {
        final Layer last = layerRange.get(layerRange.size() - 1);
        lastLayerIndex = last.getParent().getLayerIndex(last.getId());
    }
    for (int i = firstLayerIndex; i <= lastLayerIndex; ++i) {
        final Layer layer = layers.get(i);
        if (!(emptyLayers.contains(layer) || fixedLayers.contains(layer))) {
            for (final Patch patch : AlignmentUtils.filterPatches(layer, filter)) patch.updateMipMaps();
        }
    }
    Utils.log("Done.");
}

Example 19 with Project

use of ini.trakem2.Project in project TrakEM2 by trakem2.

the class ElasticMontage method exec.

public final void exec(final List<Patch> patches, final Set<Patch> fixedPatches) throws Exception {
    /* make sure that passed patches are ok */
    if (patches.size() < 2) {
        Utils.log("Elastic montage requires at least 2 patches to be montaged.  You passed me " + patches.size());
        return;
    }
    final Project project = patches.get(0).getProject();
    for (final Patch patch : patches) {
        if (patch.getProject() != project) {
            Utils.log("Elastic montage requires all patches to be member of a single project.  You passed me patches from several projects.");
            return;
        }
    }
    for (final Patch patch : fixedPatches) {
        if (patch.getProject() != project) {
            Utils.log("Elastic montage requires all fixed patches to be member of a single project.  You passed me fixed patches from several projects.");
            return;
        }
    }
    final Param param = setup();
    if (param == null)
        return;
    else
        exec(param, patches, fixedPatches);
}

Example 20 with Project

use of ini.trakem2.Project in project TrakEM2 by trakem2.

the class Util method deserializePointMatches.

protected static final ArrayList<PointMatch> deserializePointMatches(final Project project, final Object key, final String prefix, final long id1, final long id2) {
    final String name = prefix == null ? "pointmatches" : prefix + ".pointmatches";
    final Loader loader = project.getLoader();
    final Object ob = loader.deserialize(new StringBuilder(loader.getUNUIdFolder()).append("pointmatches.ser/").append(FSLoader.createIdPath(Long.toString(id1) + "_" + Long.toString(id2), name, ".ser")).toString());
    if (null != ob) {
        try {
            final PointMatches pm = (PointMatches) ob;
            if (pm.key != null && key.equals(pm.key))
                return pm.pointMatches;
        } catch (final Exception e) {
            Utils.log("Exception during pointmatch deserialization.");
            e.printStackTrace();
        }
    }
    return null;
}