Examples with Montage ini.trakem2.utils.Montage used on opensource projects

Example 1 with Montage

use of ini.trakem2.utils.Montage in project TrakEM2 by trakem2.

the class PatchStack method createColor256Copy.

// WARNING This method will fail if the stack has slices of different dimensions
/**
 * Does not respect local transform of the patches, this is intended for confocal stacks.
 */
public ImagePlus createColor256Copy() {
    final Rectangle box = patch[0].getBoundingBox();
    final int width = box.width;
    final int height = box.height;
    Loader loader = patch[0].getProject().getLoader();
    // the montage, in RGB
    patch[0].getProject().getLoader().releaseToFit(4 * patch.length * width * height);
    final ColorProcessor montage = new ColorProcessor(width * patch.length, height);
    for (int i = 0; i < patch.length; i++) {
        montage.insert(this.stack.getProcessor(i + 1), i * width, 0);
    }
    final MedianCut mc = new MedianCut(montage);
    loader.releaseToFit(patch.length * width * height);
    ImageProcessor m2 = mc.convertToByte(256);
    final ImageStack st = new ImageStack(width, height);
    for (int i = 0; i < patch.length; i++) {
        m2.setRoi(i * width, 0, width, height);
        loader.releaseToFit(width * height);
        st.addSlice(null, m2.crop());
    }
    ImagePlus imp = new ImagePlus("color256", st);
    imp.setCalibration(patch[0].getLayer().getParent().getCalibrationCopy());
    // imp.getCalibration().pixelDepth = patch[0].getLayer().getThickness();
    return imp;
}

Example 2 with Montage

use of ini.trakem2.utils.Montage in project TrakEM2 by trakem2.

the class AlignTask method alignPatches.

/**
 * @param patches: the list of Patch instances to align, all belonging to the same Layer.
 * @param fixedPatches: the list of Patch instances to keep locked in place, if any.
 * @param m: {@link AlignTask#LINEAR_SIFT_CORRESPONDENCES}, {@link AlignTask#LINEAR_PHASE_CORRELATION} or {@link AlignTask#ELASTIC_BLOCK_CORRESPONDENCES}.
 */
public static final void alignPatches(final List<Patch> patches, final Set<Patch> fixedPatches, final int m) throws Exception {
    if (patches.size() < 2) {
        Utils.log("No images to align.");
        return;
    }
    for (final Patch patch : fixedPatches) {
        if (!patches.contains(patch)) {
            Utils.log("The list of fixed patches contains at least one Patch not included in the list of patches to align!");
            return;
        }
    }
    if (ELASTIC_BLOCK_CORRESPONDENCES == m)
        new ElasticMontage().exec(patches, fixedPatches);
    else if (LINEAR_PHASE_CORRELATION == m) {
        // Montage all given patches, fixedPatches is ignored!
        if (!fixedPatches.isEmpty())
            Utils.log("Ignoring " + fixedPatches.size() + " fixed patches.");
        StitchingTEM.montageWithPhaseCorrelation(patches);
    } else if (LINEAR_SIFT_CORRESPONDENCES == m) {
        if (!Align.paramOptimize.setup("Montage Selection"))
            return;
        final GenericDialog gd = new GenericDialog("Montage Selection: Miscellaneous");
        gd.addCheckbox("tiles are roughly in place", tilesAreInPlace);
        gd.addCheckbox("sloppy overlap test (fast)", sloppyOverlapTest);
        gd.addCheckbox("consider largest graph only", largestGraphOnly);
        gd.addCheckbox("hide tiles from non-largest graph", hideDisconnectedTiles);
        gd.addCheckbox("delete tiles from non-largest graph", deleteDisconnectedTiles);
        gd.showDialog();
        if (gd.wasCanceled())
            return;
        tilesAreInPlace = gd.getNextBoolean();
        sloppyOverlapTest = gd.getNextBoolean();
        largestGraphOnly = gd.getNextBoolean();
        hideDisconnectedTiles = gd.getNextBoolean();
        deleteDisconnectedTiles = gd.getNextBoolean();
        final Align.ParamOptimize p = Align.paramOptimize.clone();
        alignPatches(p, patches, fixedPatches, tilesAreInPlace, largestGraphOnly, hideDisconnectedTiles, deleteDisconnectedTiles, sloppyOverlapTest);
    } else
        Utils.log("Don't know how to align with mode " + m);
}

Example 3 with Montage

use of ini.trakem2.utils.Montage in project TrakEM2 by trakem2.

the class AlignTask method montageLayersTask.

/**
 * Montage each layer independently.
 *  Does NOT register layers to each other.
 *  Considers visible Patches only.
 */
public static final Bureaucrat montageLayersTask(final List<Layer> layers) {
    if (null == layers || layers.isEmpty())
        return null;
    return Bureaucrat.createAndStart(new Worker.Task("Montaging layers", true) {

        @Override
        public void exec() {
            final int m = chooseAlignmentMode();
            if (ELASTIC_BLOCK_CORRESPONDENCES == m) {
                final ElasticMontage.Param p = ElasticMontage.setup();
                if (p == null)
                    return;
                else {
                    try {
                        montageLayers(p, layers);
                    } catch (final Exception e) {
                        e.printStackTrace();
                        Utils.log("Exception during montaging layers.  Operation failed.");
                    }
                }
            } else if (LINEAR_PHASE_CORRELATION == m) {
                StitchingTEM.montageWithPhaseCorrelation(layers, this);
            } else if (LINEAR_SIFT_CORRESPONDENCES == m) {
                if (!Align.paramOptimize.setup("Montage Layers"))
                    return;
                final GenericDialog gd = new GenericDialog("Montage Layers: Miscellaneous");
                gd.addCheckbox("tiles are roughly in place", tilesAreInPlace);
                gd.addCheckbox("sloppy overlap test (fast)", sloppyOverlapTest);
                gd.addCheckbox("consider largest graph only", largestGraphOnly);
                gd.addCheckbox("hide tiles from non-largest graph", hideDisconnectedTiles);
                gd.addCheckbox("delete tiles from non-largest graph", deleteDisconnectedTiles);
                gd.showDialog();
                if (gd.wasCanceled())
                    return;
                tilesAreInPlace = gd.getNextBoolean();
                sloppyOverlapTest = gd.getNextBoolean();
                largestGraphOnly = gd.getNextBoolean();
                hideDisconnectedTiles = gd.getNextBoolean();
                deleteDisconnectedTiles = gd.getNextBoolean();
                final Align.ParamOptimize p = Align.paramOptimize.clone();
                montageLayers(p, layers, tilesAreInPlace, largestGraphOnly, hideDisconnectedTiles, deleteDisconnectedTiles, sloppyOverlapTest);
            } else
                Utils.log("Don't know how to align with mode " + m);
        }
    }, layers.get(0).getProject());
}

Example 4 with Montage

use of ini.trakem2.utils.Montage 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 5 with Montage

use of ini.trakem2.utils.Montage in project TrakEM2 by trakem2.

the class ElasticMontage method exec.

@SuppressWarnings("deprecation")
public final void exec(final Param param, final List<Patch> patches, final Set<Patch> fixedPatches) throws Exception {
    /* free memory */
    patches.get(0).getProject().getLoader().releaseAll();
    /* create tiles and models for all patches */
    final ArrayList<AbstractAffineTile2D<?>> tiles = new ArrayList<AbstractAffineTile2D<?>>();
    final ArrayList<AbstractAffineTile2D<?>> fixedTiles = new ArrayList<AbstractAffineTile2D<?>>();
    Align.tilesFromPatches(param.po, patches, fixedPatches, tiles, fixedTiles);
    if (!param.isAligned) {
        Align.alignTiles(param.po, tiles, fixedTiles, param.tilesAreInPlace, param.maxNumThreads);
        /* Apply the estimated affine transform to patches */
        for (final AbstractAffineTile2D<?> t : tiles) t.getPatch().setAffineTransform(t.createAffine());
        Display.update();
    }
    /* generate tile pairs for all by now overlapping tiles */
    final ArrayList<AbstractAffineTile2D<?>[]> tilePairs = new ArrayList<AbstractAffineTile2D<?>[]>();
    AbstractAffineTile2D.pairOverlappingTiles(tiles, tilePairs);
    /* check if there was any pair */
    if (tilePairs.size() == 0) {
        Utils.log("Elastic montage could not find any overlapping patches after pre-montaging.");
        return;
    }
    Utils.log(tilePairs.size() + " pairs of patches will be block-matched...");
    /* make pairwise global models local */
    final ArrayList<Triple<AbstractAffineTile2D<?>, AbstractAffineTile2D<?>, InvertibleCoordinateTransform>> pairs = new ArrayList<Triple<AbstractAffineTile2D<?>, AbstractAffineTile2D<?>, InvertibleCoordinateTransform>>();
    /*
		 * The following casting madness is necessary to get this code compiled
		 * with Sun/Oracle Java 6 which otherwise generates an inconvertible
		 * type exception.
		 *
		 * TODO Remove as soon as this bug is fixed in Sun/Oracle javac.
		 */
    for (final AbstractAffineTile2D<?>[] pair : tilePairs) {
        final AbstractAffineModel2D<?> m;
        switch(param.po.desiredModelIndex) {
            case 0:
                final TranslationModel2D t = (TranslationModel2D) (Object) pair[1].getModel().createInverse();
                t.concatenate((TranslationModel2D) (Object) pair[0].getModel());
                m = t;
                break;
            case 1:
                final RigidModel2D r = (RigidModel2D) (Object) pair[1].getModel().createInverse();
                r.concatenate((RigidModel2D) (Object) pair[0].getModel());
                m = r;
                break;
            case 2:
                final SimilarityModel2D s = (SimilarityModel2D) (Object) pair[1].getModel().createInverse();
                s.concatenate((SimilarityModel2D) (Object) pair[0].getModel());
                m = s;
                break;
            case 3:
                final AffineModel2D a = (AffineModel2D) (Object) pair[1].getModel().createInverse();
                a.concatenate((AffineModel2D) (Object) pair[0].getModel());
                m = a;
                break;
            default:
                m = null;
        }
        pairs.add(new Triple<AbstractAffineTile2D<?>, AbstractAffineTile2D<?>, InvertibleCoordinateTransform>(pair[0], pair[1], m));
    }
    /* Elastic alignment */
    /* Initialization */
    final double springTriangleHeightTwice = 2 * Math.sqrt(0.75 * param.springLengthSpringMesh * param.springLengthSpringMesh);
    final ArrayList<SpringMesh> meshes = new ArrayList<SpringMesh>(tiles.size());
    final HashMap<AbstractAffineTile2D<?>, SpringMesh> tileMeshMap = new HashMap<AbstractAffineTile2D<?>, SpringMesh>();
    for (final AbstractAffineTile2D<?> tile : tiles) {
        final double w = tile.getWidth();
        final double h = tile.getHeight();
        final int numX = Math.max(2, (int) Math.ceil(w / param.springLengthSpringMesh) + 1);
        final int numY = Math.max(2, (int) Math.ceil(h / springTriangleHeightTwice) + 1);
        final double wMesh = (numX - 1) * param.springLengthSpringMesh;
        final double hMesh = (numY - 1) * springTriangleHeightTwice;
        final SpringMesh mesh = new SpringMesh(numX, numY, wMesh, hMesh, param.stiffnessSpringMesh, param.maxStretchSpringMesh * param.bmScale, param.dampSpringMesh);
        meshes.add(mesh);
        tileMeshMap.put(tile, mesh);
    }
    // final int blockRadius = Math.max( 32, Util.roundPos( param.springLengthSpringMesh / 2 ) );
    final int blockRadius = Math.max(Util.roundPos(16 / param.bmScale), param.bmBlockRadius);
    /**
     * TODO set this something more than the largest error by the approximate model
     */
    final int searchRadius = param.bmSearchRadius;
    final AbstractModel<?> localSmoothnessFilterModel = mpicbg.trakem2.align.Util.createModel(param.bmLocalModelIndex);
    for (final Triple<AbstractAffineTile2D<?>, AbstractAffineTile2D<?>, InvertibleCoordinateTransform> pair : pairs) {
        final AbstractAffineTile2D<?> t1 = pair.a;
        final AbstractAffineTile2D<?> t2 = pair.b;
        final SpringMesh m1 = tileMeshMap.get(t1);
        final SpringMesh m2 = tileMeshMap.get(t2);
        final ArrayList<PointMatch> pm12 = new ArrayList<PointMatch>();
        final ArrayList<PointMatch> pm21 = new ArrayList<PointMatch>();
        final ArrayList<Vertex> v1 = m1.getVertices();
        final ArrayList<Vertex> v2 = m2.getVertices();
        final String patchName1 = patchName(t1.getPatch());
        final String patchName2 = patchName(t2.getPatch());
        final PatchImage pi1 = t1.getPatch().createTransformedImage();
        if (pi1 == null) {
            Utils.log("Patch `" + patchName1 + "' failed generating a transformed image.  Skipping...");
            continue;
        }
        final PatchImage pi2 = t2.getPatch().createTransformedImage();
        if (pi2 == null) {
            Utils.log("Patch `" + patchName2 + "' failed generating a transformed image.  Skipping...");
            continue;
        }
        final FloatProcessor fp1 = (FloatProcessor) pi1.target.convertToFloat();
        final ByteProcessor mask1 = pi1.getMask();
        final FloatProcessor fpMask1 = mask1 == null ? null : scaleByte(mask1);
        final FloatProcessor fp2 = (FloatProcessor) pi2.target.convertToFloat();
        final ByteProcessor mask2 = pi2.getMask();
        final FloatProcessor fpMask2 = mask2 == null ? null : scaleByte(mask2);
        if (!fixedTiles.contains(t1)) {
            BlockMatching.matchByMaximalPMCC(fp1, fp2, fpMask1, fpMask2, param.bmScale, pair.c, blockRadius, blockRadius, searchRadius, searchRadius, param.bmMinR, param.bmRodR, param.bmMaxCurvatureR, v1, pm12, new ErrorStatistic(1));
            if (param.bmUseLocalSmoothnessFilter) {
                Utils.log("`" + patchName1 + "' > `" + patchName2 + "': found " + pm12.size() + " correspondence candidates.");
                localSmoothnessFilterModel.localSmoothnessFilter(pm12, pm12, param.bmLocalRegionSigma, param.bmMaxLocalEpsilon, param.bmMaxLocalTrust);
                Utils.log("`" + patchName1 + "' > `" + patchName2 + "': " + pm12.size() + " candidates passed local smoothness filter.");
            } else {
                Utils.log("`" + patchName1 + "' > `" + patchName2 + "': found " + pm12.size() + " correspondences.");
            }
        } else {
            Utils.log("Skipping fixed patch `" + patchName1 + "'.");
        }
        if (!fixedTiles.contains(t2)) {
            BlockMatching.matchByMaximalPMCC(fp2, fp1, fpMask2, fpMask1, param.bmScale, pair.c.createInverse(), blockRadius, blockRadius, searchRadius, searchRadius, param.bmMinR, param.bmRodR, param.bmMaxCurvatureR, v2, pm21, new ErrorStatistic(1));
            if (param.bmUseLocalSmoothnessFilter) {
                Utils.log("`" + patchName1 + "' < `" + patchName2 + "': found " + pm21.size() + " correspondence candidates.");
                localSmoothnessFilterModel.localSmoothnessFilter(pm21, pm21, param.bmLocalRegionSigma, param.bmMaxLocalEpsilon, param.bmMaxLocalTrust);
                Utils.log("`" + patchName1 + "' < `" + patchName2 + "': " + pm21.size() + " candidates passed local smoothness filter.");
            } else {
                Utils.log("`" + patchName1 + "' < `" + patchName2 + "': found " + pm21.size() + " correspondences.");
            }
        } else {
            Utils.log("Skipping fixed patch `" + patchName2 + "'.");
        }
        for (final PointMatch pm : pm12) {
            final Vertex p1 = (Vertex) pm.getP1();
            final Vertex p2 = new Vertex(pm.getP2());
            p1.addSpring(p2, new Spring(0, 1.0f));
            m2.addPassiveVertex(p2);
        }
        for (final PointMatch pm : pm21) {
            final Vertex p1 = (Vertex) pm.getP1();
            final Vertex p2 = new Vertex(pm.getP2());
            p1.addSpring(p2, new Spring(0, 1.0f));
            m1.addPassiveVertex(p2);
        }
    }
    /* initialize */
    for (final Map.Entry<AbstractAffineTile2D<?>, SpringMesh> entry : tileMeshMap.entrySet()) entry.getValue().init(entry.getKey().getModel());
    /* optimize the meshes */
    try {
        final long t0 = System.currentTimeMillis();
        IJ.log("Optimizing spring meshes...");
        if (param.useLegacyOptimizer) {
            Utils.log("  ...using legacy optimizer...");
            SpringMesh.optimizeMeshes2(meshes, param.po.maxEpsilon, param.maxIterationsSpringMesh, param.maxPlateauwidthSpringMesh, param.visualize);
        } else {
            SpringMesh.optimizeMeshes(meshes, param.po.maxEpsilon, param.maxIterationsSpringMesh, param.maxPlateauwidthSpringMesh, param.visualize);
        }
        IJ.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;
    }
    /* apply */
    for (final Map.Entry<AbstractAffineTile2D<?>, SpringMesh> entry : tileMeshMap.entrySet()) {
        final AbstractAffineTile2D<?> tile = entry.getKey();
        if (!fixedTiles.contains(tile)) {
            final Patch patch = tile.getPatch();
            final SpringMesh mesh = entry.getValue();
            final Set<PointMatch> matches = mesh.getVA().keySet();
            Rectangle box = patch.getCoordinateTransformBoundingBox();
            /* compensate for existing coordinate transform bounding box */
            for (final PointMatch pm : matches) {
                final Point p1 = pm.getP1();
                final double[] l = p1.getL();
                l[0] += box.x;
                l[1] += box.y;
            }
            final ThinPlateSplineTransform mlt = ElasticLayerAlignment.makeTPS(matches);
            patch.appendCoordinateTransform(mlt);
            box = patch.getCoordinateTransformBoundingBox();
            patch.getAffineTransform().setToTranslation(box.x, box.y);
            patch.updateInDatabase("transform");
            patch.updateBucket();
            patch.updateMipMaps();
        }
    }
    Utils.log("Done.");
}