Examples with Point3f org.scijava.vecmath.Point3f used on opensource projects

Example 26 with Point3f

use of org.scijava.vecmath.Point3f in project TrakEM2 by trakem2.

the class Polyline method generateTriangles.

/**
 * Returns a list of Point3f that define a polyline in 3D, for usage with an ij3d CustomLineMesh CONTINUOUS. @param parallels is ignored.
 */
public synchronized List<Point3f> generateTriangles(final double scale, final int parallels, final int resample, final Calibration cal) {
    if (-1 == n_points)
        setupForDisplay();
    if (0 == n_points)
        return null;
    // local pointers, since they may be transformed
    final int n_points;
    final double[][] p;
    if (!this.at.isIdentity()) {
        final Object[] ob = getTransformedData();
        p = (double[][]) ob[0];
        n_points = p[0].length;
    } else {
        n_points = this.n_points;
        p = this.p;
    }
    final ArrayList<Point3f> list = new ArrayList<Point3f>();
    final double KW = scale * cal.pixelWidth * resample;
    final double KH = scale * cal.pixelHeight * resample;
    for (int i = 0; i < n_points; i++) {
        list.add(new Point3f((float) (p[0][i] * KW), (float) (p[1][i] * KH), (float) (layer_set.getLayer(p_layer[i]).getZ() * KW)));
    }
    if (n_points < 2) {
        // Duplicate first point
        list.add(list.get(0));
    }
    return list;
}

Example 27 with Point3f

use of org.scijava.vecmath.Point3f in project TrakEM2 by trakem2.

the class Profile method generateTriangles.

/**
 * Takes a profile_list, scans for its Profile children, makes sublists of continuous profiles (if they happen to be branched), and then creates triangles for them using weighted vector strings.
 */
public static List<Point3f> generateTriangles(final ProjectThing pt, final double scale) {
    if (!pt.getType().equals("profile_list")) {
        Utils.log2("Profile: ignoring unhandable ProjectThing type.");
        return null;
    }
    // should be sorted by Z already
    final ArrayList<ProjectThing> al = pt.getChildren();
    if (al.size() < 2) {
        Utils.log("profile_list " + pt + " has less than two profiles: can't render in 3D.");
        return null;
    }
    // collect all Profile
    final HashSet<Profile> hs = new HashSet<Profile>();
    for (final ProjectThing child : al) {
        final Object ob = child.getObject();
        if (ob instanceof Profile) {
            hs.add((Profile) ob);
        } else {
            Utils.log2("Render: skipping non Profile class child");
        }
    }
    // Create sublists of profiles, following the chain of links.
    final Profile[] p = new Profile[hs.size()];
    hs.toArray(p);
    // find if at least one is visible
    boolean hidden = true;
    for (int i = 0; i < p.length; i++) {
        if (p[i].visible) {
            hidden = false;
            break;
        }
        if (null == p[i] || 0 == p[i].n_points) {
            Utils.log("Cannot generate triangle mesh: empty profile " + p[i] + (null != p[i] ? " at layer " + p[i].getLayer() : ""));
            return null;
        }
    }
    if (hidden)
        return null;
    // collect starts and ends
    final HashSet<Profile> hs_bases = new HashSet<Profile>();
    final HashSet<Profile> hs_done = new HashSet<Profile>();
    final List<Point3f> triangles = new ArrayList<Point3f>();
    do {
        Profile base = null;
        // choose among existing bases
        if (hs_bases.size() > 0) {
            base = hs_bases.iterator().next();
        } else {
            // find a new base, simply by taking the lowest Z or remaining profiles
            double min_z = Double.MAX_VALUE;
            for (int i = 0; i < p.length; i++) {
                if (hs_done.contains(p[i]))
                    continue;
                final double z = p[i].getLayer().getZ();
                if (z < min_z) {
                    min_z = z;
                    base = p[i];
                }
            }
            // add base
            if (null != base)
                hs_bases.add(base);
        }
        if (null == base) {
            Utils.log2("No more bases.");
            break;
        }
        // crawl list to get a sequence of profiles in increasing or decreasing Z order, but not mixed z trends
        final ArrayList<Profile> al_profiles = new ArrayList<Profile>();
        // Utils.log2("Calling accumulate for base " + base);
        al_profiles.add(base);
        final Profile last = accumulate(hs_done, al_profiles, base, 0);
        // if the trend was not empty, add it
        if (last != base) {
            // count as done
            hs_done.addAll(al_profiles);
            // add new possible base (which may have only 2 links if it was from a broken Z trend)
            hs_bases.add(last);
            // create 3D object from base to base
            final Profile[] profiles = new Profile[al_profiles.size()];
            al_profiles.toArray(profiles);
            final List<Point3f> tri = makeTriangles(profiles, scale);
            if (null != tri)
                triangles.addAll(tri);
        } else {
            // remove base
            hs_bases.remove(base);
        }
    } while (0 != hs_bases.size());
    return triangles;
}

Example 28 with Point3f

use of org.scijava.vecmath.Point3f in project TrakEM2 by trakem2.

the class MCCube method getTriangles.

/**
 * Create a list of triangles from the specified image data and the
 * given isovalue.
 * @param volume
 * @param thresh
 * @return
 */
public static final List<Point3f> getTriangles(final Volume volume, final int thresh) {
    final List<Point3f> tri = new ArrayList<Point3f>();
    final Carrier car = new Carrier();
    car.w = volume.xDim;
    car.h = volume.yDim;
    car.d = volume.zDim;
    car.threshold = thresh + 0.5f;
    car.volume = volume;
    if (volume instanceof ImgLibVolume && ((ImgLibVolume) volume).getImage().getContainer() instanceof ShapeList) {
        getShapeListImageTriangles((ImgLibVolume) volume, car, tri);
    } else {
        final MCCube cube = new MCCube();
        for (int z = -1; z < car.d + 1; z += 1) {
            for (int x = -1; x < car.w + 1; x += 1) {
                for (int y = -1; y < car.h + 1; y += 1) {
                    cube.init(x, y, z);
                    cube.computeEdges(car);
                    cube.getTriangles(tri, car);
                }
            }
            IJ.showProgress(z, car.d - 2);
        }
    }
    // convert pixel coordinates
    for (int i = 0; i < tri.size(); i++) {
        final Point3f p = (Point3f) tri.get(i);
        p.x = (float) (p.x * volume.pw + volume.minCoord.x);
        p.y = (float) (p.y * volume.ph + volume.minCoord.y);
        p.z = (float) (p.z * volume.pd + volume.minCoord.z);
    }
    return tri;
}

Example 29 with Point3f

use of org.scijava.vecmath.Point3f in project TrakEM2 by trakem2.

the class MCCube method getTriangles.

private void getTriangles(final List<Point3f> list, final Carrier car) {
    final int cn = caseNumber(car);
    boolean directTable = !(isAmbigous(cn));
    directTable = true;
    // address in the table
    int offset = directTable ? cn * 15 : (255 - cn) * 15;
    for (int index = 0; index < 5; index++) {
        // if there's a triangle
        if (faces[offset] != -1) {
            // pick up vertexes of the current triangle
            list.add(new Point3f(this.e[faces[offset + 0]]));
            list.add(new Point3f(this.e[faces[offset + 1]]));
            list.add(new Point3f(this.e[faces[offset + 2]]));
        }
        offset += 3;
    }
}

Example 30 with Point3f

use of org.scijava.vecmath.Point3f in project TrakEM2 by trakem2.

the class AreaTree method generateMesh.

public MeshData generateMesh(final double scale, final int resample) {
    final HashMap<Layer, Area> areas = new HashMap<Layer, Area>();
    synchronized (node_layer_map) {
        for (final Map.Entry<Layer, Set<Node<Area>>> e : node_layer_map.entrySet()) {
            final Area a = new Area();
            for (final AreaNode nd : (Collection<AreaNode>) (Collection) e.getValue()) {
                if (null != nd.aw)
                    a.add(nd.aw.getArea());
            }
            areas.put(e.getKey(), a);
        }
    }
    final List<Point3f> ps = AreaUtils.generateTriangles(this, scale, resample, areas);
    final List<Color3f> colors = new ArrayList<Color3f>();
    // Determine colors by proximity to a node, since there isn't any other way.
    // TODO
    Utils.log("WARNING: AreaTree multicolor 3D mesh is not yet implemented.");
    final Color3f cf = new Color3f(color);
    for (int i = 0; i < ps.size(); i++) colors.add(cf);
    return new MeshData(ps, colors);
}