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

Example 56 with Point3f

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

the class Profile method measure.

/**
 * Assumes Z-coord sorted list of profiles, as stored in a "profile_list" ProjectThing type. .
 */
public static ResultsTable measure(final Profile[] profiles, ResultsTable rt, final long profile_list_id) {
    Utils.log2("profiles.length" + profiles.length);
    if (null == profiles || 0 == profiles.length)
        return null;
    if (1 == profiles.length) {
        // don't measure if there is only one
        return rt;
    }
    for (final Profile p : profiles) {
        if (null == p || 0 == p.n_points) {
            Utils.log("Cannot measure: empty profile " + p + (null != p ? " at layer " + p.getLayer() : ""));
            return rt;
        }
    }
    if (null == rt)
        rt = Utils.createResultsTable("Profile list results", new String[] { "id", "interpolated surface", "surface: sum of length x thickness", "volume", "name-id" });
    final Calibration cal = profiles[0].getLayerSet().getCalibration();
    // else, interpolate skin and measure each triangle
    // already calibrated
    final List<Point3f> tri = makeTriangles(profiles, 1.0);
    final int n_tri = tri.size();
    if (0 != n_tri % 3) {
        Utils.log("Profile.measure error: triangle verts list not a multiple of 3 for profile list id " + profile_list_id);
        return rt;
    }
    // Surface: calibrated sum of the area of all triangles in the mesh.
    double surface = 0;
    for (int i = 2; i < n_tri; i += 3) {
        surface += M.measureArea(tri.get(i - 2), tri.get(i - 1), tri.get(i));
    }
    // add capping ends
    final double area_first = profiles[0].computeArea();
    final double area_last = profiles[profiles.length - 1].computeArea();
    if (profiles[0].closed)
        surface += area_first;
    if (profiles[profiles.length - 1].closed)
        surface += area_last;
    // Surface flat: sum of the perimeter lengths times the layer thickness
    double surface_flat = 0;
    for (int i = 0; i < profiles.length; i++) {
        if (0 == profiles[i].p_i[0].length)
            profiles[i].generateInterpolatedPoints(0.05);
        surface_flat += profiles[i].computeLength() * profiles[i].layer.getThickness() * cal.pixelWidth;
    }
    // Volume: area times layer thickness
    double volume = area_first * profiles[0].layer.getThickness();
    for (int i = 1; i < profiles.length - 1; i++) {
        volume += profiles[i].computeArea() * profiles[i].layer.getThickness();
    }
    volume += area_last * profiles[profiles.length - 1].layer.getThickness();
    // calibrate volume: the Z is still in pixels
    volume *= cal.pixelWidth;
    rt.incrementCounter();
    rt.addLabel("units", cal.getUnit());
    rt.addValue(0, profile_list_id);
    rt.addValue(1, surface);
    rt.addValue(2, surface_flat);
    rt.addValue(3, volume);
    double nameid = 0;
    try {
        nameid = Double.parseDouble(profiles[0].project.findProjectThing(profiles[0]).getParent().getTitle());
    } catch (final NumberFormatException nfe) {
    }
    rt.addValue(4, nameid);
    return rt;
}

Example 57 with Point3f

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

the class Tree method generateSkeleton.

/**
 * @return a CustomLineMesh.PAIRWISE list for a LineMesh.
 */
public MeshData generateSkeleton(final double scale_, final int parallels, final int resample) {
    if (null == root)
        return null;
    final ArrayList<Point3f> list = new ArrayList<Point3f>();
    final ArrayList<Color3f> colors = new ArrayList<Color3f>();
    // Simulate recursion
    final LinkedList<Node<T>> todo = new LinkedList<Node<T>>();
    todo.add(root);
    final float scale = (float) scale_;
    final Calibration cal = layer_set.getCalibration();
    final float pixelWidthScaled = (float) cal.pixelWidth * scale;
    final float pixelHeightScaled = (float) cal.pixelHeight * scale;
    final int sign = cal.pixelDepth < 0 ? -1 : 1;
    final float[] fps = new float[2];
    final Map<Node<T>, Point3f> points = new HashMap<Node<T>, Point3f>();
    // A few performance tests are needed:
    // 1 - if the map caching of points helps or recomputing every time is cheaper than lookup
    // 2 - if removing no-longer-needed points from the map helps lookup or overall slows down
    // 
    // The method, by the way, is very parallelizable: each is independent.
    final HashMap<Color, Color3f> cached_colors = new HashMap<Color, Color3f>();
    final Color3f cf = new Color3f(this.color);
    cached_colors.put(this.color, cf);
    boolean go = true;
    while (go) {
        final Node<T> node = todo.removeFirst();
        // Add children to todo list if any
        if (null != node.children) {
            for (final Node<T> nd : node.children) todo.add(nd);
        }
        go = !todo.isEmpty();
        // Get node's 3D coordinate
        Point3f p = points.get(node);
        if (null == p) {
            fps[0] = node.x;
            fps[1] = node.y;
            this.at.transform(fps, 0, fps, 0, 1);
            p = new Point3f(fps[0] * pixelWidthScaled, fps[1] * pixelHeightScaled, (float) node.la.getZ() * pixelWidthScaled * sign);
            points.put(node, p);
        }
        if (null != node.parent) {
            // Create a line to the parent
            list.add(points.get(node.parent));
            list.add(p);
            if (null == node.color) {
                colors.add(cf);
                // twice: a line segment
                colors.add(cf);
            } else {
                Color3f c = cached_colors.get(node.color);
                if (null == c) {
                    c = new Color3f(node.color);
                    cached_colors.put(node.color, c);
                }
                colors.add(c);
                // twice: a line segment
                colors.add(c);
            }
            if (go && node.parent != todo.getFirst().parent) {
                // node.parent point no longer needed (last child just processed)
                points.remove(node.parent);
            }
        }
    }
    // Utils.log2("Skeleton MeshData lists of same length: " + (list.size() == colors.size()));
    return new MeshData(list, colors);
}

Example 58 with Point3f

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

the class Treeline method addTriangles.

private static final void addTriangles(final List<Point3f> ps, final List<Point3f> parent_verts, final List<Point3f> child_verts, final int i0, final int i1) {
    // one triangle
    ps.add(new Point3f(parent_verts.get(i0)));
    ps.add(new Point3f(parent_verts.get(i1)));
    ps.add(new Point3f(child_verts.get(i0)));
    // another
    ps.add(new Point3f(parent_verts.get(i1)));
    ps.add(new Point3f(child_verts.get(i1)));
    ps.add(new Point3f(child_verts.get(i0)));
}