Model.java

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/*******************************************************************************
 * Copyright (c) 2012 Stefan Profanter. All rights reserved. This program and the accompanying
 * materials are made available under the terms of the GNU Public License v3.0 which accompanies
 * this distribution, and is available at http://www.gnu.org/licenses/gpl.html
 * 
 * Contributors: Stefan Profanter - initial API and implementation, Year: 2012 Andrei Stoica -
 * complemented implementation during Google Summer of Code 2014.
 ******************************************************************************/
package edu.tum.cs.vis.model;

import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.text.DecimalFormat;
import java.text.NumberFormat;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedList;
import java.util.List;
import java.util.Set;
import java.util.concurrent.Callable;

import javax.vecmath.Point3f;
import javax.vecmath.Tuple3f;
import javax.vecmath.Vector3f;

import org.apache.log4j.Logger;

import processing.core.PGraphics;
import edu.tum.cs.ias.knowrob.utils.ThreadPool;
import edu.tum.cs.vis.model.util.BSphere;
import edu.tum.cs.vis.model.util.DrawSettings;
import edu.tum.cs.vis.model.util.Group;
import edu.tum.cs.vis.model.util.Line;
import edu.tum.cs.vis.model.util.Region;
import edu.tum.cs.vis.model.util.Triangle;
import edu.tum.cs.vis.model.util.Vertex;
import edu.tum.cs.vis.model.util.algorithm.Miniball;

public class Model {

        private static final Logger             LOGGER                          = Logger.getLogger(Model.class);

        private String                                  textureBasePath         = null;

        private Group                                   group;

        private final List<Vertex>              vertices                        = new ArrayList<Vertex>();

        private final List<Triangle>    triangles                       = new ArrayList<Triangle>();

        private final List<Line>                lines                           = new ArrayList<Line>();

        private final List<Region>              regions                         = new ArrayList<Region>();

        private BSphere                                 boundingSphere          = null;

        private float                                   scale                           = 1f;

        private boolean                                 normalsInitialized      = false;

        private float                                   lowMeanCurvature        = Float.MAX_VALUE;

        private float                                   highMeanCurvature       = Float.MIN_VALUE;

        private float                                   lowGaussCurvature       = Float.MAX_VALUE;

        private float                                   highGaussCurvature      = Float.MIN_VALUE;

        private float                                   avgMeanCurvature        = 0f;

        private float                                   varMeanCurvature        = 0f;

        private float                                   avgGaussCurvature       = 0f;

        private float                                   varGaussCurvature       = 0f;

        public void draw(PGraphics g, DrawSettings drawSettings) {
                if (group != null)
                        group.draw(g, drawSettings);
        }

        public BSphere getBoundingSphere() {
                if (boundingSphere == null)
                        calculateBoundingsphere();
                return boundingSphere;
        }

        public Group getGroup() {
                return group;
        }

        public List<Line> getLines() {
                return lines;
        }

        public List<Region> getRegions() {
                return regions;
        }

        public HashMap<Integer, Region> getRegionsMap() {
                HashMap<Integer, Region> regionsMap = new HashMap<Integer, Region>();
                for (Region r : regions) {
                        regionsMap.put(r.getRegionId(), r);
                }
                return regionsMap;
        }

        public float getScale() {
                return scale;
        }

        public String getTextureBasePath() {
                return textureBasePath;
        }

        public List<Triangle> getTriangles() {
                return triangles;
        }

        public float getUnscaled(float scaled) {
                return scaled * 1f / scale;
        }

        public float getLowMeanCurvature() {
                return lowMeanCurvature;
        }

        public float getHighMeanCurvature() {
                return highMeanCurvature;
        }

        public float getLowGaussCurvature() {
                return lowGaussCurvature;
        }

        public float getHighGaussCurvature() {
                return highGaussCurvature;
        }

        public float getAvgMeanCurvature() {
                return avgMeanCurvature;
        }

        public float getAvgGaussCurvature() {
                return avgGaussCurvature;
        }

        public float getVarMeanCurvature() {
                return varMeanCurvature;
        }

        public float getVarGaussCurvature() {
                return varGaussCurvature;
        }

        public Tuple3f[] getUnscaled(Point3f[] corner) {
                Tuple3f[] ret = new Point3f[corner.length];
                for (int i = 0; i < corner.length; i++) {
                        ret[i] = getUnscaled(corner[i]);
                }
                return ret;
        }

        public Tuple3f getUnscaled(Tuple3f t) {
                Tuple3f tr = new Point3f(t);
                tr.scale(1f / scale);
                return tr;
        }

        public Vector3f getUnscaled(Vector3f t) {
                Vector3f tr = new Vector3f(t);
                tr.scale(1f / scale);
                return tr;
        }

        public List<Vertex> getVertices() {
                return vertices;
        }

        public void mirrorX() {
                for (Vertex v : vertices) {
                        v.x *= (-1);
                }
                group.resetMinMaxValues();
        }

        public void normalize() {
                reloadVertexList();
                float x = group.getMaxX() - group.getMinX();
                float y = group.getMaxY() - group.getMinY();
                float z = group.getMaxZ() - group.getMinZ();

                float max = Math.max(x, Math.max(y, z));

                scale(1f / max);

                scale = 1f / max;
                LOGGER.debug("Model normalized to fit a unity length cube. Scaling applied: " + scale);
        }

        public void scale(float factor) {

                for (Vertex v : vertices) {
                        v.scale(factor);
                }
                for (Triangle t : triangles) {
                        t.updateEdges();
                        t.updateCentroid();
                }
                for (Line l : lines)
                        l.updateCentroid();
                group.resetMinMaxValues();
        }

        public void setGroup(Group group) {
                this.group = group;
        }

        public void setRegions(List<Region> regions) {
                if (this.regions != null) {
                        this.regions.clear();
                        this.regions.addAll(regions);
                }
        }

        public void setTextureBasePath(String textureBasePath) {
                this.textureBasePath = textureBasePath;
        }

        public void setLowMeanCurvature(final float lowMeanCurvature) {
                this.lowMeanCurvature = lowMeanCurvature;
        }

        public void setHighMeanCurvature(final float highMeanCurvature) {
                this.highMeanCurvature = highMeanCurvature;
        }

        public void setLowGaussCurvature(final float lowGaussCurvature) {
                this.lowGaussCurvature = lowGaussCurvature;
        }

        public void setHighGaussCurvature(final float highGaussCurvature) {
                this.highGaussCurvature = highGaussCurvature;
        }

        public void setAvgMeanCurvature(final float avgMeanCurvature) {
                this.avgMeanCurvature = avgMeanCurvature;
        }

        public void setAvgGaussCurvature(final float avgGaussCurvature) {
                this.avgGaussCurvature = avgGaussCurvature;
        }

        public void setVarMeanCurvature(final float varMeanCurvature) {
                this.varMeanCurvature = varMeanCurvature;
        }

        public void setVarGaussCurvature(final float varGaussCurvature) {
                this.varGaussCurvature = varGaussCurvature;
        }

        public int removeDoubleSidedTriangles() {
                final Set<Triangle> toRemove = new HashSet<Triangle>();

                final int interval = 1000;
                List<Callable<Void>> threads = new LinkedList<Callable<Void>>();
                for (int start = 0; start < triangles.size(); start += interval) {
                        final int st = start;
                        threads.add(new Callable<Void>() {

                                @Override
                                public Void call() throws Exception {
                                        int end = Math.min(st + interval, triangles.size());
                                        for (int i = st; i < end; i++) {
                                                Triangle t1 = triangles.get(i);
                                                if (toRemove.contains(t1))
                                                        continue;
                                                for (int j = i + 1; j < triangles.size(); j++) {
                                                        Triangle t2 = triangles.get(j);

                                                        if (toRemove.contains(t2))
                                                                continue;
                                                        int eqCnt = 0;
                                                        for (int k = 0; k < 3; k++) {
                                                                Point3f p1 = t1.getPosition()[k];
                                                                for (Point3f p2 : t2.getPosition()) {
                                                                        if (p1.x == p2.x && p1.y == p2.y && p1.z == p2.z) {
                                                                                eqCnt++;
                                                                                break;
                                                                        }
                                                                }
                                                                if (eqCnt != k + 1) {
                                                                        // break if not enough vertices are equal
                                                                        break;
                                                                }
                                                        }
                                                        if (eqCnt == 3) {
                                                                // triangles are the same, so remove j

                                                                synchronized (toRemove) {
                                                                        toRemove.add(t2);
                                                                }
                                                        }
                                                }
                                        }
                                        return null;
                                }

                        });
                };

                ThreadPool.executeInPool(threads);
                if (toRemove.size() > 0) {
                        this.group.removeTriangle(toRemove);
                        reloadVertexList();
                }
                return toRemove.size();
        }

        public void reloadVertexList() {
                synchronized (triangles) {
                        triangles.clear();
                        this.group.getAllTriangles(triangles);
                }
                Set<Vertex> vertices = new HashSet<Vertex>(triangles.size() * 2);
                for (Triangle t : triangles) {
                        vertices.addAll(Arrays.asList(t.getPosition()));
                }
                for (Line l : lines) {
                        vertices.addAll(Arrays.asList(l.getPosition()));
                }
                this.vertices.clear();
                this.vertices.addAll(vertices);
        }

        public void updateVertexSharing() {

                final Set<Triangle> checkedTriangles = Collections.synchronizedSet(new HashSet<Triangle>());

                Set<Vertex> toRemove = new HashSet<Vertex>();

                for (Triangle t : triangles)
                        updateVertexSharingForTriangle(t, checkedTriangles, toRemove);
                synchronized (vertices) {
                        vertices.removeAll(toRemove);
                }
                reloadVertexList();
        }

        private void updateVertexSharingForNeighbors(final Triangle t, final Triangle n,
                        final Set<Triangle> checkedTriangles, Set<Vertex> toRemove) {
                if (t == n)
                        return;
                synchronized (n) {
                        if (checkedTriangles.contains(n))
                                return;

                        double angle = t.getDihedralAngle(n);
                        // Share vertices if angle is < 15 degree
                        boolean share = (angle < 15 / 180.0 * Math.PI);

                        for (Vertex vt : t.getPosition()) {
                                for (int i = 0; i < n.getPosition().length; i++) {
                                        Vertex vn = n.getPosition()[i];
                                        /*
                                        if ((vt.sameCoordinates(vn) && vt.getPointarea() == vn.getPointarea() && vt
                                                        .getNormalVector().equals(vn.getNormalVector()))
                                                        ||(share && vn != vt && vt.sameCoordinates(vn))) {*/
                                        if (share && vn != vt && vt.sameCoordinates(vn)) {
                                                // merge vertices
                                                n.getPosition()[i] = vt;
                                                int cnt = 0;
                                                for (Triangle tmpTri : t.getNeighbors()) {
                                                        for (Vertex tmpVer : tmpTri.getPosition())
                                                                if (tmpVer == vn) {
                                                                        cnt++;
                                                                        break;
                                                                }
                                                }
                                                if (cnt == 0) {
                                                        for (Triangle tmpTri : n.getNeighbors()) {
                                                                if (tmpTri == t)
                                                                        continue;
                                                                for (Vertex tmpVer : tmpTri.getPosition())
                                                                        if (tmpVer == vn) {
                                                                                cnt++;
                                                                                break;
                                                                        }
                                                        }
                                                }
                                                if (cnt == 0) {
                                                        toRemove.add(vn);
                                                }
                                        } else if (!share && vn == vt) {
                                                // split vertices
                                                // System.out.println("split");
                                                /*Vertex clone = (Vertex) vt.clone();
                                                synchronized (vertices) {
                                                        vertices.add(clone);
                                                }
                                                n.getPosition()[i] = clone;*/
                                        }
                                }
                        }
                }
        }

        private void updateVertexSharingForTriangle(final Triangle t,
                        final Set<Triangle> checkedTriangles, final Set<Vertex> toRemove) {
                synchronized (t) {
                        if (checkedTriangles.contains(t))
                                return;
                        synchronized (t.getNeighbors()) {
                                for (Triangle n : t.getNeighbors()) {
                                        updateVertexSharingForNeighbors(t, n, checkedTriangles, toRemove);
                                        // also check neighbors of neighbor
                                        for (Triangle nn : n.getNeighbors()) {
                                                updateVertexSharingForNeighbors(t, nn, checkedTriangles, toRemove);
                                        }
                                }

                        }
                        checkedTriangles.add(t);
                }
        }

        public void updateVertexNormals() {
                // Compute from faces

                // Reset normal vectors, because vertex normals from collada aren't correct
                for (Vertex v : vertices) {
                        v.getNormalVector().x = v.getNormalVector().y = v.getNormalVector().z = 0;
                }

                for (int i = 0; i < triangles.size(); ++i) {
                        calculateVertexNormalsForTriangle(triangles.get(i));
                }

                // Normalize all vectors.
                // Additionally search the vectors which have max x, max y and max z coordinates (needed for
                // vertex winding check / inverted normals check)

                Vertex extrema[] = new Vertex[6];

                for (Vertex v : vertices) {
                        v.getNormalVector().normalize();
                        float coord[] = new float[3];
                        v.get(coord);
                        // Set all max values
                        for (int i = 0; i < 3; i++) {
                                float extCoord[] = new float[3];
                                if (extrema[i] != null)
                                        extrema[i].get(extCoord);
                                if (extrema[i] == null || extCoord[i] < coord[i])
                                        extrema[i] = v;
                        }
                        // Set all min values
                        for (int i = 0; i < 3; i++) {
                                float extCoord[] = new float[3];
                                if (extrema[i + 3] != null)
                                        extrema[i + 3].get(extCoord);
                                if (extrema[i + 3] == null || extCoord[i] > coord[i])
                                        extrema[i + 3] = v;
                        }
                }

                int vote = 0;
                // Now the vertex normal of maxX must point in approximately the same direction as the
                // axis. If the angle between the vertex normal and the direction is smaller than 90° vote
                // for inversion.
                for (int i = 0; i < 6; i++) {
                        float coord[] = { 0, 0, 0 };
                        coord[i % 3] = i < 3 ? 1 : -1;
                        double dot = extrema[i].getNormalVector().dot((new Vector3f(coord)));
                        double angle = Math.acos(dot);
                        // System.out.println("Angle: " + (angle * 180 / Math.PI));
                        if (angle < Math.PI / 2)
                                vote--;
                        else
                                vote++;
                }
                // System.out.println("VOTE: " + vote);
                if (vote > 0) {
                        // They voted for inverting
                        LOGGER.debug("Inverting normal vertices, because vote is: " + vote);
                        for (Vertex v : vertices) {
                                v.getNormalVector().scale(-1f);
                        }
                }
                for (Triangle t : triangles) {
                        t.calculateNormalVector();
                }

                normalsInitialized = true;

        }

        private static void calculateVertexNormalsForTriangle(final Triangle t) {
                Vertex p0 = t.getPosition()[0];
                Vertex p1 = t.getPosition()[1];
                Vertex p2 = t.getPosition()[2];

                // get vectors from p0 to p1 and so on
                Vector3f a = new Vector3f(p0);
                a.sub(p1);
                Vector3f b = new Vector3f(p1);
                b.sub(p2);
                Vector3f c = new Vector3f(p2);
                c.sub(p0);
                // length of these vectors
                float l2a = a.lengthSquared(), l2b = b.lengthSquared(), l2c = c.lengthSquared();
                if (l2a == 0.0 || l2b == 0.0 || l2c == 0.0) {
                        LOGGER.debug("skipping triangle: " + t + "\n(" + p0 + p1 + p2 + ")");
                        return;
                }

                Vector3f facenormal = new Vector3f();
                facenormal.cross(a, b); // unscaled normal

                Vector3f normalP0 = (Vector3f) facenormal.clone();
                normalP0.scale(1.0f / (l2a * l2c));
                // normalP0.scale(1.0f / areaOfTriangle);
                synchronized (p0.getNormalVector()) {
                        p0.getNormalVector().add(normalP0);
                }

                Vector3f normalP1 = (Vector3f) facenormal.clone();
                normalP1.scale(1.0f / (l2b * l2a));
                // normalP1.scale(1.0f / areaOfTriangle);
                synchronized (p1.getNormalVector()) {
                        p1.getNormalVector().add(normalP1);
                }

                Vector3f normalP2 = (Vector3f) facenormal.clone();
                normalP2.scale(1.0f / (l2c * l2b));
                // normalP2.scale(1.0f / areaOfTriangle);
                synchronized (p2.getNormalVector()) {
                        p2.getNormalVector().add(normalP2);
                }
        }

        public File exportVerticesAsTxt() {
                try {
                        File tmp = File.createTempFile("knowrob_", ".txt",
                                        new File(System.getProperty("java.io.tmpdir")));
                        exportVerticesAsTxt(tmp, true);
                        return tmp;
                } catch (IOException e) {
                        LOGGER.error("Couldn't create temp file name: " + e.getMessage());
                        return null;
                }

        }

        public boolean exportVerticesAsTxt(File path, boolean overwrite) {

                try {
                        if (!overwrite && path.exists()) {
                                LOGGER.error("Couldn't export model to file. Already exists: "
                                                + path.getAbsolutePath());
                                return false;
                        }
                        FileWriter fstream = new FileWriter(path);
                        BufferedWriter out = new BufferedWriter(fstream);
                        out.write(vertices.size() + "\n");
                        NumberFormat df = new DecimalFormat("0.####################");
                        for (int i = 0; i < vertices.size(); i++) {
                                Vertex v = vertices.get(i);
                                out.write(df.format(v.x) + "\t" + df.format(v.y) + "\t" + df.format(v.z));
                                if (normalsInitialized) {
                                        out.write("\t" + df.format(v.getNormalVector().x) + "\t"
                                                        + df.format(v.getNormalVector().y) + "\t"
                                                        + df.format(v.getNormalVector().z));
                                }
                                if (i < vertices.size() - 1)
                                        out.write("\n");
                        }
                        LOGGER.info("Model exported to file " + path.getAbsolutePath());
                        out.close();
                        return true;
                } catch (IOException e) {
                        LOGGER.error("Couldn't export model to file " + path.getAbsolutePath() + ". "
                                        + e.getMessage());
                }
                return false;
        }

        public double getSizeX() {
                return group.getMaxX() - group.getMinX();
        }

        public double getSizeY() {
                return group.getMaxY() - group.getMinY();
        }

        public double getSizeZ() {
                return group.getMaxZ() - group.getMinZ();
        }

        private void calculateBoundingsphere() {
                if (vertices.size() == 0)
                        return;

                Miniball mb = new Miniball(3);
                for (Vertex v : vertices) {
                        double arr[] = new double[3];
                        arr[0] = v.x;
                        arr[1] = v.y;
                        arr[2] = v.z;
                        mb.check_in(arr);
                }
                mb.build();
                this.boundingSphere = new BSphere((float) Math.sqrt(mb.squared_radius()), new Vector3f(
                                (float) mb.center()[0], (float) mb.center()[1], (float) mb.center()[2]));

        }

        public float feature_size() {
                if (triangles.size() == 0)
                        return 0.0f;

                int nf = triangles.size();
                int nsamp = Math.min(nf / 2, 333);

                Float[] samples = new Float[nsamp * 3];

                for (int i = 0; i < nsamp; i++) {

                        int ind = (int) (Math.random() * nf);
                        final Vertex p0 = triangles.get(ind).getPosition()[0];
                        final Vertex p1 = triangles.get(ind).getPosition()[1];
                        final Vertex p2 = triangles.get(ind).getPosition()[2];
                        samples[i * 3] = p0.distanceSquared(p1);
                        samples[i * 3 + 1] = p1.distanceSquared(p2);
                        samples[i * 3 + 2] = p2.distanceSquared(p0);
                }
                Arrays.sort(samples);
                return getUnscaled((float) Math.sqrt(samples[samples.length / 2]));
        }
}