Examples with Polygon cbit.vcell.geometry.surface.Polygon used on opensource projects

Example 6 with Polygon

use of cbit.vcell.geometry.surface.Polygon in project vcell by virtualcell.

the class SurfaceRenderer method createProjectedScreenPolygons.

/**
 * Insert the method's description here.
 * Creation date: (7/7/2004 11:25:42 AM)
 * @param g java.awt.Graphics
 */
public PolygonInfo[] createProjectedScreenPolygons(SurfaceCollection surfaceCollection, int[] quickRenderSkip, BoundingBoxInfo bbi) {
    int[] xPoints = new int[4];
    int[] yPoints = new int[4];
    ArrayList<PolygonInfo> polygonInfoList = new ArrayList<PolygonInfo>(1000);
    Vect3d centroid = new Vect3d();
    Vect3d centroidProj = new Vect3d();
    Vect3d unitNormal = new Vect3d();
    Vect3d cameraVector = new Vect3d(0, 0, 1);
    Vect3d cameraVectorScene = new Vect3d();
    getTrackball().getCamera().unProjectPoint(cameraVector, cameraVectorScene);
    cameraVectorScene.unit();
    for (int i = 0; i < surfaceCollection.getSurfaceCount(); i++) {
        cbit.vcell.geometry.surface.Surface surface = surfaceCollection.getSurfaces(i);
        for (int j = 0; j < surface.getPolygonCount(); j++) {
            if (quickRenderSkip != null && (quickRenderSkip[i] == 0 || j % quickRenderSkip[i] != 0)) {
                continue;
            }
            cbit.vcell.geometry.surface.Polygon polygon = surface.getPolygons(j);
            // find centroid depth along user line of sight
            calculateProjectedCentroid(polygon, centroid, centroidProj);
            double depth = centroidProj.getZ();
            // depthCue color scale
            float notFlatShadeColorScale = (float) (1.0 - bbi.depthCue * (depth - bbi.minZ));
            // calculate flat shading scale, adjust due to normal
            polygon.getUnitNormal(unitNormal);
            double dot = unitNormal.dot(cameraVectorScene);
            float flatShadeColorScale = (float) (0.5 * notFlatShadeColorScale + 0.5 * Math.pow(Math.abs(dot), 2));
            // make sure color scale between 0 and 1
            notFlatShadeColorScale = (float) Math.min(1.0, Math.max(0.0, notFlatShadeColorScale));
            flatShadeColorScale = (float) Math.min(1.0, Math.max(0.0, flatShadeColorScale));
            polygonInfoList.add(new PolygonInfo(createScreenPolygon(polygon, xPoints, yPoints, bbi.xOffset, bbi.xScale, bbi.yOffset, bbi.yScale), depth, flatShadeColorScale, notFlatShadeColorScale, i, j));
        }
    }
    Collections.sort(polygonInfoList);
    PolygonInfo[] polygonInfoArr = new PolygonInfo[polygonInfoList.size()];
    polygonInfoList.toArray(polygonInfoArr);
    return polygonInfoArr;
}

Example 7 with Polygon

use of cbit.vcell.geometry.surface.Polygon in project vcell by virtualcell.

the class ROIMultiPaintManager method calcMinMax.

private static StatsHelper calcMinMax(File[] selectedFiles) throws Exception {
    ArrayList<SurfaceCollection> allSurfCollections = new ArrayList<>();
    TreeMap<String, TreeMap<Integer, ArrayList<TreeMap<Integer, TreeSet<Integer>>>>> fileMapSurfMapSubsurf = new TreeMap<>();
    for (int j = 0; j < selectedFiles.length; j++) {
        File selectedfiFile = selectedFiles[j];
        SurfaceCollection surfaceCollection = ClientRequestManager.createSurfaceCollectionFromSurfaceFile(selectedfiFile);
        if (surfaceCollection == null) {
            throw new Exception("Expecting .stl or .mesh(salk) from file '" + selectedfiFile + "'");
        }
        TreeMap<Integer, ArrayList<TreeMap<Integer, TreeSet<Integer>>>> fileSurf = new TreeMap<>();
        fileMapSurfMapSubsurf.put(selectedfiFile.getAbsolutePath(), fileSurf);
        // nodeMapFace.add(treeMap);
        TreeSet<Integer> allNodes = new TreeSet<>();
        for (int k = 0; k < surfaceCollection.getNodeCount(); k++) {
            allNodes.add(k);
        }
        TreeMap<Integer, ArrayList<TreeSet<Integer>>> allSubSurf = new TreeMap<>();
        int surfOutCount = 0;
        for (int i = 0; i < surfaceCollection.getSurfaceCount(); i++) {
            ArrayList<TreeMap<Integer, TreeSet<Integer>>> surfMap = new ArrayList<>();
            fileSurf.put(i, surfMap);
            TreeMap<Integer, TreeSet<Integer>> treeMap = new TreeMap<>();
            surfMap.add(treeMap);
            Surface surface = surfaceCollection.getSurfaces(i);
            for (int k = 0; k < surface.getPolygonCount(); k++) {
                Polygon polygon = surface.getPolygons(k);
                for (Node node : polygon.getNodes()) {
                    TreeSet<Integer> PolygonIndexes = treeMap.get(node.getGlobalIndex());
                    if (PolygonIndexes == null) {
                        PolygonIndexes = new TreeSet<Integer>();
                        treeMap.put(node.getGlobalIndex(), PolygonIndexes);
                    }
                    PolygonIndexes.add(k);
                }
            }
            allSubSurf.put(i, new ArrayList<>());
            while (allNodes.size() > 0) {
                surfOutCount += 1;
                TreeSet<Integer> searchNodes = new TreeSet<>(Arrays.asList(new Integer[] { allNodes.iterator().next() }));
                TreeSet<Integer> alreadySearched = new TreeSet<>();
                TreeSet<Integer> subSurf = new TreeSet<>();
                allSubSurf.get(i).add(subSurf);
                while (searchNodes.size() > 0) {
                    Integer currentNode = searchNodes.iterator().next();
                    searchNodes.remove(currentNode);
                    alreadySearched.add(currentNode);
                    allNodes.remove(currentNode);
                    TreeSet<Integer> facesForNode = treeMap.get(surfaceCollection.getNodes(currentNode).getGlobalIndex());
                    Iterator<Integer> facesIter = facesForNode.iterator();
                    while (facesIter.hasNext()) {
                        Integer faceIndex = facesIter.next();
                        subSurf.add(faceIndex);
                        Polygon poly = surfaceCollection.getSurfaces(i).getPolygons(faceIndex);
                        for (int k = 0; k < poly.getNodes().length; k++) {
                            if (poly.getNodes()[k].getGlobalIndex() != currentNode && !alreadySearched.contains(poly.getNodes()[k].getGlobalIndex())) {
                                searchNodes.add(poly.getNodes()[k].getGlobalIndex());
                            }
                        }
                    }
                }
            }
        }
        if (surfOutCount > surfaceCollection.getSurfaceCount()) {
            SurfaceCollection newSurfCollection = new SurfaceCollection();
            newSurfCollection.setNodes(surfaceCollection.getNodes());
            for (Integer origSurfIndex : allSubSurf.keySet()) {
                ArrayList<TreeSet<Integer>> newSubSurfaces = allSubSurf.get(origSurfIndex);
                for (TreeSet<Integer> subSurf : newSubSurfaces) {
                    OrigSurface os = new OrigSurface(0, 1);
                    Iterator<Integer> polyIter = subSurf.iterator();
                    while (polyIter.hasNext()) {
                        Polygon poly = surfaceCollection.getSurfaces(origSurfIndex).getPolygons(polyIter.next());
                        os.addPolygon(poly);
                    }
                    newSurfCollection.addSurface(os);
                }
            }
            allSurfCollections.add(newSurfCollection);
        } else {
            allSurfCollections.add(surfaceCollection);
        }
    // fileMapSurfMapSubsurf.get(selectedfiFile.getAbsolutePath()).get(i).add(treeMap);
    }
    StatsHelper statsHelper = new StatsHelper();
    statsHelper.recalSurfs = allSurfCollections;
    for (int j = 0; j < statsHelper.recalSurfs.size(); j++) {
        // File selectedfiFile = selectedFiles[j];
        // SurfaceCollection surfaceCollection = ClientRequestManager.createSurfaceCollectionFromSurfaceFile(selectedfiFile);
        SurfaceCollection surfaceCollection = statsHelper.recalSurfs.get(j);
        for (int i = 0; i < surfaceCollection.getNodes().length; i++) {
            if (j == 0 && i == 0) {
                statsHelper.xmin = surfaceCollection.getNodes()[i].getX();
                statsHelper.xmax = statsHelper.xmin;
                statsHelper.ymin = surfaceCollection.getNodes()[i].getY();
                statsHelper.ymax = statsHelper.ymin;
                statsHelper.zmin = surfaceCollection.getNodes()[i].getZ();
                statsHelper.zmax = statsHelper.zmin;
            }
            statsHelper.xmin = Math.min(statsHelper.xmin, surfaceCollection.getNodes()[i].getX());
            statsHelper.ymin = Math.min(statsHelper.ymin, surfaceCollection.getNodes()[i].getY());
            statsHelper.zmin = Math.min(statsHelper.zmin, surfaceCollection.getNodes()[i].getZ());
            statsHelper.xmax = Math.max(statsHelper.xmax, surfaceCollection.getNodes()[i].getX());
            statsHelper.ymax = Math.max(statsHelper.ymax, surfaceCollection.getNodes()[i].getY());
            statsHelper.zmax = Math.max(statsHelper.zmax, surfaceCollection.getNodes()[i].getZ());
        }
    }
    return statsHelper;
}

Example 8 with Polygon

use of cbit.vcell.geometry.surface.Polygon in project vcell by virtualcell.

the class AVS_UCD_Exporter method writeUCDGeometryOnly.

/**
 * Insert the method's description here.
 * Creation date: (7/19/2004 10:54:30 AM)
 * @param geometrySurfaceDescription cbit.vcell.geometry.surface.GeometrySurfaceDescription
 */
public static void writeUCDGeometryOnly(GeometrySurfaceDescription geometrySurfaceDescription, java.io.Writer writer) throws Exception {
    final String QUAD_TYPE = "quad";
    // GeometricRegion regions[] = geometrySurfaceDescription.getGeometricRegions();
    SurfaceCollection surfaceCollection = geometrySurfaceDescription.getSurfaceCollection();
    if (surfaceCollection == null) {
        geometrySurfaceDescription.updateAll();
        surfaceCollection = geometrySurfaceDescription.getSurfaceCollection();
    }
    Node[] nodes = surfaceCollection.getNodes();
    int numNodes = nodes.length;
    int numCells = 0;
    for (int i = 0; i < surfaceCollection.getSurfaceCount(); i++) {
        numCells += surfaceCollection.getSurfaces(i).getPolygonCount();
    }
    int numNodeData = 0;
    int numCellData = 0;
    int numModelData = 0;
    writer.write(numNodes + " " + numCells + " " + numNodeData + " " + numCellData + " " + numModelData + "\n");
    for (int i = 0; i < nodes.length; i++) {
        writer.write(nodes[i].getGlobalIndex() + " " + nodes[i].getX() + " " + nodes[i].getY() + " " + nodes[i].getZ() + "\n");
    }
    // 
    // print the "Cells" (polygons) for each surface (each surface has it's own material id).
    // 
    int cellID = 0;
    for (int i = 0; i < surfaceCollection.getSurfaceCount(); i++) {
        Surface surface = surfaceCollection.getSurfaces(i);
        // for material now just give it the index (later need to collect these in terms of closed objects).
        String materialType = Integer.toString(i);
        for (int j = 0; j < surface.getPolygonCount(); j++) {
            Polygon polygon = surface.getPolygons(j);
            int node0Index = polygon.getNodes(0).getGlobalIndex();
            int node1Index = polygon.getNodes(1).getGlobalIndex();
            int node2Index = polygon.getNodes(2).getGlobalIndex();
            int node3Index = polygon.getNodes(3).getGlobalIndex();
            writer.write(cellID + " " + materialType + " " + QUAD_TYPE + " " + node0Index + " " + node1Index + " " + node2Index + " " + node3Index + "\n");
            cellID++;
        }
    }
}

Example 9 with Polygon

use of cbit.vcell.geometry.surface.Polygon in project vcell by virtualcell.

the class SmoldynFileWriter method writeMeshFile.

private void writeMeshFile() throws SolverException {
    FileOutputStream fos = null;
    try {
        polygonMembaneElementMap = new HashMap<Polygon, MembraneElement>();
        cartesianMesh = CartesianMesh.createSimpleCartesianMesh(resampledGeometry, polygonMembaneElementMap);
        // Write Mesh file
        File meshFile = new File(baseFileName + SimDataConstants.MESHFILE_EXTENSION);
        fos = new FileOutputStream(meshFile);
        cartesianMesh.write(new PrintStream(fos));
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw new SolverException(e.getMessage());
    } finally {
        try {
            if (fos != null) {
                fos.close();
            }
        } catch (IOException e) {
            e.printStackTrace();
        }
    }
}