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

Example 6 with Node

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

the class RasterExporter method writeStanfordPolygonTex.

public static PolyTexHelper writeStanfordPolygonTex(RegionImage regionImage, Writer writer, /*BitSet bInDomain,*/
CartesianMesh mesh) throws IOException, MathException {
    int totalPolygons = regionImage.getSurfacecollection().getTotalPolygonCount();
    int totalVerts = totalPolygons * 4;
    final int ALL_NEIGHBOR_QUAD_BOX_SIDE = 3;
    // 2D image texture
    int imgSideSize = (int) Math.ceil(Math.sqrt((totalPolygons)));
    int texelXSize = (imgSideSize * ALL_NEIGHBOR_QUAD_BOX_SIDE);
    int[][] texIndexToFaceIndexPtrs = new int[texelXSize * texelXSize][0];
    // Arrays.fill(texImage0, Integer.MAX_VALUE);
    final int squareSize = 40;
    int fontXSize = texelXSize * squareSize;
    int fontYSize = texelXSize * squareSize;
    BufferedImage image0 = createTextureImage(fontXSize);
    // int[] texFontImage = new int[fontXSize*fontYSize];
    // Arrays.fill(texFontImage, 0xFF000000);
    // int[] bitMasks0 = new int[]{0xFF0000, 0xFF00, 0xFF, 0xFF000000};
    // SinglePixelPackedSampleModel sm0 = new SinglePixelPackedSampleModel(
    // DataBuffer.TYPE_INT, texelXSize*squareSize, texelXSize*squareSize, bitMasks0);
    // DataBufferInt db0 = new DataBufferInt(texFontImage, texFontImage.length);
    // WritableRaster wr0 = Raster.createWritableRaster(sm0, db0, new Point());
    // BufferedImage image0 = new BufferedImage(ColorModel.getRGBdefault(), wr0, false, null);
    Graphics2D g2d = image0.createGraphics();
    g2d.setColor(Color.white);
    Font bigF = Font.decode("Dialog-plain-10");
    g2d.setFont(bigF);
    float texelSize = 1.0f / texelXSize;
    writer.write("ply\n");
    writer.write("format ascii 1.0\n");
    // writer.write("comment "+geometrySurfaceDescription.getGeometry().getName()+"\n");
    writer.write("comment textureImage size is " + imgSideSize + "x" + imgSideSize + "\n");
    writer.write("element vertex " + totalVerts + "\n");
    writer.write("property float x\n");
    writer.write("property float y\n");
    writer.write("property float z\n");
    // must be 's' for blender (u texture coord)
    writer.write("property float s\n");
    // must be 't' for blender (v texture coord)
    writer.write("property float t\n");
    writer.write("element face " + totalPolygons + "\n");
    writer.write("property list uchar int vertex_index\n");
    writer.write("end_header\n");
    StringBuffer sbVert = new StringBuffer();
    StringBuffer sbFace = new StringBuffer();
    int faceIndex = 0;
    int vertIndex = 0;
    for (int currSurf = 0; currSurf < regionImage.getSurfacecollection().getSurfaceCount(); currSurf++) {
        for (int currFace = 0; currFace < regionImage.getSurfacecollection().getSurfaces(currSurf).getPolygonCount(); currFace++) {
            // if(bInDomain != null && !bInDomain.get(faceIndex)){
            // continue;
            // }
            g2d.setColor(Color.white);
            Quadrilateral quad = (Quadrilateral) regionImage.getSurfacecollection().getSurfaces(currSurf).getPolygons(currFace);
            NAHelper naHelper0 = calcNAHelper(quad);
            Point2D p2dm = Coordinate.get2DProjection(naHelper0.middle, naHelper0.normalAxis);
            int x = faceIndex % imgSideSize;
            int y = faceIndex / imgSideSize;
            int boxX = (x * ALL_NEIGHBOR_QUAD_BOX_SIDE) + 1;
            int boxY = (y * ALL_NEIGHBOR_QUAD_BOX_SIDE) + 1;
            int fontX = boxX * squareSize;
            int fontY = boxY * squareSize;
            // das.getColorFromValue(data[faceIndex]);//face color
            texIndexToFaceIndexPtrs[boxY * texelXSize + boxX] = new int[] { faceIndex };
            g2d.drawString(currSurf + "-" + currFace, fontX, fontY);
            float imgXTexelCenter = (boxX + .5f) * texelSize;
            float imgYTexelCenter = (boxY + .5f) * texelSize;
            ArrayList<RegionImage.MembraneEdgeNeighbor> neighbors = regionImage.getMembraneEdgeNeighbors()[currSurf][currFace];
            sbFace.append(quad.getNodeCount() + "");
            for (int vrt = 0; vrt < quad.getNodeCount(); vrt++) {
                g2d.setColor(Color.white);
                RegionImage.MembraneEdgeNeighbor membraneEdgeNeighbor = neighbors.get(vrt);
                MembraneElementIdentifier neighb = membraneEdgeNeighbor.getMembraneElementIdentifier();
                if (neighb != null) {
                    Quadrilateral quadNeighbor = (Quadrilateral) regionImage.getSurfacecollection().getSurfaces(neighb.surfaceIndex).getPolygons(neighb.nonMasterPolygonIndex);
                    NAHelper naHelper1 = calcNAHelper(quadNeighbor);
                    Point2D p2dmNeighb = Coordinate.get2DProjection(naHelper1.middle, naHelper0.normalAxis);
                    double xdiff = p2dmNeighb.getX() - p2dm.getX();
                    double ydiff = p2dmNeighb.getY() - p2dm.getY();
                    int dxn = (int) Math.signum((Math.abs(xdiff) < 1e-9 ? 0 : xdiff));
                    int dyn = (int) Math.signum((Math.abs(ydiff) < 1e-9 ? 0 : ydiff));
                    // das.getColorFromValue(data[membraneEdgeNeighbor.getMasterPolygonIndex()]);
                    texIndexToFaceIndexPtrs[(boxY + dyn) * texelXSize + (boxX + dxn)] = new int[] { membraneEdgeNeighbor.getMasterPolygonIndex() };
                    g2d.drawString(neighb.nonMasterPolygonIndex + "", fontX + (dxn * squareSize), fontY + (dyn * squareSize));
                    RegionImage.MembraneEdgeNeighbor membraneEdgeNeighbor2 = neighbors.get((vrt + 1 == quad.getNodeCount() ? 0 : vrt + 1));
                    MembraneElementIdentifier neighb2 = membraneEdgeNeighbor2.getMembraneElementIdentifier();
                    if (neighb2 != null) {
                        CommonNeighb commonNeighb = calculateCommonNeighbor(mesh, regionImage, mesh.getMembraneElements()[membraneEdgeNeighbor.getMasterPolygonIndex()], mesh.getMembraneElements()[membraneEdgeNeighbor2.getMasterPolygonIndex()], faceIndex);
                        if (commonNeighb != null) {
                            if (commonNeighb.neighborneighbos.size() == 0) {
                                commonNeighb.neighborneighbos.add(membraneEdgeNeighbor.getMasterPolygonIndex());
                                commonNeighb.neighborneighbos.add(membraneEdgeNeighbor2.getMasterPolygonIndex());
                            }
                            // mesh.getMembraneElements()[commonNeighb].getCentroid();
                            Coordinate commonCoord = new Coordinate(commonNeighb.node.getX(), commonNeighb.node.getY(), commonNeighb.node.getZ());
                            Point2D p2dmcommon = Coordinate.get2DProjection(commonCoord, naHelper0.normalAxis);
                            double xdiff1 = p2dmcommon.getX() - p2dm.getX();
                            double ydiff1 = p2dmcommon.getY() - p2dm.getY();
                            int dxc = (int) Math.signum((Math.abs(xdiff1) < 1e-9 ? 0 : xdiff1));
                            int dyc = (int) Math.signum((Math.abs(ydiff1) < 1e-9 ? 0 : ydiff1));
                            g2d.setColor(Color.green);
                            int xloc = fontX + (dxc * squareSize);
                            int yloc = fontY + (dyc * squareSize);
                            double avgVal = 0;
                            int texIndex = (boxY + dyc) * texelXSize + boxX + dxc;
                            texIndexToFaceIndexPtrs[texIndex] = new int[commonNeighb.neighborneighbos.size()];
                            for (int k = 0; k < commonNeighb.neighborneighbos.size(); k++) {
                                g2d.drawString(regionImage.getQuadIndexToSurfAndFace().get(commonNeighb.neighborneighbos.get(k)).getFace() + "", xloc, yloc + (k * 11));
                                // avgVal+= data[commonNeighb.neighborneighbos.get(k)];
                                // das.getColorFromValue(avgVal/commonNeighb.neighborneighbos.size());
                                texIndexToFaceIndexPtrs[texIndex][k] = commonNeighb.neighborneighbos.get(k);
                            }
                        // if(texImage0[texIndex] != Integer.MAX_VALUE){
                        // System.out.println("texture pixel used twice");
                        // }
                        }
                    }
                } else {
                    System.out.println("neighbor null");
                }
                Point2D p2dv = Coordinate.get2DProjection(new Coordinate(quad.getNodes(vrt).getX(), quad.getNodes(vrt).getY(), quad.getNodes(vrt).getZ()), naHelper0.normalAxis);
                double xdiff3 = p2dv.getX() - p2dm.getX();
                double ydiff3 = p2dv.getY() - p2dm.getY();
                int dx = (int) Math.signum((Math.abs(xdiff3) < 1e-9 ? 0 : xdiff3));
                int dy = (int) Math.signum((Math.abs(ydiff3) < 1e-9 ? 0 : ydiff3));
                float u = (float) imgXTexelCenter + ((float) dx * texelSize / 2.0f);
                float v = (float) imgYTexelCenter + ((float) dy * texelSize / 2.0f);
                Node vertex = quad.getNodes()[vrt];
                sbVert.append((float) vertex.getX() + " " + (float) vertex.getY() + " " + (float) vertex.getZ() + " " + u + " " + v + "\n");
                sbFace.append(" ");
                sbFace.append(vertIndex + "");
                vertIndex++;
            }
            sbFace.append("\n");
            faceIndex++;
        }
    }
    if (faceIndex != totalPolygons || vertIndex != totalVerts) {
        throw new IOException("Final faces and verts count don't match");
    }
    writer.write(sbVert.toString());
    writer.write(sbFace.toString());
    // ImageIO.write(op0.filter(image0, null), "png", baos);
    return new PolyTexHelper(texIndexToFaceIndexPtrs, flipPNG(image0), texelXSize);
}

Example 7 with Node

use of cbit.vcell.geometry.surface.Node 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 Node

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

the class ExportDocument method writeStanfordPolygon.

public static void writeStanfordPolygon(GeometrySurfaceDescription geometrySurfaceDescription, Writer writer) throws IOException {
    int faceCount = geometrySurfaceDescription.getSurfaceCollection().getTotalPolygonCount();
    int vertCount = geometrySurfaceDescription.getSurfaceCollection().getNodes().length;
    writer.write("ply\n");
    writer.write("format ascii 1.0\n");
    writer.write("comment " + geometrySurfaceDescription.getGeometry().getName() + "\n");
    writer.write("element vertex " + vertCount + "\n");
    writer.write("property float x\n");
    writer.write("property float y\n");
    writer.write("property float z\n");
    writer.write("element face " + faceCount + "\n");
    writer.write("property list uchar int vertex_index\n");
    writer.write("end_header\n");
    // write verts x y z
    for (int i = 0; i < vertCount; i++) {
        Node vertex = geometrySurfaceDescription.getSurfaceCollection().getNodes()[i];
        writer.write((float) vertex.getX() + " " + (float) vertex.getY() + " " + (float) vertex.getZ() + "\n");
    }
    // write faces as a set of connected vertex indexes
    for (int i = 0; i < geometrySurfaceDescription.getSurfaceCollection().getSurfaceCount(); i++) {
        for (int j = 0; j < geometrySurfaceDescription.getSurfaceCollection().getSurfaces(i).getPolygonCount(); j++) {
            Quadrilateral quad = (Quadrilateral) geometrySurfaceDescription.getSurfaceCollection().getSurfaces(i).getPolygons(j);
            writer.write(quad.getNodeCount() + "");
            for (int k = 0; k < quad.getNodeCount(); k++) {
                writer.write(" ");
                writer.write(quad.getNodes(k).getGlobalIndex() + "");
            }
            writer.write("\n");
        }
    }
}

Example 9 with Node

use of cbit.vcell.geometry.surface.Node 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++;
        }
    }
}