Examples with VisMesh org.vcell.vis.vismesh.thrift.VisMesh used on opensource projects

Example 11 with VisMesh

use of org.vcell.vis.vismesh.thrift.VisMesh in project vcell by virtualcell.

the class CartesianMeshVtkFileWriter method writeEmptyMeshFiles.

public File[] writeEmptyMeshFiles(VCellSimFiles vcellFiles, File destinationDirectory, ProgressListener progressListener) throws IOException, MathException {
    if (destinationDirectory == null || !destinationDirectory.isDirectory()) {
        throw new RuntimeException("destinationDirectory '" + destinationDirectory + " not valid");
    }
    // 
    // read the simplified cartesian mesh
    // 
    CartesianMeshFileReader reader = new CartesianMeshFileReader();
    CartesianMesh mesh = reader.readFromFiles(vcellFiles);
    // 
    // for each volume domain in mesh, extract the associated VisMesh
    // 
    List<String> volumeDomainNames = mesh.getVolumeDomainNames();
    HashMap<String, VisMesh> domainMeshMap = new HashMap<String, VisMesh>();
    for (String volumeDomainName : volumeDomainNames) {
        CartesianMeshMapping meshMapping = new CartesianMeshMapping();
        VisMesh visMesh = meshMapping.fromMeshData(mesh, volumeDomainName, true);
        domainMeshMap.put(volumeDomainName, visMesh);
    }
    // 
    // for each membrane domain in mesh, extract the associated VisMesh
    // 
    List<String> membraneDomainNames = mesh.getMembraneDomainNames();
    for (String membraneDomainName : membraneDomainNames) {
        CartesianMeshMapping meshMapping = new CartesianMeshMapping();
        VisMesh visMesh = meshMapping.fromMeshData(mesh, membraneDomainName, false);
        domainMeshMap.put(membraneDomainName, visMesh);
    }
    ArrayList<String> allDomainNames = new ArrayList<String>();
    allDomainNames.addAll(volumeDomainNames);
    allDomainNames.addAll(membraneDomainNames);
    int numFiles = vcellFiles.getTimes().size() * allDomainNames.size();
    ArrayList<File> files = new ArrayList<File>();
    int filesProcessed = 0;
    for (final String domainName : allDomainNames) {
        // 
        // find the globalIndexes for each domain element - use this to extract the domain-only data.
        // 
        VisMesh visMesh = domainMeshMap.get(domainName);
        File vtuFile = getVtuMeshFileName(vcellFiles, domainName);
        File fvIndexDataFileName = getFiniteVolumeIndexDataFileName(vcellFiles, domainName);
        VtkService.getInstance().writeFiniteVolumeSmoothedVtkGridAndIndexData(visMesh, domainName, vtuFile, fvIndexDataFileName);
        files.add(vtuFile);
        filesProcessed++;
        if (progressListener != null) {
            progressListener.progress(((double) filesProcessed) / numFiles);
        }
    }
    return files.toArray(new File[0]);
}

Example 12 with VisMesh

use of org.vcell.vis.vismesh.thrift.VisMesh in project vcell by virtualcell.

the class DebugWriteProblem method main.

/**
 * @param args
 */
public static void main(String[] args) {
    try {
        VisMesh visMesh = new VisMesh(3, new Vect3D(0, 0, 0), new Vect3D(3, 1, 1));
        VisPoint[] points0 = new VisPoint[] { new VisPoint(0, 0, 0), new VisPoint(1, 0, 0), new VisPoint(0, 1, 0), new VisPoint(0, 0, 1) };
        visMesh.addToPoints(points0[0]);
        visMesh.addToPoints(points0[1]);
        visMesh.addToPoints(points0[2]);
        visMesh.addToPoints(points0[3]);
        List<PolyhedronFace> faces0 = Arrays.asList(new PolyhedronFace(Arrays.asList(0, 1, 3)), new PolyhedronFace(Arrays.asList(0, 3, 2)), new PolyhedronFace(Arrays.asList(0, 2, 1)), new PolyhedronFace(Arrays.asList(1, 3, 2)));
        int level = 0;
        int boxNumber = 0;
        int boxIndex = 0;
        int fraction = 0;
        VisIrregularPolyhedron genPolyhedra0 = new VisIrregularPolyhedron(faces0);
        genPolyhedra0.setChomboVolumeIndex(new ChomboVolumeIndex(level, boxNumber, boxIndex, fraction));
        visMesh.addToIrregularPolyhedra(genPolyhedra0);
    // VisPoint[] points1 = new VisPoint[] {
    // new VisPoint(2+0, 0, 0),
    // new VisPoint(2+1, 0, 0),
    // new VisPoint(2+0, 1, 0),
    // new VisPoint(2+0, 0, 1)
    // };
    // 
    // visMesh.addPoint(points1[0]);
    // visMesh.addPoint(points1[1]);
    // visMesh.addPoint(points1[2]);
    // visMesh.addPoint(points1[3]);
    // 
    // vtkUnstructuredGrid vtkgrid = VtkGridUtils.getVolumeVtkGrid(visMesh);
    // String filenameASCII = "testASCII.vtk";
    // String filenameBinary = "testBinary.vtk";
    // VtkGridUtils.writeXML(vtkgrid, filenameASCII, true);
    // VtkGridUtils.writeXML(vtkgrid, filenameBinary, false);
    // vtkgrid = VtkGridUtils.read(filenameBinary);
    // vtkgrid.BuildLinks();
    // SimpleVTKViewer simpleViewer = new SimpleVTKViewer();
    // String[] varNames = visDomain.getVisMeshData().getVarNames();
    // simpleViewer.showGrid(vtkgrid, varNames[0], varNames[1]);
    } catch (Exception e) {
        e.printStackTrace(System.out);
    }
}