Examples with CartesianMesh org.vcell.vis.vcell.CartesianMesh used on opensource projects

Example 6 with CartesianMesh

use of org.vcell.vis.vcell.CartesianMesh 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]);
}