Examples with MovingBoundaryReader cbit.vcell.solvers.mb.MovingBoundaryReader used on opensource projects

Example 1 with MovingBoundaryReader

use of cbit.vcell.solvers.mb.MovingBoundaryReader in project vcell by virtualcell.

the class MovingBoundaryVtkFileWriter method getVtuMeshData.

public double[] getVtuMeshData(MovingBoundarySimFiles movingBoundarySimFiles, double[] fullRasterData, File destinationDirectory, VtuVarInfo var, int timeIndex) throws Exception {
    MovingBoundaryReader reader = new MovingBoundaryReader(movingBoundarySimFiles.hdf5OutputFile.getAbsolutePath());
    Plane plane = reader.getPlane(timeIndex);
    int numX = plane.getSizeX();
    int numY = plane.getSizeY();
    DoubleBuffer buffer = DoubleBuffer.wrap(new double[numX * numY]);
    for (int j = 0; j < numY; j++) {
        for (int i = 0; i < numX; i++) {
            Element element = plane.get(i, j);
            if (element != null) {
                if (var.variableDomain == VariableDomain.VARIABLEDOMAIN_VOLUME && var.domainName.equals(reader.getFakeInsideDomainName())) {
                    if (element.position == Position.BOUNDARY || element.position == Position.INSIDE) {
                        buffer.put(fullRasterData[i + numX * j]);
                    // buffer.put(species.mass);
                    // buffer.put(i+j*numX);
                    // buffer.put(i);
                    // buffer.put(j);
                    } else {
                    // skip this element, it is "outside" domain.
                    }
                }
            } else {
                System.out.println("found empty species at index(" + i + "," + j + ")");
            }
        }
    }
    double[] volumeData = buffer.array();
    double[] data = null;
    switch(var.variableDomain) {
        case VARIABLEDOMAIN_CONTOUR:
            {
                break;
            }
        case VARIABLEDOMAIN_MEMBRANE:
            {
                /*
				MovingBoundaryIndexData movingBoundaryIndexData = VisMeshUtils.readChomboIndexData(chomboIndexDataFile);
				List<ChomboVisMembraneIndex> cellIndices = new ArrayList<ChomboVisMembraneIndex>();
				for (ChomboSurfaceIndex chomboSurfaceIndex : chomboIndexData.chomboSurfaceIndices){
					cellIndices.add(new SimpleChomboVisMembraneIndex(chomboSurfaceIndex.index));
				}
				data = chomboMeshData.getMembraneCellData(var.name, cellIndices);
				*/
                break;
            }
        case VARIABLEDOMAIN_NONSPATIAL:
            {
                break;
            }
        case VARIABLEDOMAIN_POSTPROCESSING:
            {
                break;
            }
        case VARIABLEDOMAIN_UNKNOWN:
            {
                break;
            }
        case VARIABLEDOMAIN_VOLUME:
            {
                MovingBoundaryIndexData movingBoundaryIndexData = getMovingBoundaryIndexData(movingBoundarySimFiles, destinationDirectory, var, timeIndex);
                if (var.functionExpression != null) {
                    throw new UnsupportedOperationException();
                } else {
                    int numElements = movingBoundaryIndexData.movingBoundaryVolumeIndices.size();
                    data = new double[numElements];
                    int i = 0;
                    for (MovingBoundaryVolumeIndex mbvIndex : movingBoundaryIndexData.movingBoundaryVolumeIndices) {
                        data[i++] = volumeData[mbvIndex.index];
                    }
                }
                break;
            }
        default:
            {
                throw new RuntimeException("unsupported variable type " + var.variableDomain.name() + " for variable " + var.name);
            }
    }
    return data;
}

Example 2 with MovingBoundaryReader

use of cbit.vcell.solvers.mb.MovingBoundaryReader in project vcell by virtualcell.

the class MovingBoundaryVtkFileWriter method writeEmptyMeshFiles.

public File[] writeEmptyMeshFiles(MovingBoundarySimFiles movingBoundaryFiles, int timeIndex, File destinationDirectory, ProgressListener progressListener) throws IOException, MathException, DataAccessException {
    HashMap<String, VisMesh> domainMeshMap = new HashMap<String, VisMesh>();
    ArrayList<String> allDomainNames = new ArrayList<String>();
    File hdf5OutputFile = movingBoundaryFiles.hdf5OutputFile;
    MovingBoundaryReader reader = new MovingBoundaryReader(hdf5OutputFile.getAbsolutePath());
    // 
    // for inside volume domain in mesh, extract the associated VisMesh
    // 
    {
        String insideDomainName = reader.getFakeInsideDomainName();
        MovingBoundaryMeshMapping insideMeshMapping = new MovingBoundaryMeshMapping();
        VisMesh insideVisMesh = insideMeshMapping.fromReader(reader, DomainType.INSIDE, timeIndex);
        domainMeshMap.put(insideDomainName, insideVisMesh);
        allDomainNames.add(insideDomainName);
    }
    // {
    // String outsideDomainName = reader.getFakeOutsideDomainName();
    // MovingBoundaryMeshMapping outsideMeshMapping = new MovingBoundaryMeshMapping();
    // VisMesh outsideVisMesh = outsideMeshMapping.fromReader(reader, DomainType.OUTSIDE, timeIndex);
    // domainMeshMap.put(outsideDomainName, outsideVisMesh);
    // allDomainNames.add(outsideDomainName);
    // }
    // {
    // String membraneDomainName = reader.getFakeMembraneDomainName();
    // MovingBoundaryMeshMapping membraneMeshMapping = new MovingBoundaryMeshMapping();
    // VisMesh membraneVisMesh = membraneMeshMapping.fromReader(reader, DomainType.MEMBRANE, timeIndex);
    // domainMeshMap.put(membraneDomainName, membraneVisMesh);
    // allDomainNames.add(membraneDomainName);
    // }
    int numFiles = 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(destinationDirectory, movingBoundaryFiles, domainName, timeIndex);
        File mbIndexDataFileName = getMovingBoundaryIndexDataFileName(movingBoundaryFiles, domainName, timeIndex);
        VtkService.getInstance().writeMovingBoundaryVtkGridAndIndexData(visMesh, domainName, vtuFile, mbIndexDataFileName);
        files.add(vtuFile);
        filesProcessed++;
        if (progressListener != null) {
            progressListener.progress(((double) filesProcessed) / numFiles);
        }
    }
    return files.toArray(new File[0]);
}

Example 3 with MovingBoundaryReader

use of cbit.vcell.solvers.mb.MovingBoundaryReader in project vcell by virtualcell.

the class MovingBoundaryVtkFileWriter method getEmptyVtuMeshFiles.

public VtuFileContainer getEmptyVtuMeshFiles(MovingBoundarySimFiles movingBoundaryFiles, int timeIndex, File destinationDirectory) throws IOException, MathException, DataAccessException {
    // 
    // find mesh for each file at time 0
    // 
    File hdf5OutputFile = movingBoundaryFiles.hdf5OutputFile;
    MovingBoundaryReader reader = new MovingBoundaryReader(hdf5OutputFile.getAbsolutePath());
    // 
    // for each domain in cartesian mesh, get the mesh file
    // 
    ArrayList<String> domains = new ArrayList<String>();
    domains.add(reader.getFakeInsideDomainName());
    // domains.add(reader.getFakeOutsideDomainName());
    // domains.add(reader.getFakeMembraneDomainName());
    boolean bMeshFileMissing = false;
    for (String domainName : domains) {
        File file = getVtuMeshFileName(destinationDirectory, movingBoundaryFiles, domainName, timeIndex);
        if (!file.exists()) {
            bMeshFileMissing = true;
        }
    }
    if (bMeshFileMissing) {
        writeEmptyMeshFiles(movingBoundaryFiles, timeIndex, destinationDirectory, null);
    }
    VtuFileContainer vtuFileContainer = new VtuFileContainer();
    for (int i = 0; i < domains.size(); i++) {
        String domainName = domains.get(i);
        File vtuMeshFile = getVtuMeshFileName(destinationDirectory, movingBoundaryFiles, domainName, timeIndex);
        byte[] vtuMeshFileContents = FileUtils.readByteArrayFromFile(vtuMeshFile);
        double time = reader.getTimeInfo().generationTimes.get(timeIndex);
        vtuFileContainer.addVtuMesh(new VtuFileContainer.VtuMesh(domainName, time, vtuMeshFileContents));
    }
    return vtuFileContainer;
}