Examples with FeaturePhaseVol cbit.vcell.solvers.CartesianMeshChombo.FeaturePhaseVol used on opensource projects

Example 1 with FeaturePhaseVol

use of cbit.vcell.solvers.CartesianMeshChombo.FeaturePhaseVol in project vcell by virtualcell.

the class SimulationData method getChomboFiles.

@Override
public ChomboFiles getChomboFiles() throws IOException, XmlParseException, ExpressionException {
    if (chomboFileIterationIndices == null) {
        throw new RuntimeException("SimulationData.chomboFileIterationIndices is null, can't process Chombo HDF5 files");
    }
    if (!(getVcDataId() instanceof VCSimulationDataIdentifier)) {
        throw new RuntimeException("SimulationData.getVcDataId() is not a VCSimulationDataIdentifier (type is " + getVcDataId().getClass().getName() + "), can't process chombo HDF5 files");
    }
    VCSimulationDataIdentifier vcDataID = (VCSimulationDataIdentifier) getVcDataId();
    String expectedMeshfile = vcDataID.getID() + ".mesh.hdf5";
    File meshFile = amplistorHelper.getFile(expectedMeshfile);
    ChomboFiles chomboFiles = new ChomboFiles(vcDataID.getSimulationKey(), vcDataID.getJobIndex(), meshFile);
    String simtaskFilePath = vcDataID.getID() + "_0.simtask.xml";
    File simtaskFile = amplistorHelper.getFile(simtaskFilePath);
    if (!simtaskFile.exists()) {
        throw new RuntimeException("Chombo dataset mission .simtask.xml file, please rerun");
    }
    String xmlString = FileUtils.readFileToString(simtaskFile);
    SimulationTask simTask = XmlHelper.XMLToSimTask(xmlString);
    if (!simTask.getSimulation().getSolverTaskDescription().getChomboSolverSpec().isSaveChomboOutput() && !simTask.getSimulation().getSolverTaskDescription().isParallel()) {
        throw new RuntimeException("Export of Chombo simulations to VTK requires chombo data, select 'Chombo' data format in simulation solver options and rerun simulation.");
    }
    CartesianMeshChombo chomboMesh = (CartesianMeshChombo) mesh;
    FeaturePhaseVol[] featurePhaseVols = chomboMesh.getFeaturePhaseVols();
    for (int timeIndex : chomboFileIterationIndices) {
        if (featurePhaseVols == null) {
            // for old format which doesn't have featurephasevols, we need to try ivol up to 20 for each feature
            Enumeration<SubDomain> subdomainEnum = simTask.getSimulation().getMathDescription().getSubDomains();
            while (subdomainEnum.hasMoreElements()) {
                SubDomain subDomain = subdomainEnum.nextElement();
                if (subDomain instanceof CompartmentSubDomain) {
                    for (int ivol = 0; ivol < 20; ++ivol) {
                        // can be many vol, let us try 20
                        findChomboFeatureVolFile(chomboFiles, vcDataID, subDomain.getName(), ivol, timeIndex);
                    }
                }
            }
        } else {
            // note: some feature + ivol doesn't have a file if there are no variables defined in that feature
            for (FeaturePhaseVol pfv : featurePhaseVols) {
                findChomboFeatureVolFile(chomboFiles, vcDataID, pfv.feature, pfv.ivol, timeIndex);
            }
        }
    }
    return chomboFiles;
}

Example 2 with FeaturePhaseVol

use of cbit.vcell.solvers.CartesianMeshChombo.FeaturePhaseVol in project vcell by virtualcell.

the class ChomboFileReader method readMesh.

private static ChomboMeshData readMesh(String meshFileName, String vol0FileName) throws Exception {
    ChomboMesh chomboMesh = new ChomboMesh();
    if (H5.H5open() < 0) {
        throw new Exception("H5.H5open() failed");
    }
    FileFormat fileFormat = FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5);
    if (fileFormat == null) {
        throw new Exception("FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5) failed, returned null.");
    }
    FileFormat meshFile = fileFormat.createInstance(new File(meshFileName).getAbsolutePath(), FileFormat.READ);
    try {
        meshFile.open();
        DefaultMutableTreeNode meshRootNode = (DefaultMutableTreeNode) meshFile.getRootNode();
        Group meshRootGroup = (Group) meshRootNode.getUserObject();
        Group meshGroup = Hdf5Reader.getChildGroup(meshRootGroup, "mesh");
        chomboMesh.setDimension(Hdf5Reader.getIntAttribute(meshGroup, MESH_ATTR_DIMENSION));
        chomboMesh.setExtent(Hdf5Reader.getVect3DAttribute(meshGroup, MESH_ATTR_EXTENT, 1.0));
        chomboMesh.setOrigin(Hdf5Reader.getVect3DAttribute(meshGroup, MESH_ATTR_ORIGIN, 0.0));
        // it's very wasteful here, but what can I do?
        CartesianMeshChombo cartesianMeshChombo = CartesianMeshChombo.readMeshFile(new File(meshFileName));
        for (FeaturePhaseVol fpv : cartesianMeshChombo.getFeaturePhaseVols()) {
            chomboMesh.addFeaturePhase(fpv.feature, fpv.iphase);
        }
        // Hdf5Reader.DataColumn[] metricsColumns = Hdf5Reader.getDataTable(meshGroup,METRICS_DATASET);
        if (chomboMesh.getDimension() == 2) {
            Hdf5Reader.DataColumn[] segmentColumns = Hdf5Reader.getDataTable(meshGroup, "segments");
            Hdf5Reader.DataColumn[] verticesColumns = Hdf5Reader.getDataTable(meshGroup, "vertices");
            ChomboBoundaries boundaries = chomboMesh.getBoundaries();
            int numVertices = verticesColumns[0].getNumRows();
            int numSegments = segmentColumns[0].getNumRows();
            for (int i = 0; i < numVertices; i++) {
                double x = verticesColumns[0].getValue(i);
                double y = verticesColumns[1].getValue(i);
                double z = 0.0;
                boundaries.addPoint(new ChomboBoundaries.Point(x, y, z));
            }
            for (int i = 0; i < numSegments; i++) {
                int v1 = (int) segmentColumns[1].getValue(i);
                int v2 = (int) segmentColumns[2].getValue(i);
                // THIS COULD BE WRONG - is the chomboIndex one-to-one with the line segments? ... if not should be in the HDF5 file.
                int chomboIndex = i;
                boundaries.addSegment(new ChomboBoundaries.Segment(chomboIndex, v1, v2));
            }
        } else if (chomboMesh.getDimension() == 3) {
            Hdf5Reader.DataColumn[] surfaceTriangleColumns = Hdf5Reader.getDataTable(meshGroup, "surface triangles");
            ChomboBoundaries boundaries = chomboMesh.getBoundaries();
            int numTriangles = surfaceTriangleColumns[0].getNumRows();
            for (int row = 0; row < numTriangles; row++) {
                int index = (int) surfaceTriangleColumns[0].getValue(row);
                int faceNumber = (int) surfaceTriangleColumns[1].getValue(row);
                // not used currently
                int neighborIndex = (int) surfaceTriangleColumns[2].getValue(row);
                double x0 = surfaceTriangleColumns[3].getValue(row);
                double y0 = surfaceTriangleColumns[4].getValue(row);
                double z0 = surfaceTriangleColumns[5].getValue(row);
                int p0_index = boundaries.getOrCreatePoint(x0, y0, z0);
                double x1 = surfaceTriangleColumns[6].getValue(row);
                double y1 = surfaceTriangleColumns[7].getValue(row);
                double z1 = surfaceTriangleColumns[8].getValue(row);
                int p1_index = boundaries.getOrCreatePoint(x1, y1, z1);
                double x2 = surfaceTriangleColumns[9].getValue(row);
                double y2 = surfaceTriangleColumns[10].getValue(row);
                double z2 = surfaceTriangleColumns[11].getValue(row);
                int p2_index = boundaries.getOrCreatePoint(x2, y2, z2);
                Face face = Face.fromInteger(faceNumber);
                SurfaceTriangle surfaceTriangle = new SurfaceTriangle(index, face, p0_index, p1_index, p2_index);
                boundaries.addSurfaceTriangle(surfaceTriangle);
            }
            Hdf5Reader.DataColumn[] metricsColumns = Hdf5Reader.getDataTable(meshGroup, "membrane elements");
            MeshMetrics meshMetrics = boundaries.getMeshMetrics();
            int numMeshMetrics = metricsColumns[0].getNumRows();
            for (int row = 0; row < numMeshMetrics; row++) {
                int index = (int) metricsColumns[0].getValue(row);
                int level = (int) metricsColumns[1].getValue(row);
                // not used currently
                int i = (int) metricsColumns[2].getValue(row);
                // not used currently
                int j = (int) metricsColumns[3].getValue(row);
                // not used currently
                int k = (int) metricsColumns[4].getValue(row);
                double x = metricsColumns[5].getValue(row);
                double y = metricsColumns[6].getValue(row);
                double z = metricsColumns[7].getValue(row);
                Vect3D center = new Vect3D(x, y, z);
                double normalX = metricsColumns[8].getValue(row);
                double normalY = metricsColumns[9].getValue(row);
                double normalZ = metricsColumns[10].getValue(row);
                Vect3D normal = new Vect3D(normalX, normalY, normalZ);
                double volumeFraction = metricsColumns[11].getValue(row);
                double areaFraction = metricsColumns[12].getValue(row);
                int membraneId = (int) metricsColumns[13].getValue(row);
                int cornerPhaseMask = (int) metricsColumns[14].getValue(row);
                BorderCellInfo borderCellInfo = new BorderCellInfo(index, level, i, j, k, center, normal, volumeFraction, areaFraction, membraneId, cornerPhaseMask);
                meshMetrics.addBorderCellInfo(borderCellInfo);
            }
        } else {
            throw new Exception("failed to read chombo file, unexpected mesh dimension " + chomboMesh.getDimension());
        }
    } finally {
        meshFile.close();
    }
    FileFormat vol0File = fileFormat.createInstance(new File(vol0FileName).getAbsolutePath(), FileFormat.READ);
    try {
        vol0File.open();
        DefaultMutableTreeNode rootNode = (DefaultMutableTreeNode) vol0File.getRootNode();
        Group rootGroup = (Group) rootNode.getUserObject();
        Group level0Group = Hdf5Reader.getChildGroup(rootGroup, "level_0");
        double time = Hdf5Reader.getDoubleAttribute(level0Group, "time");
        ChomboMeshData chomboMeshData = new ChomboMeshData(chomboMesh, time);
        int numComponents = Hdf5Reader.getIntAttribute(rootGroup, "num_components");
        int numLevels = Hdf5Reader.getIntAttribute(rootGroup, "num_levels");
        int fractionComponentIndex = -1;
        for (int i = 0; i < numComponents; i++) {
            String compName = Hdf5Reader.getStringAttribute(rootGroup, "component_" + i);
            chomboMeshData.addComponentName(compName);
            if (compName.equals("fraction-0")) {
                fractionComponentIndex = i;
                chomboMeshData.setFraction0ComponentIndex(fractionComponentIndex);
            }
        }
        for (int i = 0; i < numLevels; i++) {
            Group levelGroup = Hdf5Reader.getChildGroup(rootGroup, "level_" + i);
            int refinement = 2;
            if (i == 0) {
                refinement = 1;
            }
            ChomboLevel chomboLevel = new ChomboLevel(chomboMesh, i, refinement);
            Hdf5Reader.DataColumn[] boxColumns = Hdf5Reader.getDataTable(levelGroup, "boxes");
            int[] lo_i, lo_j, lo_k, hi_i, hi_j, hi_k;
            if (chomboMesh.getDimension() == 2) {
                lo_i = ((Hdf5Reader.IntColumn) boxColumns[0]).data;
                lo_j = ((Hdf5Reader.IntColumn) boxColumns[1]).data;
                hi_i = ((Hdf5Reader.IntColumn) boxColumns[2]).data;
                hi_j = ((Hdf5Reader.IntColumn) boxColumns[3]).data;
                lo_k = new int[boxColumns[0].getNumRows()];
                hi_k = new int[boxColumns[0].getNumRows()];
            } else {
                lo_i = ((Hdf5Reader.IntColumn) boxColumns[0]).data;
                lo_j = ((Hdf5Reader.IntColumn) boxColumns[1]).data;
                lo_k = ((Hdf5Reader.IntColumn) boxColumns[2]).data;
                hi_i = ((Hdf5Reader.IntColumn) boxColumns[3]).data;
                hi_j = ((Hdf5Reader.IntColumn) boxColumns[4]).data;
                hi_k = ((Hdf5Reader.IntColumn) boxColumns[5]).data;
            }
            for (int b = 0; b < boxColumns[0].getNumRows(); b++) {
                ChomboBox chomboBox = new ChomboBox(chomboLevel, lo_i[b], hi_i[b], lo_j[b], hi_j[b], lo_k[b], hi_k[b], chomboMesh.getDimension());
                chomboLevel.addBox(chomboBox);
            }
            chomboMesh.addLevel(chomboLevel);
            // 
            // read the variables
            // 
            Hdf5Reader.DataColumn[] data = Hdf5Reader.getDataTable(levelGroup, "data:datatype=0");
            Hdf5Reader.DataColumn[] offsets = Hdf5Reader.getDataTable(levelGroup, "data:offsets=0");
            ChomboLevelData chomboLevelData = new ChomboLevelData(i, fractionComponentIndex, ((Hdf5Reader.DoubleColumn) data[0]).data, ((Hdf5Reader.LongColumn) offsets[0]).data);
            chomboMeshData.addLevelData(chomboLevelData);
        }
        readMembraneVarData(chomboMeshData, rootGroup);
        return chomboMeshData;
    } finally {
        vol0File.close();
    }
}