Examples with Group ncsa.hdf.object.Group used on opensource projects

Example 16 with Group

use of ncsa.hdf.object.Group in project vcell by virtualcell.

the class H5FileStructure method printGroup.

/**
 * Recursively print a group and its members.
 *
 * @throws Exception
 */
private static void printGroup(Group g, String indent) throws Exception {
    if (g == null)
        return;
    java.util.List members = g.getMemberList();
    int n = members.size();
    indent += "    ";
    HObject obj = null;
    for (int i = 0; i < n; i++) {
        obj = (HObject) members.get(i);
        System.out.println(indent + obj);
        if (obj instanceof Group) {
            printGroup((Group) obj, indent);
        }
        Dataset ds = BeanUtils.downcast(Dataset.class, obj);
        if (ds != null && ds.getName().equals("elements")) {
            // if (ds != null && ds.getName().equals("boundaries")) {
            VH5Dataset vds = new VH5Dataset(ds);
            vds.info();
            vds.meta();
        }
    }
}

Example 17 with Group

use of ncsa.hdf.object.Group in project vcell by virtualcell.

the class SimulationDataSpatialHdf5 method retrieveSimDataSet.

public SimDataSet retrieveSimDataSet(double time, String varName) throws Exception {
    File tempFile = getTempSimHdf5File(time);
    FileFormat fileFormat = FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5);
    FileFormat solFile = fileFormat.createInstance(tempFile.getAbsolutePath(), FileFormat.READ);
    solFile.open();
    DefaultMutableTreeNode rootNode = (DefaultMutableTreeNode) solFile.getRootNode();
    Group rootGroup = (Group) rootNode.getUserObject();
    Group solGroup = (Group) rootGroup.getMemberList().get(0);
    SimDataSet simDataSet = new SimDataSet();
    List<HObject> memberList = solGroup.getMemberList();
    for (HObject member : memberList) {
        if (!(member instanceof Dataset)) {
            continue;
        }
        Dataset dataset = (Dataset) member;
        String dsname = dataset.getName();
        if (!dsname.equals(varName)) {
            continue;
        }
        simDataSet.solValues = (double[]) dataset.read();
        List<Attribute> attrList = dataset.getMetadata();
        for (Attribute attr : attrList) {
            String attrName = attr.getName();
            Object val = attr.getValue();
            double dval = 0;
            if (val instanceof double[]) {
                dval = ((double[]) val)[0];
            }
            if (attrName.equals(SOLUTION_DATASET_ATTR_MAX_ERROR)) {
                simDataSet.maxError = dval;
            } else if (attrName.equals(SOLUTION_DATASET_ATTR_MEAN)) {
                simDataSet.mean = dval;
            } else if (attrName.equals(SOLUTION_DATASET_ATTR_RELATIVE_L2ERROR)) {
                simDataSet.l2Error = dval;
            } else if (attrName.equals(SOLUTION_DATASET_ATTR_SUM_VOLFRAC)) {
                simDataSet.sumVolFrac = dval;
            }
        }
        break;
    }
    return simDataSet;
}

Example 18 with Group

use of ncsa.hdf.object.Group in project vcell by virtualcell.

the class SimulationDataSpatialHdf5 method retriveVariableNames.

private void retriveVariableNames() throws Exception {
    // read variables only when I have never read the file since variables don't change
    if (dataSetIdentifierList.size() > 0) {
        return;
    }
    File tempFile = getTempSimHdf5File(0.0);
    FileFormat fileFormat = FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5);
    FileFormat meshFile = fileFormat.createInstance(tempFile.getAbsolutePath(), FileFormat.READ);
    meshFile.open();
    DefaultMutableTreeNode rootNode = (DefaultMutableTreeNode) meshFile.getRootNode();
    Group rootGroup = (Group) rootNode.getUserObject();
    Group solGroup = (Group) rootGroup.getMemberList().get(0);
    List<Attribute> solAttrList = solGroup.getMetadata();
    String[] varNames = null;
    int[] varTypes = null;
    for (Attribute attr : solAttrList) {
        String attrName = attr.getName();
        Object value = attr.getValue();
        if (attrName.equals(SOLUTION_ATTR_VARIABLES)) {
            varNames = (String[]) value;
        } else if (attrName.equals(SOLUTION_ATTR_VARIABLE_TYPES)) {
            varTypes = (int[]) value;
        }
    }
    for (int i = 0; i < varNames.length; i++) {
        VariableType varType = VariableType.getVariableTypeFromInteger(varTypes[i]);
        Domain domain = Variable.getDomainFromCombinedIdentifier(varNames[i]);
        String varName = Variable.getNameFromCombinedIdentifier(varNames[i]);
        dataSetIdentifierList.add(new DataSetIdentifier(varName, varType, domain));
    }
}

Example 19 with Group

use of ncsa.hdf.object.Group in project vcell by virtualcell.

the class SimulationDataSpatialHdf5 method readMeshFile.

public static ChomboMesh readMeshFile(File chomboMeshFile) throws Exception {
    // if (chomboMesh != null)
    // {
    // return;
    // }
    ChomboMesh chomboMesh = new ChomboMesh();
    // File mfile = new File(userDirectory, getMeshFileName());
    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(chomboMeshFile.getAbsolutePath(), FileFormat.READ);
    meshFile.open();
    DefaultMutableTreeNode rootNode = (DefaultMutableTreeNode) meshFile.getRootNode();
    Group rootGroup = (Group) rootNode.getUserObject();
    Group meshGroup = (Group) rootGroup.getMemberList().get(0);
    List<Attribute> meshAttrList = meshGroup.getMetadata();
    for (Attribute attr : meshAttrList) {
        String attrName = attr.getName();
        Object value = attr.getValue();
        if (attrName.equals(MESH_ATTR_DIMENSION)) {
            chomboMesh.dimension = ((int[]) value)[0];
        } else {
            String[] valueStrArray = (String[]) value;
            String value0 = valueStrArray[0];
            StringTokenizer st = new StringTokenizer(value0, "{,} ");
            List<Double> valueList = new ArrayList<Double>();
            while (st.hasMoreTokens()) {
                String token = st.nextToken();
                valueList.add(Double.parseDouble(token));
            }
            if (attrName.equals(MESH_ATTR_DX)) {
                for (int i = 0; i < valueList.size(); ++i) {
                    chomboMesh.dx[i] = valueList.get(i);
                }
            } else if (attrName.equals(MESH_ATTR_EXTENT)) {
                for (int i = 0; i < valueList.size(); ++i) {
                    chomboMesh.extent[i] = valueList.get(i);
                }
            } else if (attrName.equals(MESH_ATTR_NX)) {
                for (int i = 0; i < valueList.size(); ++i) {
                    chomboMesh.nx[i] = valueList.get(i).intValue();
                }
            } else if (attrName.equals(MESH_ATTR_ORIGIN)) {
                for (int i = 0; i < valueList.size(); ++i) {
                    chomboMesh.origin[i] = valueList.get(i);
                }
            }
        }
    }
    List<HObject> memberList = meshGroup.getMemberList();
    for (HObject member : memberList) {
        if (member instanceof Dataset) {
            Dataset dataset = (Dataset) member;
            Vector vectValues = (Vector) dataset.read();
            String name = dataset.getName();
            if (name.equals(BOXES_DATASET)) {
            // not needed right now
            } else if (name.equals(METRICS_DATASET)) {
                H5CompoundDS compoundDataSet = (H5CompoundDS) dataset;
                chomboMesh.metricsColumnNames = compoundDataSet.getMemberNames();
                int c = -1;
                int[] index = (int[]) vectValues.get(++c);
                int[] i = (int[]) vectValues.get(++c);
                int[] j = (int[]) vectValues.get(++c);
                int[] k = null;
                if (chomboMesh.dimension == 3) {
                    k = (int[]) vectValues.get(++c);
                }
                double[] x = (double[]) vectValues.get(++c);
                double[] y = (double[]) vectValues.get(++c);
                double[] z = null;
                if (chomboMesh.dimension == 3) {
                    z = (double[]) vectValues.get(++c);
                }
                double[] normalx = (double[]) vectValues.get(++c);
                double[] normaly = (double[]) vectValues.get(++c);
                double[] normalz = null;
                if (chomboMesh.dimension == 3) {
                    normalz = (double[]) vectValues.get(++c);
                }
                double[] volFrac = (double[]) vectValues.get(++c);
                double[] areaFrac = (double[]) vectValues.get(++c);
                for (int n = 0; n < index.length; ++n) {
                    ChomboMeshMetricsEntry entry = new ChomboMeshMetricsEntry(index[n], i[n], j[n], k == null ? 0 : k[n], x[n], y[n], z == null ? 0 : z[n], normalx[n], normaly[n], normalz == null ? 0 : normalz[n], volFrac[n], areaFrac[n]);
                    chomboMesh.metrics.add(entry);
                }
            } else if (name.equals(SURFACE_DATASET)) {
            // not needed right now
            } else if (name.equals(SLICE_VIEW_DATASET)) {
            // not needed right now
            }
        }
    }
    return chomboMesh;
}

Example 20 with Group

use of ncsa.hdf.object.Group 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();
    }
}