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

Example 11 with Attribute

use of ncsa.hdf.object.Attribute 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 12 with Attribute

use of ncsa.hdf.object.Attribute 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));
    }
}