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

Example 11 with FileFormat

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

the class DataSet method readHdf5SolutionMetaData.

private void readHdf5SolutionMetaData(InputStream is) throws Exception {
    File tempFile = null;
    FileFormat solFile = null;
    try {
        tempFile = createTempHdf5File(is);
        FileFormat fileFormat = FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5);
        solFile = fileFormat.createInstance(tempFile.getAbsolutePath(), FileFormat.READ);
        solFile.open();
        DefaultMutableTreeNode rootNode = (DefaultMutableTreeNode) solFile.getRootNode();
        Group rootGroup = (Group) rootNode.getUserObject();
        List<HObject> solGroups = rootGroup.getMemberList();
        for (HObject memberGroup : solGroups) {
            if (memberGroup instanceof Group && memberGroup.getName().equals("solution")) {
                Group solGroup = (Group) memberGroup;
                List<HObject> memberList = solGroup.getMemberList();
                for (HObject member : memberList) {
                    if (!(member instanceof Dataset)) {
                        continue;
                    }
                    Dataset dataset = (Dataset) member;
                    String dsname = dataset.getName();
                    int vt = -1;
                    String domain = null;
                    List<Attribute> solAttrList = dataset.getMetadata();
                    for (Attribute attr : solAttrList) {
                        String attrName = attr.getName();
                        if (attrName.equals("variable type")) {
                            Object obj = attr.getValue();
                            vt = ((int[]) obj)[0];
                        } else if (attrName.equals("domain")) {
                            Object obj = attr.getValue();
                            domain = ((String[]) obj)[0];
                        }
                    }
                    long[] dims = dataset.getDims();
                    String varName = domain == null ? dsname : domain + Variable.COMBINED_IDENTIFIER_SEPARATOR + dsname;
                    dataBlockList.addElement(DataBlock.createDataBlock(varName, vt, (int) dims[0], 0));
                }
                break;
            }
        }
    } finally {
        try {
            if (solFile != null) {
                solFile.close();
            }
            if (tempFile != null) {
                if (!tempFile.delete()) {
                    System.err.println("couldn't delete temp file " + tempFile);
                }
            }
        } catch (Exception e) {
        // ignore
        }
    }
}

Example 12 with FileFormat

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

the class DataSet method readMBSDataMetadata.

private void readMBSDataMetadata() throws Exception {
    FileFormat fileFormat = FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5);
    FileFormat solFile = null;
    try {
        solFile = fileFormat.createInstance(fileName, FileFormat.READ);
        solFile.open();
        DefaultMutableTreeNode rootNode = (DefaultMutableTreeNode) solFile.getRootNode();
        Group rootGroup = (Group) rootNode.getUserObject();
        Group solutionGroup = null;
        for (Object member : rootGroup.getMemberList()) {
            String memberName = ((HObject) member).getName();
            if (member instanceof Group) {
                MBSDataGroup group = MBSDataGroup.valueOf(memberName);
                if (group == MBSDataGroup.Solution) {
                    solutionGroup = (Group) member;
                    break;
                }
            }
        }
        if (solutionGroup == null) {
            throw new Exception("Group " + MBSDataGroup.Solution + " not found");
        }
        // find any timeGroup
        Group timeGroup = null;
        for (Object member : solutionGroup.getMemberList()) {
            String memberName = ((HObject) member).getName();
            if (member instanceof Group && memberName.startsWith("time")) {
                timeGroup = (Group) member;
                break;
            }
        }
        if (timeGroup == null) {
            throw new Exception("No time group found");
        }
        // find all the datasets in that time group
        for (Object member : timeGroup.getMemberList()) {
            if (member instanceof Dataset) {
                List<Attribute> solAttrList = ((Dataset) member).getMetadata();
                int size = 0;
                String varName = null;
                VariableType varType = null;
                for (Attribute attr : solAttrList) {
                    String attrName = attr.getName();
                    Object attrValue = attr.getValue();
                    if (attrName.equals(MSBDataAttribute.name.name())) {
                        varName = ((String[]) attrValue)[0];
                    } else if (attrName.equals(MSBDataAttribute.size.name())) {
                        size = ((int[]) attrValue)[0];
                    } else if (attrName.equals(MSBDataAttribute.type.name())) {
                        String vt = ((String[]) attrValue)[0];
                        if (vt.equals(MSBDataAttributeValue.Point.name())) {
                            varType = VariableType.POINT_VARIABLE;
                        } else if (vt.equals(MSBDataAttributeValue.Volume.name())) {
                            varType = VariableType.VOLUME;
                        } else if (vt.equals(MSBDataAttributeValue.PointSubDomain.name())) {
                        // Position for PointSubdomain
                        }
                    }
                }
                if (varType == VariableType.VOLUME) {
                    // only display volume
                    dataBlockList.addElement(DataBlock.createDataBlock(varName, varType.getType(), size, 0));
                }
                if (varType == VariableType.POINT_VARIABLE) {
                    // only display volume
                    dataBlockList.addElement(DataBlock.createDataBlock(varName, varType.getType(), size, 0));
                }
            }
        }
    } finally {
        if (solFile != null) {
            try {
                solFile.close();
            } catch (Exception e) {
            // ignore
            }
        }
    }
}

Example 13 with FileFormat

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

the class SimDataReader method getNextDataAtCurrentTimeChombo.

private void getNextDataAtCurrentTimeChombo(double[][] returnValues) throws Exception {
    if (zipFilenNames == null || zipFilenNames[masterTimeIndex] == null) {
        return;
    }
    if (currentZipFile == null || !currentZipFileName.equals(zipFilenNames[masterTimeIndex])) {
        close();
        currentZipFile = new ZipFile(zipFilenNames[masterTimeIndex]);
        currentZipFileName = zipFilenNames[masterTimeIndex];
    }
    File tempFile = null;
    FileFormat solFile = null;
    try {
        tempFile = DataSet.createTempHdf5File(currentZipFile, simDataFileNames[masterTimeIndex]);
        FileFormat fileFormat = FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5);
        solFile = fileFormat.createInstance(tempFile.getAbsolutePath(), FileFormat.READ);
        solFile.open();
        for (int k = 0; k < varNames.length; ++k) {
            try {
                boolean bExtrapolatedValue = false;
                String varName = varNames[k];
                if (varName.endsWith(InsideVariable.INSIDE_VARIABLE_SUFFIX)) {
                    bExtrapolatedValue = true;
                    varName = varName.substring(0, varName.lastIndexOf(InsideVariable.INSIDE_VARIABLE_SUFFIX));
                } else if (varName.endsWith(OutsideVariable.OUTSIDE_VARIABLE_SUFFIX)) {
                    bExtrapolatedValue = true;
                    varName = varName.substring(0, varName.lastIndexOf(OutsideVariable.OUTSIDE_VARIABLE_SUFFIX));
                }
                double[] sol = null;
                if (bExtrapolatedValue) {
                    sol = DataSet.readChomboExtrapolatedValues(varName, solFile);
                } else {
                    String varPath = Hdf5Utils.getVarSolutionPath(varNames[k]);
                    HObject solObj = FileFormat.findObject(solFile, varPath);
                    if (solObj instanceof Dataset) {
                        Dataset dataset = (Dataset) solObj;
                        sol = (double[]) dataset.read();
                    }
                }
                if (sol != null) {
                    for (int l = 0; l < varIndexes[k].length; ++l) {
                        int idx = varIndexes[k][l];
                        double val = sol[idx];
                        returnValues[k][l] = val;
                    }
                }
            } catch (Exception e) {
                e.printStackTrace(System.out);
                throw new DataAccessException(e.getMessage(), e);
            }
        }
    } finally {
        try {
            if (solFile != null) {
                solFile.close();
            }
            if (tempFile != null) {
                if (!tempFile.delete()) {
                    System.err.println("couldn't delete temp file " + tempFile.getAbsolutePath());
                }
            }
        } catch (Exception e) {
        // ignore
        }
    }
    ++masterTimeIndex;
    if (masterTimeIndex >= times.length) {
        close();
    }
}

Example 14 with FileFormat

use of ncsa.hdf.object.FileFormat 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 15 with FileFormat

use of ncsa.hdf.object.FileFormat 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;
}