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

Example 6 with Group

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

the class CartesianMeshMovingBoundary method readMeshFile.

public static CartesianMeshMovingBoundary readMeshFile(File meshFile) throws Exception {
    CartesianMeshMovingBoundary mesh = new CartesianMeshMovingBoundary();
    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 meshH5File = null;
    try {
        meshH5File = fileFormat.createInstance(meshFile.getAbsolutePath(), FileFormat.READ);
        meshH5File.open();
        DefaultMutableTreeNode rootNode = (DefaultMutableTreeNode) meshH5File.getRootNode();
        Group rootGroup = (Group) rootNode.getUserObject();
        Group meshGroup = null;
        for (Object member : rootGroup.getMemberList()) {
            if (member instanceof Group) {
                Group g = (Group) member;
                if (g.getName().equals(Group_Mesh))
                    ;
                {
                    meshGroup = g;
                    break;
                }
            }
        }
        if (meshGroup == null) {
            throw new Exception(Group_Mesh + " group not found in mesh");
        }
        for (Object member : meshGroup.getMemberList()) {
            if (member instanceof Dataset) {
                Dataset ds = (Dataset) member;
                Object data = ds.getData();
                MeshDataset mds = MeshDataset.valueOf(ds.getName());
                switch(mds) {
                    case dimension:
                        mesh.dimension = ((int[]) data)[0];
                        break;
                    case extent:
                        {
                            double[] darr = (double[]) data;
                            mesh.extent = new Extent(darr[0], darr[1], 0.5);
                            break;
                        }
                    case origin:
                        {
                            double[] darr = (double[]) data;
                            mesh.origin = new Origin(darr[0], darr[1], 0.5);
                            break;
                        }
                    case size:
                        {
                            int[] iarr = (int[]) data;
                            mesh.size = new ISize(iarr[0], iarr[1], 1);
                            break;
                        }
                }
            }
        }
    } finally {
        if (meshH5File != null) {
            meshH5File.close();
        }
    }
    return mesh;
}

Example 7 with Group

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

the class H5FileStructure method run.

// public static void main(String args[]) throws Exception {
@Test
public void run() {
    // create the file and add groups ans dataset into the file
    try {
        // createFile();
        // retrieve an instance of H5File
        FileFormat fileFormat = FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5);
        if (fileFormat == null) {
            System.err.println("Cannot find HDF5 FileFormat.");
            return;
        }
        // open the file with read-only access
        FileFormat testFile = fileFormat.createInstance(fname, FileFormat.READ);
        if (testFile == null) {
            System.err.println("Failed to open file: " + fname);
            return;
        }
        // open the file and retrieve the file structure
        testFile.open();
        Group root = (Group) ((javax.swing.tree.DefaultMutableTreeNode) testFile.getRootNode()).getUserObject();
        printGroup(root, "");
        // close file resource
        testFile.close();
    } catch (Exception e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
}

Example 8 with Group

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

the class H5FileStructure method createFile.

/**
 * create the file and add groups and dataset into the file, which is the
 * same as javaExample.H5DatasetCreate
 *
 * @see javaExample.HDF5DatasetCreate
 * @throws Exception
 */
private static void createFile() throws Exception {
    // retrieve an instance of H5File
    FileFormat fileFormat = FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5);
    if (fileFormat == null) {
        System.err.println("Cannot find HDF5 FileFormat.");
        return;
    }
    // create a new file with a given file name.
    H5File testFile = (H5File) fileFormat.createFile(fname, FileFormat.FILE_CREATE_DELETE);
    if (testFile == null) {
        System.err.println("Failed to create file:" + fname);
        return;
    }
    // open the file and retrieve the root group
    testFile.open();
    Group root = (Group) ((javax.swing.tree.DefaultMutableTreeNode) testFile.getRootNode()).getUserObject();
    // create groups at the root
    Group g1 = testFile.createGroup("integer arrays", root);
    Group g2 = testFile.createGroup("float arrays", root);
    // create 2D 32-bit (4 bytes) integer dataset of 20 by 10
    Datatype dtype = testFile.createDatatype(Datatype.CLASS_INTEGER, 4, Datatype.NATIVE, Datatype.NATIVE);
    Dataset dataset = testFile.createScalarDS("2D 32-bit integer 20x10", g1, dtype, dims2D, null, null, 0, null);
    // create 3D 8-bit (1 byte) unsigned integer dataset of 20 by 10 by 5
    dtype = testFile.createDatatype(Datatype.CLASS_INTEGER, 1, Datatype.NATIVE, Datatype.SIGN_NONE);
    dataset = testFile.createScalarDS("3D 8-bit unsigned integer 20x10x5", g1, dtype, dims3D, null, null, 0, null);
    // create 2D 64-bit (8 bytes) double dataset of 20 by 10
    dtype = testFile.createDatatype(Datatype.CLASS_FLOAT, 8, Datatype.NATIVE, -1);
    dataset = testFile.createScalarDS("2D 64-bit double 20x10", g2, dtype, dims2D, null, null, 0, null);
    // create 3D 32-bit (4 bytes) float dataset of 20 by 10 by 5
    dtype = testFile.createDatatype(Datatype.CLASS_FLOAT, 4, Datatype.NATIVE, -1);
    dataset = testFile.createScalarDS("3D 32-bit float  20x10x5", g2, dtype, dims3D, null, null, 0, null);
    // close file resource
    testFile.close();
}

Example 9 with Group

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

the class SimResultsViewer method createODEDataViewer.

/**
 * Insert the method's description here.
 * Creation date: (6/11/2004 2:33:44 PM)
 * @return javax.swing.JPanel
 * @throws DataAccessException
 */
private DataViewer createODEDataViewer() throws DataAccessException {
    odeDataViewer = new ODEDataViewer();
    odeDataViewer.setSimulation(getSimulation());
    ODESolverResultSet odesrs = ((ODEDataManager) dataManager).getODESolverResultSet();
    odeDataViewer.setOdeSolverResultSet(odesrs);
    odeDataViewer.setNFSimMolecularConfigurations(((ODEDataManager) dataManager).getNFSimMolecularConfigurations());
    odeDataViewer.setVcDataIdentifier(dataManager.getVCDataIdentifier());
    if (getSimulation() != null) {
        String ownerName = generateHDF5DescrOwner(getSimulation());
        odeDataViewer.setHDF5DescriptionText(ownerName + ":" + simulation.getName());
    }
    // odeDataViewer.setXVarName(odeDataViewer.getODESolverPlotSpecificationPanel1().getXAxisComboBox_frm().getSelectedItem().toString());
    // 
    // Example code for reading stats data from Stochastic multitrial non-histogram
    // 
    FileFormat hdf5FileFormat = null;
    File to = null;
    try {
        if (odeDataViewer.getOdeSolverResultSet() instanceof ODESimData) {
            byte[] hdf5FileBytes = ((ODESimData) odeDataViewer.getOdeSolverResultSet()).getHdf5FileBytes();
            if (hdf5FileBytes != null) {
                to = File.createTempFile("odeStats_" + getSimulation().getSimulationInfo().getAuthoritativeVCSimulationIdentifier(), ".hdf5");
                Files.write(hdf5FileBytes, to);
                FileFormat fileFormat = FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5);
                if (fileFormat == null) {
                    throw new Exception("Cannot find HDF5 FileFormat.");
                }
                // open the file with read-only access
                hdf5FileFormat = fileFormat.createInstance(to.getAbsolutePath(), FileFormat.READ);
                // open the file and retrieve the file structure
                hdf5FileFormat.open();
                Group root = (Group) ((javax.swing.tree.DefaultMutableTreeNode) hdf5FileFormat.getRootNode()).getUserObject();
                List<HObject> postProcessMembers = ((Group) root).getMemberList();
                for (HObject nextHObject : postProcessMembers) {
                    // System.out.println(nextHObject.getName()+"\n"+nextHObject.getClass().getName());
                    H5ScalarDS h5ScalarDS = (H5ScalarDS) nextHObject;
                    h5ScalarDS.init();
                    try {
                        long[] dims = h5ScalarDS.getDims();
                        System.out.println("---" + nextHObject.getName() + " " + nextHObject.getClass().getName() + " Dimensions=" + Arrays.toString(dims));
                        Object obj = h5ScalarDS.read();
                        if (dims.length == 2) {
                            // dims[0]=numTimes (will be the same as 'SimTimes' data length)
                            // dims[1]=numVars (will be the same as 'VarNames' data length)
                            // if name='StatMean' this is the same as the default data saved in the odeSolverresultSet
                            double[] columns = new double[(int) dims[1]];
                            for (int row = 0; row < dims[0]; row++) {
                                System.arraycopy(obj, row * columns.length, columns, 0, columns.length);
                                System.out.println(Arrays.toString(columns));
                            }
                        } else {
                            if (obj instanceof double[]) {
                                System.out.println(Arrays.toString((double[]) obj));
                            } else {
                                System.out.println(Arrays.toString((String[]) obj));
                            }
                        }
                    } catch (Exception e) {
                        e.printStackTrace();
                    }
                }
            }
        }
    } catch (Exception e) {
        e.printStackTrace();
    } finally {
        if (hdf5FileFormat != null) {
            try {
                hdf5FileFormat.close();
            } catch (Exception e2) {
                e2.printStackTrace();
            }
        }
        if (to != null) {
            try {
                to.delete();
            } catch (Exception e2) {
                e2.printStackTrace();
            }
        }
    }
    return odeDataViewer;
}

Example 10 with Group

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

the class ODEDataInterfaceImpl method extractColumnMin.

@Override
public double[] extractColumnMin(String columnName) throws ExpressionException, ObjectNotFoundException {
    FileFormat hdf5FileFormat = null;
    File to = null;
    try {
        ODESolverResultSet osrs = getOdeSolverResultSet();
        if (osrs instanceof ODESimData) {
            byte[] hdf5FileBytes = ((ODESimData) getOdeSolverResultSet()).getHdf5FileBytes();
            if (hdf5FileBytes != null) {
                to = File.createTempFile("odeStats_" + simulationModelInfo.getSimulationName(), ".hdf5");
                Files.write(hdf5FileBytes, to);
                FileFormat fileFormat = FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5);
                if (fileFormat == null) {
                    throw new Exception("Cannot find HDF5 FileFormat.");
                }
                // open the file with read-only access
                hdf5FileFormat = fileFormat.createInstance(to.getAbsolutePath(), FileFormat.READ);
                // open the file and retrieve the file structure
                hdf5FileFormat.open();
                Group root = (Group) ((javax.swing.tree.DefaultMutableTreeNode) hdf5FileFormat.getRootNode()).getUserObject();
                List<HObject> postProcessMembers = ((Group) root).getMemberList();
                for (HObject nextHObject : postProcessMembers) {
                    System.out.println(nextHObject.getName() + "   " + nextHObject.getClass().getName());
                    H5ScalarDS h5ScalarDS = (H5ScalarDS) nextHObject;
                    h5ScalarDS.init();
                    try {
                        long[] dims = h5ScalarDS.getDims();
                        System.out.println("---" + nextHObject.getName() + " " + nextHObject.getClass().getName() + " Dimensions=" + Arrays.toString(dims));
                        Object obj = h5ScalarDS.read();
                        if (dims.length == 2) {
                            double[] columns = new double[(int) dims[1]];
                            for (int row = 0; row < dims[0]; row++) {
                                System.arraycopy(obj, row * columns.length, columns, 0, columns.length);
                                System.out.println(Arrays.toString(columns));
                            }
                            return null;
                        // return columns;
                        } else {
                            return null;
                        }
                    } catch (Exception e) {
                        return null;
                    }
                }
            }
        }
    } catch (Exception e) {
    } finally {
        if (hdf5FileFormat != null) {
            try {
                hdf5FileFormat.close();
            } catch (Exception e2) {
                e2.printStackTrace();
            }
        }
        if (to != null) {
            try {
                to.delete();
            } catch (Exception e2) {
                e2.printStackTrace();
            }
        }
    }
    return null;
}