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

Example 1 with FileFormat

use of ncsa.hdf.object.FileFormat 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 2 with FileFormat

use of ncsa.hdf.object.FileFormat 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 3 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();
        Group solGroup = (Group) rootGroup.getMemberList().get(0);
        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));
        }
    } 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 4 with FileFormat

use of ncsa.hdf.object.FileFormat 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 5 with FileFormat

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

the class DataSet method readMBSData.

private double[] readMBSData(String varName, Double time) throws Exception {
    FileFormat fileFormat = FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5);
    FileFormat solFile = null;
    double[] data = 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");
        }
        int varIndex = -1;
        int size = 0;
        for (int i = 0; i < dataBlockList.size(); ++i) {
            DataBlock dataBlock = dataBlockList.get(i);
            if (dataBlock.getVarName().equals(varName)) {
                varIndex = i;
                size = dataBlock.getSize();
                break;
            }
        }
        if (varIndex == -1) {
            throw new Exception("Variable " + varName + " not found");
        }
        // find time group for that time
        Group timeGroup = null;
        for (Object member : solutionGroup.getMemberList()) {
            if (member instanceof Group) {
                Group group = (Group) member;
                List<Attribute> dsAttrList = group.getMetadata();
                Attribute timeAttribute = null;
                for (Attribute attr : dsAttrList) {
                    if (attr.getName().equals(MSBDataAttribute.time.name())) {
                        timeAttribute = attr;
                        break;
                    }
                }
                if (timeAttribute != null) {
                    double t = ((double[]) timeAttribute.getValue())[0];
                    if (Math.abs(t - time) < 1e-8) {
                        timeGroup = group;
                        break;
                    }
                }
            }
        }
        if (timeGroup == null) {
            throw new Exception("No time group found for time=" + time);
        }
        // find variable dataset
        Dataset varDataset = null;
        for (Object member : timeGroup.getMemberList()) {
            if (member instanceof Dataset) {
                List<Attribute> dsAttrList = ((Dataset) member).getMetadata();
                String var = null;
                for (Attribute attr : dsAttrList) {
                    if (attr.getName().equals(MSBDataAttribute.name.name())) {
                        var = ((String[]) attr.getValue())[0];
                        break;
                    }
                }
                if (var != null && var.equals(varName)) {
                    varDataset = (Dataset) member;
                    break;
                }
            }
        }
        if (varDataset == null) {
            throw new Exception("Data for Variable " + varName + " at time " + time + " not found");
        }
        data = new double[size];
        System.arraycopy((double[]) varDataset.getData(), 0, data, 0, size);
        return data;
    } finally {
        if (solFile != null) {
            try {
                solFile.close();
            } catch (Exception e) {
            // ignore
            }
        }
    }
}