H5Ex_T_ObjectReference.java

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
 * Copyright by The HDF Group.                                               *
 * All rights reserved.                                                      *
 *                                                                           *
 * This file is part of HDF5.  The full HDF5 copyright notice, including     *
 * terms governing use, modification, and redistribution, is contained in    *
 * the COPYING file, which can be found at the root of the source code       *
 * distribution tree, or in https://www.hdfgroup.org/licenses.               *
 * If you do not have access to either file, you may request a copy from     *
 * help@hdfgroup.org.                                                        *
 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */

/************************************************************
  This example shows how to read and write object references
  to a dataset.  The program first creates objects in the
  file and writes references to those objects to a dataset
  with a dataspace of DIM0, then closes the file.  Next, it
  reopens the file, dereferences the references, and outputs
  the names of their targets to the screen.
 ************************************************************/

import java.util.EnumSet;
import java.util.HashMap;
import java.util.Map;

import hdf.hdf5lib.H5;
import hdf.hdf5lib.HDF5Constants;

public class H5Ex_T_ObjectReference {
    private static String FILENAME     = "H5Ex_T_ObjectReference.h5";
    private static String DATASETNAME  = "DS1";
    private static String DATASETNAME2 = "DS2";
    private static String GROUPNAME    = "G1";
    private static final int DIM0      = 2;
    private static final int RANK      = 1;

    // Values for the status of space allocation
    enum H5G_obj {
        H5G_UNKNOWN(HDF5Constants.H5O_TYPE_UNKNOWN),     /* Unknown object type */
        H5G_GROUP(HDF5Constants.H5O_TYPE_GROUP),         /* Object is a group */
        H5G_DATASET(HDF5Constants.H5O_TYPE_DATASET),     /* Object is a dataset */
        H5G_TYPE(HDF5Constants.H5O_TYPE_NAMED_DATATYPE); /* Object is a named data type */
        private static final Map<Integer, H5G_obj> lookup = new HashMap<Integer, H5G_obj>();

        static
        {
            for (H5G_obj s : EnumSet.allOf(H5G_obj.class))
                lookup.put(s.getCode(), s);
        }

        private int code;

        H5G_obj(int layout_type) { this.code = layout_type; }

        public int getCode() { return this.code; }

        public static H5G_obj get(int code) { return lookup.get(code); }
    }

    private static void writeObjRef()
    {
        long file_id       = HDF5Constants.H5I_INVALID_HID;
        long dataspace_id  = HDF5Constants.H5I_INVALID_HID;
        long filespace_id  = HDF5Constants.H5I_INVALID_HID;
        long group_id      = HDF5Constants.H5I_INVALID_HID;
        long dataset_id    = HDF5Constants.H5I_INVALID_HID;
        long[] dims        = {DIM0};
        byte[][] dset_data = new byte[DIM0][HDF5Constants.H5R_REF_BUF_SIZE];

        // Create a new file using default properties.
        try {
            file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT,
                                   HDF5Constants.H5P_DEFAULT);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Create dataset with a scalar dataspace.
        try {
            dataspace_id = H5.H5Screate(HDF5Constants.H5S_SCALAR);
            if ((file_id >= 0) && (dataspace_id >= 0)) {
                dataset_id = H5.H5Dcreate(file_id, DATASETNAME2, HDF5Constants.H5T_STD_I32LE, dataspace_id,
                                          HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT,
                                          HDF5Constants.H5P_DEFAULT);
                if (dataset_id >= 0)
                    H5.H5Dclose(dataset_id);
                dataset_id = HDF5Constants.H5I_INVALID_HID;
                H5.H5Sclose(dataspace_id);
                dataspace_id = HDF5Constants.H5I_INVALID_HID;
            }
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Create a group in the file.
        try {
            if (file_id >= 0)
                group_id = H5.H5Gcreate(file_id, GROUPNAME, HDF5Constants.H5P_DEFAULT,
                                        HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
            if (group_id >= 0)
                H5.H5Gclose(group_id);
            group_id = HDF5Constants.H5I_INVALID_HID;
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        try {
            if (file_id >= 0) {
                try {
                    dset_data[0] = H5.H5Rcreate_object(file_id, GROUPNAME, HDF5Constants.H5P_DEFAULT);
                }
                catch (Throwable err) {
                    err.printStackTrace();
                }

                try {
                    dset_data[1] = H5.H5Rcreate_object(file_id, DATASETNAME2, HDF5Constants.H5P_DEFAULT);
                }
                catch (Throwable err) {
                    err.printStackTrace();
                }
            }

            // Create dataspace. Setting maximum size to NULL sets the maximum
            // size to be the current size.
            try {
                filespace_id = H5.H5Screate_simple(RANK, dims, null);
            }
            catch (Exception e) {
                e.printStackTrace();
            }

            // Create the dataset.
            try {
                if ((file_id >= 0) && (filespace_id >= 0))
                    dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_REF, filespace_id,
                                              HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT,
                                              HDF5Constants.H5P_DEFAULT);
            }
            catch (Exception e) {
                e.printStackTrace();
            }

            // Write the object references to it.
            try {
                if (dataset_id >= 0)
                    H5.H5Dwrite(dataset_id, HDF5Constants.H5T_STD_REF, HDF5Constants.H5S_ALL,
                                HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data);
            }
            catch (Exception e) {
                e.printStackTrace();
            }
        }
        catch (Exception ex) {
            ex.printStackTrace();
        }
        finally {
            try {
                H5.H5Rdestroy(dset_data[1]);
            }
            catch (Exception ex) {
            }
            try {
                H5.H5Rdestroy(dset_data[0]);
            }
            catch (Exception ex) {
            }
        }

        // End access to the dataset and release resources used by it.

        try {
            if (dataset_id >= 0)
                H5.H5Dclose(dataset_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        try {
            if (filespace_id >= 0)
                H5.H5Sclose(filespace_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Close the file.
        try {
            if (file_id >= 0)
                H5.H5Fclose(file_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }
    }

    private static void readObjRef()
    {
        long file_id       = HDF5Constants.H5I_INVALID_HID;
        long dataset_id    = HDF5Constants.H5I_INVALID_HID;
        long dataspace_id  = HDF5Constants.H5I_INVALID_HID;
        int object_type    = -1;
        long object_id     = HDF5Constants.H5I_INVALID_HID;
        long[] dims        = {DIM0};
        byte[][] dset_data = new byte[DIM0][HDF5Constants.H5R_REF_BUF_SIZE];

        // Open an existing file.
        try {
            file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT);

            // Open an existing dataset.
            try {
                dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT);

                try {
                    // Get dataspace and allocate memory for read buffer.
                    dataspace_id = H5.H5Dget_space(dataset_id);
                    H5.H5Sget_simple_extent_dims(dataspace_id, dims, null);

                    // Read data.
                    H5.H5Dread(dataset_id, HDF5Constants.H5T_STD_REF, HDF5Constants.H5S_ALL,
                               HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data);

                    // Output the data to the screen.
                    for (int indx = 0; indx < dims[0]; indx++) {
                        System.out.println(DATASETNAME + "[" + indx + "]:");
                        System.out.print("  ->");
                        // Open the referenced object, get its name and type.
                        try {
                            object_id = H5.H5Ropen_object(dset_data[indx], HDF5Constants.H5P_DEFAULT,
                                                          HDF5Constants.H5P_DEFAULT);
                            try {
                                object_type = H5.H5Rget_obj_type3(dset_data[indx], HDF5Constants.H5R_OBJECT);
                                String obj_name = null;
                                if (object_type >= 0) {
                                    // Get the name.
                                    obj_name = H5.H5Iget_name(object_id);
                                }
                                if ((object_id >= 0) && (object_type >= -1)) {
                                    switch (H5G_obj.get(object_type)) {
                                    case H5G_GROUP:
                                        System.out.print("H5G_GROUP");
                                        break;
                                    case H5G_DATASET:
                                        System.out.print("H5G_DATASET");
                                        break;
                                    case H5G_TYPE:
                                        System.out.print("H5G_TYPE");
                                        break;
                                    default:
                                        System.out.print("UNHANDLED");
                                    }
                                }
                                // Print the name.
                                System.out.println(": " + obj_name);
                            }
                            catch (Exception e) {
                                e.printStackTrace();
                            }
                            finally {
                                try {
                                    H5.H5Oclose(object_id);
                                }
                                catch (Exception e) {
                                }
                            }
                        }
                        catch (Exception e4) {
                            e4.printStackTrace();
                        }
                        finally {
                            try {
                                H5.H5Rdestroy(dset_data[indx]);
                            }
                            catch (Exception e4) {
                            }
                        }
                    } // end for
                }
                catch (Exception e3) {
                    e3.printStackTrace();
                }
                finally {
                    try {
                        H5.H5Sclose(dataspace_id);
                    }
                    catch (Exception e3) {
                    }
                }
            }
            catch (Exception e2) {
                e2.printStackTrace();
            }
            finally {
                try {
                    H5.H5Dclose(dataset_id);
                }
                catch (Exception e2) {
                }
            }
        }
        catch (Exception e1) {
            e1.printStackTrace();
        }
        finally {
            try {
                H5.H5Fclose(file_id);
            }
            catch (Exception e1) {
            }
        }
    }

    public static void main(String[] args)
    {
        H5Ex_T_ObjectReference.writeObjRef();
        H5Ex_T_ObjectReference.readObjRef();
    }
}