path: root/HDF5Examples/JAVA/H5T/110/H5Ex_T_ObjectReferenceAttribute.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 an attribute.  The program first creates objects in the
  file and writes references to those objects to an
  attribute 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_ObjectReferenceAttribute {
    private static String FILENAME      = "H5Ex_T_ObjectReferenceAttribute.h5";
    private static String DATASETNAME   = "DS1";
    private static String ATTRIBUTENAME = "A1";
    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 CreateDataset()
    {
        long file_id       = HDF5Constants.H5I_INVALID_HID;
        long dataspace_id  = HDF5Constants.H5I_INVALID_HID;
        long group_id      = HDF5Constants.H5I_INVALID_HID;
        long dataset_id    = HDF5Constants.H5I_INVALID_HID;
        long attribute_id  = HDF5Constants.H5I_INVALID_HID;
        long[] dims        = {DIM0};
        byte[][] dset_data = new byte[DIM0][8];

        // 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 (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();
        }

        // Create references to the previously created objects. Passing -1
        // as space_id causes this parameter to be ignored. Other values
        // besides valid dataspaces result in an error.
        try {
            if (file_id >= 0) {
                byte rbuf0[] = H5.H5Rcreate(file_id, GROUPNAME, HDF5Constants.H5R_OBJECT, -1);
                byte rbuf1[] = H5.H5Rcreate(file_id, DATASETNAME2, HDF5Constants.H5R_OBJECT, -1);
                for (int indx = 0; indx < 8; indx++) {
                    dset_data[0][indx] = rbuf0[indx];
                    dset_data[1][indx] = rbuf1[indx];
                }
            }
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Create dataset with a scalar dataspace to serve as the parent
        // for the attribute.
        try {
            dataspace_id = H5.H5Screate(HDF5Constants.H5S_SCALAR);
            if (dataspace_id >= 0) {
                dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I32LE, dataspace_id,
                                          HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT,
                                          HDF5Constants.H5P_DEFAULT);
                H5.H5Sclose(dataspace_id);
                dataspace_id = HDF5Constants.H5I_INVALID_HID;
            }
        }
        catch (Exception e) {
            e.printStackTrace();
        }

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

        // Create the attribute and write the array data to it.
        try {
            if ((dataset_id >= 0) && (dataspace_id >= 0))
                attribute_id =
                    H5.H5Acreate(dataset_id, ATTRIBUTENAME, HDF5Constants.H5T_STD_REF_OBJ, dataspace_id,
                                 HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Write the dataset.
        try {
            if (attribute_id >= 0)
                H5.H5Awrite(attribute_id, HDF5Constants.H5T_STD_REF_OBJ, dset_data);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // End access to the dataset and release resources used by it.
        try {
            if (attribute_id >= 0)
                H5.H5Aclose(attribute_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

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

        // Terminate access to the data space.
        try {
            if (dataspace_id >= 0)
                H5.H5Sclose(dataspace_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 ReadDataset()
    {
        long file_id      = HDF5Constants.H5I_INVALID_HID;
        long dataspace_id = HDF5Constants.H5I_INVALID_HID;
        long dataset_id   = HDF5Constants.H5I_INVALID_HID;
        long attribute_id = HDF5Constants.H5I_INVALID_HID;
        int object_type   = -1;
        long object_id    = HDF5Constants.H5I_INVALID_HID;
        long[] dims       = {DIM0};
        byte[][] dset_data;

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

        // Open an existing dataset.
        try {
            if (file_id >= 0)
                dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        try {
            if (dataset_id >= 0)
                attribute_id = H5.H5Aopen_by_name(dataset_id, ".", ATTRIBUTENAME, HDF5Constants.H5P_DEFAULT,
                                                  HDF5Constants.H5P_DEFAULT);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Get dataspace and allocate memory for read buffer.
        try {
            if (attribute_id >= 0)
                dataspace_id = H5.H5Aget_space(attribute_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        try {
            if (dataspace_id >= 0)
                H5.H5Sget_simple_extent_dims(dataspace_id, dims, null);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Allocate array of pointers to two-dimensional arrays (the
        // elements of the dataset.
        dset_data = new byte[(int)dims[0]][8];

        // Read data.
        try {
            if (attribute_id >= 0)
                H5.H5Aread(attribute_id, HDF5Constants.H5T_STD_REF_OBJ, dset_data);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Output the data to the screen.
        for (int indx = 0; indx < dims[0]; indx++) {
            System.out.println(ATTRIBUTENAME + "[" + indx + "]:");
            System.out.print("  ->");
            // Open the referenced object, get its name and type.
            try {
                if (dataset_id >= 0) {
                    object_id   = H5.H5Rdereference(dataset_id, HDF5Constants.H5P_DEFAULT,
                                                    HDF5Constants.H5R_OBJECT, dset_data[indx]);
                    object_type = H5.H5Rget_obj_type(dataset_id, HDF5Constants.H5R_OBJECT, dset_data[indx]);
                }
                String obj_name = null;
                if (object_type >= 0) {
                    // Get the length of the name and retrieve 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");
                        try {
                            if (object_id >= 0)
                                H5.H5Gclose(object_id);
                        }
                        catch (Exception e) {
                            e.printStackTrace();
                        }
                        break;
                    case H5G_DATASET:
                        System.out.print("H5G_DATASET");
                        try {
                            if (object_id >= 0)
                                H5.H5Dclose(object_id);
                        }
                        catch (Exception e) {
                            e.printStackTrace();
                        }
                        break;
                    case H5G_TYPE:
                        System.out.print("H5G_TYPE");
                        try {
                            if (object_id >= 0)
                                H5.H5Tclose(object_id);
                        }
                        catch (Exception e) {
                            e.printStackTrace();
                        }
                        break;
                    default:
                        System.out.print("UNHANDLED");
                    }
                }
                // Print the name.
                System.out.println(": " + obj_name);
            }
            catch (Exception e) {
                e.printStackTrace();
            }
        }

        // End access to the dataset and release resources used by it.
        try {
            if (attribute_id >= 0)
                H5.H5Aclose(attribute_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

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

        // Terminate access to the data space.
        try {
            if (dataspace_id >= 0)
                H5.H5Sclose(dataspace_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

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

    public static void main(String[] args)
    {
        H5Ex_T_ObjectReferenceAttribute.CreateDataset();
        // Now we begin the read section of this example. Here we assume
        // the dataset and array have the same name and rank, but can have
        // any size. Therefore we must allocate a new array to read in
        // data using malloc().
        H5Ex_T_ObjectReferenceAttribute.ReadDataset();
    }
}