hdf5/java/examples/datasets/H5Ex_D_External.java

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
 * Copyright by The HDF Group.                                               *
 * Copyright by the Board of Trustees of the University of Illinois.         *
 * 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 data to an
  external dataset.  The program first writes integers to an
  external dataset with dataspace dimensions of DIM_XxDIM_Y,
  then closes the file.  Next, it reopens the file, reads
  back the data, and outputs the name of the external data
  file and the data to the screen.
 ************************************************************/
package examples.datasets;

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

public class H5Ex_D_External {
    private static String FILENAME = "H5Ex_D_External.h5";
    private static String EXTERNALNAME = "H5Ex_D_External.data";
    private static String DATASETNAME = "DS1";
    private static final int DIM_X = 4;
    private static final int DIM_Y = 7;
    private static final int RANK = 2;
    private static final int NAME_BUF_SIZE = 32;

    private static void writeExternal() {
        long file_id = HDF5Constants.H5I_INVALID_HID;
        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
        long filespace_id = HDF5Constants.H5I_INVALID_HID;
        long dataset_id = HDF5Constants.H5I_INVALID_HID;
        long[] dims = { DIM_X, DIM_Y };
        int[][] dset_data = new int[DIM_X][DIM_Y];

        // Initialize the dataset.
        for (int indx = 0; indx < DIM_X; indx++)
            for (int jndx = 0; jndx < DIM_Y; jndx++)
                dset_data[indx][jndx] = indx * jndx - jndx;

        // 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 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 creation property list.
        try {
            dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // set the external file.
        try {
            if (dcpl_id >= 0)
                H5.H5Pset_external(dcpl_id, EXTERNALNAME, 0, HDF5Constants.H5F_UNLIMITED);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Create the HDF5Constants.dataset.
        try {
            if ((file_id >= 0) && (filespace_id >= 0) && (dcpl_id >= 0))
                dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I32LE, filespace_id,
                        HDF5Constants.H5P_DEFAULT, dcpl_id, HDF5Constants.H5P_DEFAULT);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Write the dataset.
        try {
            H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
                    HDF5Constants.H5P_DEFAULT, dset_data);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // 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();
        }

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

        try {
            if (dcpl_id >= 0)
                H5.H5Pclose(dcpl_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 readExternal() {
        long file_id = HDF5Constants.H5I_INVALID_HID;
        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
        long dataset_id = HDF5Constants.H5I_INVALID_HID;
        int[][] dset_data = new int[DIM_X][DIM_Y];
        String[] Xname = new String[1];

        // Open file using the default properties.
        try {
            file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

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

        // Retrieve the dataset creation property list.
        try {
            if (dataset_id >= 0)
                dcpl_id = H5.H5Dget_create_plist(dataset_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Retrieve and print the name of the external file.
        long[] Xsize = new long[NAME_BUF_SIZE];
        try {
            if (dcpl_id >= 0)
                H5.H5Pget_external(dcpl_id, 0, Xsize.length, Xname, Xsize);
        }
        catch (Exception e) {
            e.printStackTrace();
        }
        System.out.println(DATASETNAME + " is stored in file: " + Xname[0]);

        // Read the data using the default properties.
        try {
            if (dataset_id >= 0)
                H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
                        HDF5Constants.H5P_DEFAULT, dset_data);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Output the data to the screen.
        System.out.println(DATASETNAME + ":");
        for (int indx = 0; indx < DIM_X; indx++) {
            System.out.print(" [ ");
            for (int jndx = 0; jndx < DIM_Y; jndx++)
                System.out.print(dset_data[indx][jndx] + " ");
            System.out.println("]");
        }
        System.out.println();

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

        try {
            if (dcpl_id >= 0)
                H5.H5Pclose(dcpl_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_D_External.writeExternal();
        H5Ex_D_External.readExternal();
    }

}