hdf5/HDF5Examples/JAVA/H5D/H5Ex_D_Szip.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 LICENSE 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 a dataset
  using szip compression.    The program first checks if
  szip compression is available, then if it is it writes
  integers to a dataset using szip, then closes the file.
  Next, it reopens the file, reads back the data, and
  outputs the type of compression and the maximum value in
  the dataset to the screen.
 ************************************************************/

import static org.hdfgroup.javahdf5.hdf5_h.*;

import java.lang.foreign.Arena;
import java.lang.foreign.MemorySegment;
import java.lang.foreign.ValueLayout;
import java.util.EnumSet;
import java.util.HashMap;
import java.util.Map;

public class H5Ex_D_Szip {
    private static String FILENAME    = "H5Ex_D_Szip.h5";
    private static String DATASETNAME = "DS1";
    private static final int DIM_X    = 32;
    private static final int DIM_Y    = 64;
    private static final int CHUNK_X  = 4;
    private static final int CHUNK_Y  = 8;
    private static final int RANK     = 2;
    private static final int NDIMS    = 2;

    // Values for the status of space allocation
    enum H5Z_filter {
        H5Z_FILTER_ERROR(H5Z_FILTER_ERROR()),
        H5Z_FILTER_NONE(H5Z_FILTER_NONE()),
        H5Z_FILTER_DEFLATE(H5Z_FILTER_DEFLATE()),
        H5Z_FILTER_SHUFFLE(H5Z_FILTER_SHUFFLE()),
        H5Z_FILTER_FLETCHER32(H5Z_FILTER_FLETCHER32()),
        H5Z_FILTER_SZIP(H5Z_FILTER_SZIP()),
        H5Z_FILTER_NBIT(H5Z_FILTER_NBIT()),
        H5Z_FILTER_SCALEOFFSET(H5Z_FILTER_SCALEOFFSET()),
        H5Z_FILTER_RESERVED(H5Z_FILTER_RESERVED()),
        H5Z_FILTER_MAX(H5Z_FILTER_MAX());
        private static final Map<Integer, H5Z_filter> lookup = new HashMap<Integer, H5Z_filter>();

        static
        {
            for (H5Z_filter s : EnumSet.allOf(H5Z_filter.class))
                lookup.put(s.getCode(), s);
        }

        private int code;

        H5Z_filter(int layout_type) { this.code = layout_type; }

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

        public static H5Z_filter get(int code) { return lookup.get(code); }
    }

    private static boolean checkSzipFilter()
    {
        try {
            int available = H5Zfilter_avail(H5Z_FILTER_SZIP());
            if (available == 0) {
                System.out.println("szip filter not available.");
                return false;
            }
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        try {
            try (Arena arena = Arena.ofConfined()) {
                MemorySegment filterInfoSeg = arena.allocate(ValueLayout.JAVA_INT);
                H5Zget_filter_info(H5Z_FILTER_SZIP(), filterInfoSeg);
                int filter_info = filterInfoSeg.get(ValueLayout.JAVA_INT, 0);
                if (((filter_info & H5Z_FILTER_CONFIG_ENCODE_ENABLED()) == 0) ||
                    ((filter_info & H5Z_FILTER_CONFIG_DECODE_ENABLED()) == 0)) {
                    System.out.println("szip filter not available for encoding and decoding.");
                    return false;
                }
            }
        }
        catch (Exception e) {
            e.printStackTrace();
        }
        return true;
    }

    private static void writeSzip(Arena arena)
    {
        long file_id      = H5I_INVALID_HID();
        long filespace_id = H5I_INVALID_HID();
        long dataset_id   = H5I_INVALID_HID();
        long dcpl_id      = H5I_INVALID_HID();
        long[] dims       = {DIM_X, DIM_Y};
        long[] chunk_dims = {CHUNK_X, CHUNK_Y};
        int[][] dset_data = new int[DIM_X][DIM_Y];

        // Initialize data.
        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 = H5Fcreate(arena.allocateFrom(FILENAME), H5F_ACC_TRUNC(), H5P_DEFAULT(), 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 =
                H5Screate_simple(RANK, arena.allocateFrom(ValueLayout.JAVA_LONG, dims), MemorySegment.NULL);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Create the dataset creation property list, add the szip compression
        // filter.
        try {
            dcpl_id = H5Pcreate(H5P_CLS_DATASET_CREATE_ID_g());
            if (dcpl_id >= 0) {
                H5Pset_szip(dcpl_id, H5_SZIP_NN_OPTION_MASK(), 8);
                // Set the chunk size.
                H5Pset_chunk(dcpl_id, NDIMS, arena.allocateFrom(ValueLayout.JAVA_LONG, chunk_dims));
            }
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Create the dataset.
        try {
            if ((file_id >= 0) && (filespace_id >= 0) && (dcpl_id >= 0))
                dataset_id = H5Dcreate2(file_id, arena.allocateFrom(DATASETNAME), H5T_STD_I32LE_g(),
                                        filespace_id, H5P_DEFAULT(), dcpl_id, H5P_DEFAULT());
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Write the data to the dataset.
        try {
            if (dataset_id >= 0) {
                // Flatten 2D array for FFM

                int[] flatData = new int[DIM_X * DIM_Y];

                for (int i = 0; i < DIM_X; i++) {

                    for (int j = 0; j < DIM_Y; j++) {

                        flatData[i * DIM_Y + j] = dset_data[i][j];
                    }
                }

                MemorySegment dataSeg = arena.allocate(ValueLayout.JAVA_INT, flatData.length);

                for (int i = 0; i < flatData.length; i++) {

                    dataSeg.setAtIndex(ValueLayout.JAVA_INT, i, flatData[i]);
                }

                H5Dwrite(dataset_id, H5T_NATIVE_INT_g(), H5S_ALL(), H5S_ALL(), H5P_DEFAULT(), dataSeg);
            }
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // End access to the dataset and release resources used by it.
        try {
            if (dcpl_id >= 0)
                H5Pclose(dcpl_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

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

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

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

    private static void readSzip(Arena arena)
    {
        long file_id      = H5I_INVALID_HID();
        long dataset_id   = H5I_INVALID_HID();
        long dcpl_id      = H5I_INVALID_HID();
        int[][] dset_data = new int[DIM_X][DIM_Y];

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

        // Open an existing dataset.
        try {
            if (file_id >= 0)
                dataset_id = H5Dopen2(file_id, arena.allocateFrom(DATASETNAME), H5P_DEFAULT());
        }
        catch (Exception e) {
            e.printStackTrace();
        }

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

        // Retrieve and print the filter type. Here we only retrieve the
        // first filter because we know that we only added one filter.
        try {
            if (dcpl_id >= 0) {
                // FFM requires MemorySegment parameters
                MemorySegment flagsSeg   = arena.allocate(ValueLayout.JAVA_INT);
                MemorySegment cdNeltsSeg = arena.allocate(ValueLayout.JAVA_LONG);
                cdNeltsSeg.set(ValueLayout.JAVA_LONG, 0, 10L);
                MemorySegment cdValuesSeg     = arena.allocate(ValueLayout.JAVA_INT, 10);
                MemorySegment nameSegment     = arena.allocate(256);
                MemorySegment filterConfigSeg = arena.allocate(ValueLayout.JAVA_INT);
                int filter_type = H5Pget_filter2(dcpl_id, 0, flagsSeg, cdNeltsSeg, cdValuesSeg, 256,
                                                 nameSegment, filterConfigSeg);
                System.out.print("Filter type is: ");
                switch (H5Z_filter.get(filter_type)) {
                case H5Z_FILTER_DEFLATE:
                    System.out.println("H5Z_FILTER_DEFLATE");
                    break;
                case H5Z_FILTER_SHUFFLE:
                    System.out.println("H5Z_FILTER_SHUFFLE");
                    break;
                case H5Z_FILTER_FLETCHER32:
                    System.out.println("H5Z_FILTER_FLETCHER32");
                    break;
                case H5Z_FILTER_SZIP:
                    System.out.println("H5Z_FILTER_SZIP");
                    break;
                case H5Z_FILTER_NBIT:
                    System.out.println("H5Z_FILTER_NBIT");
                    break;
                case H5Z_FILTER_SCALEOFFSET:
                    System.out.println("H5Z_FILTER_SCALEOFFSET");
                    break;
                default:
                    System.out.println("H5Z_FILTER_ERROR");
                }
                System.out.println();
            }
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Read the data using the default properties.
        try {
            if (dataset_id >= 0) {
                MemorySegment dataSeg = arena.allocate(ValueLayout.JAVA_INT, DIM_X * DIM_Y);

                H5Dread(dataset_id, H5T_NATIVE_INT_g(), H5S_ALL(), H5S_ALL(), H5P_DEFAULT(), dataSeg);

                // Unflatten to 2D array

                for (int i = 0; i < DIM_X; i++) {

                    for (int j = 0; j < DIM_Y; j++) {

                        dset_data[i][j] = dataSeg.getAtIndex(ValueLayout.JAVA_INT, i * DIM_Y + j);
                    }
                }
            }
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Find the maximum value in the dataset, to verify that it was read
        // correctly.
        int max = dset_data[0][0];
        for (int indx = 0; indx < DIM_X; indx++) {
            for (int jndx = 0; jndx < DIM_Y; jndx++)
                if (max < dset_data[indx][jndx])
                    max = dset_data[indx][jndx];
        }
        // Print the maximum value.
        System.out.println("Maximum value in " + DATASETNAME + " is: " + max);

        // End access to the dataset and release resources used by it.
        try {
            if (dcpl_id >= 0)
                H5Pclose(dcpl_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

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

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

    public static void main(String[] args)
    {
        try (Arena arena = Arena.ofConfined()) {
            if (H5Ex_D_Szip.checkSzipFilter()) {
                H5Ex_D_Szip.writeSzip(arena);
                H5Ex_D_Szip.readSzip(arena);
            }
        }
    }
}