hdf5/HDF5Examples/JAVA/H5D/H5Ex_D_Nbit.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 the N-Bit filter.  The program first checks if the
 N-Bit filter is available, then if it is it writes integers
 to a dataset using N-Bit, then closes the file. Next, it
 reopens the file, reads back the data, and outputs the type
 of filter 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_Nbit {
    private static String FILENAME    = "H5Ex_D_Nbit.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 checkNbitFilter()
    {
        try {
            // Check if N-Bit compression is available and can be used for both compression and decompression.
            int available = H5Zfilter_avail(H5Z_FILTER_NBIT());
            if (available == 0) {
                System.out.println("N-Bit filter not available.");
                return false;
            }
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        try (Arena arena = Arena.ofConfined()) {
            MemorySegment filterInfoSeg = arena.allocate(ValueLayout.JAVA_INT);
            H5Zget_filter_info(H5Z_FILTER_NBIT(), 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("N-Bit filter not available for encoding and decoding.");
                return false;
            }
        }
        catch (Exception e) {
            e.printStackTrace();
        }
        return true;
    }

    private static void writeData(Arena arena) throws Exception
    {
        long file_id      = H5I_INVALID_HID();
        long filespace_id = H5I_INVALID_HID();
        long dataset_id   = H5I_INVALID_HID();
        long dtype_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;

        try {
            // Create a new file using the default properties.
            file_id = H5Fcreate(arena.allocateFrom(FILENAME), H5F_ACC_TRUNC(), H5P_DEFAULT(), H5P_DEFAULT());

            // Create dataspace. Setting maximum size to NULL sets the maximum
            // size to be the current size.
            filespace_id =
                H5Screate_simple(RANK, arena.allocateFrom(ValueLayout.JAVA_LONG, dims), MemorySegment.NULL);

            // Create the datatype to use with the N-Bit filter. It has an uncompressed size of 32 bits,
            // but will have a size of 16 bits after being packed by the N-Bit filter.
            dtype_id = H5Tcopy(H5T_STD_I32LE_g());
            H5Tset_precision(dtype_id, 16);
            H5Tset_offset(dtype_id, 5);

            // Create the dataset creation property list, add the N-Bit filter and set the chunk size.
            dcpl_id = H5Pcreate(H5P_CLS_DATASET_CREATE_ID_g());
            H5Pset_nbit(dcpl_id);
            H5Pset_chunk(dcpl_id, NDIMS, arena.allocateFrom(ValueLayout.JAVA_LONG, chunk_dims));

            // Create the dataset.
            dataset_id = H5Dcreate2(file_id, arena.allocateFrom(DATASETNAME), dtype_id, filespace_id,
                                    H5P_DEFAULT(), dcpl_id, H5P_DEFAULT());

            // Write the data to the dataset.
            // 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();
        }
        finally {
            // Close and release resources.
            if (dcpl_id >= 0)
                H5Pclose(dcpl_id);
            if (dtype_id >= 0)
                H5Tclose(dtype_id);
            if (dataset_id >= 0)
                H5Dclose(dataset_id);
            if (filespace_id >= 0)
                H5Sclose(filespace_id);
            if (file_id >= 0)
                H5Fclose(file_id);
        }
    }

    private static void readData(Arena arena) throws Exception
    {
        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()) {
            /*
             * Check if N-Bit compression is available and can be used for both compression and decompression.
             * Normally we do not perform error checking in these examples for the sake of clarity, but in
             * this case we will make an exception because this filter is an optional part of the hdf5
             * library.
             */
            if (H5Ex_D_Nbit.checkNbitFilter()) {
                try {
                    H5Ex_D_Nbit.writeData(arena);
                    H5Ex_D_Nbit.readData(arena);
                }
                catch (Exception ex) {
                    ex.printStackTrace();
                }
            }
        }
        catch (Exception ex) {
            ex.printStackTrace();
        }
    }
}