hdf5/HDF5Examples/JAVA/H5D/H5Ex_D_Sofloat.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.               *
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 * help@hdfgroup.org.                                                        *
 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */

/************************************************************
  This example shows how to read and write data to a dataset
  using the Scale-Offset filter.  The program first checks
  if the Scale-Offset filter is available, then if it is it
  writes floating point numbers to a dataset using
  Scale-Offset, 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.text.DecimalFormat;
import java.text.DecimalFormatSymbols;
import java.util.EnumSet;
import java.util.HashMap;
import java.util.Locale;
import java.util.Map;

public class H5Ex_D_Sofloat {

    private static String FILENAME    = "H5Ex_D_Sofloat.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 checkScaleoffsetFilter()
    {
        try {
            int available = H5Zfilter_avail(H5Z_FILTER_SCALEOFFSET());
            if (available == 0) {
                System.out.println("Scale-Offset 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_SCALEOFFSET(), 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("Scale-Offset filter not available for encoding and decoding.");
                    return false;
                }
            }
        }
        catch (Exception e) {
            e.printStackTrace();
        }
        return true;
    }

    private static void writeData(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};
        double[][] dset_data = new double[DIM_X][DIM_Y];

        // Initialize data.
        for (int indx = 0; indx < DIM_X; indx++)
            for (int jndx = 0; jndx < DIM_Y; jndx++) {
                double x              = indx;
                double y              = jndx;
                dset_data[indx][jndx] = (x + 1) / (y + 0.3) + y;
            }

        // Find the maximum value in the dataset, to verify that it was read correctly.
        double max = dset_data[0][0];
        double min = 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];
                if (min > dset_data[indx][jndx])
                    min = dset_data[indx][jndx];
            }

        // Print the maximum value.
        DecimalFormat df = new DecimalFormat("#,##0.000000", new DecimalFormatSymbols(Locale.US));
        System.out.println("Maximum value in write buffer is: " + df.format(max));
        System.out.println("Minimum value in write buffer is: " + df.format(min));

        // Create a new file using the 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 Scale-Offset
        // filter and set the chunk size.
        try {
            dcpl_id = H5Pcreate(H5P_CLS_DATASET_CREATE_ID_g());
            if (dcpl_id >= 0) {
                H5Pset_scaleoffset(dcpl_id, H5Z_SO_FLOAT_DSCALE(), 2);
                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_IEEE_F64LE_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

                double[] flatData = new double[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_DOUBLE, flatData.length);

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

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

                H5Dwrite(dataset_id, H5T_NATIVE_DOUBLE_g(), H5S_ALL(), H5S_ALL(), H5P_DEFAULT(), dataSeg);
            }
        }
        catch (Exception e) {
            e.printStackTrace();
        }

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

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

        // Open file using the default properties.
        try {
            file_id = H5Fopen(arena.allocateFrom(FILENAME), H5F_ACC_RDONLY(), H5P_DEFAULT());
        }
        catch (Exception e) {
            e.printStackTrace();
        }
        // Open dataset using the default properties.
        try {
            if (file_id >= 0)
                dataset_id = H5Dopen2(file_id, arena.allocateFrom(DATASETNAME), H5P_DEFAULT());
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Retrieve 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_DOUBLE, DIM_X * DIM_Y);

                H5Dread(dataset_id, H5T_NATIVE_DOUBLE_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_DOUBLE, i * DIM_Y + j);
                    }
                }
            }
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Find the maximum value in the dataset, to verify that it was read correctly.
        double max = dset_data[0][0];
        double min = 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];
                if (min > dset_data[indx][jndx])
                    min = dset_data[indx][jndx];
            }

        // Print the maximum value.
        DecimalFormat df = new DecimalFormat("#,##0.000000", new DecimalFormatSymbols(Locale.US));
        System.out.println("Maximum value in " + DATASETNAME + " is: " + df.format(max));
        System.out.println("Minimum value in " + DATASETNAME + " is: " + df.format(min));

        // 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_Sofloat.checkScaleoffsetFilter()) {
                H5Ex_D_Sofloat.writeData(arena);
                H5Ex_D_Sofloat.readData(arena);
            }
        }
    }
}