hdf5/java/examples/datasets/H5Ex_D_Shuffle.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://support.hdfgroup.org/ftp/HDF5/releases.  *
 * 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 shuffle filter with gzip compression.  The
  program first checks if the shuffle and gzip filters are
  available, then if they are it writes integers to a
  dataset using shuffle+gzip, then closes the file.  Next,
  it reopens the file, reads back the data, and outputs the
  types of filters and the maximum value in the dataset to
  the screen.
 ************************************************************/
package examples.datasets;

import java.util.EnumSet;
import java.util.HashMap;
import java.util.Map;

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

public class H5Ex_D_Shuffle {
    private static String FILENAME = "H5Ex_D_Shuffle.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(HDF5Constants.H5Z_FILTER_ERROR), H5Z_FILTER_NONE(HDF5Constants.H5Z_FILTER_NONE), H5Z_FILTER_DEFLATE(
                HDF5Constants.H5Z_FILTER_DEFLATE), H5Z_FILTER_SHUFFLE(HDF5Constants.H5Z_FILTER_SHUFFLE), H5Z_FILTER_FLETCHER32(
                HDF5Constants.H5Z_FILTER_FLETCHER32), H5Z_FILTER_SZIP(HDF5Constants.H5Z_FILTER_SZIP), H5Z_FILTER_NBIT(
                HDF5Constants.H5Z_FILTER_NBIT), H5Z_FILTER_SCALEOFFSET(HDF5Constants.H5Z_FILTER_SCALEOFFSET), H5Z_FILTER_RESERVED(
                HDF5Constants.H5Z_FILTER_RESERVED), H5Z_FILTER_MAX(HDF5Constants.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 checkGzipFilter() {
        try {
            int available = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_DEFLATE);
            if (available == 0) {
                System.out.println("gzip filter not available.");
                return false;
            }
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        try {
            int filter_info = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_DEFLATE);
            if (((filter_info & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) == 0)
                    || ((filter_info & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) == 0)) {
                System.out.println("gzip filter not available for encoding and decoding.");
                return false;
            }
        }
        catch (Exception e) {
            e.printStackTrace();
        }
        return true;
    }

    private static boolean checkShuffleFilter() {
        try {
            int available = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_SHUFFLE);
            if (available == 0) {
                System.out.println("Shuffle filter not available.");
                return false;
            }
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        try {
            int filter_info = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_SHUFFLE);
            if (((filter_info & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) == 0)
                    || ((filter_info & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) == 0)) {
                System.out.println("Shuffle filter not available for encoding and decoding.");
                return false;
            }
        }
        catch (Exception e) {
            e.printStackTrace();
        }
        return true;
    }

    private static void writeShuffle() {
        long file_id = -1;
        long filespace_id = -1;
        long dataset_id = -1;
        long dcpl_id = -1;
        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 = 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, add the shuffle
        // filter and the gzip compression filter.
        // The order in which the filters are added here is significant -
        // we will see much greater results when the shuffle is applied
        // first. The order in which the filters are added to the property
        // list is the order in which they will be invoked when writing
        // data.
        try {
            dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE);
            if (dcpl_id >= 0) {
                H5.H5Pset_shuffle(dcpl_id);
                H5.H5Pset_deflate(dcpl_id, 9);
                // Set the chunk size.
                H5.H5Pset_chunk(dcpl_id, NDIMS, chunk_dims);
            }
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Create the 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 data to the dataset.
        try {
            if (dataset_id >= 0)
                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 (dcpl_id >= 0)
                H5.H5Pclose(dcpl_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

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

        try {
            if (filespace_id >= 0)
                H5.H5Sclose(filespace_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 readShuffle() {
        long file_id = -1;
        long dataset_id = -1;
        long dcpl_id = -1;
        int[][] dset_data = new int[DIM_X][DIM_Y];

        // 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();
        }

        // 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 the number of filters, and retrieve and print the
        // type of each.
        try {
            if (dcpl_id >= 0) {
                int nfilters = H5.H5Pget_nfilters(dcpl_id);
                for (int indx = 0; indx < nfilters; indx++) {
                    // Java lib requires a valid filter_name object and cd_values
                    int[] flags = { 0 };
                    long[] cd_nelmts = { 1 };
                    int[] cd_values = { 0 };
                    String[] filter_name = { "" };
                    int[] filter_config = { 0 };
                    int filter_type = -1;
                    filter_type = H5.H5Pget_filter(dcpl_id, indx, flags, cd_nelmts, cd_values, 120, filter_name,
                            filter_config);
                    System.out.print("Filter " + indx + ": 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) {
                H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
                        HDF5Constants.H5P_DEFAULT, dset_data);
            }
        }
        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)
                H5.H5Pclose(dcpl_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        try {
            if (dataset_id >= 0)
                H5.H5Dclose(dataset_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) {
        // Check if gzip 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.
        // Similarly, check for availability of the shuffle filter.
        if (H5Ex_D_Shuffle.checkGzipFilter() && H5Ex_D_Shuffle.checkShuffleFilter()) {
            H5Ex_D_Shuffle.writeShuffle();
            H5Ex_D_Shuffle.readShuffle();
        }
    }

}