H5ObjectEx_D_Shuffle.java

/************************************************************
  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 datasets;

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

import hdf.object.Dataset;
import hdf.object.Datatype;
import hdf.object.FileFormat;
import hdf.object.Group;
import hdf.object.h5.H5Datatype;
import hdf.object.h5.H5File;
import hdf.object.h5.H5ScalarDS;

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

public class H5ObjectEx_D_Shuffle {
    private static String FILENAME         = "H5ObjectEx_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;
    private static final int DATATYPE_SIZE = 4;

    // 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()
    {
        H5File file        = null;
        Dataset dset       = null;
        long file_id       = -1;
        long filespace_id  = -1;
        long dataset_id    = -1;
        long dcpl_id       = -1;
        long type_id       = -1;
        long[] dims        = {DIM_X, DIM_Y};
        long[] chunk_dims  = {CHUNK_X, CHUNK_Y};
        int[][] dset_data  = new int[DIM_X][DIM_Y];
        H5Datatype typeInt = null;

        // 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    = new H5File(FILENAME, FileFormat.CREATE);
            file_id = file.open();
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Create datatype.
        try {
            typeInt =
                new H5Datatype(Datatype.CLASS_INTEGER, DATATYPE_SIZE, Datatype.ORDER_LE, Datatype.NATIVE);
        }
        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);
            type_id      = typeInt.createNative();
        }
        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, type_id, filespace_id,
                                          HDF5Constants.H5P_DEFAULT, dcpl_id, HDF5Constants.H5P_DEFAULT);
            dset         = new H5ScalarDS(file, DATASETNAME, "/");
            Group pgroup = (Group)file.get("/");
            pgroup.addToMemberList(dset);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Write the data to the dataset.
        try {
            dset.write(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 (type_id >= 0)
                H5.H5Tclose(type_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

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

    private static void readShuffle()
    {
        H5File file     = null;
        Dataset dset    = null;
        long dataset_id = -1;
        long dcpl_id    = -1;
        int[] dset_data = new int[DIM_X * DIM_Y];

        // Open an existing file.
        try {
            file = new H5File(FILENAME, FileFormat.READ);
            file.open();
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Open an existing dataset.
        try {
            dset       = (Dataset)file.get(DATASETNAME);
            dataset_id = dset.open();
        }
        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 {
            dset.init();
            dset_data = (int[])dset.getData();
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Find the maximum value in the dataset, to verify that it was read
        // correctly.
        int max = dset_data[0];
        for (int indx = 0; indx < DIM_X; indx++) {
            for (int jndx = 0; jndx < DIM_Y; jndx++)
                if (max < dset_data[indx * DIM_Y + jndx])
                    max = dset_data[indx * DIM_Y + 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)
                dset.close(dataset_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Close the file.
        try {
            file.close();
        }
        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 (H5ObjectEx_D_Shuffle.checkGzipFilter() && H5ObjectEx_D_Shuffle.checkShuffleFilter()) {
            H5ObjectEx_D_Shuffle.writeShuffle();
            H5ObjectEx_D_Shuffle.readShuffle();
        }
    }
}