H5ObjectEx_D_Gzip.java

/************************************************************
  This example shows how to read and write data to a dataset
  using gzip compression (also called zlib or deflate).  The
  program first checks if gzip compression is available,
  then if it is it writes integers to a dataset using gzip,
  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.
 ************************************************************/
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.h5.H5Datatype;
import hdf.object.h5.H5File;

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

public class H5ObjectEx_D_Gzip {
    private static String FILENAME         = "H5ObjectEx_D_Gzip.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 void writeGzip()
    {
        H5File file        = null;
        Dataset dset       = null;
        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.open();
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Create the datatype.
        try {
            typeInt =
                new H5Datatype(Datatype.CLASS_INTEGER, DATATYPE_SIZE, Datatype.ORDER_LE, Datatype.NATIVE);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Create the dataset.
        try {
            file.createScalarDS(DATASETNAME, null, typeInt, dims, null, chunk_dims, 9, null, dset_data);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Close the file.
        try {
            file.close();
        }
        catch (Exception e) {
            e.printStackTrace();
        }
    }

    private static void readGzip()
    {
        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 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) {
                // 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, 0, flags, cd_nelmts, cd_values, 120, filter_name,
                                               filter_config);
                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 {
            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.
        if (H5ObjectEx_D_Gzip.checkGzipFilter()) {
            H5ObjectEx_D_Gzip.writeGzip();
            H5ObjectEx_D_Gzip.readGzip();
        }
    }
}