H5ObjectEx_D_Nbit.java

/************************************************************
 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.
 ************************************************************/

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_Nbit {
    private static String FILENAME         = "H5ObjectEx_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;
    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 checkNbitFilter()
    {
        try {
            // Check if N-Bit compression is available and can be used for both compression and decompression.
            int available = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_NBIT);
            if (available == 0) {
                System.out.println("N-Bit filter not available.");
                return false;
            }
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        try {
            int filter_info = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_NBIT);
            if (((filter_info & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) == 0) ||
                ((filter_info & HDF5Constants.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() throws Exception
    {
        H5File file       = null;
        Dataset dset      = null;
        long file_id      = -1;
        long filespace_id = -1;
        long dataset_id   = -1;
        long type_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];
        final H5Datatype typeInt =
            new H5Datatype(Datatype.CLASS_INTEGER, DATATYPE_SIZE, Datatype.ORDER_LE, Datatype.NATIVE);

        // 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    = new H5File(FILENAME, FileFormat.CREATE);
            file_id = file.open();

            // Create dataspace.  Setting maximum size to NULL sets the maximum
            //  size to be the current size.
            filespace_id = H5.H5Screate_simple(RANK, dims, 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.
            type_id = typeInt.createNative();
            H5.H5Tset_precision(type_id, 16);
            H5.H5Tset_offset(type_id, 5);

            // Create the dataset creation property list, add the N-Bit filter and set the chunk size.
            dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE);
            H5.H5Pset_nbit(dcpl_id);
            H5.H5Pset_chunk(dcpl_id, NDIMS, chunk_dims);

            // Create the dataset.
            if ((file_id >= 0) && (filespace_id >= 0) && (type_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);

            // Write the data to the dataset.
            H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL,
                        HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data);
        }
        catch (Exception e) {
            e.printStackTrace();
        }
        finally {
            // Close and release resources.
            if (dcpl_id >= 0)
                H5.H5Pclose(dcpl_id);
            if (type_id >= 0)
                H5.H5Tclose(type_id);
            if (dataset_id >= 0)
                dset.close(dataset_id);
            if (filespace_id >= 0)
                H5.H5Sclose(filespace_id);
            file.close();
        }
    }

    private static void readData() throws Exception
    {
        H5File file     = null;
        H5ScalarDS 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       = (H5ScalarDS)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 {
            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];
        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 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.
         */
        try {
            if (H5ObjectEx_D_Nbit.checkNbitFilter()) {
                H5ObjectEx_D_Nbit.writeData();
                H5ObjectEx_D_Nbit.readData();
            }
        }
        catch (Exception ex) {
            ex.printStackTrace();
        }
    }
}