H5ObjectEx_D_UnlimitedGzip.java

/************************************************************
  This example shows how to create and extend an unlimited
  dataset with gzip compression.  The program first writes
  integers to a gzip compressed dataset with dataspace
  dimensions of DIM_XxDIM_Y, then closes the file.  Next, it
  reopens the file, reads back the data, outputs it to the
  screen, extends the dataset, and writes new data to the
  extended portions of the dataset.  Finally it reopens the
  file again, reads back the data, and outputs it 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_UnlimitedGzip {
    private static String FILENAME         = "H5ObjectEx_D_UnlimitedGzip.h5";
    private static String DATASETNAME      = "DS1";
    private static final int DIM_X         = 4;
    private static final int DIM_Y         = 7;
    private static final int EDIM_X        = 6;
    private static final int EDIM_Y        = 10;
    private static final int CHUNK_X       = 4;
    private static final int CHUNK_Y       = 4;
    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 writeUnlimited()
    {
        H5File file        = null;
        Dataset dset       = null;
        long file_id       = -1;
        long dcpl_id       = -1;
        long dataspace_id  = -1;
        long dataset_id    = -1;
        long type_id       = -1;
        long[] dims        = {DIM_X, DIM_Y};
        long[] chunk_dims  = {CHUNK_X, CHUNK_Y};
        long[] maxdims     = {HDF5Constants.H5S_UNLIMITED, HDF5Constants.H5S_UNLIMITED};
        int[][] dset_data  = new int[DIM_X][DIM_Y];
        H5Datatype typeInt = null;

        // Initialize the dataset.
        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 with unlimited dimensions.
        try {
            dataspace_id = H5.H5Screate_simple(RANK, dims, maxdims);
            type_id      = typeInt.createNative();
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Create the dataset creation property list, add the gzip compression
        // filter.
        try {
            dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE);
            if (dcpl_id >= 0) {
                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 unlimited dataset.
        try {
            if ((file_id >= 0) && (dataspace_id >= 0) && (dcpl_id >= 0))
                dataset_id = H5.H5Dcreate(file_id, DATASETNAME, type_id, dataspace_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)
                H5.H5Dclose(dataset_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

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

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

    private static void extendUnlimited()
    {
        H5File file       = null;
        H5ScalarDS dset   = null;
        long dataspace_id = -1;
        long dataset_id   = -1;
        long[] dims       = {DIM_X, DIM_Y};
        long[] extdims    = {EDIM_X, EDIM_Y};
        long[] start      = {0, 0};
        long[] count      = new long[2];
        int[] dset_data;
        int[][] extend_dset_data = new int[EDIM_X][EDIM_Y];

        // Open an existing file.
        try {
            file = new H5File(FILENAME, FileFormat.WRITE);
            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();
        }

        // Get dataspace and allocate memory for read buffer. This is a
        // two dimensional dataset so the dynamic allocation must be done
        // in steps.
        try {
            if (dataset_id >= 0)
                dataspace_id = H5.H5Dget_space(dataset_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        try {
            if (dataspace_id >= 0)
                H5.H5Sget_simple_extent_dims(dataspace_id, dims, null);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Allocate array of pointers to rows.
        dset_data = new int[(int)dims[0] * (int)dims[1]];

        // Read the data using the default properties.
        try {
            dset.init();
            dset_data = (int[])dset.getData();
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Output the data to the screen.
        System.out.println("Dataset before extension:");
        for (int indx = 0; indx < DIM_X; indx++) {
            System.out.print(" [ ");
            for (int jndx = 0; jndx < DIM_Y; jndx++)
                System.out.print(dset_data[indx * DIM_Y + jndx] + " ");
            System.out.println("]");
        }
        System.out.println();

        try {
            if (dataspace_id >= 0)
                H5.H5Sclose(dataspace_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Extend the dataset.
        try {
            dset.extend(extdims);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Retrieve the dataspace for the newly extended dataset.
        try {
            if (dataset_id >= 0)
                dataspace_id = H5.H5Dget_space(dataset_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Initialize data for writing to the extended dataset.
        for (int indx = 0; indx < EDIM_X; indx++)
            for (int jndx = 0; jndx < EDIM_Y; jndx++)
                extend_dset_data[indx][jndx] = jndx;

        // Select the entire dataspace.
        try {
            if (dataspace_id >= 0) {
                H5.H5Sselect_all(dataspace_id);

                // Subtract a hyperslab reflecting the original dimensions from the
                // selection. The selection now contains only the newly extended
                // portions of the dataset.
                count[0] = dims[0];
                count[1] = dims[1];
                H5.H5Sselect_hyperslab(dataspace_id, HDF5Constants.H5S_SELECT_NOTB, start, null, count, null);

                // Write the data to the selected portion of the dataset.
                if (dataset_id >= 0)
                    H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, dataspace_id,
                                HDF5Constants.H5P_DEFAULT, extend_dset_data);
            }
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // End access to the dataset and release resources used by it.
        try {
            if (dataset_id >= 0)
                dset.close(dataset_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        try {
            if (dataspace_id >= 0)
                H5.H5Sclose(dataspace_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

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

    private static void readUnlimited()
    {
        H5File file       = null;
        Dataset dset      = null;
        long dataspace_id = -1;
        long dataset_id   = -1;
        long dcpl_id      = -1;
        long[] dims       = {DIM_X, DIM_Y};
        int[] dset_data;

        // 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();
        }

        // Get dataspace and allocate memory for the read buffer as before.
        try {
            if (dataset_id >= 0)
                dataspace_id = H5.H5Dget_space(dataset_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        try {
            if (dataspace_id >= 0)
                H5.H5Sget_simple_extent_dims(dataspace_id, dims, null);
        }
        catch (Exception e) {
            e.printStackTrace();
        }
        // Allocate array of pointers to rows.
        dset_data = new int[(int)dims[0] * (int)dims[1]];

        // Read the data using the default properties.
        try {
            dset.init();
            dset_data = (int[])dset.getData();
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Output the data to the screen.
        System.out.println("Dataset after extension:");
        for (int indx = 0; indx < dims[0]; indx++) {
            System.out.print(" [ ");
            for (int jndx = 0; jndx < dims[1]; jndx++)
                System.out.print(dset_data[(int)(indx * dims[1] + jndx)] + " ");
            System.out.println("]");
        }
        System.out.println();

        // End access to the dataset and release resources used by it.
        try {
            if (dataset_id >= 0)
                dset.close(dataset_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        try {
            if (dataspace_id >= 0)
                H5.H5Sclose(dataspace_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_UnlimitedGzip.checkGzipFilter()) {
            H5ObjectEx_D_UnlimitedGzip.writeUnlimited();
            H5ObjectEx_D_UnlimitedGzip.extendUnlimited();
            H5ObjectEx_D_UnlimitedGzip.readUnlimited();
        }
    }
}