H5ObjectEx_D_Chunk.java

/************************************************************
  This example shows how to create a chunked dataset.  The
  program first writes integers in a hyperslab selection to
  a chunked dataset with dataspace dimensions of DIM_XxDIM_Y
  and chunk size of CHUNK_XxCHUNK_Y, then closes the file.
  Next, it reopens the file, reads back the data, and
  outputs it to the screen.  Finally it reads the data again
  using a different hyperslab selection, and outputs
  the result 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_Chunk {
    private static String FILENAME         = "H5ObjectEx_D_Chunk.h5";
    private static String DATASETNAME      = "DS1";
    private static final int DIM_X         = 6;
    private static final int DIM_Y         = 8;
    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 H5D_layout {
        H5D_LAYOUT_ERROR(-1),
        H5D_COMPACT(0),
        H5D_CONTIGUOUS(1),
        H5D_CHUNKED(2),
        H5D_NLAYOUTS(3);
        private static final Map<Integer, H5D_layout> lookup = new HashMap<Integer, H5D_layout>();

        static
        {
            for (H5D_layout s : EnumSet.allOf(H5D_layout.class))
                lookup.put(s.getCode(), s);
        }

        private int code;

        H5D_layout(int layout_type) { this.code = layout_type; }

        public int getCode() { return this.code; }

        public static H5D_layout get(int code) { return lookup.get(code); }
    }

    private static void writeChunk()
    {
        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 to "1", to make it easier to see the selections.
        for (int indx = 0; indx < DIM_X; indx++)
            for (int jndx = 0; jndx < DIM_Y; jndx++)
                dset_data[indx][jndx] = 1;

        // Print the data to the screen.
        System.out.println("Original Data:");
        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][jndx] + " ");
            System.out.println("]");
        }
        System.out.println();

        // 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.
        try {
            dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Set the chunk size.
        try {
            if (dcpl_id >= 0)
                H5.H5Pset_chunk(dcpl_id, NDIMS, chunk_dims);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Create the chunked 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();
        }

        // Define and select the first part of the hyperslab selection.
        long[] start  = {0, 0};
        long[] stride = {3, 3};
        long[] count  = {2, 3};
        long[] block  = {2, 2};
        try {
            if ((filespace_id >= 0))
                H5.H5Sselect_hyperslab(filespace_id, HDF5Constants.H5S_SELECT_SET, start, stride, count,
                                       block);
        }
        catch (Exception e) {
            e.printStackTrace();
        }
        // Define and select the second part of the hyperslab selection,
        // which is subtracted from the first selection by the use of
        // H5S_SELECT_NOTB
        block[0] = 1;
        block[1] = 1;
        try {
            if ((filespace_id >= 0)) {
                H5.H5Sselect_hyperslab(filespace_id, HDF5Constants.H5S_SELECT_NOTB, start, stride, count,
                                       block);

                // Write the data to the dataset.
                if (dataset_id >= 0)
                    H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, filespace_id,
                                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 (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 readChunk()
    {
        H5File file       = null;
        Dataset dset      = null;
        long filespace_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 = 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();
        }

        // Print the storage layout.
        try {
            if (dcpl_id >= 0) {
                int layout_type = H5.H5Pget_layout(dcpl_id);
                System.out.print("Storage layout for " + DATASETNAME + " is: ");
                switch (H5D_layout.get(layout_type)) {
                case H5D_COMPACT:
                    System.out.println("H5D_COMPACT");
                    break;
                case H5D_CONTIGUOUS:
                    System.out.println("H5D_CONTIGUOUS");
                    break;
                case H5D_CHUNKED:
                    System.out.println("H5D_CHUNKED");
                    break;
                }
                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();
        }

        // Output the data to the screen.
        System.out.println("Data as written to disk by hyberslabs:");
        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();

        // Initialize the read array.
        for (int indx = 0; indx < DIM_X; indx++)
            for (int jndx = 0; jndx < DIM_Y; jndx++)
                dset_data[indx * DIM_Y + jndx] = 0;

        // Define and select the hyperslab to use for reading.
        try {
            if (dataset_id >= 0) {
                filespace_id = H5.H5Dget_space(dataset_id);

                long[] start  = {0, 1};
                long[] stride = {4, 4};
                long[] count  = {2, 2};
                long[] block  = {2, 3};

                if (filespace_id >= 0) {
                    H5.H5Sselect_hyperslab(filespace_id, HDF5Constants.H5S_SELECT_SET, start, stride, count,
                                           block);

                    // Read the data using the previously defined hyperslab.
                    if ((dataset_id >= 0) && (filespace_id >= 0))
                        H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL,
                                   filespace_id, HDF5Constants.H5P_DEFAULT, dset_data);
                }
            }
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Output the data to the screen.
        System.out.println("Data as read from disk by hyberslab:");
        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();

        // 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();
        }

        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();
        }
    }

    public static void main(String[] args)
    {
        H5ObjectEx_D_Chunk.writeChunk();
        H5ObjectEx_D_Chunk.readChunk();
    }
}