H5Ex_T_Array.java

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/************************************************************
  This example shows how to read and write array datatypes
  to a dataset.  The program first writes integers arrays of
  dimension ADIM0xADIM1 to a dataset with a dataspace of
  DIM0, then closes the  file.  Next, it reopens the file,
  reads back the data, and outputs it to the screen.
 ************************************************************/

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

public class H5Ex_T_Array {
    private static String FILENAME    = "H5Ex_T_Array.h5";
    private static String DATASETNAME = "DS1";
    private static final int DIM0     = 4;
    private static final int ADIM0    = 3;
    private static final int ADIM1    = 5;
    private static final int RANK     = 1;
    private static final int NDIMS    = 2;

    private static void CreateDataset()
    {
        long file_id        = HDF5Constants.H5I_INVALID_HID;
        long filetype_id    = HDF5Constants.H5I_INVALID_HID;
        long memtype_id     = HDF5Constants.H5I_INVALID_HID;
        long dataspace_id   = HDF5Constants.H5I_INVALID_HID;
        long dataset_id     = HDF5Constants.H5I_INVALID_HID;
        long[] dims         = {DIM0};
        long[] adims        = {ADIM0, ADIM1};
        int[][][] dset_data = new int[DIM0][ADIM0][ADIM1];

        // Initialize data. indx is the element in the dataspace, jndx and kndx the
        // elements within the array datatype.
        for (int indx = 0; indx < DIM0; indx++)
            for (int jndx = 0; jndx < ADIM0; jndx++)
                for (int kndx = 0; kndx < ADIM1; kndx++)
                    dset_data[indx][jndx][kndx] = indx * jndx - jndx * kndx + indx * kndx;

        // Create a new file using default properties.
        try {
            file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT,
                                   HDF5Constants.H5P_DEFAULT);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Create array datatypes for file.
        try {
            filetype_id = H5.H5Tarray_create(HDF5Constants.H5T_STD_I64LE, NDIMS, adims);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Create array datatypes for memory.
        try {
            memtype_id = H5.H5Tarray_create(HDF5Constants.H5T_NATIVE_INT, NDIMS, adims);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Create dataspace. Setting maximum size to NULL sets the maximum
        // size to be the current size.
        try {
            dataspace_id = H5.H5Screate_simple(RANK, dims, null);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Create the dataset.
        try {
            if ((file_id >= 0) && (dataspace_id >= 0) && (filetype_id >= 0))
                dataset_id =
                    H5.H5Dcreate(file_id, DATASETNAME, filetype_id, dataspace_id, HDF5Constants.H5P_DEFAULT,
                                 HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Write the dataset.
        try {
            if ((dataset_id >= 0) && (memtype_id >= 0))
                H5.H5Dwrite(dataset_id, memtype_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
                            HDF5Constants.H5P_DEFAULT, dset_data);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // End access to the dataset and release resources used by it.
        try {
            if (dataset_id >= 0)
                H5.H5Dclose(dataset_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Terminate access to the data space.
        try {
            if (dataspace_id >= 0)
                H5.H5Sclose(dataspace_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Terminate access to the file type.
        try {
            if (filetype_id >= 0)
                H5.H5Tclose(filetype_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Terminate access to the mem type.
        try {
            if (memtype_id >= 0)
                H5.H5Tclose(memtype_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Close the file.
        try {
            if (file_id >= 0)
                H5.H5Fclose(file_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }
    }

    private static void ReadDataset()
    {
        long file_id     = HDF5Constants.H5I_INVALID_HID;
        long filetype_id = HDF5Constants.H5I_INVALID_HID;
        long memtype_id  = HDF5Constants.H5I_INVALID_HID;
        long dataset_id  = HDF5Constants.H5I_INVALID_HID;
        long[] dims      = {DIM0};
        long[] adims     = {ADIM0, ADIM1};
        int[][][] dset_data;

        // Open an existing file.
        try {
            file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Open an existing dataset.
        try {
            if (file_id >= 0)
                dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Get the datatype.
        try {
            if (dataset_id >= 0)
                filetype_id = H5.H5Dget_type(dataset_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Get the datatype's dimensions.
        try {
            if (filetype_id >= 0)
                H5.H5Tget_array_dims(filetype_id, adims);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Allocate array of pointers to two-dimensional arrays (the
        // elements of the dataset.
        dset_data = new int[(int)dims[0]][(int)(adims[0])][(int)(adims[1])];

        // Create array datatypes for memory.
        try {
            memtype_id = H5.H5Tarray_create(HDF5Constants.H5T_NATIVE_INT, 2, adims);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Read data.
        try {
            if ((dataset_id >= 0) && (memtype_id >= 0))
                H5.H5Dread(dataset_id, memtype_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
                           HDF5Constants.H5P_DEFAULT, dset_data);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

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

        // End access to the dataset and release resources used by it.
        try {
            if (dataset_id >= 0)
                H5.H5Dclose(dataset_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Terminate access to the file type.
        try {
            if (filetype_id >= 0)
                H5.H5Tclose(filetype_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Terminate access to the mem type.
        try {
            if (memtype_id >= 0)
                H5.H5Tclose(memtype_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Close the file.
        try {
            if (file_id >= 0)
                H5.H5Fclose(file_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }
    }

    public static void main(String[] args)
    {
        H5Ex_T_Array.CreateDataset();
        // Now we begin the read section of this example. Here we assume
        // the dataset and array have the same name and rank, but can have
        // any size. Therefore we must allocate a new array to read in
        // data using malloc().
        H5Ex_T_Array.ReadDataset();
    }
}