/************************************************************

  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.

  This file is intended for use with HDF5 Library verion 1.6

 ************************************************************/

package datatypes;

import ncsa.hdf.hdf5lib.H5;
import ncsa.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() {
		int file_id = -1;
		int filetype_id = -1;
		int memtype_id = -1;
		int dataspace_id = -1;
		int dataset_id = -1;
		long[] dims = { DIM0 };
		int[] 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, null);
		}
		catch (Exception e) {
			e.printStackTrace();
		}

		// Create array datatypes for memory.
		try {
			memtype_id = H5.H5Tarray_create(HDF5Constants.H5T_NATIVE_INT, NDIMS,
					adims, null);
		}
		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);
		}
		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() {
		int file_id = -1;
		int filetype_id = -1;
		int memtype_id = -1;
		int dataspace_id = -1;
		int dataset_id = -1;
		long[] dims = { DIM0 };
		int[] 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);
		}
		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, null);
		}
		catch (Exception e) {
			e.printStackTrace();
		}

		// Get dataspace and allocate memory for read buffer.
		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_ndims(dataspace_id);
		}
		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,
					null);
		}
		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 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();
		}

	}

	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();
	}

}