389 lines
9.1 KiB
Java
389 lines
9.1 KiB
Java
/************************************************************
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This example shows how to create and extend an unlimited
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dataset. The program first writes integers to a dataset
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with dataspace dimensions of DIM_XxDIM_Y, then closes the
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file. Next, it reopens the file, reads back the data,
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outputs it to the screen, extends the dataset, and writes
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new data to the extended portions of the dataset. Finally
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it reopens the file again, reads back the data, and
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outputs it to the screen.
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This file is intended for use with HDF5 Library verion 1.6
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************************************************************/
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package datasets;
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import ncsa.hdf.hdf5lib.H5;
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import ncsa.hdf.hdf5lib.HDF5Constants;
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public class H5Ex_D_UnlimitedAdd {
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private static String FILENAME = "h5ex_d_unlimadd.h5";
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private static String DATASETNAME = "DS1";
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private static final int DIM_X = 4;
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private static final int DIM_Y = 7;
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private static final int EDIM_X = 6;
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private static final int EDIM_Y = 10;
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private static final int CHUNK_X = 4;
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private static final int CHUNK_Y = 4;
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private static final int RANK = 2;
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private static final int NDIMS = 2;
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private static void writeUnlimited() {
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int file_id = -1;
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int dcpl_id = -1;
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int dataspace_id = -1;
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int dataset_id = -1;
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long[] dims = { DIM_X, DIM_Y };
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long[] chunk_dims = { CHUNK_X, CHUNK_Y };
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long[] maxdims = { HDF5Constants.H5S_UNLIMITED, HDF5Constants.H5S_UNLIMITED };
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int[][] dset_data = new int[DIM_X][DIM_Y];
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// Initialize the dataset.
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for (int indx = 0; indx < DIM_X; indx++)
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for (int jndx = 0; jndx < DIM_Y; jndx++)
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dset_data[indx][jndx] = indx * jndx - jndx;
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// Create a new file using default properties.
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try {
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file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC,
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HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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// Create dataspace with unlimited dimensions.
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try {
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dataspace_id = H5.H5Screate_simple(RANK, dims, maxdims);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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// Create the dataset creation property list.
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try {
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dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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// Set the chunk size.
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try {
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if (dcpl_id >= 0)
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H5.H5Pset_chunk(dcpl_id, NDIMS, chunk_dims);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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// Create the unlimited dataset.
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try {
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if ((file_id >= 0) && (dataspace_id >= 0) && (dcpl_id >= 0))
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dataset_id = H5.H5Dcreate(file_id, DATASETNAME,
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HDF5Constants.H5T_STD_I32LE, dataspace_id, dcpl_id);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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// Write the data to the dataset.
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try {
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if (dataset_id >= 0)
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H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT,
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HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
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HDF5Constants.H5P_DEFAULT, dset_data);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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// End access to the dataset and release resources used by it.
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try {
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if (dataset_id >= 0)
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H5.H5Dclose(dataset_id);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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try {
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if (dataspace_id >= 0)
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H5.H5Sclose(dataspace_id);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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try {
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if (dcpl_id >= 0)
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H5.H5Pclose(dcpl_id);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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// Close the file.
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try {
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if (file_id >= 0)
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H5.H5Fclose(file_id);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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}
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private static void extendUnlimited() {
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int file_id = -1;
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int dataspace_id = -1;
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int dataset_id = -1;
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long[] dims = { DIM_X, DIM_Y };
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long[] extdims = { EDIM_X, EDIM_Y };
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long[] start = { 0, 0 };
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long[] count = new long[2];
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int[][] dset_data;
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int[][] extend_dset_data = new int[EDIM_X][EDIM_Y];
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// Open an existing file.
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try {
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file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDWR,
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HDF5Constants.H5P_DEFAULT);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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// Open an existing dataset.
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try {
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if (file_id >= 0)
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dataset_id = H5.H5Dopen(file_id, DATASETNAME);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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// Get dataspace and allocate memory for read buffer. This is a
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// two dimensional dataset so the dynamic allocation must be done
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// in steps.
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try {
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if (dataset_id >= 0)
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dataspace_id = H5.H5Dget_space(dataset_id);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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try {
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if (dataspace_id >= 0)
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H5.H5Sget_simple_extent_dims(dataspace_id, dims, null);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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// Allocate array of pointers to rows.
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dset_data = new int[(int) dims[0]][(int) dims[1]];
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// Read the data using the default properties.
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try {
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if (dataset_id >= 0)
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H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT,
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HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
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HDF5Constants.H5P_DEFAULT, dset_data);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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// Output the data to the screen.
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System.out.println("Dataset before extension:");
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for (int indx = 0; indx < DIM_X; indx++) {
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System.out.print(" [ ");
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for (int jndx = 0; jndx < DIM_Y; jndx++)
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System.out.print(dset_data[indx][jndx] + " ");
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System.out.println("]");
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}
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System.out.println();
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try {
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if (dataspace_id >= 0)
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H5.H5Sclose(dataspace_id);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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// Extend the dataset.
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try {
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if (dataset_id >= 0)
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H5.H5Dextend(dataset_id, extdims);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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// Retrieve the dataspace for the newly extended dataset.
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try {
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if (dataset_id >= 0)
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dataspace_id = H5.H5Dget_space(dataset_id);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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// Initialize data for writing to the extended dataset.
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for (int indx = 0; indx < EDIM_X; indx++)
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for (int jndx = 0; jndx < EDIM_Y; jndx++)
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extend_dset_data[indx][jndx] = jndx;
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// Select the entire dataspace.
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try {
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if (dataspace_id >= 0) {
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H5.H5Sselect_all(dataspace_id);
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// Subtract a hyperslab reflecting the original dimensions from the
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// selection. The selection now contains only the newly extended
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// portions of the dataset.
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count[0] = dims[0];
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count[1] = dims[1];
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H5.H5Sselect_hyperslab(dataspace_id, HDF5Constants.H5S_SELECT_NOTB,
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start, null, count, null);
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// Write the data to the selected portion of the dataset.
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if (dataset_id >= 0)
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H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT,
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HDF5Constants.H5S_ALL, dataspace_id, HDF5Constants.H5P_DEFAULT,
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extend_dset_data);
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}
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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// End access to the dataset and release resources used by it.
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try {
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if (dataset_id >= 0)
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H5.H5Dclose(dataset_id);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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try {
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if (dataspace_id >= 0)
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H5.H5Sclose(dataspace_id);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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// Close the file.
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try {
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if (file_id >= 0)
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H5.H5Fclose(file_id);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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}
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private static void readUnlimited() {
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int file_id = -1;
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int dataspace_id = -1;
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int dataset_id = -1;
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long[] dims = { DIM_X, DIM_Y };
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int[][] dset_data;
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// Open an existing file.
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try {
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file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY,
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HDF5Constants.H5P_DEFAULT);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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// Open an existing dataset.
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try {
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if (file_id >= 0)
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dataset_id = H5.H5Dopen(file_id, DATASETNAME);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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// Get dataspace and allocate memory for the read buffer as before.
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try {
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if (dataset_id >= 0)
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dataspace_id = H5.H5Dget_space(dataset_id);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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try {
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if (dataspace_id >= 0)
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H5.H5Sget_simple_extent_dims(dataspace_id, dims, null);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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// Allocate array of pointers to rows.
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dset_data = new int[(int) dims[0]][(int) dims[1]];
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// Read the data using the default properties.
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try {
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if (dataset_id >= 0)
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H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT,
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HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
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HDF5Constants.H5P_DEFAULT, dset_data);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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// Output the data to the screen.
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System.out.println("Dataset after extension:");
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for (int indx = 0; indx < dims[0]; indx++) {
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System.out.print(" [ ");
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for (int jndx = 0; jndx < dims[1]; jndx++)
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System.out.print(dset_data[indx][jndx] + " ");
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System.out.println("]");
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}
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System.out.println();
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// End access to the dataset and release resources used by it.
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try {
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if (dataset_id >= 0)
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H5.H5Dclose(dataset_id);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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try {
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if (dataspace_id >= 0)
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H5.H5Sclose(dataspace_id);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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// Close the file.
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try {
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if (file_id >= 0)
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H5.H5Fclose(file_id);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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}
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public static void main(String[] args) {
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H5Ex_D_UnlimitedAdd.writeUnlimited();
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H5Ex_D_UnlimitedAdd.extendUnlimited();
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H5Ex_D_UnlimitedAdd.readUnlimited();
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}
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}
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