package test.hdf5lib; import static org.junit.Assert.assertTrue; import static org.junit.Assert.fail; import java.io.File; import ncsa.hdf.hdf5lib.H5; import ncsa.hdf.hdf5lib.HDF5Constants; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import org.junit.After; import org.junit.Before; import org.junit.Test; public class TestH5Dplist { private static final String H5_FILE = "test.h5"; 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 NDIMS = 2; private static final int FILLVAL = 99; private static final int RANK = 2; int H5fid = -1; int H5dsid = -1; int H5did = -1; int H5dcpl_id = -1; long[] H5dims = { DIM_X, DIM_Y }; long[] H5extdims = { EDIM_X, EDIM_Y }; long[] H5chunk_dims = { CHUNK_X, CHUNK_Y }; long[] H5maxdims = { HDF5Constants.H5S_UNLIMITED, HDF5Constants.H5S_UNLIMITED }; private final void _deleteFile(String filename) { File file = new File(filename); if (file.exists()) { try {file.delete();} catch (SecurityException e) {} } } private final void _createPDataset(int fid, int dsid, String name, int dcpl_val) { try { H5dcpl_id = H5.H5Pcreate(dcpl_val); } catch (Exception err) { err.printStackTrace(); fail("H5.H5Pcreate: " + err); } assertTrue("TestH5Dplist._createPDataset: ", H5dcpl_id > 0); // Set the chunk size. try { H5.H5Pset_chunk(H5dcpl_id, NDIMS, H5chunk_dims); } catch (Exception e) { e.printStackTrace(); } // Set the fill value for the dataset try { int[] fill_value = { FILLVAL }; H5.H5Pset_fill_value(H5dcpl_id, HDF5Constants.H5T_NATIVE_INT, fill_value); } catch (Exception e) { e.printStackTrace(); } // Set the allocation time to "early". This way we can be sure // that reading from the dataset immediately after creation will // return the fill value. try { H5.H5Pset_alloc_time(H5dcpl_id, HDF5Constants.H5D_ALLOC_TIME_EARLY); } catch (Exception e) { e.printStackTrace(); } _createDataset(H5fid, H5dsid, "dset", H5dcpl_id, HDF5Constants.H5P_DEFAULT); } private final void _createDataset(int fid, int dsid, String name, int dcpl, int dapl) { try { H5did = H5.H5Dcreate(fid, name, HDF5Constants.H5T_STD_I32BE, dsid, HDF5Constants.H5P_DEFAULT, dcpl, dapl); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Dcreate: " + err); } assertTrue("TestH5Dplist._createDataset: ",H5did > 0); } @Before public void createH5file() throws NullPointerException, HDF5Exception { assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0); try { H5fid = H5.H5Fcreate(H5_FILE, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); H5dsid = H5.H5Screate_simple(RANK, H5dims, H5maxdims); } catch (Throwable err) { err.printStackTrace(); fail("TestH5Dplist.createH5file: " + err); } assertTrue("TestH5Dplist.createH5file: H5.H5Fcreate: ",H5fid > 0); assertTrue("TestH5Dplist.createH5file: H5.H5Screate_simple: ",H5dsid > 0); H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); } @After public void deleteH5file() throws HDF5LibraryException { if (H5dcpl_id >= 0) try {H5.H5Pclose(H5dcpl_id);} catch (Exception ex) {} if (H5did > 0) try {H5.H5Dclose(H5did);} catch (Exception ex) {} if (H5dsid > 0) try {H5.H5Sclose(H5dsid);} catch (Exception ex) {} if (H5fid > 0) try {H5.H5Fclose(H5fid);} catch (Exception ex) {} _deleteFile(H5_FILE); } @Test public void testH5Dset_extent() { int[][] write_dset_data = new int[DIM_X][DIM_Y]; int[][] read_dset_data = new int[DIM_X][DIM_Y]; int[][] extend_dset_data = new int[EDIM_X][EDIM_Y]; // Initialize the dataset. for (int indx = 0; indx < DIM_X; indx++) for (int jndx = 0; jndx < DIM_Y; jndx++) write_dset_data[indx][jndx] = indx * jndx - jndx; _createPDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DATASET_CREATE); // Read values from the dataset, which has not been written to yet. try { H5.H5Dread(H5did, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, read_dset_data); } catch (Exception e) { e.printStackTrace(); } assertTrue("testH5Dset_extent - H5.H5Dread: ", read_dset_data[0][0] == 99); // Write the data to the dataset. try { H5.H5Dwrite(H5did, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, write_dset_data); } catch (Exception e) { e.printStackTrace(); } // Read the data back. try { H5.H5Dread(H5did, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, read_dset_data); } catch (Exception e) { e.printStackTrace(); } assertTrue("testH5Dset_extent - H5.H5Dread: ", read_dset_data[3][6] == 12); // Extend the dataset. try { H5.H5Dset_extent(H5did, H5extdims); } catch (Exception e) { e.printStackTrace(); } // Read from the extended dataset. try { H5.H5Dread(H5did, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, extend_dset_data); } catch (Exception e) { e.printStackTrace(); } assertTrue("testH5Dset_extent - H5.H5Dread: ", extend_dset_data[3][6] == 12); assertTrue("testH5Dset_extent - H5.H5Dread: ", extend_dset_data[4][8] == 99); } }