diff options
Diffstat (limited to 'java/test/TestH5D.java')
| -rw-r--r-- | java/test/TestH5D.java | 892 |
1 files changed, 892 insertions, 0 deletions
diff --git a/java/test/TestH5D.java b/java/test/TestH5D.java new file mode 100644 index 0000000..9e359e2 --- /dev/null +++ b/java/test/TestH5D.java @@ -0,0 +1,892 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * Copyright by The HDF Group. * + * Copyright by the Board of Trustees of the University of Illinois. * + * All rights reserved. * + * * + * This file is part of HDF5. The full HDF5 copyright notice, including * + * terms governing use, modification, and redistribution, is contained in * + * the files COPYING and Copyright.html. COPYING can be found at the root * + * of the source code distribution tree; Copyright.html can be found at the * + * root level of an installed copy of the electronic HDF5 document set and * + * is linked from the top-level documents page. It can also be found at * + * http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have * + * access to either file, you may request a copy from help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + +package test; + +import static org.junit.Assert.assertFalse; +import static org.junit.Assert.assertTrue; +import static org.junit.Assert.fail; + +import java.io.File; + +import hdf.hdf5lib.H5; +import hdf.hdf5lib.HDF5Constants; +import hdf.hdf5lib.HDFNativeData; +import hdf.hdf5lib.callbacks.H5D_iterate_cb; +import hdf.hdf5lib.callbacks.H5D_iterate_t; +import hdf.hdf5lib.exceptions.HDF5Exception; +import hdf.hdf5lib.exceptions.HDF5LibraryException; + +import org.junit.After; +import org.junit.Before; +import org.junit.Rule; +import org.junit.Test; +import org.junit.rules.TestName; + +public class TestH5D { + @Rule public TestName testname = new TestName(); + private static final String H5_FILE = "test.h5"; + private static final int DIM_X = 4; + private static final int DIM_Y = 6; + private static final int RANK = 2; + long H5fid = -1; + long H5dsid = -1; + long H5dtid = -1; + long H5did = -1; + long H5did0 = -1; + long H5dcpl_id = -1; + long[] H5dims = { DIM_X, DIM_Y }; + + // Values for the status of space allocation + enum H5D_space_status { + H5D_SPACE_STATUS_ERROR(-1), H5D_SPACE_STATUS_NOT_ALLOCATED(0), H5D_SPACE_STATUS_PART_ALLOCATED( + 1), H5D_SPACE_STATUS_ALLOCATED(2); + + private int code; + + H5D_space_status(int space_status) { + this.code = space_status; + } + + public int getCode() { + return this.code; + } + } + + private final void _deleteFile(String filename) { + File file = new File(filename); + + if (file.exists()) { + try {file.delete();} + catch (SecurityException e) {} + } + } + + private final void _createPDataset(long fid, long dsid, String name, long dcpl_val) { + + try { + H5dcpl_id = H5.H5Pcreate(dcpl_val); + } + catch (Exception err) { + err.printStackTrace(); + fail("H5.H5Pcreate: " + err); + } + assertTrue("testH5D._createPDataset: H5.H5Pcreate: ", H5dcpl_id >= 0); + + // 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(); + } + + try { + H5did0 = H5.H5Dcreate(fid, name, + HDF5Constants.H5T_STD_I32BE, dsid, + HDF5Constants.H5P_DEFAULT, H5dcpl_id, HDF5Constants.H5P_DEFAULT); + } + catch (Throwable err) { + err.printStackTrace(); + fail("H5.H5Dcreate: " + err); + } + assertTrue("TestH5D._createPDataset.H5Dcreate: ", H5did0 >= 0); + } + + private final void _createDataset(long fid, long dsid, String name, long dapl) { + try { + H5did = H5.H5Dcreate(fid, name, + HDF5Constants.H5T_STD_I32BE, dsid, + HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, dapl); + } + catch (Throwable err) { + err.printStackTrace(); + fail("H5.H5Dcreate: " + err); + } + assertTrue("TestH5D._createDataset.H5Dcreate: ", H5did >= 0); + } + + private final void _createVLDataset(long fid, long dsid, String name, long dapl) { + try { + H5dtid = H5.H5Tcopy(HDF5Constants.H5T_C_S1); + } + catch (Throwable err) { + err.printStackTrace(); + fail("H5.H5Tcopy: " + err); + } + assertTrue("TestH5D._createVLDataset.H5Tcopy: ", H5dtid >= 0); + try { + H5.H5Tset_size(H5dtid, HDF5Constants.H5T_VARIABLE); + assertTrue("TestH5D._createVLDataset.H5Tis_variable_str", H5.H5Tis_variable_str(H5dtid)); + } + catch (Throwable err) { + err.printStackTrace(); + fail("H5.H5Tset_size: " + err); + } + try { + H5did = H5.H5Dcreate(fid, name, H5dtid, dsid, + HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, dapl); + } + catch (Throwable err) { + err.printStackTrace(); + fail("H5.H5Dcreate: " + err); + } + assertTrue("TestH5D._createVLDataset.H5Dcreate: ", H5did >= 0); + } + + private final void _closeH5file() throws HDF5LibraryException { + if (H5dcpl_id >= 0) + try {H5.H5Pclose(H5dcpl_id);} catch (Exception ex) {} + if (H5did0 >= 0) + try {H5.H5Dclose(H5did0);} catch (Exception ex) {} + if (H5did >= 0) + try {H5.H5Dclose(H5did);} catch (Exception ex) {} + if (H5dtid > 0) + try {H5.H5Tclose(H5dtid);} catch (Exception ex) {} + if (H5dsid > 0) + try {H5.H5Sclose(H5dsid);} catch (Exception ex) {} + if (H5fid > 0) + try {H5.H5Fclose(H5fid);} catch (Exception ex) {} + } + + private final void _openH5file(String name, long dapl) { + try { + H5fid = H5.H5Fopen(H5_FILE, + HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT); + } + catch (Throwable err) { + err.printStackTrace(); + fail("TestH5D._openH5file: " + err); + } + assertTrue("TestH5D._openH5file: H5.H5Fopen: ",H5fid >= 0); + try { + H5did = H5.H5Dopen(H5fid, name, dapl); + } + catch (Throwable err) { + err.printStackTrace(); + fail("TestH5D._openH5file: " + err); + } + assertTrue("TestH5D._openH5file: H5.H5Dopen: ",H5did >= 0); + try { + H5dsid = H5.H5Dget_space(H5did); + } + catch (Throwable err) { + err.printStackTrace(); + fail("TestH5D._openH5file: " + err); + } + assertTrue("TestH5D._openH5file: H5.H5Screate_simple: ",H5dsid > 0); + } + + @Before + public void createH5file() + throws NullPointerException, HDF5Exception { + assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0); + System.out.print(testname.getMethodName()); + + try { + H5fid = H5.H5Fcreate(H5_FILE, HDF5Constants.H5F_ACC_TRUNC, + HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); + H5dsid = H5.H5Screate_simple(RANK, H5dims, null); + } + catch (Throwable err) { + err.printStackTrace(); + fail("TestH5D.createH5file: " + err); + } + assertTrue("TestH5D.createH5file: H5.H5Fcreate: ",H5fid >= 0); + assertTrue("TestH5D.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 (H5did0 >= 0) + try {H5.H5Dclose(H5did0);} catch (Exception ex) {} + if (H5did >= 0) + try {H5.H5Dclose(H5did);} catch (Exception ex) {} + if (H5dtid > 0) + try {H5.H5Tclose(H5dtid);} 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); + System.out.println(); + } + + @Test + public void testH5Dcreate() { + long dataset_id = -1; + try { + dataset_id = H5.H5Dcreate(H5fid, "dset", + HDF5Constants.H5T_STD_I32BE, H5dsid, + HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); + } + catch (Exception err) { + err.printStackTrace(); + fail("testH5Dcreate: " + err); + } + assertTrue(dataset_id >= 0); + + // End access to the dataset and release resources used by it. + try { + if (dataset_id >= 0) + H5.H5Dclose(dataset_id); + } + catch (Exception err) { + err.printStackTrace(); + } + } + + @Test + public void testH5Dcreate_anon() { + long dataset_id = -1; + try { + dataset_id = H5.H5Dcreate_anon(H5fid, HDF5Constants.H5T_STD_I32BE, + H5dsid, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); + } + catch (Exception err) { + err.printStackTrace(); + fail("testH5Dcreate_anon: " + err); + } + assertTrue(dataset_id >= 0); + + // End access to the dataset and release resources used by it. + try { + if (dataset_id >= 0) + H5.H5Dclose(dataset_id); + } + catch (Exception err) { + err.printStackTrace(); + } + } + + @Test + public void testH5Dopen() { + long dataset_id = -1; + _createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT); + + try { + H5.H5Dclose(H5did); + H5did = -1; + dataset_id = H5.H5Dopen(H5fid, "dset", HDF5Constants.H5P_DEFAULT); + } + catch (Exception err) { + err.printStackTrace(); + fail("testH5Dopen: " + err); + } + assertTrue("testH5Dopen: ", dataset_id >= 0); + + // End access to the dataset and release resources used by it. + try { + if (dataset_id >= 0) + H5.H5Dclose(dataset_id); + } + catch (Exception err) { + err.printStackTrace(); + } + } + + @Test + public void testH5Dget_storage_size_empty() { + long storage_size = 0; + _createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT); + + try { + storage_size = H5.H5Dget_storage_size(H5did); + } + catch (Exception err) { + err.printStackTrace(); + fail("testH5Dget_storage_size: " + err); + } + assertTrue("testH5Dget_storage_size: ", storage_size == 0); + } + + @Test + public void testH5Dget_storage_size() { + long storage_size = 0; + int[][] dset_data = new int[DIM_X][DIM_Y]; + int FILLVAL = 99; + _createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT); + + // Initialize the dataset. + for (int indx = 0; indx < DIM_X; indx++) + for (int jndx = 0; jndx < DIM_Y; jndx++) + dset_data[indx][jndx] = FILLVAL; + + try { + if (H5did >= 0) + H5.H5Dwrite(H5did, HDF5Constants.H5T_NATIVE_INT, + HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, dset_data[0]); + } + catch (Exception e) { + e.printStackTrace(); + } + + try { + storage_size = H5.H5Dget_storage_size(H5did); + } + catch (Exception err) { + err.printStackTrace(); + fail("testH5Dget_storage_size: " + err); + } + assertTrue("testH5Dget_storage_size: "+storage_size, storage_size == DIM_X*DIM_Y*4); + } + + @Test + public void testH5Dget_access_plist() { + long dapl_id = -1; + int pequal = -1; + long test_dapl_id = -1; + + try { + test_dapl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_ACCESS); + } + catch (Exception err) { + err.printStackTrace(); + fail("testH5Dget_access_plist: H5.H5Pcreate: " + err); + } + assertTrue("testH5Dget_access_plist: test_dapl_id: ", test_dapl_id >= 0); + + _createDataset(H5fid, H5dsid, "dset", test_dapl_id); + + try { + dapl_id = H5.H5Dget_access_plist(H5did); + assertTrue("testH5Dget_access_plist: dapl_id: ", dapl_id >= 0); + pequal = H5.H5Pequal(dapl_id, test_dapl_id); + } + catch (Exception err) { + err.printStackTrace(); + fail("testH5Dget_access_plist: H5.H5Dget_access_plist: " + err); + } + + // End access to the dataset and release resources used by it. + try { + if (dapl_id >= 0) + H5.H5Pclose(dapl_id); + } + catch (Exception err) { + err.printStackTrace(); + } + try { + if (test_dapl_id >= 0) + H5.H5Pclose(test_dapl_id); + } + catch (Exception err) { + err.printStackTrace(); + } + assertTrue("testH5Dget_access_plist: ", pequal > 0); + } + + @Test + public void testH5Dget_space_status() { + int[][] write_dset_data = new int[DIM_X][DIM_Y]; + int space_status = -1; + int space_status0 = -1; + + // 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, "dset0", HDF5Constants.H5P_DATASET_CREATE); + _createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT); + + // Retrieve and print space status and storage size for dset0. + try { + space_status0 = H5.H5Dget_space_status(H5did0); + } + catch (Exception e) { + e.printStackTrace(); + } + assertTrue("testH5Dget_space_status0 - H5.H5Dget_space_status: ", space_status0 == H5D_space_status.H5D_SPACE_STATUS_ALLOCATED.getCode()); + + // Retrieve and print space status and storage size for dset. + try { + space_status = H5.H5Dget_space_status(H5did); + } + catch (Exception e) { + e.printStackTrace(); + } + assertFalse("testH5Dget_space_status - H5.H5Dget_space_status: ", space_status == H5D_space_status.H5D_SPACE_STATUS_ALLOCATED.getCode()); + + // 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(); + } + + // Retrieve and print space status and storage size for dset. + try { + space_status = H5.H5Dget_space_status(H5did); + } + catch (Exception e) { + e.printStackTrace(); + } + assertTrue("testH5Dget_space_status - H5.H5Dget_space_status: ", space_status == H5D_space_status.H5D_SPACE_STATUS_ALLOCATED.getCode()); + } + + @Test(expected = HDF5LibraryException.class) + public void testH5Dget_space_closed() throws Throwable { + long dataset_id = -1; + try { + dataset_id = H5.H5Dcreate(H5fid, "dset", + HDF5Constants.H5T_STD_I32BE, H5dsid, + HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); + } + catch (Throwable err) { + err.printStackTrace(); + fail("H5.H5Dcreate: " + err); + } + assertTrue("TestH5D.testH5Dget_space_closed: ", dataset_id >= 0); + H5.H5Dclose(dataset_id); + + H5.H5Dget_space(dataset_id); + } + + @Test + public void testH5Dget_space() { + long dataspace_id = -1; + _createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT); + + try { + dataspace_id = H5.H5Dget_space(H5did); + } + catch (Exception err) { + err.printStackTrace(); + fail("H5.H5Dget_space: " + err); + } + assertTrue("TestH5D.testH5Dget_space: ", dataspace_id >= 0); + + // End access to the dataspace and release resources used by it. + try { + if (dataspace_id >= 0) + H5.H5Sclose(dataspace_id); + } + catch (Exception err) { + err.printStackTrace(); + } + } + + @Test(expected = HDF5LibraryException.class) + public void testH5Dget_type_closed() throws Throwable { + long dataset_id = -1; + try { + dataset_id = H5.H5Dcreate(H5fid, "dset", + HDF5Constants.H5T_STD_I32BE, H5dsid, + HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); + } + catch (Throwable err) { + err.printStackTrace(); + fail("H5.H5Dcreate: " + err); + } + assertTrue("TestH5D.testH5Dget_type_closed: ", dataset_id >= 0); + H5.H5Dclose(dataset_id); + + H5.H5Dget_type(dataset_id); + } + + @Test + public void testH5Dget_type() { + long datatype_id = -1; + _createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT); + + try { + datatype_id = H5.H5Dget_type(H5did); + } + catch (Exception err) { + err.printStackTrace(); + fail("H5.H5Dget_type: " + err); + } + assertTrue("TestH5D.testH5Dget_type: ", datatype_id >= 0); + + // End access to the datatype and release resources used by it. + try { + if (datatype_id >= 0) + H5.H5Tclose(datatype_id); + } + catch (Exception err) { + err.printStackTrace(); + } + } + + @Test + public void testH5Dget_offset() { + int[][] write_dset_data = new int[DIM_X][DIM_Y]; + long dset_address = 0; + _createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT); + + try { + // Test dataset address. Should be undefined. + dset_address = H5.H5Dget_offset(H5did); + } + catch (HDF5LibraryException hdfex) { + ; + } + catch (Exception err) { + err.printStackTrace(); + fail("H5.H5Dget_offset: " + err); + } + // 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(); + } + + try { + // Test dataset address. + dset_address = H5.H5Dget_offset(H5did); + } + catch (Exception err) { + err.printStackTrace(); + fail("H5.H5Dget_offset: " + err); + } + + assertTrue("TestH5D.testH5Dget_offset: ", dset_address >= 0); + } + + @Test + public void testH5Dfill_null() { + int[] buf_data = new int[DIM_X*DIM_Y]; + + // Initialize memory buffer + for (int indx = 0; indx < DIM_X; indx++) + for (int jndx = 0; jndx < DIM_Y; jndx++) { + buf_data[(indx * DIM_Y) + jndx] = indx * jndx - jndx; + } + byte[] buf_array = HDFNativeData.intToByte(0, DIM_X*DIM_Y, buf_data); + + // Fill selection in memory + try { + H5.H5Dfill(null, HDF5Constants.H5T_NATIVE_UINT, buf_array, HDF5Constants.H5T_NATIVE_UINT, H5dsid); + } + catch (Exception err) { + err.printStackTrace(); + fail("H5.H5Dfill: " + err); + } + buf_data = HDFNativeData.byteToInt(buf_array); + + // Verify memory buffer the hard way + for (int indx = 0; indx < DIM_X; indx++) + for (int jndx = 0; jndx < DIM_Y; jndx++) + assertTrue("H5.H5Dfill: [" + indx+","+jndx + "] ", buf_data[(indx * DIM_Y) + jndx] == 0); + } + + @Test + public void testH5Dfill() { + int[] buf_data = new int[DIM_X*DIM_Y]; + byte[] fill_value = HDFNativeData.intToByte(254); + + // Initialize memory buffer + for (int indx = 0; indx < DIM_X; indx++) + for (int jndx = 0; jndx < DIM_Y; jndx++) { + buf_data[(indx * DIM_Y) + jndx] = indx * jndx - jndx; + } + byte[] buf_array = HDFNativeData.intToByte(0, DIM_X*DIM_Y, buf_data); + + // Fill selection in memory + try { + H5.H5Dfill(fill_value, HDF5Constants.H5T_NATIVE_UINT, buf_array, HDF5Constants.H5T_NATIVE_UINT, H5dsid); + } + catch (Exception err) { + err.printStackTrace(); + fail("H5.H5Dfill: " + err); + } + buf_data = HDFNativeData.byteToInt(buf_array); + + // Verify memory buffer the hard way + for (int indx = 0; indx < DIM_X; indx++) + for (int jndx = 0; jndx < DIM_Y; jndx++) + assertTrue("H5.H5Dfill: [" + indx+","+jndx + "] ", buf_data[(indx * DIM_Y) + jndx] == 254); + } + + @Test + public void testH5Diterate() { + final int SPACE_RANK = 2; + final int SPACE_FILL = 254; + + class H5D_iter_data implements H5D_iterate_t { + public int fill_value; /* The fill value to check */ + public long fill_curr_coord; /* Current coordinate to examine */ + public long[] fill_coords; /* Pointer to selection's coordinates */ + } + + H5D_iterate_t iter_data = new H5D_iter_data(); + + class H5D_iter_callback implements H5D_iterate_cb { + public int callback(byte[] elem_buf, long elem_id, int ndim, long[] point, H5D_iterate_t op_data) { + //Check value in current buffer location + int element = HDFNativeData.byteToInt(elem_buf, 0); + if(element != ((H5D_iter_data)op_data).fill_value) + return -1; + //Check number of dimensions + if(ndim != SPACE_RANK) + return(-1); + //Check Coordinates + long[] fill_coords = new long[2]; + fill_coords[0] = ((H5D_iter_data)op_data).fill_coords[(int) (2 * ((H5D_iter_data)op_data).fill_curr_coord)]; + fill_coords[1] = ((H5D_iter_data)op_data).fill_coords[(int) (2 * ((H5D_iter_data)op_data).fill_curr_coord) + 1]; + ((H5D_iter_data)op_data).fill_curr_coord++; + if(fill_coords[0] != point[0]) + return(-1); + if(fill_coords[1] != point[1]) + return(-1); + + return(0); + } + } + + int[] buf_data = new int[DIM_X*DIM_Y]; + byte[] fill_value = HDFNativeData.intToByte(SPACE_FILL); + + // Initialize memory buffer + for (int indx = 0; indx < DIM_X; indx++) + for (int jndx = 0; jndx < DIM_Y; jndx++) { + buf_data[(indx * DIM_Y) + jndx] = indx * jndx - jndx; + } + byte[] buf_array = HDFNativeData.intToByte(0, DIM_X*DIM_Y, buf_data); + + // Fill selection in memory + try { + H5.H5Dfill(fill_value, HDF5Constants.H5T_NATIVE_UINT, buf_array, HDF5Constants.H5T_NATIVE_UINT, H5dsid); + } + catch (Exception err) { + err.printStackTrace(); + fail("H5.H5Diterate: " + err); + } + + // Initialize the iterator structure + ((H5D_iter_data)iter_data).fill_value = SPACE_FILL; + ((H5D_iter_data)iter_data).fill_curr_coord = 0; + // Set the coordinates of the selection + ((H5D_iter_data)iter_data).fill_coords = new long[DIM_X*DIM_Y*SPACE_RANK]; /* Coordinates of selection */ + for (int indx = 0; indx < DIM_X; indx++) + for (int jndx = 0; jndx < DIM_Y; jndx++) { + ((H5D_iter_data)iter_data).fill_coords[2*(indx * DIM_Y + jndx)] = indx; + ((H5D_iter_data)iter_data).fill_coords[2*(indx * DIM_Y + jndx) + 1] = jndx; + } /* end for */ + + // Iterate through selection, verifying correct data + H5D_iterate_cb iter_cb = new H5D_iter_callback(); + int op_status = -1; + try { + op_status = H5.H5Diterate(buf_array, HDF5Constants.H5T_NATIVE_UINT, H5dsid, iter_cb, iter_data); + } + catch (Throwable err) { + err.printStackTrace(); + fail("H5.H5Diterate: " + err); + } + assertTrue("H5Diterate ", op_status == 0); + } + + @Test + public void testH5Diterate_write() { + final int SPACE_RANK = 2; + final int SPACE_FILL = 254; + + class H5D_iter_data implements H5D_iterate_t { + public int fill_value; /* The fill value to check */ + public long fill_curr_coord; /* Current coordinate to examine */ + public long[] fill_coords; /* Pointer to selection's coordinates */ + } + + H5D_iterate_t iter_data = new H5D_iter_data(); + + class H5D_iter_callback implements H5D_iterate_cb { + public int callback(byte[] elem_buf, long elem_id, int ndim, long[] point, H5D_iterate_t op_data) { + //Check value in current buffer location + int element = HDFNativeData.byteToInt(elem_buf, 0); + if(element != ((H5D_iter_data)op_data).fill_value) + return -1; + //Check number of dimensions + if(ndim != SPACE_RANK) + return(-1); + //Check Coordinates + long[] fill_coords = new long[2]; + fill_coords[0] = ((H5D_iter_data)op_data).fill_coords[(int) (2 * ((H5D_iter_data)op_data).fill_curr_coord)]; + fill_coords[1] = ((H5D_iter_data)op_data).fill_coords[(int) (2 * ((H5D_iter_data)op_data).fill_curr_coord) + 1]; + ((H5D_iter_data)op_data).fill_curr_coord++; + if(fill_coords[0] != point[0]) + return(-1); + if(fill_coords[1] != point[1]) + return(-1); + element -= 128; + byte[] new_elembuf = HDFNativeData.intToByte(element); + elem_buf[0] = new_elembuf[0]; + elem_buf[1] = new_elembuf[1]; + elem_buf[2] = new_elembuf[2]; + elem_buf[3] = new_elembuf[3]; + return(0); + } + } + + int[] buf_data = new int[DIM_X*DIM_Y]; + byte[] fill_value = HDFNativeData.intToByte(SPACE_FILL); + + // Initialize memory buffer + for (int indx = 0; indx < DIM_X; indx++) + for (int jndx = 0; jndx < DIM_Y; jndx++) { + buf_data[(indx * DIM_Y) + jndx] = indx * jndx - jndx; + } + byte[] buf_array = HDFNativeData.intToByte(0, DIM_X*DIM_Y, buf_data); + + // Fill selection in memory + try { + H5.H5Dfill(fill_value, HDF5Constants.H5T_NATIVE_UINT, buf_array, HDF5Constants.H5T_NATIVE_UINT, H5dsid); + } + catch (Exception err) { + err.printStackTrace(); + fail("H5.H5Diterate: " + err); + } + + // Initialize the iterator structure + ((H5D_iter_data)iter_data).fill_value = SPACE_FILL; + ((H5D_iter_data)iter_data).fill_curr_coord = 0; + // Set the coordinates of the selection + ((H5D_iter_data)iter_data).fill_coords = new long[DIM_X*DIM_Y*SPACE_RANK]; /* Coordinates of selection */ + for (int indx = 0; indx < DIM_X; indx++) + for (int jndx = 0; jndx < DIM_Y; jndx++) { + ((H5D_iter_data)iter_data).fill_coords[2*(indx * DIM_Y + jndx)] = indx; + ((H5D_iter_data)iter_data).fill_coords[2*(indx * DIM_Y + jndx) + 1] = jndx; + } /* end for */ + + // Iterate through selection, verifying correct data + H5D_iterate_cb iter_cb = new H5D_iter_callback(); + int op_status = -1; + try { + op_status = H5.H5Diterate(buf_array, HDF5Constants.H5T_NATIVE_UINT, H5dsid, iter_cb, iter_data); + } + catch (Throwable err) { + err.printStackTrace(); + fail("H5.H5Diterate: " + err); + } + assertTrue("H5Diterate ", op_status == 0); + + buf_data = HDFNativeData.byteToInt(buf_array); + + // Verify memory buffer the hard way + for (int indx = 0; indx < DIM_X; indx++) + for (int jndx = 0; jndx < DIM_Y; jndx++) + assertTrue("H5.H5Diterate: [" + indx+","+jndx + "] "+buf_data[(indx * DIM_Y) + jndx], buf_data[(indx * DIM_Y) + jndx] == 126); + } + + @Test + public void testH5Dvlen_get_buf_size() { + String[] str_data = { "Parting", "is such", "sweet", "sorrow.", + "Testing", "one", "two", "three.", + "Dog,", "man's", "best", "friend.", + "Diamonds", "are", "a", "girls!", + "S A", "T U R", "D A Y", "night", + "That's", "all", "folks", "!!!" }; + long vl_size = -1; /* Number of bytes used */ + long str_data_bytes = 0; + for (int idx = 0; idx < str_data.length; idx++) + str_data_bytes += str_data[idx].length() + 1; //Account for terminating null + + _createVLDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT); + + try { + if ((H5did >= 0) && (H5dtid >= 0)) + H5.H5Dwrite_VLStrings(H5did, H5dtid, + HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, str_data); + } + catch (Exception e) { + e.printStackTrace(); + } + try { + vl_size = H5.H5Dvlen_get_buf_size(H5did, H5dtid, H5dsid); + } + catch (Exception e) { + e.printStackTrace(); + } + assertTrue("H5Dvlen_get_buf_size " + vl_size + " == " + str_data_bytes, vl_size == str_data_bytes); + } + + @Test(expected = IllegalArgumentException.class) + public void testH5Dvlen_read_invalid_buffer() throws Throwable { + String[] str_data = { "Parting", "is such", "sweet", "sorrow.", + "Testing", "one", "two", "three.", + "Dog,", "man's", "best", "friend.", + "Diamonds", "are", "a", "girls!", + "S A", "T U R", "D A Y", "night", + "That's", "all", "folks", "!!!" }; + byte[] read_data = new byte[512]; + + _createVLDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT); + + try { + H5.H5Dwrite_VLStrings(H5did, H5dtid, + HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, str_data); + } + catch (Exception e) { + e.printStackTrace(); + } + + H5.H5Dread(H5did, H5dtid, + HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, read_data); + } + + @Test + public void testH5Dvlen_write_read() { + String[] str_wdata = { "Parting", "is such", "sweet", "sorrow.", + "Testing", "one", "two", "three.", + "Dog,", "man's", "best", "friend.", + "Diamonds", "are", "a", "girls!", + "S A", "T U R", "D A Y", "night", + "That's", "all", "folks", "!!!" }; + String[] str_rdata = new String[DIM_X * DIM_Y]; + + _createVLDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT); + + try { + if ((H5did >= 0) && (H5dtid >= 0)) + H5.H5Dwrite_VLStrings(H5did, H5dtid, + HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, str_wdata); + } + catch (Exception e) { + e.printStackTrace(); + } + try { + if ((H5did >= 0) && (H5dtid >= 0)) + H5.H5Dread_VLStrings(H5did, H5dtid, + HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, + HDF5Constants.H5P_DEFAULT, str_rdata); + } + catch (Exception e) { + e.printStackTrace(); + } + for (int v = 0; v < DIM_X * DIM_Y; v++) + assertTrue("testH5Dvlen_write_read " + str_wdata[v] + " == " + str_rdata[v], str_wdata[v] == str_wdata[v]); + } + +} |