1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465
|
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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 COPYING file, which can be found at the root of the source code *
* distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. *
* 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.assertEquals;
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.exceptions.HDF5Exception;
import hdf.hdf5lib.exceptions.HDF5LibraryException;
import org.junit.After;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Rule;
import org.junit.Test;
import org.junit.rules.TestName;
public class TestH5Pvirtual {
@Rule public TestName testname = new TestName();
private static final String H5_FILE = "vds.h5";
private static final String SRC_FILE[] = {
"v-0.h5",
"v-1.h5",
"v-2.h5"
};
private static final String SRC_DATASET[] = {
"A",
"B",
"C"
};
private static final int DIM_Y = 6;
private static final int VDSDIM_X = 4;
private static final int VDSDIM_Y = 6;
private static final int fill_value = -1;
long[] H5dims = { DIM_Y };
long[] VDSH5dims = { VDSDIM_X, VDSDIM_Y };
long H5fid = -1;
long H5dsid = -1;
long H5dssid = -1;
long H5dvsid = -1;
long H5did = -1;
long H5dcplid = -1;
long H5dapl_id = -1;
private final void _deleteFile(String filename) {
File file = new File(filename);
if (file.exists()) {
try {file.delete();} catch (SecurityException e) {}
}
}
private final long _createDataset(long fid, long dsid, String name, long dcpl, long dapl) {
long did = -1;
long space_id = -1;
long[] start = {0, 0};
long[] stride = null;
long[] count = {1, 1};
long[] block = {1, VDSDIM_Y};
try {
H5dssid = H5.H5Screate_simple(1, H5dims, null);
for (int i = 0; i < 3; i++) {
start[0] = i;
/* Select i-th row in the virtual dataset; selection in the source datasets is the same. */
H5.H5Sselect_hyperslab(dsid, HDF5Constants.H5S_SELECT_SET, start, stride, count, block);
H5.H5Pset_virtual(dcpl, dsid, SRC_FILE[i], SRC_DATASET[i], H5dssid);
}
did = H5.H5Dcreate(fid, name, HDF5Constants.H5T_NATIVE_INT, dsid,
HDF5Constants.H5P_DEFAULT, dcpl, dapl);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Dcreate: " + err);
}
assertTrue("TestH5Pvirtual._createDataset: ", did > 0);
return did;
}
private final void _createH5File(long fcpl, long fapl) {
int[] dset_data = new int[DIM_Y];
// Create source files and datasets
for (int i=0; i < 3; i++) {
long space_id = -1;
long dset_id = -1;
long file_id = -1;
for (int j = 0; j < DIM_Y; j++) dset_data[j] = i+1;
try {
file_id = H5.H5Fcreate(SRC_FILE[i], HDF5Constants.H5F_ACC_TRUNC,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
space_id = H5.H5Screate_simple(1, H5dims, null);
dset_id = H5.H5Dcreate(file_id, SRC_DATASET[i], HDF5Constants.H5T_NATIVE_INT, space_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
H5.H5Dwrite (dset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT,
dset_data);
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5Pvirtual.createH5file: " + err);
}
finally {
if (dset_id > 0)
try {H5.H5Dclose(dset_id);} catch (Exception ex) {}
if (space_id > 0)
try {H5.H5Sclose(space_id);} catch (Exception ex) {}
if (file_id > 0)
try {H5.H5Fclose(file_id);} catch (Exception ex) {}
}
}
try {
int[] fill_value = {-1};
H5fid = H5.H5Fcreate(H5_FILE, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
H5dsid = H5.H5Screate_simple(2, VDSH5dims, null);
H5dcplid = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE);
H5.H5Pset_fill_value(H5dcplid, HDF5Constants.H5T_NATIVE_INT, fill_value);
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5Pvirtual.createH5file: " + err);
}
assertTrue("TestH5Pvirtual.createH5file: H5.H5Fcreate: ", H5fid > 0);
assertTrue("TestH5Pvirtual.createH5file: H5.H5Screate_simple: ", H5dsid > 0);
assertTrue("TestH5Pvirtual.createH5file: H5.H5Pcreate: ", H5dcplid > 0);
try {
H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
}
catch (Throwable err) {
err.printStackTrace();
}
}
@Before
public void createH5file()
throws NullPointerException, HDF5Exception {
assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0);
System.out.print(testname.getMethodName());
_createH5File(HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
H5dapl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_ACCESS);
assertTrue("TestH5Pvirtual.createH5file: H5.H5Pcreate: ", H5dapl_id > 0);
}
@After
public void deleteH5file() throws HDF5LibraryException {
if (H5dapl_id > 0)
try {H5.H5Pclose(H5dapl_id);} catch (Exception ex) {}
if (H5dcplid > 0)
try {H5.H5Pclose(H5dcplid);} catch (Exception ex) {}
if (H5dsid > 0)
try {H5.H5Sclose(H5dsid);} catch (Exception ex) {}
if (H5fid > 0)
try {H5.H5Fclose(H5fid);} catch (Exception ex) {}
for (int i = 0; i < 3; i++) {
_deleteFile(SRC_FILE[i]);
}
_deleteFile(H5_FILE);
System.out.println();
}
@Test
public void testH5Pvirtual_storage() {
int layout = -1;
H5did = _createDataset(H5fid, H5dsid, "VDS", H5dcplid, H5dapl_id);
try {
layout = H5.H5Pget_layout (H5dcplid);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Pget_layout: " + err);
}
finally {
if (H5dssid > 0)
try {H5.H5Sclose(H5dssid);} catch (Exception ex) {}
if (H5did > 0)
try {H5.H5Dclose(H5did);} catch (Exception ex) {}
}
assertTrue("testH5Pvirtual_storage", HDF5Constants.H5D_VIRTUAL == layout);
}
@Test
public void testH5Pget_virtual_count() {
long num_map = -1;
H5did = _createDataset(H5fid, H5dsid, "VDS", H5dcplid, H5dapl_id);
try {
num_map = H5.H5Pget_virtual_count(H5dcplid);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Pget_virtual_count: " + err);
}
finally {
if (H5dssid > 0)
try {H5.H5Sclose(H5dssid);} catch (Exception ex) {}
if (H5did > 0)
try {H5.H5Dclose(H5did);} catch (Exception ex) {}
}
assertTrue("testH5Pget_virtual_count: "+num_map, num_map >= 0);
assertEquals(3, num_map);
}
@Test
public void testH5Pget_source_filename() throws Throwable {
String filename = null;
H5did = _createDataset(H5fid, H5dsid, "VDS", H5dcplid, H5dapl_id);
try {
filename = (H5.H5Pget_virtual_filename (H5dcplid, 2));
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Pget_virtual_filename: " + err);
}
finally {
if (H5dssid > 0)
try {H5.H5Sclose(H5dssid);} catch (Exception ex) {}
if (H5did > 0)
try {H5.H5Dclose(H5did);} catch (Exception ex) {}
}
assertTrue("testH5Pget_source_filename: "+filename, filename.compareTo("v-2.h5") == 0);
}
@Test
public void testH5Pget_source_datasetname() throws Throwable {
String datasetname = null;
H5did = _createDataset(H5fid, H5dsid, "VDS", H5dcplid, H5dapl_id);
try {
datasetname = H5.H5Pget_virtual_dsetname (H5dcplid, 1);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Pget_virtual_dsetname: " + err);
}
finally {
if (H5dssid > 0)
try {H5.H5Sclose(H5dssid);} catch (Exception ex) {}
if (H5did > 0)
try {H5.H5Dclose(H5did);} catch (Exception ex) {}
}
assertTrue("testH5Pget_source_datasetname: "+datasetname, datasetname.compareTo("B") == 0);
}
@Test
public void testH5Pget_selection_source_dataset() throws Throwable {
long src_space = -1;
long src_selection = -1;
H5did = _createDataset(H5fid, H5dsid, "VDS", H5dcplid, H5dapl_id);
try {
src_space = H5.H5Pget_virtual_srcspace (H5dcplid, 0);
src_selection = H5.H5Sget_select_type(src_space);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Pget_selection_source_dataset: " + err);
}
finally {
if (src_space > 0)
try {H5.H5Sclose(src_space);} catch (Exception ex) {}
if (H5dssid > 0)
try {H5.H5Sclose(H5dssid);} catch (Exception ex) {}
if (H5did > 0)
try {H5.H5Dclose(H5did);} catch (Exception ex) {}
}
assertTrue("testH5Pget_selection_source_dataset", src_selection == HDF5Constants.H5S_SEL_ALL);
}
@Test
public void testH5Pget_mapping_parameters() {
long num_map = -1;
H5did = _createDataset(H5fid, H5dsid, "VDS", H5dcplid, H5dapl_id);
try {
try {
num_map = H5.H5Pget_virtual_count(H5dcplid);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Pget_virtual_count: " + err);
}
for (int i = 0; i < num_map; i++) {
int vselection = -1;
long vspace = -1;
long nblocks; // Number of hyperslab blocks
long blocks[] = {-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}; // List of blocks
long[] start = {i, 0};
long[] stride = {1, 1};
long[] count = {1, 1};
long[] block = {1, VDSDIM_Y};
long q_start[] = new long[2];
long q_stride[] = new long[2];
long q_count[] = new long[2];
long q_block[] = new long[2];
boolean is_regular = false;
try {
try {
vspace = H5.H5Pget_virtual_vspace (H5dcplid, i);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Pget_virtual_vspace: " + err);
}
try {
vselection = H5.H5Sget_select_type(vspace);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Sget_select_type: " + err);
}
assertTrue("testH5Pget_mapping_parameters["+i+"]", vselection == HDF5Constants.H5S_SEL_HYPERSLABS);
// Verify that there is only one block
nblocks = H5.H5Sget_select_hyper_nblocks(vspace);
assertTrue("H5Sget_select_hyper_nblocks", nblocks == 1);
// Retrieve the block defined
H5.H5Sget_select_hyper_blocklist(vspace, 0, nblocks, blocks);
// Verify that the correct block is defined
assertTrue("H5.H5Sget_select_hyper_blocklist["+i+"] [0]: "+blocks[0], start[0] == blocks[0]);
assertTrue("H5.H5Sget_select_hyper_blocklist["+i+"] [1]: "+blocks[1], start[1] == blocks[1]);
assertTrue("H5.H5Sget_select_hyper_blocklist["+i+"] [2]: "+blocks[2], (block[0]-1+i) == blocks[2]);
assertTrue("H5.H5Sget_select_hyper_blocklist["+i+"] [3]: "+blocks[3], (block[1]-1) == blocks[3]);
// We also can use new APIs to get start, stride, count and block
is_regular = H5.H5Sis_regular_hyperslab(vspace);
assertTrue("H5.H5Sis_regular_hyperslab", is_regular);
H5.H5Sget_regular_hyperslab (vspace, q_start, q_stride, q_count, q_block);
// Verify the hyperslab parameters
for(int u = 0; u < 2; u++) {
assertTrue("H5Sget_regular_hyperslab, start", start[u] == q_start[u]);
assertTrue("H5Sget_regular_hyperslab, stride", stride[u] == q_stride[u]);
assertTrue("H5Sget_regular_hyperslab, count", count[u] == q_count[u]);
assertTrue("H5Sget_regular_hyperslab, block", block[u] == q_block[u]);
}
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.testH5Pget_mapping_parameters: " + err);
}
finally {
if (vspace > 0)
try {H5.H5Sclose(vspace);} catch (Exception ex) {}
}
}
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Pget_mapping_parameters: " + err);
}
finally {
if (H5dssid > 0)
try {H5.H5Sclose(H5dssid);} catch (Exception ex) {}
if (H5did > 0)
try {H5.H5Dclose(H5did);} catch (Exception ex) {}
}
}
@Test
public void testH5Pset_get_virtual_view() {
int ret_val = -1;
H5did = _createDataset(H5fid, H5dsid, "VDS", H5dcplid, H5dapl_id);
try {
ret_val = H5.H5Pget_virtual_view(H5dapl_id);
assertTrue("H5Pget_virtual_view", ret_val >= 0);
assertEquals(HDF5Constants.H5D_VDS_LAST_AVAILABLE, ret_val);
H5.H5Pset_virtual_view(H5dapl_id, HDF5Constants.H5D_VDS_FIRST_MISSING);
ret_val = H5.H5Pget_virtual_view(H5dapl_id);
assertTrue("H5Pget_virtual_view", ret_val >= 0);
assertEquals(HDF5Constants.H5D_VDS_FIRST_MISSING, ret_val);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Pset_get_virtual_view: " + err);
}
finally {
if (H5dssid > 0)
try {H5.H5Sclose(H5dssid);} catch (Exception ex) {}
if (H5did > 0)
try {H5.H5Dclose(H5did);} catch (Exception ex) {}
}
}
@Test
public void testH5Pset_get_virtual_printf_gap() {
long ret_val = -1;
H5did = _createDataset(H5fid, H5dsid, "VDS", H5dcplid, H5dapl_id);
try {
ret_val = H5.H5Pget_virtual_printf_gap(H5dapl_id);
assertTrue("H5Pget_virtual_printf_gap", ret_val >= 0);
assertEquals(0, ret_val);
H5.H5Pset_virtual_printf_gap(H5dapl_id, 2);
ret_val = H5.H5Pget_virtual_printf_gap(H5dapl_id);
assertTrue("H5Pget_virtual_printf_gap", ret_val >= 0);
assertEquals(2, ret_val);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5Pset_get_virtual_printf_gap: " + err);
}
finally {
if (H5dssid > 0)
try {H5.H5Sclose(H5dssid);} catch (Exception ex) {}
if (H5did > 0)
try {H5.H5Dclose(H5did);} catch (Exception ex) {}
}
}
@Test
public void testH5Pset_virtual_prefix() {
String prefix = "tmp";
try {
H5.H5Pset_virtual_prefix(H5dapl_id, prefix);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5Pset_virtual_prefix: " + err);
}
}
@Test(expected = NullPointerException.class)
public void testH5Pset_virtual_prefix_null() throws Throwable{
H5.H5Pset_virtual_prefix(H5dapl_id, null);
}
@Test
public void testH5Pget_virtual_prefix() {
String prefix = "tmp";
String pre = "";
try {
H5.H5Pset_virtual_prefix(H5dapl_id, prefix);
pre = H5.H5Pget_virtual_prefix(H5dapl_id);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5Pget_virtual_prefix: " + err);
}
assertTrue("The prefix: ", prefix.equals(pre));
}
}
|