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hdf5/java/test/TestH5A.java
Allen Byrne 2376723d4a
Develop jni trans (#2266) 
* Add compound and refactor out atomic types

* Add Array String tests back

* Convert Attribute version of compound example

* Update transfer atom8ic read to return object
2022-12-05 22:29:42 -06:00

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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* 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://www.hdfgroup.org/licenses. *
* 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.assertNotNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import java.io.File;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import hdf.hdf5lib.H5;
import hdf.hdf5lib.HDF5Constants;
import hdf.hdf5lib.callbacks.H5A_iterate_cb;
import hdf.hdf5lib.callbacks.H5A_iterate_t;
import hdf.hdf5lib.exceptions.HDF5Exception;
import hdf.hdf5lib.exceptions.HDF5LibraryException;
import hdf.hdf5lib.structs.H5A_info_t;
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 TestH5A {
@Rule
public TestName testname = new TestName();
private static final String H5_FILE = "testA.h5";
private static final int DIM_X = 4;
private static final int DIM_Y = 6;
long H5fid = HDF5Constants.H5I_INVALID_HID;
long H5dsid = HDF5Constants.H5I_INVALID_HID;
long H5atid = HDF5Constants.H5I_INVALID_HID;
long H5did = HDF5Constants.H5I_INVALID_HID;
long[] H5dims = {DIM_X, DIM_Y};
long type_id = HDF5Constants.H5I_INVALID_HID;
long space_id = HDF5Constants.H5I_INVALID_HID;
long lapl_id = HDF5Constants.H5I_INVALID_HID;
long aapl_id = HDF5Constants.H5I_INVALID_HID;
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 dapl)
{
long did = HDF5Constants.H5I_INVALID_HID;
try {
did = 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("TestH5A._createDataset: ", did > 0);
return did;
}
@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);
assertTrue("TestH5A.createH5file: H5.H5Fcreate: ", H5fid > 0);
H5dsid = H5.H5Screate_simple(2, H5dims, null);
assertTrue("TestH5A.createH5file: H5.H5Screate_simple: ", H5dsid > 0);
H5did = _createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT);
assertTrue("TestH5A.createH5file: _createDataset: ", H5did > 0);
space_id = H5.H5Screate(HDF5Constants.H5S_NULL);
assertTrue(space_id > 0);
lapl_id = H5.H5Pcreate(HDF5Constants.H5P_LINK_ACCESS);
assertTrue(lapl_id > 0);
aapl_id = H5.H5Pcreate(HDF5Constants.H5P_ATTRIBUTE_ACCESS);
assertTrue(aapl_id > 0);
type_id = H5.H5Tenum_create(HDF5Constants.H5T_STD_I32LE);
assertTrue(type_id > 0);
int status = H5.H5Tenum_insert(type_id, "test", 1);
assertTrue(status >= 0);
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5A.createH5file: " + err);
}
H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
}
@After
public void deleteH5file() throws HDF5LibraryException
{
if (H5dsid > 0)
try {
H5.H5Sclose(H5dsid);
}
catch (Exception ex) {
}
if (H5did > 0)
try {
H5.H5Dclose(H5did);
}
catch (Exception ex) {
}
if (H5fid > 0)
try {
H5.H5Fclose(H5fid);
}
catch (Exception ex) {
}
if (H5atid > 0)
try {
H5.H5Tclose(H5atid);
}
catch (Exception ex) {
}
if (type_id > 0)
try {
H5.H5Tclose(type_id);
}
catch (Exception ex) {
}
if (space_id > 0)
try {
H5.H5Sclose(space_id);
}
catch (Exception ex) {
}
if (lapl_id > 0)
try {
H5.H5Pclose(lapl_id);
}
catch (Exception ex) {
}
if (aapl_id > 0)
try {
H5.H5Pclose(aapl_id);
}
catch (Exception ex) {
}
_deleteFile(H5_FILE);
System.out.println();
}
@Test
public void testH5Acreate2()
{
long attr_id = HDF5Constants.H5I_INVALID_HID;
try {
attr_id = H5.H5Acreate(H5did, "dset", type_id, space_id, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT);
assertTrue("testH5Acreate2", attr_id >= 0);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Acreate2: " + err);
}
finally {
if (attr_id > 0)
try {
H5.H5Aclose(attr_id);
}
catch (Exception ex) {
}
}
}
@Test(expected = HDF5LibraryException.class)
public void testH5Acreate2_invalidobject() throws Throwable
{
H5.H5Acreate(H5dsid, "dset", type_id, space_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
}
@Test(expected = NullPointerException.class)
public void testH5Acreate2_nullname() throws Throwable
{
H5.H5Acreate(H5did, null, type_id, space_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
}
@Test
public void testH5Aopen()
{
String attr_name = "dset";
long attribute_id = HDF5Constants.H5I_INVALID_HID;
long attr_id = HDF5Constants.H5I_INVALID_HID;
try {
attr_id = H5.H5Acreate(H5did, attr_name, type_id, space_id, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT);
// Opening the existing attribute, attr_name(Created by H5ACreate2)
// attached to an object identifier.
attribute_id = H5.H5Aopen(H5did, attr_name, HDF5Constants.H5P_DEFAULT);
assertTrue("testH5Aopen: H5Aopen", attribute_id >= 0);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Aopen: " + err);
}
finally {
if (attr_id > 0)
try {
H5.H5Aclose(attr_id);
}
catch (Exception ex) {
}
if (attribute_id > 0)
try {
H5.H5Aclose(attribute_id);
}
catch (Exception ex) {
}
}
}
@Test(expected = HDF5LibraryException.class)
public void testH5Aopen_invalidname() throws Throwable
{
H5.H5Aopen(H5did, "attr_name", HDF5Constants.H5P_DEFAULT);
}
@Test
public void testH5Aopen_by_idx()
{
long loc_id = H5did;
String obj_name = ".";
int idx_type = HDF5Constants.H5_INDEX_CRT_ORDER;
int order = HDF5Constants.H5_ITER_INC;
long n = 0;
long attr_id = HDF5Constants.H5I_INVALID_HID;
long attribute_id = HDF5Constants.H5I_INVALID_HID;
try {
attr_id = H5.H5Acreate(H5did, "file", type_id, space_id, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT);
// Opening the existing attribute, obj_name(Created by H5ACreate2)
// by index, attached to an object identifier.
attribute_id = H5.H5Aopen_by_idx(H5did, ".", HDF5Constants.H5_INDEX_CRT_ORDER,
HDF5Constants.H5_ITER_INC, 0, aapl_id, lapl_id);
assertTrue("testH5Aopen_by_idx: H5Aopen_by_idx", attribute_id >= 0);
// Negative test- Error should be thrown when H5Aopen_by_idx is
// called
// with n=5 and we do not have 5 attributes created.
try {
n = 5;
H5.H5Aopen_by_idx(loc_id, obj_name, idx_type, order, n, aapl_id, lapl_id);
fail("Negative Test Failed:- Error not Thrown when n is invalid.");
}
catch (AssertionError err) {
fail("H5.H5Aopen_by_idx: " + err);
}
catch (HDF5LibraryException err) {
}
// Negative test- Error should be thrown when H5Aopen_by_idx is
// called
// with an invalid object name(which hasn't been created).
try {
n = 0;
obj_name = "file";
H5.H5Aopen_by_idx(loc_id, obj_name, idx_type, order, n, aapl_id, lapl_id);
fail("Negative Test Failed:- Error not Thrown when attribute name is invalid.");
}
catch (AssertionError err) {
fail("H5.H5Aopen_by_idx: " + err);
}
catch (HDF5LibraryException err) {
}
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Aopen_by_idx: " + err);
}
finally {
if (attr_id > 0)
try {
H5.H5Aclose(attr_id);
}
catch (Exception ex) {
}
if (attribute_id > 0)
try {
H5.H5Aclose(attribute_id);
}
catch (Exception ex) {
}
}
}
@Test
public void testH5Acreate_by_name()
{
String obj_name = ".";
String attr_name = "DATASET";
long attribute_id = HDF5Constants.H5I_INVALID_HID;
boolean bool_val = false;
try {
attribute_id = H5.H5Acreate_by_name(H5fid, obj_name, attr_name, type_id, space_id,
HDF5Constants.H5P_DEFAULT, aapl_id, lapl_id);
assertTrue("testH5Acreate_by_name: H5Acreate_by_name", attribute_id >= 0);
// Check if the name of attribute attached to the object specified
// by loc_id and obj_name exists.It should be true.
bool_val = H5.H5Aexists_by_name(H5fid, obj_name, attr_name, lapl_id);
assertTrue("testH5Acreate_by_name: H5Aexists_by_name", bool_val == true);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Acreate_by_name " + err);
}
finally {
if (attribute_id > 0)
try {
H5.H5Aclose(attribute_id);
}
catch (Exception ex) {
}
}
}
@Test
public void testH5Arename() throws Throwable, HDF5LibraryException, NullPointerException
{
long loc_id = H5fid;
String old_attr_name = "old";
String new_attr_name = "new";
long attr_id = HDF5Constants.H5I_INVALID_HID;
int ret_val = -1;
boolean bool_val = false;
try {
attr_id =
H5.H5Acreate(loc_id, old_attr_name, type_id, space_id, HDF5Constants.H5P_DEFAULT, aapl_id);
ret_val = H5.H5Arename(loc_id, old_attr_name, new_attr_name);
// Check the return value.It should be non negative.
assertTrue("testH5Arename: H5Arename", ret_val >= 0);
// Check if the new name of attribute attached to the object
// specified by loc_id and obj_name exists.It should be true.
bool_val = H5.H5Aexists(loc_id, new_attr_name);
assertTrue("testH5Arename: H5Aexists", bool_val == true);
// Check if the old name of attribute attached to the object
// specified by loc_id and obj_name exists. It should equal false.
bool_val = H5.H5Aexists(loc_id, old_attr_name);
assertEquals(bool_val, false);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Arename " + err);
}
finally {
if (attr_id > 0)
try {
H5.H5Aclose(attr_id);
}
catch (Exception ex) {
}
}
}
@Test
public void testH5Arename_by_name()
{
long loc_id = H5fid;
String obj_name = ".";
String old_attr_name = "old";
String new_attr_name = "new";
long attr_id = HDF5Constants.H5I_INVALID_HID;
int ret_val = -1;
boolean bool_val = false;
try {
attr_id = H5.H5Acreate_by_name(loc_id, obj_name, old_attr_name, type_id, space_id,
HDF5Constants.H5P_DEFAULT, aapl_id, lapl_id);
ret_val = H5.H5Arename_by_name(loc_id, obj_name, old_attr_name, new_attr_name, lapl_id);
// Check the return value.It should be non negative.
assertTrue("testH5Arename_by_name: H5Arename_by_name", ret_val >= 0);
// Check if the new name of attribute attached to the object
// specified by loc_id and obj_name exists.It should be true.
bool_val = H5.H5Aexists_by_name(loc_id, obj_name, new_attr_name, lapl_id);
assertTrue("testH5Arename_by_name: H5Aexists_by_name", bool_val == true);
// Check if the old name of attribute attached to the object
// specified by loc_id and obj_name exists. It should equal false.
bool_val = H5.H5Aexists_by_name(loc_id, obj_name, old_attr_name, lapl_id);
assertEquals(bool_val, false);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Arename_by_name " + err);
}
finally {
if (attr_id > 0)
try {
H5.H5Aclose(attr_id);
}
catch (Exception ex) {
}
}
}
@Test
public void testH5Aget_name()
{
String obj_name = ".";
String attr_name = "DATASET1";
String ret_name = null;
long attribute_id = HDF5Constants.H5I_INVALID_HID;
try {
attribute_id = H5.H5Acreate_by_name(H5fid, obj_name, attr_name, type_id, space_id,
HDF5Constants.H5P_DEFAULT, aapl_id, lapl_id);
assertTrue("testH5Aget_name: H5Acreate_by_name ", attribute_id > 0);
ret_name = H5.H5Aget_name(attribute_id);
assertEquals(ret_name, attr_name);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Aget_name " + err);
}
finally {
if (attribute_id > 0)
try {
H5.H5Aclose(attribute_id);
}
catch (Exception ex) {
}
}
}
@Test
public void testH5Aget_name_by_idx()
{
long loc_id = H5fid;
String obj_name = ".";
String attr_name = "DATASET1", attr2_name = "DATASET2";
String ret_name = null;
int idx_type = HDF5Constants.H5_INDEX_NAME;
int order = HDF5Constants.H5_ITER_INC;
int n = 0;
long attr1_id = HDF5Constants.H5I_INVALID_HID;
long attr2_id = HDF5Constants.H5I_INVALID_HID;
try {
attr1_id = H5.H5Acreate_by_name(loc_id, obj_name, attr_name, type_id, space_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
attr2_id = H5.H5Acreate_by_name(loc_id, obj_name, attr2_name, type_id, space_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
// getting the 1st attribute name(n=0).
ret_name = H5.H5Aget_name_by_idx(loc_id, obj_name, idx_type, order, n, lapl_id);
assertFalse("H5Aget_name_by_idx ", ret_name == null);
assertEquals(ret_name, attr_name);
// getting the second attribute name(n=1)
ret_name = H5.H5Aget_name_by_idx(loc_id, obj_name, idx_type, order, 1, lapl_id);
assertFalse("H5Aget_name_by_idx ", ret_name == null);
assertEquals(ret_name, attr2_name);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Aget_name_by_idx " + err);
}
finally {
if (attr1_id > 0)
try {
H5.H5Aclose(attr1_id);
}
catch (Exception ex) {
}
if (attr2_id > 0)
try {
H5.H5Aclose(attr2_id);
}
catch (Exception ex) {
}
}
}
@Test
public void testH5Aget_storage_size()
{
long attr_id = HDF5Constants.H5I_INVALID_HID;
long attr_size = HDF5Constants.H5I_INVALID_HID;
try {
attr_id = H5.H5Acreate(H5did, "dset", type_id, space_id, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT);
attr_size = H5.H5Aget_storage_size(attr_id);
assertTrue("The size of attribute is :", attr_size == 0);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Aget_storage_size: " + err);
}
finally {
if (attr_id > 0)
try {
H5.H5Aclose(attr_id);
}
catch (Exception ex) {
}
}
}
@Test
public void testH5Aget_info()
{
H5A_info_t attr_info = null;
long attribute_id = HDF5Constants.H5I_INVALID_HID;
long attr_id = HDF5Constants.H5I_INVALID_HID;
try {
attr_id = H5.H5Acreate(H5did, "dset", type_id, space_id, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT);
attribute_id = H5.H5Aopen(H5did, "dset", HDF5Constants.H5P_DEFAULT);
// Calling H5Aget_info with attribute_id returned from H5Aopen.
attr_info = H5.H5Aget_info(attribute_id);
assertFalse("H5Aget_info ", attr_info == null);
assertTrue("Corder_Valid should be false", attr_info.corder_valid == false);
assertTrue("Character set used for attribute name",
attr_info.cset == HDF5Constants.H5T_CSET_ASCII);
assertTrue("Corder ", attr_info.corder == 0);
assertEquals(attr_info.data_size, H5.H5Aget_storage_size(attr_id));
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Aget_info: " + err);
}
finally {
if (attr_id > 0)
try {
H5.H5Aclose(attr_id);
}
catch (Exception ex) {
}
if (attribute_id > 0)
try {
H5.H5Aclose(attribute_id);
}
catch (Exception ex) {
}
}
}
@Test
public void testH5Aget_info1()
{
H5A_info_t attr_info = null;
long attribute_id = HDF5Constants.H5I_INVALID_HID;
long attr_id = HDF5Constants.H5I_INVALID_HID;
int order = HDF5Constants.H5_ITER_INC;
try {
attr_id = H5.H5Acreate(H5did, ".", type_id, space_id, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT);
attribute_id = H5.H5Aopen_by_idx(H5did, ".", HDF5Constants.H5_INDEX_CRT_ORDER, order, 0,
HDF5Constants.H5P_DEFAULT, lapl_id);
// Calling H5Aget_info with attribute_id returned from
// H5Aopen_by_idx.
attr_info = H5.H5Aget_info(attribute_id);
assertFalse("H5Aget_info ", attr_info == null);
assertTrue("Corder_Valid should be true", attr_info.corder_valid == true);
assertTrue("Character set", attr_info.cset == HDF5Constants.H5T_CSET_ASCII);
assertTrue("Corder ", attr_info.corder == 0);
assertEquals(attr_info.data_size, H5.H5Aget_storage_size(attr_id));
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Aget_info1: " + err);
}
finally {
if (attr_id > 0)
try {
H5.H5Aclose(attr_id);
}
catch (Exception ex) {
}
if (attribute_id > 0)
try {
H5.H5Aclose(attribute_id);
}
catch (Exception ex) {
}
}
}
@Test
public void testH5Aget_info_by_idx()
{
long attr_id = HDF5Constants.H5I_INVALID_HID;
long attr2_id = HDF5Constants.H5I_INVALID_HID;
;
H5A_info_t attr_info = null;
try {
attr_id = H5.H5Acreate(H5did, "dset1", type_id, space_id, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT);
attr2_id = H5.H5Acreate(H5did, "dataset2", type_id, space_id, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT);
// Verify info for 1st attribute, in increasing creation order
attr_info = H5.H5Aget_info_by_idx(H5did, ".", HDF5Constants.H5_INDEX_CRT_ORDER,
HDF5Constants.H5_ITER_INC, 0, lapl_id);
assertNotNull(attr_info);
assertTrue("Corder ", attr_info.corder ==
0); // should equal 0 as this is the order of 1st attribute created.
assertEquals(attr_info.data_size, H5.H5Aget_storage_size(attr_id));
// Verify info for 2nd attribute, in increasing creation order
attr_info = H5.H5Aget_info_by_idx(H5did, ".", HDF5Constants.H5_INDEX_CRT_ORDER,
HDF5Constants.H5_ITER_INC, 1, lapl_id);
assertNotNull(attr_info);
assertTrue("Corder", attr_info.corder == 1);
assertEquals(attr_info.data_size, H5.H5Aget_storage_size(attr2_id));
// verify info for 2nd attribute, in decreasing creation order
attr_info = H5.H5Aget_info_by_idx(H5did, ".", HDF5Constants.H5_INDEX_CRT_ORDER,
HDF5Constants.H5_ITER_DEC, 0, lapl_id);
assertNotNull(attr_info);
assertTrue("Corder", attr_info.corder ==
1); // should equal 1 as this is the order of 2nd attribute created.
// verify info for 1st attribute, in decreasing creation order
attr_info = H5.H5Aget_info_by_idx(H5did, ".", HDF5Constants.H5_INDEX_CRT_ORDER,
HDF5Constants.H5_ITER_DEC, 1, lapl_id);
assertNotNull(attr_info);
assertTrue("Corder", attr_info.corder ==
0); // should equal 0 as this is the order of 1st attribute created.
// verify info for 1st attribute, in increasing name order
attr_info = H5.H5Aget_info_by_idx(H5did, ".", HDF5Constants.H5_INDEX_NAME,
HDF5Constants.H5_ITER_INC, 1, lapl_id);
assertNotNull(attr_info);
assertTrue("Corder", attr_info.corder ==
0); // should equal 0 as this is the order of 1st attribute created.
// verify info for 2nd attribute, in decreasing name order
attr_info = H5.H5Aget_info_by_idx(H5did, ".", HDF5Constants.H5_INDEX_NAME,
HDF5Constants.H5_ITER_DEC, 1, lapl_id);
assertNotNull(attr_info);
assertTrue("Corder", attr_info.corder ==
1); // should equal 1 as this is the order of 2nd attribute created.
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Aget_info_by_idx:" + err);
}
finally {
if (attr_id > 0)
try {
H5.H5Aclose(attr_id);
}
catch (Exception ex) {
}
if (attr2_id > 0)
try {
H5.H5Aclose(attr2_id);
}
catch (Exception ex) {
}
}
}
@Test
public void testH5Aget_info_by_name()
{
long attr_id = HDF5Constants.H5I_INVALID_HID;
H5A_info_t attr_info = null;
String obj_name = ".";
String attr_name = "DATASET";
try {
attr_id = H5.H5Acreate_by_name(H5fid, obj_name, attr_name, type_id, space_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
attr_info = H5.H5Aget_info_by_name(H5fid, obj_name, attr_name, lapl_id);
assertNotNull(attr_info);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Aget_info_by_name:" + err);
}
finally {
if (attr_id > 0)
try {
H5.H5Aclose(attr_id);
}
catch (Exception ex) {
}
}
}
@Test
public void testH5Adelete_by_name()
{
long attr_id = HDF5Constants.H5I_INVALID_HID;
int ret_val = -1;
boolean bool_val = false;
boolean exists = false;
try {
attr_id = H5.H5Acreate_by_name(H5fid, ".", "DATASET", type_id, space_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
ret_val = H5.H5Adelete_by_name(H5fid, ".", "DATASET", lapl_id);
assertTrue("H5Adelete_by_name", ret_val >= 0);
// Check if the Attribute still exists.
bool_val = H5.H5Aexists_by_name(H5fid, ".", "DATASET", lapl_id);
assertFalse("testH5Adelete_by_name: H5Aexists_by_name", bool_val);
exists = H5.H5Aexists(H5fid, "DATASET");
assertFalse("testH5Adelete_by_name: H5Aexists ", exists);
// Negative test. Error thrown when we try to delete an attribute
// that has already been deleted.
try {
ret_val = H5.H5Adelete_by_name(H5fid, ".", "DATASET", lapl_id);
fail("Negative Test Failed: Error Not thrown.");
}
catch (AssertionError err) {
fail("H5.H5Adelete_by_name: " + err);
}
catch (HDF5LibraryException err) {
}
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Adelete_by_name " + err);
}
finally {
if (attr_id > 0)
try {
H5.H5Aclose(attr_id);
}
catch (Exception ex) {
}
}
}
@Test
public void testH5Aexists()
{
boolean exists = false;
long attr_id = HDF5Constants.H5I_INVALID_HID;
long attribute_id = HDF5Constants.H5I_INVALID_HID;
try {
exists = H5.H5Aexists(H5fid, "None");
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Aexists: " + err);
}
assertFalse("H5Aexists ", exists);
try {
attr_id = H5.H5Acreate(H5fid, "dset", type_id, space_id, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT);
exists = H5.H5Aexists(H5fid, "dset");
assertTrue("H5Aexists ", exists);
attribute_id =
H5.H5Acreate_by_name(H5fid, ".", "attribute", type_id, space_id, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT, lapl_id);
exists = H5.H5Aexists(H5fid, "attribute");
assertTrue("H5Aexists ", exists);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Aexists: " + err);
}
finally {
if (attr_id > 0)
try {
H5.H5Aclose(attr_id);
}
catch (Exception ex) {
}
if (attribute_id > 0)
try {
H5.H5Aclose(attribute_id);
}
catch (Exception ex) {
}
}
}
@Test
public void testH5Adelete_by_idx_order()
{
boolean exists = false;
long attr1_id = HDF5Constants.H5I_INVALID_HID;
long attr2_id = HDF5Constants.H5I_INVALID_HID;
long attr3_id = HDF5Constants.H5I_INVALID_HID;
long attr4_id = HDF5Constants.H5I_INVALID_HID;
try {
attr1_id = H5.H5Acreate_by_name(H5fid, ".", "attribute1", type_id, space_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
attr2_id = H5.H5Acreate_by_name(H5fid, ".", "attribute2", type_id, space_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
attr3_id = H5.H5Acreate_by_name(H5fid, ".", "attribute3", type_id, space_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
attr4_id = H5.H5Acreate_by_name(H5fid, ".", "attribute4", type_id, space_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
H5.H5Adelete_by_idx(H5fid, ".", HDF5Constants.H5_INDEX_CRT_ORDER, HDF5Constants.H5_ITER_INC, 3,
lapl_id);
exists = H5.H5Aexists(H5fid, "attribute4");
assertFalse("H5Adelete_by_idx: H5Aexists", exists);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Adelete_by_idx: " + err);
}
finally {
if (attr1_id > 0)
try {
H5.H5Aclose(attr1_id);
}
catch (Exception ex) {
}
if (attr2_id > 0)
try {
H5.H5Aclose(attr2_id);
}
catch (Exception ex) {
}
if (attr3_id > 0)
try {
H5.H5Aclose(attr3_id);
}
catch (Exception ex) {
}
if (attr4_id > 0)
try {
H5.H5Aclose(attr4_id);
}
catch (Exception ex) {
}
}
}
@Test
public void testH5Adelete_by_idx_name1()
{
boolean exists = false;
long attr1_id = HDF5Constants.H5I_INVALID_HID;
long attr2_id = HDF5Constants.H5I_INVALID_HID;
long attr3_id = HDF5Constants.H5I_INVALID_HID;
try {
attr1_id = H5.H5Acreate_by_name(H5fid, ".", "attribute1", type_id, space_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
attr2_id = H5.H5Acreate_by_name(H5fid, ".", "attribute2", type_id, space_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
attr3_id = H5.H5Acreate_by_name(H5fid, ".", "attribute3", type_id, space_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
H5.H5Adelete_by_idx(H5fid, ".", HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, 2,
lapl_id);
exists = H5.H5Aexists(H5fid, "attribute3");
assertFalse("H5Adelete_by_idx: H5Aexists", exists);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Adelete_by_idx: " + err);
}
finally {
if (attr1_id > 0)
try {
H5.H5Aclose(attr1_id);
}
catch (Exception ex) {
}
if (attr2_id > 0)
try {
H5.H5Aclose(attr2_id);
}
catch (Exception ex) {
}
if (attr3_id > 0)
try {
H5.H5Aclose(attr3_id);
}
catch (Exception ex) {
}
}
}
@Test
public void testH5Adelete_by_idx_name2()
{
boolean exists = false;
long attr1_id = HDF5Constants.H5I_INVALID_HID;
long attr2_id = HDF5Constants.H5I_INVALID_HID;
long attr3_id = HDF5Constants.H5I_INVALID_HID;
long attr4_id = HDF5Constants.H5I_INVALID_HID;
try {
attr1_id = H5.H5Acreate_by_name(H5fid, ".", "attribute1", type_id, space_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
attr2_id = H5.H5Acreate_by_name(H5fid, ".", "attribute2", type_id, space_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
attr3_id = H5.H5Acreate_by_name(H5fid, ".", "attribute3", type_id, space_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
attr4_id = H5.H5Acreate_by_name(H5fid, ".", "attribute4", type_id, space_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
H5.H5Adelete_by_idx(H5fid, ".", HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_DEC, 3,
lapl_id);
exists = H5.H5Aexists(H5fid, "attribute1");
assertFalse("H5Adelete_by_idx: H5Aexists", exists);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Adelete_by_idx: " + err);
}
finally {
if (attr1_id > 0)
try {
H5.H5Aclose(attr1_id);
}
catch (Exception ex) {
}
if (attr2_id > 0)
try {
H5.H5Aclose(attr2_id);
}
catch (Exception ex) {
}
if (attr3_id > 0)
try {
H5.H5Aclose(attr3_id);
}
catch (Exception ex) {
}
if (attr4_id > 0)
try {
H5.H5Aclose(attr4_id);
}
catch (Exception ex) {
}
}
}
@Test(expected = NullPointerException.class)
public void testH5Adelete_by_idx_null() throws Throwable
{
H5.H5Adelete_by_idx(H5fid, null, HDF5Constants.H5_INDEX_CRT_ORDER, HDF5Constants.H5_ITER_INC, 0,
lapl_id);
}
@Test(expected = HDF5LibraryException.class)
public void testH5Adelete_by_idx_invalidobject() throws Throwable
{
H5.H5Adelete_by_idx(H5fid, "invalid", HDF5Constants.H5_INDEX_CRT_ORDER, HDF5Constants.H5_ITER_INC, 0,
lapl_id);
}
@Test
public void testH5Aopen_by_name()
{
String obj_name = ".";
String attr_name = "DATASET";
long attribute_id = HDF5Constants.H5I_INVALID_HID;
long aid = HDF5Constants.H5I_INVALID_HID;
try {
attribute_id =
H5.H5Acreate_by_name(H5fid, obj_name, attr_name, type_id, space_id, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT, lapl_id);
// open Attribute by name
if (attribute_id >= 0) {
try {
aid = H5.H5Aopen_by_name(H5fid, obj_name, attr_name, HDF5Constants.H5P_DEFAULT, lapl_id);
assertTrue("testH5Aopen_by_name: ", aid >= 0);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Aopen_by_name " + err);
}
}
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Aopen_by_name " + err);
}
finally {
if (aid > 0)
try {
H5.H5Aclose(aid);
}
catch (Exception ex) {
}
if (attribute_id > 0)
try {
H5.H5Aclose(attribute_id);
}
catch (Exception ex) {
}
}
}
@Test
public void testH5Awrite_readVL()
{
String attr_name = "VLdata";
long attr_id = HDF5Constants.H5I_INVALID_HID;
long atype_id = HDF5Constants.H5I_INVALID_HID;
long aspace_id = HDF5Constants.H5I_INVALID_HID;
String[] str_data = {"Parting", "is such", "sweet", "sorrow."};
long[] dims = {str_data.length};
long lsize = 1;
try {
atype_id = H5.H5Tcopy(HDF5Constants.H5T_C_S1);
assertTrue("testH5Awrite_readVL.H5Tcopy: ", atype_id >= 0);
H5.H5Tset_size(atype_id, HDF5Constants.H5T_VARIABLE);
assertTrue("testH5Awrite_readVL.H5Tis_variable_str", H5.H5Tis_variable_str(atype_id));
}
catch (Exception err) {
if (atype_id > 0)
try {
H5.H5Tclose(atype_id);
}
catch (Exception ex) {
}
err.printStackTrace();
fail("H5.testH5Awrite_readVL: " + err);
}
try {
aspace_id = H5.H5Screate_simple(1, dims, null);
assertTrue(aspace_id > 0);
attr_id = H5.H5Acreate(H5did, attr_name, atype_id, aspace_id, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT);
assertTrue("testH5Awrite_readVL: ", attr_id >= 0);
H5.H5AwriteVL(attr_id, atype_id, str_data);
H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
for (int j = 0; j < dims.length; j++) {
lsize *= dims[j];
}
String[] strs = new String[(int)lsize];
for (int j = 0; j < lsize; j++) {
strs[j] = "";
}
try {
H5.H5AreadVL(attr_id, atype_id, strs);
}
catch (Exception ex) {
ex.printStackTrace();
}
assertTrue("testH5Awrite_readVL:", str_data[0].equals(strs[0]));
assertTrue("testH5Awrite_readVL:", str_data[1].equals(strs[1]));
assertTrue("testH5Awrite_readVL:", str_data[2].equals(strs[2]));
assertTrue("testH5Awrite_readVL:", str_data[3].equals(strs[3]));
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.testH5Awrite_readVL: " + err);
}
finally {
if (attr_id > 0)
try {
H5.H5Aclose(attr_id);
}
catch (Exception ex) {
}
if (aspace_id > 0)
try {
H5.H5Sclose(aspace_id);
}
catch (Exception ex) {
}
if (atype_id > 0)
try {
H5.H5Tclose(atype_id);
}
catch (Exception ex) {
}
}
}
@Test
public void testH5Aget_create_plist()
{
String attr_name = "DATASET1";
int char_encoding = 0;
long plist_id = HDF5Constants.H5I_INVALID_HID;
long attribute_id = HDF5Constants.H5I_INVALID_HID;
try {
plist_id = H5.H5Pcreate(HDF5Constants.H5P_ATTRIBUTE_CREATE);
assertTrue(plist_id > 0);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Aget_create_plist: H5Pcreate " + err);
}
try {
// Get the character encoding and ensure that it is the default (ASCII)
try {
char_encoding = H5.H5Pget_char_encoding(plist_id);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5Pget_char_encoding: " + err);
}
assertTrue("testH5Aget_create_plist: get_char_encoding",
char_encoding == HDF5Constants.H5T_CSET_ASCII);
// Create an attribute for the dataset using the property list
try {
attribute_id =
H5.H5Acreate(H5fid, attr_name, type_id, space_id, plist_id, HDF5Constants.H5P_DEFAULT);
assertTrue("testH5Aget_create_plist: H5Acreate", attribute_id >= 0);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Acreate: " + err);
}
// Close the property list, and get the attribute's property list
H5.H5Pclose(plist_id);
plist_id = H5.H5Aget_create_plist(attribute_id);
assertTrue(plist_id > 0);
// Get the character encoding and ensure that it is the default (ASCII)
try {
char_encoding = H5.H5Pget_char_encoding(plist_id);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5Pget_char_encoding: " + err);
}
assertTrue("testH5Aget_create_plist: get_char_encoding",
char_encoding == HDF5Constants.H5T_CSET_ASCII);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Aget_create_plist " + err);
}
finally {
if (plist_id > 0)
try {
H5.H5Pclose(plist_id);
}
catch (Exception ex) {
}
if (attribute_id > 0)
try {
H5.H5Aclose(attribute_id);
}
catch (Exception ex) {
}
}
}
@Test
public void testH5Aiterate()
{
long attr1_id = HDF5Constants.H5I_INVALID_HID;
long attr2_id = HDF5Constants.H5I_INVALID_HID;
long attr3_id = HDF5Constants.H5I_INVALID_HID;
long attr4_id = HDF5Constants.H5I_INVALID_HID;
class idata {
public String attr_name = null;
idata(String name) { this.attr_name = name; }
}
class H5A_iter_data implements H5A_iterate_t {
public ArrayList<idata> iterdata = new ArrayList<idata>();
}
H5A_iterate_t iter_data = new H5A_iter_data();
class H5A_iter_callback implements H5A_iterate_cb {
public int callback(long group, String name, H5A_info_t info, H5A_iterate_t op_data)
{
idata id = new idata(name);
((H5A_iter_data)op_data).iterdata.add(id);
return 0;
}
}
try {
attr1_id = H5.H5Acreate_by_name(H5fid, ".", "attribute1", type_id, space_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
attr2_id = H5.H5Acreate_by_name(H5fid, ".", "attribute2", type_id, space_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
attr3_id = H5.H5Acreate_by_name(H5fid, ".", "attribute3", type_id, space_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
attr4_id = H5.H5Acreate_by_name(H5fid, ".", "attribute4", type_id, space_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
H5A_iterate_cb iter_cb = new H5A_iter_callback();
try {
H5.H5Aiterate(H5fid, HDF5Constants.H5_INDEX_CRT_ORDER, HDF5Constants.H5_ITER_INC, 0L, iter_cb,
iter_data);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Aiterate: " + err);
}
assertFalse("H5Aiterate ", ((H5A_iter_data)iter_data).iterdata.isEmpty());
assertTrue("H5Aiterate " + ((H5A_iter_data)iter_data).iterdata.size(),
((H5A_iter_data)iter_data).iterdata.size() == 4);
assertTrue(
"H5Aiterate " + (((H5A_iter_data)iter_data).iterdata.get(0)).attr_name,
(((H5A_iter_data)iter_data).iterdata.get(0)).attr_name.compareToIgnoreCase("attribute1") ==
0);
assertTrue(
"H5Aiterate " + (((H5A_iter_data)iter_data).iterdata.get(1)).attr_name,
(((H5A_iter_data)iter_data).iterdata.get(1)).attr_name.compareToIgnoreCase("attribute2") ==
0);
assertTrue(
"H5Aiterate " + ((idata)((H5A_iter_data)iter_data).iterdata.get(2)).attr_name,
(((H5A_iter_data)iter_data).iterdata.get(2)).attr_name.compareToIgnoreCase("attribute3") ==
0);
assertTrue("H5Aiterate " + ((idata)((H5A_iter_data)iter_data).iterdata.get(3)).attr_name,
((idata)((H5A_iter_data)iter_data).iterdata.get(3))
.attr_name.compareToIgnoreCase("attribute4") == 0);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Aiterate: " + err);
}
finally {
if (attr1_id > 0)
try {
H5.H5Aclose(attr1_id);
}
catch (Exception ex) {
}
if (attr2_id > 0)
try {
H5.H5Aclose(attr2_id);
}
catch (Exception ex) {
}
if (attr3_id > 0)
try {
H5.H5Aclose(attr3_id);
}
catch (Exception ex) {
}
if (attr4_id > 0)
try {
H5.H5Aclose(attr4_id);
}
catch (Exception ex) {
}
}
}
@Test
public void testH5Aiterate_by_name()
{
long attr1_id = HDF5Constants.H5I_INVALID_HID;
long attr2_id = HDF5Constants.H5I_INVALID_HID;
long attr3_id = HDF5Constants.H5I_INVALID_HID;
long attr4_id = HDF5Constants.H5I_INVALID_HID;
class idata {
public String attr_name = null;
idata(String name) { this.attr_name = name; }
}
class H5A_iter_data implements H5A_iterate_t {
public ArrayList<idata> iterdata = new ArrayList<idata>();
}
H5A_iterate_t iter_data = new H5A_iter_data();
class H5A_iter_callback implements H5A_iterate_cb {
public int callback(long group, String name, H5A_info_t info, H5A_iterate_t op_data)
{
idata id = new idata(name);
((H5A_iter_data)op_data).iterdata.add(id);
return 0;
}
}
try {
attr1_id = H5.H5Acreate_by_name(H5fid, ".", "attribute4", type_id, space_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
attr2_id = H5.H5Acreate_by_name(H5fid, ".", "attribute3", type_id, space_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
attr3_id = H5.H5Acreate_by_name(H5fid, ".", "attribute2", type_id, space_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
attr4_id = H5.H5Acreate_by_name(H5fid, ".", "attribute1", type_id, space_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, lapl_id);
H5A_iterate_cb iter_cb = new H5A_iter_callback();
try {
H5.H5Aiterate_by_name(H5fid, ".", HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, 0L,
iter_cb, iter_data, HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Aiterate_by_name: " + err);
}
assertFalse("H5Aiterate_by_name ", ((H5A_iter_data)iter_data).iterdata.isEmpty());
assertTrue("H5Aiterate_by_name " + ((H5A_iter_data)iter_data).iterdata.size(),
((H5A_iter_data)iter_data).iterdata.size() == 4);
assertTrue("H5Aiterate_by_name " + ((idata)((H5A_iter_data)iter_data).iterdata.get(1)).attr_name,
((idata)((H5A_iter_data)iter_data).iterdata.get(1))
.attr_name.compareToIgnoreCase("attribute2") == 0);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Aiterate: " + err);
}
finally {
if (attr1_id > 0)
try {
H5.H5Aclose(attr1_id);
}
catch (Exception ex) {
}
if (attr2_id > 0)
try {
H5.H5Aclose(attr2_id);
}
catch (Exception ex) {
}
if (attr3_id > 0)
try {
H5.H5Aclose(attr3_id);
}
catch (Exception ex) {
}
if (attr4_id > 0)
try {
H5.H5Aclose(attr4_id);
}
catch (Exception ex) {
}
}
}
@Test
public void testH5AVLwr()
{
String attr_int_name = "VLIntdata";
String attr_dbl_name = "VLDbldata";
long attr_int_id = HDF5Constants.H5I_INVALID_HID;
long attr_dbl_id = HDF5Constants.H5I_INVALID_HID;
long atype_int_id = HDF5Constants.H5I_INVALID_HID;
long atype_dbl_id = HDF5Constants.H5I_INVALID_HID;
long aspace_id = HDF5Constants.H5I_INVALID_HID;
long[] dims = {4};
long lsize = 1;
ArrayList[] vl_int_data = new ArrayList[4];
ArrayList[] vl_dbl_data = new ArrayList[4];
try {
// Write Integer data
vl_int_data[0] = new ArrayList<Integer>(Arrays.asList(1));
vl_int_data[1] = new ArrayList<Integer>(Arrays.asList(2, 3));
vl_int_data[2] = new ArrayList<Integer>(Arrays.asList(4, 5, 6));
vl_int_data[3] = new ArrayList<Integer>(Arrays.asList(7, 8, 9, 10));
Class dataClass = vl_int_data.getClass();
assertTrue("testH5AVLwr.getClass: " + dataClass, dataClass.isArray());
try {
atype_int_id = H5.H5Tvlen_create(HDF5Constants.H5T_STD_U32LE);
assertTrue("testH5AVLwr.H5Tvlen_create: ", atype_int_id >= 0);
}
catch (Exception err) {
if (atype_int_id > 0)
try {
H5.H5Tclose(atype_int_id);
}
catch (Exception ex) {
}
err.printStackTrace();
fail("H5.testH5AVLwr: " + err);
}
try {
aspace_id = H5.H5Screate_simple(1, dims, null);
assertTrue(aspace_id > 0);
attr_int_id = H5.H5Acreate(H5did, attr_int_name, atype_int_id, aspace_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
assertTrue("testH5AVLwr: ", attr_int_id >= 0);
H5.H5AwriteVL(attr_int_id, atype_int_id, vl_int_data);
}
catch (Exception err) {
if (attr_int_id > 0)
try {
H5.H5Aclose(attr_int_id);
}
catch (Exception ex) {
}
if (atype_int_id > 0)
try {
H5.H5Tclose(atype_int_id);
}
catch (Exception ex) {
}
err.printStackTrace();
fail("H5.testH5AVLwr: " + err);
}
finally {
if (aspace_id > 0)
try {
H5.H5Sclose(aspace_id);
}
catch (Exception ex) {
}
}
// Write Double data
vl_dbl_data[0] = new ArrayList<Double>(Arrays.asList(1.1));
vl_dbl_data[1] = new ArrayList<Double>(Arrays.asList(2.2, 3.3));
vl_dbl_data[2] = new ArrayList<Double>(Arrays.asList(4.4, 5.5, 6.6));
vl_dbl_data[3] = new ArrayList<Double>(Arrays.asList(7.7, 8.8, 9.9, 10.0));
dataClass = vl_dbl_data.getClass();
assertTrue("testH5AVLwr.getClass: " + dataClass, dataClass.isArray());
try {
atype_dbl_id = H5.H5Tvlen_create(HDF5Constants.H5T_NATIVE_DOUBLE);
assertTrue("testH5AVLwr.H5Tvlen_create: ", atype_dbl_id >= 0);
}
catch (Exception err) {
if (atype_dbl_id > 0)
try {
H5.H5Tclose(atype_dbl_id);
}
catch (Exception ex) {
}
err.printStackTrace();
fail("H5.testH5AVLwr: " + err);
}
try {
aspace_id = H5.H5Screate_simple(1, dims, null);
assertTrue(aspace_id > 0);
attr_dbl_id = H5.H5Acreate(H5did, attr_dbl_name, atype_dbl_id, aspace_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
assertTrue("testH5AVLwr: ", attr_dbl_id >= 0);
H5.H5AwriteVL(attr_dbl_id, atype_dbl_id, vl_dbl_data);
}
catch (Exception err) {
if (attr_dbl_id > 0)
try {
H5.H5Aclose(attr_dbl_id);
}
catch (Exception ex) {
}
if (atype_dbl_id > 0)
try {
H5.H5Tclose(atype_dbl_id);
}
catch (Exception ex) {
}
err.printStackTrace();
fail("H5.testH5AVLwr: " + err);
}
finally {
if (aspace_id > 0)
try {
H5.H5Sclose(aspace_id);
}
catch (Exception ex) {
}
}
H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
for (int j = 0; j < dims.length; j++)
lsize *= dims[j];
// Read Integer data
ArrayList[] vl_readbuf = new ArrayList[4];
for (int j = 0; j < lsize; j++)
vl_readbuf[j] = new ArrayList<Integer>();
try {
H5.H5AreadVL(attr_int_id, atype_int_id, vl_readbuf);
}
catch (Exception ex) {
ex.printStackTrace();
}
assertTrue("testH5AVLwr:" + vl_readbuf[0].get(0),
vl_int_data[0].get(0).equals(vl_readbuf[0].get(0)));
assertTrue("testH5AVLwr:" + vl_readbuf[1].get(0),
vl_int_data[1].get(0).equals(vl_readbuf[1].get(0)));
assertTrue("testH5AVLwr:" + vl_readbuf[2].get(0),
vl_int_data[2].get(0).equals(vl_readbuf[2].get(0)));
assertTrue("testH5AVLwr:" + vl_readbuf[3].get(0),
vl_int_data[3].get(0).equals(vl_readbuf[3].get(0)));
// Read Double data
vl_readbuf = new ArrayList[4];
for (int j = 0; j < lsize; j++)
vl_readbuf[j] = new ArrayList<Double>();
try {
H5.H5AreadVL(attr_dbl_id, atype_dbl_id, vl_readbuf);
}
catch (Exception ex) {
ex.printStackTrace();
}
assertTrue("testH5AVLwr:" + vl_readbuf[0].get(0),
vl_dbl_data[0].get(0).equals(vl_readbuf[0].get(0)));
assertTrue("testH5AVLwr:" + vl_readbuf[1].get(0),
vl_dbl_data[1].get(0).equals(vl_readbuf[1].get(0)));
assertTrue("testH5AVLwr:" + vl_readbuf[2].get(0),
vl_dbl_data[2].get(0).equals(vl_readbuf[2].get(0)));
assertTrue("testH5AVLwr:" + vl_readbuf[3].get(0),
vl_dbl_data[3].get(0).equals(vl_readbuf[3].get(0)));
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.testH5AVLwr: " + err);
}
finally {
if (attr_dbl_id > 0)
try {
H5.H5Aclose(attr_dbl_id);
}
catch (Exception ex) {
}
if (attr_int_id > 0)
try {
H5.H5Aclose(attr_int_id);
}
catch (Exception ex) {
}
if (atype_dbl_id > 0)
try {
H5.H5Tclose(atype_dbl_id);
}
catch (Exception ex) {
}
if (atype_int_id > 0)
try {
H5.H5Tclose(atype_int_id);
}
catch (Exception ex) {
}
}
}
@Test
public void testH5AVLwrVL()
{
String attr_int_name = "VLIntdata";
long attr_int_id = HDF5Constants.H5I_INVALID_HID;
long atype_int_id = HDF5Constants.H5I_INVALID_HID;
long base_atype_int_id = HDF5Constants.H5I_INVALID_HID;
long aspace_id = HDF5Constants.H5I_INVALID_HID;
long[] dims = {4};
long lsize = 1;
ArrayList[] base_vl_int_data = new ArrayList[4];
ArrayList[] vl_int_data = new ArrayList[4];
try {
// Write Integer data
vl_int_data[0] = new ArrayList<Integer>(Arrays.asList(1));
vl_int_data[1] = new ArrayList<Integer>(Arrays.asList(2, 3));
vl_int_data[2] = new ArrayList<Integer>(Arrays.asList(4, 5, 6));
vl_int_data[3] = new ArrayList<Integer>(Arrays.asList(7, 8, 9, 10));
Class dataClass = vl_int_data.getClass();
assertTrue("testH5AVLwrVL.getClass: " + dataClass, dataClass.isArray());
// Write VL data
base_vl_int_data[0] = new ArrayList<ArrayList<Integer>>();
base_vl_int_data[0].add(vl_int_data[0]);
base_vl_int_data[1] = new ArrayList<ArrayList<Integer>>();
base_vl_int_data[1].add(vl_int_data[0]);
base_vl_int_data[1].add(vl_int_data[1]);
base_vl_int_data[2] = new ArrayList<ArrayList<Integer>>();
base_vl_int_data[2].add(vl_int_data[0]);
base_vl_int_data[2].add(vl_int_data[1]);
base_vl_int_data[2].add(vl_int_data[2]);
base_vl_int_data[3] = new ArrayList<ArrayList<Integer>>();
base_vl_int_data[3].add(vl_int_data[0]);
base_vl_int_data[3].add(vl_int_data[1]);
base_vl_int_data[3].add(vl_int_data[2]);
base_vl_int_data[3].add(vl_int_data[3]);
try {
atype_int_id = H5.H5Tvlen_create(HDF5Constants.H5T_STD_U32LE);
assertTrue("testH5AVLwr.H5Tvlen_create: ", atype_int_id >= 0);
base_atype_int_id = H5.H5Tvlen_create(atype_int_id);
assertTrue("testH5AVLwrVL.H5Tvlen_create: ", base_atype_int_id >= 0);
}
catch (Exception err) {
if (base_atype_int_id > 0)
try {
H5.H5Tclose(base_atype_int_id);
}
catch (Exception ex) {
}
if (atype_int_id > 0)
try {
H5.H5Tclose(atype_int_id);
}
catch (Exception ex) {
}
err.printStackTrace();
fail("H5.testH5AVLwrVL: " + err);
}
try {
aspace_id = H5.H5Screate_simple(1, dims, null);
assertTrue(aspace_id > 0);
attr_int_id = H5.H5Acreate(H5did, attr_int_name, base_atype_int_id, aspace_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
assertTrue("testH5AVLwrVL: ", attr_int_id >= 0);
H5.H5AwriteVL(attr_int_id, base_atype_int_id, base_vl_int_data);
}
catch (Exception err) {
if (attr_int_id > 0)
try {
H5.H5Aclose(attr_int_id);
}
catch (Exception ex) {
}
if (atype_int_id > 0)
try {
H5.H5Tclose(atype_int_id);
}
catch (Exception ex) {
}
err.printStackTrace();
fail("H5.testH5AVLwrVL: " + err);
}
finally {
if (aspace_id > 0)
try {
H5.H5Sclose(aspace_id);
}
catch (Exception ex) {
}
}
H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
for (int j = 0; j < dims.length; j++)
lsize *= dims[j];
// Read Integer data
ArrayList[] base_vl_readbuf = new ArrayList[4];
for (int j = 0; j < lsize; j++)
base_vl_readbuf[j] = new ArrayList<ArrayList<Integer>>();
try {
H5.H5AreadVL(attr_int_id, base_atype_int_id, base_vl_readbuf);
}
catch (Exception ex) {
ex.printStackTrace();
}
ArrayList<ArrayList<Integer>> vl_readbuf = (ArrayList<ArrayList<Integer>>)base_vl_readbuf[0];
assertTrue("vl_readbuf 0 exists", vl_readbuf != null);
ArrayList<Integer> vl_readbuf_int = (ArrayList<Integer>)(vl_readbuf.get(0));
/*
* System.out.println(); System.out.println("vl_readbuf: " + vl_readbuf);
* System.out.println("vl_readbuf_int: " + vl_readbuf_int);
*/
assertTrue("testHADVLwrVL:" + vl_readbuf_int.get(0),
vl_int_data[0].get(0).equals(vl_readbuf_int.get(0)));
vl_readbuf = (ArrayList<ArrayList<Integer>>)base_vl_readbuf[1];
vl_readbuf_int = (ArrayList<Integer>)(vl_readbuf.get(1));
/*
* System.out.println("vl_readbuf: " + vl_readbuf); System.out.println("vl_readbuf_int: " +
* vl_readbuf_int);
*/
assertTrue("testH5AVLwrVL:" + vl_readbuf_int.get(1),
vl_int_data[1].get(1).equals(vl_readbuf_int.get(1)));
vl_readbuf = (ArrayList<ArrayList<Integer>>)base_vl_readbuf[2];
vl_readbuf_int = (ArrayList<Integer>)(vl_readbuf.get(2));
/*
* System.out.println("vl_readbuf: " + vl_readbuf); System.out.println("vl_readbuf_int: " +
* vl_readbuf_int);
*/
assertTrue("testH5AVLwrVL:" + vl_readbuf_int.get(2),
vl_int_data[2].get(2).equals(vl_readbuf_int.get(2)));
vl_readbuf = (ArrayList<ArrayList<Integer>>)base_vl_readbuf[3];
vl_readbuf_int = (ArrayList<Integer>)(vl_readbuf.get(3));
/*
* System.out.println("vl_readbuf: " + vl_readbuf); System.out.println("vl_readbuf_int: " +
* vl_readbuf_int);
*/
assertTrue("testH5AVLwrVL:" + vl_readbuf_int.get(3),
vl_int_data[3].get(3).equals(vl_readbuf_int.get(3)));
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.testH5AVLwrVL: " + err);
}
finally {
if (attr_int_id > 0)
try {
H5.H5Aclose(attr_int_id);
}
catch (Exception ex) {
}
if (atype_int_id > 0)
try {
H5.H5Tclose(atype_int_id);
}
catch (Exception ex) {
}
if (base_atype_int_id > 0)
try {
H5.H5Tclose(base_atype_int_id);
}
catch (Exception ex) {
}
}
}
@Test
public void testH5AArraywr()
{
String att_int_name = "ArrayIntdata";
long att_int_id = HDF5Constants.H5I_INVALID_HID;
long atype_int_id = HDF5Constants.H5I_INVALID_HID;
long aspace_id = HDF5Constants.H5I_INVALID_HID;
long[] dims = {4};
long lsize = 1;
ArrayList[] arr_int_data = new ArrayList[4];
try {
// Write Integer data
arr_int_data[0] = new ArrayList<Integer>(Arrays.asList(1, 2, 3, 4));
arr_int_data[1] = new ArrayList<Integer>(Arrays.asList(2, 3, 4, 5));
arr_int_data[2] = new ArrayList<Integer>(Arrays.asList(4, 5, 6, 7));
arr_int_data[3] = new ArrayList<Integer>(Arrays.asList(7, 8, 9, 10));
Class dataClass = arr_int_data.getClass();
assertTrue("testH5AArraywr.getClass: " + dataClass, dataClass.isArray());
try {
atype_int_id = H5.H5Tarray_create(HDF5Constants.H5T_STD_U32LE, 1, dims);
assertTrue("testH5AArraywr.H5Tarray_create: ", atype_int_id >= 0);
}
catch (Exception err) {
if (atype_int_id > 0)
try {
H5.H5Tclose(atype_int_id);
}
catch (Exception ex) {
}
err.printStackTrace();
fail("H5.testH5AArraywr: " + err);
}
try {
aspace_id = H5.H5Screate_simple(1, dims, null);
assertTrue(aspace_id > 0);
att_int_id = H5.H5Acreate(H5did, att_int_name, atype_int_id, aspace_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
assertTrue("testH5AVLwr: ", att_int_id >= 0);
H5.H5AwriteVL(att_int_id, atype_int_id, arr_int_data);
}
catch (Exception err) {
if (att_int_id > 0)
try {
H5.H5Aclose(att_int_id);
}
catch (Exception ex) {
}
if (atype_int_id > 0)
try {
H5.H5Tclose(atype_int_id);
}
catch (Exception ex) {
}
err.printStackTrace();
fail("H5.testH5AVLwr: " + err);
}
finally {
if (aspace_id > 0)
try {
H5.H5Sclose(aspace_id);
}
catch (Exception ex) {
}
}
H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
for (int j = 0; j < dims.length; j++)
lsize *= dims[j];
// Read Integer data
ArrayList[] arr_readbuf = new ArrayList[4];
for (int j = 0; j < lsize; j++)
arr_readbuf[j] = new ArrayList<Integer>();
try {
H5.H5AreadVL(att_int_id, atype_int_id, arr_readbuf);
}
catch (Exception ex) {
ex.printStackTrace();
}
assertTrue("testH5AVLwr:" + arr_readbuf[0].get(0),
arr_int_data[0].get(0).equals(arr_readbuf[0].get(0)));
assertTrue("testH5AVLwr:" + arr_readbuf[1].get(0),
arr_int_data[1].get(0).equals(arr_readbuf[1].get(0)));
assertTrue("testH5AVLwr:" + arr_readbuf[2].get(0),
arr_int_data[2].get(0).equals(arr_readbuf[2].get(0)));
assertTrue("testH5AVLwr:" + arr_readbuf[3].get(0),
arr_int_data[3].get(0).equals(arr_readbuf[3].get(0)));
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.testH5AArraywr: " + err);
}
finally {
if (att_int_id > 0)
try {
H5.H5Aclose(att_int_id);
}
catch (Exception ex) {
}
if (atype_int_id > 0)
try {
H5.H5Tclose(atype_int_id);
}
catch (Exception ex) {
}
}
}
@Test
public void testH5AArray_string_buffer() throws Throwable
{
String att_str_name = "ArrayStringdata";
long att_str_id = HDF5Constants.H5I_INVALID_HID;
long atype_str_id = HDF5Constants.H5I_INVALID_HID;
long aspace_id = HDF5Constants.H5I_INVALID_HID;
long[] strdims = {4};
long[] dims = {6};
long lsize = 1;
String[] str_data0 = {"Parting", "is such", "sweet", "sorrow."};
String[] str_data1 = {"Testing", "one", "two", "three."};
String[] str_data2 = {"Dog,", "man's", "best", "friend."};
String[] str_data3 = {"Diamonds", "are", "a", "girls!"};
String[] str_data4 = {"S A", "T U R", "D A Y", "night"};
String[] str_data5 = {"That's", "all", "folks", "!!!"};
ArrayList[] arr_str_data = new ArrayList[6];
arr_str_data[0] = new ArrayList<String>(Arrays.asList(str_data0));
arr_str_data[1] = new ArrayList<String>(Arrays.asList(str_data1));
arr_str_data[2] = new ArrayList<String>(Arrays.asList(str_data2));
arr_str_data[3] = new ArrayList<String>(Arrays.asList(str_data3));
arr_str_data[4] = new ArrayList<String>(Arrays.asList(str_data4));
arr_str_data[5] = new ArrayList<String>(Arrays.asList(str_data5));
try {
H5atid = H5.H5Tcopy(HDF5Constants.H5T_C_S1);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5AArray_string_buffer.H5.H5Tcopy: " + err);
}
assertTrue("testH5AArray_string_buffer.H5Tcopy: ", H5atid >= 0);
try {
H5.H5Tset_size(H5atid, HDF5Constants.H5T_VARIABLE);
assertTrue("testH5AArray_string_buffer.H5Tis_variable_str", H5.H5Tis_variable_str(H5atid));
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5DArray_string_buffer.H5Tset_size: " + err);
}
try {
atype_str_id = H5.H5Tarray_create(H5atid, 1, strdims);
assertTrue("testH5AArray_string_buffer.H5Tarray_create: ", atype_str_id >= 0);
}
catch (Exception err) {
if (atype_str_id > 0)
try {
H5.H5Tclose(atype_str_id);
}
catch (Exception ex) {
}
err.printStackTrace();
fail("testH5AArray_string_buffer: " + err);
}
try {
aspace_id = H5.H5Screate_simple(1, dims, null);
assertTrue(aspace_id > 0);
att_str_id = H5.H5Acreate(H5did, att_str_name, atype_str_id, aspace_id, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT);
assertTrue("testH5AArray_string_buffer: ", att_str_id >= 0);
H5.H5AwriteVL(att_str_id, atype_str_id, arr_str_data);
}
catch (Exception err) {
if (att_str_id > 0)
try {
H5.H5Dclose(att_str_id);
}
catch (Exception ex) {
}
if (atype_str_id > 0)
try {
H5.H5Tclose(atype_str_id);
}
catch (Exception ex) {
}
err.printStackTrace();
fail("testH5AArray_string_buffer: " + err);
}
finally {
if (aspace_id > 0)
try {
H5.H5Sclose(aspace_id);
}
catch (Exception ex) {
}
}
H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
for (int j = 0; j < dims.length; j++)
lsize *= dims[j];
ArrayList[] arr_readbuf = new ArrayList[6];
for (int j = 0; j < lsize; j++)
arr_readbuf[j] = new ArrayList<String>();
try {
H5.H5AreadVL(att_str_id, atype_str_id, arr_readbuf);
}
catch (Exception ex) {
ex.printStackTrace();
}
finally {
if (att_str_id > 0)
try {
H5.H5Aclose(att_str_id);
}
catch (Exception ex) {
}
if (atype_str_id > 0)
try {
H5.H5Tclose(atype_str_id);
}
catch (Exception ex) {
}
}
assertTrue("testH5AArray_string_buffer:" + arr_readbuf[0].get(0),
arr_str_data[0].get(0).equals(arr_readbuf[0].get(0)));
assertTrue("testH5AArray_string_buffer:" + arr_readbuf[1].get(0),
arr_str_data[1].get(0).equals(arr_readbuf[1].get(0)));
assertTrue("testH5AArray_string_buffer:" + arr_readbuf[2].get(0),
arr_str_data[2].get(0).equals(arr_readbuf[2].get(0)));
assertTrue("testH5AArray_string_buffer:" + arr_readbuf[3].get(0),
arr_str_data[3].get(0).equals(arr_readbuf[3].get(0)));
}
}
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