mirror of
https://github.com/HDFGroup/hdf5.git
synced 2026-09-25 04:09:44 +03:00
Allen Byrne
b754dcb8f2
FFM build requires Java 25, Jextract 25. Generates FFM bindings during configure. JNI is default when the requirements are not met or can be forced. Presets added for maven and FFM - JNI is default selection. Enhanced Maven options will work with either JNI or FFM New Workflows for testing and maven uploads. Extensive documentation changes for java.
662 lines
22 KiB
Java
662 lines
22 KiB
Java
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
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* Copyright by The HDF Group. *
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* All rights reserved. *
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* *
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* This file is part of HDF5. The full HDF5 copyright notice, including *
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* terms governing use, modification, and redistribution, is contained in *
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* the LICENSE file, which can be found at the root of the source code *
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* distribution tree, or in https://www.hdfgroup.org/licenses. *
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* If you do not have access to either file, you may request a copy from *
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* help@hdfgroup.org. *
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* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
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package test;
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import static org.junit.Assert.assertFalse;
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import static org.junit.Assert.assertTrue;
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import static org.junit.Assert.fail;
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import hdf.hdf5lib.H5;
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import hdf.hdf5lib.HDF5Constants;
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import hdf.hdf5lib.exceptions.HDF5Exception;
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import hdf.hdf5lib.exceptions.HDF5FunctionArgumentException;
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import hdf.hdf5lib.exceptions.HDF5LibraryException;
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import org.junit.After;
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import org.junit.Before;
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import org.junit.Rule;
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import org.junit.Test;
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import org.junit.rules.TestName;
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public class TestH5S {
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@Rule
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public TestName testname = new TestName();
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long H5sid = HDF5Constants.H5I_INVALID_HID;
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int H5rank = 2;
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long H5dims[] = {5, 5};
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long H5maxdims[] = {10, 10};
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@Before
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public void createH5file() throws NullPointerException, HDF5Exception
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{
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assertTrue("H5 open ids is 0", H5.getOpenIDCount() == 0);
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System.out.print(testname.getMethodName());
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H5sid = H5.H5Screate_simple(H5rank, H5dims, H5maxdims);
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assertTrue("H5.H5Screate_simple_extent", H5sid > 0);
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}
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@After
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public void deleteH5file() throws HDF5LibraryException
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{
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if (H5sid > 0) {
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try {
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H5.H5Sclose(H5sid);
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}
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catch (Exception ex) {
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}
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}
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System.out.println();
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}
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@Test
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public void testH5Sget_simple_extent_ndims()
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{
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int read_rank = -1;
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try {
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read_rank = H5.H5Sget_simple_extent_ndims(H5sid);
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assertTrue("H5.H5Sget_simple_extent_ndims", H5rank == read_rank);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Sget_simple_extent_ndims: " + err);
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}
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}
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@Test
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public void testH5Sget_simple_extent_dims_null()
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{
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int read_rank = -1;
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try {
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read_rank = H5.H5Sget_simple_extent_dims(H5sid, null, null);
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assertTrue("H5.H5Sget_simple_extent_dims", H5rank == read_rank);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Sget_simple_extent_dims: " + err);
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}
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}
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@Test
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public void testH5Sget_simple_extent_dims()
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{
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int read_rank = -1;
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long dims[] = {5, 5};
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long maxdims[] = {10, 10};
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try {
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read_rank = H5.H5Sget_simple_extent_dims(H5sid, dims, maxdims);
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assertTrue("H5.H5Sget_simple_extent_dims", H5rank == read_rank);
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assertTrue("H5.H5Sget_simple_extent_dims:dims", H5dims[0] == dims[0]);
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assertTrue("H5.H5Sget_simple_extent_dims:maxdims", H5maxdims[0] == maxdims[0]);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Sget_simple_extent_dims: " + err);
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}
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}
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@Test
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public void testH5Sget_simple_extent_npoints()
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{
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long num_elements = -1;
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try {
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num_elements = H5.H5Sget_simple_extent_npoints(H5sid);
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assertTrue("H5.H5Sget_simple_extent_npoints", (H5dims[0] * H5dims[1]) == num_elements);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Sget_simple_extent_npoints: " + err);
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}
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}
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@Test
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public void testH5Sget_simple_extent_type()
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{
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int read_type = -1;
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try {
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read_type = H5.H5Sget_simple_extent_type(H5sid);
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assertTrue("H5.H5Sget_simple_extent_type", HDF5Constants.H5S_SIMPLE == read_type);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Sget_simple_extent_type: " + err);
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}
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}
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@Test
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public void testH5Sis_simple()
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{
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boolean result = false;
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try {
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result = H5.H5Sis_simple(H5sid);
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assertTrue("H5.H5Sis_simple", result);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Sis_simple: " + err);
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}
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}
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@Test
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public void testH5Sset_extent_simple()
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{
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long num_elements = -1;
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try {
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H5.H5Sset_extent_simple(H5sid, H5rank, H5maxdims, H5maxdims);
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num_elements = H5.H5Sget_simple_extent_npoints(H5sid);
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assertTrue("H5.H5Sget_simple_extent_npoints", (H5maxdims[0] * H5maxdims[1]) == num_elements);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Sset_extent_simple: " + err);
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}
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}
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@Test
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public void testH5Sget_select_type()
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{
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int read_type = -1;
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try {
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read_type = H5.H5Sget_select_type(H5sid);
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assertTrue("H5.H5Sget_select_type", HDF5Constants.H5S_SEL_ALL == read_type);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Sset_extent_none: " + err);
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}
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}
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@Test
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public void testH5Sset_extent_none()
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{
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int read_type = -1;
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try {
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H5.H5Sset_extent_none(H5sid);
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read_type = H5.H5Sget_simple_extent_type(H5sid);
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assertTrue("H5.H5Sget_simple_extent_type: " + read_type, HDF5Constants.H5S_NULL == read_type);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Sset_extent_none: " + err);
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}
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}
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@Test
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public void testH5Scopy()
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{
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long sid = HDF5Constants.H5I_INVALID_HID;
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int read_rank = -1;
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try {
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sid = H5.H5Scopy(H5sid);
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assertTrue("H5.H5Sis_simple", sid > 0);
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read_rank = H5.H5Sget_simple_extent_ndims(sid);
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assertTrue("H5.H5Screate_simple_extent_ndims", H5rank == read_rank);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Scopy: " + err);
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}
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finally {
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try {
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H5.H5Sclose(sid);
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}
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catch (Exception ex) {
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}
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}
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}
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@Test
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public void testH5Sextent_copy()
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{
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long sid = HDF5Constants.H5I_INVALID_HID;
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int class_type = -1;
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try {
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sid = H5.H5Screate(HDF5Constants.H5S_NULL);
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assertTrue("H5.H5Screate_null", sid > 0);
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H5.H5Sextent_copy(sid, H5sid);
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class_type = H5.H5Sget_simple_extent_type(sid);
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assertTrue("H5.H5Screate_null: type", class_type == HDF5Constants.H5S_SIMPLE);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Sextent_copy: " + err);
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}
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finally {
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try {
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H5.H5Sclose(sid);
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}
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catch (Exception ex) {
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}
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}
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}
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@Test
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public void testH5Sextent_equal()
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{
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long sid = HDF5Constants.H5I_INVALID_HID;
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boolean result = false;
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try {
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sid = H5.H5Screate(HDF5Constants.H5S_NULL);
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assertTrue("H5.H5Screate_null", sid > 0);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Screate: null " + err);
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}
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try {
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result = H5.H5Sextent_equal(sid, H5sid);
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assertFalse("H5.testH5Sextent_equal", result);
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H5.H5Sextent_copy(sid, H5sid);
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result = H5.H5Sextent_equal(sid, H5sid);
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assertTrue("H5.testH5Sextent_equal", result);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Sextent_copy " + err);
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}
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finally {
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try {
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H5.H5Sclose(sid);
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}
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catch (Exception ex) {
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}
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}
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}
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@Test
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public void testH5Sencode_decode_null_dataspace()
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{
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long sid = HDF5Constants.H5I_INVALID_HID;
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long decoded_sid = HDF5Constants.H5I_INVALID_HID;
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byte[] null_sbuf = null;
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boolean result = false;
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try {
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sid = H5.H5Screate(HDF5Constants.H5S_NULL);
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assertTrue("H5.H5Screate_null", sid > 0);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Screate: null " + err);
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}
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try {
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null_sbuf = H5.H5Sencode(sid);
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assertFalse("H5.testH5Sencode", null_sbuf == null);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Sencode " + err);
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}
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finally {
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if (null_sbuf == null) {
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try {
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H5.H5Sclose(sid);
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}
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catch (Exception ex) {
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}
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}
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}
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try {
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decoded_sid = H5.H5Sdecode(null_sbuf);
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assertTrue("H5.testH5Sdecode", decoded_sid > 0);
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result = H5.H5Sextent_equal(sid, decoded_sid);
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assertTrue("H5.testH5Sextent_equal", result);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Sdecode " + err);
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}
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finally {
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try {
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H5.H5Sclose(decoded_sid);
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}
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catch (Exception ex) {
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}
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try {
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H5.H5Sclose(sid);
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}
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catch (Exception ex) {
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}
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}
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}
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@Test
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public void testH5Sencode_decode_scalar_dataspace()
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{
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long sid = HDF5Constants.H5I_INVALID_HID;
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long decoded_sid = HDF5Constants.H5I_INVALID_HID;
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byte[] scalar_sbuf = null;
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boolean result = false;
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int iresult = -1;
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long lresult = -1;
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try {
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sid = H5.H5Screate(HDF5Constants.H5S_SCALAR);
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assertTrue("H5.H5Screate_null", sid > 0);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Screate: null " + err);
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}
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try {
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scalar_sbuf = H5.H5Sencode(sid);
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assertFalse("H5.testH5Sencode", scalar_sbuf == null);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Sencode " + err);
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}
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finally {
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if (scalar_sbuf == null) {
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try {
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H5.H5Sclose(sid);
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}
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catch (Exception ex) {
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}
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}
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}
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try {
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decoded_sid = H5.H5Sdecode(scalar_sbuf);
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assertTrue("H5.testH5Sdecode", decoded_sid > 0);
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result = H5.H5Sextent_equal(sid, decoded_sid);
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assertTrue("H5.testH5Sextent_equal", result);
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/* Verify decoded dataspace */
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lresult = H5.H5Sget_simple_extent_npoints(decoded_sid);
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assertTrue("H5.testH5Sget_simple_extent_npoints", lresult == 1);
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iresult = H5.H5Sget_simple_extent_ndims(decoded_sid);
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assertTrue("H5.testH5Sget_simple_extent_ndims", iresult == 0);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Sdecode " + err);
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}
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finally {
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try {
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H5.H5Sclose(decoded_sid);
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}
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catch (Exception ex) {
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}
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try {
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H5.H5Sclose(sid);
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}
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catch (Exception ex) {
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}
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}
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}
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@Test
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public void testH5Sselect_none()
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{
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int read_type = -1;
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try {
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H5.H5Sselect_none(H5sid);
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read_type = H5.H5Sget_select_type(H5sid);
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assertTrue("H5.H5Sget_select_type: " + read_type, HDF5Constants.H5S_SEL_NONE == read_type);
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H5.H5Sselect_all(H5sid);
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read_type = H5.H5Sget_select_type(H5sid);
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assertTrue("H5.H5Sget_select_type: " + read_type, HDF5Constants.H5S_SEL_ALL == read_type);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Sset_extent_none: " + err);
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}
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}
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@Test
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public void testH5Sget_select_npoints()
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{
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long coord[][] = {{0, 1}, {2, 4}, {5, 6}}; /* Coordinates for point selection */
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long num_elements = -1;
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try {
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H5.H5Sselect_elements(H5sid, HDF5Constants.H5S_SELECT_SET, 3, coord);
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num_elements = H5.H5Sget_select_npoints(H5sid);
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assertTrue("H5.H5Sget_select_npoints: " + num_elements, 3 == num_elements);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Sget_select_npoints: " + err);
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}
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}
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@Test(expected = HDF5FunctionArgumentException.class)
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public void testH5Sget_select_elem_pointlist_invalid() throws Throwable
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{
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long coord[][] = {{0, 1}, {2, 4}, {5, 6}}; /* Coordinates for point selection */
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long getcoord[] = {-1, -1}; /* Coordinates for get point selection */
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try {
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H5.H5Sselect_elements(H5sid, HDF5Constants.H5S_SELECT_SET, 3, coord);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Sget_select_elem_pointlist: " + err);
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}
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H5.H5Sget_select_elem_pointlist(H5sid, 0, 3, getcoord);
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}
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@Test
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public void testH5Sget_select_elem_pointlist()
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{
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long coord[][] = {{0, 1}, {2, 3}, {4, 5}}; /* Coordinates for point selection */
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long getcoord[] = {-1, -1, -1, -1, -1, -1}; /* Coordinates for get point selection */
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try {
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H5.H5Sselect_elements(H5sid, HDF5Constants.H5S_SELECT_SET, 3, coord);
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H5.H5Sget_select_elem_pointlist(H5sid, 0, 3, getcoord);
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assertTrue("H5.H5Sget_select_elem_pointlist:" + getcoord[0], coord[0][0] == getcoord[0]);
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assertTrue("H5.H5Sget_select_elem_pointlist:" + getcoord[1], coord[0][1] == getcoord[1]);
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assertTrue("H5.H5Sget_select_elem_pointlist:" + getcoord[2], coord[1][0] == getcoord[2]);
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assertTrue("H5.H5Sget_select_elem_pointlist:" + getcoord[3], coord[1][1] == getcoord[3]);
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assertTrue("H5.H5Sget_select_elem_pointlist:" + getcoord[4], coord[2][0] == getcoord[4]);
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assertTrue("H5.H5Sget_select_elem_pointlist:" + getcoord[5], coord[2][1] == getcoord[5]);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Sget_select_elem_pointlist: " + err);
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}
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}
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@Test
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public void testH5Sget_select_bounds()
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{
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long lowbounds[] = {-1, -1};
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long hibounds[] = {-1, -1};
|
|
try {
|
|
H5.H5Sget_select_bounds(H5sid, lowbounds, hibounds);
|
|
assertTrue("H5.H5Sget_select_bounds:" + lowbounds[0], 0 == lowbounds[0]);
|
|
assertTrue("H5.H5Sget_select_bounds:" + lowbounds[1], 0 == lowbounds[1]);
|
|
assertTrue("H5.H5Sget_select_bounds:" + hibounds[0], (H5dims[0] - 1) == hibounds[0]);
|
|
assertTrue("H5.H5Sget_select_bounds:" + hibounds[1], (H5dims[1] - 1) == hibounds[1]);
|
|
}
|
|
catch (Throwable err) {
|
|
err.printStackTrace();
|
|
fail("H5.H5Sget_select_bounds: " + err);
|
|
}
|
|
}
|
|
|
|
@Test
|
|
public void testH5Soffset_simple()
|
|
{
|
|
long coord[][] = {{2, 2}, {2, 4}, {4, 2}, {4, 4}}; /* Coordinates for point selection */
|
|
long lowbounds[] = {-1, -1};
|
|
long hibounds[] = {-1, -1};
|
|
try {
|
|
H5.H5Sselect_elements(H5sid, HDF5Constants.H5S_SELECT_SET, 4, coord);
|
|
H5.H5Sget_select_bounds(H5sid, lowbounds, hibounds);
|
|
assertTrue("H5.H5Sget_select_bounds:" + lowbounds[0], 2 == lowbounds[0]);
|
|
assertTrue("H5.H5Sget_select_bounds:" + lowbounds[1], 2 == lowbounds[1]);
|
|
assertTrue("H5.H5Sget_select_bounds:" + hibounds[0], (H5dims[0] - 1) == hibounds[0]);
|
|
assertTrue("H5.H5Sget_select_bounds:" + hibounds[1], (H5dims[1] - 1) == hibounds[1]);
|
|
}
|
|
catch (Throwable err) {
|
|
err.printStackTrace();
|
|
fail("H5.H5Sget_select_bounds: " + err);
|
|
}
|
|
try {
|
|
long offset[] = {-1, -1};
|
|
H5.H5Soffset_simple(H5sid, offset);
|
|
H5.H5Sget_select_bounds(H5sid, lowbounds, hibounds);
|
|
assertTrue("H5.H5Sget_select_bounds:" + lowbounds[0], 1 == lowbounds[0]);
|
|
assertTrue("H5.H5Sget_select_bounds:" + lowbounds[1], 1 == lowbounds[1]);
|
|
assertTrue("H5.H5Sget_select_bounds:" + hibounds[0], (H5dims[0] - 2) == hibounds[0]);
|
|
assertTrue("H5.H5Sget_select_bounds:" + hibounds[1], (H5dims[1] - 2) == hibounds[1]);
|
|
}
|
|
catch (Throwable err) {
|
|
err.printStackTrace();
|
|
fail("H5.H5Soffset_simple: " + err);
|
|
}
|
|
}
|
|
|
|
@Test
|
|
public void testH5Sget_select_hyper()
|
|
{
|
|
long space1 = HDF5Constants.H5I_INVALID_HID;
|
|
long start[] = {0, 0};
|
|
long stride[] = {1, 1};
|
|
long count[] = {1, 1};
|
|
long block[] = {4, 4};
|
|
long nblocks; // Number of hyperslab blocks
|
|
long blocks[] = {-1, -1, -1, -1, -1, -1, -1, -1}; // List of blocks
|
|
try {
|
|
// Copy "all" selection & space
|
|
space1 = H5.H5Scopy(H5sid);
|
|
assertTrue("H5.H5Scopy", H5sid > 0);
|
|
// 'AND' "all" selection with another hyperslab
|
|
H5.H5Sselect_hyperslab(space1, HDF5Constants.H5S_SELECT_AND, start, stride, count, block);
|
|
|
|
// Verify that there is only one block
|
|
nblocks = H5.H5Sget_select_hyper_nblocks(space1);
|
|
assertTrue("H5Sget_select_hyper_nblocks", nblocks == 1);
|
|
|
|
// Retrieve the block defined
|
|
H5.H5Sget_select_hyper_blocklist(space1, 0, nblocks, blocks);
|
|
|
|
// Verify that the correct block is defined
|
|
assertTrue("H5.H5Sget_select_hyper_blocklist:" + blocks[0], start[0] == blocks[0]);
|
|
assertTrue("H5.H5Sget_select_hyper_blocklist:" + blocks[1], start[1] == blocks[1]);
|
|
assertTrue("H5.H5Sget_select_hyper_blocklist:" + blocks[2], (block[0] - 1) == blocks[2]);
|
|
assertTrue("H5.H5Sget_select_hyper_blocklist:" + blocks[3], (block[1] - 1) == blocks[3]);
|
|
}
|
|
catch (Throwable err) {
|
|
err.printStackTrace();
|
|
fail("H5.H5Sget_select_bounds: " + err);
|
|
}
|
|
finally {
|
|
try {
|
|
H5.H5Sclose(space1);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
}
|
|
}
|
|
|
|
@Test
|
|
public void testH5Sget_select_valid()
|
|
{
|
|
long space1 = HDF5Constants.H5I_INVALID_HID;
|
|
long start[] = {1, 0};
|
|
long stride[] = {1, 1};
|
|
long count[] = {2, 3};
|
|
long block[] = {1, 1};
|
|
long offset[] = {0, 0}; // Offset of selection
|
|
|
|
try {
|
|
// Copy "all" selection & space
|
|
space1 = H5.H5Scopy(H5sid);
|
|
assertTrue("H5.H5Scopy", H5sid > 0);
|
|
// 'AND' "all" selection with another hyperslab
|
|
H5.H5Sselect_hyperslab(space1, HDF5Constants.H5S_SELECT_SET, start, stride, count, block);
|
|
|
|
// Check a valid offset
|
|
offset[0] = -1;
|
|
offset[1] = 0;
|
|
H5.H5Soffset_simple(space1, offset);
|
|
assertTrue("H5Sselect_valid", H5.H5Sselect_valid(space1));
|
|
|
|
// Check an invalid offset
|
|
offset[0] = 10;
|
|
offset[1] = 0;
|
|
H5.H5Soffset_simple(space1, offset);
|
|
assertFalse("H5Sselect_valid", H5.H5Sselect_valid(space1));
|
|
|
|
/* Reset offset */
|
|
offset[0] = 0;
|
|
offset[1] = 0;
|
|
H5.H5Soffset_simple(space1, offset);
|
|
assertTrue("H5Sselect_valid", H5.H5Sselect_valid(space1));
|
|
}
|
|
catch (Throwable err) {
|
|
err.printStackTrace();
|
|
fail("testH5Sget_select_valid: " + err);
|
|
}
|
|
finally {
|
|
try {
|
|
H5.H5Sclose(space1);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
}
|
|
}
|
|
|
|
@Test
|
|
public void testH5Shyper_regular()
|
|
{
|
|
long start[] = {1, 0};
|
|
long stride[] = {1, 1};
|
|
long count[] = {2, 3};
|
|
long block[] = {1, 1};
|
|
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 {
|
|
// Set "regular" hyperslab selection
|
|
H5.H5Sselect_hyperslab(H5sid, HDF5Constants.H5S_SELECT_SET, start, stride, count, block);
|
|
|
|
// Query if 'hyperslab' selection is regular hyperslab (should be TRUE)
|
|
is_regular = H5.H5Sis_regular_hyperslab(H5sid);
|
|
assertTrue("H5.H5Sis_regular_hyperslab", is_regular);
|
|
|
|
// Retrieve the hyperslab parameters
|
|
H5.H5Sget_regular_hyperslab(H5sid, q_start, q_stride, q_count, q_block);
|
|
|
|
/* Verify the hyperslab parameters */
|
|
for (int u = 0; u < H5rank; 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]);
|
|
} /* end for */
|
|
}
|
|
catch (Throwable err) {
|
|
err.printStackTrace();
|
|
fail("testH5Sget_select_valid: " + err);
|
|
}
|
|
}
|
|
}
|