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.
1951 lines
72 KiB
Java
1951 lines
72 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 java.io.File;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.List;
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import hdf.hdf5lib.H5;
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import hdf.hdf5lib.HDF5Constants;
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import hdf.hdf5lib.HDFNativeData;
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import hdf.hdf5lib.callbacks.H5D_iterate_cb;
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import hdf.hdf5lib.callbacks.H5D_iterate_t;
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import hdf.hdf5lib.exceptions.HDF5Exception;
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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.Ignore;
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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 TestH5D {
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@Rule
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public TestName testname = new TestName();
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private static final String H5_FILE = "testD.h5";
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private static final int DIM_X = 4;
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private static final int DIM_Y = 6;
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private static final int RANK = 2;
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long H5fid = HDF5Constants.H5I_INVALID_HID;
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long H5faplid = HDF5Constants.H5I_INVALID_HID;
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long H5dsid = HDF5Constants.H5I_INVALID_HID;
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long H5dtid = HDF5Constants.H5I_INVALID_HID;
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long H5did = HDF5Constants.H5I_INVALID_HID;
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long H5did0 = HDF5Constants.H5I_INVALID_HID;
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long H5dcpl_id = HDF5Constants.H5I_INVALID_HID;
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long[] H5dims = {DIM_X, DIM_Y};
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// Values for the status of space allocation
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enum H5D_space_status {
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H5D_SPACE_STATUS_ERROR(-1),
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H5D_SPACE_STATUS_NOT_ALLOCATED(0),
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H5D_SPACE_STATUS_PART_ALLOCATED(1),
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H5D_SPACE_STATUS_ALLOCATED(2);
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private int code;
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H5D_space_status(int space_status) { this.code = space_status; }
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public int getCode() { return this.code; }
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}
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private final void _deleteFile(String filename)
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{
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File file = new File(filename);
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if (file.exists()) {
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try {
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file.delete();
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}
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catch (SecurityException e) {
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}
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}
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}
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private final void _createPDataset(long fid, long dsid, String name, long dcpl_val)
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{
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try {
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H5dcpl_id = H5.H5Pcreate(dcpl_val);
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}
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catch (Exception err) {
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err.printStackTrace();
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fail("H5.H5Pcreate: " + err);
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}
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assertTrue("testH5D._createPDataset: H5.H5Pcreate: ", H5dcpl_id >= 0);
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// Set the allocation time to "early". This way we can be sure
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// that reading from the dataset immediately after creation will
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// return the fill value.
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try {
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H5.H5Pset_alloc_time(H5dcpl_id, HDF5Constants.H5D_ALLOC_TIME_EARLY);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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try {
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H5did0 = H5.H5Dcreate(fid, name, HDF5Constants.H5T_STD_I32BE, dsid, HDF5Constants.H5P_DEFAULT,
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H5dcpl_id, HDF5Constants.H5P_DEFAULT);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Dcreate: " + err);
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}
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assertTrue("TestH5D._createPDataset.H5Dcreate: ", H5did0 >= 0);
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}
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private final void _createChunkDataset(long fid, long dsid, String name, long dapl)
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{
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try {
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H5dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE);
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}
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catch (Exception err) {
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err.printStackTrace();
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fail("H5.H5Pcreate: " + err);
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}
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assertTrue("testH5D._createChunkDataset: H5.H5Pcreate: ", H5dcpl_id >= 0);
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// Set the chunking.
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long[] chunk_dim = {4, 4};
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try {
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H5.H5Pset_chunk(H5dcpl_id, RANK, chunk_dim);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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try {
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H5did = H5.H5Dcreate(fid, name, HDF5Constants.H5T_STD_I32BE, dsid, HDF5Constants.H5P_DEFAULT,
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H5dcpl_id, dapl);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Dcreate: " + err);
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}
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assertTrue("TestH5D._createChunkDataset.H5Dcreate: ", H5did >= 0);
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}
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private final void _createDataset(long fid, long dsid, String name, long dapl)
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{
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try {
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H5did = H5.H5Dcreate(fid, name, HDF5Constants.H5T_STD_I32BE, dsid, HDF5Constants.H5P_DEFAULT,
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HDF5Constants.H5P_DEFAULT, dapl);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Dcreate: " + err);
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}
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assertTrue("TestH5D._createDataset.H5Dcreate: ", H5did >= 0);
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}
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private final void _createVLStrDataset(String name, long dapl)
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{
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try {
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H5dtid = H5.H5Tcopy(HDF5Constants.H5T_C_S1);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Tcopy: " + err);
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}
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assertTrue("TestH5D._createVLStrDataset.H5Tcopy: ", H5dtid >= 0);
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try {
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H5.H5Tset_size(H5dtid, HDF5Constants.H5T_VARIABLE);
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assertTrue("TestH5D._createVLStrDataset.H5Tis_variable_str", H5.H5Tis_variable_str(H5dtid));
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Tset_size: " + err);
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}
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try {
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H5did = H5.H5Dcreate(H5fid, name, H5dtid, H5dsid, HDF5Constants.H5P_DEFAULT,
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HDF5Constants.H5P_DEFAULT, dapl);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Dcreate: " + err);
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}
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assertTrue("TestH5D._createVLStrDataset.H5Dcreate: ", H5did >= 0);
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}
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private final void _closeH5file() throws HDF5LibraryException
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{
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if (H5dcpl_id >= 0)
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try {
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H5.H5Pclose(H5dcpl_id);
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}
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catch (Exception ex) {
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}
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if (H5did0 >= 0)
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try {
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H5.H5Dclose(H5did0);
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}
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catch (Exception ex) {
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}
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if (H5did >= 0)
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try {
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H5.H5Dclose(H5did);
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}
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catch (Exception ex) {
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}
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if (H5dtid > 0)
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try {
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H5.H5Tclose(H5dtid);
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}
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catch (Exception ex) {
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}
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if (H5dsid > 0)
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try {
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H5.H5Sclose(H5dsid);
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}
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catch (Exception ex) {
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}
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if (H5fid > 0)
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try {
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H5.H5Fclose(H5fid);
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}
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catch (Exception ex) {
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}
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}
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private final void _openH5file(String filename, String dsetname, long dapl)
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{
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try {
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H5fid = H5.H5Fopen(filename, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("TestH5D._openH5file: " + err);
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}
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assertTrue("TestH5D._openH5file: H5.H5Fopen: ", H5fid >= 0);
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try {
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H5did = H5.H5Dopen(H5fid, dsetname, dapl);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("TestH5D._openH5file: " + err);
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}
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assertTrue("TestH5D._openH5file: H5.H5Dopen: ", H5did >= 0);
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try {
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H5dsid = H5.H5Dget_space(H5did);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("TestH5D._openH5file: " + err);
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}
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assertTrue("TestH5D._openH5file: H5.H5Screate_simple: ", H5dsid > 0);
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}
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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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try {
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H5faplid = H5.H5Pcreate(HDF5Constants.H5P_FILE_ACCESS);
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H5fid = H5.H5Fcreate(H5_FILE, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, H5faplid);
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H5dsid = H5.H5Screate_simple(RANK, H5dims, null);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("TestH5D.createH5file: " + err);
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}
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assertTrue("TestH5D.createH5file: H5.H5Fcreate: ", H5fid >= 0);
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assertTrue("TestH5D.createH5file: H5.H5Screate_simple: ", H5dsid >= 0);
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H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
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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 (H5dcpl_id >= 0)
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try {
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H5.H5Pclose(H5dcpl_id);
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}
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catch (Exception ex) {
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}
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if (H5did0 >= 0)
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try {
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H5.H5Dclose(H5did0);
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}
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catch (Exception ex) {
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}
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if (H5did >= 0)
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try {
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H5.H5Dclose(H5did);
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}
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catch (Exception ex) {
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}
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if (H5dtid > 0)
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try {
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H5.H5Tclose(H5dtid);
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}
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catch (Exception ex) {
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}
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if (H5dsid > 0)
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try {
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H5.H5Sclose(H5dsid);
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}
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catch (Exception ex) {
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}
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if (H5faplid >= 0)
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try {
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H5.H5Pclose(H5faplid);
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}
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catch (Exception ex) {
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}
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if (H5fid > 0)
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try {
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H5.H5Fclose(H5fid);
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}
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catch (Exception ex) {
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}
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_deleteFile(H5_FILE);
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System.out.println();
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}
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@Test
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public void testH5Dcreate()
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{
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long dataset_id = HDF5Constants.H5I_INVALID_HID;
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try {
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dataset_id =
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H5.H5Dcreate(H5fid, "dset", HDF5Constants.H5T_STD_I32BE, H5dsid, HDF5Constants.H5P_DEFAULT,
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HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
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}
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catch (Exception err) {
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err.printStackTrace();
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fail("testH5Dcreate: " + err);
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}
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assertTrue(dataset_id >= 0);
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// End access to the dataset and release resources used by it.
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try {
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if (dataset_id >= 0)
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H5.H5Dclose(dataset_id);
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}
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catch (Exception err) {
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err.printStackTrace();
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}
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}
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@Test
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public void testH5Dcreate_anon()
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{
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long dataset_id = HDF5Constants.H5I_INVALID_HID;
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try {
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dataset_id = H5.H5Dcreate_anon(H5fid, HDF5Constants.H5T_STD_I32BE, H5dsid,
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HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
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}
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catch (Exception err) {
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err.printStackTrace();
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fail("testH5Dcreate_anon: " + err);
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}
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assertTrue(dataset_id >= 0);
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// End access to the dataset and release resources used by it.
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try {
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if (dataset_id >= 0)
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H5.H5Dclose(dataset_id);
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}
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catch (Exception err) {
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err.printStackTrace();
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}
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}
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@Test
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public void testH5Dopen()
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{
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long dataset_id = HDF5Constants.H5I_INVALID_HID;
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_createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT);
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try {
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H5.H5Dclose(H5did);
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H5did = HDF5Constants.H5I_INVALID_HID;
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dataset_id = H5.H5Dopen(H5fid, "dset", HDF5Constants.H5P_DEFAULT);
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}
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catch (Exception err) {
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err.printStackTrace();
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fail("testH5Dopen: " + err);
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}
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assertTrue("testH5Dopen: ", dataset_id >= 0);
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// End access to the dataset and release resources used by it.
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try {
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if (dataset_id >= 0)
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H5.H5Dclose(dataset_id);
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}
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catch (Exception err) {
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err.printStackTrace();
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}
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}
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@Test
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public void testH5Dget_storage_size_empty()
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{
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long storage_size = 0;
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_createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT);
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try {
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storage_size = H5.H5Dget_storage_size(H5did);
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}
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catch (Exception err) {
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err.printStackTrace();
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fail("testH5Dget_storage_size: " + err);
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}
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assertTrue("testH5Dget_storage_size: ", storage_size == 0);
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}
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@Test
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public void testH5Dget_storage_size()
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{
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long storage_size = 0;
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int[][] dset_data = new int[DIM_X][DIM_Y];
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int FILLVAL = 99;
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_createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT);
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// Initialize the dataset.
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for (int indx = 0; indx < DIM_X; indx++)
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for (int jndx = 0; jndx < DIM_Y; jndx++)
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dset_data[indx][jndx] = FILLVAL;
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try {
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if (H5did >= 0)
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H5.H5Dwrite(H5did, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
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HDF5Constants.H5P_DEFAULT, dset_data[0]);
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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try {
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storage_size = H5.H5Dget_storage_size(H5did);
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}
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catch (Exception err) {
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err.printStackTrace();
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fail("testH5Dget_storage_size: " + err);
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}
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assertTrue("testH5Dget_storage_size: " + storage_size, storage_size == DIM_X * DIM_Y * 4);
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}
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@Test
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public void testH5Dget_access_plist()
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{
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long dapl_id = HDF5Constants.H5I_INVALID_HID;
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long test_dapl_id = HDF5Constants.H5I_INVALID_HID;
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int[] mdc_nelmts1 = {0};
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int[] mdc_nelmts2 = {0};
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long[] rdcc_nelmts1 = {0};
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long[] rdcc_nelmts2 = {0};
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long[] rdcc_nbytes1 = {0};
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long[] rdcc_nbytes2 = {0};
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double[] rdcc_w01 = {0};
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double[] rdcc_w02 = {0};
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try {
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test_dapl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_ACCESS);
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}
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catch (Exception err) {
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err.printStackTrace();
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fail("testH5Dget_access_plist: H5.H5Pcreate: " + err);
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}
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assertTrue("testH5Dget_access_plist: test_dapl_id: ", test_dapl_id >= 0);
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try {
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H5.H5Pget_cache(H5faplid, mdc_nelmts1, rdcc_nelmts1, rdcc_nbytes1, rdcc_w01);
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}
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catch (Exception err) {
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err.printStackTrace();
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fail("testH5Dget_access_plist: H5.H5Pget_cache: " + err);
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}
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|
_createChunkDataset(H5fid, H5dsid, "dset", test_dapl_id);
|
|
|
|
try {
|
|
dapl_id = H5.H5Dget_access_plist(H5did);
|
|
assertTrue("testH5Dget_access_plist: dapl_id: ", dapl_id >= 0);
|
|
H5.H5Pget_chunk_cache(dapl_id, rdcc_nelmts2, rdcc_nbytes2, rdcc_w02);
|
|
}
|
|
catch (Exception err) {
|
|
err.printStackTrace();
|
|
fail("testH5Dget_access_plist: H5.H5Dget_access_plist: " + err);
|
|
}
|
|
|
|
// End access to the dataset and release resources used by it.
|
|
try {
|
|
if (dapl_id >= 0)
|
|
H5.H5Pclose(dapl_id);
|
|
}
|
|
catch (Exception err) {
|
|
err.printStackTrace();
|
|
}
|
|
try {
|
|
if (test_dapl_id >= 0)
|
|
H5.H5Pclose(test_dapl_id);
|
|
}
|
|
catch (Exception err) {
|
|
err.printStackTrace();
|
|
}
|
|
assertTrue("testH5Dget_access_plist: ", rdcc_nelmts2 == rdcc_nelmts2 && rdcc_nbytes2 == rdcc_nbytes2);
|
|
}
|
|
|
|
@Test
|
|
public void testH5Dget_space_status()
|
|
{
|
|
int[][] write_dset_data = new int[DIM_X][DIM_Y];
|
|
int space_status = -1;
|
|
int space_status0 = -1;
|
|
|
|
// Initialize the dataset.
|
|
for (int indx = 0; indx < DIM_X; indx++)
|
|
for (int jndx = 0; jndx < DIM_Y; jndx++)
|
|
write_dset_data[indx][jndx] = indx * jndx - jndx;
|
|
|
|
_createPDataset(H5fid, H5dsid, "dset0", HDF5Constants.H5P_DATASET_CREATE);
|
|
_createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT);
|
|
|
|
// Retrieve and print space status and storage size for dset0.
|
|
try {
|
|
space_status0 = H5.H5Dget_space_status(H5did0);
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
assertTrue("testH5Dget_space_status0 - H5.H5Dget_space_status: ",
|
|
space_status0 == H5D_space_status.H5D_SPACE_STATUS_ALLOCATED.getCode());
|
|
|
|
// Retrieve and print space status and storage size for dset.
|
|
try {
|
|
space_status = H5.H5Dget_space_status(H5did);
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
assertFalse("testH5Dget_space_status - H5.H5Dget_space_status: ",
|
|
space_status == H5D_space_status.H5D_SPACE_STATUS_ALLOCATED.getCode());
|
|
|
|
// Write the data to the dataset.
|
|
try {
|
|
H5.H5Dwrite(H5did, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
|
|
HDF5Constants.H5P_DEFAULT, write_dset_data);
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
|
|
// Retrieve and print space status and storage size for dset.
|
|
try {
|
|
space_status = H5.H5Dget_space_status(H5did);
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
assertTrue("testH5Dget_space_status - H5.H5Dget_space_status: ",
|
|
space_status == H5D_space_status.H5D_SPACE_STATUS_ALLOCATED.getCode());
|
|
}
|
|
|
|
@Test(expected = HDF5LibraryException.class)
|
|
public void testH5Dget_space_closed() throws Throwable
|
|
{
|
|
long dataset_id = HDF5Constants.H5I_INVALID_HID;
|
|
try {
|
|
dataset_id =
|
|
H5.H5Dcreate(H5fid, "dset", HDF5Constants.H5T_STD_I32BE, H5dsid, HDF5Constants.H5P_DEFAULT,
|
|
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
|
|
}
|
|
catch (Throwable err) {
|
|
err.printStackTrace();
|
|
fail("H5.H5Dcreate: " + err);
|
|
}
|
|
assertTrue("TestH5D.testH5Dget_space_closed: ", dataset_id >= 0);
|
|
H5.H5Dclose(dataset_id);
|
|
|
|
H5.H5Dget_space(dataset_id);
|
|
}
|
|
|
|
@Test
|
|
public void testH5Dget_space()
|
|
{
|
|
long dataspace_id = HDF5Constants.H5I_INVALID_HID;
|
|
_createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT);
|
|
|
|
try {
|
|
dataspace_id = H5.H5Dget_space(H5did);
|
|
}
|
|
catch (Exception err) {
|
|
err.printStackTrace();
|
|
fail("H5.H5Dget_space: " + err);
|
|
}
|
|
assertTrue("TestH5D.testH5Dget_space: ", dataspace_id >= 0);
|
|
|
|
// End access to the dataspace and release resources used by it.
|
|
try {
|
|
if (dataspace_id >= 0)
|
|
H5.H5Sclose(dataspace_id);
|
|
}
|
|
catch (Exception err) {
|
|
err.printStackTrace();
|
|
}
|
|
}
|
|
|
|
@Test(expected = HDF5LibraryException.class)
|
|
public void testH5Dget_type_closed() throws Throwable
|
|
{
|
|
long dataset_id = HDF5Constants.H5I_INVALID_HID;
|
|
try {
|
|
dataset_id =
|
|
H5.H5Dcreate(H5fid, "dset", HDF5Constants.H5T_STD_I32BE, H5dsid, HDF5Constants.H5P_DEFAULT,
|
|
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
|
|
}
|
|
catch (Throwable err) {
|
|
err.printStackTrace();
|
|
fail("H5.H5Dcreate: " + err);
|
|
}
|
|
assertTrue("TestH5D.testH5Dget_type_closed: ", dataset_id >= 0);
|
|
H5.H5Dclose(dataset_id);
|
|
|
|
H5.H5Dget_type(dataset_id);
|
|
}
|
|
|
|
@Test
|
|
public void testH5Dget_type()
|
|
{
|
|
long datatype_id = HDF5Constants.H5I_INVALID_HID;
|
|
_createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT);
|
|
|
|
try {
|
|
datatype_id = H5.H5Dget_type(H5did);
|
|
}
|
|
catch (Exception err) {
|
|
err.printStackTrace();
|
|
fail("H5.H5Dget_type: " + err);
|
|
}
|
|
assertTrue("TestH5D.testH5Dget_type: ", datatype_id >= 0);
|
|
|
|
// End access to the datatype and release resources used by it.
|
|
try {
|
|
if (datatype_id >= 0)
|
|
H5.H5Tclose(datatype_id);
|
|
}
|
|
catch (Exception err) {
|
|
err.printStackTrace();
|
|
}
|
|
}
|
|
|
|
@Test
|
|
public void testH5Dget_offset()
|
|
{
|
|
int[][] write_dset_data = new int[DIM_X][DIM_Y];
|
|
long dset_address = 0;
|
|
_createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT);
|
|
|
|
try {
|
|
// Test dataset address. Should be undefined.
|
|
dset_address = H5.H5Dget_offset(H5did);
|
|
}
|
|
catch (HDF5LibraryException hdfex) {
|
|
;
|
|
}
|
|
catch (Exception err) {
|
|
err.printStackTrace();
|
|
fail("H5.H5Dget_offset: " + err);
|
|
}
|
|
// Write the data to the dataset.
|
|
try {
|
|
H5.H5Dwrite(H5did, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
|
|
HDF5Constants.H5P_DEFAULT, write_dset_data);
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
|
|
try {
|
|
// Test dataset address.
|
|
dset_address = H5.H5Dget_offset(H5did);
|
|
}
|
|
catch (Exception err) {
|
|
err.printStackTrace();
|
|
fail("H5.H5Dget_offset: " + err);
|
|
}
|
|
|
|
assertTrue("TestH5D.testH5Dget_offset: ", dset_address >= 0);
|
|
}
|
|
|
|
@Test
|
|
public void testH5Dfill_null()
|
|
{
|
|
int[] buf_data = new int[DIM_X * DIM_Y];
|
|
|
|
// Initialize memory buffer
|
|
for (int indx = 0; indx < DIM_X; indx++)
|
|
for (int jndx = 0; jndx < DIM_Y; jndx++) {
|
|
buf_data[(indx * DIM_Y) + jndx] = indx * jndx - jndx;
|
|
}
|
|
byte[] buf_array = HDFNativeData.intToByte(0, DIM_X * DIM_Y, buf_data);
|
|
|
|
// Fill selection in memory
|
|
try {
|
|
H5.H5Dfill(null, HDF5Constants.H5T_NATIVE_UINT, buf_array, HDF5Constants.H5T_NATIVE_UINT, H5dsid);
|
|
}
|
|
catch (Exception err) {
|
|
err.printStackTrace();
|
|
fail("H5.H5Dfill: " + err);
|
|
}
|
|
buf_data = HDFNativeData.byteToInt(buf_array);
|
|
|
|
// Verify memory buffer the hard way
|
|
for (int indx = 0; indx < DIM_X; indx++)
|
|
for (int jndx = 0; jndx < DIM_Y; jndx++)
|
|
assertTrue("H5.H5Dfill: [" + indx + "," + jndx + "] ", buf_data[(indx * DIM_Y) + jndx] == 0);
|
|
}
|
|
|
|
@Test
|
|
public void testH5Dfill()
|
|
{
|
|
int[] buf_data = new int[DIM_X * DIM_Y];
|
|
byte[] fill_value = HDFNativeData.intToByte(254);
|
|
|
|
// Initialize memory buffer
|
|
for (int indx = 0; indx < DIM_X; indx++)
|
|
for (int jndx = 0; jndx < DIM_Y; jndx++) {
|
|
buf_data[(indx * DIM_Y) + jndx] = indx * jndx - jndx;
|
|
}
|
|
byte[] buf_array = HDFNativeData.intToByte(0, DIM_X * DIM_Y, buf_data);
|
|
|
|
// Fill selection in memory
|
|
try {
|
|
H5.H5Dfill(fill_value, HDF5Constants.H5T_NATIVE_UINT, buf_array, HDF5Constants.H5T_NATIVE_UINT,
|
|
H5dsid);
|
|
}
|
|
catch (Exception err) {
|
|
err.printStackTrace();
|
|
fail("H5.H5Dfill: " + err);
|
|
}
|
|
buf_data = HDFNativeData.byteToInt(buf_array);
|
|
|
|
// Verify memory buffer the hard way
|
|
for (int indx = 0; indx < DIM_X; indx++)
|
|
for (int jndx = 0; jndx < DIM_Y; jndx++)
|
|
assertTrue("H5.H5Dfill: [" + indx + "," + jndx + "] ",
|
|
buf_data[(indx * DIM_Y) + jndx] == 254);
|
|
}
|
|
|
|
@Test
|
|
public void testH5Diterate()
|
|
{
|
|
final int SPACE_RANK = 2;
|
|
final int SPACE_FILL = 254;
|
|
|
|
class H5D_iter_data implements H5D_iterate_t {
|
|
public int fill_value; /* The fill value to check */
|
|
public long fill_curr_coord; /* Current coordinate to examine */
|
|
public long[] fill_coords; /* Pointer to selection's coordinates */
|
|
}
|
|
|
|
H5D_iterate_t iter_data = new H5D_iter_data();
|
|
|
|
class H5D_iter_callback implements H5D_iterate_cb {
|
|
public int callback(byte[] elem_buf, long elem_id, int ndim, long[] point, H5D_iterate_t op_data)
|
|
{
|
|
// Check value in current buffer location
|
|
int element = HDFNativeData.byteToInt(elem_buf, 0);
|
|
if (element != ((H5D_iter_data)op_data).fill_value)
|
|
return -1;
|
|
// Check number of dimensions
|
|
if (ndim != SPACE_RANK)
|
|
return (-1);
|
|
// Check Coordinates
|
|
long[] fill_coords = new long[2];
|
|
fill_coords[0] =
|
|
((H5D_iter_data)op_data).fill_coords[(int)(2 * ((H5D_iter_data)op_data).fill_curr_coord)];
|
|
fill_coords[1] = ((H5D_iter_data)op_data)
|
|
.fill_coords[(int)(2 * ((H5D_iter_data)op_data).fill_curr_coord) + 1];
|
|
((H5D_iter_data)op_data).fill_curr_coord++;
|
|
if (fill_coords[0] != point[0])
|
|
return (-1);
|
|
if (fill_coords[1] != point[1])
|
|
return (-1);
|
|
|
|
return (0);
|
|
}
|
|
}
|
|
|
|
int[] buf_data = new int[DIM_X * DIM_Y];
|
|
byte[] fill_value = HDFNativeData.intToByte(SPACE_FILL);
|
|
|
|
// Initialize memory buffer
|
|
for (int indx = 0; indx < DIM_X; indx++)
|
|
for (int jndx = 0; jndx < DIM_Y; jndx++) {
|
|
buf_data[(indx * DIM_Y) + jndx] = indx * jndx - jndx;
|
|
}
|
|
byte[] buf_array = HDFNativeData.intToByte(0, DIM_X * DIM_Y, buf_data);
|
|
|
|
// Fill selection in memory
|
|
try {
|
|
H5.H5Dfill(fill_value, HDF5Constants.H5T_NATIVE_UINT, buf_array, HDF5Constants.H5T_NATIVE_UINT,
|
|
H5dsid);
|
|
}
|
|
catch (Exception err) {
|
|
err.printStackTrace();
|
|
fail("H5.H5Diterate: " + err);
|
|
}
|
|
|
|
// Initialize the iterator structure
|
|
((H5D_iter_data)iter_data).fill_value = SPACE_FILL;
|
|
((H5D_iter_data)iter_data).fill_curr_coord = 0;
|
|
// Set the coordinates of the selection
|
|
((H5D_iter_data)iter_data).fill_coords =
|
|
new long[DIM_X * DIM_Y * SPACE_RANK]; /* Coordinates of selection */
|
|
for (int indx = 0; indx < DIM_X; indx++)
|
|
for (int jndx = 0; jndx < DIM_Y; jndx++) {
|
|
((H5D_iter_data)iter_data).fill_coords[2 * (indx * DIM_Y + jndx)] = indx;
|
|
((H5D_iter_data)iter_data).fill_coords[2 * (indx * DIM_Y + jndx) + 1] = jndx;
|
|
} /* end for */
|
|
|
|
// Iterate through selection, verifying correct data
|
|
H5D_iterate_cb iter_cb = new H5D_iter_callback();
|
|
int op_status = -1;
|
|
try {
|
|
op_status = H5.H5Diterate(buf_array, HDF5Constants.H5T_NATIVE_UINT, H5dsid, iter_cb, iter_data);
|
|
}
|
|
catch (Throwable err) {
|
|
err.printStackTrace();
|
|
fail("H5.H5Diterate: " + err);
|
|
}
|
|
assertTrue("H5Diterate ", op_status == 0);
|
|
}
|
|
|
|
@Test
|
|
public void testH5Diterate_write()
|
|
{
|
|
final int SPACE_RANK = 2;
|
|
final int SPACE_FILL = 254;
|
|
|
|
class H5D_iter_data implements H5D_iterate_t {
|
|
public int fill_value; /* The fill value to check */
|
|
public long fill_curr_coord; /* Current coordinate to examine */
|
|
public long[] fill_coords; /* Pointer to selection's coordinates */
|
|
}
|
|
|
|
H5D_iterate_t iter_data = new H5D_iter_data();
|
|
|
|
class H5D_iter_callback implements H5D_iterate_cb {
|
|
public int callback(byte[] elem_buf, long elem_id, int ndim, long[] point, H5D_iterate_t op_data)
|
|
{
|
|
// Check value in current buffer location
|
|
int element = HDFNativeData.byteToInt(elem_buf, 0);
|
|
if (element != ((H5D_iter_data)op_data).fill_value)
|
|
return -1;
|
|
// Check number of dimensions
|
|
if (ndim != SPACE_RANK)
|
|
return (-1);
|
|
// Check Coordinates
|
|
long[] fill_coords = new long[2];
|
|
fill_coords[0] =
|
|
((H5D_iter_data)op_data).fill_coords[(int)(2 * ((H5D_iter_data)op_data).fill_curr_coord)];
|
|
fill_coords[1] = ((H5D_iter_data)op_data)
|
|
.fill_coords[(int)(2 * ((H5D_iter_data)op_data).fill_curr_coord) + 1];
|
|
((H5D_iter_data)op_data).fill_curr_coord++;
|
|
if (fill_coords[0] != point[0])
|
|
return (-1);
|
|
if (fill_coords[1] != point[1])
|
|
return (-1);
|
|
element -= 128;
|
|
byte[] new_elembuf = HDFNativeData.intToByte(element);
|
|
elem_buf[0] = new_elembuf[0];
|
|
elem_buf[1] = new_elembuf[1];
|
|
elem_buf[2] = new_elembuf[2];
|
|
elem_buf[3] = new_elembuf[3];
|
|
return (0);
|
|
}
|
|
}
|
|
|
|
int[] buf_data = new int[DIM_X * DIM_Y];
|
|
byte[] fill_value = HDFNativeData.intToByte(SPACE_FILL);
|
|
|
|
// Initialize memory buffer
|
|
for (int indx = 0; indx < DIM_X; indx++)
|
|
for (int jndx = 0; jndx < DIM_Y; jndx++) {
|
|
buf_data[(indx * DIM_Y) + jndx] = indx * jndx - jndx;
|
|
}
|
|
byte[] buf_array = HDFNativeData.intToByte(0, DIM_X * DIM_Y, buf_data);
|
|
|
|
// Fill selection in memory
|
|
try {
|
|
H5.H5Dfill(fill_value, HDF5Constants.H5T_NATIVE_UINT, buf_array, HDF5Constants.H5T_NATIVE_UINT,
|
|
H5dsid);
|
|
}
|
|
catch (Exception err) {
|
|
err.printStackTrace();
|
|
fail("H5.H5Diterate: " + err);
|
|
}
|
|
|
|
// Initialize the iterator structure
|
|
((H5D_iter_data)iter_data).fill_value = SPACE_FILL;
|
|
((H5D_iter_data)iter_data).fill_curr_coord = 0;
|
|
// Set the coordinates of the selection
|
|
((H5D_iter_data)iter_data).fill_coords =
|
|
new long[DIM_X * DIM_Y * SPACE_RANK]; /* Coordinates of selection */
|
|
for (int indx = 0; indx < DIM_X; indx++)
|
|
for (int jndx = 0; jndx < DIM_Y; jndx++) {
|
|
((H5D_iter_data)iter_data).fill_coords[2 * (indx * DIM_Y + jndx)] = indx;
|
|
((H5D_iter_data)iter_data).fill_coords[2 * (indx * DIM_Y + jndx) + 1] = jndx;
|
|
} /* end for */
|
|
|
|
// Iterate through selection, verifying correct data
|
|
H5D_iterate_cb iter_cb = new H5D_iter_callback();
|
|
int op_status = -1;
|
|
try {
|
|
op_status = H5.H5Diterate(buf_array, HDF5Constants.H5T_NATIVE_UINT, H5dsid, iter_cb, iter_data);
|
|
}
|
|
catch (Throwable err) {
|
|
err.printStackTrace();
|
|
fail("H5.H5Diterate: " + err);
|
|
}
|
|
assertTrue("H5Diterate ", op_status == 0);
|
|
|
|
buf_data = HDFNativeData.byteToInt(buf_array);
|
|
|
|
// Verify memory buffer the hard way
|
|
for (int indx = 0; indx < DIM_X; indx++)
|
|
for (int jndx = 0; jndx < DIM_Y; jndx++)
|
|
assertTrue("H5.H5Diterate: [" + indx + "," + jndx + "] " + buf_data[(indx * DIM_Y) + jndx],
|
|
buf_data[(indx * DIM_Y) + jndx] == 126);
|
|
}
|
|
|
|
@Ignore
|
|
public void testH5Dvlen_get_buf_size()
|
|
{
|
|
String[] str_data = {"Parting", "is such", "sweet", "sorrow.", "Testing", "one", "two", "three.",
|
|
"Dog,", "man's", "best", "friend.", "Diamonds", "are", "a", "girls!",
|
|
"S A", "T U R", "D A Y", "night", "That's", "all", "folks", "!!!"};
|
|
long vl_size = -1; /* Number of bytes used */
|
|
long str_data_bytes = 0;
|
|
for (int idx = 0; idx < str_data.length; idx++)
|
|
str_data_bytes += str_data[idx].length() + 1; // Account for terminating null
|
|
|
|
_createVLStrDataset("dset", HDF5Constants.H5P_DEFAULT);
|
|
|
|
try {
|
|
if ((H5did >= 0) && (H5dtid >= 0))
|
|
H5.H5DwriteVL(H5did, H5dtid, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
|
|
HDF5Constants.H5P_DEFAULT, str_data);
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
try {
|
|
vl_size = H5.H5Dvlen_get_buf_size(H5did, H5dtid, H5dsid);
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
assertTrue("H5Dvlen_get_buf_size " + vl_size + " == " + str_data_bytes, vl_size == str_data_bytes);
|
|
}
|
|
|
|
@Ignore
|
|
public void testH5Dvlen_string_buffer() throws Throwable
|
|
{
|
|
String dset_str_name = "VLStringdata";
|
|
long dset_str_id = HDF5Constants.H5I_INVALID_HID;
|
|
long dtype_str_id = HDF5Constants.H5I_INVALID_HID;
|
|
long dspace_id = HDF5Constants.H5I_INVALID_HID;
|
|
long[] dims = {64};
|
|
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[] vl_str_data = new ArrayList[6];
|
|
vl_str_data[0] = new ArrayList<String>(Arrays.asList(str_data0));
|
|
vl_str_data[1] = new ArrayList<String>(Arrays.asList(str_data1));
|
|
vl_str_data[2] = new ArrayList<String>(Arrays.asList(str_data2));
|
|
vl_str_data[3] = new ArrayList<String>(Arrays.asList(str_data3));
|
|
vl_str_data[4] = new ArrayList<String>(Arrays.asList(str_data4));
|
|
vl_str_data[5] = new ArrayList<String>(Arrays.asList(str_data5));
|
|
|
|
try {
|
|
H5dtid = H5.H5Tcopy(HDF5Constants.H5T_C_S1);
|
|
}
|
|
catch (Throwable err) {
|
|
err.printStackTrace();
|
|
fail("testH5Dvlen_string_buffer.H5.H5Tcopy: " + err);
|
|
}
|
|
assertTrue("testH5Dvlen_string_buffer.H5Tcopy: ", H5dtid >= 0);
|
|
try {
|
|
H5.H5Tset_size(H5dtid, HDF5Constants.H5T_VARIABLE);
|
|
assertTrue("testH5Dvlen_string_buffer.H5Tis_variable_str", H5.H5Tis_variable_str(H5dtid));
|
|
}
|
|
catch (Throwable err) {
|
|
err.printStackTrace();
|
|
fail("testH5Dvlen_string_buffer.H5Tset_size: " + err);
|
|
}
|
|
try {
|
|
dtype_str_id = H5.H5Tvlen_create(H5dtid);
|
|
assertTrue("testH5Dvlen_string_buffer.H5Tvlen_create: ", dtype_str_id >= 0);
|
|
}
|
|
catch (Exception err) {
|
|
if (dtype_str_id > 0)
|
|
try {
|
|
H5.H5Tclose(dtype_str_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
err.printStackTrace();
|
|
fail("testH5Dvlen_string_buffer: " + err);
|
|
}
|
|
|
|
try {
|
|
dspace_id = H5.H5Screate_simple(1, dims, null);
|
|
assertTrue(dspace_id > 0);
|
|
dset_str_id =
|
|
H5.H5Dcreate(H5fid, dset_str_name, dtype_str_id, dspace_id, HDF5Constants.H5P_DEFAULT,
|
|
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
|
|
assertTrue("testH5Dvlen_string_buffer: ", dset_str_id >= 0);
|
|
|
|
H5.H5DwriteVL(dset_str_id, dtype_str_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
|
|
HDF5Constants.H5P_DEFAULT, vl_str_data);
|
|
}
|
|
catch (Exception err) {
|
|
if (dset_str_id > 0)
|
|
try {
|
|
H5.H5Dclose(dset_str_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
if (dtype_str_id > 0)
|
|
try {
|
|
H5.H5Tclose(dtype_str_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
err.printStackTrace();
|
|
fail("testH5Dvlen_string_buffer: " + err);
|
|
}
|
|
finally {
|
|
if (dspace_id > 0)
|
|
try {
|
|
H5.H5Sclose(dspace_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
}
|
|
|
|
H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
|
|
|
|
for (int j = 0; j < dims.length; j++)
|
|
lsize *= dims[j];
|
|
|
|
ArrayList[] vl_readbuf = new ArrayList[4];
|
|
for (int j = 0; j < lsize; j++)
|
|
vl_readbuf[j] = new ArrayList<String>();
|
|
|
|
try {
|
|
H5.H5DreadVL(dset_str_id, dtype_str_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
|
|
HDF5Constants.H5P_DEFAULT, vl_readbuf);
|
|
}
|
|
catch (Exception ex) {
|
|
ex.printStackTrace();
|
|
}
|
|
assertTrue("testH5Dvlen_string_buffer:" + vl_readbuf[0].get(0),
|
|
vl_str_data[0].get(0).equals(vl_readbuf[0].get(0)));
|
|
assertTrue("testH5Dvlen_string_buffer:" + vl_readbuf[1].get(0),
|
|
vl_str_data[1].get(0).equals(vl_readbuf[1].get(0)));
|
|
assertTrue("testH5Dvlen_string_buffer:" + vl_readbuf[2].get(0),
|
|
vl_str_data[2].get(0).equals(vl_readbuf[2].get(0)));
|
|
assertTrue("testH5Dvlen_string_buffer:" + vl_readbuf[3].get(0),
|
|
vl_str_data[3].get(0).equals(vl_readbuf[3].get(0)));
|
|
}
|
|
|
|
@Test
|
|
public void testH5Dvlen_write_read()
|
|
{
|
|
String[] str_wdata = {"Parting", "is such", "sweet", "sorrow.", "Testing", "one", "two", "three.",
|
|
"Dog,", "man's", "best", "friend.", "Diamonds", "are", "a", "girls!",
|
|
"S A", "T U R", "D A Y", "night", "That's", "all", "folks", "!!!"};
|
|
String[] str_rdata = new String[DIM_X * DIM_Y];
|
|
|
|
_createVLStrDataset("dset", HDF5Constants.H5P_DEFAULT);
|
|
|
|
try {
|
|
if ((H5did >= 0) && (H5dtid >= 0))
|
|
H5.H5DwriteVL(H5did, H5dtid, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
|
|
HDF5Constants.H5P_DEFAULT, str_wdata);
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
|
|
try {
|
|
if ((H5did >= 0) && (H5dtid >= 0))
|
|
H5.H5DreadVL(H5did, H5dtid, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
|
|
HDF5Constants.H5P_DEFAULT, str_rdata);
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
for (int v = 0; v < DIM_X * DIM_Y; v++)
|
|
assertTrue("testH5Dvlen_write_read " + str_wdata[v] + " == " + str_rdata[v],
|
|
str_wdata[v] == str_wdata[v]);
|
|
}
|
|
|
|
@Test
|
|
public void testH5DVLwr()
|
|
{
|
|
String dset_int_name = "VLIntdata";
|
|
String dset_dbl_name = "VLDbldata";
|
|
long dset_int_id = HDF5Constants.H5I_INVALID_HID;
|
|
long dset_dbl_id = HDF5Constants.H5I_INVALID_HID;
|
|
long dtype_int_id = HDF5Constants.H5I_INVALID_HID;
|
|
long dtype_dbl_id = HDF5Constants.H5I_INVALID_HID;
|
|
long dspace_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("testH5DVLwr.getClass: " + dataClass, dataClass.isArray());
|
|
|
|
try {
|
|
dtype_int_id = H5.H5Tvlen_create(HDF5Constants.H5T_STD_U32LE);
|
|
assertTrue("testH5DVLwr.H5Tvlen_create: ", dtype_int_id >= 0);
|
|
}
|
|
catch (Exception err) {
|
|
if (dtype_int_id > 0)
|
|
try {
|
|
H5.H5Tclose(dtype_int_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
err.printStackTrace();
|
|
fail("H5.testH5DVLwr: " + err);
|
|
}
|
|
|
|
try {
|
|
dspace_id = H5.H5Screate_simple(1, dims, null);
|
|
assertTrue(dspace_id > 0);
|
|
dset_int_id =
|
|
H5.H5Dcreate(H5fid, dset_int_name, dtype_int_id, dspace_id, HDF5Constants.H5P_DEFAULT,
|
|
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
|
|
assertTrue("testH5DVLwr: ", dset_int_id >= 0);
|
|
|
|
H5.H5DwriteVL(dset_int_id, dtype_int_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
|
|
HDF5Constants.H5P_DEFAULT, vl_int_data);
|
|
}
|
|
catch (Exception err) {
|
|
if (dset_int_id > 0)
|
|
try {
|
|
H5.H5Dclose(dset_int_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
if (dtype_int_id > 0)
|
|
try {
|
|
H5.H5Tclose(dtype_int_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
err.printStackTrace();
|
|
fail("H5.testH5DVLwr: " + err);
|
|
}
|
|
finally {
|
|
if (dspace_id > 0)
|
|
try {
|
|
H5.H5Sclose(dspace_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("testH5DVLwr.getClass: " + dataClass, dataClass.isArray());
|
|
|
|
try {
|
|
dtype_dbl_id = H5.H5Tvlen_create(HDF5Constants.H5T_NATIVE_DOUBLE);
|
|
assertTrue("testH5DVLwr.H5Tvlen_create: ", dtype_dbl_id >= 0);
|
|
}
|
|
catch (Exception err) {
|
|
if (dtype_dbl_id > 0)
|
|
try {
|
|
H5.H5Tclose(dtype_dbl_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
err.printStackTrace();
|
|
fail("H5.testH5DVLwr: " + err);
|
|
}
|
|
|
|
try {
|
|
dspace_id = H5.H5Screate_simple(1, dims, null);
|
|
assertTrue(dspace_id > 0);
|
|
dset_dbl_id =
|
|
H5.H5Dcreate(H5fid, dset_dbl_name, dtype_dbl_id, dspace_id, HDF5Constants.H5P_DEFAULT,
|
|
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
|
|
assertTrue("testH5DVLwr: ", dset_dbl_id >= 0);
|
|
|
|
H5.H5DwriteVL(dset_dbl_id, dtype_dbl_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
|
|
HDF5Constants.H5P_DEFAULT, vl_dbl_data);
|
|
}
|
|
catch (Exception err) {
|
|
if (dset_dbl_id > 0)
|
|
try {
|
|
H5.H5Dclose(dset_dbl_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
if (dtype_dbl_id > 0)
|
|
try {
|
|
H5.H5Tclose(dtype_dbl_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
err.printStackTrace();
|
|
fail("H5.testH5DVLwr: " + err);
|
|
}
|
|
finally {
|
|
if (dspace_id > 0)
|
|
try {
|
|
H5.H5Sclose(dspace_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_int_readbuf = new ArrayList[4];
|
|
for (int j = 0; j < lsize; j++)
|
|
vl_int_readbuf[j] = new ArrayList<Integer>();
|
|
|
|
try {
|
|
H5.H5DreadVL(dset_int_id, dtype_int_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
|
|
HDF5Constants.H5P_DEFAULT, vl_int_readbuf);
|
|
}
|
|
catch (Exception ex) {
|
|
ex.printStackTrace();
|
|
}
|
|
assertTrue("testH5DVLwr:" + vl_int_readbuf[0].get(0),
|
|
vl_int_data[0].get(0).equals(vl_int_readbuf[0].get(0)));
|
|
assertTrue("testH5DVLwr:" + vl_int_readbuf[1].get(0),
|
|
vl_int_data[1].get(0).equals(vl_int_readbuf[1].get(0)));
|
|
assertTrue("testH5DVLwr:" + vl_int_readbuf[2].get(0),
|
|
vl_int_data[2].get(0).equals(vl_int_readbuf[2].get(0)));
|
|
assertTrue("testH5DVLwr:" + vl_int_readbuf[3].get(0),
|
|
vl_int_data[3].get(0).equals(vl_int_readbuf[3].get(0)));
|
|
|
|
// Read Double data
|
|
ArrayList[] vl_dbl_readbuf = new ArrayList[4];
|
|
for (int j = 0; j < lsize; j++)
|
|
vl_dbl_readbuf[j] = new ArrayList<Double>();
|
|
|
|
try {
|
|
H5.H5DreadVL(dset_dbl_id, dtype_dbl_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
|
|
HDF5Constants.H5P_DEFAULT, vl_dbl_readbuf);
|
|
}
|
|
catch (Exception ex) {
|
|
ex.printStackTrace();
|
|
}
|
|
assertTrue("testH5DVLwr:" + vl_dbl_readbuf[0].get(0),
|
|
vl_dbl_data[0].get(0).equals(vl_dbl_readbuf[0].get(0)));
|
|
assertTrue("testH5DVLwr:" + vl_dbl_readbuf[1].get(0),
|
|
vl_dbl_data[1].get(0).equals(vl_dbl_readbuf[1].get(0)));
|
|
assertTrue("testH5DVLwr:" + vl_dbl_readbuf[2].get(0),
|
|
vl_dbl_data[2].get(0).equals(vl_dbl_readbuf[2].get(0)));
|
|
assertTrue("testH5DVLwr:" + vl_dbl_readbuf[3].get(0),
|
|
vl_dbl_data[3].get(0).equals(vl_dbl_readbuf[3].get(0)));
|
|
}
|
|
catch (Throwable err) {
|
|
err.printStackTrace();
|
|
fail("H5.testH5DVLwr: " + err);
|
|
}
|
|
finally {
|
|
if (dset_dbl_id > 0)
|
|
try {
|
|
H5.H5Dclose(dset_dbl_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
if (dset_int_id > 0)
|
|
try {
|
|
H5.H5Dclose(dset_int_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
if (dtype_dbl_id > 0)
|
|
try {
|
|
H5.H5Tclose(dtype_dbl_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
if (dtype_int_id > 0)
|
|
try {
|
|
H5.H5Tclose(dtype_int_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
}
|
|
}
|
|
|
|
@Test
|
|
public void testH5DVLwrVL()
|
|
{
|
|
String dset_int_name = "VLIntdata";
|
|
long dset_int_id = HDF5Constants.H5I_INVALID_HID;
|
|
long dtype_int_id = HDF5Constants.H5I_INVALID_HID;
|
|
long base_dtype_int_id = HDF5Constants.H5I_INVALID_HID;
|
|
long dspace_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("testH5DVLwrVL.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 {
|
|
dtype_int_id = H5.H5Tvlen_create(HDF5Constants.H5T_STD_U32LE);
|
|
assertTrue("testH5DVLwrVL.H5Tvlen_create: ", dtype_int_id >= 0);
|
|
base_dtype_int_id = H5.H5Tvlen_create(dtype_int_id);
|
|
assertTrue("testH5DVLwrVL.H5Tvlen_create: ", base_dtype_int_id >= 0);
|
|
}
|
|
catch (Exception err) {
|
|
if (base_dtype_int_id > 0)
|
|
try {
|
|
H5.H5Tclose(base_dtype_int_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
if (dtype_int_id > 0)
|
|
try {
|
|
H5.H5Tclose(dtype_int_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
err.printStackTrace();
|
|
fail("H5.testH5DVLwrVL: " + err);
|
|
}
|
|
|
|
try {
|
|
dspace_id = H5.H5Screate_simple(1, dims, null);
|
|
assertTrue(dspace_id > 0);
|
|
dset_int_id = H5.H5Dcreate(H5fid, dset_int_name, base_dtype_int_id, dspace_id,
|
|
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT,
|
|
HDF5Constants.H5P_DEFAULT);
|
|
assertTrue("testH5DVLwrVL: ", dset_int_id >= 0);
|
|
|
|
H5.H5DwriteVL(dset_int_id, base_dtype_int_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
|
|
HDF5Constants.H5P_DEFAULT, base_vl_int_data);
|
|
}
|
|
catch (Exception err) {
|
|
if (dset_int_id > 0)
|
|
try {
|
|
H5.H5Dclose(dset_int_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
if (dtype_int_id > 0)
|
|
try {
|
|
H5.H5Tclose(dtype_int_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
err.printStackTrace();
|
|
fail("H5.testH5DVLwrVL: " + err);
|
|
}
|
|
finally {
|
|
if (dspace_id > 0)
|
|
try {
|
|
H5.H5Sclose(dspace_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.H5DreadVL(dset_int_id, base_dtype_int_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
|
|
HDF5Constants.H5P_DEFAULT, 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("testH5DVLwrVL:" + 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("testH5DVLwrVL:" + 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("testH5DVLwrVL:" + 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("testH5DVLwrVL:" + vl_readbuf_int.get(3),
|
|
vl_int_data[3].get(3).equals(vl_readbuf_int.get(3)));
|
|
}
|
|
catch (Throwable err) {
|
|
err.printStackTrace();
|
|
fail("H5.testH5DVLwrVL: " + err);
|
|
}
|
|
finally {
|
|
if (dset_int_id > 0)
|
|
try {
|
|
H5.H5Dclose(dset_int_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
if (dtype_int_id > 0)
|
|
try {
|
|
H5.H5Tclose(dtype_int_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
if (base_dtype_int_id > 0)
|
|
try {
|
|
H5.H5Tclose(base_dtype_int_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
}
|
|
}
|
|
|
|
@Test
|
|
public void testH5DArraywr()
|
|
{
|
|
String dset_int_name = "ArrayIntdata";
|
|
long dset_int_id = HDF5Constants.H5I_INVALID_HID;
|
|
long dtype_int_id = HDF5Constants.H5I_INVALID_HID;
|
|
long dspace_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("testH5DArraywr.getClass: " + dataClass, dataClass.isArray());
|
|
|
|
try {
|
|
dtype_int_id = H5.H5Tarray_create(HDF5Constants.H5T_STD_U32LE, 1, dims);
|
|
assertTrue("testH5DArraywr.H5Tarray_create: ", dtype_int_id >= 0);
|
|
}
|
|
catch (Exception err) {
|
|
if (dtype_int_id > 0)
|
|
try {
|
|
H5.H5Tclose(dtype_int_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
err.printStackTrace();
|
|
fail("H5.testH5DArraywr: " + err);
|
|
}
|
|
|
|
try {
|
|
dspace_id = H5.H5Screate_simple(1, dims, null);
|
|
assertTrue(dspace_id > 0);
|
|
dset_int_id =
|
|
H5.H5Dcreate(H5fid, dset_int_name, dtype_int_id, dspace_id, HDF5Constants.H5P_DEFAULT,
|
|
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
|
|
assertTrue("testH5DVLwr: ", dset_int_id >= 0);
|
|
|
|
H5.H5DwriteVL(dset_int_id, dtype_int_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
|
|
HDF5Constants.H5P_DEFAULT, arr_int_data);
|
|
}
|
|
catch (Exception err) {
|
|
if (dset_int_id > 0)
|
|
try {
|
|
H5.H5Dclose(dset_int_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
if (dtype_int_id > 0)
|
|
try {
|
|
H5.H5Tclose(dtype_int_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
err.printStackTrace();
|
|
fail("H5.testH5DVLwr: " + err);
|
|
}
|
|
finally {
|
|
if (dspace_id > 0)
|
|
try {
|
|
H5.H5Sclose(dspace_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.H5DreadVL(dset_int_id, dtype_int_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
|
|
HDF5Constants.H5P_DEFAULT, arr_readbuf);
|
|
}
|
|
catch (Exception ex) {
|
|
ex.printStackTrace();
|
|
}
|
|
assertTrue("testH5DVLwr:" + arr_readbuf[0].get(0),
|
|
arr_int_data[0].get(0).equals(arr_readbuf[0].get(0)));
|
|
assertTrue("testH5DVLwr:" + arr_readbuf[1].get(0),
|
|
arr_int_data[1].get(0).equals(arr_readbuf[1].get(0)));
|
|
assertTrue("testH5DVLwr:" + arr_readbuf[2].get(0),
|
|
arr_int_data[2].get(0).equals(arr_readbuf[2].get(0)));
|
|
assertTrue("testH5DVLwr:" + arr_readbuf[3].get(0),
|
|
arr_int_data[3].get(0).equals(arr_readbuf[3].get(0)));
|
|
}
|
|
catch (Throwable err) {
|
|
err.printStackTrace();
|
|
fail("H5.testH5DArraywr: " + err);
|
|
}
|
|
finally {
|
|
if (dset_int_id > 0)
|
|
try {
|
|
H5.H5Dclose(dset_int_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
if (dtype_int_id > 0)
|
|
try {
|
|
H5.H5Tclose(dtype_int_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
}
|
|
}
|
|
|
|
@Test
|
|
public void testH5DArray_string_buffer() throws Throwable
|
|
{
|
|
String dset_str_name = "ArrayStringdata";
|
|
long dset_str_id = HDF5Constants.H5I_INVALID_HID;
|
|
long dtype_str_id = HDF5Constants.H5I_INVALID_HID;
|
|
long dspace_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 {
|
|
H5dtid = H5.H5Tcopy(HDF5Constants.H5T_C_S1);
|
|
}
|
|
catch (Throwable err) {
|
|
err.printStackTrace();
|
|
fail("testH5DArray_string_buffer.H5.H5Tcopy: " + err);
|
|
}
|
|
assertTrue("testH5DArray_string_buffer.H5Tcopy: ", H5dtid >= 0);
|
|
try {
|
|
H5.H5Tset_size(H5dtid, HDF5Constants.H5T_VARIABLE);
|
|
assertTrue("testH5DArray_string_buffer.H5Tis_variable_str", H5.H5Tis_variable_str(H5dtid));
|
|
}
|
|
catch (Throwable err) {
|
|
err.printStackTrace();
|
|
fail("testH5DArray_string_buffer.H5Tset_size: " + err);
|
|
}
|
|
try {
|
|
dtype_str_id = H5.H5Tarray_create(H5dtid, 1, strdims);
|
|
assertTrue("testH5DArray_string_buffer.H5Tarray_create: ", dtype_str_id >= 0);
|
|
}
|
|
catch (Exception err) {
|
|
if (dtype_str_id > 0)
|
|
try {
|
|
H5.H5Tclose(dtype_str_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
err.printStackTrace();
|
|
fail("testH5DArray_string_buffer: " + err);
|
|
}
|
|
|
|
try {
|
|
dspace_id = H5.H5Screate_simple(1, dims, null);
|
|
assertTrue(dspace_id > 0);
|
|
dset_str_id =
|
|
H5.H5Dcreate(H5fid, dset_str_name, dtype_str_id, dspace_id, HDF5Constants.H5P_DEFAULT,
|
|
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
|
|
assertTrue("testH5DArray_string_buffer: ", dset_str_id >= 0);
|
|
|
|
H5.H5DwriteVL(dset_str_id, dtype_str_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
|
|
HDF5Constants.H5P_DEFAULT, arr_str_data);
|
|
}
|
|
catch (Exception err) {
|
|
if (dset_str_id > 0)
|
|
try {
|
|
H5.H5Dclose(dset_str_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
if (dtype_str_id > 0)
|
|
try {
|
|
H5.H5Tclose(dtype_str_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
err.printStackTrace();
|
|
fail("testH5DArray_string_buffer: " + err);
|
|
}
|
|
finally {
|
|
if (dspace_id > 0)
|
|
try {
|
|
H5.H5Sclose(dspace_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.H5DreadVL(dset_str_id, dtype_str_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
|
|
HDF5Constants.H5P_DEFAULT, arr_readbuf);
|
|
}
|
|
catch (Exception ex) {
|
|
ex.printStackTrace();
|
|
}
|
|
finally {
|
|
if (dset_str_id > 0)
|
|
try {
|
|
H5.H5Dclose(dset_str_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
if (dtype_str_id > 0)
|
|
try {
|
|
H5.H5Tclose(dtype_str_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
}
|
|
assertTrue("testH5DArray_string_buffer:" + arr_readbuf[0].get(0),
|
|
arr_str_data[0].get(0).equals(arr_readbuf[0].get(0)));
|
|
assertTrue("testH5DArray_string_buffer:" + arr_readbuf[1].get(0),
|
|
arr_str_data[1].get(0).equals(arr_readbuf[1].get(0)));
|
|
assertTrue("testH5DArray_string_buffer:" + arr_readbuf[2].get(0),
|
|
arr_str_data[2].get(0).equals(arr_readbuf[2].get(0)));
|
|
assertTrue("testH5DArray_string_buffer:" + arr_readbuf[3].get(0),
|
|
arr_str_data[3].get(0).equals(arr_readbuf[3].get(0)));
|
|
}
|
|
|
|
@Test
|
|
public void testH5DArrayenum_rw()
|
|
{
|
|
String dset_enum_name = "ArrayEnumdata";
|
|
long dset_enum_id = HDF5Constants.H5I_INVALID_HID;
|
|
long dtype_enum_id = HDF5Constants.H5I_INVALID_HID;
|
|
long dtype_arr_enum_id = HDF5Constants.H5I_INVALID_HID;
|
|
long dspace_id = HDF5Constants.H5I_INVALID_HID;
|
|
long[] dims = {4};
|
|
long lsize = 1;
|
|
String enum_type = "Enum_type";
|
|
byte[] enum_val = new byte[1];
|
|
String enum_name = null;
|
|
|
|
// Create a enumerate datatype
|
|
try {
|
|
dtype_enum_id = H5.H5Tcreate(HDF5Constants.H5T_ENUM, (long)1);
|
|
assertTrue("testH5DArrayenum_wr.H5Tarray_create: ", dtype_enum_id >= 0);
|
|
}
|
|
catch (Throwable err) {
|
|
if (dtype_enum_id > 0)
|
|
try {
|
|
H5.H5Tclose(dtype_enum_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
err.printStackTrace();
|
|
fail("testH5DArrayenum_rw:H5Tcreate " + err);
|
|
}
|
|
|
|
try {
|
|
enum_val[0] = 10;
|
|
H5.H5Tenum_insert(dtype_enum_id, "RED", enum_val);
|
|
enum_val[0] = 11;
|
|
H5.H5Tenum_insert(dtype_enum_id, "GREEN", enum_val);
|
|
enum_val[0] = 12;
|
|
H5.H5Tenum_insert(dtype_enum_id, "BLUE", enum_val);
|
|
enum_val[0] = 13;
|
|
H5.H5Tenum_insert(dtype_enum_id, "ORANGE", enum_val);
|
|
enum_val[0] = 14;
|
|
H5.H5Tenum_insert(dtype_enum_id, "YELLOW", enum_val);
|
|
|
|
// Query member number and member index by member name, for enumeration type.
|
|
assertTrue("Can't get member number", H5.H5Tget_nmembers(dtype_enum_id) == 5);
|
|
assertTrue("Can't get correct index number",
|
|
H5.H5Tget_member_index(dtype_enum_id, "ORANGE") == 3);
|
|
|
|
// Commit enumeration datatype and close it */
|
|
H5.H5Tcommit(H5fid, enum_type, dtype_enum_id, HDF5Constants.H5P_DEFAULT,
|
|
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
|
|
|
|
H5.H5Tclose(dtype_enum_id);
|
|
|
|
// Open the dataytpe for query
|
|
dtype_enum_id = H5.H5Topen(H5fid, enum_type, HDF5Constants.H5P_DEFAULT);
|
|
assertTrue("testH5DArrayenum_rw:H5Tcreate", dtype_enum_id >= 0);
|
|
|
|
// Query member number and member index by member name, for enumeration type
|
|
assertTrue("Can't get member number", H5.H5Tget_nmembers(dtype_enum_id) == 5);
|
|
assertTrue("Can't get correct index number",
|
|
H5.H5Tget_member_index(dtype_enum_id, "ORANGE") == 3);
|
|
|
|
// Query member value by member name, for enumeration type
|
|
H5.H5Tenum_valueof(dtype_enum_id, "ORANGE", enum_val);
|
|
assertTrue("Incorrect value for enum member", enum_val[0] == 13);
|
|
|
|
// Query member value by member index, for enumeration type
|
|
H5.H5Tget_member_value(dtype_enum_id, 2, enum_val);
|
|
assertTrue("Incorrect value for enum member", enum_val[0] == 12);
|
|
|
|
// Query member name by member value, for enumeration type
|
|
enum_val[0] = 14;
|
|
enum_name = H5.H5Tenum_nameof(dtype_enum_id, enum_val, 16);
|
|
assertTrue("Incorrect name for enum member", enum_name.compareTo("YELLOW") == 0);
|
|
|
|
ArrayList[] arr_enum_data = new ArrayList[4];
|
|
try {
|
|
// Write Integer data
|
|
arr_enum_data[0] = new ArrayList<Integer>(Arrays.asList(10, 11, 12, 13));
|
|
arr_enum_data[1] = new ArrayList<Integer>(Arrays.asList(11, 12, 13, 14));
|
|
arr_enum_data[2] = new ArrayList<Integer>(Arrays.asList(12, 13, 14, 10));
|
|
arr_enum_data[3] = new ArrayList<Integer>(Arrays.asList(13, 14, 10, 11));
|
|
Class dataClass = arr_enum_data.getClass();
|
|
assertTrue("testH5DArrayenum_wr.getClass: " + dataClass, dataClass.isArray());
|
|
|
|
try {
|
|
dtype_arr_enum_id = H5.H5Tarray_create(HDF5Constants.H5T_STD_U32LE, 1, dims);
|
|
assertTrue("testH5DArrayenum_wr.H5Tarray_create: ", dtype_arr_enum_id >= 0);
|
|
}
|
|
catch (Exception err) {
|
|
if (dtype_arr_enum_id > 0)
|
|
try {
|
|
H5.H5Tclose(dtype_arr_enum_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
err.printStackTrace();
|
|
fail("H5.testH5DArrayenum_wr: " + err);
|
|
}
|
|
|
|
dspace_id = H5.H5Screate_simple(1, dims, null);
|
|
assertTrue(dspace_id > 0);
|
|
dset_enum_id = H5.H5Dcreate(H5fid, dset_enum_name, dtype_arr_enum_id, dspace_id,
|
|
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT,
|
|
HDF5Constants.H5P_DEFAULT);
|
|
assertTrue("testH5DVLwr: ", dset_enum_id >= 0);
|
|
|
|
H5.H5DwriteVL(dset_enum_id, dtype_arr_enum_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
|
|
HDF5Constants.H5P_DEFAULT, arr_enum_data);
|
|
}
|
|
catch (Throwable err) {
|
|
if (dset_enum_id > 0)
|
|
try {
|
|
H5.H5Dclose(dset_enum_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
if (dtype_enum_id > 0)
|
|
try {
|
|
H5.H5Tclose(dtype_enum_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
if (dtype_arr_enum_id > 0)
|
|
try {
|
|
H5.H5Tclose(dtype_arr_enum_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
err.printStackTrace();
|
|
fail("testH5DArrayenum_rw:query " + err);
|
|
}
|
|
finally {
|
|
if (dspace_id > 0)
|
|
try {
|
|
H5.H5Sclose(dspace_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.H5DreadVL(dset_enum_id, dtype_arr_enum_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
|
|
HDF5Constants.H5P_DEFAULT, arr_readbuf);
|
|
}
|
|
catch (Exception ex) {
|
|
ex.printStackTrace();
|
|
}
|
|
assertTrue("testH5DVLArrayenum_wr:" + arr_readbuf[0].get(0),
|
|
arr_enum_data[0].get(0).equals(arr_readbuf[0].get(0)));
|
|
assertTrue("testH5DVLArrayenum_wr:" + arr_readbuf[1].get(0),
|
|
arr_enum_data[1].get(0).equals(arr_readbuf[1].get(0)));
|
|
assertTrue("testH5DVLArrayenum_wr:" + arr_readbuf[2].get(0),
|
|
arr_enum_data[2].get(0).equals(arr_readbuf[2].get(0)));
|
|
assertTrue("testH5DVLArrayenum_wr:" + arr_readbuf[3].get(0),
|
|
arr_enum_data[3].get(0).equals(arr_readbuf[3].get(0)));
|
|
}
|
|
catch (Throwable err) {
|
|
err.printStackTrace();
|
|
fail("H5.testH5DArrayenum_wr: " + err);
|
|
}
|
|
finally {
|
|
if (dset_enum_id > 0)
|
|
try {
|
|
H5.H5Dclose(dset_enum_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
if (dtype_enum_id > 0)
|
|
try {
|
|
H5.H5Tclose(dtype_enum_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
if (dtype_arr_enum_id > 0)
|
|
try {
|
|
H5.H5Tclose(dtype_arr_enum_id);
|
|
}
|
|
catch (Exception ex) {
|
|
}
|
|
}
|
|
}
|
|
}
|