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e94071fe53
hdf5/java/test/TestH5D.java
Allen Byrne 2376723d4a
Develop jni trans (#2266) 
* Add compound and refactor out atomic types

* Add Array String tests back

* Convert Attribute version of compound example

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

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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the COPYING file, which can be found at the root of the source code *
* distribution tree, or in https://www.hdfgroup.org/licenses. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
package test;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import java.io.File;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import hdf.hdf5lib.H5;
import hdf.hdf5lib.HDF5Constants;
import hdf.hdf5lib.HDFNativeData;
import hdf.hdf5lib.callbacks.H5D_iterate_cb;
import hdf.hdf5lib.callbacks.H5D_iterate_t;
import hdf.hdf5lib.exceptions.HDF5Exception;
import hdf.hdf5lib.exceptions.HDF5LibraryException;
import org.junit.After;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Rule;
import org.junit.Test;
import org.junit.rules.TestName;
public class TestH5D {
@Rule
public TestName testname = new TestName();
private static final String H5_FILE = "testD.h5";
private static final int DIM_X = 4;
private static final int DIM_Y = 6;
private static final int RANK = 2;
long H5fid = HDF5Constants.H5I_INVALID_HID;
long H5faplid = HDF5Constants.H5I_INVALID_HID;
long H5dsid = HDF5Constants.H5I_INVALID_HID;
long H5dtid = HDF5Constants.H5I_INVALID_HID;
long H5did = HDF5Constants.H5I_INVALID_HID;
long H5did0 = HDF5Constants.H5I_INVALID_HID;
long H5dcpl_id = HDF5Constants.H5I_INVALID_HID;
long[] H5dims = {DIM_X, DIM_Y};
// Values for the status of space allocation
enum H5D_space_status {
H5D_SPACE_STATUS_ERROR(-1),
H5D_SPACE_STATUS_NOT_ALLOCATED(0),
H5D_SPACE_STATUS_PART_ALLOCATED(1),
H5D_SPACE_STATUS_ALLOCATED(2);
private int code;
H5D_space_status(int space_status) { this.code = space_status; }
public int getCode() { return this.code; }
}
private final void _deleteFile(String filename)
{
File file = new File(filename);
if (file.exists()) {
try {
file.delete();
}
catch (SecurityException e) {
}
}
}
private final void _createPDataset(long fid, long dsid, String name, long dcpl_val)
{
try {
H5dcpl_id = H5.H5Pcreate(dcpl_val);
}
catch (Exception err) {
err.printStackTrace();
fail("H5.H5Pcreate: " + err);
}
assertTrue("testH5D._createPDataset: H5.H5Pcreate: ", H5dcpl_id >= 0);
// Set the allocation time to "early". This way we can be sure
// that reading from the dataset immediately after creation will
// return the fill value.
try {
H5.H5Pset_alloc_time(H5dcpl_id, HDF5Constants.H5D_ALLOC_TIME_EARLY);
}
catch (Exception e) {
e.printStackTrace();
}
try {
H5did0 = H5.H5Dcreate(fid, name, HDF5Constants.H5T_STD_I32BE, dsid, HDF5Constants.H5P_DEFAULT,
H5dcpl_id, HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Dcreate: " + err);
}
assertTrue("TestH5D._createPDataset.H5Dcreate: ", H5did0 >= 0);
}
private final void _createChunkDataset(long fid, long dsid, String name, long dapl)
{
try {
H5dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE);
}
catch (Exception err) {
err.printStackTrace();
fail("H5.H5Pcreate: " + err);
}
assertTrue("testH5D._createChunkDataset: H5.H5Pcreate: ", H5dcpl_id >= 0);
// Set the chunking.
long[] chunk_dim = {4, 4};
try {
H5.H5Pset_chunk(H5dcpl_id, RANK, chunk_dim);
}
catch (Exception e) {
e.printStackTrace();
}
try {
H5did = H5.H5Dcreate(fid, name, HDF5Constants.H5T_STD_I32BE, dsid, HDF5Constants.H5P_DEFAULT,
H5dcpl_id, dapl);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Dcreate: " + err);
}
assertTrue("TestH5D._createChunkDataset.H5Dcreate: ", H5did >= 0);
}
private final void _createDataset(long fid, long dsid, String name, long dapl)
{
try {
H5did = H5.H5Dcreate(fid, name, HDF5Constants.H5T_STD_I32BE, dsid, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT, dapl);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Dcreate: " + err);
}
assertTrue("TestH5D._createDataset.H5Dcreate: ", H5did >= 0);
}
private final void _createVLStrDataset(String name, long dapl)
{
try {
H5dtid = H5.H5Tcopy(HDF5Constants.H5T_C_S1);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Tcopy: " + err);
}
assertTrue("TestH5D._createVLStrDataset.H5Tcopy: ", H5dtid >= 0);
try {
H5.H5Tset_size(H5dtid, HDF5Constants.H5T_VARIABLE);
assertTrue("TestH5D._createVLStrDataset.H5Tis_variable_str", H5.H5Tis_variable_str(H5dtid));
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Tset_size: " + err);
}
try {
H5did = H5.H5Dcreate(H5fid, name, H5dtid, H5dsid, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT, dapl);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Dcreate: " + err);
}
assertTrue("TestH5D._createVLStrDataset.H5Dcreate: ", H5did >= 0);
}
private final void _closeH5file() throws HDF5LibraryException
{
if (H5dcpl_id >= 0)
try {
H5.H5Pclose(H5dcpl_id);
}
catch (Exception ex) {
}
if (H5did0 >= 0)
try {
H5.H5Dclose(H5did0);
}
catch (Exception ex) {
}
if (H5did >= 0)
try {
H5.H5Dclose(H5did);
}
catch (Exception ex) {
}
if (H5dtid > 0)
try {
H5.H5Tclose(H5dtid);
}
catch (Exception ex) {
}
if (H5dsid > 0)
try {
H5.H5Sclose(H5dsid);
}
catch (Exception ex) {
}
if (H5fid > 0)
try {
H5.H5Fclose(H5fid);
}
catch (Exception ex) {
}
}
private final void _openH5file(String filename, String dsetname, long dapl)
{
try {
H5fid = H5.H5Fopen(filename, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5D._openH5file: " + err);
}
assertTrue("TestH5D._openH5file: H5.H5Fopen: ", H5fid >= 0);
try {
H5did = H5.H5Dopen(H5fid, dsetname, dapl);
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5D._openH5file: " + err);
}
assertTrue("TestH5D._openH5file: H5.H5Dopen: ", H5did >= 0);
try {
H5dsid = H5.H5Dget_space(H5did);
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5D._openH5file: " + err);
}
assertTrue("TestH5D._openH5file: H5.H5Screate_simple: ", H5dsid > 0);
}
@Before
public void createH5file() throws NullPointerException, HDF5Exception
{
assertTrue("H5 open ids is 0", H5.getOpenIDCount() == 0);
System.out.print(testname.getMethodName());
try {
H5faplid = H5.H5Pcreate(HDF5Constants.H5P_FILE_ACCESS);
H5fid = H5.H5Fcreate(H5_FILE, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, H5faplid);
H5dsid = H5.H5Screate_simple(RANK, H5dims, null);
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5D.createH5file: " + err);
}
assertTrue("TestH5D.createH5file: H5.H5Fcreate: ", H5fid >= 0);
assertTrue("TestH5D.createH5file: H5.H5Screate_simple: ", H5dsid >= 0);
H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
}
@After
public void deleteH5file() throws HDF5LibraryException
{
if (H5dcpl_id >= 0)
try {
H5.H5Pclose(H5dcpl_id);
}
catch (Exception ex) {
}
if (H5did0 >= 0)
try {
H5.H5Dclose(H5did0);
}
catch (Exception ex) {
}
if (H5did >= 0)
try {
H5.H5Dclose(H5did);
}
catch (Exception ex) {
}
if (H5dtid > 0)
try {
H5.H5Tclose(H5dtid);
}
catch (Exception ex) {
}
if (H5dsid > 0)
try {
H5.H5Sclose(H5dsid);
}
catch (Exception ex) {
}
if (H5faplid >= 0)
try {
H5.H5Pclose(H5faplid);
}
catch (Exception ex) {
}
if (H5fid > 0)
try {
H5.H5Fclose(H5fid);
}
catch (Exception ex) {
}
_deleteFile(H5_FILE);
System.out.println();
}
@Test
public void testH5Dcreate()
{
long dataset_id = 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 (Exception err) {
err.printStackTrace();
fail("testH5Dcreate: " + err);
}
assertTrue(dataset_id >= 0);
// End access to the dataset and release resources used by it.
try {
if (dataset_id >= 0)
H5.H5Dclose(dataset_id);
}
catch (Exception err) {
err.printStackTrace();
}
}
@Test
public void testH5Dcreate_anon()
{
long dataset_id = HDF5Constants.H5I_INVALID_HID;
try {
dataset_id = H5.H5Dcreate_anon(H5fid, HDF5Constants.H5T_STD_I32BE, H5dsid,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
}
catch (Exception err) {
err.printStackTrace();
fail("testH5Dcreate_anon: " + err);
}
assertTrue(dataset_id >= 0);
// End access to the dataset and release resources used by it.
try {
if (dataset_id >= 0)
H5.H5Dclose(dataset_id);
}
catch (Exception err) {
err.printStackTrace();
}
}
@Test
public void testH5Dopen()
{
long dataset_id = HDF5Constants.H5I_INVALID_HID;
_createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT);
try {
H5.H5Dclose(H5did);
H5did = HDF5Constants.H5I_INVALID_HID;
dataset_id = H5.H5Dopen(H5fid, "dset", HDF5Constants.H5P_DEFAULT);
}
catch (Exception err) {
err.printStackTrace();
fail("testH5Dopen: " + err);
}
assertTrue("testH5Dopen: ", dataset_id >= 0);
// End access to the dataset and release resources used by it.
try {
if (dataset_id >= 0)
H5.H5Dclose(dataset_id);
}
catch (Exception err) {
err.printStackTrace();
}
}
@Test
public void testH5Dget_storage_size_empty()
{
long storage_size = 0;
_createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT);
try {
storage_size = H5.H5Dget_storage_size(H5did);
}
catch (Exception err) {
err.printStackTrace();
fail("testH5Dget_storage_size: " + err);
}
assertTrue("testH5Dget_storage_size: ", storage_size == 0);
}
@Test
public void testH5Dget_storage_size()
{
long storage_size = 0;
int[][] dset_data = new int[DIM_X][DIM_Y];
int FILLVAL = 99;
_createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT);
// Initialize the dataset.
for (int indx = 0; indx < DIM_X; indx++)
for (int jndx = 0; jndx < DIM_Y; jndx++)
dset_data[indx][jndx] = FILLVAL;
try {
if (H5did >= 0)
H5.H5Dwrite(H5did, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
HDF5Constants.H5P_DEFAULT, dset_data[0]);
}
catch (Exception e) {
e.printStackTrace();
}
try {
storage_size = H5.H5Dget_storage_size(H5did);
}
catch (Exception err) {
err.printStackTrace();
fail("testH5Dget_storage_size: " + err);
}
assertTrue("testH5Dget_storage_size: " + storage_size, storage_size == DIM_X * DIM_Y * 4);
}
@Test
public void testH5Dget_access_plist()
{
long dapl_id = HDF5Constants.H5I_INVALID_HID;
long test_dapl_id = HDF5Constants.H5I_INVALID_HID;
int[] mdc_nelmts1 = {0};
int[] mdc_nelmts2 = {0};
long[] rdcc_nelmts1 = {0};
long[] rdcc_nelmts2 = {0};
long[] rdcc_nbytes1 = {0};
long[] rdcc_nbytes2 = {0};
double[] rdcc_w01 = {0};
double[] rdcc_w02 = {0};
try {
test_dapl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_ACCESS);
}
catch (Exception err) {
err.printStackTrace();
fail("testH5Dget_access_plist: H5.H5Pcreate: " + err);
}
assertTrue("testH5Dget_access_plist: test_dapl_id: ", test_dapl_id >= 0);
try {
H5.H5Pget_cache(H5faplid, mdc_nelmts1, rdcc_nelmts1, rdcc_nbytes1, rdcc_w01);
}
catch (Exception err) {
err.printStackTrace();
fail("testH5Dget_access_plist: H5.H5Pget_cache: " + err);
}
_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) {
}
}
}
}
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