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Code Issues Packages Projects Releases Wiki Activity
e94071fe53
hdf5/java/test/TestH5R.java
Allen Byrne 9c61f7b1e1
JNI: Improve varlen datatype handling in H5A/H5D read/write functions (#2156) 
* Improve JNI VL datatype read/write to handle complex combinations

* Implement VL of VL JNI writes and reads

* Add Java VLofVL test for attributtes

* Changes to address review issues

* Fix H5Aread vl blocks
2022-10-25 23:33:30 -05:00

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Java
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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the COPYING file, which can be found at the root of the source code *
* distribution tree, or in https://www.hdfgroup.org/licenses. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
package test;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import java.io.File;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import hdf.hdf5lib.H5;
import hdf.hdf5lib.HDF5Constants;
import hdf.hdf5lib.exceptions.HDF5Exception;
import hdf.hdf5lib.exceptions.HDF5FunctionArgumentException;
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 TestH5R {
@Rule
public TestName testname = new TestName();
private static final String H5_FILE = "testH5R.h5";
private static final int DIM_X = 4;
private static final int DIM_Y = 6;
long H5fid = HDF5Constants.H5I_INVALID_HID;
long H5dsid = HDF5Constants.H5I_INVALID_HID;
long H5did = HDF5Constants.H5I_INVALID_HID;
long H5gid = HDF5Constants.H5I_INVALID_HID;
long H5did2 = HDF5Constants.H5I_INVALID_HID;
long[] H5dims = {DIM_X, DIM_Y};
int[][] dset_data = new int[DIM_X][DIM_Y];
int FILLVAL = 99;
private final void _deleteFile(String filename)
{
File file = null;
try {
file = new File(filename);
}
catch (Throwable err) {
}
if (file.exists()) {
try {
file.delete();
}
catch (SecurityException e) {
e.printStackTrace();
}
}
assertFalse("TestH5R._deleteFile file still exists ", file.exists());
}
private final long _createDataset(long fid, long dsid, String name, long dapl)
{
long did = HDF5Constants.H5I_INVALID_HID;
try {
did = H5.H5Dcreate(fid, name, HDF5Constants.H5T_STD_I32BE, dsid, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT, dapl);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Dcreate: " + err);
}
assertTrue("TestH5R._createDataset: ", did > 0);
return did;
}
private final long _createGroup(long fid, String name)
{
long gid = HDF5Constants.H5I_INVALID_HID;
try {
gid = H5.H5Gcreate(fid, name, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Gcreate: " + err);
}
assertTrue("TestH5R._createGroup: ", gid > 0);
return gid;
}
@Before
public void createH5file() throws NullPointerException, HDF5Exception
{
assertTrue("H5 open ids is 0", H5.getOpenIDCount() == 0);
System.out.print(testname.getMethodName());
try {
H5fid = H5.H5Fcreate(H5_FILE, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT);
H5dsid = H5.H5Screate_simple(2, H5dims, null);
H5gid = _createGroup(H5fid, "Group1");
H5did2 = _createDataset(H5gid, H5dsid, "dset2", HDF5Constants.H5P_DEFAULT);
H5did = _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();
}
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5R.createH5file: " + err);
}
assertTrue("TestH5R.createH5file: H5.H5Fcreate: ", H5fid > 0);
assertTrue("TestH5R.createH5file: H5.H5Screate_simple: ", H5dsid > 0);
assertTrue("TestH5R.createH5file: _createDataset: ", H5did > 0);
H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
}
@After
public void deleteH5file() throws HDF5LibraryException
{
if (H5dsid > 0)
try {
H5.H5Sclose(H5dsid);
}
catch (Exception ex) {
}
if (H5did > 0)
try {
H5.H5Dclose(H5did);
}
catch (Exception ex) {
}
if (H5fid > 0)
try {
H5.H5Fclose(H5fid);
}
catch (Exception ex) {
}
if (H5gid > 0)
try {
H5.H5Gclose(H5gid);
}
catch (Exception ex) {
}
if (H5did2 > 0)
try {
H5.H5Dclose(H5did2);
}
catch (Exception ex) {
}
_deleteFile(H5_FILE);
System.out.println();
}
// Test v1.12 APIs params
@Test
public void testH5Rget_object()
{
int ref_type = HDF5Constants.H5R_OBJECT2;
long ret_val = -1;
byte[] ref = null;
String name = "";
String objName = "/dset";
try {
ref = H5.H5Rcreate_object(H5fid, objName, HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Rget_object: H5Rcreate_object " + err);
}
try {
ret_val = H5.H5Rget_type(ref);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Rget_object: H5Rget_type: " + err);
}
assertTrue("testH5Rget_object: H5Rget_type", ret_val == ref_type);
try {
name = H5.H5Rget_file_name(ref);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Rget_object: H5Rget_file_name: " + err);
}
assertTrue("testH5Rget_object: H5Rget_file_name", H5_FILE.equals(name));
try {
name = H5.H5Rget_obj_name(ref, HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Rget_object: H5Rget_obj_name: " + err);
}
assertTrue("The name of the object: ", objName.equals(name));
H5.H5Rdestroy(ref);
}
@Test
public void testH5Rget_obj_type3()
{
int obj_type = -1;
byte[] ref = null;
String objName = "/dset";
try {
ref = H5.H5Rcreate_object(H5fid, objName, HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Rget_obj_type3: H5Rcreate_object " + err);
}
try {
obj_type = H5.H5Rget_obj_type3(ref, HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Rget_obj_type3: H5.H5Rget_obj_type3: " + err);
}
assertEquals(obj_type, HDF5Constants.H5O_TYPE_DATASET);
H5.H5Rdestroy(ref);
}
@Test
public void testH5Rcreate_regionref_object()
{
byte[] ref = null;
String objName = "/dset";
long start[] = {2, 2}; // Starting location of hyperslab
long stride[] = {1, 1}; // Stride of hyperslab
long count[] = {1, 1}; // Element count of hyperslab
long block[] = {3, 3}; // Block size of hyperslab
// Select 3x3 hyperslab for reference
try {
H5.H5Sselect_hyperslab(H5dsid, HDF5Constants.H5S_SELECT_SET, start, stride, count, block);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Rget_object: H5Sselect_hyperslab " + err);
}
try {
ref = H5.H5Rcreate_region(H5fid, objName, H5dsid, HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Rget_object: H5Rcreate_region " + err);
}
assertNotNull(ref);
H5.H5Rdestroy(ref);
}
// These tests need to be updated with new APIs
// @Test//
// public void testH5Rget_group() {
// long loc_id = H5fid;
// int ref_type = HDF5Constants.H5R_OBJECT2;
// long ret_val = -1;
// byte[] ref = null;
// String name = "";
// String objName = "/dset";
//
// try {
// ref = H5.H5Rcreate_object(H5fid, objName, HDF5Constants.H5P_DEFAULT);
// }
// catch (Throwable err) {
// err.printStackTrace();
// fail("testH5Rget_object: H5Rcreate_object " + err);
// }
// try {
// dataset_id= H5.H5Rdereference(H5fid, HDF5Constants.H5P_DEFAULT,
// HDF5Constants.H5R_DATASET_REGION, ref1);
//
// //Create reference on group
// ref2 = H5.H5Rcreate(H5gid, "/Group1", HDF5Constants.H5R_OBJECT, -1);
// group_id= H5.H5Rdereference(H5gid, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5R_OBJECT,
// ref2); assertNotNull(ref1); assertNotNull(ref2); assertTrue(dataset_id >= 0);
// assertTrue(group_id >= 0);
// }
// catch (Throwable err) {
// err.printStackTrace();
// fail("TestH5Rdereference " + err);
// }
// finally {
// try {H5.H5Dclose(dataset_id);} catch (Exception ex) {}
// try {H5.H5Gclose(group_id);} catch (Exception ex) {}
// }
// }
// @Test//
// public void testH5Rget_region_dataset() {
// long loc_id = H5fid;
// int ref_type = HDF5Constants.H5R_OBJECT2;
// long ret_val = -1;
// byte[] ref = null;
// String name = "";
// String objName = "/dset";
//
// try {
// ref = H5.H5Rcreate_object(H5fid, objName, HDF5Constants.H5P_DEFAULT);
// }
// catch (Throwable err) {
// err.printStackTrace();
// fail("testH5Rget_object: H5Rcreate_object " + err);
// }
// try {
// dsid = H5.H5Rget_region(H5fid, HDF5Constants.H5R_DATASET_REGION, ref);
// assertNotNull(ref);
// assertTrue(dsid >= 0);
// }
// catch (Throwable err) {
// err.printStackTrace();
// fail("TestH5Rget_region: " + err);
// }
// finally {
// try {H5.H5Sclose(dsid);} catch (Exception ex) {}
// }
// }
// @Test//
// public void testH5Rget_attr() {
// long loc_id = H5fid;
// int ref_type = HDF5Constants.H5R_OBJECT2;
// long ret_val = -1;
// byte[] ref = null;
// String name = "";
// String objName = "/dset";
//
// try {
// ref = H5.H5Rcreate_object(H5fid, objName, HDF5Constants.H5P_DEFAULT);
// }
// catch (Throwable err) {
// err.printStackTrace();
// fail("testH5Rget_object: H5Rcreate_object " + err);
// }
// try {
// dsid = H5.H5Rget_region(H5fid, HDF5Constants.H5R_DATASET_REGION, ref);
// assertNotNull(ref);
// assertTrue(dsid >= 0);
// }
// catch (Throwable err) {
// err.printStackTrace();
// fail("TestH5Rget_region: " + err);
// }
// finally {
// try {H5.H5Sclose(dsid);} catch (Exception ex) {}
// }
// }
// Test parameters to H5Rcreate_object
@Test(expected = NullPointerException.class)
public void testH5Rcreate_object_Nullname() throws Throwable
{
String name = null;
H5.H5Rcreate_object(H5fid, name, HDF5Constants.H5P_DEFAULT);
}
@Test(expected = HDF5FunctionArgumentException.class)
public void testH5Rget_name_Invalidloc() throws Throwable
{
String name = "";
H5.H5Rcreate_object(-1, name, HDF5Constants.H5P_DEFAULT);
}
// Test parameters to H5Rcreate_region
@Test(expected = NullPointerException.class)
public void testH5Rcreate_region_Nullname() throws Throwable
{
String name = null;
H5.H5Rcreate_region(H5fid, name, -1, HDF5Constants.H5P_DEFAULT);
}
@Test(expected = HDF5FunctionArgumentException.class)
public void testH5Rcreate_region_Invalidloc() throws Throwable
{
String name = "";
H5.H5Rcreate_region(-1, name, -1, HDF5Constants.H5P_DEFAULT);
}
// Test parameters to H5Rcreate_attr
@Test(expected = NullPointerException.class)
public void testH5Rcreate_attr_Nullname() throws Throwable
{
String name = null;
String attrname = "";
H5.H5Rcreate_attr(H5fid, name, attrname, HDF5Constants.H5P_DEFAULT);
}
@Test(expected = NullPointerException.class)
public void testH5Rcreate_attr_Nullattrname() throws Throwable
{
String name = "";
String attrname = null;
H5.H5Rcreate_attr(H5fid, name, attrname, HDF5Constants.H5P_DEFAULT);
}
@Test(expected = HDF5FunctionArgumentException.class)
public void testH5Rcreate_attr_Invalidloc() throws Throwable
{
String name = "";
String attrname = "";
H5.H5Rcreate_attr(-1, name, attrname, HDF5Constants.H5P_DEFAULT);
}
// Test parameters to H5Rdestroy
@Test(expected = NullPointerException.class)
public void testH5Rdestroy_Nullref() throws Throwable
{
byte[] ref = null;
H5.H5Rdestroy(ref);
}
// Test parameters to H5Rget_type
@Test(expected = NullPointerException.class)
public void testH5Rget_type_Nullref() throws Throwable
{
byte[] ref = null;
H5.H5Rget_type(ref);
}
// Test parameters to H5Requal
@Test(expected = NullPointerException.class)
public void testH5Requal_Nullref1() throws Throwable
{
byte[] ref1 = null;
byte[] ref2 = {0, 0, 0, 0};
H5.H5Requal(ref1, ref2);
}
@Test(expected = NullPointerException.class)
public void testH5Requal_Nullref2() throws Throwable
{
byte[] ref1 = {0, 0, 0, 0};
byte[] ref2 = null;
H5.H5Requal(ref1, ref2);
}
// Test parameters to H5Rcopy
@Test(expected = NullPointerException.class)
public void testH5Rcopy_Nullref1() throws Throwable
{
byte[] ref1 = null;
byte[] ref2 = H5.H5Rcopy(ref1);
}
// Test parameters to H5Ropen_object
@Test(expected = NullPointerException.class)
public void testH5Ropen_object_Nullref() throws Throwable
{
byte[] ref = null;
H5.H5Ropen_object(ref, -1, -1);
}
// Test parameters to H5Ropen_region
@Test(expected = NullPointerException.class)
public void testH5Ropen_region_Nullref() throws Throwable
{
byte[] ref = null;
H5.H5Ropen_region(ref, -1, -1);
}
// Test parameters to H5Ropen_attr
@Test(expected = NullPointerException.class)
public void testH5Ropen_attr_Nullref() throws Throwable
{
byte[] ref = null;
H5.H5Ropen_attr(ref, -1, -1);
}
// Test parameters to H5Rget_obj_type3
@Test(expected = NullPointerException.class)
public void testH5Rget_obj_type3_Nullref() throws Throwable
{
byte[] ref = null;
H5.H5Rget_obj_type3(ref, -1);
}
// Test parameters to H5Rget_file_name
@Test(expected = NullPointerException.class)
public void testH5Rget_file_name_Nullref() throws Throwable
{
byte[] ref = null;
H5.H5Rget_file_name(ref);
}
// Test parameters to H5Rget_obj_name
@Test(expected = NullPointerException.class)
public void testH5Rget_obj_name_Nullref() throws Throwable
{
byte[] ref = null;
H5.H5Rget_obj_name(ref, -1);
}
// Test parameters to H5Rget_attr_name
@Test(expected = NullPointerException.class)
public void testH5Rget_attr_name_Nullref() throws Throwable
{
byte[] ref = null;
H5.H5Rget_attr_name(ref);
}
@Test
public void testH5RVLattr_ref()
{
String attr_obj_name = "VLObjRefdata";
String attr_reg_name = "VLRegRefdata";
long attr_obj_id = HDF5Constants.H5I_INVALID_HID;
long attr_reg_id = HDF5Constants.H5I_INVALID_HID;
long atype_obj_id = HDF5Constants.H5I_INVALID_HID;
long atype_reg_id = HDF5Constants.H5I_INVALID_HID;
long aspace_id = HDF5Constants.H5I_INVALID_HID;
long[] dims = {4};
long lsize = 1;
byte[] ref1 = null;
byte[] ref2 = null;
byte[] ref3 = null;
byte[] ref4 = null;
try {
// Create reference on dataset
ref1 = H5.H5Rcreate(H5fid, "/dset", HDF5Constants.H5R_DATASET_REGION, H5dsid);
assertNotNull(ref1);
ref2 = H5.H5Rcreate(H5gid, "dset2", HDF5Constants.H5R_DATASET_REGION, H5dsid);
assertNotNull(ref2);
ref3 = H5.H5Rcreate(H5gid, "/dset", HDF5Constants.H5R_OBJECT, -1);
assertNotNull(ref3);
// Create reference on group
ref4 = H5.H5Rcreate(H5gid, "/Group1", HDF5Constants.H5R_OBJECT, -1);
assertNotNull(ref3);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5RVLattr_ref: " + err);
}
ArrayList[] vl_obj_data = new ArrayList[4];
ArrayList[] vl_reg_data = new ArrayList[4];
try {
// Write Object Reference data
vl_obj_data[0] = new ArrayList<byte[]>(Arrays.asList(ref3));
vl_obj_data[1] = new ArrayList<byte[]>(Arrays.asList(ref3, ref4));
vl_obj_data[2] = new ArrayList<byte[]>(Arrays.asList(ref3, ref3, ref3));
vl_obj_data[3] = new ArrayList<byte[]>(Arrays.asList(ref4, ref4, ref4, ref4));
Class dataClass = vl_obj_data.getClass();
assertTrue("testH5RVLattr_ref.getClass: " + dataClass, dataClass.isArray());
try {
atype_obj_id = H5.H5Tvlen_create(HDF5Constants.H5T_STD_REF_OBJ);
assertTrue("testH5RVLattr_ref.H5Tvlen_create: ", atype_obj_id >= 0);
}
catch (Exception err) {
if (atype_obj_id > 0)
try {
H5.H5Tclose(atype_obj_id);
}
catch (Exception ex) {
}
err.printStackTrace();
fail("H5.testH5RVLattr_ref: " + err);
}
try {
aspace_id = H5.H5Screate_simple(1, dims, null);
assertTrue(aspace_id > 0);
attr_obj_id = H5.H5Acreate(H5did, attr_obj_name, atype_obj_id, aspace_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
assertTrue("testH5RVLattr_ref: ", attr_obj_id >= 0);
H5.H5Awrite(attr_obj_id, atype_obj_id, vl_obj_data);
}
catch (Exception err) {
if (attr_obj_id > 0)
try {
H5.H5Aclose(attr_obj_id);
}
catch (Exception ex) {
}
if (atype_obj_id > 0)
try {
H5.H5Tclose(atype_obj_id);
}
catch (Exception ex) {
}
err.printStackTrace();
fail("H5.testH5RVLattr_ref: " + err);
}
finally {
if (aspace_id > 0)
try {
H5.H5Sclose(aspace_id);
}
catch (Exception ex) {
}
}
// Write Region Reference data
vl_reg_data[0] = new ArrayList<byte[]>(Arrays.asList(ref1));
vl_reg_data[1] = new ArrayList<byte[]>(Arrays.asList(ref1, ref2));
vl_reg_data[2] = new ArrayList<byte[]>(Arrays.asList(ref1, ref1, ref1));
vl_reg_data[3] = new ArrayList<byte[]>(Arrays.asList(ref2, ref2, ref2, ref2));
dataClass = vl_reg_data.getClass();
assertTrue("testH5RVLattr_ref.getClass: " + dataClass, dataClass.isArray());
try {
atype_reg_id = H5.H5Tvlen_create(HDF5Constants.H5T_STD_REF_DSETREG);
assertTrue("testH5RVLattr_ref.H5Tvlen_create: ", atype_reg_id >= 0);
}
catch (Exception err) {
if (atype_reg_id > 0)
try {
H5.H5Tclose(atype_reg_id);
}
catch (Exception ex) {
}
err.printStackTrace();
fail("H5.testH5RVLattr_ref: " + err);
}
try {
aspace_id = H5.H5Screate_simple(1, dims, null);
assertTrue(aspace_id > 0);
attr_reg_id = H5.H5Acreate(H5did, attr_reg_name, atype_reg_id, aspace_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
assertTrue("testH5RVLattr_ref: ", attr_reg_id >= 0);
H5.H5Awrite(attr_reg_id, atype_reg_id, vl_reg_data);
}
catch (Exception err) {
if (attr_reg_id > 0)
try {
H5.H5Aclose(attr_reg_id);
}
catch (Exception ex) {
}
if (atype_reg_id > 0)
try {
H5.H5Tclose(atype_reg_id);
}
catch (Exception ex) {
}
err.printStackTrace();
fail("H5.testH5RVLattr_ref: " + err);
}
finally {
if (aspace_id > 0)
try {
H5.H5Sclose(aspace_id);
}
catch (Exception ex) {
}
}
H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
for (int j = 0; j < dims.length; j++) {
lsize *= dims[j];
}
// Read Object Reference data
ArrayList[] vl_readbuf = new ArrayList[4];
for (int j = 0; j < lsize; j++)
vl_readbuf[j] = new ArrayList<byte[]>();
try {
H5.H5Aread(attr_obj_id, atype_obj_id, vl_readbuf);
}
catch (Exception ex) {
ex.printStackTrace();
}
assertTrue("testH5RVLattr_ref:" + ((byte[])vl_readbuf[0].get(0))[0],
((byte[])vl_obj_data[0].get(0))[0] == ((byte[])vl_readbuf[0].get(0))[0]);
assertTrue("testH5RVLattr_ref:" + ((byte[])vl_readbuf[1].get(0))[0],
((byte[])vl_obj_data[1].get(0))[0] == ((byte[])vl_readbuf[1].get(0))[0]);
assertTrue("testH5RVLattr_ref:" + ((byte[])vl_readbuf[2].get(0))[0],
((byte[])vl_obj_data[2].get(0))[0] == ((byte[])vl_readbuf[2].get(0))[0]);
assertTrue("testH5RVLattr_ref:" + ((byte[])vl_readbuf[3].get(0))[0],
((byte[])vl_obj_data[3].get(0))[0] == ((byte[])vl_readbuf[3].get(0))[0]);
// Read Region Reference data
vl_readbuf = new ArrayList[4];
for (int j = 0; j < lsize; j++)
vl_readbuf[j] = new ArrayList<byte[]>();
try {
H5.H5Aread(attr_reg_id, atype_reg_id, vl_readbuf);
}
catch (Exception ex) {
ex.printStackTrace();
}
assertTrue("testH5RVLattr_ref:" + ((byte[])vl_readbuf[0].get(0))[0],
((byte[])vl_reg_data[0].get(0))[0] == ((byte[])vl_readbuf[0].get(0))[0]);
assertTrue("testH5RVLattr_ref:" + ((byte[])vl_readbuf[1].get(0))[0],
((byte[])vl_reg_data[1].get(0))[0] == ((byte[])vl_readbuf[1].get(0))[0]);
assertTrue("testH5RVLattr_ref:" + ((byte[])vl_readbuf[2].get(0))[0],
((byte[])vl_reg_data[2].get(0))[0] == ((byte[])vl_readbuf[2].get(0))[0]);
assertTrue("testH5RVLattr_ref:" + ((byte[])vl_readbuf[3].get(0))[0],
((byte[])vl_reg_data[3].get(0))[0] == ((byte[])vl_readbuf[3].get(0))[0]);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.testH5RVLattr_ref: " + err);
}
finally {
if (attr_reg_id > 0)
try {
H5.H5Aclose(attr_reg_id);
}
catch (Exception ex) {
}
if (attr_obj_id > 0)
try {
H5.H5Aclose(attr_obj_id);
}
catch (Exception ex) {
}
if (atype_reg_id > 0)
try {
H5.H5Tclose(atype_reg_id);
}
catch (Exception ex) {
}
if (atype_obj_id > 0)
try {
H5.H5Tclose(atype_obj_id);
}
catch (Exception ex) {
}
}
}
@Test
public void testH5RVLdset_ref()
{
String dset_obj_name = "VLObjRefdata";
String dset_reg_name = "VLRegRefdata";
long dset_obj_id = HDF5Constants.H5I_INVALID_HID;
long dset_reg_id = HDF5Constants.H5I_INVALID_HID;
long dtype_obj_id = HDF5Constants.H5I_INVALID_HID;
long dtype_reg_id = HDF5Constants.H5I_INVALID_HID;
long dspace_id = HDF5Constants.H5I_INVALID_HID;
long[] dims = {4};
long lsize = 1;
byte[] ref1 = null;
byte[] ref2 = null;
byte[] ref3 = null;
byte[] ref4 = null;
try {
// Create reference on dataset
ref1 = H5.H5Rcreate(H5fid, "/dset", HDF5Constants.H5R_DATASET_REGION, H5dsid);
assertNotNull(ref1);
ref2 = H5.H5Rcreate(H5gid, "dset2", HDF5Constants.H5R_DATASET_REGION, H5dsid);
assertNotNull(ref2);
ref3 = H5.H5Rcreate(H5gid, "/dset", HDF5Constants.H5R_OBJECT, -1);
assertNotNull(ref3);
// Create reference on group
ref4 = H5.H5Rcreate(H5gid, "/Group1", HDF5Constants.H5R_OBJECT, -1);
assertNotNull(ref3);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5RVLattr_ref: " + err);
}
ArrayList[] vl_obj_data = new ArrayList[4];
ArrayList[] vl_reg_data = new ArrayList[4];
try {
// Write Object Reference data
vl_obj_data[0] = new ArrayList<byte[]>(Arrays.asList(ref3));
vl_obj_data[1] = new ArrayList<byte[]>(Arrays.asList(ref3, ref4));
vl_obj_data[2] = new ArrayList<byte[]>(Arrays.asList(ref3, ref3, ref3));
vl_obj_data[3] = new ArrayList<byte[]>(Arrays.asList(ref4, ref4, ref4, ref4));
Class dataClass = vl_obj_data.getClass();
assertTrue("testH5RVLdset_ref.getClass: " + dataClass, dataClass.isArray());
try {
dtype_obj_id = H5.H5Tvlen_create(HDF5Constants.H5T_STD_REF_OBJ);
assertTrue("testH5RVLdset_ref.H5Tvlen_create: ", dtype_obj_id >= 0);
}
catch (Exception err) {
if (dtype_obj_id > 0)
try {
H5.H5Tclose(dtype_obj_id);
}
catch (Exception ex) {
}
err.printStackTrace();
fail("H5.testH5RVLdset_ref: " + err);
}
try {
dspace_id = H5.H5Screate_simple(1, dims, null);
assertTrue(dspace_id > 0);
dset_obj_id =
H5.H5Dcreate(H5fid, dset_obj_name, dtype_obj_id, dspace_id, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
assertTrue("testH5RVLdset_ref: ", dset_obj_id >= 0);
H5.H5Dwrite(dset_obj_id, dtype_obj_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
HDF5Constants.H5P_DEFAULT, vl_obj_data);
}
catch (Exception err) {
if (dset_obj_id > 0)
try {
H5.H5Dclose(dset_obj_id);
}
catch (Exception ex) {
}
if (dtype_obj_id > 0)
try {
H5.H5Tclose(dtype_obj_id);
}
catch (Exception ex) {
}
err.printStackTrace();
fail("H5.testH5RVLdset_ref: " + err);
}
finally {
if (dspace_id > 0)
try {
H5.H5Sclose(dspace_id);
}
catch (Exception ex) {
}
}
// Write Region Reference data
vl_reg_data[0] = new ArrayList<byte[]>(Arrays.asList(ref1));
vl_reg_data[1] = new ArrayList<byte[]>(Arrays.asList(ref1, ref2));
vl_reg_data[2] = new ArrayList<byte[]>(Arrays.asList(ref1, ref1, ref1));
vl_reg_data[3] = new ArrayList<byte[]>(Arrays.asList(ref2, ref2, ref2, ref2));
dataClass = vl_reg_data.getClass();
assertTrue("testH5RVLdset_ref.getClass: " + dataClass, dataClass.isArray());
try {
dtype_reg_id = H5.H5Tvlen_create(HDF5Constants.H5T_STD_REF_DSETREG);
assertTrue("testH5RVLdset_ref.H5Tvlen_create: ", dtype_reg_id >= 0);
}
catch (Exception err) {
if (dtype_reg_id > 0)
try {
H5.H5Tclose(dtype_reg_id);
}
catch (Exception ex) {
}
err.printStackTrace();
fail("H5.testH5RVLdset_ref: " + err);
}
try {
dspace_id = H5.H5Screate_simple(1, dims, null);
assertTrue(dspace_id > 0);
dset_reg_id =
H5.H5Dcreate(H5fid, dset_reg_name, dtype_reg_id, dspace_id, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
assertTrue("testH5RVLdset_ref: ", dset_reg_id >= 0);
H5.H5Dwrite(dset_reg_id, dtype_reg_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
HDF5Constants.H5P_DEFAULT, vl_reg_data);
}
catch (Exception err) {
if (dset_reg_id > 0)
try {
H5.H5Dclose(dset_reg_id);
}
catch (Exception ex) {
}
if (dtype_reg_id > 0)
try {
H5.H5Tclose(dtype_reg_id);
}
catch (Exception ex) {
}
err.printStackTrace();
fail("H5.testH5RVLdset_ref: " + 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 Object Reference data
ArrayList[] vl_readbuf = new ArrayList[4];
for (int j = 0; j < lsize; j++)
vl_readbuf[j] = new ArrayList<byte[]>();
try {
H5.H5Dread(dset_obj_id, dtype_obj_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
HDF5Constants.H5P_DEFAULT, vl_readbuf);
}
catch (Exception ex) {
ex.printStackTrace();
}
assertTrue("testH5RVLdset_ref:" + ((byte[])vl_readbuf[0].get(0))[0],
((byte[])vl_obj_data[0].get(0))[0] == ((byte[])vl_readbuf[0].get(0))[0]);
assertTrue("testH5RVLdset_ref:" + ((byte[])vl_readbuf[1].get(0))[0],
((byte[])vl_obj_data[1].get(0))[0] == ((byte[])vl_readbuf[1].get(0))[0]);
assertTrue("testH5RVLdset_ref:" + ((byte[])vl_readbuf[2].get(0))[0],
((byte[])vl_obj_data[2].get(0))[0] == ((byte[])vl_readbuf[2].get(0))[0]);
assertTrue("testH5RVLdset_ref:" + ((byte[])vl_readbuf[3].get(0))[0],
((byte[])vl_obj_data[3].get(0))[0] == ((byte[])vl_readbuf[3].get(0))[0]);
// Read Region Reference data
vl_readbuf = new ArrayList[4];
for (int j = 0; j < lsize; j++)
vl_readbuf[j] = new ArrayList<byte[]>();
try {
H5.H5Dread(dset_reg_id, dtype_reg_id, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
HDF5Constants.H5P_DEFAULT, vl_readbuf);
}
catch (Exception ex) {
ex.printStackTrace();
}
assertTrue("testH5RVLdset_ref:" + ((byte[])vl_readbuf[0].get(0))[0],
((byte[])vl_reg_data[0].get(0))[0] == ((byte[])vl_readbuf[0].get(0))[0]);
assertTrue("testH5RVLdset_ref:" + ((byte[])vl_readbuf[1].get(0))[0],
((byte[])vl_reg_data[1].get(0))[0] == ((byte[])vl_readbuf[1].get(0))[0]);
assertTrue("testH5RVLdset_ref:" + ((byte[])vl_readbuf[2].get(0))[0],
((byte[])vl_reg_data[2].get(0))[0] == ((byte[])vl_readbuf[2].get(0))[0]);
assertTrue("testH5RVLdset_ref:" + ((byte[])vl_readbuf[3].get(0))[0],
((byte[])vl_reg_data[3].get(0))[0] == ((byte[])vl_readbuf[3].get(0))[0]);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.testH5RVLdset_ref: " + err);
}
finally {
if (dset_reg_id > 0)
try {
H5.H5Dclose(dset_reg_id);
}
catch (Exception ex) {
}
if (dset_obj_id > 0)
try {
H5.H5Dclose(dset_obj_id);
}
catch (Exception ex) {
}
if (dtype_reg_id > 0)
try {
H5.H5Tclose(dtype_reg_id);
}
catch (Exception ex) {
}
if (dtype_obj_id > 0)
try {
H5.H5Tclose(dtype_obj_id);
}
catch (Exception ex) {
}
}
}
}
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