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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.assertTrue;
import static org.junit.Assert.fail;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.io.Reader;
import java.io.StreamTokenizer;
import hdf.hdf5lib.H5;
import hdf.hdf5lib.HDF5Constants;
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;
/**
* @author xcao
*
*/
public class TestH5 {
@Rule public TestName testname = new TestName();
private static final String H5_FILE = "testData.h5";
private static final String EXPORT_FILE = "testExport.txt";
private static final String H5_DREG_FILE = "trefer_reg.h5";
private static final String EXPORT_DREG_FILE = "testExportReg.txt";
private static final String H5_AREG_FILE = "tattrreg.h5";
private static final String EXPORT_AREG_FILE = "testExportAReg.txt";
private static final int DIM_X = 4;
private static final int DIM_Y = 6;
private static final int DIM_BLKS = 36;
private static final int DIM_PNTS = 10;
private static final int DIM_ATTR = 12;
private static final int RANK = 2;
long H5fid = HDF5Constants.H5I_INVALID_HID;
long H5dsid = HDF5Constants.H5I_INVALID_HID;
long H5did = HDF5Constants.H5I_INVALID_HID;
long[] H5dims = { DIM_X, DIM_Y };
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) {}
}
}
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_I32LE, dsid,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, dapl);
}
catch (Throwable err) {
err.printStackTrace();
fail("H5.H5Dcreate: " + err);
}
assertTrue("TestH5._createDataset: ", did > 0);
return did;
}
private final void _createH5File() {
try {
H5fid = H5.H5Fcreate(H5_FILE, HDF5Constants.H5F_ACC_TRUNC,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
H5dsid = H5.H5Screate_simple(2, H5dims, null);
H5did = _createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5Pfapl.createH5file: " + err);
}
assertTrue("TestH5.createH5file: H5.H5Fcreate: ", H5fid > 0);
assertTrue("TestH5.createH5file: H5.H5Screate_simple: ", H5dsid > 0);
assertTrue("TestH5.createH5file: _createDataset: ", H5did > 0);
try {
H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
}
catch (Throwable err) {
err.printStackTrace();
}
}
private final void _closeH5File() {
if (H5did >= 0)
try {H5.H5Dclose(H5did);} catch (Exception ex) {}
if (H5dsid > 0)
try {H5.H5Sclose(H5dsid);} catch (Exception ex) {}
if (H5fid > 0)
try {H5.H5Fclose(H5fid);} catch (Exception ex) {}
H5fid = HDF5Constants.H5I_INVALID_HID;
H5dsid = HDF5Constants.H5I_INVALID_HID;
H5did = HDF5Constants.H5I_INVALID_HID;
}
public void _openH5File(String filename, String dsetname) {
try {
H5fid = H5.H5Fopen(filename,
HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5._openH5file: " + err);
}
assertTrue("TestH5._openH5file: H5.H5Fopen: ", H5fid >= 0);
try {
H5did = H5.H5Dopen(H5fid, dsetname, HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5._openH5file: " + err);
}
assertTrue("TestH5._openH5file: H5.H5Dopen: ", H5did >= 0);
try {
H5dsid = H5.H5Dget_space(H5did);
}
catch (Throwable err) {
err.printStackTrace();
fail("TestH5._openH5file: " + err);
}
assertTrue("TestH5._openH5file: H5.H5Screate_simple: ",H5dsid > 0);
}
public final void _deleteH5file() {
_closeH5File();
_deleteFile(H5_FILE);
}
@After
public void closeH5File() throws HDF5LibraryException {
_closeH5File();
assertTrue("H5 open ids is 0", H5.getOpenIDCount()==0);
System.out.println();
}
@Before
public void verifyCount()
throws NullPointerException, HDF5Exception {
assertTrue("H5 open ids is 0", H5.getOpenIDCount()==0);
System.out.print(testname.getMethodName());
}
/**
* Test method for {@link hdf.hdf5lib.H5#J2C(int)}.
* NOTE:
* H5F_ACC_DEBUG no longer prints any special debug info. Even though the symbol is
* being retained hdf java does not access the symbol.
*/
@Test
public void testJ2C() {
int H5F_ACC_RDONLY = 0x0000;
int H5F_ACC_RDWR = 0x0001;
int H5F_ACC_TRUNC = 0x0002;
int H5F_ACC_EXCL = 0x0004;
int H5F_ACC_CREAT = 0x0010;
int H5F_OBJ_FILE = 0x0001;
int H5F_OBJ_DATASET = 0x0002;
int H5F_OBJ_GROUP = 0x0004;
int H5F_OBJ_DATATYPE = 0x0008;
int H5F_OBJ_ATTR = 0x0010;
int H5F_OBJ_ALL = H5F_OBJ_FILE | H5F_OBJ_DATASET | H5F_OBJ_GROUP
| H5F_OBJ_DATATYPE | H5F_OBJ_ATTR;
int H5F_OBJ_LOCAL = 0x0020;
int definedValues[] = { H5F_ACC_RDONLY, H5F_ACC_RDWR, H5F_ACC_TRUNC,
H5F_ACC_EXCL, H5F_ACC_CREAT, H5F_OBJ_FILE,
H5F_OBJ_DATASET, H5F_OBJ_GROUP, H5F_OBJ_DATATYPE, H5F_OBJ_ATTR,
H5F_OBJ_ALL, H5F_OBJ_LOCAL };
int j2cValues[] = { HDF5Constants.H5F_ACC_RDONLY,
HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5F_ACC_TRUNC,
HDF5Constants.H5F_ACC_EXCL,
HDF5Constants.H5F_ACC_CREAT, HDF5Constants.H5F_OBJ_FILE,
HDF5Constants.H5F_OBJ_DATASET, HDF5Constants.H5F_OBJ_GROUP,
HDF5Constants.H5F_OBJ_DATATYPE, HDF5Constants.H5F_OBJ_ATTR,
HDF5Constants.H5F_OBJ_ALL, HDF5Constants.H5F_OBJ_LOCAL };
for (int i = 0; i < definedValues.length; i++) {
assertEquals(definedValues[i], j2cValues[i]);
}
assertFalse(H5F_ACC_RDONLY == HDF5Constants.H5F_ACC_RDWR);
assertFalse(H5F_OBJ_FILE == HDF5Constants.H5F_OBJ_GROUP);
}
/**
* Test method for {@link hdf.hdf5lib.H5#H5error_off()}.
*/
@Test
public void testH5error_off() {
try {
H5.H5error_off();
}
catch (Throwable err) {
fail("H5.H5error_off failed: " + err);
}
}
/**
* Test method for {@link hdf.hdf5lib.H5#H5open()}.
*/
@Test
public void testH5open() {
try {
H5.H5open();
}
catch (Throwable err) {
fail("H5.H5open failed: " + err);
}
}
/**
* Test method for {@link hdf.hdf5lib.H5#H5garbage_collect()}.
*/
@Test
public void testH5garbage_collect() {
try {
H5.H5garbage_collect();
}
catch (Throwable err) {
fail("H5.H5garbage_collect failed: " + err);
}
}
/**
* Test method for
* {@link hdf.hdf5lib.H5#H5set_free_list_limits(int, int, int, int, int, int)}
* .
*/
@Test
public void testH5set_free_list_limits() {
int reg_global_lim = 1;
int reg_list_lim = 1;
int arr_global_lim = 1;
int arr_list_lim = 1;
int blk_global_lim = 1;
int blk_list_lim = 1;
try {
H5.H5set_free_list_limits(reg_global_lim, reg_list_lim,
arr_global_lim, arr_list_lim, blk_global_lim, blk_list_lim);
}
catch (Throwable err) {
fail("H5.H5set_free_list_limits failed: " + err);
}
}
/**
* Test method for {@link hdf.hdf5lib.H5#H5get_libversion(int[])}.
*/
@Test
public void testH5get_libversion() {
int libversion[] = { 1, 10, 8 };
try {
H5.H5get_libversion(libversion);
}
catch (Throwable err) {
fail("H5.H5get_libversion: " + err);
}
for (int i = 0; i < 2; i++)
assertEquals(H5.LIB_VERSION[i], libversion[i]);
for (int i = 0; i < 2; i++)
assertFalse(libversion[i] == 0);
}
/**
* Test method for {@link hdf.hdf5lib.H5#H5get_libversion(int[])}
* to ensure a null libversion parameter causes the function to
* fail.
*/
@Test
public void testH5get_libversion_null_param() {
try {
H5.H5get_libversion(null);
}
catch (Throwable err) {
return;
}
fail("H5.H5get_libversion: succeeded with a null libversion parameter!");
}
/**
* Test method for
* {@link hdf.hdf5lib.H5#H5check_version(int, int, int)}.
*/
@Test
public void testH5check_version() {
int majnum = 1, minnum = 10, relnum = 8;
try {
H5.H5check_version(majnum, minnum, relnum);
}
catch (Throwable err) {
fail("H5.H5check_version failed: " + err);
}
try {
H5.H5check_version(-1, 0, 0);
}
catch (Throwable err) {
fail("H5.H5check_version failed: " + err);
}
}
@Test
public void testIsSerializable() {
H5 test = new H5();
ByteArrayOutputStream out = new ByteArrayOutputStream();
ObjectOutputStream oos;
try {
oos = new ObjectOutputStream(out);
oos.writeObject(test);
oos.close();
}
catch (IOException err) {
err.printStackTrace();
fail("ObjectOutputStream failed: " + err);
}
assertTrue(out.toByteArray().length > 0);
}
@SuppressWarnings("static-access")
@Test
public void serializeToDisk()
{
try {
H5 test = new H5();
FileOutputStream fos = new FileOutputStream("temph5.ser");
ObjectOutputStream oos = new ObjectOutputStream(fos);
oos.writeObject(test);
oos.close();
}
catch (Exception ex) {
fail("Exception thrown during test: " + ex.toString());
}
try {
FileInputStream fis = new FileInputStream("temph5.ser");
ObjectInputStream ois = new ObjectInputStream(fis);
H5 test = (hdf.hdf5lib.H5) ois.readObject();
ois.close();
assertTrue("H5.LIB_VERSION[0]", test.LIB_VERSION[0]==H5.LIB_VERSION[0]);
assertTrue("H5.LIB_VERSION[1]", test.LIB_VERSION[1]==H5.LIB_VERSION[1]);
// assertTrue("H5.LIB_VERSION[2]", test.LIB_VERSION[2]==H5.LIB_VERSION[2]);
// Clean up the file
new File("temph5.ser").delete();
}
catch (Exception ex) {
fail("Exception thrown during test: " + ex.toString());
}
}
@Test
public void testH5export_dataset() {
int[][] dset_data = new int[DIM_X][DIM_Y];
int[][] dset_indata = new int[DIM_X][DIM_Y];
int FILLVAL = 99;
_createH5File();
// 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_STD_I32LE,
HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
HDF5Constants.H5P_DEFAULT, dset_data);
}
catch (Exception e) {
e.printStackTrace();
}
_closeH5File();
_openH5File(H5_FILE, "/dset");
try {
H5.H5export_dataset(EXPORT_FILE, H5fid, "/dset", 99);
}
catch (HDF5LibraryException err) {
err.printStackTrace();
fail("H5export_dataset failed: " + err);
}
File file = new File(EXPORT_FILE);
try {
Reader reader = new FileReader(EXPORT_FILE);
StreamTokenizer streamTokenizer = new StreamTokenizer(reader);
int indx = 0;
int jndx = 0;
while(streamTokenizer.nextToken() != StreamTokenizer.TT_EOF){
if(streamTokenizer.ttype == StreamTokenizer.TT_NUMBER) {
dset_indata[indx][jndx] = (int)streamTokenizer.nval;
jndx++;
if (jndx >= DIM_Y) {
jndx = 0;
indx++;
}
}
}
reader.close();
}
catch (IOException err) {
err.printStackTrace();
fail("read file failed: " + err);
}
for(int row = 0; row < DIM_X; row++)
for(int col = 0; col < DIM_Y; col++) {
assertTrue("H5export_dataset: <"+row+","+col+">"+dset_indata[row][col]+"=99", dset_indata[row][col]==99);
}
_deleteH5file();
}
@Test
public void testH5export_regdataset() {
int[] dset_data_expect = {66, 69, 72, 75, 78, 81, 96, 99, 102, 105, 108,
111, 126, 129, 132, 135, 138, 141, 156, 159, 162, 165, 168, 171,
186, 189, 192, 195, 198, 201, 216, 219, 222, 225, 228, 231,
207, 66, 252, 48, 84, 96, 12, 14, 213, 99};
int[] dset_indata = new int[DIM_BLKS+DIM_PNTS];
String objName = "/Dataset1";
_openH5File(H5_DREG_FILE, objName);
try {
H5.H5export_dataset(EXPORT_DREG_FILE, H5fid, objName, 99);
}
catch (HDF5LibraryException err) {
err.printStackTrace();
fail("H5export_dataset failed: " + err);
}
File file = new File(EXPORT_DREG_FILE);
try {
Reader reader = new FileReader(EXPORT_DREG_FILE);
StreamTokenizer streamTokenizer = new StreamTokenizer(reader);
int indx = 0;
while(streamTokenizer.nextToken() != StreamTokenizer.TT_EOF){
if(streamTokenizer.ttype == StreamTokenizer.TT_NUMBER) {
dset_indata[indx] = (int)streamTokenizer.nval;
indx++;
}
}
reader.close();
}
catch (IOException err) {
err.printStackTrace();
fail("read file failed: " + err);
}
for(int row = 0; row < DIM_X; row++)
assertTrue("testH5export_regdataset: <"+row+">"+dset_indata[row], dset_indata[row]==dset_data_expect[row]);
}
@Test
public void testH5export_attrdataset() {
int[] dset_data_expect = {66, 69, 72, 75, 78, 81, 96, 99, 102, 105, 108,
111, 126, 129, 132, 135, 138, 141, 156, 159, 162, 165, 168, 171,
186, 189, 192, 195, 198, 201, 216, 219, 222, 225, 228, 231,
207, 66, 252, 48, 84, 96, 12, 14, 213, 99};
int[] dset_indata = new int[DIM_BLKS+DIM_PNTS];
String dsetName = "/Dataset1";
String objName = "Attribute1";
_openH5File(H5_AREG_FILE, dsetName);
try {
H5.H5export_attribute(EXPORT_AREG_FILE, H5did, objName, 99);
}
catch (HDF5LibraryException err) {
err.printStackTrace();
fail("H5export_attribute failed: " + err);
}
File file = new File(EXPORT_AREG_FILE);
try {
Reader reader = new FileReader(EXPORT_AREG_FILE);
StreamTokenizer streamTokenizer = new StreamTokenizer(reader);
int indx = 0;
int jndx = 0;
while(streamTokenizer.nextToken() != StreamTokenizer.TT_EOF){
if(streamTokenizer.ttype == StreamTokenizer.TT_NUMBER) {
dset_indata[indx] = (int)streamTokenizer.nval;
indx++;
}
}
reader.close();
}
catch (IOException err) {
err.printStackTrace();
fail("read file failed: " + err);
}
for(int row = 0; row < DIM_X; row++)
assertTrue("testH5export_attrdataset: <"+row+">"+dset_indata[row], dset_indata[row]==dset_data_expect[row]);
}
}
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