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/**
*
*/
package test.object;
import java.util.Vector;
import junit.framework.TestCase;
import ncsa.hdf.hdf5lib.H5;
import ncsa.hdf.hdf5lib.HDF5Constants;
import ncsa.hdf.object.Dataset;
import ncsa.hdf.object.FileFormat;
import ncsa.hdf.object.h5.H5CompoundDS;
import ncsa.hdf.object.h5.H5File;
/**
* TestCase for bug fixes.
* <p>
* This class tests all the public methods in H5CompoundDS class.
* <p>
* The test file contains the following objects.
*
* <pre>
*
*
* /dataset_byte Dataset {50, 10}
* /dataset_comp Dataset {50, 10}
* /dataset_enum Dataset {50, 10}
* /dataset_float Dataset {50, 10}
* /dataset_image Dataset {50, 10}
* /dataset_int Dataset {50, 10}
* /dataset_str Dataset {50, 10}
* /g0 Group
* /g0/dataset_comp Dataset {50, 10}
* /g0/dataset_int Dataset {50, 10}
* /g0/datatype_float Type
* /g0/datatype_int Type
* /g0/datatype_str Type
* /g0/g00 Group
* /g0/g00/dataset_float Dataset {50, 10}
* /g0_attr Group
*
* </pre>
*
*@author Peter Cao, The HDF Group
*/
public class H5BugFixTest extends TestCase {
private static final int NLOOPS = 10;
private static final H5File H5FILE = new H5File();
private H5File testFile = null;
/**
* @param arg0
*/
public H5BugFixTest(final String arg0) {
super(arg0);
}
private static void collectGarbage() {
try {
System.gc();
Thread.sleep(100);
System.runFinalization();
Thread.sleep(100);
}
catch (final Exception ex) {
ex.printStackTrace();
}
}
/*
* (non-Javadoc)
*
* @see junit.framework.TestCase#setUp()
*/
@Override
protected void setUp() throws Exception {
super.setUp();
testFile = (H5File) H5FILE.open(H5TestFile.NAME_FILE_H5,
FileFormat.WRITE);
assertNotNull(testFile);
}
/*
* (non-Javadoc)
*
* @see junit.framework.TestCase#tearDown()
*/
@Override
protected void tearDown() throws Exception {
super.tearDown();
if (testFile != null) {
try {
testFile.close();
}
catch (final Exception ex) {
}
testFile = null;
}
}
/**
* The following program fails because dataset.init() does not reset the
* selection of dataspace.
* <p>
* The bug appears on hdf-java 2.4 beta04 or earlier version. It is fixed at
* later version.
*
* <pre>
* 1) read the table cell (using dataset selection to select only that row of the table)
* 2) re-initialize the Dataset
* 3) call 'Dataset.clearData()'
* 4) call 'Dataset.getData()'
* 5) change the correct column/row **
* 6) call 'Dataset.write()'
* 7) close the file
* 8) reopen the file and read the table cell as in step 1
* 9) assert that the value has been changed and is correct
* This sequence of actions works correctly on the hdf-java library built for
* 64-bit solaris that we received in August 2006. On the latest (beta-d), This
* fails when attempting to change the value of the 1st and 4th rows (however, it
* works for the 0th row).
* </pre>
* <p>
*/
public final void testBug847() throws Exception {
Vector data = null;
final H5CompoundDS dset = (H5CompoundDS) testFile
.get(H5TestFile.NAME_DATASET_COMPOUND);
assertNotNull(dset);
for (int loop = 0; loop < NLOOPS; loop++) {
// read the whole dataset by default
dset.init();
try {
data = (Vector) dset.getData();
}
catch (final Exception ex) {
fail("getData() failed. " + ex);
}
assertNotNull(data);
assertTrue(data.size() > 0);
// check the data values
int[] ints = (int[]) data.get(0);
float[] floats = (float[]) data.get(1);
String[] strs = (String[]) data.get(2);
assertNotNull(ints);
assertNotNull(floats);
assertNotNull(strs);
for (int i = 0; i < H5TestFile.DIM_SIZE; i++) {
assertEquals(H5TestFile.DATA_INT[i], ints[i]);
assertEquals(H5TestFile.DATA_FLOAT[i], floats[i],
Float.MIN_VALUE);
assertTrue(H5TestFile.DATA_STR[i].equals(strs[i]));
}
final int rank = dset.getRank();
final long[] dims = dset.getDims();
final long[] start = dset.getStartDims();
final long[] count = dset.getSelectedDims();
final int[] selectedIndex = dset.getSelectedIndex();
// read data row by row
for (int i = 0; i < rank; i++) {
start[i] = 0;
count[i] = 1;
}
final int nrows = dset.getHeight();
for (int i = 0; i < nrows; i++) {
dset.clearData();
dset.init();
// select one row only
for (int j = 0; j < rank; j++) {
count[j] = 1;
}
// select different rows
start[0] = i;
try {
data = (Vector) dset.getData();
}
catch (final Exception ex) {
fail("getData() failed. " + ex);
}
ints = (int[]) data.get(0);
floats = (float[]) data.get(1);
strs = (String[]) data.get(2);
assertNotNull(ints);
assertNotNull(floats);
assertNotNull(strs);
assertEquals(H5TestFile.DATA_INT[i], ints[0]);
assertEquals(H5TestFile.DATA_FLOAT[i], floats[0],
Float.MIN_VALUE);
assertTrue(H5TestFile.DATA_STR[i].equals(strs[0]));
} // for (int i=0; i<nrows; i++) {
// read field by field
final int nmembers = dset.getMemberCount();
for (int i = 0; i < nmembers; i++) {
dset.clearData();
dset.init();
dset.setMemberSelection(false);
dset.selectMember(i);
try {
data = (Vector) dset.getData();
}
catch (final Exception ex) {
fail("getData() failed. " + ex);
}
assertNotNull(data);
assertTrue(data.size() == 1);
switch (i) {
case 0:
ints = (int[]) data.get(0);
assertNotNull(ints);
for (int j = 0; j < H5TestFile.DIM_SIZE; j++) {
assertEquals(H5TestFile.DATA_INT[j], ints[j]);
}
break;
case 1:
floats = (float[]) data.get(0);
assertNotNull(floats);
for (int j = 0; j < H5TestFile.DIM_SIZE; j++) {
assertEquals(H5TestFile.DATA_FLOAT[j], floats[j],
Float.MIN_VALUE);
}
break;
case 2:
strs = (String[]) data.get(0);
assertNotNull(strs);
for (int j = 0; j < H5TestFile.DIM_SIZE; j++) {
assertTrue(H5TestFile.DATA_STR[j].equals(strs[j]));
}
break;
}
} // for (int i=0; i<nmembers; i++) {
} // for (int loop=0; loop<NLOOPS; loop++) {
}
/**
* The following operation causes memory leak because a group is left open
* at file.get().
* <p>
* The bug appears on hdf-java 2.4 beta05 or earlier version. It is fixed at
* later version.
*
* <pre>
* while (true) {
* H5File file = new H5File(H5TestFile.NAME_FILE_H5, H5File.READ);
* //file.open();
* file.get("/Table0");
* file.get("/Group0");
*
* int n = H5.H5Fget_obj_count(file.getFID(), HDF5Constants.H5F_OBJ_ALL);
* if (n > 1)
* System.out.println("*** Possible memory leak!!!");
*
* file.close();
* }
* </pre>
*/
public final void testBug863() throws Exception {
int nObjs = 0; // number of object left open
Dataset dset = null;
final String dnames[] = { H5TestFile.NAME_DATASET_CHAR,
H5TestFile.NAME_DATASET_COMPOUND,
H5TestFile.NAME_DATASET_COMPOUND_SUB,
H5TestFile.NAME_DATASET_ENUM, H5TestFile.NAME_DATASET_FLOAT,
H5TestFile.NAME_DATASET_IMAGE, H5TestFile.NAME_DATASET_INT,
H5TestFile.NAME_DATASET_STR, H5TestFile.NAME_DATASET_INT_SUB,
H5TestFile.NAME_DATASET_FLOAT_SUB_SUB };
// test two open options: open full tree or open individual object only
for (int openOption = 0; openOption < 2; openOption++) {
for (int i = 0; i < NLOOPS; i++) {
nObjs = 0;
final H5File file = new H5File(H5TestFile.NAME_FILE_H5,
FileFormat.WRITE);
if (openOption == 0) {
try {
file.open(); // opent the full tree
}
catch (final Exception ex) {
fail("file.open() failed. " + ex);
}
}
try {
// datasets
for (int j = 0; j < dnames.length; j++) {
dset = (Dataset) file.get(dnames[j]);
dset.init();
final Object data = dset.getData();
dset.write(data);
dset.getMetadata();
}
// groups
file.get(H5TestFile.NAME_GROUP);
file.get(H5TestFile.NAME_GROUP_ATTR);
file.get(H5TestFile.NAME_GROUP_SUB);
// datatypes
file.get(H5TestFile.NAME_DATATYPE_INT);
file.get(H5TestFile.NAME_DATATYPE_FLOAT);
file.get(H5TestFile.NAME_DATATYPE_STR);
}
catch (final Exception ex) {
fail("file.get() failed. " + ex);
}
try {
nObjs = H5.H5Fget_obj_count(file.getFID(),
HDF5Constants.H5F_OBJ_ALL);
}
catch (final Exception ex) {
fail("H5.H5Fget_obj_count() failed. " + ex);
}
try {
file.close();
}
catch (final Exception ex) {
fail("file.close() failed. " + ex);
}
assertTrue(nObjs <= 1); // file id should be the only this left
// open
} // for (int i=0; i<NLOOPS; i++)
} // for (int openOption=0; openOption<2; openOption++)
}
}