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package test.object;
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.ByteArrayOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.util.Vector;
import ncsa.hdf.hdf5lib.H5;
import ncsa.hdf.hdf5lib.HDF5Constants;
import ncsa.hdf.object.Attribute;
import ncsa.hdf.object.Datatype;
import ncsa.hdf.object.FileFormat;
import ncsa.hdf.object.h5.H5Datatype;
import ncsa.hdf.object.h5.H5File;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.BeforeClass;
import org.junit.Test;
/**
* TestCase for H5Datatype.
* <p>
* This class tests all the public methods in H5ScalarDS 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>
* <p>
* We use the following template to test all the methods:
* <p>
* What to test:
* <ul>
* <li>Test for boundary conditions
* <ul>
* <li>
* </ul>
* <li>Test for failure
* <ul>
* <li>
* </ul>
* <li>Test for success on general functionality
* <ul>
* <li>
* </ul>
* </ul>
*
* @author Peter Cao, The HDF Group
*/
public class H5DatatypeTest {
private final static org.slf4j.Logger log = org.slf4j.LoggerFactory.getLogger(H5DatatypeTest.class);
private static final H5File H5FILE = new H5File();
private static final int NLOOPS = 10;
private static final int TEST_VALUE_INT = Integer.MAX_VALUE;
private static final float TEST_VALUE_FLOAT = Float.MAX_VALUE;
private static final String TEST_VALUE_STR = "Test";
private static final String TNAME = H5TestFile.NAME_DATATYPE_INT;
private H5Datatype typeInt = null;
private H5Datatype typeUInt = null;
private H5Datatype typeFloat = null;
private H5Datatype typeStr = null;
private H5File testFile = null;
private H5Datatype testDatatype = null;
@BeforeClass
public static void createFile() throws Exception {
try {
int openID = H5.getOpenIDCount();
if (openID > 0)
System.out.println("H5DatatypeTest BeforeClass: Number of IDs still open: " + openID);
}
catch (Exception ex) {
ex.printStackTrace();
}
try {
H5TestFile.createTestFile(null);
}
catch (final Exception ex) {
System.out.println("*** Unable to create HDF5 test file. " + ex);
System.exit(-1);
}
}
@AfterClass
public static void checkIDs() throws Exception {
try {
int openID = H5.getOpenIDCount();
if (openID > 0)
System.out.println("H5DatatypeTest AfterClass: Number of IDs still open: " + openID);
}
catch (Exception ex) {
ex.printStackTrace();
}
}
@Before
public void openFiles() throws Exception {
try {
int openID = H5.getOpenIDCount();
if (openID > 0)
log.debug("Before: Number of IDs still open: " + openID);
}
catch (Exception ex) {
ex.printStackTrace();
}
typeInt = new H5Datatype(Datatype.CLASS_INTEGER, H5TestFile.DATATYPE_SIZE, -1, -1);
typeUInt = new H5Datatype(Datatype.CLASS_INTEGER, H5TestFile.DATATYPE_SIZE, -1, Datatype.SIGN_NONE);
typeFloat = new H5Datatype(Datatype.CLASS_FLOAT, H5TestFile.DATATYPE_SIZE, -1, -1);
typeStr = new H5Datatype(Datatype.CLASS_STRING, H5TestFile.STR_LEN, -1, -1);
testFile = (H5File) H5FILE.open(H5TestFile.NAME_FILE_H5, FileFormat.WRITE);
assertNotNull(testFile);
testFile.open();
testDatatype = (H5Datatype) testFile.get(TNAME);
assertNotNull(testDatatype);
}
@After
public void removeFiles() throws Exception {
if (testFile != null) {
try {
testFile.close();
}
catch (final Exception ex) {
}
testFile = null;
}
try {
int openID = H5.getOpenIDCount();
if (openID > 0)
log.debug("After: Number of IDs still open: " + openID);
}
catch (Exception ex) {
ex.printStackTrace();
}
}
/**
* Test method for {@link ncsa.hdf.object.h5.H5Datatype#open()}.
* <p>
* What to test:
* <ul>
* <li>Open a datatype identifier
* <li>Check the class and size of the datatype
* <li>Close the datatype
* <li>Repeat all above
* </ul>
*/
@Test
public void testOpen() {
log.debug("testOpen");
int tid = -1, tclass = -1, tsize = -1;
for (int loop = 0; loop < NLOOPS; loop++) {
tid = tclass = tsize = -1;
try {
tid = testDatatype.open();
}
catch (final Exception ex) {
fail("open() failed. " + ex);
}
assertTrue(tid > 0);
try {
tclass = H5.H5Tget_class(tid);
tsize = H5.H5Tget_size(tid);
}
catch (final Exception ex) {
fail("open() failed. " + ex);
}
assertEquals(4, tsize);
assertEquals(HDF5Constants.H5T_INTEGER, tclass);
try {
H5.H5Tclose(tid);
}
catch (final Exception ex) {
}
}
int nObjs = 0;
try {
nObjs = H5.H5Fget_obj_count(testFile.getFID(), HDF5Constants.H5F_OBJ_ALL);
}
catch (final Exception ex) {
fail("H5.H5Fget_obj_count() failed. " + ex);
}
assertEquals(1, nObjs); // file id should be the only one left open
}
/**
* Test method for {@link ncsa.hdf.object.h5.H5Datatype#close(int)}.
* <p>
* What to test:
* <ul>
* <li>Open a datatype identifier
* <li>Check the class and size of the datatype
* <li>Close the datatype
* <li>Access the closed datatype (expect to fail)
* <li>Repeat all above
* </ul>
*/
@Test
public void testClose() {
log.debug("testClose");
int tid = -1, tclass = -1, tsize = -1;
for (int loop = 0; loop < NLOOPS; loop++) {
tid = tclass = tsize = -1;
try {
tid = testDatatype.open();
}
catch (final Exception ex) {
fail("open() failed. " + ex);
}
assertTrue(tid > 0);
try {
tclass = H5.H5Tget_class(tid);
tsize = H5.H5Tget_size(tid);
}
catch (final Exception ex) {
fail("open() failed. " + ex);
}
assertEquals(4, tsize);
assertEquals(HDF5Constants.H5T_INTEGER, tclass);
try {
H5.H5Tclose(tid);
}
catch (final Exception ex) {
}
try {
tclass = H5.H5Tget_class(tid);
}
catch (final Exception ex) {
; // Expected - intentional
}
}
int nObjs = 0;
try {
nObjs = H5.H5Fget_obj_count(testFile.getFID(), HDF5Constants.H5F_OBJ_ALL);
}
catch (final Exception ex) {
fail("H5.H5Fget_obj_count() failed. " + ex);
}
assertEquals(1, nObjs); // file id should be the only one left open
}
/**
* Test method for {@link ncsa.hdf.object.h5.H5Datatype#toNative()}.
* <p>
* What to test:
* <ul>
* <li>Create integer, float and string datatypes in memory
* <li>Call toNative() to get datatype identifiers
* <li>Check the classes and sizes of the datatypes from toNative()
* </ul>
*/
@Test
public void testToNative() {
log.debug("testToNative");
int tid = -1, tclass = -1, tsize = -1;
// test integer datatype
try {
tid = typeInt.toNative();
}
catch (final Exception ex) {
fail("testToNative() failed. " + ex);
}
try {
tclass = H5.H5Tget_class(tid);
tsize = H5.H5Tget_size(tid);
}
catch (final Exception ex) {
fail("open() failed. " + ex);
}
assertEquals(4, tsize);
assertEquals(HDF5Constants.H5T_INTEGER, tclass);
try {
H5.H5Tclose(tid);
}
catch (final Exception ex) {
}
// test float datatype
try {
tid = typeFloat.toNative();
}
catch (final Exception ex) {
fail("testToNative() failed. " + ex);
}
try {
tclass = H5.H5Tget_class(tid);
tsize = H5.H5Tget_size(tid);
}
catch (final Exception ex) {
fail("open() failed. " + ex);
}
assertEquals(4, tsize);
assertEquals(HDF5Constants.H5T_FLOAT, tclass);
try {
H5.H5Tclose(tid);
}
catch (final Exception ex) {
}
// test String datatype
try {
tid = typeStr.toNative();
}
catch (final Exception ex) {
fail("testToNative() failed. " + ex);
}
try {
tclass = H5.H5Tget_class(tid);
tsize = H5.H5Tget_size(tid);
}
catch (final Exception ex) {
fail("open() failed. " + ex);
}
assertEquals(H5TestFile.STR_LEN, tsize);
assertEquals(HDF5Constants.H5T_STRING, tclass);
try {
H5.H5Tclose(tid);
}
catch (final Exception ex) {
}
int nObjs = 0;
try {
nObjs = H5.H5Fget_obj_count(testFile.getFID(), HDF5Constants.H5F_OBJ_ALL);
}
catch (final Exception ex) {
fail("H5.H5Fget_obj_count() failed. " + ex);
}
assertEquals(1, nObjs); // file id should be the only one left open
}
/**
* Test method for {@link ncsa.hdf.object.h5.H5Datatype#fromNative(int)}.
* <p>
* What to test:
* <ul>
* <li>Create empty datatype object in memory
* <li>Test faillure on the class and size of the datatype
* <li>Open datatype identifier from file
* <li>Call fromNative(int tid) to fill the datatype object
* <li>Check the class and size of the datatype
* </ul>
*/
@Test
public void testFromNative() {
log.debug("testFromNative");
int tid = -1;
H5Datatype type = new H5Datatype(-1);
assertFalse(Datatype.CLASS_INTEGER == type.getDatatypeClass());
assertFalse(type.getDatatypeSize() == 4);
try {
tid = H5.H5Topen(testFile.getFID(), TNAME);
}
catch (final Exception ex) {
fail("H5Topen() failed. " + ex);
}
assertTrue(tid > 0);
type.fromNative(tid);
assertTrue(Datatype.CLASS_INTEGER == type.getDatatypeClass());
assertTrue(type.getDatatypeSize() == 4);
try {
H5.H5Tclose(tid);
}
catch (final Exception ex) {
}
int nObjs = 0;
try {
nObjs = H5.H5Fget_obj_count(testFile.getFID(), HDF5Constants.H5F_OBJ_ALL);
}
catch (final Exception ex) {
fail("H5.H5Fget_obj_count() failed. " + ex);
}
assertEquals(1, nObjs); // file id should be the only one left open
int tids[] = { HDF5Constants.H5T_STD_I32LE, HDF5Constants.H5T_STD_U16LE, HDF5Constants.H5T_STD_I32BE };
int sizes[] = { 4, 2, 4 };
int signs[] = { Datatype.SIGN_2, Datatype.SIGN_NONE, Datatype.SIGN_2 };
int orders[] = { Datatype.ORDER_LE, Datatype.ORDER_LE, Datatype.ORDER_BE };
for (int i = 0; i < tids.length; i++) {
type = new H5Datatype(tids[i]);
assertEquals("sizes#" + i, sizes[i], type.getDatatypeSize());
assertEquals("signs#" + i, signs[i], type.getDatatypeSign());
assertEquals("orders#" + i, orders[i], type.getDatatypeOrder());
}
}
/**
* Test method for {@link ncsa.hdf.object.h5.H5Datatype#isUnsigned()}.
* <p>
* What to test:
* <ul>
* <li>Check unsigned integer datatype
* <li>check signed integer datatype
* <li>Check non-integer datatype
* </ul>
*/
@Test
public void testIsUnsigned() {
log.debug("testIsUnsigned");
assertFalse(typeInt.isUnsigned());
assertFalse(typeFloat.isUnsigned());
assertFalse(typeStr.isUnsigned());
assertTrue(typeUInt.isUnsigned());
}
/**
* Test method for {@link ncsa.hdf.object.h5.H5Datatype#getMetadata()}.
* <p>
* What to test:
* <ul>
* <li>Get all the attributes
* <li>Check the content of the attributes
* </ul>
*/
@Test
public void testGetMetadata() {
log.debug("testGetMetadata");
Vector attrs = null;
try {
attrs = (Vector) testDatatype.getMetadata();
}
catch (final Exception ex) {
fail("getMetadata() failed. " + ex);
}
assertNotNull(attrs);
assertTrue(attrs.size() > 0);
final int n = attrs.size();
for (int i = 0; i < n; i++) {
final Attribute attr = (Attribute) attrs.get(i);
final H5Datatype dtype = (H5Datatype) attr.getType();
if (dtype.getDatatypeClass() == Datatype.CLASS_STRING) {
assertTrue(H5TestFile.ATTRIBUTE_STR.getName().equals(attr.getName()));
assertTrue(((String[]) H5TestFile.ATTRIBUTE_STR.getValue())[0].equals(((String[]) attr.getValue())[0]));
}
else if (dtype.getDatatypeClass() == Datatype.CLASS_INTEGER) {
assertTrue(H5TestFile.ATTRIBUTE_INT_ARRAY.getName().equals(attr.getName()));
final int[] expected = (int[]) H5TestFile.ATTRIBUTE_INT_ARRAY.getValue();
assertNotNull(expected);
final int[] ints = (int[]) attr.getValue();
assertNotNull(ints);
for (int j = 0; j < expected.length; j++) {
assertEquals(expected[j], ints[j]);
}
}
} // for (int i=0; i<n; i++) {
int nObjs = 0;
try {
nObjs = H5.H5Fget_obj_count(testFile.getFID(), HDF5Constants.H5F_OBJ_ALL);
}
catch (final Exception ex) {
fail("H5.H5Fget_obj_count() failed. " + ex);
}
assertEquals(1, nObjs); // file id should be the only one left open
}
/**
* Test method for {@link ncsa.hdf.object.h5.H5Datatype#writeMetadata(java.lang.Object)}.
* <p>
* What to test:
* <ul>
* <li>Update the value of an existing attribute
* <li>Attach a new attribute
* <li>Close and re-open file to check if the change is made in file
* <li>Restore to the orginal state
* </ul>
*/
@Test
public void testWriteMetadata() {
log.debug("testWriteMetadata");
Vector attrs = null;
Attribute attr = null;
try {
attrs = (Vector) testDatatype.getMetadata();
}
catch (final Exception ex) {
fail("getMetadata() failed. " + ex);
}
assertNotNull(attrs);
assertTrue(attrs.size() > 0);
// update existing attribute
int n = attrs.size();
for (int i = 0; i < n; i++) {
attr = (Attribute) attrs.get(i);
final H5Datatype dtype = (H5Datatype) attr.getType();
if (dtype.getDatatypeClass() == Datatype.CLASS_STRING) {
final String[] strs = (String[]) attr.getValue();
strs[0] = TEST_VALUE_STR;
}
else if (dtype.getDatatypeClass() == Datatype.CLASS_INTEGER) {
final int[] ints = (int[]) attr.getValue();
assertNotNull(ints);
for (int j = 0; j < ints.length; j++) {
ints[j] = TEST_VALUE_INT;
}
}
try {
testDatatype.writeMetadata(attr);
}
catch (final Exception ex) {
fail("writeMetadata() failed. " + ex);
}
} // for (int i=0; i<n; i++) {
// attache a new attribute
attr = new Attribute("float attribute", typeFloat, new long[] { 1 }, new float[] { TEST_VALUE_FLOAT });
try {
testDatatype.writeMetadata(attr);
}
catch (final Exception ex) {
fail("writeMetadata() failed. " + ex);
}
// close the file and reopen it
try {
testFile.close();
testFile.open();
testDatatype = (H5Datatype) testFile.get(TNAME);
}
catch (final Exception ex) {
fail("write() failed. " + ex);
}
// check the change in file
try {
attrs = (Vector) testDatatype.getMetadata();
}
catch (final Exception ex) {
fail("getMetadata() failed. " + ex);
}
assertNotNull(attrs);
assertTrue(attrs.size() > 0);
n = attrs.size();
Attribute newAttr = null;
for (int i = 0; i < n; i++) {
attr = (Attribute) attrs.get(i);
final H5Datatype dtype = (H5Datatype) attr.getType();
if (dtype.getDatatypeClass() == Datatype.CLASS_STRING) {
assertTrue(H5TestFile.ATTRIBUTE_STR.getName().equals(attr.getName()));
assertTrue(TEST_VALUE_STR.equals(((String[]) attr.getValue())[0]));
}
else if (dtype.getDatatypeClass() == Datatype.CLASS_INTEGER) {
assertTrue(H5TestFile.ATTRIBUTE_INT_ARRAY.getName().equals(attr.getName()));
final int[] ints = (int[]) attr.getValue();
assertNotNull(ints);
for (int j = 0; j < ints.length; j++) {
assertEquals(TEST_VALUE_INT, ints[j]);
}
}
else if (dtype.getDatatypeClass() == Datatype.CLASS_FLOAT) {
newAttr = attr;
final float[] floats = (float[]) attr.getValue();
assertEquals(TEST_VALUE_FLOAT, floats[0], Float.MIN_VALUE);
}
} // for (int i=0; i<n; i++) {
// remove the new attribute
try {
testDatatype.removeMetadata(newAttr);
}
catch (final Exception ex) {
fail("removeMetadata() failed. " + ex);
}
// set the value to original
n = attrs.size();
for (int i = 0; i < n; i++) {
attr = (Attribute) attrs.get(i);
final H5Datatype dtype = (H5Datatype) attr.getType();
if (dtype.getDatatypeClass() == Datatype.CLASS_STRING) {
final String[] strs = (String[]) attr.getValue();
strs[0] = ((String[]) H5TestFile.ATTRIBUTE_STR.getValue())[0];
}
else if (dtype.getDatatypeClass() == Datatype.CLASS_INTEGER) {
final int[] ints = (int[]) attr.getValue();
assertNotNull(ints);
for (int j = 0; j < ints.length; j++) {
final int[] expected = (int[]) H5TestFile.ATTRIBUTE_INT_ARRAY.getValue();
ints[j] = expected[j];
}
}
try {
testDatatype.writeMetadata(attr);
}
catch (final Exception ex) {
fail("writeMetadata() failed. " + ex);
}
} // for (int i=0; i<n; i++) {
int nObjs = 0;
try {
nObjs = H5.H5Fget_obj_count(testFile.getFID(), HDF5Constants.H5F_OBJ_ALL);
}
catch (final Exception ex) {
fail("H5.H5Fget_obj_count() failed. " + ex);
}
assertEquals(1, nObjs); // file id should be the only one left open
}
/**
* Test method for {@link ncsa.hdf.object.h5.H5Datatype#removeMetadata(java.lang.Object)}.
* <p>
* What to test:
* <ul>
* <li>Remove all existing attributes
* <li>Close and reopen file to check if all attribute are removed from file
* <li>Restore to the orginal state
* </ul>
*/
@Test
public void testRemoveMetadata() {
log.debug("testRemoveMetadata");
Vector attrs = null;
try {
attrs = (Vector) testDatatype.getMetadata();
}
catch (final Exception ex) {
fail("getMetadata() failed. " + ex);
}
assertNotNull(attrs);
assertTrue(attrs.size() > 0);
// remove all attributes
final int n = attrs.size();
final Object[] arrayAttr = attrs.toArray();
for (int i = 0; i < n; i++) {
try {
testDatatype.removeMetadata(arrayAttr[i]);
}
catch (final Exception ex) {
fail("removeMetadata() failed. " + ex);
}
}
// close the file and reopen it
try {
testFile.close();
testFile.open();
testDatatype = (H5Datatype) testFile.get(TNAME);
}
catch (final Exception ex) {
fail("write() failed. " + ex);
}
attrs = null;
try {
attrs = (Vector) testDatatype.getMetadata();
}
catch (final Exception ex) {
fail("getMetadata() failed. " + ex);
}
assertNotNull(attrs);
assertFalse(attrs.size() > 0);
// restor to the original
try {
testDatatype.writeMetadata(H5TestFile.ATTRIBUTE_STR);
testDatatype.writeMetadata(H5TestFile.ATTRIBUTE_INT_ARRAY);
}
catch (final Exception ex) {
fail("writeMetadata() failed. " + ex);
}
int nObjs = 0;
try {
nObjs = H5.H5Fget_obj_count(testFile.getFID(), HDF5Constants.H5F_OBJ_ALL);
}
catch (final Exception ex) {
fail("H5.H5Fget_obj_count() failed. " + ex);
}
assertEquals(1, nObjs); // file id should be the only one left open
}
/**
* Test method for {@link ncsa.hdf.object.h5.H5Datatype} IsSerializable.
*/
@Test
public void testIsSerializable() {
log.debug("testIsSerializable");
ByteArrayOutputStream out = new ByteArrayOutputStream();
ObjectOutputStream oos;
try {
oos = new ObjectOutputStream(out);
oos.writeObject(testDatatype);
oos.close();
}
catch (IOException err) {
err.printStackTrace();
fail("ObjectOutputStream failed: " + err);
}
assertTrue(out.toByteArray().length > 0);
}
/**
* Test method for {@link ncsa.hdf.object.h5.H5Datatype} SerializeToDisk.
* <p>
* What to test:
* <ul>
* <li>serialize a dataset identifier
* <li>deserialize a dataset identifier
* <li>Open a datatype identifier
* <li>Check the class and size of the datatype
* <li>Close the datatype
* </ul>
*/
@Test
public void testSerializeToDisk() {
log.debug("testSerializeToDisk");
try {
FileOutputStream fos = new FileOutputStream("temph5dtype.ser");
ObjectOutputStream oos = new ObjectOutputStream(fos);
oos.writeObject(testDatatype);
oos.close();
}
catch (Exception ex) {
fail("Exception thrown during test: " + ex.toString());
}
H5Datatype test = null;
try {
FileInputStream fis = new FileInputStream("temph5dtype.ser");
ObjectInputStream ois = new ObjectInputStream(fis);
test = (ncsa.hdf.object.h5.H5Datatype) ois.readObject();
ois.close();
// Clean up the file
new File("temph5dtype.ser").delete();
}
catch (Exception ex) {
fail("Exception thrown during test: " + ex.toString());
}
int tid = -1, tclass = -1, tsize = -1;
for (int loop = 0; loop < NLOOPS; loop++) {
tid = tclass = tsize = -1;
try {
tid = test.open();
}
catch (final Exception ex) {
fail("open() failed. " + ex);
}
assertTrue(tid > 0);
try {
tclass = H5.H5Tget_class(tid);
tsize = H5.H5Tget_size(tid);
}
catch (final Exception ex) {
fail("open() failed. " + ex);
}
assertEquals(4, tsize);
assertEquals(HDF5Constants.H5T_INTEGER, tclass);
try {
H5.H5Tclose(tid);
}
catch (final Exception ex) {
}
}
int nObjs = 0;
try {
nObjs = H5.H5Fget_obj_count(testFile.getFID(), HDF5Constants.H5F_OBJ_ALL);
}
catch (final Exception ex) {
fail("H5.H5Fget_obj_count() failed. " + ex);
}
assertEquals(1, nObjs); // file id should be the only one left open
}
}
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