@Test
public void testNoValid2DVariable() throws Exception {
final File file = TestData.file(this, "noVars.nc");
NetcdfDataset dataset = NetcdfDataset.acquireDataset(file.getAbsolutePath(), null);
List<Variable> variables = dataset.getVariables();
boolean speedVariableIsPresent = false;
String speedVariableName = "";
for (Variable variable : variables) {
if (variable.getShortName().equals("spd")) {
speedVariableIsPresent = true;
speedVariableName = variable.getFullName();
break;
}
}
assertTrue(speedVariableIsPresent);
final NetCDFImageReaderSpi unidataImageReaderSpi = new NetCDFImageReaderSpi();
assertTrue(unidataImageReaderSpi.canDecodeInput(file));
NetCDFImageReader reader = null;
try {
// sample dataset containing a water_speed variable having
// only time, depth dimensions. No lon/lat dims are present
// resulting into variable not usable.
reader = (NetCDFImageReader) unidataImageReaderSpi.createReaderInstance();
reader.setInput(file);
final List<Name> names = reader.getCoveragesNames();
boolean isSpeedCoverageAvailable = false;
for (Name name : names) {
if (name.toString().equals(speedVariableName)) {
isSpeedCoverageAvailable = true;
break;
}
}
// Checking that only "mask" variable is found
assertFalse(isSpeedCoverageAvailable);
} finally {
if (dataset != null) {
dataset.close();
}
if (reader != null) {
try {
reader.dispose();
} catch (Throwable t) {
// Does nothing
}
}
}
}
public void testReadRegularNetCDF() throws IOException {
NetCDFImageReaderSpi readerSpi = new NetCDFImageReaderSpi();
File file = null;
String name = "2DLatLonCoverageHDF5.nc";
try {
file = TestData.file(this, name);
} catch (IOException e) {
warnNoFile(name);
return;
}
assertTrue(readerSpi.canDecodeInput(file));
}
@Test
public void testImageReaderPolyphemusSimple() throws Exception {
final File file = TestData.file(this, "O3-NO2.nc");
final NetCDFImageReaderSpi unidataImageReaderSpi = new NetCDFImageReaderSpi();
assertTrue(unidataImageReaderSpi.canDecodeInput(file));
NetCDFImageReader reader = null;
try {
// checking low level
reader = (NetCDFImageReader) unidataImageReaderSpi.createReaderInstance();
reader.setInput(file);
int numImages = reader.getNumImages(true);
LOGGER.info("Found " + numImages + " images.");
for (int i = 0; i < numImages; i++) {
Slice2DIndex sliceIndex = reader.getSlice2DIndex(i);
assertNotNull(sliceIndex);
spitOutSliceInformation(i, sliceIndex);
}
// checking slice catalog
final CoverageSlicesCatalog cs = reader.getCatalog();
assertNotNull(cs);
// get typenames
final String[] typeNames = cs.getTypeNames();
for (String typeName : typeNames) {
final List<CoverageSlice> granules = cs.getGranules(new Query(typeName, Filter.INCLUDE));
assertNotNull(granules);
assertFalse(granules.isEmpty());
for (CoverageSlice slice : granules) {
final SimpleFeature sf = slice.getOriginator();
if (TestData.isInteractiveTest()) {
LOGGER.info(DataUtilities.encodeFeature(sf));
}
// checks
for (Property p : sf.getProperties()) {
assertNotNull("Property " + p.getName() + " had a null value!", p.getValue());
}
}
}
} finally {
if (reader != null) {
try {
reader.dispose();
} catch (Throwable t) {
// Does nothing
}
}
}
}
@Test
public void testImageReaderIASI() throws Exception {
File file = null;
try {
file = TestData.file(this, "IASI_C_EUMP_20121120062959_31590_eps_o_l2.nc");
} catch (IOException e) {
LOGGER.warning("Unable to find file IASI_C_EUMP_20121120062959_31590_eps_o_l2.nc");
return;
}
if (!file.exists()) {
LOGGER.warning("Unable to find file IASI_C_EUMP_20121120062959_31590_eps_o_l2.nc");
return;
}
final NetCDFImageReaderSpi unidataImageReaderSpi = new NetCDFImageReaderSpi();
assertTrue(unidataImageReaderSpi.canDecodeInput(file));
NetCDFImageReader reader = null;
try {
reader = (NetCDFImageReader) unidataImageReaderSpi.createReaderInstance();
reader.setInput(file);
int numImages = reader.getNumImages(true);
for (int i = 0; i < numImages; i++) {
Slice2DIndex sliceIndex = reader.getSlice2DIndex(i);
assertNotNull(sliceIndex);
spitOutSliceInformation(i, sliceIndex);
}
// cloud_phase
CoverageSourceDescriptor cd = reader.getCoverageDescriptor(new NameImpl("cloud_phase"));
final List<AdditionalDomain> additionalDomains = cd.getAdditionalDomains();
assertTrue(!additionalDomains.isEmpty());
final AdditionalDomain ad = additionalDomains.get(0);
assertTrue(ad.getType().equals(DomainType.NUMBER));
assertEquals("cloud_phase", ad.getName());
} finally {
if (reader != null) {
try {
reader.dispose();
} catch (Throwable t) {
// Does nothing
}
}
}
}
@Test
public void testReadNC4() throws IOException {
NetCDFImageReaderSpi readerSpi = new NetCDFImageReaderSpi();
boolean isNC4available = NetCDFUtilities.isNC4CAvailable();
if (!isNC4available) {
LOGGER.warning(
"NetCDF4 reading test will be skipped due to "
+ "missing NetCDF C library.\nIf you want test to be executed, make sure you have "
+ "added the NetCDF C libraries location to the PATH environment variable");
return;
}
String name = "temperatureisobaricNC4.nc";
File file = null;
try {
file = TestData.file(this, name);
} catch (IOException e) {
warnNoFile(name);
return;
}
assertTrue(readerSpi.canDecodeInput(file));
}
@Test
public void testImageReaderPolyphemunsComplex() throws Exception {
File file = null;
try {
file = TestData.file(this, "polyphemus_20130301.nc");
} catch (IOException e) {
LOGGER.warning("Unable to find file polyphemus_20130301.nc");
return;
}
if (!file.exists()) {
LOGGER.warning("Unable to find file polyphemus_20130301.nc");
return;
}
final NetCDFImageReaderSpi unidataImageReaderSpi = new NetCDFImageReaderSpi();
assertTrue(unidataImageReaderSpi.canDecodeInput(file));
NetCDFImageReader reader = null;
try {
reader = (NetCDFImageReader) unidataImageReaderSpi.createReaderInstance();
reader.setInput(file);
int numImages = reader.getNumImages(true);
assertEquals(1008, numImages);
for (int i = 0; i < numImages; i++) {
Slice2DIndex sliceIndex = reader.getSlice2DIndex(i);
assertNotNull(sliceIndex);
spitOutSliceInformation(i, sliceIndex);
}
// check coverage names
final List<Name> names = reader.getCoveragesNames();
assertNotNull(names);
assertTrue(!names.isEmpty());
assertTrue(3 == names.size());
assertTrue(names.contains(new NameImpl("NO2")));
assertTrue(names.contains(new NameImpl("O3")));
assertTrue(names.contains(new NameImpl("V")));
// checking slice catalog
final CoverageSlicesCatalog cs = reader.getCatalog();
assertNotNull(cs);
// get typenames
final String[] typeNames = cs.getTypeNames();
for (String typeName : typeNames) {
final List<CoverageSlice> granules = cs.getGranules(new Query(typeName, Filter.INCLUDE));
assertNotNull(granules);
assertFalse(granules.isEmpty());
for (CoverageSlice slice : granules) {
final SimpleFeature sf = slice.getOriginator();
if (TestData.isInteractiveTest()) {
LOGGER.info(DataUtilities.encodeFeature(sf));
}
// checks
for (Property p : sf.getProperties()) {
assertNotNull("Property " + p.getName() + " had a null value!", p.getValue());
}
}
}
} finally {
if (reader != null) {
try {
reader.dispose();
} catch (Throwable t) {
// Does nothing
}
}
}
}
@Test
public void testImageReaderPolyphemunsComplex2() throws Exception {
File file = null;
try {
file = TestData.file(this, "polyphemus_20130301.nc");
} catch (IOException e) {
LOGGER.warning("Unable to find file polyphemus_20130301.nc");
return;
}
if (!file.exists()) {
LOGGER.warning("Unable to find file polyphemus_20130301.nc");
return;
}
FileUtils.copyFile(file, new File(TestData.file(this, null), "polyphemus.nc"));
file = TestData.file(this, "polyphemus.nc");
final NetCDFImageReaderSpi unidataImageReaderSpi = new NetCDFImageReaderSpi();
assertTrue(unidataImageReaderSpi.canDecodeInput(file));
NetCDFImageReader reader = null;
try {
reader = (NetCDFImageReader) unidataImageReaderSpi.createReaderInstance();
reader.setInput(file);
int numImages = reader.getNumImages(true);
assertEquals(1008, numImages);
for (int i = 0; i < numImages; i++) {
Slice2DIndex sliceIndex = reader.getSlice2DIndex(i);
assertNotNull(sliceIndex);
spitOutSliceInformation(i, sliceIndex);
}
// check dimensions
CoverageSourceDescriptor cd = reader.getCoverageDescriptor(new NameImpl("NO2"));
final List<AdditionalDomain> additionalDomains = cd.getAdditionalDomains();
assertNull(additionalDomains);
final List<DimensionDescriptor> dimensions = cd.getDimensionDescriptors();
assertNotNull(dimensions);
assertTrue(!dimensions.isEmpty());
assertEquals("wrong dimensions", 2, dimensions.size());
DimensionDescriptor dim = dimensions.get(0);
assertTrue(dim.getName().equals("TIME"));
assertTrue(dim.getStartAttribute().equals("time"));
dim = dimensions.get(1);
assertTrue(dim.getName().equals("ELEVATION"));
assertTrue(dim.getStartAttribute().equals("z"));
// check coverage names
final List<Name> names = reader.getCoveragesNames();
assertNotNull(names);
assertTrue(!names.isEmpty());
assertTrue(3 == names.size());
assertTrue(names.contains(new NameImpl("NO2")));
assertTrue(names.contains(new NameImpl("O3")));
assertTrue(names.contains(new NameImpl("V")));
// checking slice catalog
final CoverageSlicesCatalog cs = reader.getCatalog();
assertNotNull(cs);
// get typenames
final String[] typeNames = cs.getTypeNames();
for (String typeName : typeNames) {
final List<CoverageSlice> granules = cs.getGranules(new Query(typeName, Filter.INCLUDE));
assertNotNull(granules);
assertFalse(granules.isEmpty());
for (CoverageSlice slice : granules) {
final SimpleFeature sf = slice.getOriginator();
if (TestData.isInteractiveTest()) {
LOGGER.info(DataUtilities.encodeFeature(sf));
}
// checks
for (Property p : sf.getProperties()) {
assertNotNull("Property " + p.getName() + " had a null value!", p.getValue());
}
}
}
} finally {
// close reader
if (reader != null) {
try {
reader.dispose();
} catch (Throwable t) {
// Does nothing
}
}
// specific clean up
FileUtils.deleteDirectory(TestData.file(this, ".polyphemus"));
}
}
@Test
public void testImageReaderAscat() throws Exception {
File file = null;
try {
file = TestData.file(this, "ascatl1.nc");
} catch (IOException e) {
LOGGER.warning("Unable to find file ascatl1.nc");
return;
}
if (!file.exists()) {
LOGGER.warning("Unable to find file ascatl1.nc");
return;
}
final NetCDFImageReaderSpi unidataImageReaderSpi = new NetCDFImageReaderSpi();
assertTrue(unidataImageReaderSpi.canDecodeInput(file));
NetCDFImageReader reader = null;
try {
reader = (NetCDFImageReader) unidataImageReaderSpi.createReaderInstance();
reader.setInput(file);
int numImages = reader.getNumImages(true);
for (int i = 0; i < numImages; i++) {
Slice2DIndex sliceIndex = reader.getSlice2DIndex(i);
assertNotNull(sliceIndex);
spitOutSliceInformation(i, sliceIndex);
}
// check coverage names
final List<Name> names = reader.getCoveragesNames();
assertNotNull(names);
assertTrue(!names.isEmpty());
assertTrue(2 == names.size());
assertEquals("cell_index", names.get(0).toString());
assertEquals("f_land", names.get(1).toString());
// checking slice catalog
final CoverageSlicesCatalog cs = reader.getCatalog();
assertNotNull(cs);
// get typenames
final String[] typeNames = cs.getTypeNames();
for (String typeName : typeNames) {
final List<CoverageSlice> granules = cs.getGranules(new Query(typeName, Filter.INCLUDE));
assertNotNull(granules);
assertFalse(granules.isEmpty());
for (CoverageSlice slice : granules) {
final SimpleFeature sf = slice.getOriginator();
if (TestData.isInteractiveTest()) {
LOGGER.info(DataUtilities.encodeFeature(sf));
}
// checks
for (Property p : sf.getProperties()) {
final String pName = p.getName().toString();
if (!pName.equalsIgnoreCase("time") && !pName.equalsIgnoreCase("elevation")) {
assertNotNull("Property " + p.getName() + " had a null value!", p.getValue());
} else {
assertNull("Property " + p.getName() + " did not have a null value!", p.getValue());
}
}
}
}
} finally {
if (reader != null) {
try {
reader.dispose();
} catch (Throwable t) {
// Does nothing
}
}
}
}
@Test
public void testImageReaderGOME2AncillaryFiles() throws Exception {
final File file = TestData.file(this, "20130101.METOPA.GOME2.NO2.DUMMY.nc");
final NetCDFImageReaderSpi unidataImageReaderSpi = new NetCDFImageReaderSpi();
assertTrue(unidataImageReaderSpi.canDecodeInput(file));
NetCDFImageReader reader = null;
try {
// checking low level
reader = (NetCDFImageReader) unidataImageReaderSpi.createReaderInstance();
reader.setInput(file);
int numImages = reader.getNumImages(true);
assertEquals(1, numImages);
LOGGER.info("Found " + numImages + " images.");
for (int i = 0; i < numImages; i++) {
Slice2DIndex sliceIndex = reader.getSlice2DIndex(i);
assertNotNull(sliceIndex);
spitOutSliceInformation(i, sliceIndex);
}
// check coverage names
final List<Name> names = reader.getCoveragesNames();
assertNotNull(names);
assertTrue(!names.isEmpty());
assertTrue(1 == names.size());
assertEquals("NO2", names.get(0).toString());
// checking slice catalog
final CoverageSlicesCatalog cs = reader.getCatalog();
assertNotNull(cs);
MessageDigest md = MessageDigest.getInstance("SHA-1");
md.update(file.getCanonicalPath().getBytes());
String hashCode = AncillaryFileManager.convertToHex(md.digest());
// Check if the auxiliary files directory is present
File parentDir = file.getParentFile();
String auxiliaryDirPath =
parentDir
+ File.separator
+ "."
+ FilenameUtils.getBaseName(file.getName())
+ "_"
+ hashCode;
File auxiliaryDir = new File(auxiliaryDirPath);
assertTrue(auxiliaryDir.exists());
assertTrue(auxiliaryDir.isDirectory());
// Check if the Auxiliary File Directory contains the origin.txt file
FilenameFilter nameFileFilter = FileFilterUtils.nameFileFilter("origin.txt");
File[] files = auxiliaryDir.listFiles(nameFileFilter);
assertTrue(files != null);
assertTrue(files[0].exists());
} finally {
if (reader != null) {
try {
reader.dispose();
} catch (Throwable t) {
// Does nothing
}
}
}
}