@Test
public void NetCDFProjectedEnvelopeTest()
throws NoSuchAuthorityCodeException, FactoryException, IOException, ParseException {
File mosaic = new File(TestData.file(this, "."), "NetCDFProjection");
if (mosaic.exists()) {
FileUtils.deleteDirectory(mosaic);
}
assertTrue(mosaic.mkdirs());
File file = TestData.file(this, "wind.nc");
FileUtils.copyFileToDirectory(file, mosaic);
file = new File(mosaic, "wind.nc");
// Get format
final NetCDFReader reader = new NetCDFReader(file, null);
try {
String[] names = reader.getGridCoverageNames();
String coverageName = names[0];
// subsetting the envelope
final ParameterValue<GridGeometry2D> gg =
AbstractGridFormat.READ_GRIDGEOMETRY2D.createValue();
final GeneralEnvelope originalEnvelope = reader.getOriginalEnvelope(coverageName);
final CoordinateReferenceSystem epsg3857 = CRS.decode("EPSG:3857", true);
final GeneralEnvelope projectedEnvelope = CRS.transform(originalEnvelope, epsg3857);
gg.setValue(
new GridGeometry2D(new GridEnvelope2D(new Rectangle(0, 0, 30, 30)), projectedEnvelope));
GeneralParameterValue[] values = new GeneralParameterValue[] {gg};
GridCoverage2D coverage = reader.read(coverageName, values);
// reader doesn't perform reprojection. It simply transforms reprojected envelope
// to native envelope so BBOX and CRS should be wgs84
CoordinateReferenceSystem coverageCRS = coverage.getCoordinateReferenceSystem();
final int code = CRS.lookupEpsgCode(coverageCRS, false);
assertEquals(4326, code);
Extent extent = coverageCRS.getDomainOfValidity();
Collection<? extends GeographicExtent> geoElements = extent.getGeographicElements();
GeographicExtent geographicExtent = geoElements.iterator().next();
GeographicBoundingBoxImpl impl = (GeographicBoundingBoxImpl) geographicExtent;
// Getting the coverage Envelope for coordinates check
Envelope coverageEnvelope = coverage.getEnvelope();
assertTrue(impl.getEastBoundLongitude() >= coverageEnvelope.getMaximum(0));
assertTrue(impl.getWestBoundLongitude() <= coverageEnvelope.getMinimum(0));
assertTrue(impl.getNorthBoundLatitude() >= coverageEnvelope.getMaximum(1));
assertTrue(impl.getSouthBoundLatitude() <= coverageEnvelope.getMinimum(1));
} catch (Throwable t) {
throw new RuntimeException(t);
} finally {
if (reader != null) {
try {
reader.dispose();
} catch (Throwable t) {
// Does nothing
}
}
}
}
@Test
public void NetCDFNoDataOperation()
throws NoSuchAuthorityCodeException, FactoryException, IOException, ParseException {
File mosaic = new File(TestData.file(this, "."), "NetCDFGOME2");
if (mosaic.exists()) {
FileUtils.deleteDirectory(mosaic);
}
assertTrue(mosaic.mkdirs());
File file = TestData.file(this, "DUMMY.GOME2.NO2.PGL.nc");
FileUtils.copyFileToDirectory(file, mosaic);
file = new File(mosaic, "DUMMY.GOME2.NO2.PGL.nc");
final Hints hints =
new Hints(Hints.DEFAULT_COORDINATE_REFERENCE_SYSTEM, CRS.decode("EPSG:4326", true));
// Get format
final AbstractGridFormat format =
(AbstractGridFormat) GridFormatFinder.findFormat(file.toURI().toURL(), hints);
final NetCDFReader reader = (NetCDFReader) format.getReader(file.toURI().toURL(), hints);
assertNotNull(format);
GridCoverage2D gc = null;
try {
String[] names = reader.getGridCoverageNames();
names = new String[] {names[0]};
gc = reader.read(null);
} catch (Throwable t) {
throw new RuntimeException(t);
} finally {
if (reader != null) {
try {
reader.dispose();
} catch (Throwable t) {
// Does nothing
}
}
}
// Checking NoData
Object noData = CoverageUtilities.getNoDataProperty(gc);
assertNotNull(noData);
assertTrue(noData instanceof NoDataContainer);
Double d = ((NoDataContainer) noData).getAsSingleValue();
assertEquals(d, -999d, DELTA);
// Try to execute an operation on the NoData and check if the result contains also NoData
CoverageProcessor instance = CoverageProcessor.getInstance();
Operation scale = instance.getOperation("Scale");
ParameterValueGroup params = scale.getParameters();
params.parameter("Source0").setValue(gc);
params.parameter("backgroundValues").setValue(new double[] {0});
GridCoverage2D result = (GridCoverage2D) instance.doOperation(params);
noData = CoverageUtilities.getNoDataProperty(result);
assertNotNull(noData);
assertTrue(noData instanceof NoDataContainer);
d = ((NoDataContainer) noData).getAsSingleValue();
assertEquals(d, 0d, DELTA);
}
@Test
public void testNetCDFWithDifferentTimeDimensions() throws MalformedURLException, IOException {
// Selection of the input file
final File workDir = new File(TestData.file(this, "."), "times");
if (!workDir.mkdir()) {
FileUtils.deleteDirectory(workDir);
assertTrue("Unable to create workdir:" + workDir, workDir.mkdir());
}
FileUtils.copyFile(TestData.file(this, "times.zip"), new File(workDir, "times.zip"));
TestData.unzipFile(this, "times/times.zip");
final File inputFile = TestData.file(this, "times/times.nc");
// Get format
final AbstractGridFormat format =
(AbstractGridFormat) GridFormatFinder.findFormat(inputFile.toURI().toURL(), null);
final NetCDFReader reader = new NetCDFReader(inputFile, null);
Assert.assertNotNull(format);
Assert.assertNotNull(reader);
try {
// Selection of all the Coverage names
String[] names = reader.getGridCoverageNames();
assertNotNull(names);
assertEquals(2, names.length);
// Parsing metadata values
assertEquals("true", reader.getMetadataValue(names[0], "HAS_TIME_DOMAIN"));
List<DimensionDescriptor> descriptors = reader.getDimensionDescriptors(names[0]);
assertEquals(1, descriptors.size());
DimensionDescriptor descriptor = descriptors.get(0);
assertEquals("time", descriptor.getStartAttribute());
assertEquals("TIME", descriptor.getName());
descriptors = reader.getDimensionDescriptors(names[1]);
assertEquals(1, descriptors.size());
descriptor = descriptors.get(0);
assertEquals("time1", descriptor.getStartAttribute());
assertEquals("TIME", descriptor.getName());
assertEquals("true", reader.getMetadataValue(names[1], "HAS_TIME_DOMAIN"));
} finally {
if (reader != null) {
try {
reader.dispose();
} catch (Throwable t) {
// Does nothing
}
}
FileUtils.deleteDirectory(TestData.file(this, "times"));
}
}
@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 NetCDFGOME2()
throws NoSuchAuthorityCodeException, FactoryException, IOException, ParseException {
File mosaic = new File(TestData.file(this, "."), "NetCDFGOME2");
if (mosaic.exists()) {
FileUtils.deleteDirectory(mosaic);
}
assertTrue(mosaic.mkdirs());
File file = TestData.file(this, "DUMMY.GOME2.NO2.PGL.nc");
FileUtils.copyFileToDirectory(file, mosaic);
file = new File(mosaic, "DUMMY.GOME2.NO2.PGL.nc");
final Hints hints =
new Hints(Hints.DEFAULT_COORDINATE_REFERENCE_SYSTEM, CRS.decode("EPSG:4326", true));
// Get format
final AbstractGridFormat format =
(AbstractGridFormat) GridFormatFinder.findFormat(file.toURI().toURL(), hints);
final NetCDFReader reader = (NetCDFReader) format.getReader(file.toURI().toURL(), hints);
assertNotNull(format);
try {
String[] names = reader.getGridCoverageNames();
names = new String[] {names[0]};
for (String coverageName : names) {
final String[] metadataNames = reader.getMetadataNames(coverageName);
assertNotNull(metadataNames);
assertEquals(metadataNames.length, 12);
// Parsing metadata values
assertEquals("false", reader.getMetadataValue(coverageName, "HAS_TIME_DOMAIN"));
final String timeMetadata = reader.getMetadataValue(coverageName, "TIME_DOMAIN");
assertNull(timeMetadata);
assertEquals("false", reader.getMetadataValue(coverageName, "HAS_ELEVATION_DOMAIN"));
final String elevationMetadata = reader.getMetadataValue(coverageName, "ELEVATION_DOMAIN");
assertNull(elevationMetadata);
}
} catch (Throwable t) {
throw new RuntimeException(t);
} finally {
if (reader != null) {
try {
reader.dispose();
} catch (Throwable t) {
// Does nothing
}
}
}
}
@Before
public void cleanup() throws IOException {
// clean up
testMosaic = new File(TestData.file(this, "."), "footprintMosaic");
if (testMosaic.exists()) {
FileUtils.deleteDirectory(testMosaic);
}
// create the base mosaic we are going to use
File mosaicSource = TestData.file(this, "rgb");
FileUtils.copyDirectory(mosaicSource, testMosaic);
testMosaicUrl = DataUtilities.fileToURL(testMosaic);
// footprint source
footprintsSource = TestData.file(this, "rgb-footprints");
}
/**
* Test using this netcdf image: data: LAI= 20,20,20,30,30, 40,40,40,50,50, 60,60,60,70,70,
* 80,80,80,90,90; lon= 10,15,20,25,30; lat= 70,60,50,40;
*
* @throws IOException
*/
@Test
public void testHDF5Image() throws IOException, FactoryException {
final File testURL = TestData.file(this, "2DLatLonCoverage.nc");
// Get format
// final AbstractGridFormat format = (AbstractGridFormat)
GridFormatFinder.findFormat(testURL.toURI().toURL(), null);
final NetCDFReader reader = new NetCDFReader(testURL, null);
// assertNotNull(format);
assertNotNull(reader);
try {
String[] names = reader.getGridCoverageNames();
assertNotNull(names);
assertEquals(2, names.length);
assertEquals("ROOT/LEVEL1/V2", names[1]);
GridCoverage2D grid = reader.read("ROOT/LAI", null);
assertNotNull(grid);
byte[] byteValue =
grid.evaluate(new DirectPosition2D(DefaultGeographicCRS.WGS84, 12, 70), new byte[1]);
assertEquals(20, byteValue[0]);
byteValue =
grid.evaluate(new DirectPosition2D(DefaultGeographicCRS.WGS84, 23, 40), new byte[1]);
assertEquals(90, byteValue[0]);
} finally {
if (reader != null) {
try {
reader.dispose();
} catch (Throwable t) {
// Does nothing
}
}
}
}
@Override
protected void tearDownInternal() throws Exception {
// clean up disk
if (!ImageMosaicReaderTest.INTERACTIVE) {
FileUtils.deleteDirectory(TestData.file(this, "watertemp4"));
}
// delete tables
Class.forName("org.postgresql.Driver");
Connection connection =
DriverManager.getConnection(
"jdbc:postgresql://"
+ fixture.getProperty("host")
+ ":"
+ fixture.getProperty("port")
+ "/"
+ fixture.getProperty("database"),
fixture.getProperty("user"),
fixture.getProperty("passwd"));
Statement st = connection.createStatement();
st.execute("DROP TABLE IF EXISTS watertemp4");
st.close();
connection.close();
System.clearProperty("org.geotools.referencing.forceXY");
super.tearDownInternal();
}
@After
public void tearDown() throws FileNotFoundException, IOException {
if (TestData.isInteractiveTest()) {
return;
}
cleanUp();
}
@Test
@Ignore
public void filtered() throws Exception {
// JAI.getDefaultInstance().getTileCache().setMemoryCapacity(512*1024*1024);
// JAI.getDefaultInstance().getTileScheduler().setParallelism(10);
// JAI.getDefaultInstance().getTileScheduler().setPrefetchParallelism(10);
final OverviewsEmbedder oe = new OverviewsEmbedder();
oe.setDownsampleStep(2);
oe.setNumSteps(5);
oe.setScaleAlgorithm(OverviewsEmbedder.SubsampleAlgorithm.Filtered.toString());
// use default
oe.setTileCache(JAI.getDefaultInstance().getTileCache());
oe.setTileWidth(256);
oe.setTileHeight(256);
oe.setSourcePath(TestData.file(this, "DEM_.tiff").getAbsolutePath());
final List<Throwable> exceptions = new ArrayList<Throwable>();
oe.addProcessingEventListener(
new ProcessingEventListener() {
@Override
public void getNotification(ProcessingEvent event) {
LOGGER.info(event.toString());
}
@Override
public void exceptionOccurred(ExceptionEvent event) {
LOGGER.warning(event.toString());
exceptions.add(event.getException());
event.getException().printStackTrace();
}
});
oe.run();
// fail if any exception was reported
if (exceptions.size() > 0) {
exceptions.get(0).printStackTrace();
fail("Failed with " + exceptions.size() + " exceptions during overview embedding: ");
}
// now red it back and check that things are coherent
final ImageReader reader = new TIFFImageReaderSpi().createReaderInstance();
reader.setInput(
ImageIO.createImageInputStream(org.geotools.test.TestData.file(this, "DEM_.tiff")));
assertEquals(6, reader.getNumImages(true));
reader.dispose();
}
/*
* https://osgeo-org.atlassian.net/browse/GEOT-5287
*/
@Test
public void testEmptyGeometryRendering() throws Exception {
MapContent mc = new MapContent();
/*
* We simulate reading empty geometries with this properties and mocking the capability to
* filter, so that no filter layer is installed over our data and the empty geometry reaches
* rendering code. These geometries are in EPSG:32717 because the 0,0 coordinate is in the
* pole.
*/
File dir = new File(TestData.getResource(this, "empty-geom-rendering.properties").toURI());
PropertyDataStore dataStore =
new PropertyDataStore(dir.getParentFile()) {
@Override
protected ContentFeatureSource createFeatureSource(ContentEntry entry)
throws IOException {
return new PropertyFeatureSource(entry, Query.ALL) {
@Override
protected boolean canFilter() {
return true;
}
};
}
};
/*
* Set up the rendering of previous empty geometry
*/
StyleBuilder sb = new StyleBuilder();
Style style = sb.createStyle(sb.createPolygonSymbolizer());
Layer layer = new FeatureLayer(dataStore.getFeatureSource("empty-geom-rendering"), style);
mc.addLayer(layer);
StreamingRenderer sr = new StreamingRenderer();
sr.setMapContent(mc);
BufferedImage img = new BufferedImage(40, 40, BufferedImage.TYPE_INT_ARGB);
Graphics2D graphics = img.createGraphics();
Rectangle paintArea = new Rectangle(40, 40);
// An EPSG:8357 extent on the EPSG:32717 area of application.
double minx = -8929252.1;
double maxx = -8708634.6;
double miny = -491855.7;
double maxy = -271204.3;
ReferencedEnvelope referencedEnvelope =
new ReferencedEnvelope(
new Rectangle2D.Double(minx, miny, maxx - minx, maxy - miny), CRS.decode("EPSG:3857"));
sr.addRenderListener(
new RenderListener() {
public void featureRenderer(SimpleFeature feature) {}
public void errorOccurred(Exception e) {
errors++;
}
});
errors = 0;
sr.paint(graphics, paintArea, referencedEnvelope);
assertTrue(errors == 0);
}
@Test
// @Ignore
public void nearestExternal() throws Exception {
final OverviewsEmbedder oe = new OverviewsEmbedder();
oe.setDownsampleStep(2);
oe.setNumSteps(5);
oe.setScaleAlgorithm(OverviewsEmbedder.SubsampleAlgorithm.Nearest.toString());
// use default
oe.setTileCache(JAI.getDefaultInstance().getTileCache());
oe.setTileWidth(256);
oe.setTileHeight(256);
oe.setExternalOverviews(true);
oe.setSourcePath(TestData.file(this, "DEM_.tiff").getAbsolutePath());
oe.addProcessingEventListener(
new ProcessingEventListener() {
@Override
public void getNotification(ProcessingEvent event) {
LOGGER.info(event.toString());
}
@Override
public void exceptionOccurred(ExceptionEvent event) {
LOGGER.warning(event.toString());
}
});
oe.run();
// now red it back and check that things are coherent
final ImageReader reader = new TIFFImageReaderSpi().createReaderInstance();
reader.setInput(
ImageIO.createImageInputStream(org.geotools.test.TestData.file(this, "DEM_.tiff")));
assertTrue(reader.getNumImages(true) == 1);
reader.reset();
assertTrue(org.geotools.test.TestData.file(this, "DEM_.tif.ovr").exists());
reader.setInput(
ImageIO.createImageInputStream(org.geotools.test.TestData.file(this, "DEM_.tif.ovr")));
assertTrue(reader.getNumImages(true) == 5);
assertTrue(reader.isImageTiled(0));
assertEquals(256, reader.getTileHeight(0));
assertEquals(256, reader.getTileWidth(0));
reader.dispose();
}
private Style loadStyle(String sldFilename) throws IOException {
StyleFactory factory = StyleFactoryFinder.createStyleFactory();
java.net.URL surl = TestData.getResource(this, sldFilename);
SLDParser stylereader = new SLDParser(factory, surl);
Style style = stylereader.readXML()[0];
return style;
}
@Test
public void NetCDFNoData()
throws NoSuchAuthorityCodeException, FactoryException, IOException, ParseException {
File mosaic = new File(TestData.file(this, "."), "NetCDFGOME2");
if (mosaic.exists()) {
FileUtils.deleteDirectory(mosaic);
}
assertTrue(mosaic.mkdirs());
File file = TestData.file(this, "DUMMY.GOME2.NO2.PGL.nc");
FileUtils.copyFileToDirectory(file, mosaic);
file = new File(mosaic, "DUMMY.GOME2.NO2.PGL.nc");
final Hints hints =
new Hints(Hints.DEFAULT_COORDINATE_REFERENCE_SYSTEM, CRS.decode("EPSG:4326", true));
// Get format
final AbstractGridFormat format =
(AbstractGridFormat) GridFormatFinder.findFormat(file.toURI().toURL(), hints);
final NetCDFReader reader = (NetCDFReader) format.getReader(file.toURI().toURL(), hints);
assertNotNull(format);
try {
String[] names = reader.getGridCoverageNames();
names = new String[] {names[0]};
GridCoverage2D gc = reader.read(null);
Object noData = CoverageUtilities.getNoDataProperty(gc);
assertNotNull(noData);
assertTrue(noData instanceof NoDataContainer);
Double d = ((NoDataContainer) noData).getAsSingleValue();
assertEquals(d, -999d, DELTA);
} catch (Throwable t) {
throw new RuntimeException(t);
} finally {
if (reader != null) {
try {
reader.dispose();
} catch (Throwable t) {
// Does nothing
}
}
}
}
@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 nearest() throws Exception {
final OverviewsEmbedder oe = new OverviewsEmbedder();
oe.setDownsampleStep(2);
oe.setNumSteps(5);
oe.setScaleAlgorithm(OverviewsEmbedder.SubsampleAlgorithm.Nearest.toString());
// use default
oe.setTileCache(JAI.getDefaultInstance().getTileCache());
oe.setTileWidth(256);
oe.setTileHeight(256);
oe.setSourcePath(TestData.file(this, "DEM_.tiff").getAbsolutePath());
oe.addProcessingEventListener(
new ProcessingEventListener() {
private double lastProgress = -1;
@Override
public void getNotification(ProcessingEvent event) {
assertTrue(lastProgress <= event.getPercentage());
lastProgress = event.getPercentage();
assertTrue(lastProgress <= 100);
assertTrue(lastProgress >= 0);
LOGGER.info(event.toString());
}
@Override
public void exceptionOccurred(ExceptionEvent event) {
LOGGER.warning(event.toString());
}
});
oe.run();
// now red it back and check that things are coherent
final ImageReader reader = new TIFFImageReaderSpi().createReaderInstance();
reader.setInput(
ImageIO.createImageInputStream(org.geotools.test.TestData.file(this, "DEM_.tiff")));
assertTrue(reader.getNumImages(true) == 6);
reader.dispose();
}
@Test
// @Ignore
public void bilinear() throws Exception {
// JAI.getDefaultInstance().getTileCache().setMemoryCapacity(512*1024*1024);
// JAI.getDefaultInstance().getTileScheduler().setParallelism(10);
// JAI.getDefaultInstance().getTileScheduler().setPrefetchParallelism(10);
final OverviewsEmbedder oe = new OverviewsEmbedder();
oe.setDownsampleStep(2);
oe.setNumSteps(5);
oe.setScaleAlgorithm(OverviewsEmbedder.SubsampleAlgorithm.Bilinear.toString());
// use default
oe.setTileCache(JAI.getDefaultInstance().getTileCache());
oe.setTileWidth(256);
oe.setTileHeight(256);
oe.setSourcePath(TestData.file(this, "DEM_.tiff").getAbsolutePath());
oe.addProcessingEventListener(
new ProcessingEventListener() {
@Override
public void getNotification(ProcessingEvent event) {
LOGGER.info(event.toString());
}
@Override
public void exceptionOccurred(ExceptionEvent event) {
LOGGER.warning(event.toString());
}
});
oe.run();
// now red it back and check that things are coherent
final ImageReader reader = new TIFFImageReaderSpi().createReaderInstance();
reader.setInput(
ImageIO.createImageInputStream(org.geotools.test.TestData.file(this, "DEM_.tiff")));
assertTrue(reader.getNumImages(true) == 6);
reader.dispose();
}
/**
* @param i
* @param sliceIndex
*/
private void spitOutSliceInformation(int i, Slice2DIndex sliceIndex) {
if (TestData.isInteractiveTest()) {
String variableName = sliceIndex.getVariableName();
StringBuilder sb = new StringBuilder();
sb.append("\n").append("\n").append("\n");
sb.append("IMAGE: ").append(i).append("\n");
sb.append(" Variable Name = ").append(variableName);
sb.append(" ( Z = ");
sb.append(sliceIndex.getZIndex());
sb.append("; T = ");
sb.append(sliceIndex.getTIndex());
sb.append(")");
LOGGER.info(sb.toString());
}
}
/**
* Cleaning up the generated files (shape and properties so that we recreate them).
*
* @throws FileNotFoundException
* @throws IOException
*/
private void cleanUp() throws FileNotFoundException, IOException {
File dir = TestData.file(this, "heterogeneous/");
File[] files =
dir.listFiles(
(FilenameFilter)
FileFilterUtils.notFileFilter(
FileFilterUtils.or(
FileFilterUtils.or(
FileFilterUtils.suffixFileFilter("tif"),
FileFilterUtils.suffixFileFilter("aux")),
FileFilterUtils.nameFileFilter("datastore.properties"))));
for (File file : files) {
file.delete();
}
}
@Override
protected void setUp() throws Exception {
// setup data
File property = new File(TestData.getResource(this, "diaglines.properties").toURI());
PropertyDataStore ds = new PropertyDataStore(property.getParentFile());
fs = ds.getFeatureSource("diaglines");
bounds = new ReferencedEnvelope(0, 10, 0, 10, DefaultGeographicCRS.WGS84);
renderer = new StreamingRenderer();
Map rendererParams = new HashMap();
LabelCacheImpl labelCache = new LabelCacheImpl();
rendererParams.put(StreamingRenderer.LABEL_CACHE_KEY, labelCache);
renderer.setRendererHints(rendererParams);
renderer.setJava2DHints(new RenderingHints(KEY_ANTIALIASING, VALUE_ANTIALIAS_ON));
// System.setProperty("org.geotools.test.interactive", "true");
}
@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
}
}
}
}
public void testRandomProcess() throws Exception {
File f = TestData.file(this, "all_data.shp");
// System.out.println(f + " " + f.exists());
URL url = DataUtilities.fileToURL(f);
DataStoreFactorySpi dataStoreFactory = new ShapefileDataStoreFactory();
Map<String, Serializable> params2 = new HashMap<String, Serializable>();
params2.put("url", url);
params2.put("create spatial index", Boolean.TRUE);
ShapefileDataStore store = (ShapefileDataStore) dataStoreFactory.createNewDataStore(params2);
// ShapefileDataStore store = new ShapefileDataStore(url);
assertNotNull(store);
FeatureSource featureSource = store.getFeatureSource();
final FeatureCollection features = featureSource.getFeatures();
Map<String, Object> params = new HashMap<String, Object>();
params.put(ClusterMethodFactory.NAME.key, "random");
params.put(ClusterMethodFactory.POPULATION.key, features);
params.put(ClusterMethodFactory.POPATTRIBUTE.key, "pop");
params.put(ClusterMethodFactory.CANCER.key, features);
params.put(ClusterMethodFactory.CANATTRIBUTE.key, "cases");
params.put(ClusterMethodFactory.MINRAD.key, 1000.0);
params.put(ClusterMethodFactory.MAXRAD.key, 5000.0);
params.put(ClusterMethodFactory.NCIRCLES.key, 500.0);
params.put(ClusterMethodFactory.TESTNAME.key, "poisson");
ClusterMethodFactory factory = new ClusterMethodFactory();
Process process = factory.create(params);
assertNotNull(process);
long start = System.currentTimeMillis();
Map<String, Object> results = process.execute(params, new ClusterMonitor());
long end = System.currentTimeMillis();
System.out.println("process took " + ((end - start) / 1000) + " seconds");
GridCoverage2D grid = (GridCoverage2D) results.get(ClusterMethodFactory.RESULT.key);
String basename = f.toString();
basename = basename.substring(0, basename.length() - 4);
String filename = basename + "_rand.tiff";
Utilities.writeGrid(filename, grid);
FeatureCollection outfeatures =
(FeatureCollection) results.get(ClusterMethodFactory.CIRCLES.key);
Utilities.writeCircles(basename + "_rand.shp", outfeatures);
}
@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 testFullReadOnCoverageWithIncreasingLat() throws IOException, FactoryException {
final File testURL = TestData.file(this, "O3-NO2.nc");
// Get format
// final AbstractGridFormat format = (AbstractGridFormat)
GridFormatFinder.findFormat(testURL.toURI().toURL(), null);
final NetCDFReader reader = new NetCDFReader(testURL, null);
// assertNotNull(format);
assertNotNull(reader);
try {
String[] names = reader.getGridCoverageNames();
assertNotNull(names);
assertEquals(2, names.length);
GridCoverage2D grid = reader.read("O3", null);
assertFalse(grid.getSampleDimension(0).getDescription().toString().endsWith(":sd"));
assertNotNull(grid);
float[] value =
grid.evaluate(
(DirectPosition) new DirectPosition2D(DefaultGeographicCRS.WGS84, 5, 45),
new float[1]);
assertEquals(47.63341f, value[0], 0.00001);
value =
grid.evaluate(
(DirectPosition) new DirectPosition2D(DefaultGeographicCRS.WGS84, 5, 45.125),
new float[1]);
assertEquals(52.7991f, value[0], 0.000001);
} 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
}
}
}
}
@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"));
}
}
private void cleanUp() throws FileNotFoundException, IOException {
final File dir = TestData.file(this, ".");
removeIndexes(dir);
}
@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
}
}
}
}
