@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);
}
/**
* Gets resolution information about the coverage itself.
*
* @param reader an {@link ImageReader} to use for getting the resolution information.
* @throws IOException
* @throws TransformException
* @throws DataSourceException
*/
private void getResolutionInfo(ImageReader reader) throws IOException, TransformException {
// //
//
// get the dimension of the high resolution image and compute the
// resolution
//
// //
final Rectangle originalDim = new Rectangle(0, 0, reader.getWidth(0), reader.getHeight(0));
if (originalGridRange == null) {
originalGridRange = new GridEnvelope2D(originalDim);
}
// ///
//
// setting the higher resolution available for this coverage
//
// ///
highestRes = CoverageUtilities.getResolution((AffineTransform) raster2Model);
if (LOGGER.isLoggable(Level.FINE))
LOGGER.fine(
new StringBuffer("Highest Resolution = [")
.append(highestRes[0])
.append(",")
.append(highestRes[1])
.toString());
}
public void handleSampleDimensionNilValues(GridCoverage2D gc2d, double[] nodataValues) {
start("swe:nilValues");
start("swe:NilValues");
if (nodataValues != null && nodataValues.length > 0) {
for (double nodata : nodataValues) {
final AttributesImpl nodataAttr = new AttributesImpl();
nodataAttr.addAttribute(
"", "reason", "reason", "", "http://www.opengis.net/def/nil/OGC/0/unknown");
element("swe:nilValue", String.valueOf(nodata), nodataAttr);
}
} else if (gc2d != null) {
// do we have already a a NO_DATA value at hand?
if (gc2d.getProperties().containsKey("GC_NODATA")) {
String nodata = (String) gc2d.getProperties().get("GC_NODATA"); // TODO test me
final AttributesImpl nodataAttr = new AttributesImpl();
nodataAttr.addAttribute(
"", "reason", "reason", "", "http://www.opengis.net/def/nil/OGC/0/unknown");
element("swe:nilValue", nodata, nodataAttr);
} else {
// let's suggest some meaningful value from the data type of the underlying image
Number nodata =
CoverageUtilities.suggestNoDataValue(
gc2d.getRenderedImage().getSampleModel().getDataType());
final AttributesImpl nodataAttr = new AttributesImpl();
nodataAttr.addAttribute(
"", "reason", "reason", "", "http://www.opengis.net/def/nil/OGC/0/unknown");
element("swe:nilValue", nodata.toString(), nodataAttr);
}
}
end("swe:NilValues");
end("swe:nilValues");
}
@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
}
}
}
}
/**
* Applies the band select operation to a grid coverage.
*
* @param cropEnvelope the target envelope; always not null
* @param cropROI the target ROI shape; nullable
* @param roiTolerance; as read from op's params
* @param sourceCoverage is the source {@link GridCoverage2D} that we want to crop.
* @param hints A set of rendering hints, or {@code null} if none.
* @param sourceGridToWorldTransform is the 2d grid-to-world transform for the source coverage.
* @return The result as a grid coverage.
*/
private static GridCoverage2D buildResult(
final GeneralEnvelope cropEnvelope,
final Geometry cropROI,
final double roiTolerance,
final boolean forceMosaic,
final Hints hints,
final GridCoverage2D sourceCoverage,
final AffineTransform sourceGridToWorldTransform) {
//
// Getting the source coverage and its child geolocation objects
//
final RenderedImage sourceImage = sourceCoverage.getRenderedImage();
final GridGeometry2D sourceGridGeometry = ((GridGeometry2D) sourceCoverage.getGridGeometry());
final GridEnvelope2D sourceGridRange = sourceGridGeometry.getGridRange2D();
//
// Now we try to understand if we have a simple scale and translate or a
// more elaborated grid-to-world transformation n which case a simple
// crop could not be enough, but we may need a more elaborated chain of
// operation in order to do a good job. As an instance if we
// have a rotation which is not multiple of PI/2 we have to use
// the mosaic with a ROI
//
final boolean isSimpleTransform =
CoverageUtilities.isSimpleGridToWorldTransform(sourceGridToWorldTransform, EPS);
// Do we need to explode the Palette to RGB(A)?
//
int actionTaken = 0;
// //
//
// Layout
//
// //
final RenderingHints targetHints = new RenderingHints(null);
if (hints != null) targetHints.add(hints);
final ImageLayout layout = initLayout(sourceImage, targetHints);
targetHints.put(JAI.KEY_IMAGE_LAYOUT, layout);
//
// prepare the processor to use for this operation
//
final JAI processor = OperationJAI.getJAI(targetHints);
final boolean useProvidedProcessor = !processor.equals(JAI.getDefaultInstance());
try {
if (cropROI != null) {
// replace the cropEnvelope with the envelope of the intersection
// of the ROI and the cropEnvelope.
// Remember that envelope(intersection(roi,cropEnvelope)) != intersection(cropEnvelope,
// envelope(roi))
final Polygon modelSpaceROI = FeatureUtilities.getPolygon(cropEnvelope, GFACTORY);
Geometry intersection = IntersectUtils.intersection(cropROI, modelSpaceROI);
Envelope2D e2d =
JTS.getEnvelope2D(
intersection.getEnvelopeInternal(), cropEnvelope.getCoordinateReferenceSystem());
GeneralEnvelope ge = new GeneralEnvelope((org.opengis.geometry.Envelope) e2d);
cropEnvelope.setEnvelope(ge);
}
// //
//
// Build the new range by keeping into
// account translation of grid geometry constructor for respecting
// OGC PIXEL-IS-CENTER ImageDatum assumption.
//
// //
final AffineTransform sourceWorldToGridTransform = sourceGridToWorldTransform.createInverse();
// //
//
// finalRasterArea will hold the smallest rectangular integer raster area that contains the
// floating point raster
// area which we obtain when applying the world-to-grid transform to the cropEnvelope. Note
// that we need to intersect
// such an area with the area covered by the source coverage in order to be sure we do not try
// to crop outside the
// bounds of the source raster.
//
// //
final Rectangle2D finalRasterAreaDouble =
XAffineTransform.transform(
sourceWorldToGridTransform, cropEnvelope.toRectangle2D(), null);
final Rectangle finalRasterArea = finalRasterAreaDouble.getBounds();
// intersection with the original range in order to not try to crop outside the image bounds
Rectangle.intersect(finalRasterArea, sourceGridRange, finalRasterArea);
if (finalRasterArea.isEmpty())
throw new CannotCropException(Errors.format(ErrorKeys.CANT_CROP));
// //
//
// It is worth to point out that doing a crop the G2W transform
// should not change while the envelope might change as
// a consequence of the rounding of the underlying image datum
// which uses integer factors or in case the G2W is very
// complex. Note that we will always strive to
// conserve the original grid-to-world transform.
//
// //
// we do not have to crop in this case (should not really happen at
// this time)
if (finalRasterArea.equals(sourceGridRange) && isSimpleTransform && cropROI == null)
return sourceCoverage;
// //
//
// if I get here I have something to crop
// using the world-to-grid transform for going from envelope to the
// new grid range.
//
// //
final double minX = finalRasterArea.getMinX();
final double minY = finalRasterArea.getMinY();
final double width = finalRasterArea.getWidth();
final double height = finalRasterArea.getHeight();
// //
//
// Check if we need to use mosaic or crop
//
// //
final PlanarImage croppedImage;
final ParameterBlock pbj = new ParameterBlock();
pbj.addSource(sourceImage);
java.awt.Polygon rasterSpaceROI = null;
String operatioName = null;
if (!isSimpleTransform || cropROI != null) {
// /////////////////////////////////////////////////////////////////////
//
// We don't have a simple scale and translate transform, JAI
// crop MAY NOT suffice. Let's decide whether or not we'll use
// the Mosaic.
//
// /////////////////////////////////////////////////////////////////////
Polygon modelSpaceROI = FeatureUtilities.getPolygon(cropEnvelope, GFACTORY);
// //
//
// Now convert this polygon back into a shape for the source
// raster space.
//
// //
final List<Point2D> points = new ArrayList<Point2D>(5);
rasterSpaceROI =
FeatureUtilities.convertPolygonToPointArray(
modelSpaceROI, ProjectiveTransform.create(sourceWorldToGridTransform), points);
if (rasterSpaceROI == null || rasterSpaceROI.getBounds().isEmpty())
if (finalRasterArea.isEmpty())
throw new CannotCropException(Errors.format(ErrorKeys.CANT_CROP));
final boolean doMosaic =
forceMosaic
? true
: decideJAIOperation(roiTolerance, rasterSpaceROI.getBounds2D(), points);
if (doMosaic || cropROI != null) {
// prepare the params for the mosaic
final ROI[] roiarr;
try {
if (cropROI != null) {
final LiteShape2 cropRoiLS2 =
new LiteShape2(
cropROI, ProjectiveTransform.create(sourceWorldToGridTransform), null, false);
ROI cropRS = new ROIShape(cropRoiLS2);
Rectangle2D rt = cropRoiLS2.getBounds2D();
if (!hasIntegerBounds(rt)) {
// Approximate Geometry
Geometry geo = (Geometry) cropRoiLS2.getGeometry().clone();
transformGeometry(geo);
cropRS = new ROIShape(new LiteShape2(geo, null, null, false));
}
roiarr = new ROI[] {cropRS};
} else {
final ROIShape roi = new ROIShape(rasterSpaceROI);
roiarr = new ROI[] {roi};
}
} catch (FactoryException ex) {
throw new CannotCropException(Errors.format(ErrorKeys.CANT_CROP), ex);
}
pbj.add(MosaicDescriptor.MOSAIC_TYPE_OVERLAY);
pbj.add(null);
pbj.add(roiarr);
pbj.add(null);
pbj.add(CoverageUtilities.getBackgroundValues(sourceCoverage));
// prepare the final layout
final Rectangle bounds = rasterSpaceROI.getBounds2D().getBounds();
Rectangle.intersect(bounds, sourceGridRange, bounds);
if (bounds.isEmpty()) throw new CannotCropException(Errors.format(ErrorKeys.CANT_CROP));
// we do not have to crop in this case (should not really happen at
// this time)
if (!doMosaic && bounds.getBounds().equals(sourceGridRange) && isSimpleTransform)
return sourceCoverage;
// nice trick, we use the layout to do the actual crop
final Rectangle boundsInt = bounds.getBounds();
layout.setMinX(boundsInt.x);
layout.setWidth(boundsInt.width);
layout.setMinY(boundsInt.y);
layout.setHeight(boundsInt.height);
operatioName = "Mosaic";
}
}
// do we still have to set the operation name? If so that means we have to go for crop.
if (operatioName == null) {
// executing the crop
pbj.add((float) minX);
pbj.add((float) minY);
pbj.add((float) width);
pbj.add((float) height);
operatioName = "GTCrop";
}
// //
//
// Apply operation
//
// //
if (!useProvidedProcessor) {
croppedImage = JAI.create(operatioName, pbj, targetHints);
} else {
croppedImage = processor.createNS(operatioName, pbj, targetHints);
}
// conserve the input grid to world transformation
Map sourceProperties = sourceCoverage.getProperties();
Map properties = null;
if (sourceProperties != null && !sourceProperties.isEmpty()) {
properties = new HashMap(sourceProperties);
}
if (rasterSpaceROI != null) {
if (properties != null) {
properties.put("GC_ROI", rasterSpaceROI);
} else {
properties = Collections.singletonMap("GC_ROI", rasterSpaceROI);
}
}
return new GridCoverageFactory(hints)
.create(
sourceCoverage.getName(),
croppedImage,
new GridGeometry2D(
new GridEnvelope2D(croppedImage.getBounds()),
sourceGridGeometry.getGridToCRS2D(PixelOrientation.CENTER),
sourceCoverage.getCoordinateReferenceSystem()),
(GridSampleDimension[])
(actionTaken == 1 ? null : sourceCoverage.getSampleDimensions().clone()),
new GridCoverage[] {sourceCoverage},
properties);
} catch (TransformException e) {
throw new CannotCropException(Errors.format(ErrorKeys.CANT_CROP), e);
} catch (NoninvertibleTransformException e) {
throw new CannotCropException(Errors.format(ErrorKeys.CANT_CROP), e);
}
}