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Gets NODATA values from Raster metadata if not set, fixes shift and resampling for different resolutions #280

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Merged
AM1729 merged 3 commits into from
Nov 19, 2025
Merged

Gets NODATA values from Raster metadata if not set, fixes shift and resampling for different resolutions #280

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44d4287
gets nodata from raster metadata, fixes shifts and resampling for obs…
AM1729 Nov 18, 2025
45f2081
Merge branch 'develop' of https://github.com/integratedmodelling/klab…
AM1729 Nov 19, 2025
fe8d0f2
fixes
AM1729 Nov 19, 2025
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9 changes: 9 additions & 0 deletions adapters/klab.ogc/src/main/java/org/integratedmodelling/klab/raster/files/RasterEncoder.java
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Original file line number Diff line number Diff line change
Expand Up @@ -69,6 +69,8 @@
import org.integratedmodelling.klab.utils.NumberUtils;
import org.opengis.coverage.grid.GridCoverage;
import org.opengis.referencing.crs.CoordinateReferenceSystem;
import org.geotools.coverage.util.CoverageUtilities;
import it.geosolutions.jaiext.range.NoDataContainer;

import groovy.lang.Binding;
import groovy.lang.GroovyShell;
Expand Down Expand Up @@ -113,6 +115,13 @@ public void encodeFromCoverage(IResource resource, Map<String, String> urnParame
}
int nBands = coverage.getNumSampleDimensions();
Set<Double> nodata = getNodata(resource, coverage, band);

if (nodata.isEmpty()) {
NoDataContainer nodataContainer = CoverageUtilities.getNoDataProperty((GridCoverage2D) coverage);
double nodataValue = nodataContainer.getAsSingleValue();
nodata.add(nodataValue);
}

GroovyShell shell = null;
Binding binding = null;
Script transformation = null;
Expand Down
33 changes: 31 additions & 2 deletions adapters/klab.ogc/src/main/java/org/integratedmodelling/klab/stac/STACEncoder.java
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@
import org.hortonmachine.gears.io.stac.HMStacItem;
import org.hortonmachine.gears.io.stac.HMStacManager;
import org.hortonmachine.gears.libs.modules.HMRaster;
import org.hortonmachine.gears.libs.modules.HMRaster.HMRasterWritableBuilder;
import org.hortonmachine.gears.libs.modules.HMRaster.MergeMode;
import org.hortonmachine.gears.libs.monitor.LogProgressMonitor;
import org.hortonmachine.gears.utils.CrsUtilities;
Expand All @@ -36,6 +37,7 @@
import org.integratedmodelling.klab.api.provenance.IArtifact;
import org.integratedmodelling.klab.api.runtime.IContextualizationScope;
import org.integratedmodelling.klab.api.runtime.monitoring.IMonitor;
import org.integratedmodelling.klab.components.geospace.extents.Projection;
import org.integratedmodelling.klab.components.geospace.extents.Space;
import org.integratedmodelling.klab.components.runtime.observations.Observation;
import org.integratedmodelling.klab.components.time.extents.Time;
Expand All @@ -60,6 +62,9 @@
import org.locationtech.jts.geom.Polygon;
import org.opengis.feature.simple.SimpleFeature;
import org.opengis.feature.simple.SimpleFeatureType;
import org.opengis.geometry.DirectPosition;
import org.geotools.referencing.CRS;
import org.opengis.referencing.FactoryException;
import org.opengis.referencing.crs.CoordinateReferenceSystem;

import com.github.davidmoten.aws.lw.client.Client;
Expand Down Expand Up @@ -199,8 +204,32 @@ public void getEncodedData(IResource resource, Map<String, String> urnParameters
COGURL = resource.getParameters().get("cog", String.class);
scope.getMonitor().info("Getting requested extent from the COG Asset from url" + COGURL);
GridCoverage2D coverage = COGAssetExtension.getCOGWindowCoverage(bbox, COGURL);
encoder = new RasterEncoder();
((RasterEncoder) encoder).encodeFromCoverage(resource, urnParameters, coverage, geometry, builder, scope);

String rcrs = geometry.getDimension(IGeometry.Dimension.Type.SPACE).getParameters().get(
org.integratedmodelling.klab.common.Geometry.PARAMETER_SPACE_PROJECTION,
String.class);

Projection crs = Projection.create(rcrs);
org.locationtech.jts.geom.Envelope requestedExtend = new org.locationtech.jts.geom.Envelope(bbox.get(0),
bbox.get(1), bbox.get(2), bbox.get(3));

HMRaster raster = HMRaster.fromGridCoverage(coverage);
HMRaster outRaster = new HMRasterWritableBuilder().setRegion(RegionMap.fromEnvelopeAndGrid(requestedExtend,
(int) space.shape()[0],
(int) space.shape()[1])).setCrs(crs.getCoordinateReferenceSystem())
.setNoValue(raster.getNovalue())
.build();

GridCoverage2D adjCoverage = null;
try {
outRaster.mapRaster(null, raster, null);
adjCoverage = outRaster.buildCoverage();
} catch (Exception e) {
throw new KlabResourceAccessException("Cannot build COG Output " + e.getMessage());
}

encoder = new RasterEncoder();
((RasterEncoder) encoder).encodeFromCoverage(resource, urnParameters, adjCoverage, geometry, builder, scope);
return;
}

Expand Down