[SEDONA-735] Fix RS_Clip bug caused by AOI geometries smaller than pixel size (#1952)

* profiling1

* profiling4

* profiling...

* profiling 8

* remove redundant cropping

* fix lenient mode

* Use rasterizeGeomExtent from Rasterization class

* add comment

* add test for small AOI geometries

* make rasterizeGeomExtent a protected method

* add test geotif

* undo pom changes

* Address comments

* spotless fix

Author: prantogg

common/src/main/java/org/apache/sedona/common/raster/RasterBandEditors.java

@@ -31,7 +31,10 @@
 import org.geotools.coverage.grid.GridCoverage2D;
 import org.geotools.coverage.processing.CannotCropException;
 import org.geotools.coverage.processing.operation.Crop;
+import org.geotools.geometry.Envelope2D;
+import org.geotools.geometry.jts.JTS;
 import org.locationtech.jts.geom.Geometry;
+import org.opengis.geometry.BoundingBox;
 import org.opengis.parameter.ParameterValueGroup;
 import org.opengis.referencing.FactoryException;
 import org.opengis.referencing.operation.TransformException;
@@ -298,13 +301,19 @@ public static GridCoverage2D clip(
     singleBandRaster = pair.getLeft();
     geometry = pair.getRight();
 
+    // Use rasterizeGeomExtent for AOI geometries smaller than a pixel
+    double[] metadata = RasterAccessors.metadata(singleBandRaster);
+    Envelope2D geomEnvelope =
+        Rasterization.rasterizeGeomExtent(geometry, singleBandRaster, metadata, allTouched);
+    Geometry geomExtent = JTS.toGeometry((BoundingBox) geomEnvelope);
+
     // Crop the raster
     // this will shrink the extent of the raster to the geometry
     Crop cropObject = new Crop();
     ParameterValueGroup parameters = cropObject.getParameters();
     parameters.parameter("Source").setValue(singleBandRaster);
     parameters.parameter(Crop.PARAMNAME_DEST_NODATA).setValue(new double[] {noDataValue});
-    parameters.parameter(Crop.PARAMNAME_ROI).setValue(geometry);
+    parameters.parameter(Crop.PARAMNAME_ROI).setValue(geomExtent);
 
     GridCoverage2D newRaster;
     try {

common/src/main/java/org/apache/sedona/common/raster/Rasterization.java

@@ -303,7 +303,7 @@ private static boolean isInsideBounds(
     return x >= minX && x <= maxX && y >= minY && y <= maxY;
   }
 
-  private static Envelope2D rasterizeGeomExtent(
+  protected static Envelope2D rasterizeGeomExtent(
       Geometry geom, GridCoverage2D raster, double[] metadata, boolean allTouched) {
 
     if (Objects.equals(geom.getGeometryType(), "MultiLineString")) {

common/src/test/java/org/apache/sedona/common/raster/RasterBandEditorsTest.java

@@ -201,6 +201,28 @@ public void testClipWithGeometryTransform()
     assertTrue(Arrays.equals(expectedValues, actualValues));
   }
 
+  @Test
+  public void testClip_smallAOI() throws FactoryException, TransformException, ParseException {
+    // Test for AOI geometries smaller than a pixel
+    GridCoverage2D raster =
+        RasterConstructors.makeEmptyRaster(1, "F", 4, 4, 401805.039562261, 2095852.150947876, 30);
+    raster = RasterEditors.setSrid(raster, 5070);
+    double[] bandValues = {1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16};
+    raster = MapAlgebra.addBandFromArray(raster, bandValues, 1);
+    String polygon =
+        "POLYGON ((401866.1071465613 2095803.8989834636, 401850.9983055725 2095803.1375789386, 401850.039562261 2095822.150947876, 401865.14840359957 2095822.9124532426, 401880.2572475523 2095823.6738547424, 401881.2159852499 2095804.6604855175, 401866.1071465613 2095803.8989834636))";
+    Geometry geom = Constructors.geomFromWKT(polygon, 5070);
+
+    GridCoverage2D clippedRaster = RasterBandEditors.clip(raster, 1, geom, false, 0, true);
+    double bandNoDataValue = RasterBandAccessors.getBandNoDataValue(clippedRaster);
+    double expectedBandNoDataValue = 0.0;
+    double[] actualValues = MapAlgebra.bandAsArray(clippedRaster, 1);
+    double[] expectedValues = {2.0, 3.0, 6.0, 7.0};
+
+    assertEquals(expectedBandNoDataValue, bandNoDataValue, FP_TOLERANCE);
+    assertTrue(Arrays.equals(expectedValues, actualValues));
+  }
+
   @Test
   public void testClip()
       throws IOException, FactoryException, TransformException, ParseException,
@@ -244,7 +266,7 @@ public void testClip()
     points.add(Constructors.geomFromWKT("POINT(237919 4.20357e+06)", 26918));
     points.add(Constructors.geomFromWKT("POINT(223802 4.20465e+06)", 26918));
     actualValues = PixelFunctions.values(croppedRaster, points, 1).toArray(new Double[0]);
-    expectedValues = new Double[] {0.0, 0.0, 0.0, 0.0, null};
+    expectedValues = new Double[] {0.0, 0.0, 0.0, 0.0, 255.0};
     assertTrue(Arrays.equals(expectedValues, actualValues));
   }