Make polygonize work for polygons with holes (#1794)

Fixes #1793 

# Description

In case of a grid such as:

```
1 1 1
1 2 1
1 1 1
```

``polygonize`` would not set the hole in polygon 1 where polygon 2 is
located. Instead polygon 1 would overlap 2 entirely, as we forgot to
pass the interiors that were computed by shapely. This fixes this and
adds a unit test.

# Checklist
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Before requesting review, please go through this checklist:
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- [x] Links to correct issue
- [x] Update changelog, if changes affect users
- [x] PR title starts with ``Issue #nr``, e.g. ``Issue #737``
- [x] Unit tests were added
- [ ] **If feature added**: Added/extended example
- [ ] **If feature added**: Added feature to API documentation
- [ ] **If pixi.lock was changed**: Ran `pixi run generate-sbom` and
committed changes

Author: JoerivanEngelen

docs/api/changelog.rst

@@ -55,6 +55,7 @@ Fixed
   layer, when the stage and bottom_elevation were exactly equal to the bottom of
   a layer in the model discretization, which would cause these cells to be
   dropped when distributing conductances later.
+- Fixed :func:`imod.prepare.spatial.polygonize` for polygons with holes.
 
 Changed
 ~~~~~~~

imod/tests/test_spatial.py

@@ -7,6 +7,7 @@
 import shapely.geometry as sg
 import xarray as xr
 from pytest_cases import parametrize_with_cases
+from shapely.geometry import Polygon
 
 import imod
 from imod.testing import assert_frame_equal
@@ -118,6 +119,50 @@ def test_polygonize():
     assert sorted(gdf["value"]) == [1.0, 2.0, 3.0]
 
 
+def fits_exact_hole(parent: Polygon, child: Polygon, tol=0.0) -> bool:
+    hole_polys = Polygon(parent.interiors[0])
+    exterior = Polygon(child.exterior)
+    return exterior.equals(hole_polys)
+
+
+def test_polygonize_with_holes():
+    """
+    Polygonize should be able to handle polygons with holes. In this test, we
+    create a 5x5 grid of values as follows:
+
+    1 1 1 1 1
+    1 2 2 2 1
+    1 2 3 2 1
+    1 2 2 2 1
+    1 1 1 1 1
+
+    The polygon for the value 1.0 should be a large square that contains the
+    entire grid, but has a hole in the middle that corresponds to the polygon
+    for the value 2.0. The polygon for the value 2.0 should have a hole that
+    corresponds exactly to the polygon for the value 3.0.
+    """
+    # Arrange
+    nrow, ncol = 5, 5
+    dx, dy = 1.0, -1.0
+    xmin, xmax = 0.0, 5.0
+    ymin, ymax = 0.0, 5.0
+    coords = imod.util.spatial._xycoords((xmin, xmax, ymin, ymax), (dx, dy))
+    kwargs = {"name": "test", "coords": coords, "dims": ("y", "x")}
+    data = np.ones((nrow, ncol), dtype=np.float32)
+    data[1:-1, 1:-1] = 2.0
+    data[2, 2] = 3.0
+    da = xr.DataArray(data, **kwargs)
+    # Act
+    gdf = imod.prepare.polygonize(da)
+    gdf = gdf.sort_values("value").reset_index(drop=True)
+    # Assert
+    assert len(gdf) == 3
+    assert sorted(gdf["value"]) == [1.0, 2.0, 3.0]
+    p1, p2, p3 = gdf.geometry
+    ok = fits_exact_hole(p1, p2) and fits_exact_hole(p2, p3)
+    assert ok
+
+
 def test_handle_dtype():
     assert imod.prepare.spatial._handle_dtype(np.uint8, None) == (1, 0)
     assert imod.prepare.spatial._handle_dtype(np.uint16, None) == (2, 0)

imod/util/spatial.py

@@ -730,7 +730,13 @@ def _polygonize(da: xr.DataArray) -> "gpd.GeoDataFrame":
     geometries = []
     colvalues = []
     for geom, colval in shapes:
-        geometries.append(shapely.geometry.Polygon(geom["coordinates"][0]))
+        coordinates = geom["coordinates"]
+        exterior = coordinates[0]
+        if len(coordinates) > 1:
+            interiors = coordinates[1:]
+        else:
+            interiors = None
+        geometries.append(shapely.geometry.Polygon(exterior, interiors))
         colvalues.append(colval)
 
     gdf = gpd.GeoDataFrame({"value": colvalues, "geometry": geometries})