Some minor changes

nlmod/dims/base.py

@@ -206,7 +206,7 @@ def to_model_ds(
     return ds
 
 
-def extrapolate_ds(ds, mask=None, layer="layer"):
+def extrapolate_ds(ds, mask=None, layer="layer", mask_values=None):
     """Fill missing data in layermodel based on nearest interpolation.
 
     Used for ensuring layer model contains data everywhere. Useful for
@@ -223,6 +223,10 @@ def extrapolate_ds(ds, mask=None, layer="layer"):
         variable. The default is None.
     layer : str, optional
         The name of the layer dimension. The default is 'layer'.
+    mask_values : np.ndarray, optional
+        Boolean mask for each cell, with a value of True if its value is used to fill
+        data in mask. When mask_values is None, it is determined from mask. The default
+        is None.
 
     Returns
     -------
@@ -234,6 +238,8 @@ def extrapolate_ds(ds, mask=None, layer="layer"):
     if not mask.any():
         # all of the model cells are is inside the known area
         return ds
+    if mask_values is None:
+        mask_values = ~mask
     if mask.all():
         raise (ValueError("The model only contains NaNs"))
     if "gridtype" in ds.attrs and ds.gridtype == "vertex":
@@ -243,7 +249,7 @@ def extrapolate_ds(ds, mask=None, layer="layer"):
     else:
         x, y = np.meshgrid(ds.x, ds.y)
         dims = ("y", "x")
-    points = np.stack((x[~mask], y[~mask]), axis=1)
+    points = np.stack((x[mask_values], y[mask_values]), axis=1)
     xi = np.stack((x[mask], y[mask]), axis=1)
     # geneterate the tree only once, to increase speed
     tree = cKDTree(points)
@@ -254,11 +260,11 @@ def extrapolate_ds(ds, mask=None, layer="layer"):
         data = ds[key].data
         if ds[key].dims == dims:
             if np.isnan(data[mask]).sum() > 0:  # do not update if no NaNs
-                data[mask] = data[~mask][i]
+                data[mask] = data[mask_values][i]
         elif ds[key].dims == (layer,) + dims:
             for lay in range(len(ds[layer])):
                 if np.isnan(data[lay, mask]).sum() > 0:  # do not update if no NaNs
-                    data[lay, mask] = data[lay, ~mask][i]
+                    data[lay, mask] = data[lay, mask_values][i]
         else:
             logger.warning(
                 f"Data variable '{key}' not extrapolated because "

nlmod/dims/grid.py

@@ -702,8 +702,6 @@ def update_ds_from_layer_ds(ds, layer_ds, method="nearest", **kwargs):
         Dataset with variables from layer_ds.
     """
     if not layer_ds.layer.equals(ds.layer):
-        # do not change the original Dataset
-        layer_ds = layer_ds.copy()
         # update layers in ds
         drop_vars = []
         for var in ds.data_vars:
@@ -1201,7 +1199,7 @@ def gdf_to_data_array_struc(
         DESCRIPTION.
     """
     warnings.warn(
-        "The method gdf_to_data_array_struc is deprecated. Please use gdf_to_da instead",
+        "The method gdf_to_data_array_struc is deprecated. Please use gdf_to_da instead.",
         DeprecationWarning,
     )
 
@@ -1770,7 +1768,7 @@ def get_thickness_from_topbot(top, bot):
         or (layer, icell2d).
     """
     warnings.warn(
-        "The method get_thickness_from_topbot is deprecated. Please use nlmod.layers.calculate_thickness instead",
+        "The method get_thickness_from_topbot is deprecated. Please use nlmod.layers.calculate_thickness instead.",
         DeprecationWarning,
     )
 

nlmod/dims/resample.py

@@ -583,7 +583,7 @@ def structured_da_to_ds(da, ds, method="average", nodata=np.nan):
 def extent_to_polygon(extent):
     logger.warning(
         "nlmod.resample.extent_to_polygon is deprecated. "
-        "Use nlmod.util.extent_to_polygon instead"
+        "Use nlmod.util.extent_to_polygon instead."
     )
     from ..util import extent_to_polygon
 
@@ -594,7 +594,7 @@ def get_extent_polygon(ds, rotated=True):
     """Get the model extent, as a shapely Polygon."""
     logger.warning(
         "nlmod.resample.get_extent_polygon is deprecated. "
-        "Use nlmod.grid.get_extent_polygon instead"
+        "Use nlmod.grid.get_extent_polygon instead."
     )
     from .grid import get_extent_polygon
 
@@ -605,7 +605,7 @@ def affine_transform_gdf(gdf, affine):
     """Apply an affine transformation to a geopandas GeoDataFrame."""
     logger.warning(
         "nlmod.resample.affine_transform_gdf is deprecated. "
-        "Use nlmod.grid.affine_transform_gdf instead"
+        "Use nlmod.grid.affine_transform_gdf instead."
     )
     from .grid import affine_transform_gdf
 
@@ -615,7 +615,7 @@ def affine_transform_gdf(gdf, affine):
 def get_extent(ds, rotated=True):
     """Get the model extent, corrected for angrot if necessary."""
     logger.warning(
-        "nlmod.resample.get_extent is deprecated. Use nlmod.grid.get_extent instead"
+        "nlmod.resample.get_extent is deprecated. Use nlmod.grid.get_extent instead."
     )
     from .grid import get_extent
 
@@ -626,7 +626,7 @@ def get_affine_mod_to_world(ds):
     """Get the affine-transformation from model to real-world coordinates."""
     logger.warning(
         "nlmod.resample.get_affine_mod_to_world is deprecated. "
-        "Use nlmod.grid.get_affine_mod_to_world instead"
+        "Use nlmod.grid.get_affine_mod_to_world instead."
     )
     from .grid import get_affine_mod_to_world
 
@@ -637,7 +637,7 @@ def get_affine_world_to_mod(ds):
     """Get the affine-transformation from real-world to model coordinates."""
     logger.warning(
         "nlmod.resample.get_affine_world_to_mod is deprecated. "
-        "Use nlmod.grid.get_affine_world_to_mod instead"
+        "Use nlmod.grid.get_affine_world_to_mod instead."
     )
     from .grid import get_affine_world_to_mod
 
@@ -647,7 +647,7 @@ def get_affine_world_to_mod(ds):
 def get_affine(ds, sx=None, sy=None):
     """Get the affine-transformation, from pixel to real-world coordinates."""
     logger.warning(
-        "nlmod.resample.get_affine is deprecated. Use nlmod.grid.get_affine instead"
+        "nlmod.resample.get_affine is deprecated. Use nlmod.grid.get_affine instead."
     )
     from .grid import get_affine