Merge branch 'main' into math

docs/index.qmd

@@ -1,5 +1,6 @@
 ---
 toc: false
+format-links: false
 ---
 
 ![](MIKE-IO-Logo-Pos-RGB.svg)

docs/user-guide/dataarray.qmd

@@ -175,6 +175,7 @@ Other methods that also return a DataArray:
 * [`interp_like`](`mikeio.DataArray.interp_like`) - Spatio (temporal) interpolation (see example [Dfsu interpolation](../examples/dfsu/spatial_interpolation.qmd)
 * [`interp_time()`](`mikeio.DataArray.interp_time`) - Temporal interpolation (see example [Time interpolation](../examples/Time-interpolation.qmd))
 * [`dropna()`](`mikeio.DataArray.dropna`) - Remove time steps where all items are NaN
+* [`fillna()`](`mikeio.DataArray.fillna`) - Fill missing values with a constant value
 * [`squeeze()`](`mikeio.DataArray.squeeze`) - Remove axes of length 1
 
 ### Conversion:

docs/user-guide/dataset.qmd

@@ -179,6 +179,7 @@ Other methods that also return a Dataset:
 * [`interp_like`](`mikeio.Dataset.interp_like`) - Spatio (temporal) interpolation (see [Dfsu interpolation notebook](../examples/dfsu/spatial_interpolation.qmd)
 * [`interp_time()`](`mikeio.Dataset.interp_time`) - Temporal interpolation (see [Time interpolation notebook](../examples/Time-interpolation.qmd))
 * [`dropna()`](`mikeio.Dataset.dropna`) - Remove time steps where all items are NaN
+* [`fillna()`](`mikeio.Dataset.fillna`) - Fill missing values with a constant value
 * [`squeeze()`](`mikeio.Dataset.squeeze`) - Remove axes of length 1
 
 ### Conversion:

mikeio/dataset/_dataarray.py

@@ -484,6 +484,34 @@ def to_numpy(self) -> np.ndarray:
     def _has_time_axis(self) -> bool:
         return self.dims[0][0] == "t"
 
+    def fillna(self, value: float = 0.0) -> "DataArray":
+        """Fill NA/NaN value.
+
+        Parameters
+        ----------
+        value: float, optional
+            Value used to fill missing values. Default is 0.0.
+
+        Examples
+        --------
+        ```{python}
+        import numpy as np
+        import mikeio
+
+        da = mikeio.DataArray([np.nan, 1.0])
+        da
+        ```
+
+        ```{python}
+        da.fillna(0.0)
+        ```
+
+        """
+        da = self.copy()
+        x = da.values
+        x[np.isnan(x)] = value
+        return da
+
     def dropna(self) -> "DataArray":
         """Remove time steps where values are NaN."""
         if not self._has_time_axis:

mikeio/dataset/_dataset.py

@@ -416,6 +416,19 @@ def copy(self) -> "Dataset":
         """Returns a copy of this dataset."""
         return deepcopy(self)
 
+    def fillna(self, value: float = 0.0) -> "Dataset":
+        """Fill NA/NaN value.
+
+        Parameters
+        ----------
+        value: float, optional
+            Value used to fill missing values. Default is 0.0.
+
+        """
+        res = {name: da.fillna(value=value) for name, da in self._data_vars.items()}
+
+        return Dataset(data=res, validate=False)
+
     def dropna(self) -> "Dataset":
         """Remove time steps where all items are NaN."""
         if not self[0]._has_time_axis:  # type: ignore

mikeio/pfs/_pfsdocument.py

@@ -339,6 +339,9 @@ def _parse_line(self, line: str, level: int = 0) -> tuple[str, int]:
     def _parse_param(self, value: str) -> str:
         if len(value) == 0:
             return "[]"
+        if value[0] == "|" and value[-1] == "|":
+            if value.count("|") == 2:
+                return self._parse_token(value)
         if "MULTIPOLYGON" in value:
             return value
         if "," in value:

tests/test_dataset.py

@@ -1679,3 +1679,23 @@ def test_read_write_single_timestep_preserves_dt(tmp_path):
 
     dfs2 = mikeio.open(outfn)
     assert dfs2.timestep == pytest.approx(10800.0)
+
+
+def test_fillna() -> None:
+    ds = mikeio.Dataset(
+        {
+            "foo": mikeio.DataArray(np.array([np.nan, 1.0])),
+            "bar": mikeio.DataArray(np.array([2.0, np.nan])),
+            "baz": mikeio.DataArray(np.array([2.0, 3.0])),
+        }
+    )
+    assert np.isnan(ds["foo"].to_numpy()[0])
+    assert np.isnan(ds["bar"].to_numpy()[-1])
+
+    ds_filled = ds.fillna()
+
+    assert ds_filled["foo"].to_numpy()[0] == pytest.approx(0.0)
+    assert ds_filled["bar"].to_numpy()[-1] == pytest.approx(0.0)
+
+    # original dataset is not modified
+    assert np.isnan(ds["foo"].to_numpy()[0])

tests/test_pfs.py

@@ -215,7 +215,7 @@ def test_pfssection_insert_pfssection(d1) -> None:
 
     for j in range(10):
         dj = dict(val=j, lst=[0.3, 0.7])
-        key = f"FILE_{j+1}"
+        key = f"FILE_{j + 1}"
         sct[key] = mikeio.PfsSection(dj)
 
     assert sct.FILE_6.val == 5
@@ -226,7 +226,7 @@ def test_pfssection_find_replace(d1) -> None:
 
     for j in range(10):
         dj = dict(val=j, lst=[0.3, 0.7])
-        key = f"FILE_{j+1}"
+        key = f"FILE_{j + 1}"
         sct[key] = mikeio.PfsSection(dj)
 
     assert sct.FILE_6.lst == [0.3, 0.7]
@@ -1250,3 +1250,8 @@ def test_ignores_comments_in_quotes() -> None:
 """
     pfs = mikeio.PfsDocument.from_text(text)
     assert pfs.SymbologyModule.SymbologyTreeView == "//"
+
+
+def test_filenames_may_contain_comma() -> None:
+    pfs = mikeio.read_pfs("tests/testdata/pfs/tidal.21t")
+    assert pfs.m21_tideph.Setup.File_1.mesh_file == "|.\\b,athy.mesh|"

tests/testdata/pfs/tidal.21t

@@ -0,0 +1,26 @@
+[m21_tideph]
+   CLSID = 'TidePredictionHeights.dll'
+   TypeName = 'm21_tideph'
+   CREATEDTIME = '2018-01-25T08:27:01'
+   MODIFIEDTIME = '2018-01-25T08:28:25'
+   NOTES = ''
+   [Setup]
+      Name = 'Esbjerg1989Global_Area'
+      Prediction_type = 1
+      constituent_file_name = |..\..\..\..\..\..\..\..\Program Files (x86)\DHI\MIKE Zero\2024\Application Data\Tide_Constituents\global_tide_constituents_height_0.25deg.dfs2|
+      start_date = 1989, 1, 1
+      end_date = 1990, 1, 4
+      timestep = 1.0
+      number_of_files = 1
+      [File_1]
+         format = 3
+         mesh_file = |.\b,athy.mesh|
+         file_name = |.\Esbjerg1989PredictedGlobal.dfsu|
+         description = 'Predicted tide level'
+      EndSect  // File_1
+
+      logfilelocation = |.\|
+   EndSect  // Setup
+
+EndSect  // m21_tideph
+