Merge pull request #1566 from OceanParcels/fieldset_from_directory

Creating a new `Fieldset.from_modulefile()` method

Author: erikvansebille

parcels/fieldset.py

@@ -1,3 +1,5 @@
+import importlib.util
+import sys
 from copy import deepcopy
 from glob import glob
 from os import path
@@ -1062,6 +1064,32 @@ def from_xarray_dataset(cls, ds, variables, dimensions, mesh='spherical', allow_
         v = fields.pop('V', None)
         return cls(u, v, fields=fields)
 
+    @classmethod
+    def from_modulefile(cls, filename, modulename="create_fieldset", **kwargs):
+        """Initialises FieldSet data from a file containing a python module file with a create_fieldset() function.
+
+        Parameters
+        ----------
+        filename: path to a python file containing at least a function which returns a FieldSet object.
+        modulename: name of the function in the python file that returns a FieldSet object. Default is "create_fieldset".
+        """
+        # check if filename exists
+        if not path.exists(filename):
+            raise IOError(f"FieldSet module file {filename} does not exist")
+
+        # Importing the source file directly (following https://docs.python.org/3/library/importlib.html#importing-a-source-file-directly)
+        spec = importlib.util.spec_from_file_location(modulename, filename)
+        fieldset_module = importlib.util.module_from_spec(spec)
+        sys.modules[modulename] = fieldset_module
+        spec.loader.exec_module(fieldset_module)
+
+        if not hasattr(fieldset_module, modulename):
+            raise IOError(f"{filename} does not contain a {modulename} function")
+        fieldset = getattr(fieldset_module, modulename)(**kwargs)
+        if not isinstance(fieldset, FieldSet):
+            raise IOError(f"Module {filename}.{modulename} does not return a FieldSet object")
+        return fieldset
+
     def get_fields(self):
         """Returns a list of all the :class:`parcels.field.Field` and :class:`parcels.field.VectorField`
         objects associated with this FieldSet.

tests/test_data/fieldset_nemo.py

@@ -0,0 +1,18 @@
+from os import path
+
+import parcels
+
+
+def create_fieldset(indices=None):
+    data_path = path.join(path.dirname(__file__))
+
+    filenames = {'U': {'lon': path.join(data_path, 'mask_nemo_cross_180lon.nc'),
+                       'lat': path.join(data_path, 'mask_nemo_cross_180lon.nc'),
+                       'data': path.join(data_path, 'Uu_eastward_nemo_cross_180lon.nc')},
+                 'V': {'lon': path.join(data_path, 'mask_nemo_cross_180lon.nc'),
+                       'lat': path.join(data_path, 'mask_nemo_cross_180lon.nc'),
+                       'data': path.join(data_path, 'Vv_eastward_nemo_cross_180lon.nc')}}
+    variables = {'U': 'U', 'V': 'V'}
+    dimensions = {'lon': 'glamf', 'lat': 'gphif', 'time': 'time_counter'}
+    indices = indices or {}
+    return parcels.FieldSet.from_nemo(filenames, variables, dimensions, indices=indices)

tests/test_data/fieldset_nemo_error.py

@@ -0,0 +1,21 @@
+from os import path
+
+import parcels
+
+
+def random_function_name():
+    data_path = path.join(path.dirname(__file__))
+
+    filenames = {'U': {'lon': path.join(data_path, 'mask_nemo_cross_180lon.nc'),
+                       'lat': path.join(data_path, 'mask_nemo_cross_180lon.nc'),
+                       'data': path.join(data_path, 'Uu_eastward_nemo_cross_180lon.nc')},
+                 'V': {'lon': path.join(data_path, 'mask_nemo_cross_180lon.nc'),
+                       'lat': path.join(data_path, 'mask_nemo_cross_180lon.nc'),
+                       'data': path.join(data_path, 'Vv_eastward_nemo_cross_180lon.nc')}}
+    variables = {'U': 'U', 'V': 'V'}
+    dimensions = {'lon': 'glamf', 'lat': 'gphif', 'time': 'time_counter'}
+    return parcels.FieldSet.from_nemo(filenames, variables, dimensions)
+
+
+def none_returning_function():
+    return None

tests/test_fieldset.py

@@ -200,6 +200,24 @@ def test_field_from_netcdf(with_timestamps):
         Field.from_netcdf(filenames, variable, dimensions, interp_method='cgrid_velocity')
 
 
+def test_fieldset_from_modulefile():
+    data_path = path.join(path.dirname(__file__), 'test_data/')
+    fieldset = FieldSet.from_modulefile(data_path + 'fieldset_nemo.py')
+    assert fieldset.U.creation_log == 'from_nemo'
+
+    indices = {'lon': range(6, 10)}
+    fieldset = FieldSet.from_modulefile(data_path + 'fieldset_nemo.py', indices=indices)
+    assert fieldset.U.grid.lon.shape[1] == 4
+
+    with pytest.raises(IOError):
+        FieldSet.from_modulefile(data_path + 'fieldset_nemo_error.py')
+
+    FieldSet.from_modulefile(data_path + 'fieldset_nemo_error.py', modulename='random_function_name')
+
+    with pytest.raises(IOError):
+        FieldSet.from_modulefile(data_path + 'fieldset_nemo_error.py', modulename='none_returning_function')
+
+
 def test_field_from_netcdf_fieldtypes():
     data_path = path.join(path.dirname(__file__), 'test_data/')