Merge branch 'master' into save_interpolators

opendrift/models/oceandrift.py

@@ -199,7 +199,7 @@ def update(self):
         # Optional machine learning correction
         self.machine_learning_correction()
 
-    def simulate_trajectories(self, outfile, trajectories,
+    def simulate_trajectories(self, outfile, trajectories, number=1,
                               wind_drift_factors=None, current_drift_factors=None,
                               time_step=None, time_step_output=None,
                               simulation_duration=None, simulation_interval=None):
@@ -208,7 +208,7 @@ def simulate_trajectories(self, outfile, trajectories,
         time_step_output = pd.Timedelta(time_step_output)
         simulation_interval = pd.Timedelta(simulation_interval)
         # Interpolate trajectories to output time step
-        trajectories = trajectories.traj.gridtime(time_step_output)
+        #trajectories = trajectories.traj.gridtime(time_step_output)
         # Find all seed combinations: position, time, wdf, cdf
         #  Loop også over trajektorier -> origin_marker
         step = int(simulation_interval / time_step_output)
@@ -217,11 +217,13 @@ def simulate_trajectories(self, outfile, trajectories,
         start_lats = trajectories.isel(time=tind).isel(trajectory=0).lat.values
         start_times = trajectories.time[tind]
         self.set_config('drift:max_age_seconds', simulation_duration.total_seconds())
+        kwargs = {'wind_drift_factor': wind_drift_factors[0],
+                  'current_drift_factor': current_drift_factors[0]}
         for (lo,la,ti) in zip(start_lons, start_lats, start_times):
             if np.isnan(lo):
                 continue
             ti = pd.Timestamp(ti.values).to_pydatetime()
-            self.seed_elements(lon=lo, lat=la, time=ti)
+            self.seed_elements(lon=lo, lat=la, time=ti, number=number, **kwargs)
         print(self)
         self.run(outfile=outfile, end_time=pd.Timestamp(start_times[-1].values).to_pydatetime()+simulation_duration)
         # Simulate and save to file

opendrift/readers/reader_ROMS_native.py

@@ -45,7 +45,6 @@ class Reader(BaseReader, StructuredReader):
         :param interpolator_path: If save_interpolator is True, user can input this string to control where interpolator is saved.
         :type interpolator_path: Path, str, optional
 
-
     Example:
 
     .. code::

opendrift/readers/reader_netCDF_CF_generic.py

@@ -247,12 +247,12 @@ def __init__(self, filename=None, zarr_storage_options=None, name=None, proj4=No
             # We load lon and lat arrays into memory
             lon_var = self.Dataset.variables[lon_var_name]
             lat_var = self.Dataset.variables[lat_var_name]
+            self.xname = lon_var_name
+            self.yname = lat_var_name
             if lon_var.ndim == 1:
                 logger.debug('Lon and lat are 1D arrays - using as projection coordinates')
                 x = lon_var.data
                 y = lat_var.data
-                self.xname = lon_var_name
-                self.yname = lat_var_name
                 self.dimensions['x'] = lon_var.dims[0]
                 self.dimensions['y'] = lat_var.dims[0]
                 if self.proj4 is None:
@@ -261,11 +261,15 @@ def __init__(self, filename=None, zarr_storage_options=None, name=None, proj4=No
                 logger.debug('Lon and lat are 2D arrays - dataset is unprojected')
                 self.lon = lon_var.data
                 self.lat = lat_var.data
+                self.dimensions['x'] = lon_var.dims[0]
+                self.dimensions['y'] = lat_var.dims[1]
                 self.projected = False
             elif lon_var.ndim == 3:
                 logger.debug('Lon lat are 3D arrays, reading first time')
                 self.lon = lon_var[0,:,:].data
                 self.lat = lat_var[0,:,:].data
+                self.dimensions['x'] = lon_var.dims[1]
+                self.dimensions['y'] = lat_var.dims[2]
                 self.projected = False
         else:
             if self.proj4 is None:
@@ -511,6 +515,9 @@ def get_variables(self, requested_variables, time=None,
                 from opendrift.readers.basereader import vector_pairs_xy
                 for vectorpair in vector_pairs_xy:
                     if vectorpair[0] in self.rotate_mapping and vectorpair[0] in variables.keys():
+                        if self.proj.__class__.__name__ == 'fakeproj':
+                            logger.warning('Rotation from fakeproj is not yet implemented, skipping.')
+                            continue
                         logger.debug(f'Rotating vector from east/north to xy orientation: {vectorpair[0:2]}')
                         variables[vectorpair[0]], variables[vectorpair[1]] = self.rotate_vectors(
                             lon, lat, variables[vectorpair[0]], variables[vectorpair[1]],