Remove default value of argument orientation

On second thought, I find the default value confusing. We are
reverting commit b328ab6f.

Common/util_eddies.py

@@ -79,7 +79,8 @@ class SHPC_class:
                     = self._ishape_last[i_slice]["Cyclones"].size
             else:
                 try:
-                    self._n_dates[i_slice] = self.get_ishape_last(i_slice).size
+                    self._n_dates[i_slice] \
+                        = self.get_ishape_last(i_slice, self.def_orient).size
                 except AttributeError:
                     # Try the other orientation:
                     orientation = other_orient(self.def_orient)
@@ -88,9 +89,7 @@ class SHPC_class:
 
         return self._n_dates[i_slice]
 
-    def get_ishape_last(self, i_slice, orientation = None):
-        if orientation is None: orientation = self.def_orient
-
+    def get_ishape_last(self, i_slice, orientation):
         if self._ishape_last[i_slice][orientation] is None:
             fname = path.join(self.dir, f"Slice_{i_slice}", orientation,
                               "ishape_last.txt")
@@ -106,9 +105,7 @@ class SHPC_class:
 
         return self._ishape_last[i_slice][orientation]
 
-    def get_reader(self, i_slice, layer, orientation = None):
-        if orientation is None: orientation = self.def_orient
-
+    def get_reader(self, i_slice, layer, orientation):
         if layer not in self._readers[i_slice][orientation]:
             my_shapefile = path.join(self.dir, f"Slice_{i_slice}", orientation,
                                      layer)
@@ -123,9 +120,7 @@ class SHPC_class:
 
         return self._readers[i_slice][orientation][layer]
 
-    def get_n_shapes(self, i_slice, orientation = None):
-        if orientation is None: orientation = self.def_orient
-
+    def get_n_shapes(self, i_slice, orientation):
         if self._n_shapes[i_slice][orientation] == 0:
             reader = self.get_reader(i_slice, layer = "extremum",
                                      orientation = orientation)
@@ -169,7 +164,7 @@ class SHPC_class:
         assert i_slice >= 0
         return i_slice
 
-    def comp_ishape(self, date, eddy_index, i_slice, orientation = None):
+    def comp_ishape(self, date, eddy_index, i_slice, orientation):
         """Compute the location in the shapefiles."""
 
         assert date >= self.d_init[i_slice]

Inst_eddies/Analysis/eddy_dump.py

@@ -44,7 +44,8 @@ for layer in ["extremum", "outermost_contour", "max_speed_contour", "centroid"]:
     print()
 
     try:
-        shapeRec = SHPC.get_reader(0, layer).shapeRecord(ishape)
+        shapeRec = SHPC.get_reader(0, layer, args.orientation)\
+                       .shapeRecord(ishape)
     except AttributeError:
         pass
     else:

Overlap/report_graph.py

@@ -38,21 +38,21 @@ def read_eddy_graph(edgelist, shpc_dir = None, orientation = "Cyclones"):
         if shpc_dir is not None:
             # Read and set attributes of eddies:
             SHPC = util_eddies.SHPC_class(shpc_dir, orientation)
-            set_attribute(G, SHPC)
+            set_attribute(G, SHPC, orientation)
     else:
         print(edgelist, "not readable")
         G = nx.DiGraph()
 
     return G
 
-def set_attribute(G, SHPC):
-    reader = SHPC.get_reader(0, "extremum")
+def set_attribute(G, SHPC, orientation):
+    reader = SHPC.get_reader(0, "extremum", orientation)
 
-    if G.number_of_nodes() <= SHPC.get_n_shapes(0) / 100:
+    if G.number_of_nodes() <= SHPC.get_n_shapes(0, orientation) / 100:
         for n in G:
             date_index, eddy_index = node_to_date_eddy(n,
                                                        G.graph["e_overestim"])
-            ishape = SHPC.comp_ishape(date_index, eddy_index, 0)
+            ishape = SHPC.comp_ishape(date_index, eddy_index, 0, orientation)
             shape_rec = reader.shapeRecord(ishape)
             G.add_node(n, coordinates = tuple(shape_rec.shape.points[0]),
                        speed = shape_rec.record.speed,

Trajectories/cost_function.py

@@ -52,7 +52,7 @@ def calculate_radii_rossby(properties):
     if n_valid_Rossby != 0: avg_Rossby /= n_valid_Rossby
     return avg_rad, avg_Rossby
 
-def node_to_prop(node_list, e_overestim, SHPC):
+def node_to_prop(node_list, e_overestim, SHPC, orientation):
     """node_list is a list of node identification numbers for
     instantaneous eddies. This function returns some properties of the
     eddies, read from shapefiles: position of extremum, radius of
@@ -66,14 +66,16 @@ def node_to_prop(node_list, e_overestim, SHPC):
     for n in node_list:
         date_index, eddy_index = report_graph.node_to_date_eddy(n, e_overestim)
         i_slice = SHPC.get_slice(date_index)
-        ishape = SHPC.comp_ishape(date_index, eddy_index, i_slice)
-        shapeRec = SHPC.get_reader(i_slice, "extremum").shapeRecord(ishape)
+        ishape = SHPC.comp_ishape(date_index, eddy_index, i_slice, orientation)
+        shapeRec = SHPC.get_reader(i_slice, "extremum", orientation)\
+                       .shapeRecord(ishape)
         prop = {"pos": shapeRec.shape.points[0], "speed": shapeRec.record.speed}
-        prop["radius"] = SHPC.get_reader(i_slice, "max_speed_contour")\
-            .record(ishape).r_eq_area
+        prop["radius"] = SHPC.get_reader(i_slice, "max_speed_contour",
+                                         orientation).record(ishape).r_eq_area
 
         if prop["radius"] < 0:
-            prop["radius"] = SHPC.get_reader(i_slice, "outermost_contour")\
+            prop["radius"] = SHPC.get_reader(i_slice, "outermost_contour",
+                                             orientation)\
                 .record(ishape).r_eq_area
 
         properties.append(prop)
@@ -129,7 +131,7 @@ for n in g.vertices():
     if n.in_degree() != 0:
         # Define properties for beginning of the segment:
         properties = node_to_prop(g.vp.inst_eddies[n][:n_days_avg], e_overestim,
-                                  SHPC)
+                                  SHPC, args.orientation)
         g.vp.first_av_rad[n], g.vp.first_av_ros[n] \
             = calculate_radii_rossby(properties)
         g.vp.pos_first[n] = properties[0]["pos"] # in degrees
@@ -147,7 +149,7 @@ for n in g.vertices():
                 # We cannot use part of properties from the beginning
                 # of the segment.
                 properties = node_to_prop(g.vp.inst_eddies[n][- n_days_avg:],
-                                          e_overestim, SHPC)
+                                          e_overestim, SHPC, args.orientation)
             else:
                 # assertion: n.in_degree() != 0 and n_days_avg <
                 # len_seg < 2 * n_days_avg
@@ -156,7 +158,7 @@ for n in g.vertices():
                 # of the segment.
                 properties = properties[len_seg - n_days_avg:] \
                     + node_to_prop(g.vp.inst_eddies[n][n_days_avg:],
-                                   e_overestim, SHPC)
+                                   e_overestim, SHPC, args.orientation)
 
             g.vp.last_av_rad[n], g.vp.last_av_ros[n] \
                 = calculate_radii_rossby(properties)

Trajectories/plot_traj.py

@@ -3,7 +3,7 @@
 import report_graph
 import random
 
-def get_extr_coord(traj, e_overestim, SHPC):
+def get_extr_coord(traj, e_overestim, SHPC, orientation):
     x = []
     y = []
 
@@ -11,15 +11,17 @@ def get_extr_coord(traj, e_overestim, SHPC):
         date_index, eddy_index = report_graph.node_to_date_eddy(node,
                                                                 e_overestim)
         i_slice = SHPC.get_slice(date_index)
-        ishape = SHPC.comp_ishape(date_index, eddy_index, i_slice)
-        shape = SHPC.get_reader(i_slice, layer = "extremum").shape(ishape)
+        ishape = SHPC.comp_ishape(date_index, eddy_index, i_slice, orientation)
+        shape = SHPC.get_reader(i_slice, layer = "extremum",
+                                orientation = orientation).shape(ishape)
         x.append(shape.points[0][0])
         y.append(shape.points[0][1])
 
     return x, y
 
-def plot_single_traj(traj, e_overestim, SHPC, ax, src_crs, annotate_flag):
-    x, y = get_extr_coord(traj, e_overestim, SHPC)
+def plot_single_traj(traj, e_overestim, SHPC, orientation, ax, src_crs,
+                     annotate_flag):
+    x, y = get_extr_coord(traj, e_overestim, SHPC, orientation)
     ax.plot(x, y, color = "red", linewidth = 0.5, transform = src_crs)
     ax.plot(x[0], y[0], marker = "s", markersize = 2, color = "black",
             transform = src_crs)
@@ -75,8 +77,8 @@ if __name__ == "__main__":
                                                  only_date = True)
         if args.min_duration == 1 or duration >= args.min_duration:
             if args.min_duration > 1: n_long_traj += 1
-            plot_single_traj(traj, e_overestim, SHPC, ax, src_crs,
-                             args.annotate)
+            plot_single_traj(traj, e_overestim, SHPC, args.orientation, ax,
+                             src_crs, args.annotate)
 
     ax.add_feature(cfeature.LAND, edgecolor = "black")
     ax.gridlines(draw_labels = True)