bug fix: map plotting supports vlim different from None

track_analyzer/plotting.py

@@ -981,11 +981,17 @@ def plot_all_scalar_fields(data_dir, df, data, field, image={'image_fn': None, '
 
     # get vlim
     map_param_ = dict(map_param)
+    vlim_default = tca.compute_vlim(df, data, field)
+
     if map_param_['vlim'] is None:
-        vlim = tca.compute_vlim(df, data, field)
-        map_param_['vlim'] = vlim
+        map_param_['vlim'] = vlim_default
+    else: 
+        for i,vl in enumerate(map_param_['vlim']):
+            if vl is None:
+                map_param_['vlim'][i] = vlim_default[i]
+
     label = tpr.make_param_label(field, l_unit=info['length_unit'], t_unit=info['time_unit'])
-    plot_cmap(plot_dir, label, map_param_['cmap'], vlim[0], vlim[1])
+    plot_cmap(plot_dir, label, map_param_['cmap'], map_param_['vlim'][0], map_param_['vlim'][1])
 
     for frame in df['frame'].unique():
         frame = int(frame)
@@ -1011,11 +1017,16 @@ def plot_all_vector_fields(data_dir, df, data, field, plot_on_field=None, dim=3,
 
     # get vlim
     if plot_on_field is not None:
+        vlim_default = tca.compute_vlim(df, data, plot_on_field['plot_on'])
         if plot_on_field['vlim'] is None:
-            vlim = tca.compute_vlim(df, data, plot_on_field['plot_on'])
-            plot_on_field['vlim'] = vlim
-            label = tpr.make_param_label(plot_on_field['plot_on'], l_unit=info['length_unit'], t_unit=info['time_unit'])
-            plot_cmap(plot_dir, label, plot_on_field['cmap'], vlim[0], vlim[1])
+            plot_on_field['vlim'] = vlim_default
+        else: 
+            for i,vl in enumerate(plot_on_field['vlim']):
+                if vl is None:
+                    plot_on_field['vlim'][i] = vlim_default[i]
+
+        label = tpr.make_param_label(plot_on_field['plot_on'], l_unit=info['length_unit'], t_unit=info['time_unit'])
+        plot_cmap(plot_dir, label, plot_on_field['cmap'], plot_on_field['vlim'][0], plot_on_field['vlim'][1])
 
     for frame in df['frame'].unique():
         frame = int(frame)
@@ -1056,12 +1067,16 @@ def plot_all_Voronoi(data_dir, df, data, show_local_area=True, df_mean = None,
     # get vlim
     if show_local_area:
         if 'area' in df.columns:
+            vlim_default = [df['area'].min(), df['area'].max()]
             if map_param['vlim'] is None:
-                vlim = [df['area'].min(), df['area'].max()]
-                if vlim == [np.nan, np.nan]:
+                if vlim_default == [np.nan, np.nan]:
                     show_local_area = False
                 else:
-                    map_param['vlim'] = vlim
+                    map_param['vlim'] = vlim_default
+            else: 
+                for i,vl in enumerate(map_param['vlim']):
+                    if vl is None:
+                        map_param['vlim'][i] = vlim_default[i]
         else:
             show_local_area = False