improve notebook comments

track_analyzer/prepare.py

@@ -1301,7 +1301,6 @@ def get_image(data_dir, filename=None, verbose=False):
                                                                                                               y_size,
                                                                                                               t_size,
                                                                                                               z_size))
-                print("If the time and z dimensions are mixed up, you can swap them.")
 
         image_dict = {'image_fn': filename, 't_dim': t_dim, 'z_dim': z_dim, 'image_size': im.shape[-2:]}
     else:

track_analyzer/scripts/analyze_tracks.py

@@ -77,7 +77,7 @@ def make_traj_config(data_dir=None,export_config=True):
                    # list of variables averaged along the whole track to be plotted in histogram
                    }
 
-    centered_traj_config = {'run': True,  # run plot_centered_traj
+    total_traj_config = {'run': True,  # run plot_centered_traj
                             'hide_labels': False,  # hide trajectory ID
                             'label_size': 5,  # label size in points if hide_labels is False
                             'dont_center': False,  # to keep initial position at its true position
@@ -93,7 +93,7 @@ def make_traj_config(data_dir=None,export_config=True):
               'MSD_config': MSD_config,
               'scatter_config': scatter_config,
               'hist_config': hist_config,
-              'centered_traj_config': centered_traj_config
+              'total_traj_config': total_traj_config
               }
 
     if export_config:
@@ -134,7 +134,7 @@ def traj_analysis(data_dir, data=None, image=None, refresh=False, parallelize=Fa
     traj_config = traj_config_default if traj_config is None else traj_config
     
     # check that all configs are in traj_confign, if not load default
-    for key in ["traj_config_","MSD_config","scatter_config","hist_config","centered_traj_config"]:
+    for key in ["traj_config_","MSD_config","scatter_config","hist_config","total_traj_config"]:
         if key not in traj_config.keys():
             traj_config[key] = traj_config_default[key]
 
@@ -142,7 +142,7 @@ def traj_analysis(data_dir, data=None, image=None, refresh=False, parallelize=Fa
     MSD_config = traj_config["MSD_config"]
     scatter_config = traj_config["scatter_config"]
     hist_config = traj_config["hist_config"]
-    centered_traj_config = traj_config["centered_traj_config"]
+    total_traj_config = traj_config["total_traj_config"]
 
     ### Filter data
 
@@ -215,10 +215,10 @@ def traj_analysis(data_dir, data=None, image=None, refresh=False, parallelize=Fa
                 tpl.plot_param_vs_param(data_dir, x_param, y_param, df_prop, plot_dir=sub_dir, plot_config=plot_config,
                                         prefix='track_')
 
-        if centered_traj_config['run']:
-            print("Plotting centered trajectories")
-            tpl.plot_centered_traj(data_dir, df, dim=dim, plot_dir=sub_dir, plot_config=plot_config,
-                                   specific_config=centered_traj_config)
+        if total_traj_config['run']:
+            print("Plotting total trajectories")
+            tpl.plot_total_traj(data_dir, df, dim=dim, plot_dir=sub_dir, plot_config=plot_config,
+                                   specific_config=total_traj_config)
 
     return df_list
 
@@ -285,7 +285,7 @@ def main(args=None):
 
     # get traj_config
     traj_config = {}
-    for key in ["traj_config_","MSD_config","scatter_config","hist_config","centered_traj_config"]:
+    for key in ["traj_config_","MSD_config","scatter_config","hist_config","total_traj_config"]:
         if key in config.keys():
             traj_config[key] = config[key]