minor bug fix in compare module + bug fix in plot_on maps computed even if not...

minor bug fix in compare module + bug fix in plot_on maps computed even if not computed in scalar maps

requirements.txt

@@ -2,7 +2,7 @@ pandas
 matplotlib
 scikit-image
 scipy
-seaborn
+seaborn >= 0.11.2
 lmfit
 napari[all]
 tifffile

track_analyzer/plotting.py

@@ -737,8 +737,9 @@ def plot_param_hist(data_dir, param, df=None, hue=None, hue_order=None, hist=Tru
     df = df[np.isfinite(df[param])]
 
     kind = "hist" if hist else "kde"
-    g = sns.displot(data=df, x=param, hue=hue, kind=kind, kde=kde)
-    fig = g.fig
+    g = sns.displot(data=df, x=param, hue=hue, kind=kind, kde=kde,facet_kws={'legend_out':False})
+    sns.move_legend(g, "upper right", frameon=False)
+    fig = g.figure
     ax = g.ax
     fig.set_size_inches(figsize[0], figsize[1])
     ax.set_xlabel(param_label)

track_analyzer/prepare.py

@@ -26,7 +26,6 @@
 import os
 import os.path as osp
 import csv
-import time
 
 import matplotlib.pyplot as plt
 from matplotlib import cm
@@ -510,7 +509,7 @@ def pool_datasets(df_list, name_list):
         if df is None:
             continue
         df['dataset'] = name_list[i]
-        df_out = pd.concat([df_out, df])
+        df_out = pd.concat([df_out, df], ignore_index=True)
 
     return df_out
 

track_analyzer/scripts/analyze_maps.py

@@ -130,6 +130,7 @@ def map_analysis(data_dir, data=None, image=None, refresh=False, parallelize=Fal
                           plot_grid=grid_param['plot_grid'],
                           save_plot_fn=osp.join(map_dir, 'grids{}'.format(plot_config['format'])))
 
+    special_fields = ['div', 'curl', 'v_mean', 'a_mean'] # special scalar fields that need to be calculated and not interpolated 
     # Compute fields
     for i, df in enumerate(df_list):
         # name subset directory
@@ -157,7 +158,7 @@ def map_analysis(data_dir, data=None, image=None, refresh=False, parallelize=Fal
 
         # list required fields to interpolate
         all_fields = list(set(list(scalar_fields.keys()) + list(vector_fields.keys()) + list(vector_mean.keys())))
-        interp_fields = [f for f in all_fields if f not in ['div', 'curl', 'v_mean', 'a_mean']]  # fields to interpolate
+        interp_fields = [f for f in all_fields if f not in special_fields]  # fields to interpolate
         vel_fields = ['v' + d for d in dimensions]
         acc_fields = ['a' + d for d in dimensions]
 
@@ -177,11 +178,19 @@ def map_analysis(data_dir, data=None, image=None, refresh=False, parallelize=Fal
                 if af not in interp_fields:
                     interp_fields.append(af)
 
+        # add plot_on fields to fields to compute
+        plot_on_fields = []
+        for k in vector_fields.keys():
+            plot_on_f = vector_fields[k]['plot_on']
+            plot_on_fields.append(plot_on_f)
+            if plot_on_f not in interp_fields and plot_on_f not in special_fields:
+                interp_fields.append(plot_on_f)
+
         # compute data
         field_data = tca.interpolate_all_fields(data_dir, df, grids, field_values=interp_fields,
                                                 temporal_average=map_param['temporal_average'],
                                                 export_field=map_param['export_field'], outdir=sub_dir)
-        if 'div' in all_fields or 'curl' in all_fields:
+        if 'div' in all_fields or 'curl' in all_fields or 'div' in plot_on_fields or 'curl' in plot_on_fields:
             field_data = tca.compute_all_div_curl(data_dir, df, field_data, lengthscale,
                                                   export_field=map_param['export_field'], outdir=sub_dir)
         for mf in ['v_mean', 'a_mean']:

track_analyzer/scripts/compare_datasets.py

@@ -73,7 +73,7 @@ def compare_datasets(data_dir, df_list=[], track_df_list=[], MSD_df_list=[], dat
 
     if param_couples is not None:
         if len(param_couples['couples']) > 0:
-            print("plotting scatter plots")
+            print("Plotting couples of parameters...")
         for param_couple in param_couples['couples']:
             tpl.plot_param_vs_param(data_dir, param_couple[0], param_couple[1], df=pooled_all_df, hue=hue,
                                     hue_order=hue_order, set_axis_lim=param_couples['axis_lim'], plot_config=plot_config,
@@ -81,15 +81,15 @@ def compare_datasets(data_dir, df_list=[], track_df_list=[], MSD_df_list=[], dat
 
     if param_track_couples is not None:
         if len(param_track_couples['couples']) > 0:
-            print("plotting scatter plots")
+            print("Plotting couples of whole-track parameters...")
         for param_couple in param_track_couples['couples']:
             tpl.plot_param_vs_param(data_dir, param_couple[0], param_couple[1], df=pooled_track_df, hue=hue,
                                     hue_order=hue_order, set_axis_lim=param_track_couples['axis_lim'],
-                                    plot_config=plot_config, plot_dir=plot_dir, suffix='_' + names_str)
+                                    plot_config=plot_config, plot_dir=plot_dir, suffix='_' + names_str, prefix='track_')
 
     if param_hist is not None:
         if len(param_hist['param']) > 0:
-            print("plotting histograms")
+            print("Plotting parameters histograms...")
         for param in param_hist['param']:
             tpl.plot_param_hist(data_dir, param, df=pooled_all_df, hue=hue, hue_order=hue_order,
                                 hist=param_hist['hist'], kde=param_hist['kde'],
@@ -97,15 +97,15 @@ def compare_datasets(data_dir, df_list=[], track_df_list=[], MSD_df_list=[], dat
 
     if param_track_hist is not None:
         if len(param_track_hist['param']) > 0:
-            print("plotting histograms")
+            print("Plotting whole-track parameters histograms...")
         for param in param_track_hist['param']:
             tpl.plot_param_hist(data_dir, param, df=pooled_track_df, hue=hue, hue_order=hue_order,
                                 hist=param_track_hist['hist'], kde=param_track_hist['kde'],
-                                plot_config=plot_config, plot_dir=plot_dir, suffix='_' + names_str)
+                                plot_config=plot_config, plot_dir=plot_dir, suffix='_' + names_str, prefix='track_')
 
     if param_boxplot is not None:
         if len(param_boxplot['param']) > 0:
-            print("plotting boxplots")
+            print("Plotting parameters boxplots...")
         for param in param_boxplot['param']:
             tpl.plot_param_boxplot(data_dir, df=pooled_all_df, x_param=x_param, param=param, order=order,
                                    save_stat=param_boxplot['save_stat'], boxplot=param_boxplot['boxplot'],
@@ -114,12 +114,12 @@ def compare_datasets(data_dir, df_list=[], track_df_list=[], MSD_df_list=[], dat
 
     if param_track_boxplot is not None:
         if len(param_track_boxplot['param']) > 0:
-            print("plotting boxplots")
+            print("Plotting whole-track parameters boxplots...")
         for param in param_track_boxplot['param']:
             tpl.plot_param_boxplot(data_dir, df=pooled_track_df, x_param=x_param, param=param, order=order,
                                    save_stat=param_track_boxplot['save_stat'], boxplot=param_track_boxplot['boxplot'],
                                    swarmplot=param_track_boxplot['swarmplot'], plot_config=plot_config, plot_dir=plot_dir,
-                                   suffix='_' + names_str)
+                                   suffix='_' + names_str, prefix='track_')
 
     if MSD_plot_param is not None:
         # add parameters