Update batch simulation plotting and run() docstring

Co-authored-by: Nicholas Tolley <[email protected]>
Signed-off-by: samadpls <[email protected]>

examples/howto/plot_batch_simulate.py

@@ -110,27 +110,32 @@ def summary_func(results):
 # backend='dask' if installed
 print("Simulation results:", simulation_results)
 ###############################################################################
-# Extract and Plot Results
-###############################################################################
+# This plot shows an overlay of all smoothed dipole waveforms from the
+# batch simulation. Each line represents a different set of parameters,
+# allowing us to visualize the range of responses across the parameter space.
+
 
-# Extract and overlay dipole waveforms
 dpl_waveforms = []
 for data_list in simulation_results['simulated_data']:
     for data in data_list:
-        dpl_waveforms.append(data['dpl'][0].data['agg'].copy().smooth(30))
+        window_len = 30
+        dpl_smooth = data['dpl'][0].copy().smooth(window_len)
+        dpl_waveforms.append(dpl_smooth.data['agg'])
 
 plt.figure(figsize=(10, 6))
 for waveform in dpl_waveforms:
-    plt.plot(waveform, alpha=0.5)
+    plt.plot(waveform, alpha=0.5, linewidth=3)
 plt.title('Overlay of Dipole Waveforms')
 plt.xlabel('Time (ms)')
 plt.ylabel('Dipole Amplitude (nAm)')
 plt.grid(True)
 plt.tight_layout()
-plt.savefig("image.png")
 plt.show()
+###############################################################################
+# This plot displays the minimum and maximum dipole peaks across
+# different synaptic strengths. This allows us to see how the range of
+# dipole activity changes as we vary the synaptic strength parameter.
 
-# Extract min and max peaks for plotting
 min_peaks, max_peaks, param_values = [], [], []
 for summary_list, data_list in zip(simulation_results['summary_statistics'],
                                    simulation_results['simulated_data']):

hnn_core/batch_simulate.py

@@ -179,9 +179,15 @@ def run(self, param_grid, return_output=True,
         Returns
         -------
         results : dict
-            Dictionary containing summary statistics and simulation data
-            if return_output is True and clear_cache is False. Otherwise,
-            a dictionary containing only summary statistics.
+            Dictionary containing 'summary_statistics' and optionally
+            'simulated_data'.
+            'simulated_data' may include keys: 'dpl', 'lfp', 'spikes',
+            'voltages', 'param_values', 'net', 'times'.
+
+        Notes
+        -----
+        Return content depends on summary_func, return_output, and
+        clear_cache settings.
 
         """
         _validate_type(param_grid, types=(dict,), item_name='param_grid')