Change of default behavior for MAXIMA_THRESHOLD_WINDOW

- MAXIMA_THRESHOLD_WINDOW has now a default value equal to 'None', corresponding to set it equal to the entire signal duration. Also accepts float values.
- Little fix involving plot_minima function in minima.py script, now plotting the interpolated position of minima when required.

pipeline/stage03_trigger_detection/Snakefile

@@ -13,7 +13,7 @@ def filtered_triggers(wildcards):
     return prev_rule_output(wildcards, rule_list=config.TRIGGER_FILTER,
                             default_input=default_input)
 
-#### UTILTY BLOCKS ####
+#### UTILITY BLOCKS ####
 
 use rule template_all as all with:
     input:

pipeline/stage03_trigger_detection/configs/config_template.yaml

@@ -66,7 +66,8 @@ MIN_PEAK_DISTANCE: 0.28
 # amplitude fraction to set the threshold detecting local maxima
 MAXIMA_THRESHOLD_FRACTION: .5
 # time window to use to set the threshold detecting local maxima (s)
-MAXIMA_THRESHOLD_WINDOW: 3
+# default value 'None' is meant to set the time window equal to the entire signal length
+MAXIMA_THRESHOLD_WINDOW: 'None'
 # minimum time the signal must be increasing after a minima candidate (s)
 MINIMA_PERSISTENCE: 0.16
 

pipeline/stage03_trigger_detection/scripts/minima.py

@@ -140,8 +140,8 @@ def plot_minima(asig, event, channel, maxima_threshold_window,
 
     idx_ch = np.where(event.array_annotations['channels'] == channel)[0]
 
-    ax.plot(times[peaks], signal[peaks], 'x', color='r', label='detected maxima') 
-    ax.plot(event.times[idx_ch], signal[(event.times[idx_ch]*sampling_rate).astype(int)], 
+    ax.plot(times[peaks], signal[peaks], 'x', color='r', label='detected maxima')
+    ax.plot(event.times[idx_ch], np.interp(event.times[idx_ch], times, signal), 
             'x', color='g', label='selected minima')
 
     ax.set_title(f'channel {channel}')
@@ -164,8 +164,8 @@ def plot_minima(asig, event, channel, maxima_threshold_window,
                      help="minimum time minima (s)")
     CLI.add_argument("--maxima_threshold_fraction", nargs='?', type=float, default=0.5,
                      help="amplitude fraction to set the threshold detecting local maxima")
-    CLI.add_argument("--maxima_threshold_window", nargs='?', type=int, default=2,
-                     help="time window to use to set the threshold detecting local maxima [s]")
+    CLI.add_argument("--maxima_threshold_window", nargs='?', type=none_or_float, default=None,
+                     help="time window to use to set the threshold detecting local maxima (s)")
     CLI.add_argument("--min_peak_distance", nargs='?', type=float, default=0.200,
                      help="minimum distance between peaks (s)")
     CLI.add_argument("--img_dir", nargs='?', type=Path,
@@ -183,13 +183,16 @@ def plot_minima(asig, event, channel, maxima_threshold_window,
 
     block = load_neo(args.data)
     asig = block.segments[0].analogsignals[0]
+
+    if args.maxima_threshold_window is None or args.maxima_threshold_window > asig.t_stop - asig.t_start:
+         args.maxima_threshold_window = asig.t_stop - asig.t_start
 
     transition_event = detect_minima(asig,
-                                     interpolation_points=args.num_interpolation_points,
-                                     maxima_threshold_fraction=args.maxima_threshold_fraction,
-                                     maxima_threshold_window=args.maxima_threshold_window,
-                                     min_peak_distance=args.min_peak_distance,
-                                     minima_persistence=args.minima_persistence)
+                                     interpolation_points = args.num_interpolation_points,
+                                     maxima_threshold_fraction = args.maxima_threshold_fraction,
+                                     maxima_threshold_window = args.maxima_threshold_window,
+                                     min_peak_distance = args.min_peak_distance,
+                                     minima_persistence = args.minima_persistence)
 
     block.segments[0].events.append(transition_event)
 
@@ -200,7 +203,7 @@ def plot_minima(asig, event, channel, maxima_threshold_window,
             plot_minima(asig=time_slice(asig, args.plot_tstart, args.plot_tstop),
                         event=time_slice(transition_event, args.plot_tstart, args.plot_tstop),
                         channel=int(channel),
-                        maxima_threshold_window = args.maxima_threshold_window,
+                        maxima_threshold_window = min(args.maxima_threshold_window, args.plot_tstop-args.plot_tstart),
                         maxima_threshold_fraction = args.maxima_threshold_fraction, 
                         min_peak_distance = args.min_peak_distance)
             output_path = args.img_dir / args.img_name.replace('_channel0', f'_channel{channel}')