Merge branch 'master' into alex

code/chirpdetection.py

@@ -187,22 +187,9 @@ def main(datapath: str) -> None:
         # start_index = t0 * data.samplerate
         # stop_index = (t0 + dt) * data.samplerate
 
-        fig, axs = plt.subplots(
-            7,
-            2,
-            figsize=(20 / 2.54, 12 / 2.54),
-            constrained_layout=True,
-            sharex=True,
-            sharey='row',
-        )
-
         # iterate through all fish
         for i, track_id in enumerate(np.unique(ident[~np.isnan(ident)])[:2]):
 
-            # load region of interest of raw data file
-            data_oi = data[start_index:stop_index, :]
-            time_oi = raw_time[start_index:stop_index]
-
             # get indices for time array in time window
             window_index = np.arange(len(idx))[
                 (ident == track_id) & (time[idx] >= t0) & (
@@ -220,10 +207,25 @@ def main(datapath: str) -> None:
             if len(freq_temp) < expected_duration * 0.9:
                 continue
 
+            fig, axs = plt.subplots(
+                7,
+                config.electrodes,
+                figsize=(20 / 2.54, 12 / 2.54),
+                constrained_layout=True,
+                sharex=True,
+                sharey='row',
+            )
             # get best electrode
-            electrode = np.argsort(np.nanmean(powers_temp, axis=0))[-1]
+            best_electrodes = np.argsort(np.nanmean(
+                powers_temp, axis=0))[-config.electrodes:]
             # <------------------------------------------ Iterate through electrodes
 
+            for i, electrode in enumerate(best_electrodes):
+
+                # load region of interest of raw data file
+                data_oi = data[start_index:stop_index, :]
+                time_oi = raw_time[start_index:stop_index]
+
                 # plot wavetracker tracks to spectrogram
                 # for track_id in np.unique(ident):  # <---------- Find freq gaps later
                 # here
@@ -424,7 +426,8 @@ def main(datapath: str) -> None:
                 axs[3, i].set_title("Fitered above")
                 axs[4, i].set_title("Filtered envelope of baseline envelope")
                 axs[5, i].set_title("Search envelope")
-            axs[6, i].set_title("Filtered absolute instantaneous frequency")
+                axs[6, i].set_title(
+                    "Filtered absolute instantaneous frequency")
 
             plt.show()
 

code/chirpdetector_conf.yml

@@ -1,6 +1,7 @@
 # Duration and overlap of the analysis window in seconds
 window: 5
-overlap: 0.5
+overlap: 1
+edges: 0.25
 
 # Number of electrodes to go over
 electrodes: 3