diff --git a/code/behavior.py b/code/behavior.py index 73ddcc5..2e0eb3d 100644 --- a/code/behavior.py +++ b/code/behavior.py @@ -6,6 +6,7 @@ import matplotlib.pyplot as plt from IPython import embed from pandas import read_csv from modules.logger import makeLogger +from scipy.ndimage import gaussian_filter1d logger = makeLogger(__name__) @@ -106,7 +107,6 @@ def correct_chasing_events( logger.info('Chasing events are equal') return category, timestamps - # Correct the wrong chasing events; delete double events wrong_ids = [] for i in range(len(longer_array)-(len_diff+1)): @@ -123,6 +123,32 @@ def correct_chasing_events( return category, timestamps +def event_triggered_chirps( + event: np.ndarray, + chirps:np.ndarray, + time_before_event: int, + time_after_event: int + )-> tuple[np.ndarray, np.ndarray]: + + + + event_chirps = [] # chirps that are in specified window around event + centered_chirps = [] # timestamps of chirps around event centered on the event timepoint + + for event_timestamp in event: + start = event_timestamp - time_before_event # timepoint of window start + stop = event_timestamp + time_after_event # timepoint of window ending + chirps_around_event = [c for c in chirps if (c >= start) & (c <= stop)] # get chirps that are in a -5 to +5 sec window around event + event_chirps.append(chirps_around_event) + if len(chirps_around_event) == 0: + continue + else: + centered_chirps.append(chirps_around_event - event_timestamp) + centered_chirps = np.concatenate(centered_chirps, axis=0) # convert list of arrays to one array for plotting + + return event_chirps, centered_chirps + + def main(datapath: str): # behavior is pandas dataframe with all the data @@ -144,11 +170,6 @@ def main(datapath: str): chasing_offset = timestamps[category == 1] physical_contact = timestamps[category == 2] - ##### TODO Physical contact-triggered chirps (PTC) mit Rasterplot ##### - # Wahrscheinlichkeit von Phys auf Ch und vice versa - # Chasing-triggered chirps (CTC) mit Rasterplot - # Wahrscheinlichkeit von Chase auf Ch und vice versa - # First overview plot fig1, ax1 = plt.subplots() ax1.scatter(chirps, np.ones_like(chirps), marker='*', color='royalblue', label='Chirps') @@ -160,11 +181,41 @@ def main(datapath: str): plt.close() # Get fish ids - all_fish_ids = np.unique(chirps_fish_ids) + fish_ids = np.unique(chirps_fish_ids) + + ##### Chasing triggered chirps CTC ##### + # Evaluate how many chirps were emitted in specific time window around the chasing onset events + + # Iterate over chasing onsets (later over fish) + time_around_event = 5 # time window around the event in which chirps are counted, 5 = -5 to +5 sec around event + + #### Loop crashes at concatenate in function #### + for i in range(len(fish_ids)): + fish = fish_ids[i] + chirps = chirps[chirps_fish_ids == fish] + print(fish) + + chasing_chirps, centered_chasing_chirps = event_triggered_chirps(chasing_onset, chirps, time_around_event, time_around_event) + physical_chirps, centered_physical_chirps = event_triggered_chirps(physical_contact, chirps, time_around_event, time_around_event) + + # Kernel density estimation ??? + # centered_chasing_chirps_convolved = gaussian_filter1d(centered_chasing_chirps, 5) + + # centered_chasing = chasing_onset[0] - chasing_onset[0] ## get the 0 timepoint for plotting; set one chasing event to 0 + offsets = [0.5, 1] + fig4, ax4 = plt.subplots(figsize=(20 / 2.54, 12 / 2.54), constrained_layout=True) + ax4.eventplot(np.array([centered_chasing_chirps, centered_physical_chirps]), lineoffsets=offsets, linelengths=0.25, colors=['g', 'r']) + ax4.vlines(0, 0, 1.5, 'tab:grey', 'dashed', 'Timepoint of event') + # ax4.plot(centered_chasing_chirps_convolved) + ax4.set_yticks(offsets) + ax4.set_yticklabels(['Chasings', 'Physical \n contacts']) + ax4.set_xlabel('Time[s]') + ax4.set_ylabel('Type of event') + plt.show() # Associate chirps to inidividual fish - fish1 = chirps[chirps_fish_ids == all_fish_ids[0]] - fish2 = chirps[chirps_fish_ids == all_fish_ids[1]] + fish1 = chirps[chirps_fish_ids == fish_ids[0]] + fish2 = chirps[chirps_fish_ids == fish_ids[1]] fish = [len(fish1), len(fish2)] #### Chirp counts per fish general ##### @@ -196,36 +247,15 @@ def main(datapath: str): fig3 , ax3 = plt.subplots() ax3.bar(['Chirps in chasing events', 'Chasing events without Chirps'], [counts_chirps_chasings, chasings_without_chirps], width=width) plt.ylabel('Count') - plt.show() + # plt.show() plt.close() # comparison between chasing events with and without chirps - ##### Chasing triggered chirps CTC ##### - # Evaluate how many chirps were emitted in specific time window around the chasing onset events - - # Goal: - # Plot with Chasing onsets centered at t = 0 on x-axis as a function of event type (0, 1, 2) (or later as a function of recordings) with chirps as rasterplot in background - # Chasing onset is defined at the point event 'chasing' - # Iterate over chasing onsets (later over fish) - # Get chirps which in a time window of -5 to +5 seconds aroung the chasing onset and save them - # Set Chasing onset at timepoint 0: Chasing onset timestamp - chasing onset timestamp - # Calculate chirp timestamps relative to chasing onset: Chirp timestamp - Chasing onset timestamp - # For rasterplot look at plt.eventplot() function - # Do the plot - # Then same with physical onset events (PTC) - - - - - - - embed() - - + exit()