import os import numpy as np 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__) class Behavior: """Load behavior data from csv file as class attributes Attributes ---------- behavior: 0: chasing onset, 1: chasing offset, 2: physical contact behavior_type: behavioral_category: comment_start: comment_stop: dataframe: pandas dataframe with all the data duration_s: media_file: observation_date: observation_id: start_s: start time of the event in seconds stop_s: stop time of the event in seconds total_length: """ def __init__(self, folder_path: str) -> None: LED_on_time_BORIS = np.load(os.path.join(folder_path, 'LED_on_time.npy'), allow_pickle=True) self.time = np.load(os.path.join(folder_path, "times.npy"), allow_pickle=True) csv_filename = [f for f in os.listdir(folder_path) if f.endswith('.csv')][0] # check if there are more than one csv file self.dataframe = read_csv(os.path.join(folder_path, csv_filename)) self.chirps = np.load(os.path.join(folder_path, 'chirps.npy'), allow_pickle=True) self.chirps_ids = np.load(os.path.join(folder_path, 'chirps_ids.npy'), allow_pickle=True) for k, key in enumerate(self.dataframe.keys()): key = key.lower() if ' ' in key: key = key.replace(' ', '_') if '(' in key: key = key.replace('(', '') key = key.replace(')', '') setattr(self, key, np.array(self.dataframe[self.dataframe.keys()[k]])) last_LED_t_BORIS = LED_on_time_BORIS[-1] real_time_range = self.time[-1] - self.time[0] factor = 1.034141 shift = last_LED_t_BORIS - real_time_range * factor self.start_s = (self.start_s - shift) / factor self.stop_s = (self.stop_s - shift) / factor """ 1 - chasing onset 2 - chasing offset 3 - physical contact event temporal encpding needs to be corrected ... not exactly 25FPS. ### correspinding python code ### factor = 1.034141 LED_on_time_BORIS = np.load(os.path.join(folder_path, 'LED_on_time.npy'), allow_pickle=True) last_LED_t_BORIS = LED_on_time_BORIS[-1] real_time_range = times[-1] - times[0] shift = last_LED_t_BORIS - real_time_range * factor data = pd.read_csv(os.path.join(folder_path, file[1:-7] + '.csv')) boris_times = data['Start (s)'] data_times = [] for Cevent_t in boris_times: Cevent_boris_times = (Cevent_t - shift) / factor data_times.append(Cevent_boris_times) data_times = np.array(data_times) behavior = data['Behavior'] """ def correct_chasing_events( category: np.ndarray, timestamps: np.ndarray ) -> tuple[np.ndarray, np.ndarray]: onset_ids = np.arange( len(category))[category == 0] offset_ids = np.arange( len(category))[category == 1] # Check whether on- or offset is longer and calculate length difference if len(onset_ids) > len(offset_ids): len_diff = len(onset_ids) - len(offset_ids) longer_array = onset_ids shorter_array = offset_ids logger.info(f'Onsets are greater than offsets by {len_diff}') elif len(onset_ids) < len(offset_ids): len_diff = len(offset_ids) - len(onset_ids) longer_array = offset_ids shorter_array = onset_ids logger.info(f'Offsets are greater than offsets by {len_diff}') elif len(onset_ids) == len(offset_ids): 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)): if (shorter_array[i] > longer_array[i]) & (shorter_array[i] < longer_array[i+1]): pass else: wrong_ids.append(longer_array[i]) longer_array = np.delete(longer_array, i) category = np.delete( category, wrong_ids) timestamps = np.delete( timestamps, wrong_ids) 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 bh = Behavior(datapath) # chirps are not sorted in time (presumably due to prior groupings) # get and sort chirps and corresponding fish_ids of the chirps chirps = bh.chirps[np.argsort(bh.chirps)] chirps_fish_ids = bh.chirps_ids[np.argsort(bh.chirps)] category = bh.behavior timestamps = bh.start_s # Correct for doubles in chasing on- and offsets to get the right on-/offset pairs # Get rid of tracking faults (two onsets or two offsets after another) category, timestamps = correct_chasing_events(category, timestamps) # split categories chasing_onset = timestamps[category == 0] chasing_offset = timestamps[category == 1] physical_contact = timestamps[category == 2] # First overview plot fig1, ax1 = plt.subplots() ax1.scatter(chirps, np.ones_like(chirps), marker='*', color='royalblue', label='Chirps') ax1.scatter(chasing_onset, np.ones_like(chasing_onset)*2, marker='.', color='forestgreen', label='Chasing onset') ax1.scatter(chasing_offset, np.ones_like(chasing_offset)*2.5, marker='.', color='firebrick', label='Chasing offset') ax1.scatter(physical_contact, np.ones_like(physical_contact)*3, marker='x', color='black', label='Physical contact') plt.legend() # plt.show() plt.close() # Get 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 == fish_ids[0]] fish2 = chirps[chirps_fish_ids == fish_ids[1]] fish = [len(fish1), len(fish2)] ### Plots: # 1. All recordings, all fish, all chirps # One CTC, one PTC # 2. All recordings, only winners # One CTC, one PTC # 3. All recordings, all losers # One CTC, one PTC #### Chirp counts per fish general ##### fig2, ax2 = plt.subplots() x = ['Fish1', 'Fish2'] width = 0.35 ax2.bar(x, fish, width=width) ax2.set_ylabel('Chirp count') # plt.show() plt.close() ##### Count chirps emitted during chasing events and chirps emitted out of chasing events ##### chirps_in_chasings = [] for onset, offset in zip(chasing_onset, chasing_offset): chirps_in_chasing = [c for c in chirps if (c > onset) & (c < offset)] chirps_in_chasings.append(chirps_in_chasing) # chirps out of chasing events counts_chirps_chasings = 0 chasings_without_chirps = 0 for i in chirps_in_chasings: if i: chasings_without_chirps += 1 else: counts_chirps_chasings += 1 # chirps in chasing events 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.close() # comparison between chasing events with and without chirps embed() exit() if __name__ == '__main__': # Path to the data datapath = '../data/mount_data/2020-05-13-10_00/' main(datapath)