import os import numpy as np from IPython import embed from pandas import read_csv import matplotlib.pyplot as plt 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 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_ids = bh.chirps_ids[np.argsort(bh.chirps)] category = bh.behavior timestamps = bh.start_s # split categories chasing_onset = timestamps[category == 0] chasing_offset = timestamps[category == 1] physical_contact = timestamps[category == 2] # 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 fig, ax = plt.subplots() ax.scatter(chirps, np.ones_like(chirps), marker='*', color='royalblue', label='Chirps') ax.scatter(chasing_onset, np.ones_like(chasing_onset)*2, marker='.', color='forestgreen', label='Chasing onset') ax.scatter(chasing_offset, np.ones_like(chasing_offset)*2.5, marker='.', color='firebrick', label='Chasing offset') ax.scatter(physical_contact, np.ones_like(physical_contact)*3, marker='x', color='black', label='Physical contact') plt.legend() plt.show() embed() exit() if __name__ == '__main__': # Path to the data datapath = '../data/mount_data/2020-05-13-10_00/' main(datapath)