diff --git a/code/plot_event_timeline.py b/code/plot_event_timeline.py new file mode 100644 index 0000000..6c984be --- /dev/null +++ b/code/plot_event_timeline.py @@ -0,0 +1,203 @@ +import numpy as np + +import os + +import numpy as np +import matplotlib.pyplot as plt +from thunderfish.powerspectrum import decibel + +from IPython import embed +from pandas import read_csv +from modules.logger import makeLogger +from modules.plotstyle import PlotStyle + +ps = PlotStyle() + +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) + + csv_filename = [f for f in os.listdir(folder_path) if f.endswith('.csv')][0] + logger.info(f'CSV file: {csv_filename}') + 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) + + self.ident = np.load(os.path.join(folder_path, 'ident_v.npy'), allow_pickle=True) + self.idx = np.load(os.path.join(folder_path, 'idx_v.npy'), allow_pickle=True) + self.freq = np.load(os.path.join(folder_path, 'fund_v.npy'), allow_pickle=True) + self.time = np.load(os.path.join(folder_path, "times.npy"), allow_pickle=True) + self.spec = np.load(os.path.join(folder_path, "spec.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 + +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 main(datapath: str): + # behabvior 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]/ 60) /60 + chasing_offset = (timestamps[category == 1]/ 60) /60 + physical_contact = (timestamps[category == 2] / 60) /60 + + all_fish_ids = np.unique(chirps_fish_ids) + fish1_id = all_fish_ids[0] + fish2_id = all_fish_ids[1] + # Associate chirps to inidividual fish + fish1 = (chirps[chirps_fish_ids == fish1_id] / 60) /60 + fish2 = (chirps[chirps_fish_ids == fish2_id] / 60) /60 + fish1_color = ps.red + fish2_color = ps.orange + + fig, ax = plt.subplots(4, 1, figsize=(10, 5), height_ratios=[0.5, 0.5, 0.5, 6], sharex=True) + # marker size + s = 200 + ax[0].scatter(physical_contact, np.ones(len(physical_contact)), color='firebrick', marker='|', s=s) + ax[1].scatter(chasing_onset, np.ones(len(chasing_onset)), color='green', marker='|', s=s ) + ax[2].scatter(fish1, np.ones(len(fish1))-0.25, color=fish1_color, marker='|', s=s) + ax[2].scatter(fish2, np.zeros(len(fish2))+0.25, color=fish2_color, marker='|', s=s) + + + freq_temp = bh.freq[bh.ident==fish1_id] + time_temp = bh.time[bh.idx[bh.ident==fish1_id]] + ax[3].plot((time_temp/ 60) /60, freq_temp, color=fish1_color) + + freq_temp = bh.freq[bh.ident==fish2_id] + time_temp = bh.time[bh.idx[bh.ident==fish2_id]] + ax[3].plot((time_temp/ 60) /60, freq_temp, color=fish2_color) + + #ax[3].imshow(decibel(bh.spec), extent=[bh.time[0]/60/60, bh.time[-1]/60/60, 0, 2000], aspect='auto', origin='lower') + + # Hide grid lines + ax[0].grid(False) + ax[0].set_frame_on(False) + ax[0].set_xticks([]) + ax[0].set_yticks([]) + ps.hide_ax(ax[0]) + + + ax[1].grid(False) + ax[1].set_frame_on(False) + ax[1].set_xticks([]) + ax[1].set_yticks([]) + ps.hide_ax(ax[1]) + + ax[2].grid(False) + ax[2].set_frame_on(False) + ax[2].set_yticks([]) + ax[2].set_xticks([]) + ps.hide_ax(ax[2]) + + + + ax[3].axvspan(0, 3, 0, 5, facecolor='grey', alpha=0.5) + ax[3].set_xticks(np.arange(0, 6.1, 0.5)) + + labelpad = 40 + ax[0].set_ylabel('Physical contact', rotation=0, labelpad=labelpad) + ax[1].set_ylabel('Chasing events', rotation=0, labelpad=labelpad) + ax[2].set_ylabel('Chirps', rotation=0, labelpad=labelpad) + ax[3].set_ylabel('EODf') + + ax[3].set_xlabel('Time [h]') + + plt.show() + embed() + + # plot chirps + + +if __name__ == '__main__': + # Path to the data + datapath = '../data/mount_data/2020-05-13-10_00/' + main(datapath)