129 lines
4.4 KiB
Python
129 lines
4.4 KiB
Python
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
|
|
from modules.behaviour_handling import Behavior, correct_chasing_events
|
|
|
|
from extract_chirps import get_valid_datasets
|
|
ps = PlotStyle()
|
|
|
|
logger = makeLogger(__name__)
|
|
|
|
|
|
def main(datapath: str):
|
|
foldernames = [
|
|
datapath + x + '/' for x in os.listdir(datapath) if os.path.isdir(datapath+x)]
|
|
foldernames, _ = get_valid_datasets(datapath)
|
|
|
|
for foldername in foldernames[3:4]:
|
|
print(foldername)
|
|
# foldername = foldernames[0]
|
|
if foldername == '../data/mount_data/2020-05-12-10_00/':
|
|
continue
|
|
# behabvior is pandas dataframe with all the data
|
|
bh = Behavior(foldername)
|
|
# 2020-06-11-10
|
|
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(bh.chirps_ids)
|
|
fish1_id = all_fish_ids[0]
|
|
fish2_id = all_fish_ids[1]
|
|
# Associate chirps to inidividual fish
|
|
fish1 = (bh.chirps[bh.chirps_ids == fish1_id] / 60) / 60
|
|
fish2 = (bh.chirps[bh.chirps_ids == fish2_id] / 60) / 60
|
|
embed()
|
|
exit()
|
|
fish1_color = ps.gblue2
|
|
fish2_color = ps.gblue1
|
|
fig, ax = plt.subplots(5, 1, figsize=(
|
|
21*ps.cm, 10*ps.cm), height_ratios=[0.5, 0.5, 0.5, 0.2, 6], sharex=True)
|
|
# marker size
|
|
s = 80
|
|
ax[0].scatter(physical_contact, np.ones(
|
|
len(physical_contact)), color=ps.gray, marker='|', s=s)
|
|
ax[1].scatter(chasing_onset, np.ones(len(chasing_onset)),
|
|
color=ps.gray, 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[4].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[4].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[4].axvspan(0, 3, 0, 5, facecolor='grey', alpha=0.5)
|
|
ax[4].set_xticks(np.arange(0, 6.1, 0.5))
|
|
ps.hide_ax(ax[3])
|
|
|
|
labelpad = 30
|
|
fsize = 12
|
|
|
|
ax[0].set_ylabel('Contact', rotation=0,
|
|
labelpad=labelpad, fontsize=fsize)
|
|
ax[0].yaxis.set_label_coords(-0.062, -0.08)
|
|
ax[1].set_ylabel('Chasing', rotation=0,
|
|
labelpad=labelpad, fontsize=fsize)
|
|
ax[1].yaxis.set_label_coords(-0.06, -0.08)
|
|
ax[2].set_ylabel('Chirps', rotation=0,
|
|
labelpad=labelpad, fontsize=fsize)
|
|
ax[2].yaxis.set_label_coords(-0.07, -0.08)
|
|
ax[4].set_ylabel('EODf')
|
|
|
|
ax[4].set_xlabel('Time [h]')
|
|
# ax[0].set_title(foldername.split('/')[-2])
|
|
# 2020-03-31-9_59
|
|
plt.subplots_adjust(left=0.158, right=0.987, top=0.918, bottom=0.136)
|
|
plt.savefig('../poster/figs/timeline.svg')
|
|
plt.show()
|
|
|
|
# plot chirps
|
|
|
|
|
|
if __name__ == '__main__':
|
|
# Path to the data
|
|
datapath = '../data/mount_data/'
|
|
main(datapath)
|