- Author:
- David Nickerson <david.nickerson@gmail.com>
- Date:
- 2021-11-25 11:13:34+13:00
- Desc:
- making internal links in overview relative instead of absolute
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/702/rawfile/430939c5c1b887fcf0d899b0dd11370b77bf495f/Experiments/fig3-new.py
import os
import matplotlib
matplotlib.use('agg')
import numpy as np
import matplotlib.pyplot as plt
import opencor as opencor
# root = "C:/Nima/ABI/Physiome Journal/pluripotent stem cell/src/cellml/Channels/"
def load_sedml(filename):
return opencor.open_simulation(filename)
def get_data(filename):
data = filename.data()
data.set_ending_point(10)
data.set_point_interval(1)
return data
def run_sim(data, filename, var1, var2):
voltage = np.arange(-150, 51, 1)
x1_list = [99.1744, 1.1541e+03, 1.080458e+02, 1.169173e+02, 0.0063, 0.0037, 0.0036, 9.6060e-04, 6.4626e-04, 6.1214e-04, 5.1226e-04, 2.7837e-04]
x2_list = [12.8324, 7.9836, 13.1070, 13.3819, -21.6256, -20.7042, -19.8394, -17.1882, -69.4174, -70.7590, -66.5838, -59.575]
x5_list = [0.0039, 2.2902e-04, 0.0023, 7.8562e-04, 1.7575e4, 4.04e3, 9.6633e+03, 8.0546e3, 1.7575e+04, 4.0423e3, 9.6633e+03, 8.0546e+03]
x6_list = [-8.2139, -6.4445, -7.9177, -7.6216, 6.7241, 8.7507, 7.3955, 8.8259, 6.7241, 8.7507, 7.3955, 8.8259]
x7_list = [0.0374, 0.0289, 0.0320, 0.0296, 0.2, 0.1496, 0.1673, 0.1524, 1.3219, 0.78967, 0.9511, 0.7417]
key_ids = ["one", "two", "three", "four", "five", "six", "seven", "eight", "nine", "ten", "eleven", "twelve"]
results1 = {}
results2 = {}
file = load_sedml(filename)
for x1, x2, x5, x6, x7, index in zip(x1_list, x2_list, x5_list, x6_list, x7_list, key_ids):
file.reset(True)
file.clear_results()
data.constants()["main/x1"] = x1
data.constants()["main/x2"] = x2
data.constants()["main/x5"] = x5
data.constants()["main/x6"] = x6
data.constants()["main/x7"] = x7
results1[index] = []
results2[index] = []
for v in voltage:
data.constants()["main/v"] = v
file.run()
ds = file.results().data_store()
value1 = (ds.voi_and_variables()["main/%s" % var1].values()[-1])
value2 = ds.voi_and_variables()["main/%s" % var2].values()[-1]
results1[index].append(value1)
results2[index].append(value2)
return results1, results2
if __name__ == '__main__':
act_inact_file = "act_inact.sedml"
# inact_file = "inact.sedml"
act_inact = load_sedml(act_inact_file)
# inact = load_sedml(inact_file)
data1 = get_data(act_inact)
# data2 = get_data(inact)
#
act_inact_list = run_sim(data1, act_inact_file, 'act_inact', 'tau')
# inact_list = run_sim(data2, inact_file,'inact', 'tau_h')
# tau_m_list = run_sim(data1, act_file, 'tau_m')
# tau_h_list = run_sim(data2, inact_file, 'tau_h')
voltage = np.arange(-150, 51, 1)
for i in voltage:
act_inact_list[0]['one'][i] = (act_inact_list[0]['one'][i])**3
act_inact_list[0]['two'][i] = (act_inact_list[0]['two'][i]) ** 3
act_inact_list[0]['three'][i] = (act_inact_list[0]['three'][i]) ** 3
act_inact_list[0]['four'][i] = (act_inact_list[0]['four'][i]) ** 3
act_inact_list[0]['five'][i] = (act_inact_list[0]['five'][i]) ** 2
act_inact_list[0]['six'][i] = (act_inact_list[0]['six'][i]) ** 2
act_inact_list[0]['seven'][i] = (act_inact_list[0]['seven'][i]) ** 2
act_inact_list[0]['eight'][i] = (act_inact_list[0]['eight'][i]) ** 2
plt.figure(figsize= (15,13))
plt.subplot(2,2,1)
plt.plot(voltage, (act_inact_list[0]['one']), color='blue', label= 'Ma et al.', linewidth= 4)
plt.plot(voltage, (act_inact_list[0]['five']), color= 'blue', linewidth= 4)
plt.plot(voltage, (act_inact_list[0]['two']), color='purple', label= 'Jalife Immature', linewidth= 4)
plt.plot(voltage, (act_inact_list[0]['six']), color='purple', linewidth= 4)
plt.plot(voltage, (act_inact_list[0]['three']), color= 'black', label= 'Baseline Model', linewidth= 4)
plt.plot(voltage, (act_inact_list[0]['seven']), color='black', linewidth= 4)
plt.plot(voltage, (act_inact_list[0]['four']), color='green', label= 'Jalife Mature', linewidth= 4)
plt.plot(voltage, (act_inact_list[0]['eight']), color='green', linewidth= 4)
plt.xlabel('Voltage (mV)', fontsize= 18)
plt.ylabel('Normalized I$_{Na}$', fontsize= 18)
plt.tick_params(axis='both', labelsize=18)
plt.xlim(-150,50,50)
plt.ylim(0,1,0.1)
plt.title('A', fontsize=18)
plt.legend(fontsize= '15')
plt.subplot(2,2,2)
plt.plot(voltage, act_inact_list[1]['one'], color='blue', label='Ma et al.', linewidth=4)
plt.plot(voltage, act_inact_list[1]['two'], color='purple', label='Jalife Immature', linewidth=4)
plt.plot(voltage, act_inact_list[1]['three'], color='black', label='Baseline Model', linewidth=4)
plt.plot(voltage, act_inact_list[1]['four'], color='green', label='Jalife Mature', linewidth=4)
plt.xlabel('Voltage (mV)', fontsize=18)
plt.ylabel('Tau$_m$ (ms)', fontsize=18)
plt.tick_params(axis='both', labelsize=18)
plt.xlim(-150, 50, 50)
plt.ylim(0, 0.5, 0.05)
plt.title('C', fontsize=18)
#
plt.subplot(2,2,3)
plt.plot(voltage, act_inact_list[1]['five'], color='blue', label='Ma et al.', linewidth=4)
plt.plot(voltage, act_inact_list[1]['six'], color='purple', label='Jalife Immature', linewidth=4)
plt.plot(voltage, act_inact_list[1]['seven'], color='black', label='Baseline Model', linewidth=4)
plt.plot(voltage, act_inact_list[1]['eight'], color='green', label='Jalife Mature', linewidth=4)
plt.xlabel('Voltage (mV)', fontsize=18)
plt.ylabel('Tau$_h$ (ms)', fontsize=18)
plt.tick_params(axis='both', labelsize=18)
plt.xlim(-150, 50, 50)
plt.ylim(0, 6, 1)
plt.title('D', fontsize=18)
#
plt.subplot(2,2,4)
plt.plot(voltage, act_inact_list[1]['nine'], color='blue', label='Ma et al.', linewidth=4)
plt.plot(voltage, act_inact_list[1]['ten'], color='purple', label='Jalife Immature', linewidth=4)
plt.plot(voltage, act_inact_list[1]['eleven'], color='black', label='Baseline Model', linewidth=4)
plt.plot(voltage, act_inact_list[1]['twelve'], color='green', label='Jalife Mature', linewidth=4)
plt.xlabel('Voltage (mV)', fontsize=18)
plt.ylabel('Tau$_j$ (ms)', fontsize=18)
plt.tick_params(axis='both', labelsize=18)
plt.xlim(-150, 50, 50)
plt.ylim(0, 700, 100)
plt.title('E', fontsize= 18)
# plt.show()
plt.savefig('Figure03.png')
