- 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/fig4-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 = [7.7247, 14.5675, 12.9663, 8.7706, 15.5608, 0.0016, 3.455e-04, 5.12589e-04, 5.9251e-04, 5.997599860362688e-04]
x2_list = [6.3888, 7.5014, 7.0791, 7.8748, 5.8612, -82.4603, -43.4169, -49.5057, -52.7783, -52.321981320856140]
x5_list = [0.088, 0.0326, 0.0449, 0.0622, 0.04, 8.18207e+02, 1.5809e+03, 1.9312e+03, 7.290227e+02, 3.483755573348795e+03]
x6_list = [-6.2658, -7.3054, -6.9099, -7.6681, -5.7562, 4.3523, 6.1311, 5.73, 6.1849, 4.874098339328655]
x7_list = [1.7362, 1.6123, 1.6582, 1.6665, 1.696, 97.7424, 99.5232, 100.4626, 97.1476, 104.716837489749]
key_ids = ["one", "two", "three", "four", "five", "six", "seven", "eight", "nine", "ten"]
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)
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]['six'], color= 'blue', linewidth= 4)
plt.plot(voltage, act_inact_list[0]['two'], color='orange', label= 'Veerman1', linewidth= 4)
plt.plot(voltage, act_inact_list[0]['seven'], color='orange', linewidth= 4)
plt.plot(voltage, act_inact_list[0]['three'], color= 'black', label= 'Baseline Model', linewidth= 4)
plt.plot(voltage, act_inact_list[0]['eight'], color= 'black', linewidth= 4)
plt.plot(voltage, act_inact_list[0]['four'], color='purple', label= 'Veerman2', linewidth= 4)
plt.plot(voltage, act_inact_list[0]['nine'], color='purple', linewidth=4)
plt.plot(voltage, act_inact_list[0]['five'], color='green', label='Essalah', linewidth=4)
plt.plot(voltage, act_inact_list[0]['ten'], 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(-100,50,50)
plt.ylim(0,1,0.1)
plt.title('A', fontsize=18)
plt.legend(fontsize= '15')
plt.subplot(2,2,3)
plt.plot(voltage, act_inact_list[1]['one'], color='blue', linewidth=4)
plt.plot(voltage, act_inact_list[1]['two'], color='orange', linewidth=4)
plt.plot(voltage, act_inact_list[1]['three'], color='black', linewidth=4)
plt.plot(voltage, act_inact_list[1]['four'], color='purple', linewidth=4)
plt.plot(voltage, act_inact_list[1]['five'], color='green', linewidth=4)
plt.xlabel('Voltage (mV)', fontsize=18)
plt.ylabel('Tau$_m$ (ms)', fontsize=18)
plt.tick_params(axis= 'both', labelsize= '18')
plt.xlim(-100, 50, 50)
plt.ylim(1.5, 3.5, 0.5)
plt.title('C', fontsize=18)
#
plt.subplot(2,2,4)
plt.plot(voltage, act_inact_list[1]['six'], color='blue', linewidth=4)
plt.plot(voltage, act_inact_list[1]['seven'], color='orange', linewidth=4)
plt.plot(voltage, act_inact_list[1]['eight'], color='black', linewidth=4)
plt.plot(voltage, act_inact_list[1]['nine'], color='purple', linewidth=4)
plt.plot(voltage, act_inact_list[1]['ten'], color='green', linewidth=4)
plt.xlabel('Voltage (mV)', fontsize= 18)
plt.ylabel('Tau$_{inact},I_{CaL}$ (ms)', fontsize= 18)
plt.tick_params(axis= 'both', labelsize= '18')
plt.xlim(-100,50,50)
plt.ylim(0,1000,500)
plt.title('D', fontsize=18)
# plt.show()
plt.savefig('Figure04.png')
