- Author:
- nima <nafs080@aucklanduni.ac.nz>
- Date:
- 2021-10-13 17:22:04+13:00
- Desc:
- Updated Documentation
- Permanent Source URI:
- https://models.cellml.org/workspace/702/rawfile/63554fa72b7ca4c4e2bab44f0a05f8334c95f4a1/Experiments/Fig7/fig7-new.py
import os
import matplotlib
matplotlib.use('agg')
import numpy as np
import matplotlib.pyplot as plt
import opencor as opencor
# root = "../Channels/"
def load_sedml(filename):
return opencor.open_simulation(filename)
def get_data(filename):
data = filename.data()
data.set_ending_point(100)
data.set_point_interval(1)
return data
def run_sim(data, filename, var1, var2):
voltage = np.arange(-100, 101, 1)
x1_list = [9.3840e-4, 0.0013, 0.0013, 0.0012]
x2_list = [180.5160, 1e5, 1e5, 6.6727e4]
x5_list = [0.3532, 0.2614, 0.2268, 0.2805]
x6_list = [-14.6633, -22.0906, -19.8509, -18.8670]
x7_list = [1.4223e-05, 2e-11, 2e-11, 4.7411e-6]
key_ids = ["one", "two", "three", "four"]
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(-100, 101, 1)
plt.figure(figsize= (19,8))
plt.subplot(1,3,1)
plt.plot(voltage, act_inact_list[0]['one'], color='blue', label= 'Ma et al.', linewidth= 4)
plt.plot(voltage, act_inact_list[0]['two'], color='orange', label='Ma, Wei et al. patient', linewidth=4)
plt.plot(voltage, act_inact_list[0]['three'], color='purple', label= 'Ma, Wie et al. iCell', linewidth= 4)
plt.plot(voltage, act_inact_list[0]['four'], color='black', label= 'Baseline Model', linewidth= 4)
plt.xlabel('Voltage (mV)', fontsize= 14)
plt.ylabel('Normalized I$_{Ks}$', fontsize= 14)
plt.xlim(-100,100,50)
plt.ylim(0,1,0.5)
plt.tick_params(axis='both', labelsize='18')
plt.title('A', fontsize=18)
plt.legend(fontsize= '14')
# #
plt.subplot(1,3,2)
plt.plot(voltage, act_inact_list[1]['one'], color='blue', linewidth=4)
plt.plot(voltage, act_inact_list[1]['three'], color='orange', linewidth=4)
plt.plot(voltage, act_inact_list[1]['two'], color='green', linewidth=4)
plt.plot(voltage, act_inact_list[1]['four'], color='black', linewidth=4)
plt.xlabel('Voltage (mV)', fontsize= 14)
plt.ylabel('Tau$_{act},I_{Ks}$ (ms)', fontsize= 14)
plt.xlim(-100,100,50)
plt.ylim(0,1000,500)
plt.tick_params(axis= 'both', labelsize= '18')
plt.title('B', fontsize=18)
# plt.show()
plt.savefig("Figure07.png")