- Author:
- nima <nafs080@aucklanduni.ac.nz>
- Date:
- 2021-10-08 09:28:17+13:00
- Desc:
- Update the figure in documentation
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/6b9/rawfile/509a0c339805d7ffa9ed45605ab696eddbc46c68/Fig3D.py
# To reproduce Figure 3 in the associated Physiome paper,
# execute this script from the command line:
# cd [PathToThisFile]
# [PathToOpenCOR]/pythonshell Figure3D.py
import os
import matplotlib
matplotlib.use('agg')
import numpy as np
import matplotlib.pyplot as plt
import opencor as opencor
root = "C:/Users/nafs080/work/BG-python-project/resources"
simulation = opencor.open_simulation(os.path.join(root, 'AE1-BG.sedml'))
data = simulation.data()
data.set_ending_point(10)
data.set_point_interval(1)
result = []
q_Cl_o_vec = [20,25,30,35,40,45,50,60,70,80,90,100,110,120]
for q in q_Cl_o_vec:
simulation.reset(True)
simulation.clear_results()
data.constants()["AE1/q_Cl_i"] = 29
data.constants()["AE1/q_HCO3_i"] = 26
data.constants()["AE1/q_HCO3_o"] = 26
data.constants()["AE1/K_Cl_o"] = 1.34784535e+00
data.constants()["AE1/K_Cl_i"] = 1.34809503e+00
data.constants()["AE1/K_HCO3_i"] = 8.37243345e-01
data.constants()["AE1/K_HCO3_o"] = 8.37398440e-01
data.constants()["AE1/K_E_o"] = 3.42812779e+00
data.constants()["AE1/K_E_i"] = 3.71610024e-01
data.constants()["AE1/K_ECl_o"] = 2.30943735e+02
data.constants()["AE1/K_ECl_i"] = 2.50575623e+01
data.constants()["AE1/K_EHCO3_o"] = 5.68610961e+02
data.constants()["AE1/K_EHCO3_i"] = 6.15805309e+01
data.constants()["AE1/K_Re1"] = 2.16462852e+01
data.constants()["AE1/K_Re2"] = 2.43394395e+00
data.constants()["AE1/K_Re3"] = 1.99577523e+02
data.constants()["AE1/K_Re4"] = 3.21470643e+02
data.constants()["AE1/K_Re5"] = 2.19265742e+00
data.constants()["AE1/K_Re6"] = 3.48281500e+01
data.states()["AE1/q_E_o"] = 0.01738
data.states()["AE1/q_E_i"] = 0.473
data.states()["AE1/q_ECl_o"] = 0.0396
data.states()["AE1/q_ECl_i"] = 0.274
data.states()["AE1/q_EHCO3_i"] = 0.0621
data.states()["AE1/q_EHCO3_o"] = 0.00228
data.constants()["AE1/q_Cl_o"] = q
simulation.run()
ds = simulation.results().data_store()
value = ds.voi_and_variables()["AE1/v_Re2"].values()[-1]
result.append(value)
# print(result)
simulation1 = opencor.open_simulation(os.path.join(root, 'Weinstein_2000_AE1_Fig3.sedml'))
data1 = simulation1.data()
data1.set_ending_point(10)
data1.set_point_interval(1)
result_cellml = []
for q in q_Cl_o_vec:
simulation1.reset(True)
simulation1.clear_results()
data1.states()["concentrations/Cl_ext"] = q
simulation1.run()
ds = simulation1.results().data_store()
value1 = ds.voi_and_variables()["fluxes/J_AE1_HCO3"].values()
result_cellml.append(value1)
# print(result_cellml)
plt.plot(q_Cl_o_vec, result, color= 'green')
plt.plot(q_Cl_o_vec, result_cellml, color= 'blue')
plt.xlim(0,120)
plt.ylim()
plt.xlabel('Cl_o')
plt.ylabel('HCO3 flux')
# plt.show()
plt.savefig("Figure3D.png")
