- Author:
- Leyla <noroozbabaee@gmail.com>
- Date:
- 2022-05-10 14:01:08+12:00
- Desc:
- Adding Tong_2011 to PMR
- Permanent Source URI:
- https://models.cellml.org/workspace/85c/rawfile/a03f680a69226c515cd789723c8036028406852b/Experiments/Figure_11/Fig11_sim.py
# with the following commands at the prompt in the OpenCOR Python console:
#
# In [1]: cd path/to/folder_this_file_is_in
# In [2]: run Fig1_sim.py
import opencor as oc
import matplotlib.pyplot as plt
import numpy as np
# The prefix of the saved output file name
prefilename = 'Fig11'
# Load the simulation file
sub =['A','B','C','D','E']
varName = np.array(["Time", "Force", "I_tot", "v", "cai"])
# # simulation.reset(True)
simfile = 'Tong_2011_newVersion.sedml'
simulation = oc.open_simulation(simfile)
data = simulation.data()
# Set constant values
start = 0
end = 20000
pointInterval = 0.1
# Reset states variables
data.set_starting_point(start)
data.set_ending_point(end)
data.set_point_interval(pointInterval)
# I_st =[-0.1, -0.4, -0.4, -1.2]
# ca = [0.000216]#, 0.001,0.0001,0.00001]
# ca = [0.0000116, 0.000116, 0.000116, 0.000156]
v_init = [-53, -50, -50, -40]
# v_init =[-53.9915441282156]
ca = [0.000350061161001, 0.0001, 0.00012, 0.0001]
I_st = [-0.18, -0.25, -0.4, -1.236]
sf = [1.00, 1, 1, 1]
gna = [0.12, 0.09, 0.045, 0.00]
k0 = [6, 6, 7, 6]
for i in range(len(I_st)):
simulation.reset(True)
#
# if i==0 :
#
# if i==1:
# #
# data.constants()['interface/I_CaL/sf'] = sf[i]
# # data.constants()['interface/I_test_swt'] = 1
# # data.constants()['interface/test_start'] = 1000
# # data.constants()['interface/test_end'] = 10000
# # data.constants()['interface/I_test'] = I_st[i]
# # data.constants()['interface/Ca_Concentrations/cai_hold_swtch'] = 0
# # data.constants()['interface/membrane_potential/v_var'] = 1
# # data.constants()['interface/membrane_potential/a_correction'] = 1
# # data.constants()['interface/Ca_Concentrations/cai_init'] = ca[i]
# # data.constants()['interface/membrane_potential/v_init'] = -53 # v_init[i]
# else:
# data.constants()['interface/I_CaL/sf'] = 1
# # data.constants()['interface/parameters/ko'] = 5
# if i==2:
# data.constants()['interface/parameters/ko'] = 10
# else:
# data.constants()['interface/parameters/ko'] = 5
data.constants()['interface/I_CaL/s_clamp'] = sf[i]
data.constants()['interface/I_test_swt'] = 1
data.constants()['interface/parameters/gna'] = gna[i]
data.constants()['interface/test_start'] = 1000
data.constants()['interface/test_end'] = 10000
data.constants()['interface/I_test'] = I_st[i]
data.constants()['interface/Ca_Concentrations/cai_hold_swtch'] = 0
data.constants()['interface/membrane_potential/v_var'] = 1
data.constants()['interface/membrane_potential/a_correction'] = 1
data.constants()['interface/Ca_Concentrations/cai_init'] = ca[i]
data.constants()['interface/membrane_potential/v_init'] = v_init[i]
data.constants()['interface/parameters/ko'] = k0[i]
simulation.run()
# Access simulation results
results = simulation.results()
# Data to save
rows = end * 10 + 1
vars = np.reshape(varName, (1,5))
# Grab a some algebraic variable results
r = np.zeros((rows, len(varName)))
r[:, 0] = results.voi().values()
r[:, 1] = results.algebraic()['interface/Ca_dependent_Force/Force'].values()
r[:, 2] = results.algebraic()['interface/membrane_potential/I_tot'].values()
r[:, 3] = results.algebraic()['interface/membrane_potential/v'].values()
r[:, 4] = results.algebraic()['interface/Ca_Concentrations/cai'].values()
filename = '%s_%s.csv' % (prefilename, sub[i])
np.savetxt(filename, vars, fmt='%s', delimiter=",")
with open(filename, "ab") as f:
np.savetxt(f, r, delimiter=",")
f.close
