- 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_10/Fig10_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 = 'Fig10'
# Load the simulation file
sub =['A','B','C','D','E']
varName = np.array([ "Time", "css", "ctc", "icl", "c", "v", "cai" ])
# simulation.reset(True)
# cai = [100000000, 250000000, 500000000, 1000000000]
#cai = [100, 250, 500, 1000]
# cai = [0.000100, 0.000250, 0.000500, 0.001]
# for i in range(len(cai)):
# simfile = 'Tong_2011_newVersion.sedml'
# simulation = oc.open_simulation(simfile)
# data = simulation.data()
# # Set constant values
# start = 0
# end = 400
# pointInterval = 0.1
# # Reset states variables and parameters
# data.set_starting_point(start)
# data.set_ending_point(end)
# data.set_point_interval(pointInterval)
#
# rows = end * 10 + 1
# #
# simulation.reset(True)
# data.constants()['interface/membrane_potential/v_var'] = 1
# data.constants() [ 'interface/membrane_potential/v_init' ] = 150
# data.constants()['interface/Ca_Concentrations/cai_hold'] = cai[i]
# data.constants()['interface/Ca_Concentrations/cai_hold_swtch'] = 1
# simulation.run()
# # Access simulation results
# results = simulation.results()
# # # Data to save
# vars = np.reshape(varName, (1, 7))
# # Grab a some algebraic variable results
# r = np.zeros((rows, len(varName)))
# r [ :, 0 ] = results.voi().values()
# r [ :, 1 ] = results.algebraic()['interface/I_Cl/css'].values()
# r [ :, 2 ] = results.algebraic()['interface/I_Cl/ctc'].values()
# r [ :, 3 ] = results.algebraic() [ 'interface/I_Cl/icl'].values()
# r [ :, 4 ] = results.states() [ 'interface/I_Cl/c'].values()
# r [ :, 5 ] = results.algebraic() [ 'interface/membrane_potential/v'].values()
# r [ :, 6 ] = results.algebraic() [ 'interface/Ca_Concentrations/cai'].values()
# filename = '%s_%s_%s.csv' % (prefilename,sub[0],i)
# np.savetxt(filename, vars, fmt='%s', delimiter=",")
# with open(filename, "ab") as f:
# np.savetxt(f, r, delimiter=",")
# f.close
# v_hold = [-60, -30 , 0, 30]
#
# for i in range(len(v_hold)):
# simfile = 'Tong_2011_newVersion.sedml'
# simulation = oc.open_simulation(simfile)
# data = simulation.data()
# simulation.reset(True)
# # Reset states variables and parameters
#
# # Set constant values
# start = 0
# end = 10000
# pointInterval = 0.1
# # Reset states variables
# data.set_starting_point(start)
# data.set_ending_point(end)
# data.set_point_interval(pointInterval)
#
#
# data.constants() [ 'interface/membrane_potential/v_hold' ] = v_hold [ i ]
#
# data.constants() [ 'interface/membrane_potential/v_clamp' ] = v_hold [ i ]
# print(v_hold [ i ])
# data.constants() [ 'interface/Ca_Concentrations/cai_init' ] = 0.001
# data.constants() [ 'interface/Ca_Concentrations/cai_hold_swtch' ] = 0
# data.constants() [ 'interface/membrane_potential/v_var' ] = 0
# data.constants() [ 'interface/membrane_potential/time_clamp_strt' ] = end
# data.constants() [ 'interface/membrane_potential/time_clamp_stp' ] = end
# simulation.run()
# # Access simulation results
# results = simulation.results()
# # Data to save
# rows = end * 10 + 1
# r = np.zeros((rows, len(varName)))
# r [ :, 0 ] = results.voi().values()
# r [ :, 1 ] = results.algebraic() [ 'interface/I_Cl/css' ].values() # q2
# r [ :, 2 ] = results.algebraic() [ 'interface/I_Cl/ctc' ].values()
# r [ :, 3 ] = results.algebraic() [ 'interface/I_Cl/icl' ].values()
# r [ :, 4 ] = results.states() [ 'interface/I_Cl/c' ].values()
# r [ :, 5 ] = results.algebraic() [ 'interface/membrane_potential/v' ].values()
# r [ :, 6 ] = results.algebraic() [ 'interface/Ca_Concentrations/cai' ].values()
# filename = '%s_%s_%s.csv' % (prefilename, sub [ 1 ], i)
# np.savetxt(filename, vars, fmt='%s', delimiter=",")
# with open(filename, "ab") as f:
# np.savetxt(f, r, delimiter=",")
# f.close
v_hold =[-60]
# # simulation.reset(True)
simfile = 'Tong_2011_newVersion.sedml'
simulation = oc.open_simulation(simfile)
data = simulation.data()
simulation.reset(True)
#
v_clamp = [40, 30, 20, 10, 0, -10, -20, -30, -40, -50]
for i in range(len(v_clamp)):
# Reset states variables and parameters
# Set constant values
start = 0
end = 400
pointInterval = 0.1
# Reset states variables
data.set_starting_point(start)
data.set_ending_point(end)
data.set_point_interval(pointInterval)
data.constants() [ 'interface/membrane_potential/v_hold' ] = v_hold
data.constants() [ 'interface/membrane_potential/v_clamp' ] = v_clamp [ i ]
data.constants() [ 'interface/Ca_Concentrations/cai_hold_swtch' ] = 0
data.constants() [ 'interface/membrane_potential/v_var' ] = 0
data.constants() [ 'interface/membrane_potential/time_clamp_strt' ] = 100
data.constants() [ 'interface/membrane_potential/time_clamp_stp' ] = 200
data.constants() [ 'interface/membrane_potential/a_correction'] = 0
data.constants()['interface/Ca_Concentrations/cai_init'] = 0.00016
# data.constants() [ 'interface/parameters/ki' ] = 110
# data.constants() [ 'interface/parameters/ko' ] = 5
simulation.run()
# Access simulation results
results = simulation.results()
# Data to save
rows = end * 10 + 1
vars = np.reshape(varName, (1, 7))
# Grab a some algebraic variable results
r = np.zeros((rows, len(varName)))
r [ :, 0 ] = results.voi().values()
r [ :, 1 ] = results.algebraic()['interface/I_Cl/css'].values()
r [ :, 2 ] = results.algebraic()['interface/I_Cl/ctc'].values()
r [ :, 3 ] = results.algebraic() [ 'interface/I_Cl/icl'].values()
r [ :, 4 ] = results.states() [ 'interface/I_Cl/c'].values()
r [ :, 5 ] = results.algebraic() [ 'interface/membrane_potential/v'].values()
r [ :, 6 ] = results.algebraic() [ 'interface/Ca_Concentrations/cai'].values()
filename = '%s_%s_%s.csv' % (prefilename,sub[3],i)
np.savetxt(filename, vars, fmt='%s', delimiter=",")
with open(filename, "ab") as f:
np.savetxt(f, r, delimiter=",")
f.close
