- 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_9/Fig9_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
Sub_A=0
prefilename = 'Fig9'
# Load the simulation file
simfile = 'Tong_2011_newVersion.sedml'
simulation = oc.open_simulation(simfile)
data = simulation.data()
# Reset states variables and parameters
# Set constant values
start = 0
end = 300
pointInterval = 0.1
data.set_starting_point(start)
data.set_ending_point(end)
data.set_point_interval(pointInterval)
sub =['A','B']
varName = np.array([ "Time", "ik1", "ik2", "iBKa", "iBKab", "ika", "ib", "v", "I_K_tot" ])
vars = np.reshape(varName, (1, 9))
rows = end * 10 + 1
# simulation.reset(True)
if Sub_A:
data.constants()['interface/membrane_potential/v_var'] = 0
data.constants() [ 'interface/membrane_potential/v_hold' ] = -80
data.constants() [ 'interface/membrane_potential/v_clamp' ] = 40
simulation.run()
# Access simulation results
results = simulation.results()
# # Data to save
# varName = np.array(["Time", "ik1", "ik2" , "iBKa","iBKab","ika","ib","v"])
# vars = np.reshape(varName, (1,8))
# rows = end * 10 + 1
#"Time", "ik1", "ik2", "iBKa", "iBKab", "ika", "ib", "v"
# Grab a some algebraic variable results
r = np.zeros((rows, len(varName)))
r [ :, 0 ] = results.voi().values()
r [ :, 1 ] = results.algebraic()['interface/I_K1/ik1'].values()#q2
r [ :, 2 ] = results.algebraic()['interface/I_K2/ik2'].values()
r [ :, 3 ] = results.algebraic() [ 'interface/I_BKa/iBKa'].values()
r [ :, 4 ] = results.algebraic() [ 'interface/I_BKab/iBKab'].values()
r [ :, 5 ] = results.algebraic() [ 'interface/I_Ka/ika'].values()
r [ :, 6 ] = results.algebraic() [ 'interface/I_b/ib'].values()
r [ :, 7 ] = results.algebraic() [ 'interface/membrane_potential/v'].values()
r [ :, 8 ] = results.algebraic() [ 'interface/membrane_potential/I_K_tot'].values()
filename = '%s_%s.csv' % (prefilename,sub[0])
np.savetxt(filename, vars, fmt='%s', delimiter=",")
with open(filename, "ab") as f:
np.savetxt(f, r, delimiter=",")
f.close
else:
# simulation.reset(True)
simfile = 'Tong_2011_newVersion.sedml'
simulation = oc.open_simulation(simfile)
data = simulation.data()
simulation.reset(True)
# Reset states variables and parameters
#
# Set constant values
#v_hold =[-40]
# v_clamp = [-40,70]
v_hold =[-80,-40]
# simulation.reset(True)
data.constants() [ 'interface/membrane_potential/v_var' ] = 0
data.constants() [ 'interface/membrane_potential/time_clamp_strt' ] = 10
data.constants() [ 'interface/membrane_potential/time_clamp_stp' ] = 280
for i in range(len(v_hold)):
v_clamp = [ -40, -30, -20, -10, 0, 10, 20, 30, 40, 50, 60, 70 ]
for j in range(len(v_clamp)):
print(v_hold [ i ])
data.constants() [ 'interface/membrane_potential/v_hold' ] = v_hold [ i ]
data.constants() [ 'interface/membrane_potential/v_clamp' ] = v_clamp [ j ]
data.constants() [ 'interface/parameters/ki' ] = 160
data.constants() [ 'interface/parameters/ko' ] = 6
simulation.run()
# Access simulation results
results = simulation.results()
# Data to save
# Grab a some algebraic variable results
r = np.zeros((rows, len(varName)))
r [ :, 0 ] = results.voi().values()
r [ :, 1 ] = results.algebraic()['interface/I_K1/ik1'].values()#q2
r [ :, 2 ] = results.algebraic()['interface/I_K2/ik2'].values()
r [ :, 3 ] = results.algebraic() [ 'interface/I_BKa/iBKa'].values()
r [ :, 4 ] = results.algebraic() [ 'interface/I_BKab/iBKab'].values()
r [ :, 5 ] = results.algebraic() [ 'interface/I_Ka/ika'].values()
r [ :, 6 ] = results.algebraic() [ 'interface/I_b/ib'].values()
r [ :, 7 ] = results.algebraic() [ 'interface/membrane_potential/v' ].values()
r [ :, 8 ] = results.algebraic() [ 'interface/membrane_potential/I_K_tot' ].values()
filename = '%s_%s_%s.csv' % (prefilename, sub[i], j)
np.savetxt(filename, vars, fmt='%s', delimiter=",")
with open(filename, "ab") as f:
np.savetxt(f, r, delimiter=",")
f.close
#simulation.reset(True)#
