- 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/Fig10D_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_D'
# 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 = 400
pointInterval = 0.1
data.set_starting_point(start)
data.set_ending_point(end)
data.set_point_interval(pointInterval)
varName = np.array([ "Time", "css", "ctc", "icl", "c", "v", "cai", "I_tot", "I_inward"])
#simulation.reset(True)
vars = np.reshape(varName, (1, 9))
rows = end * 10 + 1
v_clamp = [50, 40, 30, 20, 10, 0, -10, -20, -30, -40, -50]
# v_clamp = [ -20, -15,-10,-5, 0,5, 10]
for i in range(len(v_clamp)):
data.constants() [ 'interface/I_test_swt' ] = 1
data.constants() [ 'interface/test_start' ] = 100
data.constants() [ 'interface/test_end' ] = 200
data.constants() [ 'interface/I_test' ] = -1
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'] = 0.000116
data.constants() [ 'interface/membrane_potential/v_hold'] = -60
data.constants() [ 'interface/membrane_potential/v_clamp'] = v_clamp [ i ]
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_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/membrane_potential/v' ].values()
r [ :, 7 ] = results.algebraic() [ 'interface/membrane_potential/I_tot' ].values()
r [ :, 8 ] = results.algebraic() [ 'interface/membrane_potential/I_inward' ].values()
filename = '%s_%s.csv' % (prefilename, i)
np.savetxt(filename, vars, fmt='%s', delimiter=",")
with open(filename, "ab") as f:
np.savetxt(f, r, delimiter=",")
f.close
