- 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_4/Fig4_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
V_var = 0;
V_clmp = 0;
if V_var:
prefilename = 'Fig4'
# Load the simulation file
simfile = 'Tong_2011.sedml'
simulation = oc.open_simulation(simfile)
data = simulation.data()
# Reset states variables and parameters
# simulation.reset(True)
# Set constant values
start = 0
end = 10000
pointInterval = 0.1
data.set_starting_point(start)
data.set_ending_point(end)
data.set_point_interval(pointInterval)
# simulation.reset(True)
data.constants()['interface/membrane_potential/v_init'] = -150
data.constants()['interface/parameters/kmca'] = 0.001
data.constants()['interface/I_h/a_correction'] = 3.5
simulation.run()
# Access simulation results
results = simulation.results()
# Data to save
varName = np.array(["Time", "yss", "ya", "yb", "ytc", "ih", "v" ])
vars = np.reshape(varName, (1,7))
rows = end * 10 + 1
print(rows)
# Access simulation results
results = simulation.results()
# Grab a some algebraic variable results
r = np.zeros((rows, len(varName)))
r [ :, 0 ] = results.voi().values()
r [ :, 1 ] = results.algebraic()['interface/I_h/yss'].values()
r [ :, 2 ] = results.algebraic()['interface/I_h/ya'].values()
r [ :, 3 ] = results.algebraic() [ 'interface/I_h/yb' ].values()
r [ :, 4 ] = results.algebraic() [ 'interface/I_h/ytc' ].values()
r [ :, 5 ] = results.algebraic() [ 'interface/I_h/ih' ].values()
r [ :, 6 ] = results.states() [ 'interface/membrane_potential/v' ].values()
filename = '%s.csv' % (prefilename)
np.savetxt(filename, vars, fmt='%s', delimiter=",")
with open(filename, "ab") as f:
np.savetxt(f, r, delimiter=",")
f.close
else:
prefilename = 'Fig4_3'
# Load the simulation file
simfile = 'VoltageVAR_Tong_2011.sedml'
simulation = oc.open_simulation(simfile)
data = simulation.data()
simulation.reset(True)
# Reset states variables and parameters
#simulation.reset(True)
# Set constant values
start = 0
end = 300
pointInterval = 0.001
data.set_starting_point(start)
data.set_ending_point(end)
data.set_point_interval(pointInterval)
time_clamp = 100
v_clamp = [-130, -110, -90, -80, -70, -60, -50, -40, -30]
for i in range(len(v_clamp)):
simulation.reset(True)
data.constants() [ 'interface/membrane_potential/v_init' ] = -150
data.constants()['interface/membrane_potential/v_hold'] = -30
data.constants() ['interface/parameters/kmca' ] = 0.001
data.constants() [ 'interface/membrane_potential/v_clamp' ] = v_clamp[i]
data.constants() [ 'interface/membrane_potential/time_clamp' ] = time_clamp
# data.constants() [ 'interface/parameters/ecat' ] = 25
simulation.run()
# Access simulation results
results = simulation.results()
# Data to save
varName = np.array([ "Time", "ih", "v" ])
vars = np.reshape(varName, (1, 3))
rows = end * 1000 + 1
# Grab a some algebraic variable results
r = np.zeros((rows, len(varName)))
r [ :, 0 ] = results.voi().values()
r [ :, 1 ] = results.algebraic() [ 'interface/I_h/ih' ].values()
r [ :, 2 ] = results.algebraic() [ 'interface/membrane_potential/v' ].values()
# r [ :, 7 ] = results.algebric() ['membrane_potential/v' ].values()
# Save the simulation result of the last run
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
