- Author:
- GitHub <noreply@github.com>
- Date:
- 2022-06-20 15:59:19+12:00
- Desc:
- Create README.md
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/8aa/rawfile/b46a0350f264bd9f94ef8b042d12ba826112d874/Experiments/Figure_1/Fig1_sim.py
# Author : Leyla Noroozbabaee
# Date: 12/02/2022
# FOR the case of time dependent state variable such as membrane potential the following definition was used.
# var v: mV {init: v_init, pub: out};
# ode(v, time) = - I_tot;
#
# FOR the case of step-wise changes in state variable such as membrane potential the following definition
# var v: mV {pub: out};
# v = sel
# case (time <= time_clamp_sta) and (v_var == 0{dimensionless}):
# v_hold;
# case (time > time_clamp_sta) and (time <= time_clamp_end) and (v_var == 0{dimensionless}):
# v_clamp;
# otherwise:
# v_hold;
# endsel;
# To reproduce the data needed for Figure 1 in associated original paper,
# execute this script in the Python console in OpenCOR. This can be done
# 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 numpy as np
Fig_ABCD = 1
Fig_EF = 1
if Fig_ABCD:
prefilename = 'Fig1'
# Load the simulation file
simfile = 'C:/Users/lnor300/Documents/CellML/12_Labors/Tong_2011/Simulations/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 = 6000
pointInterval = 0.1
data.set_starting_point(start)
data.set_ending_point(end)
data.set_point_interval(pointInterval)
data.constants()['interface/membrane_potential/v_init'] = -100
data.constants() [ 'interface/parameters/kmca' ] = 0.001
data.constants() [ 'interface/parameters/ecal' ] = 45
simulation.run()
# Access simulation results
results = simulation.results()
# Data to save
varName = np.array(["Time", "fss", "dss", "f1tc", "f2tc", "dtc", "ical", "v", "I_Ca_tot"])
vars = np.reshape(varName, (1,9))
rows = end * 10 + 1
# Grab some algebraic results
r = np.zeros((rows, len(varName)))
r [ :, 0 ] = results.voi().values()
r [ :, 1 ] = results.algebraic()['interface/I_CaL/fss'].values()
r [ :, 2 ] = results.algebraic()['interface/I_CaL/dss'].values()
r [ :, 3 ] = results.constants() [ 'interface/I_CaL/f1tc' ].values()
r [ :, 4 ] = results.algebraic() [ 'interface/I_CaL/f2tc' ].values()
r [ :, 5 ] = results.algebraic() [ 'interface/I_CaL/dtc' ].values()
r [ :, 6 ] = results.algebraic() [ 'interface/I_CaL/ical'].values()
r [ :, 7 ] = results.states() [ 'interface/membrane_potential/v' ].values()
r [ :, 8 ] = results.algebraic() [ 'interface/membrane_potential/I_Ca_tot' ].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
if Fig_EF:
prefilename = 'Fig1_5'
# Load the simulation file
simfile = 'C:/Users/lnor300/Documents/CellML/12_Labors/Tong_2011_V1/Simulations/VoltageVAR_Tong_2011.sedml'
simulation = oc.open_simulation(simfile)
data = simulation.data()
# Set the time interval and total time for the simulation
start = 0
end = 60
pointInterval = 0.01
data.set_starting_point(start)
data.set_ending_point(end)
data.set_point_interval(pointInterval)
v_clamp =[50, 40, 30, 20, 10, 0, -10, -20, -30, -40, -50]
for i in range(11):
# Reset states variables and parameters
simulation.reset(True)
data.constants()['interface/membrane_potential/v_hold'] = -60
data.constants()['interface/membrane_potential/v_var'] = 0
data.constants()['interface/parameters/kmca'] = 0.001
data.constants() [ 'interface/membrane_potential/v_clamp' ] = v_clamp[i]
data.constants() [ 'interface/membrane_potential/time_clamp_end']= end
data.constants() [ 'interface/membrane_potential/time_clamp_sta' ] = 6
simulation.run()
# Access simulation results
results = simulation.results()
# Data to save
varName = np.array(["Time", "ical", "I_tot","I_Ca_tot","v"])
vars = np.reshape(varName, (1,5))
rows = end * 100 + 1
# Grab some algebraic variable results
r = np.zeros((rows, len(varName)))
r [ :, 0 ] = results.voi().values()
r [ :, 1 ] = results.algebraic() [ 'interface/I_CaL/ical'].values()
r [ :, 2 ] = results.algebraic() [ 'interface/membrane_potential/I_tot'].values()
r [ :, 3 ] = results.algebraic() [ 'interface/membrane_potential/I_Ca_tot'].values()
r [ :, 4 ] = results.algebraic() [ 'interface/membrane_potential/v' ].values()
# Save the simulation result
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
