- 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_8/Fig8_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
cai_var = 1;
cai_var_ka = 0;
sub =['a', 'b']
V_hold = 0;
if cai_var:
prefilename = 'Fig8'
# Load the simulation file
simfile = 'CaVAR_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 = 2000
pointInterval = 1
data.set_starting_point(start)
data.set_ending_point(end)
data.set_point_interval(pointInterval)
# data.constants() ['interface/parameters/kmca'] = 0.001
# data.constants() [ 'interface/I_h/a_correction' ] = 1
ca_i = [0.00001, 0.00005, 0.0001, 0.0005, 0.001, 0.005, 0.01, 0.05, 0.1, 0.5, 0.8, 1.0, 5.0, 10, 50, 100]
for j in range(len(ca_i)):
simulation.reset(True)
data.constants()['interface/membrane_potential/v_init'] = 280#-200
data.constants() [ 'interface/Ca_Concentrations/cai' ] = ca_i [ j ]
simulation.run()
# Access simulation results
results = simulation.results()
# Data to save
if cai_var_ka:
varName = np.array(["Time", "xass_z", "xass_vh", "xatc", "xass", "iBKa","xa", "v"])
vars = np.reshape(varName, (1,8))
rows = end * 1 + 1
print(rows)
# Grab a some algebraic variable results
r = np.zeros((rows, len(varName)))
r [ :, 0 ] = results.voi().values()
r [ :, 1 ] = results.constants()['interface/I_BKa/xass_z'].values()
r [ :, 2 ] = results.constants()['interface/I_BKa/xass_vh'].values()
r [ :, 3 ] = results.algebraic() [ 'interface/I_BKa/xatc'].values()
r [ :, 4 ] = results.algebraic() [ 'interface/I_BKa/xass' ].values()
r [ :, 5 ] = results.algebraic() [ 'interface/I_BKa/iBKa'].values()
r [ :, 6 ] = results.states() [ 'interface/I_BKa/xa' ].values()
r [ :, 7] = results.states() [ 'interface/membrane_potential/v' ].values()
filename = '%s_%s_%s.csv' % (prefilename, sub[0],j)
np.savetxt(filename, vars, fmt='%s', delimiter=",")
with open(filename, "ab") as f:
np.savetxt(f, r, delimiter=",")
f.close
else:
varName = np.array([ "Time", "xabss_z", "xabss_vh", "xabtc", "xabss", "iBKab","xab", "v" ])
vars = np.reshape(varName, (1, 8))
rows = end * 1 + 1
print(rows)
# Grab a some algebraic variable results
r = np.zeros((rows, len(varName)))
r [ :, 0 ] = results.voi().values()
r [ :, 1 ] = results.constants() [ 'interface/I_BKab/xabss_z' ].values()
r [ :, 2 ] = results.constants() [ 'interface/I_BKab/xabss_vh' ].values()
r [ :, 3 ] = results.algebraic() [ 'interface/I_BKab/xabtc' ].values()
r [ :, 4 ] = results.algebraic() [ 'interface/I_BKab/xabss' ].values()
r [ :, 5 ] = results.algebraic() [ 'interface/I_BKab/iBKab' ].values()
r [ :, 6 ] = results.states() [ 'interface/I_BKab/xab' ].values()
r [ :, 7 ] = results.states() [ 'interface/membrane_potential/v' ].values()
filename = '%s_%s_%s.csv' % (prefilename, sub[1],j)
np.savetxt(filename, vars, fmt='%s', delimiter=",")
with open(filename, "ab") as f:
np.savetxt(f, r, delimiter=",")
f.close
elif V_hold:
# 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 = 1000
pointInterval = 1
data.set_starting_point(start)
data.set_ending_point(end)
data.set_point_interval(pointInterval)
time_clamp = 40
v_clamp = [ -200,-180,-160,-140,-120,-100,-80,-60,-40,-30, -20, -10, 0, 10, 20, 30, 40,60]
v_hold = [-80, -40]
simulation.reset(True)
for j in range(len(v_hold)):
data.constants()['interface/membrane_potential/v_hold'] = v_hold[j]
for i in range(len(v_clamp)):
prefilename = 'Fig8_c'
data.constants() [ 'interface/membrane_potential/v_clamp' ] = v_clamp [ i ]
print(i,j)
data.constants() [ 'interface/membrane_potential/time_clamp' ] = time_clamp
data.constants() [ 'interface/parameters/ki' ] = 110
data.constants() [ 'interface/parameters/ko' ] = 5
#data.constants() [ 'interface/membrane_potential/v_clamp' ] = v[ i ]
simulation.run()
# Access simulation results
results = simulation.results()
# Data to save
# Data to save
varName = np.array([ "Time", "ik2", "v","max" ])
vars = np.reshape(varName, (1, 4))
rows = end * 1 + 1
# Grab a some algebraic variable results
r = np.zeros((rows, len(varName)))
r [ :, 0 ] = results.voi().values()
r [ :, 1 ] = results.algebraic() [ 'interface/I_BKa/ik2' ].values()
r [ :, 2 ] = results.algebraic() [ 'interface/membrane_potential/v' ].values()
r[:,3] = max (r [ :, 1 ])
# Save the simulation result of the last run
filename = '%s_%s_%s.csv' % (prefilename, j,i)
np.savetxt(filename, vars, fmt='%s', delimiter=",")
with open(filename, "ab") as f:
np.savetxt(f, r, delimiter=",")
f.close
else:
prefilename = 'Fig8_5'
# Load the simulation file
simfile = 'VoltageVAR_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 = 0.5
data.set_starting_point(start)
data.set_ending_point(end)
data.set_point_interval(pointInterval)
time_clamp = 60
v_clamp = [-40,-30,-20,-10,0, 10 ]
for i in range(len(v_clamp)):
data.constants() [ 'interface/membrane_potential/v_hold' ] = -80
simulation.reset(True)
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
simulation.run()
# Access simulation results
results = simulation.results()
# Data to save
# Data to save
varName = np.array([ "Time", "ik2", "v" ])
vars = np.reshape(varName, (1, 3))
rows = end * 2 + 1
# Grab a some algebraic variable results
r = np.zeros((rows, len(varName)))
r [ :, 0 ] = results.voi().values()
r [ :, 1 ] = results.algebraic() ['interface/I_BKa/ik2'].values()
r [ :, 2 ] = results.algebraic() [ 'interface/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
