- 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_3/Fig3_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 = 1;
V_clmp = 1;
if V_var:
prefilename = 'Fig3'
# 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'] = -80
data.constants() ['interface/parameters/kmca'] = 0.001
simulation.run()
# Access simulation results
results = simulation.results()
# Data to save
varName = np.array(["Time", "bss", "gss", "btc", "gtc", "icat", "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_CaT/bss'].values()
r [ :, 2 ] = results.algebraic()['interface/I_CaT/gss'].values()
r [ :, 3 ] = results.algebraic() [ 'interface/I_CaT/btc' ].values()
r [ :, 4 ] = results.algebraic() [ 'interface/I_CaT/gtc' ].values()
r [ :, 5 ] = results.algebraic() [ 'interface/I_CaT/icat' ].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
elif V_clmp:
prefilename = 'Fig3_4'
# 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 = 100
pointInterval = 0.001
data.set_starting_point(start)
data.set_ending_point(end)
data.set_point_interval(pointInterval)
time_clamp = 13
# v_clamp = [-65,-55.-45,-35,-25,-15,-5,-15,25]
# v_clamp =[50, 40, 30, 25, 20, 10, 0,-10,-20,-30,-40,-50,-60, -70,-80]
v_clamp = [-60, -50, -40, -30, -20, -10, 0, 10, 20]
for i in range(len(v_clamp)):
data.constants()['interface/membrane_potential/v_hold'] = -80
data.constants() [ 'interface/parameters/kmca' ] = 0.001
simulation.reset(True)
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", "icat", "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_CaT/icat' ].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
else:
prefilename = 'Fig3_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 = 100
pointInterval = 0.001
data.set_starting_point(start)
data.set_ending_point(end)
data.set_point_interval(pointInterval)
time_clamp = 13
v_clamp = [ 50, 40, 30, 25, 20, 10, 0, -10, -20, -30, -40, -50, -60, -70, -80 ]
# v_clamp =[50, 40, 30, 20, 10, 0,-10,-20,-30,-40,-50]
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
data.constants() [ 'interface/parameters/ecat' ] = 25
simulation.run()
# Access simulation results
results = simulation.results()
# Data to save
# Data to save
varName = np.array([ "Time", "icat", "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_CaT/icat' ].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
# # # The prefix of the saved output file name
# prefilename = 'Fig3_3'
# # 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 = 100
# pointInterval = 0.001
# data.set_starting_point(start)
# data.set_ending_point(end)
# data.set_point_interval(pointInterval)
#
# # # # The prefix of the saved output file name
# # prefilename = 'Fig2_3'
# # # Load the simulation file
# #
# # v_clamp =[-60, -50, -40, -30, -20, -10, 0, 10, 20, 25]
#
# v_clamp = [-60]
