- Author:
- Leyla <lnor300>
- Date:
- 2022-11-02 15:33:57+13:00
- Desc:
- ..
- Permanent Source URI:
- https://models.cellml.org/workspace/763/rawfile/81e638b3f094d00aade965d9e2ca7bd101f33371/Simulation/Figure6/Fig6_sim.py
# Author : Leyla Noroozbabaee
# Date: 12/09/2021
# To reproduce the data needed for Figure 3 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 Fig6_sim.py
import opencor as oc
import numpy as np
# The prefix of the saved output file name
prefilename = 'Fig6'
# Load the simulation file
simfile = 'Fig6_IP3_Imtiaz_2002.sedml'
simulation = oc.open_simulation(simfile)
# The data object houses all the relevant information
# and pointers to the OpenCOR internal data representations
data = simulation.data()
# Set the experiments, the stimulus range
I_clamp1 = np.linspace(-35, 35, num=30)
# Define the interval of interest for this simulation experiment
duration = 3
start, end, pointInterval = 0, duration, 0.001
data.set_starting_point(start)
data.set_ending_point(end)
data.set_point_interval(pointInterval)
# Data to save
varName = np.array(["Time", "vm", "I_stim"])
vars = np.reshape(varName, (1, len(varName)))
rows = duration * 1000 + 1
r = np.zeros((rows, len(varName)))
for index, i in enumerate(I_clamp1):
# Reset states and parameters
simulation.reset(True)
# Set constant parameter values
data.constants()['vm/cm'] = 0.5
data.constants()['vm/I_clamp1'] = i
simulation.run()
# Access simulation results
results = simulation.results()
# Grab a specific algebraic variable results
r [:, 0] = results.voi().values()
r [ :, 1 ] = results.states()['vm/vm'].values()
r [ :, 2 ] = results.algebraic()['vm/I_stim'].values()
simulation.clear_results()
# Save the simulation result of the last run
filename = '%s_%s.csv' % (prefilename, index)
np.savetxt(filename, vars, fmt='%s', delimiter=",")
with open(filename, "ab") as f:
np.savetxt(f, r, delimiter=",")
f.close
