Location: Imtiaz_IP3_2002 @ 2a5540078c04 / Simulation / Figure8 / Fig8_sim.py

Author:

Leyla <noroozbabaee@gmail.com>

Date:

2022-03-21 23:51:54+13:00

Desc:

removed.

Permanent Source URI:

https://models.cellml.org/workspace/763/rawfile/2a5540078c04d07172f2517b5fd94e9f5c9cc41f/Simulation/Figure8/Fig8_sim.py

# Author : Leyla Noroozbabaee
# Date: 12/09/2021

# To reproduce the data needed for Figure 8 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 Fig8_sim.py
import opencor as oc
import matplotlib.pyplot as plt
import numpy as np
# The prefix of the saved output file name
prefilename = 'Fig8'

# Load the simulation file
simfile = 'Fig8_IP3_Imtiaz_2002.sedml'
simulation = oc.open_simulation(simfile)
data = simulation.data()

# Reset states variables and parameters
simulation.reset(True)
# Set constant values
start = 0
end = 35
pointInterval = 0.01
data.set_starting_point(start)
data.set_ending_point(end)
data.set_point_interval(pointInterval)
# Parameters to Genarate  the Current (Stimulus)
t_d_init = [5.36, 2.36]
t_d_end = [6, 3]

for j in range(2):
    # Reset states variables and parameters
    simulation.reset(True)
    data.constants()['vm/vm_init'] = -65.4
    data.constants()['vm/t_1'] = t_d_init[j]
    data.constants()['vm/t_2'] = t_d_end[j]
    simulation.run()
    # Access simulation results
    results = simulation.results()
    # Data to save
    varName = np.array(["Time", "vm", "I_inj"])
    vars = np.reshape(varName, (1, 3))
    rows = end * 100 + 1
    r = np.zeros((rows, len(varName)))
    r[:, 0] = results.voi().values()
    # print(varName, vars, rows)
    r = np.zeros((rows, len(varName)))
    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_inj'].values()
    # Save the Simulation Results
    filename = '%s_%s.csv' % (prefilename, j)
    np.savetxt(filename, vars, fmt='%s', delimiter=",")
    with open(filename, "ab") as f:
        np.savetxt(f, r, delimiter=",")
    f.close