- Author:
- WeiweiAi <wai484@aucklanduni.ac.nz>
- Date:
- 2021-06-21 15:32:15+12:00
- Desc:
- Correct the figure numbers in the doc and typos;
Change the default temerature back to 310K for Periodic_stimulation.
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/692/rawfile/209ecb42181f3204db0c1119bff2279b6a9b50e0/Simulation/Fig8_sim0.py
# To reproduce the data needed for Figure 7 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]: Fig8_sim.py
import opencor as oc
import numpy as np
# The prefix of the saved output file name
prefilename = 'simFig8'
# Load the simulation file
simfile='new_poh_2012.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()
# Define the interval of interest for this simulation experiment
pointInterval = 0.1
data.set_point_interval(pointInterval)
N=30
varName = np.array(["time","V", "Cai"])
vars = np.reshape(varName, (1, 3))
rows=40*1000*10
r = np.zeros((rows,len(varName)))
# Reset states and parameters
simulation.reset(True)
for i in range(N):
# Set constant parameter values
start=i*60000
end=start+60000
data.set_starting_point(start)
data.set_ending_point(end)
simulation.run()
# Access simulation results
results = simulation.results()
# Grab a specific algebraic variable results
r[:,0] = results.voi().values()[-rows:]
r[:,1] = results.states()['membrane/V'].values()[-rows:]
r[:,2] = results.states()['ionic_concentrations/Cai'].values()[-rows:]
# clear the results except the last run
simulation.clear_results()
# Save the simulation result of the last run
filename='%s.csv' % (prefilename)
np.savetxt(filename, vars, fmt='%s',delimiter=",")
with open(filename, "ab") as f:
np.savetxt(f, r, delimiter=",")
f.close
