/
utils.py
executable file
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/
utils.py
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import math
import os
import sys
import opencor as oc
def header(title, first=True):
if not first:
print()
print('---------------------------------------')
print(' ' * math.floor((39 - len(title)) / 2) + title)
print('---------------------------------------')
def open_simulation(file_name_or_url):
if file_name_or_url.startswith('https://'):
return oc.open_simulation(file_name_or_url)
original_directory = os.getcwd()
os.chdir(os.path.dirname(__file__) + '/../../../../../../models/')
simulation = oc.open_simulation(file_name_or_url)
os.chdir(original_directory)
return simulation
def str_value(value):
res = format(value, '.1f')
if res == '-0.0':
return '0.0'
return res
def print_values(data):
if data is None:
print('None')
else:
data_len = len(data)
print('[ %s, %s, %s, ..., %s, %s, %s ]'
% (str_value(data[0]), str_value(data[1]), str_value(data[2]),
str_value(data[data_len - 3]), str_value(data[data_len - 2]), str_value(data[data_len - 1])))
def values(data, data_type, indent=''):
if data:
print('%s - %s:' % (indent, data_type))
for item in data.values():
print('%s - %s = ' % (indent, item.uri()), end='')
try:
print_values(item.values())
except Exception:
print(str_value(item.value()))
else:
print('%s - %s: empty' % (indent, data_type))
def run_simulation(simulation, step):
# Run the simulation
print(' - Run simulation [%d]:' % step)
print(' - Settings:')
data = simulation.data()
print(' - Starting point: %f' % data.starting_point())
print(' - Ending point: %f' % data.ending_point())
print(' - Point interval: %f' % data.point_interval())
print(' - ODE solver: %s' % data.ode_solver_name())
print(' - Initial values:')
values(data.constants(), 'Constants', ' ')
values(data.states(), 'States', ' ')
values(data.rates(), 'Rates', ' ')
values(data.algebraic(), 'Algebraic', ' ')
simulation.run()
# Retrieve the number of data points and output some or all of the
# simulation values
results = simulation.results()
states = results.states()
print(' - Result values:')
print(' - Number of points: %d' % len(states['main/x'].values()))
values(results.constants(), 'Constants', ' ')
values(states, 'States', ' ')
values(results.rates(), 'Rates', ' ')
values(results.algebraic(), 'Algebraic', ' ')
def test_simulation(title, file_name_or_url, first=True):
# Header
header(title, first)
# Open the simulation
print(' - Open simulation')
simulation = open_simulation(file_name_or_url)
# Check whether the simulation is valid and has issues, and list some
# information about it
print(' - Check simulation:')
print(' - Valid: %s' % ('yes' if simulation.valid() else 'no'))
issues = simulation.issues()
if issues:
print(' - Issues:\n - %s' % '\n - '.join(issues))
else:
print(' - Issues: none')
# Run #1: run the simulation using the default settings, except if we are
# dealing with a CellML file, in which case we set a few initial
# settings
if file_name_or_url.endswith('.cellml'):
data = simulation.data()
data.set_ending_point(50.0)
data.set_point_interval(0.001)
print(' - Initial settings:')
print(' - Ending point: %f' % data.ending_point())
print(' - Point interval: %f' % data.point_interval())
run_simulation(simulation, 1)
# Run #2: change a few settings and rerun the simulation
simulation.reset()
simulation.clear_results()
data = simulation.data()
data.set_starting_point(10.0)
data.set_ending_point(30.0)
data.set_point_interval(0.1)
data.set_ode_solver('Euler (forward)')
data.set_ode_solver_property('Step', 0.01)
print(' - New settings:')
print(' - Starting point: %f' % data.starting_point())
print(' - Ending point: %f' % data.ending_point())
print(' - Point interval: %f' % data.point_interval())
print(' - ODE solver: %s' % data.ode_solver_name())
run_simulation(simulation, 2)
# Run #3: carry on from the previous run
run_simulation(simulation, 3)
# Close the simulation
oc.close_simulation(simulation)
def run_solver_simulation(simulation, solver_name):
data = simulation.data()
data.set_ode_solver(solver_name)
data.set_ode_solver_property('Step', 0.01)
simulation.reset()
simulation.clear_results()
simulation.run()
results = simulation.results()
print(' - %s:' % solver_name)
values(results.constants(), 'Constants')
values(results.states(), 'States')
values(results.rates(), 'Rates')
values(results.algebraic(), 'Algebraic')
def run_simulations(model, title):
header(title)
simulation = open_simulation(model)
run_solver_simulation(simulation, 'CVODE')
run_solver_simulation(simulation, 'Euler (forward)')
run_solver_simulation(simulation, 'Heun')
run_solver_simulation(simulation, 'Runge-Kutta (2nd order)')
run_solver_simulation(simulation, 'Runge-Kutta (4th order)')
oc.close_simulation(simulation)