OpenCOR comes bundled with Python, providing OpenCOR with Python support. The following Python packages are included:
Matplotlib: a comprehensive library for creating static, animated, and interactive visualizations in Python;
NumPy: the fundamental package for scientific computing with Python; and
SciPy: the fundamental algorithms for scientific computing in Python.
Some code illustrating the use of the OpenCOR Python module and wrappers can be found here.
Additional Python packages can be installed either from the CLI (using the jupyterconsole[.bat] script) or through the GUI (using the Python Console window plugin):
!pip install package_name
A Python module, opencor, is available and can be used to handle simulations in OpenCOR:
open_simulation(file_name_or_url): open and return a Simulation object for the given local or remote CellML file, SED-ML file, or COMBINE archive.
close_simulation(simulation): close the given Simulation object.
simulation(): return the active Simulation object, if any.
Note: simulation() is only available when using the Python Console window plugin.
The following OpenCOR classes have Python wrappers that can be used to handle a simulation, some simulation data, some simulation results, a data store, and a data store variable:
Simulation:
clear_results(): clear the simulation results.
data(): return the simulation data as a SimulationData object.
issues(): return a list of issues with the simulation.
release_all_values(): release all the values retrieved as a NumPy array (see DataStoreVariable.values()).
release_values(values): release the values retrieved as a NumPy array (see DataStoreVariable.values()).
reset(all = True): reset all the model parameters (all = True) or only the state model parameters (all = False).
results(): return the results as a SimulationResults object.
run(): run the simulation.
valid(): return whether the simulation is valid.
SimulationData:
algebraic(): return the algebraic values as a Python dictionary of DataStoreValue objects.
constants(): return the constant values as a Python dictionary of DataStoreValue objects.
ending_point(): return the ending point.
nla_solver_name(): return the name of the NLA solver.
nla_solver_property(name): return the value of the given NLA solver property.
ode_solver_name(): return the name of the ODE solver.
ode_solver_property(name): return the value of the given ODE solver property.
point_interval(): return the point interval.
rates(): return the rate values as a Python dictionary of DataStoreValue objects.
set_ending_point(value): set the ending point to the given value.
set_nla_solver(name): set the NLA solver to the given NLA solver name.
set_nla_solver_property(name, value): set the given NLA solver property to the given value.
set_ode_solver(name): set the ODE solver to the given ODE solver name.
set_ode_solver_property(name, value): set the given ODE solver property to the given value.
set_point_interval(value): set the point interval to the given value.
set_starting_point(value): set the starting point to the given value.
starting_point(): return the starting point.
states(): return the state values as a Python dictionary of DataStoreValue objects.
Note: set_ode_solver(), set_ode_solver_property(), set_nla_solver(), and set_nla_solver_property() do not currently update the GUI.
SimulationResults:
algebraic(): return the algebraic values as a Python dictionary of DataStoreVariable objects.
constants(): return the constant values as a Python dictionary of DataStoreVariable objects.
data_store(): return the associated data store as a DataStore object.
rates(): return the rate values as a Python dictionary of DataStoreVariable objects.
states(): return the state values as a Python dictionary of DataStoreVariable objects.
voi(): return the variable of integration as a DataStoreVariable object.
DataStore:
variables(): return the variables as a Python dictionary of DataStoreVariable objects.
voi(): return the variable of integration as a DataStoreVariable object.
voi_and_variables(): return the variable of integration and variables as a Python dictionary of DataStoreVariable objects.
DataStoreValue:
set_value(value): set the value.
uri(): return the URI.
value(): return the value.
DataStoreVariable:
name(): return the name.
runs_count(): return the number of runs.
type(): return the type of the variable (1: variable of integration, 2: state, 3: rate, 4: constant, 5: computed constant, and 6: algebraic).
unit(): return the unit.
uri(): return the URI.
value(position, run = -1): return the value at the given position and for the given run (run = -1 corresponds to the last run).
values(run = -1): return the values for the given run (run = -1 corresponds to the last run) as a NumPy array.
values_count(run = -1): return the number of values for the given run (run = -1 corresponds to the last run).