8000 Include functionality for modifying parameters · Issue #350 · opencor/libopencor · GitHub
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Include functionality for modifying parameters #350

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FinbarArgus opened this issue Nov 18, 2024 · 1 comment
Open

Include functionality for modifying parameters #350

FinbarArgus opened this issue Nov 18, 2024 · 1 comment
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@agarny
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@FinbarArgus
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FinbarArgus commented Nov 18, 2024 •
edited by agarny
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For replacing the Python OpenCOR API with LibOpenCOR, we need to be able to run the following commands:

self.simulation = oc.open_simulation(cellml_path)
self.simulation.valid():
self.simulation.data()
self.data.odeSolverProperties():
self.data.set_ode_solver_property(key, value)
self.data.set_point_interval(self.dt)  # time interval for data storage
self.data.set_starting_point(0)
self.data.set_ending_point(self.stop_time)

self.simulation.run()
self.simulation.reset()
self.simulation.release_all_values()
self.simulation.clear_results()
self.simulation.reset(False) # True resets everything, False resets only the states

self.simulation.results().states():
self.simulation.results().states()[variable_name].values()[-self.n_steps - 1:].copy())
self.simulation.results().algebraic():
self.simulation.results().algebraic()[variable_name].values()[-self.n_steps-1:].copy())
self.data.constants():
self.data.constants()[variable_name])

self.data.states()[param_name] = param_vals[JJ]
self.data.constants()[param_name] = param_vals[JJ]

Or equivalent commands.

For context see https://github.com/FinbarArgus/circulatory_autogen/blob/devel/src/utilities/opencor_helper.py
@agarny agarny self-assigned this Nov 18, 2024
@agarny agarny added the Feature label Nov 18, 2024
@agarny agarny added this to the 0.1 milestone Nov 18, 2024
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agarny commented Nov 18, 2024

FTR, for ISAN 2024, we quickly added a way to change model parameters by adding removeAllInitialConditions() and addInitialCondition(const std::string &pParameter, double pValue) to SedInstance. Corresponding methods were also added in the private implementation of SedInstanceTask, as well as applyInitialConditions() which was called during the initialisation of a model during a uniform time course (only supported case at this stage).

It was done this way in the interest of time since the values for the states, rates, constants, computed constants, and algebraic variables are all stored in the private implementation of SedInstanceTask. So, we probably ought to have some API on SedInstanceTask to modify the value of those different types of variables.

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