7.6.1. pyafv.calibrate.auto_calibrate

auto_calibrate(phys, ext_forces=None, dt=0.001, nsteps=50000, show=None)[source]

Auto-calibrate the parameters phys against the deformable polygon (DP) model.

In this calibration, we simulate an initially steady-state cell doublet under increasing external force dipoles using the DP model; the external force starts from 0 to max(ext_forces). We identify the detachment force as the first external force at which detachment occurs. We then search for the delta value in the finite Voronoi (FV) model to match this detachment force.

Parameters:

  • phys (PhysicalParams) – The initial physical parameters.

  • ext_forces (ndarray | None) – An array of external forces to apply during calibration; defaults to None, which uses np.linspace(0, 10, 101)[1:]; should start from a small positive value.

  • dt (float) – Time step for each simulation step.

  • nsteps (int) – Number of simulation steps to run for each external force.

  • show (bool | None) – Whether to print progress information; no need to set it if tqdm is installed.

Raises:

TypeError – If phys is not an instance of PhysicalParams.

Returns:

A tuple containing the detachment force and the calibrated PhysicalParams. If detachment does not occur within the given force range, return a NaN force.

Return type:

tuple[float, PhysicalParams]

Warning

This function may take some time to run, depending on the parameters. (If tqdm is installed, a progress bar will be shown automatically.)

Do not change defaults unless you understand the implications. If you only need a rough or faster calibration, you may change the external force range or interval. Adjusting dt and nsteps may also speed up simulations, but may affect accuracy; test the DeformablePolygonSimulator model separately to ensure accuracy is acceptable.