Port over solution creation and scaling code

[ebrahimebrahim]

In #104 the focus was on porting over the solution analysis function.

In this issue we are indicating that we also need

• something like calc_solution to act as a simulation runner. Note that Plan in matlab becomes Protocol in openlifu-python, and also note that there was an initial attempt to do something similar to calc_solution here in SlicerOpenLIFU.
• especially the scale_solution aspect which uses part of the solution analysis to rescale the solution and Pulse. This is the criticial part that we need for a minimal workflow to be viable: to determine the amplitude of pulse

Depends on #104
Would be nice to have #125 done before starting on this

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Traceability Information:

• Issue: OpenLIFU-python#126
• SOFTREQ: SlicerOpenLIFU#36
• Comment: This issue is related to the requirements defined in SlicerOpenLIFU#36.

This information was populated automatically by a script on 2025-06-09T18:01:38Z.

[ebrahimebrahim]

When we port over calc_solution we will want to stack simulation outputs over foci.

In the initial attempt in SlicerOpenLIFU (linked above) you can see that it was done by List[PlanFocus] where a PlanFocus contained a simulation output xarray. We will get away from this, because of the fix introduced in #127 .

After the fix in #127 here is a way to stack multiple simulation outputs into the correct sort of xarray dataset.

combined_dataset = xarray.concat(
    [
        sim.assign_coords(focal_point_index=i)
        for i,sim in enumerate(sims)
    ],
    dim='focal_point_index',
)

assuming sims is a list of individual xarray datasets (one for each focal point and ordered in the same order as the list of focal points) that are output of openlifu.sim.run_similation.