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PhysiCell-Tools / PhysiCell-Studio

PhysiCell Studio is a graphical tool to allow easy editing of a (XML) model, create initial positions of cells, run a simulation, and visualize results. To contribute, fork and make PRs to the development branch.
GNU General Public License v3.0
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Parameter distributions to initialize cells #222

Closed drbergman closed 2 months ago

drbergman commented 4 months ago

WARNING: DO NOT MERGE UNTIL PHYSICELL UPDATES TO INCLUDE INITIALIZATION OF PARAMETER DISTRIBUTIONS.

This gets studio ready for a future PhysiCell commit that will allow parameters to be initialized from distributions. Namely, https://github.com/MathCancer/PhysiCell/pull/203

To do this, I add a Misc tab at the end of the cell def tab. Possible improvement: check that parameter values are sensible/will not raise errors when run in PhysiCell. We're talking min < max and bounds on log-scale parameters are strictly positive (if you want a lognormal par to be arbitrarily small, then don't put on a lower_bound)

drbergman commented 3 months ago

Another to do: display a table of distributions defined for a single cell type/all cell types.

rheiland commented 2 months ago

Was this PR superseded by another, or is it still relevant?

drbergman commented 2 months ago

No. I do have another local branch that fixes the custom var bug found while making this. I've kept them separate though just to modularize the PRs. If it's better for you, I can combine. Looks like there's conflicts to resolve here anyways