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IMSY-DKFZ / simpa

The Simulation and Image Processing for Photonics and Acoustics (SIMPA) toolkit.
https://simpa.readthedocs.io/en/main/
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Add MCX simulation reflection flag -b #337

Open RecurvedBow opened 4 months ago

RecurvedBow commented 4 months ago

Please describe your :rocket: feature request. Add the -b / --reflect flag to the MCX simulation without breaking any existing reflectance behavior (https://mcx.space/wiki/index.cgi?Doc/mcx_help).

Describe the solution you'd like Update the MCXAdapter to accept a boolean flag whether the photons should be reflected or transmitted at the simulation borders.

RecurvedBow commented 4 months ago

Will only apply reflection on the volume faces along the x-axis and z-axis

RecurvedBow commented 4 months ago

Since there are multiple possible behaviors, will define an enum instead of a boolean flag instead. Will include: default, fresnel reflection, mirror reflection, cyclic

kdreher commented 4 months ago

This issue is related to #286 and we'll wait until that one is resolved :)

leoyala commented 4 months ago

This could also be resolved by #311 since user-defined flags could be passed and would overwrite the default ones.

RecurvedBow commented 4 months ago

I have found out that the command flags for capturing reflectance are set incorrectly: we do not need --saveref; and there is actually a bug with saving photon direction and position on exit. I will address the first case in this issue, and add the second as a bug issue