Possible unit mismatch for particle_diameter

[eugenejyuan]

Hi, thanks for the great tool!

I noticed a possible inconsistency in how particle_diameter is interpreted in the code:

In command_line.py L33
particle_diameter seems to be treated as a pixel-based radius.

But in RELION’s original code (e.g. ml_optimiser.cpp L642)
particle_diameter is defined as an Ångström-based diameter.

In command_line.py L185
it again appears to be used as an Ångström diameter, consistent with RELION.

This makes me wonder:
Is the unit/meaning of particle_diameter intended to differ here, or is this a small oversight?

Just raising the question in case this was unintentional. Thanks!

[biochem-fan]

Thank you very much for pointing this out.

I think

relion-blush/relion_blush/command_line.py

Line 35 in 87c01af

radius = particle_diameter * pixel_size + mask_edge_width / 2.

should be:

radius = (particle_diameter / pixel_size + mask_edge_width) / 2

Can @dkimanius confirm?