3d classification error which I haven't seen before

3D Classification
1

Hi all,

I am trying to run a 3d classification to clear up my particle stack for 3dflex, and
i get the following error:

[CPU: 720.3 MB Avail: 170.76 GB]
Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 96, in cryosparc_compute.run.main
File “cryosparc_master/cryosparc_compute/jobs/class3D/run.py”, line 262, in cryosparc_compute.jobs.class3D.run.run_class_3D
File “/opt/cryosparc2/cryosparc2_worker/cryosparc_compute/plotutil.py”, line 471, in plot_central_slices_with_mask
mask_plot[mask_plot < 1e-8] = n.nan
ValueError: cannot convert float NaN to integer

Any ideas? My first instinct is to resample the particles to give an integer pixel and box size, but
i feel like this can’t really be the problem… any help much appreciated

2

Hi @sheff_diamond_em,

Looks like there might be an issue with your focus mask? Can you tell us where this comes from? One way this error might occur is if the focus mask is a ‘binary’ mask full of integers (which we do not recommend or support). If that’s the case, perhaps using Volume Tools to pad/dilate this mask may fix things.

Hope that helps!
Valentin

1 Like
3

Hi, sorry for the slow reply!

You’re absolutely right, making the mask afresh in cryosparc solved the problem, many thanks

Fred