Cannot convert float NaN to integer

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
38/100
Issue type
Bug
Clarity
Needs clarification
Activity status
Stale
Tech stack
python
Domain
data

Research direction

Start with python-icebreaker/src/icebreaker/cli/ib_group.py and the icebreaker/ice_groups.py traceback location, using the attached STAR files to reproduce the failure. Compare the grouped_micrographs.star and selected particles.star inputs and trace which value becomes NaN before the integer conversion. Done means the input cause is understood and the job reports or handles it without this traceback.

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Description

Hi I run the test jobs to "flatten" and to "group" micrographs through relion. These jobs completed successfully. Now, I selected my particles in relion and I am trying to assign ice thickness coeficient. I use the ib_group.py, input mics from grouped_micrographs.star and selected particles.star without any parameter settings and single-threaded.

The job throws this error:

Traceback (most recent call last):
File "python-icebreaker-master/src/icebreaker/cli/ib_group.py", line 79, in
main()
File "python-icebreaker-master/src/icebreaker/cli/ib_group.py", line 70, in main
run_job(project_dir, job_dir, other_args)
File "python-icebreaker-master/src/icebreaker/cli/ib_group.py", line 34, in run_job
ib_igroups.main

File "/home/exx/Application/anaconda3/lib/python3.8/site-packages/icebreaker_em-0.3.5-py3.8.egg/icebreaker/ice_groups.py", line 65, in main
ice_groups.append(int(micro_now[y1][x1] * 10000))
ValueError: cannot convert float NaN to integer

What could be the reason? I tried converting group_micrographs.star file using relion_convert_star to match the format of the native particle.star. Files I used by default are attached.

Could you please take a lot, as I would really like to test the capacity of the IceBreaker.

Thank you
icebreaker_ptcl-proc-inputs.zip

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