DiamondLightSource / DiamondLightSource/python-icebreaker

Cannot convert float NaN to integer

Open
#10 1 comment 0 reactions 0 assignees View on GitHub
Dominant language
Python
Stars
11
Forks
6
PR merge metrics
No merged PRs in 30d

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](https://github.com/DiamondLightSource/python-icebreaker/files/8672898/icebreaker_ptcl-proc-inputs.zip)

Contributor guide

No contributing guide indexed for this repository

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.