New local refinement error

Troubleshooting
1

I’m trying to do a new local refinement. The job fails after the iteration 0. I haven’t had this issue with the old local refinement:

[CPU: 1.95 GB]   Traceback (most recent call last):
  File "/home/yunior/Yunior/Projects/cryoSPARC/cryosparc2/cryosparc_worker/cryosparc_compute/jobs/runcommon.py", line 1726, in run_with_except_hook
    run_old(*args, **kw)
  File "/home/yunior/Yunior/Projects/cryoSPARC/cryosparc2/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/threading.py", line 870, in run
    self._target(*self._args, **self._kwargs)
  File "cryosparc_worker/cryosparc_compute/engine/newengine.py", line 2109, in cryosparc_compute.engine.newengine.process.work
  File "cryosparc_worker/cryosparc_compute/engine/newengine.py", line 2157, in cryosparc_compute.engine.newengine.process.work
  File "cryosparc_worker/cryosparc_compute/engine/newengine.py", line 1171, in cryosparc_compute.engine.newengine.EngineThread.find_best_pose_shift_class
  File "<__array_function__ internals>", line 6, in unravel_index
ValueError: index 1069559411 is out of bounds for array with size 22589
2

Hi @cfonseca,

Thanks for reporting this error. We’ve seen this a few times and we’re trying to reproduce this on our end. Could I ask you to send a screenshot of the job parameters? As well, would you be open to (confidentially) sharing particle data to help us debug?

Best,
Michael

3

Hi, Michael,

I used the default parameters values.

cs_error1
cs_error11884×755 77.2 KB
cs_error2
cs_error21889×763 128 KB
cs_error3
cs_error31880×716 148 KB
cs_error4
cs_error41895×764 137 KB
cs_error5
cs_error51878×767 136 KB

4

There is no problem in sharing the particles. If you give me an email address, I’ll share them by google drive.

5

Hi @cfonseca,

Thank you for the reply and the parameter screenshots – I will follow up over email.

Best,
Michael

6

For posterity, the error was due to a binary mask being used – workaround mentioned here resolved the issue.