ValueError: zero-size array to reduction operation minimum which has no identity

Troubleshooting
1

Dear Cryosparc team,

I have done a local refinement a job using input files of particles, volume and mask from another local refinement job. The job result shows tight resolution up to 2.9 A.

The 2.9 A job’s output files of volume and mask were used to create the local resolution map.

But, I ended up with the following error

[CPU: 3.13 GB] Traceback (most recent call last):
File “cryosparc_worker/cryosparc_compute/run.py”, line 84, in cryosparc_compute.run.main
File “cryosparc_master/cryosparc_compute/jobs/local_resolution/run.py”, line 654, in cryosparc_compute.jobs.local_resolution.run.run_locres
File “cryosparc_master/cryosparc_compute/jobs/local_resolution/run.py”, line 1059, in cryosparc_compute.jobs.local_resolution.run.standalone_locres
File “<array_function internals>”, line 6, in amin
File “/mnt/ssd/cryosparc_user/cryosparc2_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages/numpy/core/fromnumeric.py”, line 2831, in amin
keepdims=keepdims, initial=initial, where=where)
File “/mnt/ssd/cryosparc_user/cryosparc2_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages/numpy/core/fromnumeric.py”, line 87, in _wrapreduction
return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
ValueError: zero-size array to reduction operation minimum which has no identity

Please give me some suggestion to create local resolution map.

Cheers

Vijaya

2

Hi @Vijaya,

I believe this is due to a known error discussed here, which we’re planning to address soon. If this is the same problem, it is caused by the mask not being scaled correctly to the range of [0,1]. Can you check the mask that was input to the job in the mask_refine slot has the correct range, and that values are between [0,1] and not some other range? If the mask is alright, can you then follow the GIF posted here to connect the inputs?

Best,
Michael