Hello all,
I’m running RBMC, which seems to be running fine, apart from some missing thumbnails:
For instance, the FCC thumbnail is displayed, whereas the FCC fit and the Empirical dose weights contain no data. During subsequent MC, the particle trajectories are displayed without a problem, yet the corresponding particle thumbnails remain blank as well. I’m assuming this is merely a bug, and I’m also assuming that the RBMC is running as intended.
@msleutel Please can you describe the sequence of upstream processing steps, including
Hello, I have the same problem. In my case, the job finishes as expected, but downstream refinements crash with the error I attached below. I am not 100% sure these two are connected, but I have run reference based motion correction on other data sets and it worked fine (both the thumbnails as well as downstream refinements).
It might be noteworthy that in the case where it does not work, the underlying raw data is Falcon4 EER data, but they were converted to Tifs at the facility as part of the on the fly processing pipeline. Can this be a problem? In cases where RBMC worked, it was always K3 data.
[CPU: 2.52 GB]
Traceback (most recent call last):
File “/net/black/data/shared/cryosparc/dfci-cryosparc/cryosparc_worker/cryosparc_compute/jobs/runcommon.py”, line 2192, in run_with_except_hook
run_old(*args, **kw)
File “cryosparc_master/cryosparc_compute/gpu/gpucore.py”, line 134, in cryosparc_master.cryosparc_compute.gpu.gpucore.GPUThread.run
File “cryosparc_master/cryosparc_compute/gpu/gpucore.py”, line 135, in cryosparc_master.cryosparc_compute.gpu.gpucore.GPUThread.run
File “cryosparc_master/cryosparc_compute/engine/engine.py”, line 1142, in cryosparc_master.cryosparc_compute.engine.engine.process.work
File “cryosparc_master/cryosparc_compute/engine/engine.py”, line 432, in cryosparc_master.cryosparc_compute.engine.engine.EngineThread.find_and_set_best_pose_shift
File “<array_function internals>”, line 5, in unravel_index
ValueError: index 2147483647 is out of bounds for array with size 5376
For what it’s worth, in my case the problem came from combining 2 particle sets from two grids. I re-extracted them individually and ran RBMC on each set, and now all looks normal (thumbnails and downstream refinements).
Hi @Moritz. For what it’s worth, it looks like the last column of pixels in the FCC plot contained NaNs or infinities, which is probably the immediate cause of the blank model fit. As for why that occurred, I’m not entirely sure, but I’m glad that you were able to work around the issue.
