RBMC 0% Cross-Validation Scores

[joonpark]

Hi,

I am currently having a problem running reference based motion correction on a dataset. The job gives following error message during the last step (particle motion correction) “Non-fatal error during computation of summary stats: need at least one array to concatenate”. I noticed that the cross-validation scores computed stay at 0%, which results in weird plots for subsequent steps. What may be going wrong here?

Thank you,
Joon

[CPU: 1.65 GB Avail: 490.60 GB]

    STARTING: OPTIMIZE HYPERPARAMETERS

---

[CPU: 1.69 GB Avail: 490.56 GB]
Working with 2515 movies containing 125024 particles

[CPU: 1.69 GB Avail: 490.56 GB]
Computing intended data cache configuration

[CPU: 2.04 GB Avail: 490.20 GB]
SEARCH RANGES:
zs:
6.2146
8.0064
thetas:
-1.9373
-2.0420
-2.1468
-2.2515
-2.3562
-2.4609
-2.5656
-2.6704
-2.7751
r start:
0.1000
r end:
30.0000
r step:
1.9933

[CPU: 2.04 GB Avail: 490.18 GB]
==================== BEGINNING ITERATION 1 ====================

[CPU: 2.04 GB Avail: 490.18 GB]
Iteration overview (parameters to be tried):
—r— -theta- —z— | -spatial- -dist.- --accel–
0.100 -1.937 6.215 | 9.65e-01 500 9.11e-01
0.100 -2.042 6.215 | 9.56e-01 500 9.15e-01
0.100 -2.147 6.215 | 9.47e-01 500 9.20e-01
0.100 -2.251 6.215 | 9.39e-01 500 9.25e-01
0.100 -2.356 6.215 | 9.32e-01 500 9.32e-01
0.100 -2.461 6.215 | 9.25e-01 500 9.39e-01
0.100 -2.566 6.215 | 9.20e-01 500 9.47e-01
0.100 -2.670 6.215 | 9.15e-01 500 9.56e-01
0.100 -2.775 6.215 | 9.11e-01 500 9.65e-01
0.100 -1.937 8.006 | 9.65e-01 3000 9.11e-01
0.100 -2.042 8.006 | 9.56e-01 3000 9.15e-01
0.100 -2.147 8.006 | 9.47e-01 3000 9.20e-01
0.100 -2.251 8.006 | 9.39e-01 3000 9.25e-01
0.100 -2.356 8.006 | 9.32e-01 3000 9.32e-01
0.100 -2.461 8.006 | 9.25e-01 3000 9.39e-01
0.100 -2.566 8.006 | 9.20e-01 3000 9.47e-01
0.100 -2.670 8.006 | 9.15e-01 3000 9.56e-01
0.100 -2.775 8.006 | 9.11e-01 3000 9.65e-01

[CPU: 2.04 GB Avail: 490.18 GB]
Cross-validation scores computed:
[--------------------------------------------------------------------------------] 0/45270 (0%)

[CPU: 2.77 GB Avail: 492.46 GB]
Terminating ray theta=-1.9373, z=6.2146 (~zero trajectories)

[CPU: 2.77 GB Avail: 492.46 GB]
Terminating ray theta=-2.0420, z=6.2146 (~zero trajectories)

[CPU: 2.77 GB Avail: 492.46 GB]
Terminating ray theta=-2.1468, z=6.2146 (~zero trajectories)

[CPU: 2.77 GB Avail: 492.46 GB]
Terminating ray theta=-2.2515, z=6.2146 (~zero trajectories)

[CPU: 2.77 GB Avail: 492.46 GB]
Terminating ray theta=-2.3562, z=6.2146 (~zero trajectories)

[CPU: 2.77 GB Avail: 492.46 GB]
Terminating ray theta=-2.4609, z=6.2146 (~zero trajectories)

[CPU: 2.77 GB Avail: 492.46 GB]
Terminating ray theta=-2.5656, z=6.2146 (~zero trajectories)

[CPU: 2.77 GB Avail: 492.46 GB]
Terminating ray theta=-2.6704, z=6.2146 (~zero trajectories)

[CPU: 2.77 GB Avail: 492.46 GB]
Terminating ray theta=-2.7751, z=6.2146 (~zero trajectories)

[CPU: 2.77 GB Avail: 492.46 GB]
Terminating ray theta=-1.9373, z=8.0064 (~zero trajectories)

[CPU: 2.77 GB Avail: 492.46 GB]
Terminating ray theta=-2.0420, z=8.0064 (~zero trajectories)

[CPU: 2.77 GB Avail: 492.46 GB]
Terminating ray theta=-2.1468, z=8.0064 (~zero trajectories)

[CPU: 2.77 GB Avail: 492.46 GB]
Terminating ray theta=-2.2515, z=8.0064 (~zero trajectories)

[CPU: 2.77 GB Avail: 492.46 GB]
Terminating ray theta=-2.3562, z=8.0064 (~zero trajectories)

[CPU: 2.77 GB Avail: 492.46 GB]
Terminating ray theta=-2.4609, z=8.0064 (~zero trajectories)

[CPU: 2.77 GB Avail: 492.46 GB]
Terminating ray theta=-2.5656, z=8.0064 (~zero trajectories)

[CPU: 2.77 GB Avail: 492.46 GB]
Terminating ray theta=-2.6704, z=8.0064 (~zero trajectories)

[CPU: 2.77 GB Avail: 492.46 GB]
Terminating ray theta=-2.7751, z=8.0064 (~zero trajectories)

[hsnyder]

Hi @joonpark, thanks for bringing this up, I haven’t seen this exact behaviour before. Could you please check the job’s text log to see if there’s any additional information? In the job dialog box, go to the metadata tab and then click “log” on the line below the tabs.

Thanks
– Harris

[joonpark]

Hi @hsnyder

I looked at the log, and it couldn’t read the files. It turned out that I forgot that I compressed the movie files. I will decompress and try again.

Thank you,
Joon

[Saeed]

Hi @joonpark
I am also facing the exact same problem. Can you tell how did you troubleshoot. And what do you mean by “I compressed the movie”.

[wtempel]

@Saeed Did you observe any error messages in the job log, which you can read under the Metadata|Log tab?

[joonpark]

Hi @Saeed
I compressed mrc into mrc.bz2 files for storage and later uncompressed them for RBMC. What worked for me is not checking the “16-bit” option in the patch motion correction.