Hey Team,
I have been having this error when I am running the Local Refinement Job with some maps: UnboundLocalError: local variable ‘map_r’ referenced before assignment
I cannot pinpoint which maps cause this issue, but it occurs in Cryosparc v5.0.6
It happens even when I “clone” jobs in old project folders.
Update:
This occurs when “Re-Estimate Gray Scale of Input structure” is selected.
Please can you post the full traceback?
Does this mean that you did not observe the error when this option was disabled?
Yes, basically when I enable this option, I get this error.
Here’s the traceback:
Progress: [▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇▇] 56/56 (100%)
Transferred: subtracted_particles_B_9.mrcs (76.29 MiB)
Threads: 2
Avg speed: 490.65 MiB/s
Remaining: 0h 00m 00s (0.00 B)
Elapsed: 0h 00m 08s
Active jobs: P1-J444, P1-J443
SSD cache complete for 56 file(s)
──────────────────────────────────────────────────────────────CPU: 563.9 MBDone.
CPU: 563.9 MBWindowing particles
CPU: 564.5 MBDone.
CPU: 564.5 MB====== Box sizes ======
CPU: 564.5 MBInput particles have box size 200
CPU: 564.6 MBInput particles have pixel size 3.4264
CPU: 564.6 MBParticles will be zeropadded/truncated to size 200 during alignment
CPU: 564.6 MBVolume refinement will be done with effective box size 200
CPU: 564.6 MBVolume refinement will be done with pixel size 3.4264
CPU: 564.6 MBParticles will be zeropadded/truncated to size 200 during backprojection
CPU: 564.6 MBParticles will be backprojected with box size 200
CPU: 564.7 MBVolume will be internally cropped and stored with box size 200
CPU: 564.7 MBVolume will be interpolated with box size 200 (zeropadding factor 1.00)
CPU: 564.7 MB====== Masking ======
CPU: 747.9 MBA mask input was connected.
CPU: 747.9 MBResampling initial mask to specified volume representation size and pixel-size..
CPU: 778.5 MBStatic masking was enabled.
CPU: 778.5 MB====== Local Refinement ======
CPU: 778.9 MBSearching over rotation extent of 5.00 degrees.
CPU: 778.9 MBSearching over shift extent of 5.00 Angstroms.
CPU: 778.9 MBUsing a rotation prior with stdev of 15.00 degrees.
CPU: 778.9 MBUsing a shift prior with stdev of 7.00 Angstroms.
CPU: 778.9 MBRe-centering poses each iteration.
CPU: 778.9 MBRe-centering shifts each iteration.
CPU: 778.9 MBRunning 7 branch and bound iterations to align particles to 0.020 degrees
CPU: 779.1 MB====== Non-Uniform Refinement ======
CPU: 779.1 MBNon-Uniform Refinement is enabled.
CPU: 779.1 MBUsing AWF of 3.00.
CPU: 779.1 MBUsing butterworth filter with order 2.
CPU: 779.1 MB====== Gold Standard Split ======
CPU: 779.1 MBParticles have input alignments3D connected, so reusing pre-existing split
CPU: 779.1 MBSet A is smaller than set B by 125 particles (0.46 percent difference relative to the total dataset).
CPU: 779.1 MBSplit A has 13515 particles
CPU: 779.1 MBSplit B has 13640 particles
CPU: 779.1 MB====== Refinement ======
CPU: 779.1 MBDC components of images will be ignored and volume will be floated at each iteration.
CPU: 779.1 MBSpherical windowing of maps is enabled
CPU: 833.9 MBRefining with T symmetry enforced
CPU: 833.9 MBResetting input per-particle scale factors to 1.0
CPU: 834.0 MBStarting at initial resolution 12.000A (radwn 57.107).
CPU: 834.2 MBInitializing noise model… (1/2)
CPU: 1.03 GBDone in 3.876s.Noise Model Initialization (1/2)
CPU: 1.04 GB====== Initial Model ======
Input Mask Real Space Slices
CPU: 1.04 GBResampling initial model to specified volume representation size and pixel-size…
CPU: 1.08 GBEstimating scale of initial reference.
CPU: 1.20 GBRescaling initial reference by a factor of 1.157
CPU: 942.0 MBTraceback (most recent call last):
File “cli/run.py”, line 106, in cli.run.run_job
File “cli/run.py”, line 211, in cli.run.run_job_function
File “compute/jobs/local_refine/run_localrefine.py”, line 606, in compute.jobs.local_refine.run_localrefine.run_local_refine
UnboundLocalError: local variable ‘map_r’ referenced before assignment
Thanks @stavros for your report and the additional details. This is a bug; we made a note about it internally.