In a dataset I'm working with, the lamellae was straightened during the AreTomo alignment (through the warptools aretomo wrapper) and that leads to the tilt angles changing absolute values (though their relative orientation is kept constant).
/scratch/dobbs/t4infection/untreated/20241220_first_bw/tomo_processing/subtomo_70s_Rasmus/subtomo/newEcoli_L01_ts_010/newEcoli_L01_ts_010_0000000_ctf_5.00A.csv tilt assignment error!
Traceback (most recent call last):
File "/struct/mahamid/rasmus/software/opus/opusTomo/cryodrgn/starfile.py", line 492, in get_warp3dctfs
dummy_tlt[mask_indices] = def_tlt
ValueError: shape mismatch: value array of shape (39,9) could not be broadcast to indexing result of shape (29,9)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/struct/mahamid/rasmus/software/opus/opusTomo/cryodrgn/dataset.py", line 91, in load_warp_subtomos
warp_ctfs, ctf_files, ctf_params = star.get_warp3dctfs(datadir=datadir, lazy=lazy, tilt_step=tilt_step, tilt_range=tilt_range, tilt_limit=tilt_limit)
File "/struct/mahamid/rasmus/software/opus/opusTomo/cryodrgn/starfile.py", line 495, in get_warp3dctfs
raise RuntimeError
RuntimeError
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/kjeldsen/.conda/envs/opus_n4/bin/dsd", line 7, in <module>
sys.exit(main())
File "/struct/mahamid/rasmus/software/opus/opusTomo/cryodrgn/__main__.py", line 65, in main
args.func(args)
File "/struct/mahamid/rasmus/software/opus/opusTomo/cryodrgn/commands/train_tomo.py", line 681, in main
data = dataset.LazyTomoWARPMRCData(args.particles, norm=args.norm,
File "/struct/mahamid/rasmus/software/opus/opusTomo/cryodrgn/dataset.py", line 412, in __init__
particles, ctfs, ctf_files, warp_ctfs = load_warp_subtomos(mrcfile, True, datadir=datadir, relion31=relion31,
File "/struct/mahamid/rasmus/software/opus/opusTomo/cryodrgn/dataset.py", line 97, in load_warp_subtomos
else: raise RuntimeError(e)
RuntimeError
Let me know if you need any additional information. As several people in our lab uses the aretomo wrapper in WarpTools we would appreciate if it would be possbile to fix this issue.
Dear AlnCat,
In a dataset I'm working with, the lamellae was straightened during the AreTomo alignment (through the warptools aretomo wrapper) and that leads to the tilt angles changing absolute values (though their relative orientation is kept constant).
I therefore get an error when trying to train a model on the data:
Let me know if you need any additional information. As several people in our lab uses the aretomo wrapper in WarpTools we would appreciate if it would be possbile to fix this issue.
Thank you,
Rasmus