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Description
I'm seeing this error with topaz 0.3.7, but topaz 0.2.5 works fine with the same command. Is it because the model was trained with the older version?
The command was originally generated by the cryoSPARC wrapper but I am running it directly, using the topaz conda environment.
(topaz-0.3.7) host:/path$ topaz extract --radius 28 --threshold -6 --up-scale 4 --assignment-radius -1 --min-radius 5 --max-radius 100 --step-radius 5 --num-workers 4 --device 0 --model model_epoch48.sav -o topaz_particles_prediction.txt X-2Y-2-2_aligned_mic_DW.mrc X+0Y+0-2_aligned_mic_DW.mrc X-1Y+0-3_aligned_mic_DW.mrc
# Beginning extraction
Traceback (most recent call last):
File "/apps/software/miniforge3/envs/topaz-0.3.7/bin/topaz", line 33, in <module>
sys.exit(load_entry_point('topaz-em==0.3.7', 'console_scripts', 'topaz')())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/software/miniforge3/envs/topaz-0.3.7/lib/python3.11/site-packages/topaz/main.py", line 148, in main
args.func(args)
File "/apps/software/miniforge3/envs/topaz-0.3.7/lib/python3.11/site-packages/topaz/commands/extract.py", line 64, in main
extract_particles(args.paths, args.model, args.device, args.batch_size, args.threshold, args.radius, args.num_workers,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/software/miniforge3/envs/topaz-0.3.7/lib/python3.11/site-packages/topaz/extract.py", line 333, in extract_particles
for path,score,coords in nms_iterator(stream, radius, threshold, pool=pool, dims=dims, verbose=verbose):
File "/apps/software/miniforge3/envs/topaz-0.3.7/lib/python3.11/site-packages/topaz/extract.py", line 99, in nms_iterator
for name,score,coords in pool.imap_unordered(process, paths_scores):
File "/apps/software/miniforge3/envs/topaz-0.3.7/lib/python3.11/multiprocessing/pool.py", line 873, in next
raise value
AttributeError: Can't get attribute 'BasicConv2d' on <module 'topaz.model.features.resnet' from '/apps/software/miniforge3/envs/topaz-0.3.7/lib/python3.11/site-packages/topaz/model/features/resnet.py'>
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