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"NameError: name 'shutil' is not defined, line 231 "shutil.copy(classorig, classfile)" in "roi_detect _and_extract(ops) #171

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vickerse1 opened this issue Jul 12, 2019 · 0 comments

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@vickerse1
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Hello,

I get this error just after suite2p finishes detecting ROIs. I'm running the "run_pipeline_tiffs_or_batch.ipynb" jupyter notebook in jupyter lab.


NameError Traceback (most recent call last)
in
13
14 # run one experiment
---> 15 opsEnd = run_s2p(ops=ops,db=db)

~/miniconda3/envs/suite2p/lib/python3.7/site-packages/suite2p/run_s2p.py in run_s2p(ops, db)
201 t11=tic()
202 print('----------- ROI DETECTION AND EXTRACTION')
--> 203 ops1[ipl] = roiextract.roi_detect_and_extract(ops1[ipl])
204 ops = ops1[ipl]
205 fpath = ops['save_path']

~/miniconda3/envs/suite2p/lib/python3.7/site-packages/suite2p/roiextract.py in roi_detect_and_extract(ops)
229 "classifiers/classifier.npy"
230 )
--> 231 shutil.copy(classorig, classfile)
232 print('NOTE: applying classifier %s'%classfile)
233 iscell = classifier.run(classfile, stat, keys=['npix_norm', 'compact', 'skew'])

NameError: name 'shutil' is not defined

Do you have an idea what the problem might be?

Thanks,

Evan

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