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copy files instead of move to maintain original behavior #9

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merged 3 commits into from
Jun 27, 2024
Merged

copy files instead of move to maintain original behavior #9

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5a3ec02
fix: copy files instead of move to maintain original behavior
ttngu207 Jun 26, 2024
ffcff31
fix: minor bugfix
ttngu207 Jun 26, 2024
11417cc
fix: use copy2
ttngu207 Jun 26, 2024
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5 changes: 3 additions & 2 deletions caiman/source_extraction/cnmf/cnmf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,7 @@
import logging
import numpy as np
import os
import shutil
import pathlib
import psutil
import scipy
Expand Down Expand Up @@ -388,14 +389,14 @@ def fit_file(self, motion_correct=False, indices=None, include_eval=False, outpu
os.remove(log_file)

if output_dir is not None:
# copy the result files to the specified output directory
output_dir = pathlib.Path(output_dir)
# move the result files to the specified output directory
files_to_move = [fname_new, fname_init_hdf5, fname_hdf5]
if motion_correct:
files_to_move += fname_mc
for f in files_to_move:
f = pathlib.Path(f)
os.rename(f, output_dir / f.name)
shutil.copy2(f, output_dir)

if return_mc & motion_correct:
return cnm2, mc
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