diff --git a/caiman/source_extraction/cnmf/cnmf.py b/caiman/source_extraction/cnmf/cnmf.py index e5f78452d..36d996a59 100644 --- a/caiman/source_extraction/cnmf/cnmf.py +++ b/caiman/source_extraction/cnmf/cnmf.py @@ -21,6 +21,7 @@ import logging import numpy as np import os +import shutil import pathlib import psutil import scipy @@ -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