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use CAIMAN_TEMP to store mcorr memmap and then move back to parent dir #22

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merged 2 commits into from
May 25, 2022
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Merged

use CAIMAN_TEMP to store mcorr memmap and then move back to parent dir #22

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use caiman to store mcorr memmaps and move them back to parent dir w…
kushalkolar May 24, 2022
e1182ef
Merge branch 'master' into caiman-tempdir-mcorr
kushalkolar May 24, 2022
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29 changes: 23 additions & 6 deletions mesmerize_core/algorithms/mcorr.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@
import os
from pathlib import Path
import numpy as np
from shutil import move as move_file


# prevent circular import
Expand All @@ -29,7 +30,14 @@ def main(batch_path, uuid, data_path: str = None):
set_parent_data_path(data_path)
input_movie_path = str(get_full_data_path(input_movie_path))

params = item["params"]
# because caiman doesn't let you specify filename to save memmap files
# create dir with uuid as the dir name
caiman_temp_dir = str(Path(input_movie_path).parent.joinpath(str(uuid)))
os.makedirs(caiman_temp_dir, exist_ok=True)
os.environ["CAIMAN_TEMP"] = caiman_temp_dir
os.environ["CAIMAN_NEW_TEMPFILE"] = "True"

params = item['params']

# adapted from current demo notebook
if "MESMERIZE_N_PROCESSES" in os.environ.keys():
Expand All @@ -52,8 +60,8 @@ def main(batch_path, uuid, data_path: str = None):
try:
# Run MC
fnames = [input_movie_path]
mc = MotionCorrect(fnames, dview=dview, **opts.get_group("motion"))
mc.motion_correct(save_movie=True, base_name_prefix=uuid)
mc = MotionCorrect(fnames, dview=dview, **opts.get_group('motion'))
mc.motion_correct(save_movie=True)

# Find path to mmap file
output_path = Path(mc.mmap_file[0])
Expand Down Expand Up @@ -106,22 +114,31 @@ def main(batch_path, uuid, data_path: str = None):
shift_path = Path(input_movie_path).parent.joinpath(f"{uuid}_shifts.npy")
np.save(str(shift_path), shifts)

# filename to move the output back to data dir
mcorr_memmap = Path(input_movie_path).parent.joinpath(
f"{uuid}_{output_path.stem}.mmap"
)

# move the output file
move_file(get_full_data_path(output_path), mcorr_memmap)
os.removedirs(caiman_temp_dir)

if data_path is not None:
cn_path = cn_path.relative_to(data_path)
output_path = get_full_data_path(output_path).relative_to(data_path)
mcorr_memmap = get_full_data_path(mcorr_memmap).relative_to(data_path)
shift_path = shift_path.relative_to(data_path)
for proj_type in proj_paths.keys():
d[f"{proj_type}-projection-path"] = proj_paths[proj_type].relative_to(
data_path
)
else:
cn_path = cn_path
output_path = get_full_data_path(output_path)
mcorr_memmap = get_full_data_path(mcorr_memmap)
shift_path = shift_path.resolve()

d.update(
{
"mcorr-output-path": output_path,
"mcorr-output-path": mcorr_memmap,
"corr-img-path": cn_path,
"shifts": shift_path,
"success": True,
Expand Down