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Fix multiprocess in dev tracking #676

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merged 4 commits into from
Mar 1, 2023
Merged

Fix multiprocess in dev tracking #676

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3721716
Fix multiprocessing Pool arg during tracking
EmmaRenauld Feb 17, 2023
50f4e90
Removing some style warnings
EmmaRenauld Feb 17, 2023
7fe5fba
Fix nibabel use with python 3.10
EmmaRenauld Mar 1, 2023
87c3079
Change tmp dir to a more thread-safe option
EmmaRenauld Mar 1, 2023
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2 changes: 1 addition & 1 deletion scilpy/tracking/seed.py
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Original file line number Diff line number Diff line change
Expand Up @@ -110,7 +110,7 @@ def get_next_n_pos(self, random_generator, indices, which_seeds):

Return
------
seed_pos: List[tuple]
seed_pos: List[List]
Positions of next seeds expressed seed_generator's space and
origin.
"""
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17 changes: 9 additions & 8 deletions scilpy/tracking/tracker.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,14 +4,14 @@
import multiprocessing
import os
import sys
import traceback
from tempfile import TemporaryDirectory
from time import perf_counter
import traceback
from typing import Union

import nibabel as nib
import numpy as np

from dipy.data import get_sphere
from dipy.io.stateful_tractogram import Space, StatefulTractogram
from dipy.io.stateful_tractogram import Space
from dipy.reconst.shm import sh_to_sf_matrix
from dipy.tracking.streamlinespeed import compress_streamlines

Expand All @@ -31,7 +31,8 @@ class Tracker(object):
def __init__(self, propagator: AbstractPropagator, mask: DataVolume,
seed_generator: SeedGenerator, nbr_seeds, min_nbr_pts,
max_nbr_pts, max_invalid_dirs, compression_th=0.1,
nbr_processes=1, save_seeds=False, mmap_mode=None,
nbr_processes=1, save_seeds=False,
mmap_mode: Union[str, None] = None,
rng_seed=1234, track_forward_only=False, skip=0):
"""
Parameters
Expand Down Expand Up @@ -131,7 +132,7 @@ def track(self):
else:
# Each process will use get_streamlines_at_seeds
chunk_ids = np.arange(self.nbr_processes)
with nib.tmpdirs.InTemporaryDirectory() as tmpdir:
with TemporaryDirectory() as tmpdir:

pool = self._prepare_multiprocessing_pool(tmpdir)

Expand Down Expand Up @@ -198,10 +199,10 @@ def _prepare_multiprocessing_pool(self, tmpdir):
pool = multiprocessing.Pool(
self.nbr_processes,
initializer=self._send_multiprocess_args_to_global,
initargs={
initargs=({
'data_file_name': data_file_name,
'mmap_mode': self.mmap_mode
})
},))

return pool

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