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Adding thread control #39

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Adding thread control #39

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a5c35d8
Adding thread control
jrdalenberg Dec 5, 2022
a365d0e
Fix threads check
jrdalenberg Mar 16, 2023
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16 changes: 15 additions & 1 deletion HD_BET/hd-bet
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Original file line number Diff line number Diff line change
@@ -1,11 +1,13 @@
#!/usr/bin/env python

import os
import multiprocessing
from HD_BET.run import run_hd_bet
from HD_BET.utils import maybe_mkdir_p, subfiles
import HD_BET



if __name__ == "__main__":
print("\n########################")
print("If you are using hd-bet, please cite the following paper:")
Expand Down Expand Up @@ -33,6 +35,10 @@ if __name__ == "__main__":
'\'cpu\' to run on CPU. When using CPU you should '
'consider disabling tta. Default for -device is: 0',
required=False)
parser.add_argument('-threads', default=0, type=int, help='used to set the number of cpu threads. '
'Must be either int or str. Use 0 for max available cpus.'
'Default for -threads is: 0',
required=False)
parser.add_argument('-tta', default=1, required=False, type=int, help='whether to use test time data augmentation '
'(mirroring). 1= True, 0=False. Disable this '
'if you are using CPU to speed things up! '
Expand All @@ -58,6 +64,7 @@ if __name__ == "__main__":

mode = args.mode
device = args.device
threads = args.threads
tta = args.tta
pp = args.pp
save_mask = args.save_mask
Expand Down Expand Up @@ -90,6 +97,13 @@ if __name__ == "__main__":
output_files = [output_file_or_dir]
input_files = [input_file_or_dir]

max_cpu_count = multiprocessing.cpu_count()
if threads == 0:
threads = max_cpu_count
elif threads not in range(1, max_cpu_count + 1):
raise ValueError(f"Unknown value for threads: {threads}. Expected: value between 1 and maximum number of available threads ({max_cpu_count}) \
Tip: A value of 0 will pick the maximum available number.")

if tta == 0:
tta = False
elif tta == 1:
Expand Down Expand Up @@ -118,4 +132,4 @@ if __name__ == "__main__":
else:
raise ValueError("Unknown value for pp: %s. Expected: 0 or 1" % str(pp))

run_hd_bet(input_files, output_files, mode, config_file, device, pp, tta, save_mask, overwrite_existing)
run_hd_bet(input_files, output_files, mode, config_file, device, threads, pp, tta, save_mask, overwrite_existing)
4 changes: 3 additions & 1 deletion HD_BET/run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ def apply_bet(img, bet, out_fname):


def run_hd_bet(mri_fnames, output_fnames, mode="accurate", config_file=os.path.join(HD_BET.__path__[0], "config.py"), device=0,
postprocess=False, do_tta=True, keep_mask=True, overwrite=True):
threads=0, postprocess=False, do_tta=True, keep_mask=True, overwrite=True):
"""

:param mri_fnames: str or list/tuple of str
Expand All @@ -35,6 +35,8 @@ def run_hd_bet(mri_fnames, output_fnames, mode="accurate", config_file=os.path.j
:return:
"""

torch.set_num_threads(threads)

list_of_param_files = []

if mode == 'fast':
Expand Down