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Set minimum dwi_denoise_window to 3 #1064

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Merged
tsalo merged 3 commits into from
Jun 12, 2026
Merged

Set minimum dwi_denoise_window to 3 #1064

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0cac201
Set minimum dwi_denoise_window to 3.
tsalo Jun 12, 2026
9a13f8d
Clean up the checks.
tsalo Jun 12, 2026
6f74cb4
Potential fix for pull request finding
tsalo Jun 12, 2026
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10 changes: 5 additions & 5 deletions qsiprep/cli/parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -105,19 +105,19 @@ def _min_one(value, parser):
return value

def _int_or_auto(value, parser):
"""Ensure an argument is an integer or 'auto'."""
"""Ensure an argument is an odd integer >= 3 or 'auto'."""
if value.lower() == 'auto':
return value
return 'auto'
try:
value = int(value)
except ValueError as exc:
raise parser.error('Argument must be an integer or "auto".') from exc

if value < 1:
raise parser.error('Argument must be greater than zero.')
if value < 3:
raise parser.error('Argument must be an odd integer >= 3.')

if value % 2 == 0:
raise parser.error('Argument must be an odd integer.')
raise parser.error('Argument must be an odd integer >= 3.')

return value

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3 changes: 2 additions & 1 deletion qsiprep/workflows/dwi/merge.py
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Expand Up @@ -445,11 +445,12 @@ def get_buffernode():

dwi_denoise_window = config.workflow.dwi_denoise_window
auto_str = ''
if denoise_method == 'dwidenoise' and config.workflow.dwi_denoise_window == 'auto':
if denoise_method == 'dwidenoise' and dwi_denoise_window == 'auto':
# Configure the denoising window
import numpy as np

dwi_denoise_window = closest_odd(int(np.ceil(np.cbrt(n_volumes))))
dwi_denoise_window = max(dwi_denoise_window, 3)
config.loggers.workflow.info(
f'Automatically using {dwi_denoise_window}, {dwi_denoise_window}, '
f'{dwi_denoise_window} window for dwidenoise'
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