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ENH: Make tractogram downsampling results reproducible by default #147

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merged 2 commits into from
Sep 21, 2023
Merged

ENH: Make tractogram downsampling results reproducible by default #147

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fea55a3
ENH: Make tractogram downsampling results reproducible by default
jhlegarreta Sep 10, 2023
96f6719
ENH: Allow non-identical results in tractogram downsampling
jhlegarreta Sep 9, 2023
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11 changes: 9 additions & 2 deletions bin/wm_preprocess_all.py
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Original file line number Diff line number Diff line change
Expand Up @@ -47,6 +47,9 @@ def main():
parser.add_argument(
'-retaindata', action='store_true', dest="flag_retaindata",
help='If given, all point and cell data stored along the tractography will be retained.')
parser.add_argument(
'--nonidentical', action='store_true',
help='Obtain nonidentical results across runs for downsampling.')

args = parser.parse_args()

Expand Down Expand Up @@ -88,7 +91,11 @@ def main():
else:
print("Remove all data stored along the tractography and only keep fiber streamlines.")
retaindata = args.flag_retaindata


random_seed = 1234
if args.nonidentical:
random_seed = None

print("==========================")

# =======================================================================
Expand Down Expand Up @@ -154,7 +161,7 @@ def pipeline(inputPolyDatas, sidx, args):
print(id_msg + msg)

# , preserve_point_data=True needs editing of preprocess function to use mask function
wm3 = wma.filter.downsample(wm2, args.numberOfFibers, preserve_point_data=retaindata, preserve_cell_data=retaindata, verbose=False)
wm3 = wma.filter.downsample(wm2, args.numberOfFibers, preserve_point_data=retaindata, preserve_cell_data=retaindata, verbose=False, random_seed=random_seed)
print("Number of fibers retained: ", wm3.GetNumberOfLines(), "/", num_lines)

if wm3 is None:
Expand Down
2 changes: 1 addition & 1 deletion whitematteranalysis/filter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -250,7 +250,7 @@ def preprocess(inpd, min_length_mm,
else:
return outpd

def downsample(inpd, output_number_of_lines, return_indices=False, preserve_point_data=False, preserve_cell_data=True, initial_indices=None, verbose=True, random_seed=None):
def downsample(inpd, output_number_of_lines, return_indices=False, preserve_point_data=False, preserve_cell_data=True, initial_indices=None, verbose=True, random_seed=1234):
""" Random (down)sampling of fibers without replacement. """

if initial_indices is None:
Expand Down
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