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uint8 in compute_density when possible #685

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merged 2 commits into from
Mar 6, 2023
Merged

uint8 in compute_density when possible #685

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6eb3ef9
Use uint8 if == 1
frheault Mar 2, 2023
7949012
Add documentation
frheault Mar 6, 2023
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13 changes: 8 additions & 5 deletions scripts/scil_compute_seed_density_map.py
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Original file line number Diff line number Diff line change
Expand Up @@ -29,10 +29,10 @@ def _build_arg_parser():
help='Output seed density filename. Format must be Nifti.')
p.add_argument('--binary',
metavar='FIXED_VALUE', type=int, nargs='?', const=1,
help='If set, will store the same value for all '
'intersected voxels, creating a binary map.\nWhen set '
'without a value, 1 is used.\n If a value is given, '
'will be used as the stored value.')
help='If set, will store the same value for all intersected'
' voxels, creating a binary map.\n'
'When set without a value, 1 is used (and dtype uint8).\n'
'If a value is given, will be used as the stored value.')
add_overwrite_arg(p)

return p
Expand Down Expand Up @@ -86,13 +86,16 @@ def main():
for seed in seeds:
# Set value at mask, either binary or increment
seed_voxel = np.round(seed).astype(int)
dtype_to_use = np.int32
if args.binary is not None:
if args.binary == 1:
dtype_to_use = np.uint8
seed_density[tuple(seed_voxel)] = args.binary
else:
seed_density[tuple(seed_voxel)] += 1

# Save seed density map
dm_img = Nifti1Image(seed_density.astype(np.int32), affine)
dm_img = Nifti1Image(seed_density.astype(dtype_to_use), affine)
dm_img.to_filename(args.seed_density_filename)


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11 changes: 7 additions & 4 deletions scripts/scil_compute_streamlines_density_map.py
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Original file line number Diff line number Diff line change
Expand Up @@ -31,9 +31,9 @@ def _build_arg_parser():
p.add_argument('--binary', metavar='FIXED_VALUE', type=int,
nargs='?', const=1,
help='If set, will store the same value for all intersected'
' voxels, creating a binary map.\n'
'When set without a value, 1 is used.\n'
'If a value is given, will be used as the stored value.')
' voxels, creating a binary map.\n'
'When set without a value, 1 is used (and dtype uint8).\n'
'If a value is given, will be used as the stored value.')
add_reference_arg(p)
add_overwrite_arg(p)
return p
Expand All @@ -60,10 +60,13 @@ def main():

streamline_count = compute_tract_counts_map(streamlines, dimensions)

dtype_to_use = np.int32
if args.binary is not None:
if args.binary == 1:
dtype_to_use = np.uint8
streamline_count[streamline_count > 0] = args.binary

nib.save(nib.Nifti1Image(streamline_count.astype(np.int16), transformation),
nib.save(nib.Nifti1Image(streamline_count.astype(dtype_to_use), transformation),
args.out_img)


Expand Down