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Fix typo in testing data #157

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Merged
daducci merged 5 commits into from
Dec 17, 2025
Merged

Fix typo in testing data #157

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fc24b71
Update macOS version in build configurationSwitching from macos-13 to…
daducci Dec 12, 2025
5a11e2e
Update macOS architecture version in build config
daducci Dec 12, 2025
7c3aef8
Fixed typo in test script and reference results ("rel _x")
ilariagabusi Dec 16, 2025
32f6c38
Update CHANGELOG
ilariagabusi Dec 16, 2025
849bcd8
Merge branch 'master' of https://github.com/daducci/COMMIT into relea…
ilariagabusi Dec 17, 2025
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10 changes: 5 additions & 5 deletions .github/workflows/build_wheels.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -59,23 +59,23 @@ jobs:
[
{
py: cp38,
arch: [x86_64, macosx_x86_64, 12.0, macos-13]
arch: [x86_64, macosx_x86_64, 12.0, macos-14]
},
{
py: cp39,
arch: [x86_64, macosx_x86_64, 12.0, macos-13]
arch: [x86_64, macosx_x86_64, 12.0, macos-14]
},
{
py: cp310,
arch: [x86_64, macosx_x86_64, 12.0, macos-13]
arch: [x86_64, macosx_x86_64, 12.0, macos-14]
},
{
py: cp311,
arch: [x86_64, macosx_x86_64, 12.0, macos-13]
arch: [x86_64, macosx_x86_64, 12.0, macos-14]
},
{
py: cp312,
arch: [x86_64, macosx_x86_64, 12.0, macos-13]
arch: [x86_64, macosx_x86_64, 12.0, macos-14]
},
{
py: cp38,
Expand Down
1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -8,6 +8,7 @@
- Error in verifying voxel correspondence between the lesion mask passed through the dictionary and the ISO weights map
- Error when checking the number of streamlines in the grouping structure for group LASSO regularization
- Added check on empty groups when setting group LASSO regularization
- Typo in test script and reference results

---
---
Expand Down
Binary file modified tests/demo_data/ref_results/ref_results_BallandStick.pickle
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Binary file modified tests/demo_data/ref_results/ref_results_StickZeppelinBall.pickle
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42 changes: 22 additions & 20 deletions tests/test_demo.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,23 +19,23 @@ def run_commit_StickZeppelinBall(local_path):
trk2dictionary.run(
filename_tractogram=os.path.join(local_path, 'demo01_fibers.tck'),
filename_peaks=os.path.join(local_path, 'peaks.nii.gz'),
filename_mask=os.path.join(local_path, 'WM.nii.gz'), # 'WM.nii.gz',
filename_mask=os.path.join(local_path, 'WM.nii.gz'),
fiber_shift=0.5,
peaks_use_affine=True
)

amico.util.fsl2scheme(os.path.join(local_path, 'bvals.txt'), os.path.join(
local_path, 'bvecs.txt'), os.path.join(local_path, 'DWI.scheme'))
amico.util.fsl2scheme(os.path.join(local_path, 'bvals.txt'),
os.path.join(local_path, 'bvecs.txt'),
os.path.join(local_path, 'DWI.scheme'))

mit = commit.Evaluation(local_path, '.')
mit.load_data(os.path.join(local_path, 'DWI.nii.gz'),
os.path.join(local_path, 'DWI.scheme'))

mit.set_model('StickZeppelinBall')
d_par = 1.7E-3 # Parallel diffusivity [mm^2/s]
d_perps = [0.51E-3] # Perpendicular diffusivity(s) [mm^2/s]
# d_perps = [] # Perpendicular diffusivity(s) [mm^2/s]
d_isos = [1.7E-3, 3.0E-3] # Isotropic diffusivity(s) [mm^2/s]
d_par = 1.7E-3 # Parallel diffusivity [mm^2/s]
d_perps = [0.51E-3] # Perpendicular diffusivity(s) [mm^2/s]
d_isos = [1.7E-3, 3.0E-3] # Isotropic diffusivity(s) [mm^2/s]
mit.model.set(d_par, d_perps, d_isos)
mit.generate_kernels(regenerate=True)
mit.load_kernels()
Expand All @@ -53,22 +53,23 @@ def run_commit_BallandStick(local_path):
trk2dictionary.run(
filename_tractogram=os.path.join(local_path, 'demo01_fibers.tck'),
filename_peaks=os.path.join(local_path, 'peaks.nii.gz'),
filename_mask=os.path.join(local_path, 'WM.nii.gz'), # 'WM.nii.gz',
filename_mask=os.path.join(local_path, 'WM.nii.gz'),
fiber_shift=0.5,
peaks_use_affine=True
)

amico.util.fsl2scheme(os.path.join(local_path, 'bvals.txt'), os.path.join(
local_path, 'bvecs.txt'), os.path.join(local_path, 'DWI.scheme'))
amico.util.fsl2scheme(os.path.join(local_path, 'bvals.txt'),
os.path.join(local_path, 'bvecs.txt'),
os.path.join(local_path, 'DWI.scheme'))

mit = commit.Evaluation(local_path, '.')
mit.load_data(os.path.join(local_path, 'DWI.nii.gz'),
os.path.join(local_path, 'DWI.scheme'))

mit.set_model('StickZeppelinBall')
d_par = 1.7E-3 # Parallel diffusivity [mm^2/s]
d_perps = [] # Perpendicular diffusivity(s) [mm^2/s]
d_isos = [1.7E-3, 3.0E-3] # Isotropic diffusivity(s) [mm^2/s]
d_par = 1.7E-3 # Parallel diffusivity [mm^2/s]
d_perps = [] # Perpendicular diffusivity(s) [mm^2/s]
d_isos = [1.7E-3, 3.0E-3] # Isotropic diffusivity(s) [mm^2/s]
mit.model.set(d_par, d_perps, d_isos)
mit.generate_kernels(regenerate=True)
mit.load_kernels()
Expand All @@ -86,22 +87,23 @@ def run_commit_VolumeFractions(local_path):
trk2dictionary.run(
filename_tractogram=os.path.join(local_path, 'demo01_fibers.tck'),
filename_peaks=os.path.join(local_path, 'peaks.nii.gz'),
filename_mask=os.path.join(local_path, 'WM.nii.gz'), # 'WM.nii.gz',
filename_mask=os.path.join(local_path, 'WM.nii.gz'),
fiber_shift=0.5,
peaks_use_affine=True
)

amico.util.fsl2scheme(os.path.join(local_path, 'bvals.txt'), os.path.join(
local_path, 'bvecs.txt'), os.path.join(local_path, 'DWI.scheme'))
amico.util.fsl2scheme(os.path.join(local_path, 'bvals.txt'),
os.path.join(local_path, 'bvecs.txt'),
os.path.join(local_path, 'DWI.scheme'))

mit = commit.Evaluation(local_path, '.')
mit.load_data(os.path.join(local_path, 'DWI.nii.gz'),
os.path.join(local_path, 'DWI.scheme'))

mit.set_model('StickZeppelinBall')
d_par = 1.7E-3 # Parallel diffusivity [mm^2/s]
d_perps = [] # Perpendicular diffusivity(s) [mm^2/s]
d_isos = [1.7E-3, 3.0E-3] # Isotropic diffusivity(s) [mm^2/s]
d_par = 1.7E-3 # Parallel diffusivity [mm^2/s]
d_perps = [] # Perpendicular diffusivity(s) [mm^2/s]
d_isos = [1.7E-3, 3.0E-3] # Isotropic diffusivity(s) [mm^2/s]
mit.model.set(d_par, d_perps, d_isos)
mit.generate_kernels(regenerate=True)
mit.load_kernels()
Expand Down Expand Up @@ -131,7 +133,7 @@ def check_results(pickle_result, ref_pickle):
assert abs(result_optimization["fit_details"]["abs_cost"] - ref_optimization["fit_details"]["abs_cost"]) < 1e-4
assert abs(result_optimization["fit_details"]["rel_cost"] - ref_optimization["fit_details"]["rel_cost"]) < 1e-4
assert abs(result_optimization["fit_details"]["abs_x"] - ref_optimization["fit_details"]["abs_x"]) < 1e-4
assert abs(result_optimization["fit_details"]["rel_x"] - ref_optimization["fit_details"]["rel _x"]) < 1e-4 #NOTE: There is a space in the key name
assert abs(result_optimization["fit_details"]["rel_x"] - ref_optimization["fit_details"]["rel_x"]) < 1e-4
assert result_optimization["fit_details"]["iterations"] == ref_optimization["fit_details"]["iterations"]

except AssertionError:
Expand Down