diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml index 47b953b..ed4718f 100644 --- a/.github/workflows/build_wheels.yml +++ b/.github/workflows/build_wheels.yml @@ -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, diff --git a/CHANGELOG.md b/CHANGELOG.md index b5a19f7..de3bfb2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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 --- --- diff --git a/tests/demo_data/ref_results/ref_results_BallandStick.pickle b/tests/demo_data/ref_results/ref_results_BallandStick.pickle index c0b7bde..9ca004a 100644 Binary files a/tests/demo_data/ref_results/ref_results_BallandStick.pickle and b/tests/demo_data/ref_results/ref_results_BallandStick.pickle differ diff --git a/tests/demo_data/ref_results/ref_results_StickZeppelinBall.pickle b/tests/demo_data/ref_results/ref_results_StickZeppelinBall.pickle index 7435916..7cceab8 100644 Binary files a/tests/demo_data/ref_results/ref_results_StickZeppelinBall.pickle and b/tests/demo_data/ref_results/ref_results_StickZeppelinBall.pickle differ diff --git a/tests/test_demo.py b/tests/test_demo.py index ef2ab28..e6118d6 100644 --- a/tests/test_demo.py +++ b/tests/test_demo.py @@ -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() @@ -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() @@ -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() @@ -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: