diff --git a/scripts/scil_tractogram_commit.py b/scripts/scil_tractogram_commit.py index 34c4b5331..2f7e16792 100755 --- a/scripts/scil_tractogram_commit.py +++ b/scripts/scil_tractogram_commit.py @@ -447,6 +447,7 @@ def main(): kernels_dir = os.path.join(tmp_dir.name, 'kernels', mit.model.id) regenerate_kernels = True mit.set_config('ATOMS_path', kernels_dir) + mit.generate_kernels(ndirs=args.nbr_dir, regenerate=regenerate_kernels) if args.compute_only: return @@ -455,12 +456,14 @@ def main(): mit.load_dictionary(tmp_dir.name, use_all_voxels_in_mask=use_mask) mit.set_threads(args.nbr_processes) + mit.build_operator(build_dir=os.path.join(tmp_dir.name, 'build/')) tol_fun = 1e-2 if args.commit2 else 1e-3 mit.fit(tol_fun=tol_fun, max_iter=args.nbr_iter, verbose=False) mit.save_results() _save_results_wrapper(args, tmp_dir, ext, hdf5_file, offsets_list, 'commit_1/', False) + if args.commit2: tmp = np.insert(np.cumsum(bundle_groups_len), 0, 0) group_idx = np.array([np.arange(tmp[i], tmp[i+1]) diff --git a/scripts/tests/test_tractogram_commit.py b/scripts/tests/test_tractogram_commit.py index cda0e16b1..bb5ac7598 100644 --- a/scripts/tests/test_tractogram_commit.py +++ b/scripts/tests/test_tractogram_commit.py @@ -13,6 +13,7 @@ fetch_data(get_testing_files_dict(), keys=['commit_amico.zip']) tmp_dir = tempfile.TemporaryDirectory() + def test_help_option(script_runner): ret = script_runner.run('scil_tractogram_commit.py', '--help') assert ret.success