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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,188 @@ | ||
| from pathlib import Path | ||
| from typing import Optional, Tuple, Union | ||
| from unittest.mock import patch | ||
|
|
||
| import nibabel as nib | ||
| import numpy as np | ||
| import pytest | ||
| from numpy.testing import assert_array_equal | ||
|
|
||
| from clinica.pipelines.utils import ( | ||
| AntsRegistrationSynQuickTransformType, | ||
| AntsRegistrationTransformType, | ||
| ) | ||
|
|
||
|
|
||
| def n4biasfieldcorrection_mock( | ||
| input_image: Path, | ||
| bspline_fitting_distance: int, | ||
| save_bias: bool = False, | ||
| verbose: bool = False, | ||
| ): | ||
| """The mock simply returns the input image without any processing.""" | ||
| return nib.load(input_image) | ||
|
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||
|
|
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| def test_run_n4biasfieldcorrection_no_bias_saving(tmp_path): | ||
| from clinica.pipelines.utils import run_n4biasfieldcorrection | ||
|
|
||
| data = np.random.random((10, 10, 10)) | ||
| nib.save(nib.Nifti1Image(data, np.eye(4)), tmp_path / "test.nii.gz") | ||
| output_dir = tmp_path / "out" | ||
| output_dir.mkdir() | ||
|
|
||
| with patch("ants.image_write", wraps=nib.save) as image_write_mock: | ||
| with patch( | ||
| "clinica.pipelines.utils._call_n4_bias_field_correction", | ||
| wraps=n4biasfieldcorrection_mock, | ||
| ) as ants_bias_correction_mock: | ||
| bias_corrected_image = run_n4biasfieldcorrection( | ||
| tmp_path / "test.nii.gz", | ||
| bspline_fitting_distance=300, | ||
| output_prefix="sub-01_ses-M000", | ||
| output_dir=output_dir, | ||
| ) | ||
| image_write_mock.assert_called_once() | ||
| ants_bias_correction_mock.assert_called_once_with( | ||
| tmp_path / "test.nii.gz", | ||
| 300, | ||
| save_bias=False, | ||
| verbose=False, | ||
| ) | ||
| # Verify that the bias corrected image exists | ||
| # If all went well, it will be the same as the input image because of the mocks. | ||
| assert [f.name for f in output_dir.iterdir()] == [ | ||
| "sub-01_ses-M000_bias_corrected_image.nii.gz" | ||
| ] | ||
| assert bias_corrected_image.exists() | ||
| bias_corrected_nifti = nib.load(bias_corrected_image) | ||
| assert_array_equal(bias_corrected_nifti.affine, np.eye(4)) | ||
| assert_array_equal(bias_corrected_nifti.get_fdata(), data) | ||
|
|
||
|
|
||
| def test_run_n4biasfieldcorrection(tmp_path): | ||
| from clinica.pipelines.utils import run_n4biasfieldcorrection | ||
|
|
||
| data = np.random.random((10, 10, 10)) | ||
| nib.save(nib.Nifti1Image(data, np.eye(4)), tmp_path / "test.nii.gz") | ||
| output_dir = tmp_path / "out" | ||
| output_dir.mkdir() | ||
|
|
||
| with patch("ants.image_write", wraps=nib.save) as image_write_mock: | ||
| with patch( | ||
| "clinica.pipelines.utils._call_n4_bias_field_correction", | ||
| wraps=n4biasfieldcorrection_mock, | ||
| ) as ants_bias_correction_mock: | ||
| bias_corrected_image = run_n4biasfieldcorrection( | ||
| tmp_path / "test.nii.gz", | ||
| bspline_fitting_distance=300, | ||
| output_prefix="sub-01_ses-M000", | ||
| output_dir=output_dir, | ||
| save_bias=True, | ||
| verbose=True, | ||
| ) | ||
| image_write_mock.assert_called() | ||
| ants_bias_correction_mock.assert_called_with( | ||
| tmp_path / "test.nii.gz", | ||
| 300, | ||
| save_bias=True, | ||
| verbose=True, | ||
| ) | ||
| assert set([f.name for f in output_dir.iterdir()]) == { | ||
| "sub-01_ses-M000_bias_corrected_image.nii.gz", | ||
| "sub-01_ses-M000_bias_image.nii.gz", | ||
| } | ||
| assert bias_corrected_image.exists() | ||
| bias_corrected_nifti = nib.load(bias_corrected_image) | ||
| assert_array_equal(bias_corrected_nifti.affine, np.eye(4)) | ||
| assert_array_equal(bias_corrected_nifti.get_fdata(), data) | ||
|
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||
|
|
||
| def generate_fake_fixed_and_moving_images(folder: Path): | ||
| data = np.random.random((10, 10, 10)) | ||
| nib.save(nib.Nifti1Image(data, np.eye(4)), folder / "fixed.nii.gz") | ||
| nib.save(nib.Nifti1Image(data, np.eye(4)), folder / "moving.nii.gz") | ||
|
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|
|
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| def test_run_ants_registration_synquick_error(tmp_path, mocker): | ||
| import re | ||
|
|
||
| from clinica.pipelines.utils import run_ants_registration_synquick | ||
|
|
||
| generate_fake_fixed_and_moving_images(tmp_path) | ||
| mocker.patch( | ||
| "clinica.pipelines.utils._call_ants_registration", | ||
| return_value={}, | ||
| ) | ||
| with pytest.raises( | ||
| RuntimeError, | ||
| match=re.escape( | ||
| "Something went wrong when calling antsRegistration with the following parameters :\n" | ||
| f"- fixed_image = {tmp_path / 'fixed.nii.gz'}\n" | ||
| f"- moving_image = {tmp_path / 'moving.nii.gz'}\n" | ||
| f"- random_seed = 0\n" | ||
| f"- type_of_transformation='antsRegistrationSyN[a]'\n" | ||
| ), | ||
| ): | ||
| run_ants_registration_synquick( | ||
| tmp_path / "fixed.nii.gz", | ||
| tmp_path / "moving.nii.gz", | ||
| random_seed=0, | ||
| transform_type=AntsRegistrationSynQuickTransformType.AFFINE, | ||
| ) | ||
|
|
||
|
|
||
| def ants_registration_mock( | ||
| fixed_image: Path, | ||
| moving_image: Path, | ||
| random_seed: int, | ||
| transform_type: Union[ | ||
| AntsRegistrationTransformType, AntsRegistrationSynQuickTransformType | ||
| ], | ||
| verbose: bool = False, | ||
| shrink_factors: Optional[Tuple[int, ...]] = None, | ||
| smoothing_sigmas: Optional[Tuple[int, ...]] = None, | ||
| number_of_iterations: Optional[Tuple[int, ...]] = None, | ||
| ) -> dict: | ||
| workdir = fixed_image.parent / "workdir" | ||
| workdir.mkdir() | ||
| mocked_transform = workdir / "transform.mat" | ||
| mocked_transform.touch() | ||
| return { | ||
| "warpedmovout": nib.load(fixed_image), | ||
| "fwdtransforms": ["fooo.txt", mocked_transform], | ||
| "invtransforms": [mocked_transform], | ||
| "foo": "bar", | ||
| } | ||
|
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|
|
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| def test_run_ants_registration_synquick(tmp_path): | ||
| from clinica.pipelines.utils import run_ants_registration_synquick | ||
|
|
||
| output_dir = tmp_path / "out" | ||
| output_dir.mkdir() | ||
| generate_fake_fixed_and_moving_images(tmp_path) | ||
|
|
||
| with patch( | ||
| "clinica.pipelines.utils._call_ants_registration", | ||
| wraps=ants_registration_mock, | ||
| ) as mock1: | ||
| with patch("ants.image_write", wraps=nib.save) as mock2: | ||
| run_ants_registration_synquick( | ||
| tmp_path / "fixed.nii.gz", | ||
| tmp_path / "moving.nii.gz", | ||
| random_seed=12, | ||
| transform_type=AntsRegistrationSynQuickTransformType.AFFINE, | ||
| output_dir=output_dir, | ||
| ) | ||
| mock1.assert_called_once_with( | ||
| tmp_path / "fixed.nii.gz", | ||
| tmp_path / "moving.nii.gz", | ||
| 12, | ||
| AntsRegistrationSynQuickTransformType.AFFINE, | ||
| verbose=False, | ||
| shrink_factors=None, | ||
| smoothing_sigmas=None, | ||
| number_of_iterations=None, | ||
| ) | ||
| mock2.assert_called_once() |