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57
.github/workflows/test_pipeline_dwi_preprocessing_using_phase_diff.yml
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,57 @@ | ||
| name: DWI Preprocessing Using Phase Diff Pipelines Tests | ||
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| on: | ||
| push: | ||
| branches: [dev] | ||
| pull_request: | ||
| branches: [dev] | ||
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| permissions: | ||
| contents: read | ||
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| concurrency: | ||
| group: '${{ github.workflow }} @ ${{ github.event.pull_request.head.label || github.head_ref || github.ref }}' | ||
| cancel-in-progress: true | ||
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| env: | ||
| POETRY_VERSION: '1.6.1' | ||
| PYTHON_VERSION: '3.10' | ||
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| jobs: | ||
| test-pipelines-dwi-preprocessing-using-phase-diff-MacOS: | ||
| runs-on: | ||
| - self-hosted | ||
| - macOS | ||
| - aramis | ||
| timeout-minutes: 720 | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| - uses: snok/install-poetry@v1 | ||
| - name: Run tests for dwi preprocessing using phase diff pipeline | ||
| run: ./scripts/run_nonregression.sh | ||
| env: | ||
| TEST: dwi/preprocessing/using_phase_diff | ||
| MODALITY: dwi_preprocessing_using_phase_diff | ||
| WORKSPACE: ${{ github.workspace }} | ||
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| test-pipelines-dwi-preprocessing-using-phase-diff-Linux: | ||
| runs-on: | ||
| - self-hosted | ||
| - Linux | ||
| timeout-minutes: 720 | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| - uses: snok/install-poetry@v1 | ||
| with: | ||
| version: ${{ env.POETRY_VERSION }} | ||
| virtualenvs-create: false | ||
| - uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: ${{ env.PYTHON_VERSION }} | ||
| cache: poetry | ||
| - name: Run tests for dwi preprocessing using phase diff pipeline | ||
| run: ./scripts/run_nonregression.sh | ||
| env: | ||
| TEST: dwi/preprocessing/using_phase_diff | ||
| MODALITY: dwi_preprocessing_using_phase_diff | ||
| WORKSPACE: ${{ github.workspace }} |
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61
...nregression/pipelines/dwi/preprocessing/using_phase_diff/test_full_phase_diff_pipeline.py
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,61 @@ | ||
| from os import fspath | ||
| from pathlib import Path | ||
| from test.nonregression.testing_tools import configure_paths, similarity_measure | ||
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| import pytest | ||
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| @pytest.mark.slow | ||
| def test_dwi_preprocessing_using_phase_diff_field_map(cmdopt, tmp_path): | ||
| base_dir = Path(cmdopt["input"]) | ||
| working_dir = Path(cmdopt["wd"]) | ||
| input_dir, tmp_dir, ref_dir = configure_paths( | ||
| base_dir, | ||
| tmp_path, | ||
| "DWIPreprocessingUsingPhaseDiffFieldmap", | ||
| ) | ||
| run_dwi_preprocessing_using_phase_diff_field_map( | ||
| input_dir, tmp_dir, ref_dir, working_dir | ||
| ) | ||
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| def run_dwi_preprocessing_using_phase_diff_field_map( | ||
| input_dir: Path, output_dir: Path, ref_dir: Path, working_dir: Path | ||
| ) -> None: | ||
| from clinica.pipelines.dwi_preprocessing_using_fmap.dwi_preprocessing_using_phasediff_fmap_pipeline import ( | ||
| DwiPreprocessingUsingPhaseDiffFMap, | ||
| ) | ||
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| caps_dir = output_dir / "caps" | ||
| tsv = input_dir / "subjects.tsv" | ||
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| parameters = { | ||
| "initrand": True, | ||
| "low_bval": 5, | ||
| "use_cuda": False, | ||
| "delete_cache": True, | ||
| } | ||
| pipeline = DwiPreprocessingUsingPhaseDiffFMap( | ||
| bids_directory=fspath(input_dir / "bids"), | ||
| caps_directory=fspath(caps_dir), | ||
| tsv_file=fspath(tsv), | ||
| base_dir=fspath(working_dir), | ||
| parameters=parameters, | ||
| ) | ||
| pipeline.build() | ||
| pipeline.run(plugin="MultiProc", plugin_args={"n_procs": 4}, bypass_check=True) | ||
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| out_file = fspath( | ||
| caps_dir | ||
| / "subjects" | ||
| / "sub-PREVDEMALS0010025PG" | ||
| / "ses-M000" | ||
| / "dwi" | ||
| / "preprocessing" | ||
| / "sub-PREVDEMALS0010025PG_ses-M000_dwi_space-b0_preproc.nii.gz" | ||
| ) | ||
| ref_file = fspath( | ||
| ref_dir / "sub-PREVDEMALS0010025PG_ses-M000_dwi_space-b0_preproc.nii.gz" | ||
| ) | ||
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| assert similarity_measure(out_file, ref_file, 0.95) |
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66
test/nonregression/pipelines/dwi/preprocessing/using_t1/test_full_t1_pipeline.py
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,66 @@ | ||
| """Non regression test for the full DWIPreprocessingUsingT1 pipeline.""" | ||
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| from os import fspath | ||
| from pathlib import Path | ||
| from test.nonregression.testing_tools import ( | ||
| configure_paths, | ||
| similarity_measure_large_nifti, | ||
| ) | ||
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| import pytest | ||
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| @pytest.mark.slow | ||
| def test_dwi_preprocessing_using_t1(cmdopt, tmp_path): | ||
| base_dir = Path(cmdopt["input"]) | ||
| working_dir = Path(cmdopt["wd"]) | ||
| input_dir, tmp_dir, ref_dir = configure_paths( | ||
| base_dir, tmp_path, "DWIPreprocessingUsingT1" | ||
| ) | ||
| run_dwi_preprocessing_using_t1(input_dir, tmp_dir, ref_dir, working_dir) | ||
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| def run_dwi_preprocessing_using_t1( | ||
| input_dir: Path, output_dir: Path, ref_dir: Path, working_dir: Path | ||
| ) -> None: | ||
| from clinica.pipelines.dwi_preprocessing_using_t1.dwi_preprocessing_using_t1_pipeline import ( | ||
| DwiPreprocessingUsingT1, | ||
| ) | ||
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| caps_dir = output_dir / "caps" | ||
| tsv = input_dir / "subjects.tsv" | ||
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| parameters = { | ||
| "initrand": True, | ||
| "low_bval": 5, | ||
| "use_cuda": False, | ||
| "random_seed": 42, | ||
| } | ||
| pipeline = DwiPreprocessingUsingT1( | ||
| bids_directory=fspath(input_dir / "bids"), | ||
| caps_directory=fspath(caps_dir), | ||
| tsv_file=fspath(tsv), | ||
| base_dir=fspath(working_dir), | ||
| parameters=parameters, | ||
| ) | ||
| pipeline.build() | ||
| pipeline.run(plugin="MultiProc", plugin_args={"n_procs": 4}, bypass_check=True) | ||
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| output_folder = ( | ||
| caps_dir | ||
| / "subjects" | ||
| / "sub-PREVDEMALS0010025PG" | ||
| / "ses-M000" | ||
| / "dwi" | ||
| / "preprocessing" | ||
| ) | ||
| out_preprocessed_image = ( | ||
| output_folder / "sub-PREVDEMALS0010025PG_ses-M000_dwi_space-T1w_preproc.nii.gz" | ||
| ) | ||
| ref_preprocessed_image = ( | ||
| ref_dir / "sub-PREVDEMALS0010025PG_ses-M000_dwi_space-T1w_preproc.nii.gz" | ||
| ) | ||
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| assert similarity_measure_large_nifti( | ||
| out_preprocessed_image, ref_preprocessed_image, 0.99 | ||
| ) |
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