simplify imports for dwi preproc using t1

clinica/pipelines/dwi_preprocessing_using_fmap/dwi_preprocessing_using_phasediff_fmap_pipeline.py

@@ -291,7 +291,7 @@ def build_core_nodes(self):
         import nipype.interfaces.utility as niu
         import nipype.pipeline.engine as npe
 
-        from clinica.pipelines.dwi_preprocessing_using_t1.dwi_preprocessing_using_t1_workflows import (
+        from clinica.pipelines.dwi_preprocessing_using_t1.workflows import (
             eddy_fsl_pipeline,
         )
         from clinica.utils.dwi import compute_average_b0_task

clinica/pipelines/dwi_preprocessing_using_fmap/dwi_preprocessing_using_phasediff_fmap_workflows.py

@@ -217,9 +217,7 @@ def compute_reference_b0(
     import nipype.interfaces.utility as niu
     import nipype.pipeline.engine as npe
 
-    from clinica.pipelines.dwi_preprocessing_using_t1.dwi_preprocessing_using_t1_workflows import (
-        eddy_fsl_pipeline,
-    )
+    from clinica.pipelines.dwi_preprocessing_using_t1.workflows import eddy_fsl_pipeline
     from clinica.utils.dwi import compute_average_b0
 
     from .dwi_preprocessing_using_phasediff_fmap_utils import get_grad_fsl

clinica/pipelines/dwi_preprocessing_using_t1/__init__.py

@@ -1 +1 @@
-from . import dwi_preprocessing_using_t1_cli
+from . import cli

clinica/pipelines/dwi_preprocessing_using_t1/dwi_preprocessing_using_t1_cli.py → clinica/pipelines/dwi_preprocessing_using_t1/cli.py

@@ -43,7 +43,7 @@ def cli(
 
     from clinica.utils.ux import print_end_pipeline
 
-    from .dwi_preprocessing_using_t1_pipeline import DwiPreprocessingUsingT1
+    from .pipeline import DwiPreprocessingUsingT1
 
     parameters = {
         "low_bval": low_bval,

clinica/pipelines/dwi_preprocessing_using_t1/dwi_preprocessing_using_t1_pipeline.py → clinica/pipelines/dwi_preprocessing_using_t1/pipeline.py

@@ -176,7 +176,7 @@ def build_output_node(self):
 
         from clinica.utils.nipype import container_from_filename, fix_join
 
-        from .dwi_preprocessing_using_t1_utils import rename_into_caps
+        from .utils import rename_into_caps
 
         container_path = npe.Node(
             nutil.Function(
@@ -257,15 +257,12 @@ def build_core_nodes(self):
 
         from clinica.utils.dwi import compute_average_b0_task
 
-        from .dwi_preprocessing_using_t1_utils import (
+        from .utils import (
             init_input_node,
             prepare_reference_b0_task,
             print_end_pipeline,
         )
-        from .dwi_preprocessing_using_t1_workflows import (
-            eddy_fsl_pipeline,
-            epi_pipeline,
-        )
+        from .workflows import eddy_fsl_pipeline, epi_pipeline
 
         init_node = npe.Node(
             interface=nutil.Function(

clinica/pipelines/dwi_preprocessing_using_t1/dwi_preprocessing_using_t1_utils.py → clinica/pipelines/dwi_preprocessing_using_t1/utils.py

@@ -88,7 +88,7 @@ def broadcast_matrix_filename_to_match_b_vector_length(
     """Return a list of the matrix filename repeated as many times as there are B-vectors."""
     import numpy as np
 
-    from clinica.pipelines.dwi_preprocessing_using_t1.dwi_preprocessing_using_t1_utils import (  # noqa
+    from clinica.pipelines.dwi_preprocessing_using_t1.utils import (  # noqa
         broadcast_filename_into_list,
     )
 
@@ -287,7 +287,7 @@ def prepare_reference_b0_task(
     """Task called be Nipype to execute prepare_reference_b0."""
     from pathlib import Path
 
-    from clinica.pipelines.dwi_preprocessing_using_t1.dwi_preprocessing_using_t1_utils import (  # noqa
+    from clinica.pipelines.dwi_preprocessing_using_t1.utils import (  # noqa
         prepare_reference_b0,
     )
     from clinica.utils.dwi import DWIDataset
@@ -496,9 +496,7 @@ def register_b0(
         If the pipeline ran successfully, this file should be located in :
         working_directory / b0_coregistration / concat_ref_moving / merged_files.nii.gz
     """
-    from clinica.pipelines.dwi_preprocessing_using_t1.dwi_preprocessing_using_t1_workflows import (
-        b0_flirt_pipeline,
-    )
+    from clinica.pipelines.dwi_preprocessing_using_t1.workflows import b0_flirt_pipeline
 
     b0_flirt = b0_flirt_pipeline(num_b0s=nb_b0s)
     b0_flirt.inputs.inputnode.in_file = str(extracted_b0_filename)

clinica/pipelines/dwi_preprocessing_using_t1/dwi_preprocessing_using_t1_workflows.py → clinica/pipelines/dwi_preprocessing_using_t1/workflows.py

@@ -83,10 +83,7 @@ def eddy_fsl_pipeline(
     from nipype.interfaces.fsl import BET
     from nipype.interfaces.fsl.epi import Eddy
 
-    from .dwi_preprocessing_using_t1_utils import (
-        generate_acq_file_task,
-        generate_index_file_task,
-    )
+    from .utils import generate_acq_file_task, generate_index_file_task
 
     inputnode = pe.Node(
         niu.IdentityInterface(
@@ -397,7 +394,7 @@ def perform_ants_registration(
     import nipype.interfaces.utility as niu
     import nipype.pipeline.engine as pe
 
-    from .dwi_preprocessing_using_t1_utils import (
+    from .utils import (
         broadcast_matrix_filename_to_match_b_vector_length,
         change_itk_transform_type,
         rotate_b_vectors,
@@ -605,8 +602,6 @@ def perform_dwi_epi_correction(
     This workflow benefits a lot from parallelization as most operations are done on
     single DWI direction.
     """
-    import os
-
     import nipype.interfaces.ants as ants
     import nipype.interfaces.fsl as fsl
     import nipype.interfaces.io as nio

test/instantiation/test_instantiate_all_pipelines.py

@@ -120,7 +120,7 @@ def test_instantiate_t1_volume_parcellation(cmdopt):
 
 
 def test_instantiate_dwi_preprocessing_using_t1(cmdopt):
-    from clinica.pipelines.dwi_preprocessing_using_t1.dwi_preprocessing_using_t1_pipeline import (
+    from clinica.pipelines.dwi_preprocessing_using_t1.pipeline import (
         DwiPreprocessingUsingT1,
     )
 

test/nonregression/pipelines/dwi/preprocessing/using_t1/test_full_t1_pipeline.py

@@ -23,7 +23,7 @@ def test_dwi_preprocessing_using_t1(cmdopt, tmp_path):
 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 (
+    from clinica.pipelines.dwi_preprocessing_using_t1.pipeline import (
         DwiPreprocessingUsingT1,
     )
 

test/nonregression/pipelines/dwi/preprocessing/using_t1/test_t1_sub_workflows.py

@@ -15,9 +15,7 @@
 
 @pytest.mark.fast
 def test_dwi_b0_flirt(cmdopt, tmp_path):
-    from clinica.pipelines.dwi_preprocessing_using_t1.dwi_preprocessing_using_t1_workflows import (
-        b0_flirt_pipeline,
-    )
+    from clinica.pipelines.dwi_preprocessing_using_t1.workflows import b0_flirt_pipeline
 
     base_dir = Path(cmdopt["input"])
     input_dir, tmp_dir, ref_dir = configure_paths(base_dir, tmp_path, "DWIB0Flirt")
@@ -41,9 +39,7 @@ def test_dwi_b0_flirt(cmdopt, tmp_path):
 
 @pytest.mark.slow
 def test_dwi_epi_pipeline(cmdopt, tmp_path):
-    from clinica.pipelines.dwi_preprocessing_using_t1.dwi_preprocessing_using_t1_workflows import (
-        epi_pipeline,
-    )
+    from clinica.pipelines.dwi_preprocessing_using_t1.workflows import epi_pipeline
 
     base_dir = Path(cmdopt["input"])
     input_dir, tmp_dir, ref_dir = configure_paths(base_dir, tmp_path, "DWIEPIPipeline")
@@ -89,7 +85,7 @@ def test_dwi_perform_ants_registration(cmdopt, tmp_path):
 
     import nibabel as nib
 
-    from clinica.pipelines.dwi_preprocessing_using_t1.dwi_preprocessing_using_t1_workflows import (
+    from clinica.pipelines.dwi_preprocessing_using_t1.workflows import (
         perform_ants_registration,
     )
 
@@ -152,7 +148,7 @@ def test_dwi_perform_ants_registration(cmdopt, tmp_path):
 
 @pytest.mark.slow
 def test_dwi_perform_dwi_epi_correction(cmdopt, tmp_path):
-    from clinica.pipelines.dwi_preprocessing_using_t1.dwi_preprocessing_using_t1_workflows import (
+    from clinica.pipelines.dwi_preprocessing_using_t1.workflows import (
         perform_dwi_epi_correction,
     )
 
@@ -192,9 +188,7 @@ def test_dwi_perform_dwi_epi_correction(cmdopt, tmp_path):
 
 @pytest.mark.slow
 def test_dwi_eddy_fsl(cmdopt, tmp_path):
-    from clinica.pipelines.dwi_preprocessing_using_t1.dwi_preprocessing_using_t1_workflows import (
-        eddy_fsl_pipeline,
-    )
+    from clinica.pipelines.dwi_preprocessing_using_t1.workflows import eddy_fsl_pipeline
 
     base_dir = Path(cmdopt["input"])
     input_dir, tmp_dir, ref_dir = configure_paths(base_dir, tmp_path, "DWIEddyFSL")

test/unittests/pipelines/dwi_preprocessing_using_t1/test_dwi_preprocessing_using_t1_utils.py

@@ -2,7 +2,7 @@
 import pytest
 from numpy.testing import assert_array_almost_equal, assert_array_equal
 
-from clinica.pipelines.dwi_preprocessing_using_t1.dwi_preprocessing_using_t1_utils import (
+from clinica.pipelines.dwi_preprocessing_using_t1.utils import (
     broadcast_matrix_filename_to_match_b_vector_length,
     change_itk_transform_type,
     extract_sub_ses_folder_name,
@@ -181,7 +181,7 @@ def test_rotate_b_vectors_wrong_content_in_vector_file(tmp_path):
 def test_configure_working_directory(tmp_path):
     import hashlib
 
-    from clinica.pipelines.dwi_preprocessing_using_t1.dwi_preprocessing_using_t1_utils import (
+    from clinica.pipelines.dwi_preprocessing_using_t1.utils import (
         configure_working_directory,
     )
 
@@ -199,9 +199,7 @@ def test_configure_working_directory(tmp_path):
 def test_compute_reference_b0_errors(tmp_path):
     import numpy as np
 
-    from clinica.pipelines.dwi_preprocessing_using_t1.dwi_preprocessing_using_t1_utils import (
-        compute_reference_b0,
-    )
+    from clinica.pipelines.dwi_preprocessing_using_t1.utils import compute_reference_b0
 
     (tmp_path / "b0.nii.gz").touch()
     np.savetxt(tmp_path / "foo.bval", [1000] * 9)
@@ -221,9 +219,7 @@ def test_compute_reference_b0_with_single_b0(tmp_path):
     import numpy as np
     from numpy.testing import assert_array_equal
 
-    from clinica.pipelines.dwi_preprocessing_using_t1.dwi_preprocessing_using_t1_utils import (
-        compute_reference_b0,
-    )
+    from clinica.pipelines.dwi_preprocessing_using_t1.utils import compute_reference_b0
 
     b0_data = 4.0 * np.ones((5, 5, 5, 1))
     b0_img = nib.Nifti1Image(b0_data, affine=np.eye(4))
@@ -258,9 +254,7 @@ def test_compute_reference_b0_with_multiple_b0(tmp_path, mocker, clean_working_d
     import numpy as np
     from numpy.testing import assert_array_equal
 
-    from clinica.pipelines.dwi_preprocessing_using_t1.dwi_preprocessing_using_t1_utils import (
-        compute_reference_b0,
-    )
+    from clinica.pipelines.dwi_preprocessing_using_t1.utils import compute_reference_b0
 
     working_directory = tmp_path / "tmp"
     working_directory.mkdir()
@@ -273,7 +267,7 @@ def test_compute_reference_b0_with_multiple_b0(tmp_path, mocker, clean_working_d
     assert not mocked_output.exists()
     mocked_output.parent.mkdir(parents=True)
     mocker.patch(
-        "clinica.pipelines.dwi_preprocessing_using_t1.dwi_preprocessing_using_t1_utils.register_b0",
+        "clinica.pipelines.dwi_preprocessing_using_t1.utils.register_b0",
         return_value=mocked_output,
     )
     # Build a dataset with 3 B0 volumes
@@ -325,14 +319,12 @@ def test_prepare_reference_b0(tmp_path, mocker):
     import numpy as np
     from numpy.testing import assert_array_equal
 
-    from clinica.pipelines.dwi_preprocessing_using_t1.dwi_preprocessing_using_t1_utils import (
-        prepare_reference_b0,
-    )
+    from clinica.pipelines.dwi_preprocessing_using_t1.utils import prepare_reference_b0
     from clinica.utils.dwi import DWIDataset
 
     mocked_output = tmp_path / "reference_b0_volume.nii.gz"
     mocker.patch(
-        "clinica.pipelines.dwi_preprocessing_using_t1.dwi_preprocessing_using_t1_utils.compute_reference_b0",
+        "clinica.pipelines.dwi_preprocessing_using_t1.utils.compute_reference_b0",
         return_value=mocked_output,
     )
     ref_b0_data = 5.0 * np.ones((5, 5, 5, 1))