[MAINT] Delete clinica.utils.mri_registration module (#1139)

clinica/pipelines/dwi/connectome/pipeline.py

@@ -272,10 +272,10 @@ def _build_core_nodes(self):
         )
 
         from clinica.utils.exceptions import ClinicaCAPSError
-        from clinica.utils.mri_registration import (
-            convert_flirt_transformation_to_mrtrix_transformation,
-        )
 
+        from .tasks import (
+            convert_flirt_to_mrtrix_transformation_task,
+        )
         from .utils import (
             get_caps_filenames,
             get_conversion_luts,
@@ -344,13 +344,13 @@ def _build_core_nodes(self):
             name="Reg-2-FSL2MrtrixConversion",
             interface=niu.Function(
                 input_names=[
-                    "in_source_image",
-                    "in_reference_image",
-                    "in_flirt_matrix",
+                    "source_image",
+                    "reference_image",
+                    "flirt_matrix",
                     "name_output_matrix",
                 ],
                 output_names=["out_mrtrix_matrix"],
-                function=convert_flirt_transformation_to_mrtrix_transformation,
+                function=convert_flirt_to_mrtrix_transformation_task,
             ),
         )
 
@@ -556,17 +556,17 @@ def _build_core_nodes(self):
                     (
                         t1_brain_conv_node,
                         fsl2mrtrix_conv_node,
-                        [("out_file", "in_source_image")],
+                        [("out_file", "source_image")],
                     ),
                     (
                         mask_node,
                         fsl2mrtrix_conv_node,
-                        [("out_file", "in_reference_image")],
+                        [("out_file", "reference_image")],
                     ),
                     (
                         t12b0_reg_node,
                         fsl2mrtrix_conv_node,
-                        [("out_matrix_file", "in_flirt_matrix")],
+                        [("out_matrix_file", "flirt_matrix")],
                     ),
                     # Apply registration without resampling on parcellations
                     (

clinica/pipelines/dwi/connectome/tasks.py

@@ -0,0 +1,32 @@
+"""This module contains Nipype tasks used by the connectome pipeline.
+
+Nipype tasks must be 'self-contained' such that only primitive type hints can be
+used. The tasks are simple wrappers around a properly implemented Python function.
+"""
+
+
+def convert_flirt_to_mrtrix_transformation_task(
+    source_image: str,
+    reference_image: str,
+    flirt_matrix: str,
+    name_output_matrix=None,
+) -> str:
+    """Adapter for Nipype"""
+
+    from pathlib import Path
+
+    from clinica.pipelines.dwi.connectome.utils import (
+        convert_flirt_to_mrtrix_transformation,
+    )
+
+    if name_output_matrix is not None:
+        name_output_matrix = Path(name_output_matrix)
+
+    return str(
+        convert_flirt_to_mrtrix_transformation(
+            Path(source_image),
+            Path(reference_image),
+            Path(flirt_matrix),
+            name_output_matrix,
+        )
+    )

clinica/pipelines/dwi/connectome/utils.py

@@ -1,7 +1,7 @@
 """This module contains utilities used by the DWIConnectome pipeline."""
 
 from pathlib import Path
-from typing import List
+from typing import List, Optional
 
 __all__ = [
     "get_luts",
@@ -10,6 +10,7 @@
     "get_caps_filenames",
     "print_begin_pipeline",
     "print_end_pipeline",
+    "convert_flirt_to_mrtrix_transformation",
 ]
 
 
@@ -120,3 +121,71 @@ def print_end_pipeline(in_bids_or_caps_file: str, final_file: str) -> None:
     from clinica.utils.ux import print_end_image
 
     print_end_image(get_subject_id(in_bids_or_caps_file))
+
+
+def _check_file_presence(
+    file: Path,
+) -> None:
+    if not file.is_file():
+        raise FileNotFoundError(f"The file {file} was not found.")
+
+
+def _get_transformation_cmd(
+    source_image: Path,
+    reference_image: Path,
+    flirt_matrix: Path,
+    mrtrix_matrix: Path,
+) -> str:
+    for file in (source_image, reference_image, flirt_matrix):
+        _check_file_presence(file)
+
+    return f"transformconvert {flirt_matrix} {source_image} {reference_image} flirt_import {mrtrix_matrix}"
+
+
+def convert_flirt_to_mrtrix_transformation(
+    source_image: Path,
+    reference_image: Path,
+    flirt_matrix: Path,
+    name_output_matrix: Optional[str] = None,
+) -> Path:
+    """Convert flirt matrix to mrtrix matrix.
+
+    This function converts a transformation matrix produced by FSL's flirt
+    command into a format usable by MRtrix. The output of this function
+    is usually for the mrtransform command.
+
+    Parameters
+    ----------
+    source_image : Path
+        File containing the source image used in FSL flirt with the -in flag.
+
+    reference_image : Path
+        File containing the reference image used in FSL flirt with the -ref flag.
+
+    flirt_matrix : Path
+        File containing the transformation matrix obtained by FSL flirt.
+
+    name_output_matrix : Path, optional
+        Name of the output matrix. Defaults to "mrtrix_matrix.mat".
+
+    Returns
+    -------
+    mrtrix_matrix : Path
+        Transformation matrix in MRtrix format.
+    """
+    import os
+
+    from clinica.utils.check_dependency import ThirdPartySoftware, check_software
+
+    check_software(ThirdPartySoftware.MRTRIX)
+
+    name_output_matrix = name_output_matrix or "mrtrix_matrix.mat"
+    mrtrix_matrix = Path(name_output_matrix)
+    mrtrix_matrix = mrtrix_matrix.resolve()
+
+    cmd = _get_transformation_cmd(
+        source_image, reference_image, flirt_matrix, mrtrix_matrix
+    )
+    os.system(cmd)
+
+    return mrtrix_matrix

test/unittests/pipelines/dwi/test_connectome_utils.py

@@ -144,3 +144,74 @@ def test_get_containers(subjects, sessions, expected):
     from clinica.pipelines.dwi.connectome.utils import get_containers
 
     assert get_containers(subjects, sessions) == expected
+
+
+def _create_files_helper(tmp_path: Path) -> tuple[Path, Path, Path, Path]:
+    flirt_matrix = tmp_path / "flirt.mat"
+    flirt_matrix.touch()
+
+    source_image = tmp_path / "src.nii.gz"
+    source_image.touch()
+
+    reference_image = tmp_path / "ref.nii.gz"
+    reference_image.touch()
+
+    mrtrix_matrix = tmp_path / "mrtrix_matrix.mat"
+    mrtrix_matrix.touch()
+
+    return source_image, reference_image, flirt_matrix, mrtrix_matrix
+
+
+def test_get_transformation_cmd(tmp_path):
+    from clinica.pipelines.dwi.connectome.utils import _get_transformation_cmd
+
+    source_image, reference_image, flirt_matrix, mrtrix_matrix = _create_files_helper(
+        tmp_path
+    )
+
+    assert (
+        _get_transformation_cmd(
+            source_image, reference_image, flirt_matrix, mrtrix_matrix
+        )
+        == f"transformconvert {flirt_matrix} {source_image} {reference_image} flirt_import {mrtrix_matrix}"
+    )
+
+
+def test_get_transformation_cmd_error(tmp_path):
+    from clinica.pipelines.dwi.connectome.utils import _get_transformation_cmd
+
+    with pytest.raises(
+        FileNotFoundError, match=f"The file {tmp_path / 'src.nii.gz'} was not found"
+    ):
+        _get_transformation_cmd(
+            tmp_path / "src.nii.gz",
+            tmp_path / "ref.nii.gz",
+            tmp_path / "flirt.mat",
+            tmp_path / "mrtx.mat",
+        )
+
+
+def test_convert_flirt_to_mrtrix_transformation(tmp_path, mocker):
+    from clinica.pipelines.dwi.connectome.utils import (
+        convert_flirt_to_mrtrix_transformation,
+    )
+
+    mocker.patch("clinica.utils.check_dependency.check_software", return_value=None)
+    mocker.patch("os.system", return_value=None)
+
+    source_image, reference_image, flirt_matrix, output_matrix = _create_files_helper(
+        tmp_path
+    )
+
+    assert (
+        convert_flirt_to_mrtrix_transformation(
+            source_image, reference_image, flirt_matrix, output_matrix.name
+        )
+        == Path(output_matrix.name).resolve()
+    )
+    assert (
+        convert_flirt_to_mrtrix_transformation(
+            source_image, reference_image, flirt_matrix, None
+        )
+        == Path("mrtrix_matrix.mat").resolve()
+    )