[ENH] Remove interactivity for image centering check (#1419)

* remove interactivity for image centering check * extend to check_relative_volume_location_in_world_coordinate_system * add a note in t1-freesurfer doc * Apply suggestions from code review Co-authored-by: AliceJoubert <[email protected]> * add a note in pet-volume doc * add a note in pet-surface doc * add a note in t1-volume doc --------- Co-authored-by: AliceJoubert <[email protected]>
aramis-lab · Jan 24, 2025 · d08c0e7 · d08c0e7
1 parent 80530a5
commit d08c0e7
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diff --git a/clinica/iotools/utils/data_handling/__init__.py b/clinica/iotools/utils/data_handling/__init__.py
@@ -1,8 +1,8 @@
 from ._centering import (
+    are_images_centered_around_origin_of_world_coordinate_system,
     center_all_nifti,
     center_nifti_origin,
     check_relative_volume_location_in_world_coordinate_system,
-    check_volume_location_in_world_coordinate_system,
 )
 from ._files import create_subs_sess_list, write_list_of_files
 from ._merging import create_merge_file
@@ -16,6 +16,6 @@
     "compute_missing_processing",
     "create_subs_sess_list",
     "write_list_of_files",
-    "check_volume_location_in_world_coordinate_system",
+    "are_images_centered_around_origin_of_world_coordinate_system",
     "check_relative_volume_location_in_world_coordinate_system",
 ]
diff --git a/clinica/iotools/utils/data_handling/_centering.py b/clinica/iotools/utils/data_handling/_centering.py
@@ -8,7 +8,7 @@
 
 __all__ = [
     "center_nifti_origin",
-    "check_volume_location_in_world_coordinate_system",
+    "are_images_centered_around_origin_of_world_coordinate_system",
     "check_relative_volume_location_in_world_coordinate_system",
     "center_all_nifti",
 ]
@@ -60,36 +60,32 @@ def _compute_qform(header: nib.Nifti1Header) -> np.ndarray:
     return qform
 
 
-def check_volume_location_in_world_coordinate_system(
-    nifti_list: List[PathLike],
-    bids_dir: PathLike,
+def are_images_centered_around_origin_of_world_coordinate_system(
+    images: Iterable[Path],
+    bids_dir: Path,
     modality: str = "t1w",
-    skip_question: bool = False,
 ) -> bool:
     """Check if images are centered around the origin of the world coordinate.
 
     Parameters
     ----------
-    nifti_list : list of PathLike
-        List of path to nifti files.
+    images : Iterable of Path
+        The paths to nifti files.
 
-    bids_dir : PathLike
-        Path to bids directory associated with this check.
+    bids_dir : Path
+        The path to bids directory associated with this check.
 
     modality : str, optional
         The modality of the image. Default='t1w'.
 
-    skip_question : bool, optional
-        If True, assume answer is yes. Default=False.
-
     Returns
     -------
     bool :
-        True if they are centered, False otherwise
+        True if all images are centered, False otherwise.
 
     Warns
     ------
-    If volume is not centered on origin of the world coordinate system
+    If at least one volume is not centered on origin of the world coordinate system.
 
     Notes
     -----
@@ -98,40 +94,25 @@ def check_volume_location_in_world_coordinate_system(
     When not centered, we warn the user of the problem propose to exit clinica to run clinica iotools center-nifti
     or to continue with the execution of the pipeline.
     """
-    import click
     import numpy as np
 
-    bids_dir = Path(bids_dir)
-    list_non_centered_files = [
-        Path(file) for file in nifti_list if not _is_centered(Path(file))
-    ]
-    if len(list_non_centered_files) == 0:
+    from clinica.utils.stream import cprint
+
+    non_centered_images = [image for image in images if not _is_centered(image)]
+    if len(non_centered_images) == 0:
         return True
-    centers = [
-        _get_world_coordinate_of_center(file) for file in list_non_centered_files
-    ]
+    centers = [_get_world_coordinate_of_center(image) for image in non_centered_images]
     l2_norm = [np.linalg.norm(center, ord=2) for center in centers]
-    click.echo(
+    cprint(
         _build_warning_message(
-            list_non_centered_files, centers, l2_norm, bids_dir, modality
-        )
+            non_centered_images, centers, l2_norm, bids_dir, modality
+        ),
+        lvl="warning",
     )
-    if not skip_question:
-        _ask_for_confirmation()
 
     return False
 
 
-def _ask_for_confirmation() -> None:
-    import sys
-
-    import click
-
-    if not click.confirm("Do you still want to launch the pipeline?"):
-        click.echo("Clinica will now exit...")
-        sys.exit(0)
-
-
 def _build_warning_message(
     non_centered_files: List[Path],
     centers: List[np.array],
@@ -170,12 +151,11 @@ def _build_warning_message(
 
 def check_relative_volume_location_in_world_coordinate_system(
     label_1: str,
-    nifti_list1: List[PathLike],
+    nifti_list1: list[PathLike],
     label_2: str,
-    nifti_list2: List[PathLike],
+    nifti_list2: list[PathLike],
     bids_dir: PathLike,
     modality: str,
-    skip_question: bool = False,
 ):
     """Check if the NIfTI file list `nifti_list1` and `nifti_list2` provided in argument are not too far apart,
     otherwise coreg in SPM may fail. Norm between center of volumes of 2 files must be less than 80 mm.
@@ -201,21 +181,15 @@ def check_relative_volume_location_in_world_coordinate_system(
         String that must be used in argument of:
         clinica iotools bids --modality <MODALITY>
         (used in potential warning message).
-
-    skip_question : bool, optional
-        Disable prompts for user input (default is False)
     """
-    import warnings
+    from clinica.utils.stream import log_and_warn
 
-    from clinica.utils.stream import cprint
-
-    warning_message = _build_warning_message_relative_volume_location(
-        label_1, nifti_list1, label_2, nifti_list2, bids_dir, modality
-    )
-    cprint(msg=warning_message, lvl="warning")
-    warnings.warn(warning_message)
-    if not skip_question:
-        _ask_for_confirmation()
+    if (
+        msg := _build_warning_message_relative_volume_location(
+            label_1, nifti_list1, label_2, nifti_list2, bids_dir, modality
+        )
+    ) is not None:
+        log_and_warn(msg, UserWarning)
 
 
 def _build_warning_message_relative_volume_location(
@@ -225,15 +199,15 @@ def _build_warning_message_relative_volume_location(
     nifti_list2: List[PathLike],
     bids_dir: PathLike,
     modality: str,
-) -> str:
+) -> Optional[str]:
     bids_dir = Path(bids_dir)
     file_couples = [(Path(f1), Path(f2)) for f1, f2 in zip(nifti_list1, nifti_list2)]
     df = pd.DataFrame(
         _get_problematic_pairs_with_l2_norm(file_couples),
         columns=[label_1, label_2, "Relative distance"],
     )
     if len(df) == 0:
-        return
+        return None
     warning_message = (
         f"It appears that {len(df)} pairs of files have an important relative offset. "
         "SPM co-registration has a high probability to fail on these files:\n\n"
@@ -391,8 +365,7 @@ def _is_centered(nii_volume: Path, threshold_l2: int = 50) -> bool:
     the volume did not exceed 100 mm. Above this distance, either the volume is either not segmented (SPM error), or the
     produced segmentation is wrong (not the shape of a brain anymore)
     """
-    center = _get_world_coordinate_of_center(nii_volume)
-    if center is None:
+    if (center := _get_world_coordinate_of_center(nii_volume)) is None:
         raise ValueError(
             f"Unable to compute the world coordinates of center for image {nii_volume}."
             "Please verify the image data and header."

diff --git a/clinica/pipelines/anatomical/freesurfer/t1/cli.py b/clinica/pipelines/anatomical/freesurfer/t1/cli.py
@@ -29,7 +29,6 @@
 @cli_param.option.subjects_sessions_tsv
 @cli_param.option.working_directory
 @cli_param.option.overwrite_outputs
-@cli_param.option.yes
 @cli_param.option.atlas_path
 @option.global_option_group
 @option.n_procs
@@ -44,7 +43,6 @@ def cli(
     subjects_sessions_tsv: Optional[str] = None,
     n_procs: Optional[int] = None,
     overwrite_outputs: bool = False,
-    yes: bool = False,
     atlas_path: Optional[str] = None,
     caps_name: Optional[str] = None,
 ) -> None:
@@ -64,10 +62,7 @@ def cli(
         caps_directory=caps_directory,
         tsv_file=subjects_sessions_tsv,
         base_dir=working_directory,
-        parameters={
-            "recon_all_args": recon_all_args,
-            "skip_question": yes,
-        },
+        parameters={"recon_all_args": recon_all_args},
         name=pipeline_name,
         overwrite_caps=overwrite_outputs,
         caps_name=caps_name,

diff --git a/clinica/pipelines/anatomical/freesurfer/t1/pipeline.py b/clinica/pipelines/anatomical/freesurfer/t1/pipeline.py
@@ -89,7 +89,7 @@ def _build_input_node(self):
         import nipype.pipeline.engine as npe
 
         from clinica.iotools.utils.data_handling import (
-            check_volume_location_in_world_coordinate_system,
+            are_images_centered_around_origin_of_world_coordinate_system,
         )
         from clinica.utils.exceptions import ClinicaException
         from clinica.utils.filemanip import (
@@ -155,10 +155,9 @@ def _build_input_node(self):
             synchronize=True,
             interface=nutil.IdentityInterface(fields=self.get_input_fields()),
         )
-        check_volume_location_in_world_coordinate_system(
-            t1w_files,
+        are_images_centered_around_origin_of_world_coordinate_system(
+            [Path(f) for f in t1w_files],
             self.bids_directory,
-            skip_question=self.parameters["skip_question"],
         )
 
         self.connect(

diff --git a/clinica/pipelines/pet/volume/cli.py b/clinica/pipelines/pet/volume/cli.py
@@ -23,7 +23,6 @@
 @cli_param.option.reconstruction_method
 @cli_param.option.subjects_sessions_tsv
 @cli_param.option.working_directory
-@cli_param.option.yes
 @option.global_option_group
 @option.n_procs
 @cli_param.option_group.advanced_pipeline_options
@@ -74,7 +73,6 @@ def cli(
     subjects_sessions_tsv: Optional[str] = None,
     working_directory: Optional[str] = None,
     n_procs: Optional[int] = None,
-    yes: bool = False,
 ) -> None:
     """SPM-based pre-processing of PET images.
 
@@ -106,7 +104,6 @@ def cli(
         "mask_threshold": mask_threshold,
         "pvc_mask_tissues": pvc_mask_tissues,
         "smooth": smooth,
-        "skip_question": yes,
     }
 
     pipeline = PETVolume(

diff --git a/clinica/pipelines/pet/volume/pipeline.py b/clinica/pipelines/pet/volume/pipeline.py
@@ -232,7 +232,6 @@ def _build_input_node(self):
             pet_bids,
             self.bids_directory,
             self.parameters["acq_label"],
-            skip_question=self.parameters["skip_question"],
         )
 
         # Save subjects to process in <WD>/<Pipeline.name>/participants.tsv

diff --git a/clinica/pipelines/pet_surface/pet_surface_cli.py b/clinica/pipelines/pet_surface/pet_surface_cli.py
@@ -20,7 +20,6 @@
 @cli_param.option.reconstruction_method
 @cli_param.option.subjects_sessions_tsv
 @cli_param.option.working_directory
-@cli_param.option.yes
 @option.global_option_group
 @option.n_procs
 def cli(
@@ -33,7 +32,6 @@ def cli(
     subjects_sessions_tsv: Optional[str] = None,
     working_directory: Optional[str] = None,
     n_procs: Optional[int] = None,
-    yes: bool = False,
 ) -> None:
     """Surface-based processing of PET images.
 
@@ -61,7 +59,6 @@ def cli(
         "reconstruction_method": reconstruction_method,
         "pvc_psf_tsv": pvc_psf_tsv,
         "longitudinal": False,
-        "skip_question": yes,
     }
 
     pipeline = PetSurface(

diff --git a/clinica/pipelines/pet_surface/pet_surface_longitudinal_cli.py b/clinica/pipelines/pet_surface/pet_surface_longitudinal_cli.py
@@ -19,7 +19,6 @@
 @cli_param.option_group.common_pipelines_options
 @cli_param.option.subjects_sessions_tsv
 @cli_param.option.working_directory
-@cli_param.option.yes
 @option.global_option_group
 @option.n_procs
 def cli(
@@ -31,7 +30,6 @@ def cli(
     subjects_sessions_tsv: Optional[str] = None,
     working_directory: Optional[str] = None,
     n_procs: Optional[int] = None,
-    yes: bool = False,
 ) -> None:
     """Longitudinal surface-based processing of PET images.
 
@@ -58,7 +56,6 @@ def cli(
         "suvr_reference_region": suvr_reference_region,
         "pvc_psf_tsv": pvc_psf_tsv,
         "longitudinal": True,
-        "skip_question": yes,
     }
 
     pipeline = PetSurface(

diff --git a/clinica/pipelines/pet_surface/pet_surface_pipeline.py b/clinica/pipelines/pet_surface/pet_surface_pipeline.py
@@ -142,7 +142,6 @@ def _build_input_node_longitudinal(self):
             read_parameters_node.inputs.pet,
             self.bids_directory,
             self.parameters["acq_label"],
-            skip_question=self.parameters["skip_question"],
         )
 
         # fmt: off
@@ -232,7 +231,6 @@ def _build_input_node_cross_sectional(self):
             read_parameters_node.inputs.pet,
             self.bids_directory,
             self.parameters["acq_label"],
-            skip_question=self.parameters["skip_question"],
         )
 
         # fmt: off

diff --git a/clinica/pipelines/t1_volume_tissue_segmentation/t1_volume_tissue_segmentation_cli.py b/clinica/pipelines/t1_volume_tissue_segmentation/t1_volume_tissue_segmentation_cli.py
@@ -16,7 +16,6 @@
 @cli_param.option_group.common_pipelines_options
 @cli_param.option.subjects_sessions_tsv
 @cli_param.option.working_directory
-@cli_param.option.yes
 @option.global_option_group
 @option.n_procs
 @cli_param.option_group.advanced_pipeline_options
@@ -37,7 +36,6 @@ def cli(
     subjects_sessions_tsv: Optional[str] = None,
     working_directory: Optional[str] = None,
     n_procs: Optional[int] = None,
-    yes: bool = False,
     caps_name: Optional[str] = None,
 ) -> None:
     """Tissue segmentation, bias correction and spatial normalization to MNI space of T1w images with SPM.
@@ -56,7 +54,6 @@ def cli(
         "tissue_probability_maps": tissue_probability_maps,
         "save_warped_unmodulated": not dont_save_warped_unmodulated,
         "save_warped_modulated": save_warped_modulated,
-        "skip_question": yes,
     }
 
     pipeline = T1VolumeTissueSegmentation(

diff --git a/clinica/pipelines/t1_volume_tissue_segmentation/t1_volume_tissue_segmentation_pipeline.py b/clinica/pipelines/t1_volume_tissue_segmentation/t1_volume_tissue_segmentation_pipeline.py
@@ -1,3 +1,4 @@
+from pathlib import Path
 from typing import List
 
 from nipype import config
@@ -73,7 +74,7 @@ def _build_input_node(self):
         import nipype.pipeline.engine as npe
 
         from clinica.iotools.utils.data_handling import (
-            check_volume_location_in_world_coordinate_system,
+            are_images_centered_around_origin_of_world_coordinate_system,
         )
         from clinica.utils.exceptions import ClinicaBIDSError, ClinicaException
         from clinica.utils.input_files import T1W_NII
@@ -90,12 +91,10 @@ def _build_input_node(self):
         self.subjects = subjects
         self.sessions = sessions
 
-        check_volume_location_in_world_coordinate_system(
-            t1w_files,
+        are_images_centered_around_origin_of_world_coordinate_system(
+            [Path(f) for f in t1w_files],
             self.bids_directory,
-            skip_question=self.parameters["skip_question"],
         )
-
         if len(self.subjects):
             print_images_to_process(self.subjects, self.sessions)
             cprint("The pipeline will last approximately 10 minutes per image.")