move PETSurface pipeline to new pet module

clinica/pipelines/pet/surface/cli.py

@@ -0,0 +1,89 @@
+from typing import Optional
+
+import click
+
+from clinica import option
+from clinica.pipelines import cli_param
+from clinica.pipelines.engine import clinica_pipeline
+
+pipeline_name = "pet-surface"
+
+
+@clinica_pipeline
+@click.command(name=pipeline_name)
+@cli_param.argument.bids_directory
+@cli_param.argument.caps_directory
+@cli_param.argument.acq_label
+@cli_param.argument.suvr_reference_region
+@cli_param.argument.pvc_psf_tsv
+@cli_param.option_group.common_pipelines_options
+@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(
+    bids_directory: str,
+    caps_directory: str,
+    acq_label: str,
+    suvr_reference_region: str,
+    pvc_psf_tsv: str,
+    reconstruction_method: Optional[str] = None,
+    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.
+
+       ACQ_LABEL corresponds to the label given to the PET acquisition, specifying the tracer used.
+    Frequently used values are '18FFDG' or '18FAV45'.
+
+       The reference region must be specified to perform intensity normalization.
+    Accepted values include: 'pons', 'cerebellumPons', 'pons2', 'cerebellumPons2'.
+
+       PVC_PSF_TSV is the TSV file containing the psf_x, psf_y and psf_z of the PSF for each PET image.
+
+    Prerequisite: You need to have performed the t1-freesurfer pipeline on your T1-weighted MR images.
+
+    See https://aramislab.paris.inria.fr/clinica/docs/public/latest/Pipelines/PET_Surface/
+    """
+    from networkx import Graph
+
+    from clinica.utils.ux import print_end_pipeline
+
+    from .pipeline import PetSurface
+
+    parameters = {
+        "acq_label": acq_label,
+        "suvr_reference_region": suvr_reference_region,
+        "reconstruction_method": reconstruction_method,
+        "pvc_psf_tsv": pvc_psf_tsv,
+        "longitudinal": False,
+        "skip_question": yes,
+    }
+
+    pipeline = PetSurface(
+        bids_directory=bids_directory,
+        caps_directory=caps_directory,
+        tsv_file=subjects_sessions_tsv,
+        base_dir=working_directory,
+        parameters=parameters,
+        name=pipeline_name,
+    )
+
+    exec_pipeline = (
+        pipeline.run(plugin="MultiProc", plugin_args={"n_procs": n_procs})
+        if n_procs
+        else pipeline.run()
+    )
+
+    if isinstance(exec_pipeline, Graph):
+        print_end_pipeline(
+            pipeline_name, pipeline.base_dir, pipeline.base_dir_was_specified
+        )
+
+
+if __name__ == "__main__":
+    cli()