[FIX] Fix some issues around the usage of Tracer and `SUVRReference…

…Region` (aramis-lab#1280)

clinica/pipelines/machine_learning/classification_cli.py

@@ -1,11 +1,12 @@
-from typing import Optional
+from typing import Optional, Union
 
 import click
 
 from clinica import option
 from clinica.pipelines import cli_param
 from clinica.pipelines.engine import clinica_pipeline
 from clinica.utils.atlas import T1AndPetVolumeAtlasName
+from clinica.utils.pet import SUVRReferenceRegion, Tracer
 
 pipeline_name = "machinelearning-classification"
 
@@ -62,8 +63,8 @@ def cli(
     subjects_visits_tsv: str,
     diagnoses_tsv: str,
     output_directory: str,
-    acq_label: Optional[str] = None,
-    suvr_reference_region: Optional[str] = None,
+    acq_label: Optional[Union[str, Tracer]] = None,
+    suvr_reference_region: Optional[Union[str, SUVRReferenceRegion]] = None,
     atlas: Optional[str] = None,
     n_procs: Optional[int] = None,
 ) -> None:

clinica/pipelines/machine_learning/input.py

@@ -296,9 +296,9 @@ def get_images(self):
                     "preprocessing",
                     f"group-{self._input_params['group_label']}",
                     "atlas_statistics",
-                    f"{self._subjects[i]}_{self._sessions[i]}_trc-{self._input_params['acq_label']}_pet"
+                    f"{self._subjects[i]}_{self._sessions[i]}_trc-{self._input_params['acq_label'].value}_pet"
                     f"_space-{self._input_params['atlas']}{pvc_key_value}"
-                    f"_suvr-{self._input_params['suvr_reference_region']}_statistics.tsv",
+                    f"_suvr-{self._input_params['suvr_reference_region'].value}_statistics.tsv",
                 )
                 for i in range(len(self._subjects))
             ]
@@ -383,8 +383,8 @@ def get_images(self):
                             self._sessions[i],
                             "pet",
                             "surface",
-                            f"{self._subjects[i]}_{self._sessions[i]}_trc-{self._input_params['acq_label']}_pet"
-                            f"_space-fsaverage_suvr-{self._input_params['suvr_reference_region']}"
+                            f"{self._subjects[i]}_{self._sessions[i]}_trc-{self._input_params['acq_label'].value}_pet"
+                            f"_space-fsaverage_suvr-{self._input_params['suvr_reference_region'].value}"
                             f"_pvc-iy_hemi-{h}_fwhm-{self._input_params['fwhm']}_projection.mgh",
                         )
                         for h in hemi
@@ -579,8 +579,8 @@ def get_images(self):
                     "pet",
                     "preprocessing",
                     f"group-{self._input_params['group_label']}",
-                    f"{self._subjects[i]}_{self._sessions[i]}_trc-{self._input_params['acq_label']}_pet"
-                    f"_space-Ixi549Space{pvc_key_value}_suvr-{self._input_params['suvr_reference_region']}"
+                    f"{self._subjects[i]}_{self._sessions[i]}_trc-{self._input_params['acq_label'].value}_pet"
+                    f"_space-Ixi549Space{pvc_key_value}_suvr-{self._input_params['suvr_reference_region'].value}"
                     f"_mask-brain{fwhm_key_value}_pet.nii.gz",
                 )
                 for i in range(len(self._subjects))

clinica/pipelines/machine_learning/ml_workflows.py

@@ -1,6 +1,9 @@
+from typing import Optional, Union
+
 import numpy as np
 
 from clinica.pipelines.machine_learning import algorithm, base, input, validation
+from clinica.utils.pet import SUVRReferenceRegion, Tracer
 
 
 class VoxelBasedKFoldDualSVM(base.MLWorkflow):
@@ -14,11 +17,11 @@ def __init__(
         output_dir,
         fwhm=0,
         modulated="on",
-        acq_label=None,
-        suvr_reference_region=None,
+        acq_label: Optional[Union[str, Tracer]] = None,
+        suvr_reference_region: Optional[Union[str, SUVRReferenceRegion]] = None,
         use_pvc_data=False,
         precomputed_kernel=None,
-        mask_zeros=True,
+        mask_zeros: bool = True,
         n_threads=15,
         n_folds=10,
         grid_search_folds=10,
@@ -46,8 +49,8 @@ def __init__(
         output_dir,
         fwhm=0,
         modulated="on",
-        acq_label=None,
-        suvr_reference_region=None,
+        acq_label: Optional[Union[str, Tracer]] = None,
+        suvr_reference_region: Optional[Union[str, SUVRReferenceRegion]] = None,
         use_pvc_data=False,
         precomputed_kernel=None,
         mask_zeros=True,
@@ -79,8 +82,8 @@ def __init__(
         output_dir,
         fwhm=0,
         modulated="on",
-        acq_label=None,
-        suvr_reference_region=None,
+        acq_label: Optional[Union[str, Tracer]] = None,
+        suvr_reference_region: Optional[Union[str, SUVRReferenceRegion]] = None,
         use_pvc_data=False,
         precomputed_kernel=None,
         mask_zeros=True,
@@ -110,8 +113,8 @@ def __init__(
         group_label,
         output_dir,
         image_type="PET",
-        acq_label=None,
-        suvr_reference_region=None,
+        acq_label: Optional[Union[str, Tracer]] = None,
+        suvr_reference_region: Optional[Union[str, SUVRReferenceRegion]] = None,
         fwhm=20,
         precomputed_kernel=None,
         n_threads=15,
@@ -141,8 +144,8 @@ def __init__(
         image_type,
         atlas,
         output_dir,
-        acq_label=None,
-        suvr_reference_region=None,
+        acq_label: Optional[Union[str, Tracer]] = None,
+        suvr_reference_region: Optional[Union[str, SUVRReferenceRegion]] = None,
         use_pvc_data=False,
         n_threads=15,
         n_iterations=100,
@@ -171,8 +174,8 @@ def __init__(
         image_type,
         atlas,
         output_dir,
-        acq_label=None,
-        suvr_reference_region=None,
+        acq_label: Optional[Union[str, Tracer]] = None,
+        suvr_reference_region: Optional[Union[str, SUVRReferenceRegion]] = None,
         use_pvc_data=False,
         n_threads=15,
         n_iterations=100,
@@ -201,8 +204,8 @@ def __init__(
         image_type,
         atlas,
         output_dir,
-        acq_label=None,
-        suvr_reference_region=None,
+        acq_label: Optional[Union[str, Tracer]] = None,
+        suvr_reference_region: Optional[Union[str, SUVRReferenceRegion]] = None,
         use_pvc_data=False,
         n_threads=15,
         n_iterations=100,
@@ -234,8 +237,8 @@ def __init__(
         image_type,
         atlas,
         output_dir,
-        acq_label=None,
-        suvr_reference_region=None,
+        acq_label: Optional[Union[str, Tracer]] = None,
+        suvr_reference_region: Optional[Union[str, SUVRReferenceRegion]] = None,
         use_pvc_data=False,
         precomputed_kernel=None,
         n_threads=15,
@@ -266,8 +269,8 @@ def __init__(
         output_dir,
         fwhm=0,
         modulated="on",
-        acq_label=None,
-        suvr_reference_region=None,
+        acq_label: Optional[Union[str, Tracer]] = None,
+        suvr_reference_region: Optional[Union[str, SUVRReferenceRegion]] = None,
         use_pvc_data=False,
         precomputed_kernel=None,
         mask_zeros=True,
@@ -298,8 +301,8 @@ def __init__(
         image_type,
         atlas,
         output_dir,
-        acq_label=None,
-        suvr_reference_region=None,
+        acq_label: Optional[Union[str, Tracer]] = None,
+        suvr_reference_region: Optional[Union[str, SUVRReferenceRegion]] = None,
         use_pvc_data=False,
         n_threads=15,
         n_iterations=100,
@@ -330,8 +333,8 @@ def __init__(
         atlas,
         dataset,
         output_dir,
-        acq_label=None,
-        suvr_reference_region=None,
+        acq_label: Optional[Union[str, Tracer]] = None,
+        suvr_reference_region: Optional[Union[str, SUVRReferenceRegion]] = None,
         use_pvc_data=False,
         n_threads=15,
         n_iterations=100,
@@ -361,8 +364,8 @@ def __init__(
         atlas,
         dataset,
         output_dir,
-        acq_label=None,
-        suvr_reference_region=None,
+        acq_label: Optional[Union[str, Tracer]] = None,
+        suvr_reference_region: Optional[Union[str, SUVRReferenceRegion]] = None,
         use_pvc_data=False,
         n_threads=15,
         n_iterations=100,
@@ -398,8 +401,8 @@ def __init__(
         output_dir,
         fwhm=0,
         modulated="on",
-        acq_label=None,
-        suvr_reference_region=None,
+        acq_label: Optional[Union[str, Tracer]] = None,
+        suvr_reference_region: Optional[Union[str, SUVRReferenceRegion]] = None,
         use_pvc_data=False,
         precomputed_kernel=None,
         mask_zeros=True,

clinica/pipelines/pet/engine.py

@@ -1,26 +1,31 @@
 from clinica.pipelines.engine import Pipeline
+from clinica.utils.pet import ReconstructionMethod, Tracer
+from clinica.utils.stream import log_and_raise
 
 
 class PETPipeline(Pipeline):
     def _check_pipeline_parameters(self) -> None:
         """Check pipeline parameters."""
-        if "acq_label" not in self.parameters.keys():
-            raise KeyError("Missing compulsory acq_label key in pipeline parameter.")
-        self.parameters.setdefault("reconstruction_method", None)
+        from clinica.utils.exceptions import ClinicaPipelineConfigurationError
+
+        if "acq_label" not in self.parameters:
+            log_and_raise(
+                "Missing compulsory 'acq_label' key in pipeline parameter.",
+                ClinicaPipelineConfigurationError,
+            )
+        self.parameters["acq_label"] = Tracer(self.parameters["acq_label"])
+        if "reconstruction_method" in self.parameters:
+            if self.parameters["reconstruction_method"]:
+                self.parameters["reconstruction_method"] = ReconstructionMethod(
+                    self.parameters["reconstruction_method"]
+                )
+        else:
+            self.parameters["reconstruction_method"] = None
 
     def _get_pet_scans_query(self) -> dict:
         """Return the query to retrieve PET scans."""
         from clinica.utils.input_files import bids_pet_nii
-        from clinica.utils.pet import ReconstructionMethod, Tracer
-
-        pet_tracer = None
-        if self.parameters["acq_label"] is not None:
-            pet_tracer = Tracer(self.parameters["acq_label"])
-
-        reconstruction_method = None
-        if self.parameters["reconstruction_method"] is not None:
-            reconstruction_method = ReconstructionMethod(
-                self.parameters["reconstruction_method"]
-            )
 
-        return bids_pet_nii(pet_tracer, reconstruction_method)
+        return bids_pet_nii(
+            self.parameters["acq_label"], self.parameters["reconstruction_method"]
+        )

clinica/pipelines/pet/volume/cli.py

@@ -1,10 +1,11 @@
-from typing import List, Optional
+from typing import List, Optional, Union
 
 import click
 
 from clinica import option
 from clinica.pipelines import cli_param
 from clinica.pipelines.engine import clinica_pipeline
+from clinica.utils.pet import ReconstructionMethod, SUVRReferenceRegion, Tracer
 
 pipeline_name = "pet-volume"
 
@@ -62,9 +63,9 @@ def cli(
     bids_directory: str,
     caps_directory: str,
     group_label: str,
-    acq_label: str,
-    suvr_reference_region: Optional[str] = None,
-    reconstruction_method: Optional[str] = None,
+    acq_label: Union[str, Tracer],
+    suvr_reference_region: Optional[Union[str, SUVRReferenceRegion]] = None,
+    reconstruction_method: Optional[Union[str, ReconstructionMethod]] = None,
     pvc_psf_tsv: Optional[str] = None,
     mask_tissues: List[int] = (1, 2, 3),
     mask_threshold: float = 0.3,

clinica/utils/exceptions.py

@@ -42,6 +42,10 @@ class ClinicaXMLParserError(ClinicaParserError):
     """Base class for XML parser errors."""
 
 
+class ClinicaPipelineConfigurationError(ClinicaException):
+    """Base class for configuration errors of clinica pipelines."""
+
+
 class ClinicaInconsistentDatasetError(ClinicaException):
     """Base class for inconsistent datasets errors."""