[REF] Move PETVolume pipeline to new clinica.pipelines.pet module (…

…aramis-lab#1226)

* move PETVolume pipeline to new pet module

* update tests

* forgot to update pipeline code...

* fix broken pet linear pipeline

clinica/pipelines/__init__.py

@@ -6,7 +6,6 @@
     machine_learning_spatial_svm,
     pet,
     pet_surface,
-    pet_volume,
     statistics_surface,
     statistics_volume,
     statistics_volume_correction,

clinica/pipelines/pet/__init__.py

@@ -1 +1 @@
-from . import linear
+from . import linear, volume

clinica/pipelines/pet/linear/pipeline.py

@@ -59,6 +59,7 @@ def _build_input_node(self):
         import nipype.interfaces.utility as nutil
         import nipype.pipeline.engine as npe
 
+        from clinica.pipelines.pet.utils import get_suvr_mask
         from clinica.utils.exceptions import (
             ClinicaBIDSError,
             ClinicaCAPSError,
@@ -67,7 +68,6 @@ def _build_input_node(self):
         from clinica.utils.image import get_mni_template
         from clinica.utils.input_files import T1W_NII, T1W_TO_MNI_TRANSFORM
         from clinica.utils.inputs import clinica_file_reader
-        from clinica.utils.pet import get_suvr_mask
         from clinica.utils.stream import cprint
         from clinica.utils.ux import print_images_to_process
 

clinica/pipelines/pet/utils.py

@@ -0,0 +1,137 @@
+from pathlib import Path
+from typing import List, Union
+
+import pandas as pd
+
+from clinica.utils.pet import SUVRReferenceRegion, Tracer
+
+__all__ = [
+    "get_suvr_mask",
+    "read_psf_information",
+]
+
+
+def get_suvr_mask(region: Union[str, SUVRReferenceRegion]) -> Path:
+    """Returns the path to the SUVR mask from SUVR reference region label.
+
+    Parameters
+    ----------
+    region : str or SUVRReferenceRegion
+        The label of the SUVR reference region.
+        Supported labels are: 'pons', 'cerebellumPons', 'pons2', and 'cerebellumPons2'
+
+    Returns
+    -------
+    Path :
+        The path to the SUVR mask.
+    """
+    masks_dir = Path(__file__).resolve().parents[2] / "resources" / "masks"
+
+    return masks_dir / _get_suvr_reference_region_labels_filename(
+        SUVRReferenceRegion(region)
+    )
+
+
+def _get_suvr_reference_region_labels_filename(region: SUVRReferenceRegion) -> str:
+    if region == SUVRReferenceRegion.PONS:
+        return "region-pons_eroded-6mm_mask.nii.gz"
+    if region == SUVRReferenceRegion.CEREBELLUM_PONS:
+        return "region-cerebellumPons_eroded-6mm_mask.nii.gz"
+    if region == SUVRReferenceRegion.PONS2:
+        return "region-pons_remove-extrabrain_eroded-2it_mask.nii.gz"
+    if region == SUVRReferenceRegion.CEREBELLUM_PONS2:
+        return "region-cerebellumPons_remove-extrabrain_eroded-3it_mask.nii.gz"
+
+
+def read_psf_information(
+    pvc_psf_tsv_path: Path,
+    subject_ids: List[str],
+    session_ids: List[str],
+    pet_tracer: Union[str, Tracer],
+) -> List[List[int]]:
+    """Read PSF information from TSV file.
+
+    Parameters
+    ----------
+    pvc_psf_tsv_path : Path
+        The path to the TSV file containing the following columns:
+        'participant_id', 'session_id', 'acq_label', 'psf_x',
+        'psf_y', and 'psf_z'
+
+    subject_ids : List[str]
+        List of participant IDs.
+        ex: ['sub-CLNC01', 'sub-CLNC01']
+
+        .. warning::
+            Must have the same length as `session_ids`.
+
+    session_ids : List[str]
+        List of session IDs.
+        ex: ['ses-M000', 'ses-M018']
+
+        .. warning::
+            Must have the same length as `subject_ids`.
+
+    pet_tracer : str or Tracer
+        The tracer we want to select in the 'acq_label' column.
+        Other tracers will not be read in this function
+
+    Returns
+    -------
+    psf : List[List[int]]
+        The PSF information following [subject_ids, session_ids] order.
+
+    Examples
+    --------
+    Example of pvc_psf_tsv:
+
+    participant_id    session_id     acq_label     psf_x    psf_y    psf_z
+    sub-CLNC01        ses-M000        FDG           8        9        10
+    sub-CLNC01        ses-M018        FDG           8        9        10
+    sub-CLNC01        ses-M000        AV45          7        6        5
+    sub-CLNC02        ses-M000        FDG           8        9        10
+    sub-CLNC03        ses-M000        FDG           8        9        10
+    """
+    pet_tracer = Tracer(pet_tracer)
+    df = _read_psf_dataframe(pvc_psf_tsv_path)
+    psf = []
+    for subject, session in zip(subject_ids, session_ids):
+        result = df.query(
+            f"participant_id == '{subject}' and session_id == '{session}' and acq_label == '{pet_tracer.value}'"
+        )
+        if len(result) == 0:
+            raise RuntimeError(
+                f"Subject {subject} with session {session} and tracer {pet_tracer.value} "
+                f"that you want to proceed was not found in the TSV file containing "
+                f"PSF specifications ({pvc_psf_tsv_path})."
+            )
+        if len(result) > 1:
+            raise RuntimeError(
+                f"Subject {subject} with session {session} and tracer {pet_tracer.value} "
+                f"that you want to proceed was found multiple times "
+                f"in the TSV file containing PSF specifications ({pvc_psf_tsv_path})."
+            )
+        psf.append(result[["psf_x", "psf_y", "psf_z"]].values.tolist()[0])
+
+    return psf
+
+
+def _read_psf_dataframe(filename: Path) -> pd.DataFrame:
+    valid_columns = {
+        "participant_id",
+        "session_id",
+        "acq_label",
+        "psf_x",
+        "psf_y",
+        "psf_z",
+    }
+    df = pd.read_csv(filename, sep="\t")
+    column_mismatch = valid_columns.symmetric_difference(set(df.columns))
+    if column_mismatch:
+        raise IOError(
+            f"The file {filename} must contain the following columns (separated by tabulations):\n"
+            f"{valid_columns}\n"
+            f"The provided TSV file contains the following columns instead:{list(df.columns)}\n"
+            f"Pay attention to the spaces (there should be none)."
+        )
+    return df

clinica/pipelines/pet/volume/__init__.py

@@ -0,0 +1 @@
+from . import cli

clinica/pipelines/pet_volume/pet_volume_cli.py → clinica/pipelines/pet/volume/cli.py

@@ -1,4 +1,4 @@
-from typing import List, Optional, Tuple
+from typing import List, Optional
 
 import click
 
@@ -92,9 +92,10 @@ def cli(
     """
     from networkx import Graph
 
-    from clinica.pipelines.pet_volume.pet_volume_pipeline import PETVolume
     from clinica.utils.ux import print_end_pipeline
 
+    from .pipeline import PETVolume
+
     parameters = {
         "group_label": group_label,
         "acq_label": acq_label,

clinica/pipelines/pet_volume/info.json → clinica/pipelines/pet/volume/info.json

@@ -11,4 +11,4 @@
             "version": ">=12"
         }
     ]
-}
+}