From 10bce0a37908b02b15f20c10fe0dbc615db367c7 Mon Sep 17 00:00:00 2001
From: NicolasGensollen <nicolas.gensollen@gmail.com>
Date: Tue, 3 Dec 2024 10:17:01 +0100
Subject: [PATCH] Add test for handling pet images registered on T1w image

---
 clinica/utils/testing_utils.py                |  9 ++++++++
 .../pipelines/pet/test_pet_linear_pipeline.py | 23 +++++++++++++++++++
 2 files changed, 32 insertions(+)

diff --git a/clinica/utils/testing_utils.py b/clinica/utils/testing_utils.py
index 03c978285..2da6b0853 100644
--- a/clinica/utils/testing_utils.py
+++ b/clinica/utils/testing_utils.py
@@ -236,6 +236,15 @@ def _build_pet_linear(directory: Path, sub: str, ses: str, config: dict) -> None
 
     tracer = Tracer(config["acq_label"])
     suvr = SUVRReferenceRegion(config["suvr_reference_region"])
+    if config.get("save_PETinT1w", False):
+        (
+            directory
+            / "subjects"
+            / sub
+            / ses
+            / "pet_linear"
+            / f"{sub}_{ses}_trc-{tracer.value}_pet_space-T1w_pet.nii.gz"
+        ).touch()
     for filename in (
         f"{sub}_{ses}_trc-{tracer.value}_pet_space-MNI152NLin2009cSym_desc-Crop_res-1x1x1_suvr-{suvr.value}_pet.nii.gz",
         f"{sub}_{ses}_trc-{tracer.value}_pet_space-T1w_rigid.mat",
diff --git a/test/unittests/pipelines/pet/test_pet_linear_pipeline.py b/test/unittests/pipelines/pet/test_pet_linear_pipeline.py
index 41e85af54..f25bd88a3 100644
--- a/test/unittests/pipelines/pet/test_pet_linear_pipeline.py
+++ b/test/unittests/pipelines/pet/test_pet_linear_pipeline.py
@@ -88,6 +88,7 @@ def test_pet_linear_get_processed_visits(tmp_path, mocker):
             ├── ses-M000
             │         └── pet_linear
             │             ├── sub-02_ses-M000_trc-18FFDG_pet_space-MNI152NLin2009cSym_desc-Crop_res-1x1x1_suvr-pons_pet.nii.gz
+            │             ├── sub-02_ses-M000_trc-18FFDG_pet_space-T1w_pet.nii.gz
             │             └── sub-02_ses-M000_trc-18FFDG_pet_space-T1w_rigid.mat
             └── ses-M006
                 └── pet_linear
@@ -116,6 +117,7 @@ def test_pet_linear_get_processed_visits(tmp_path, mocker):
                     "acq_label": Tracer.FDG,
                     "suvr_reference_region": SUVRReferenceRegion.PONS,
                     "uncropped_image": False,
+                    "save_PETinT1w": True,
                 }
             },
             "subjects": {
@@ -140,6 +142,26 @@ def test_pet_linear_get_processed_visits(tmp_path, mocker):
             },
         },
     )
+    # We remove the pet image registered on the T1w image for sub-01 and session M006
+    (
+        caps
+        / "subjects"
+        / "sub-01"
+        / "ses-M006"
+        / "pet_linear"
+        / "sub-01_ses-M006_trc-18FFDG_pet_space-T1w_pet.nii.gz"
+    ).unlink()
+    pipeline = PETLinear(
+        bids_directory=str(bids),
+        caps_directory=str(caps),
+        parameters={
+            "acq_label": Tracer.FDG,
+            "suvr_reference_region": SUVRReferenceRegion.PONS,
+            "uncropped_image": False,
+            "save_PETinT1w": True,
+        },
+    )
+    assert pipeline.get_processed_visits() == [Visit("sub-02", "ses-M000")]
 
     pipeline = PETLinear(
         bids_directory=str(bids),
@@ -148,6 +170,7 @@ def test_pet_linear_get_processed_visits(tmp_path, mocker):
             "acq_label": Tracer.FDG,
             "suvr_reference_region": SUVRReferenceRegion.PONS,
             "uncropped_image": False,
+            "save_PETinT1w": False,
         },
     )