Remove entity pet in the middle of the filename as this was done in t…

…he pipeline some time ago
aramis-lab · Dec 4, 2024 · 0492f90 · 0492f90
1 parent d046d10
commit 0492f90
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Showing 4 changed files with 23 additions and 23 deletions.
diff --git a/clinica/utils/input_files.py b/clinica/utils/input_files.py
@@ -724,7 +724,7 @@ def pet_linear_nii(
     information = {
         "pattern": Path("pet_linear")
         / _clean_pattern(
-            f"*{tracer_filter}_pet{space_filer}{description}{resolution_filter}{region_filter}_pet.nii.gz"
+            f"*{tracer_filter}{space_filer}{description}{resolution_filter}{region_filter}_pet.nii.gz"
         ),
         "description": (
             f"{'Cropped ' if space == 'mni' and not uncropped_image else ''}PET nifti image{resolution_description}"
@@ -741,7 +741,7 @@ def pet_linear_transformation_matrix(tracer: Union[str, Tracer]) -> dict:
     tracer = Tracer(tracer)
 
     return {
-        "pattern": Path("pet_linear") / f"*_trc-{tracer.value}_pet_space-T1w_rigid.mat",
+        "pattern": Path("pet_linear") / f"*_trc-{tracer.value}_space-T1w_rigid.mat",
         "description": "Rigid transformation matrix between the PET and T1w images estimated with ANTs.",
         "needed_pipeline": "pet-linear",
     }

diff --git a/clinica/utils/testing_utils.py b/clinica/utils/testing_utils.py
@@ -243,11 +243,11 @@ def _build_pet_linear(directory: Path, sub: str, ses: str, config: dict) -> None
             / sub
             / ses
             / "pet_linear"
-            / f"{sub}_{ses}_trc-{tracer.value}_pet_space-T1w_pet.nii.gz"
+            / f"{sub}_{ses}_trc-{tracer.value}_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",
+        f"{sub}_{ses}_trc-{tracer.value}_space-MNI152NLin2009cSym_desc-Crop_res-1x1x1_suvr-{suvr.value}_pet.nii.gz",
+        f"{sub}_{ses}_trc-{tracer.value}_space-T1w_rigid.mat",
     ):
         (directory / "subjects" / sub / ses / "pet_linear" / filename).touch()
 

diff --git a/test/unittests/pipelines/pet/test_pet_linear_pipeline.py b/test/unittests/pipelines/pet/test_pet_linear_pipeline.py
@@ -76,24 +76,24 @@ def test_pet_linear_get_processed_visits(tmp_path, mocker):
         ├── sub-01
         │         ├── ses-M000
         │         │         └── pet_linear
-        │         │             ├── sub-01_ses-M000_trc-18FAV45_pet_space-MNI152NLin2009cSym_desc-Crop_res-1x1x1_suvr-pons2_pet.nii.gz
-        │         │             └── sub-01_ses-M000_trc-18FAV45_pet_space-T1w_rigid.mat
+        │         │             ├── sub-01_ses-M000_trc-18FAV45_space-MNI152NLin2009cSym_desc-Crop_res-1x1x1_suvr-pons2_pet.nii.gz
+        │         │             └── sub-01_ses-M000_trc-18FAV45_space-T1w_rigid.mat
         │         └── ses-M006
         │             └── pet_linear
-        │                 ├── sub-01_ses-M006_trc-18FAV45_pet_space-MNI152NLin2009cSym_desc-Crop_res-1x1x1_suvr-pons2_pet.nii.gz
-        │                 ├── sub-01_ses-M006_trc-18FAV45_pet_space-T1w_rigid.mat
-        │                 ├── sub-01_ses-M006_trc-18FFDG_pet_space-MNI152NLin2009cSym_desc-Crop_res-1x1x1_suvr-pons_pet.nii.gz
-        │                 └── sub-01_ses-M006_trc-18FFDG_pet_space-T1w_rigid.mat
+        │                 ├── sub-01_ses-M006_trc-18FAV45_space-MNI152NLin2009cSym_desc-Crop_res-1x1x1_suvr-pons2_pet.nii.gz
+        │                 ├── sub-01_ses-M006_trc-18FAV45_space-T1w_rigid.mat
+        │                 ├── sub-01_ses-M006_trc-18FFDG_space-MNI152NLin2009cSym_desc-Crop_res-1x1x1_suvr-pons_pet.nii.gz
+        │                 └── sub-01_ses-M006_trc-18FFDG_space-T1w_rigid.mat
         └── sub-02
             ├── 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
+            │             ├── sub-02_ses-M000_trc-18FFDG_space-MNI152NLin2009cSym_desc-Crop_res-1x1x1_suvr-pons_pet.nii.gz
+            │             ├── sub-02_ses-M000_trc-18FFDG_space-T1w_pet.nii.gz
+            │             └── sub-02_ses-M000_trc-18FFDG_space-T1w_rigid.mat
             └── ses-M006
                 └── pet_linear
-                    ├── sub-02_ses-M006_trc-18FAV45_pet_space-MNI152NLin2009cSym_desc-Crop_res-1x1x1_suvr-pons2_pet.nii.gz
-                    └── sub-02_ses-M006_trc-18FAV45_pet_space-T1w_rigid.mat
+                    ├── sub-02_ses-M006_trc-18FAV45_space-MNI152NLin2009cSym_desc-Crop_res-1x1x1_suvr-pons2_pet.nii.gz
+                    └── sub-02_ses-M006_trc-18FAV45_space-T1w_rigid.mat
 
     And make sure that a PETLinear pipeline with tracer 18FFDG et pons SUVR will only consider
     (sub-01, ses-M006) and (sub-02, ses-M000) as already processed. The other folders contain
@@ -149,7 +149,7 @@ def test_pet_linear_get_processed_visits(tmp_path, mocker):
         / "sub-01"
         / "ses-M006"
         / "pet_linear"
-        / "sub-01_ses-M006_trc-18FFDG_pet_space-T1w_pet.nii.gz"
+        / "sub-01_ses-M006_trc-18FFDG_space-T1w_pet.nii.gz"
     ).unlink()
     pipeline = PETLinear(
         bids_directory=str(bids),
@@ -186,7 +186,7 @@ def test_pet_linear_get_processed_visits(tmp_path, mocker):
         / "sub-01"
         / "ses-M006"
         / "pet_linear"
-        / "sub-01_ses-M006_trc-18FFDG_pet_space-T1w_rigid.mat"
+        / "sub-01_ses-M006_trc-18FFDG_space-T1w_rigid.mat"
     ).unlink()
 
     # The corresponding visit is not considered as "processed" anymore because the transformation is

diff --git a/test/unittests/utils/test_input_files.py b/test/unittests/utils/test_input_files.py
@@ -98,7 +98,7 @@ def test_dwi_dti_query_error():
                 "Cropped PET nifti image affinely registered to the MNI152NLin2009cSym "
                 "template resulting from the pet-linear pipeline"
             ),
-            "pet_linear/*_pet_space-MNI152NLin2009cSym_desc-Crop*_pet.nii.gz",
+            "pet_linear/*_space-MNI152NLin2009cSym_desc-Crop*_pet.nii.gz",
         ),
         (
             {
@@ -108,7 +108,7 @@ def test_dwi_dti_query_error():
                 "Cropped PET nifti image obtained with tracer 18FFDG affinely registered to the "
                 "MNI152NLin2009cSym template resulting from the pet-linear pipeline"
             ),
-            "pet_linear/*_trc-18FFDG_pet_space-MNI152NLin2009cSym_desc-Crop*_pet.nii.gz",
+            "pet_linear/*_trc-18FFDG_space-MNI152NLin2009cSym_desc-Crop*_pet.nii.gz",
         ),
         (
             {
@@ -121,7 +121,7 @@ def test_dwi_dti_query_error():
                 "PET nifti image of resolution 2x2x2 obtained with tracer 18FAV45 for SUVR region "
                 "pons affinely registered to the MNI152NLin2009cSym template resulting from the pet-linear pipeline"
             ),
-            "pet_linear/*_trc-18FAV45_pet_space-MNI152NLin2009cSym*_res-2x2x2_suvr-pons_pet.nii.gz",
+            "pet_linear/*_trc-18FAV45_space-MNI152NLin2009cSym*_res-2x2x2_suvr-pons_pet.nii.gz",
         ),
         (
             {
@@ -133,7 +133,7 @@ def test_dwi_dti_query_error():
                 "PET nifti image of resolution 2x2x2 for SUVR region pons2 affinely "
                 "registered to the associated T1w image resulting from the pet-linear pipeline"
             ),
-            "pet_linear/*_pet_space-T1w*_res-2x2x2_suvr-pons2_pet.nii.gz",
+            "pet_linear/*_space-T1w*_res-2x2x2_suvr-pons2_pet.nii.gz",
         ),
         (
             {
@@ -144,7 +144,7 @@ def test_dwi_dti_query_error():
                 "PET nifti image obtained with tracer 18FFDG affinely registered to the "
                 "associated T1w image resulting from the pet-linear pipeline"
             ),
-            "pet_linear/*_trc-18FFDG_pet_space-T1w*_pet.nii.gz",
+            "pet_linear/*_trc-18FFDG_space-T1w*_pet.nii.gz",
         ),
     ],
 )