[FIX] Fix usage of group labels in non-regression tests (#1371)

aramis-lab · Nov 13, 2024 · 93292a0 · 93292a0
1 parent 88afa1e
commit 93292a0
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Showing 4 changed files with 14 additions and 22 deletions.
diff --git a/test/nonregression/pipelines/anat/test_t1_volume.py b/test/nonregression/pipelines/anat/test_t1_volume.py
@@ -86,7 +86,7 @@ def run_t1_volume_create_dartel(
         caps_directory=fspath(output_dir / "caps"),
         tsv_file=fspath(input_dir / "subjects.tsv"),
         base_dir=fspath(working_dir),
-        parameters={"group_label": "UnitTest"},
+        group_label="UnitTest",
     )
     pipeline.build()
     pipeline.run(plugin="MultiProc", plugin_args={"n_procs": 4}, bypass_check=True)
@@ -162,7 +162,7 @@ def run_t1_volume_dartel_to_mni(
         caps_directory=fspath(output_dir / "caps"),
         tsv_file=fspath(input_dir / "subjects.tsv"),
         base_dir=fspath(working_dir),
-        parameters={"group_label": "UnitTest"},
+        group_label="UnitTest",
     )
     pipeline.build()
     pipeline.run(plugin="MultiProc", plugin_args={"n_procs": 4}, bypass_check=True)
@@ -222,7 +222,7 @@ def run_t1_volume_register_dartel(
         caps_directory=fspath(output_dir / "caps"),
         tsv_file=fspath(input_dir / "subjects.tsv"),
         base_dir=fspath(working_dir),
-        parameters={"group_label": "UnitTest"},
+        group_label="UnitTest",
     )
     pipeline.build()
     pipeline.run(plugin="MultiProc", plugin_args={"n_procs": 4}, bypass_check=True)
@@ -282,7 +282,7 @@ def run_t1_volume_parcellation(
         caps_directory=fspath(output_dir / "caps"),
         tsv_file=fspath(input_dir / "subjects.tsv"),
         base_dir=fspath(working_dir),
-        parameters={"group_label": "UnitTest"},
+        group_label="UnitTest",
     )
     pipeline.build()
     pipeline.run(plugin="MultiProc", plugin_args={"n_procs": 4}, bypass_check=True)

diff --git a/test/nonregression/pipelines/pet/test_pet_volume.py b/test/nonregression/pipelines/pet/test_pet_volume.py
@@ -24,7 +24,6 @@ def run_pet_volume(
     region = SUVRReferenceRegion.PONS
 
     parameters = {
-        "group_label": "UnitTest",
         "acq_label": tracer,
         "suvr_reference_region": region,
         "skip_question": True,
@@ -34,6 +33,7 @@ def run_pet_volume(
         caps_directory=fspath(output_dir / "caps"),
         tsv_file=fspath(input_dir / "subjects.tsv"),
         base_dir=fspath(working_dir),
+        group_label="UnitTest",
         parameters=parameters,
     )
     pipeline.build()

diff --git a/test/nonregression/pipelines/test_run_pipelines_ml.py b/test/nonregression/pipelines/test_run_pipelines_ml.py
@@ -150,12 +150,12 @@ def run_spatial_svm(
     # Copy necessary data from in to out
     shutil.copytree(input_dir / "caps", caps_dir, copy_function=shutil.copy)
 
-    parameters = {"group_label": "ADNIbl", "orig_input_data_ml": "t1-volume"}
     pipeline = SpatialSVM(
         caps_directory=fspath(caps_dir),
         tsv_file=fspath(tsv),
         base_dir=fspath(working_dir),
-        parameters=parameters,
+        group_label="ADNIbl",
+        parameters={"orig_input_data_ml": "t1-volume"},
     )
     pipeline.build()
     pipeline.run(plugin="MultiProc", plugin_args={"n_procs": 4}, bypass_check=True)

diff --git a/test/nonregression/pipelines/test_run_pipelines_stats.py b/test/nonregression/pipelines/test_run_pipelines_stats.py
@@ -85,7 +85,6 @@ def run_statistics_surface(
     shutil.copytree(input_dir / "caps", caps_dir, copy_function=shutil.copy)
 
     parameters = {
-        "group_label": "UnitTest",
         "orig_input_data": "t1-freesurfer",
         "glm_type": "group_comparison",
         "contrast": "group",
@@ -95,6 +94,7 @@ def run_statistics_surface(
         caps_directory=caps_dir,
         tsv_file=tsv,
         base_dir=working_dir,
+        group_label="UnitTest",
         parameters=parameters,
     )
     pipeline.build()
@@ -154,25 +154,22 @@ def run_statistics_volume_pet(
     # Copy necessary data from in to out
     shutil.copytree(input_dir / "caps", caps_dir, copy_function=shutil.copy)
 
-    # Instantiate pipeline and run()
     parameters = {
         # Clinica compulsory parameters
-        "group_label": "UnitTest",
         "orig_input_data_volume": "pet-volume",
         "contrast": "group",
         # Optional arguments for inputs from pet-volume pipeline
         "acq_label": Tracer.FDG,
         "use_pvc_data": False,
         "suvr_reference_region": SUVRReferenceRegion.PONS,
     }
-
     pipeline = StatisticsVolume(
         caps_directory=fspath(caps_dir),
         tsv_file=fspath(tsv),
         base_dir=fspath(working_dir),
+        group_label="UnitTest",
         parameters=parameters,
     )
-
     pipeline.run(plugin="MultiProc", plugin_args={"n_procs": 2}, bypass_check=True)
 
     output_t_stat = (
@@ -217,21 +214,16 @@ def run_statistics_volume_t1(
     # Copy necessary data from in to out
     shutil.copytree(input_dir / "caps", caps_dir, copy_function=shutil.copy)
 
-    # Instantiate pipeline and run()
-    parameters = {
-        # Clinica compulsory parameters
-        "group_label": "UnitTest",
-        "orig_input_data_volume": "t1-volume",
-        "contrast": "group",
-    }
-
     pipeline = StatisticsVolume(
         caps_directory=fspath(caps_dir),
         tsv_file=fspath(tsv),
         base_dir=fspath(working_dir),
-        parameters=parameters,
+        group_label="UnitTest",
+        parameters={
+            "orig_input_data_volume": "t1-volume",
+            "contrast": "group",
+        },
     )
-
     pipeline.run(plugin="MultiProc", plugin_args={"n_procs": 2}, bypass_check=True)
 
     output_t_stat = (