testing

Author: jpillai00

src/rbc/cli/all.py

@@ -51,6 +51,8 @@ class AllArgs(BaseArgs):
     def validate_namespace(cls, ns: argparse.Namespace) -> AllArgs:
         """Validate all-workflow arguments."""
         _validate_task(ns.task)
+        if ns.smooth is not None:
+            _validate_positive(ns.smooth, "smooth")
         _validate_positive(ns.start_tr, "Start TR")
         _validate_positive(ns.tr, "TR")
         atlas_files = _resolve_atlas_args(ns.atlas)

src/rbc/cli/functional.py

@@ -45,6 +45,8 @@ class FunctionalArgs(BaseArgs):
     def validate_namespace(cls, ns: argparse.Namespace) -> FunctionalArgs:
         """Validation of functional workflow specific arguments to NamedTuple."""
         _validate_task(ns.task)
+        if ns.smooth is not None:
+            _validate_positive(ns.smooth, "smooth")
         _validate_positive(ns.tr, "TR")
         return cls(
             **BaseArgs.validate_namespace(ns).__dict__,

src/rbc/cli/metrics.py

@@ -59,6 +59,8 @@ class MetricsArgs(BaseArgs):
     def validate_namespace(cls, ns: argparse.Namespace) -> MetricsArgs:
         """Validate metrics-specific arguments."""
         _validate_task(ns.task)
+        if ns.smooth is not None:
+            _validate_positive(ns.smooth, "smooth")
         _validate_positive(ns.tr, "TR")
         atlas_files = _resolve_atlas_args(ns.atlas)
         return cls(

tests/unit/bids/test_exports.py

@@ -73,9 +73,7 @@ def _make_func_outputs(w: Path, regressors: list[str]) -> FunctionalOutputs:
         template_bold=_dummy(w, "template_bold.nii.gz"),
         regressed_bold={r: _dummy(w, f"regressed_{r}.nii.gz") for r in regressors},
         cleaned_bold={r: _dummy(w, f"cleaned_{r}.nii.gz") for r in regressors},
-        cleaned_bold_smooth={
-            r: _dummy(w, f"cleaned_{r}_smooth.nii.gz") for r in regressors
-        },
+        cleaned_bold_smooth=None,
         regressor_file={r: _dummy(w, f"regressors_{r}.1D") for r in regressors},
         template_brain_mask=_dummy(w, "template_mask.nii.gz"),
     )
@@ -222,6 +220,31 @@ def test_file_count_two_regressors(
         saved = list(pipe_ctx.output_dir.rglob("*.*"))
         assert len(saved) == 16
 
+    def test_bold_smooth_not_exported_if_none(
+        self, func_bids: Bids, workdir: Path, pipe_ctx: RunContext
+    ) -> None:
+        """No smoothed BOLD files are exported when cleaned_bold_smooth is None."""
+        outputs = _make_func_outputs(workdir, ["36-parameter"])
+        export_functional(func_bids, outputs, regressors=["36-parameter"])
+        saved = [p.name for p in pipe_ctx.output_dir.rglob("*.nii.gz")]
+        assert not any("desc-sm" in name for name in saved)
+
+    def test_cleaned_bold_smooth_exported_with_correct_desc(
+        self, func_bids: Bids, workdir: Path, pipe_ctx: RunContext
+    ) -> None:
+        """Smoothed BOLD is exported with correct fwhm label."""
+        smooth_outputs = _make_func_outputs(workdir, ["36-parameter"])._replace(
+            cleaned_bold_smooth={
+                "36-parameter": _dummy(workdir, "cleaned_smooth.nii.gz")
+            }
+        )
+        export_functional(
+            func_bids, smooth_outputs, regressors=["36-parameter"], smooth=8.0
+        )
+        saved = [p.name for p in pipe_ctx.output_dir.rglob("*.nii.gz")]
+        sm_files = [n for n in saved if "desc-sm8preproc" in n]
+        assert len(sm_files) == 1
+
 
 # ---------------------------------------------------------------------------
 # Metrics exports
@@ -238,7 +261,11 @@ def test_sanitizes_atlas_labels(
         mni = func_bids.derive(space="MNI152NLin6Asym")
         outputs = _make_metrics_outputs(workdir, ["schaefer_200"])
         export_metrics(
-            mni, outputs, regressor="36-parameter", atlases=["schaefer_200"], smooth=6.0
+            mni,
+            outputs,
+            regressor="36-parameter",
+            atlases=["schaefer_200"],
+            smooth=None,
         )
         atlas_files = [
             p.name for p in pipe_ctx.output_dir.rglob("*.*") if "atlas-" in p.name
@@ -255,7 +282,7 @@ def test_sanitizes_regressor_labels(
         mni = func_bids.derive(space="MNI152NLin6Asym")
         outputs = _make_metrics_outputs(workdir, ["aal"])
         export_metrics(
-            mni, outputs, regressor="36-parameter", atlases=["aal"], smooth=6.0
+            mni, outputs, regressor="36-parameter", atlases=["aal"], smooth=None
         )
         all_names = [p.name for p in pipe_ctx.output_dir.rglob("*.*")]
         reg_files = [n for n in all_names if "reg-" in n]
@@ -270,7 +297,7 @@ def test_file_count_single_atlas(
         mni = func_bids.derive(space="MNI152NLin6Asym")
         outputs = _make_metrics_outputs(workdir, ["schaefer_200"])
         export_metrics(
-            mni, outputs, regressor="aCompCor", atlases=["schaefer_200"], smooth=6.0
+            mni, outputs, regressor="aCompCor", atlases=["schaefer_200"], smooth=None
         )
         saved = list(pipe_ctx.output_dir.rglob("*.*"))
         assert len(saved) == 8
@@ -282,10 +309,59 @@ def test_file_count_multiple_atlases(
         atlases = ["schaefer_200", "aal"]
         mni = func_bids.derive(space="MNI152NLin6Asym")
         outputs = _make_metrics_outputs(workdir, atlases)
-        export_metrics(mni, outputs, regressor="aCompCor", atlases=atlases, smooth=6.0)
+        export_metrics(mni, outputs, regressor="aCompCor", atlases=atlases, smooth=None)
         saved = list(pipe_ctx.output_dir.rglob("*.*"))
         assert len(saved) == 10
 
+    def test_file_count_single_atlas_with_smooth(
+        self, func_bids: Bids, workdir: Path, pipe_ctx: RunContext
+    ) -> None:
+        """3 raw + 3 zscored + 3 smooth + 3 smooth zscored + 2 atlas files = 14."""
+        mni = func_bids.derive(space="MNI152NLin6Asym")
+        smooth_outputs = _make_metrics_outputs(workdir, ["schaefer_200"])._replace(
+            alff_smooth=_dummy(workdir, "alff_sm.nii.gz"),
+            falff_smooth=_dummy(workdir, "falff_sm.nii.gz"),
+            reho_smooth=_dummy(workdir, "reho_sm.nii.gz"),
+            alff_smooth_zscored=_dummy(workdir, "alff_sm_z.nii.gz"),
+            falff_smooth_zscored=_dummy(workdir, "falff_sm_z.nii.gz"),
+            reho_smooth_zscored=_dummy(workdir, "reho_sm_z.nii.gz"),
+        )
+        export_metrics(
+            mni,
+            smooth_outputs,
+            regressor="aCompCor",
+            atlases=["schaefer_200"],
+            smooth=6.0,
+        )
+        saved = list(pipe_ctx.output_dir.rglob("*.*"))
+        assert len(saved) == 14
+
+    def test_smooth_maps_have_correct_desc(
+        self, func_bids: Bids, workdir: Path, pipe_ctx: RunContext
+    ) -> None:
+        """Smoothed maps are exported with correct fwhm labels."""
+        mni = func_bids.derive(space="MNI152NLin6Asym")
+        smooth_outputs = _make_metrics_outputs(workdir, ["schaefer_200"])._replace(
+            alff_smooth=_dummy(workdir, "alff_sm.nii.gz"),
+            falff_smooth=_dummy(workdir, "falff_sm.nii.gz"),
+            reho_smooth=_dummy(workdir, "reho_sm.nii.gz"),
+            alff_smooth_zscored=_dummy(workdir, "alff_sm_z.nii.gz"),
+            falff_smooth_zscored=_dummy(workdir, "falff_sm_z.nii.gz"),
+            reho_smooth_zscored=_dummy(workdir, "reho_sm_z.nii.gz"),
+        )
+        export_metrics(
+            mni,
+            smooth_outputs,
+            regressor="aCompCor",
+            atlases=["schaefer_200"],
+            smooth=8.0,
+        )
+        saved = [p.name for p in pipe_ctx.output_dir.rglob("*.nii.gz")]
+        sm_only = [n for n in saved if "desc-sm8" in n and "Zstd" not in n]
+        sm_zstd = [n for n in saved if "desc-sm8Zstd" in n]
+        assert len(sm_only) == 3
+        assert len(sm_zstd) == 3
+
 
 # ---------------------------------------------------------------------------
 # QC exports

tests/unit/cli/test_all.py

@@ -30,7 +30,7 @@ def base_args(tmp_path: Path) -> argparse.Namespace:
         regressor=["36-parameter"],
         task=None,
         atlas=["schaefer_200"],
-        fwhm=6.0,
+        smooth=None,
         start_tr=2,
         tr=None,
         tmp_dir=None,
@@ -64,7 +64,7 @@ def test_defaults(self, base_args: argparse.Namespace) -> None:
         assert args.regressor == ["36-parameter"]
         assert args.task is None
         assert "schaefer_200" in args.atlas_files
-        assert args.smooth == 6.0
+        assert args.smooth is None
         assert args.start_tr == 2
         assert args.participant_label == []
         assert args.session_label == []
@@ -184,11 +184,11 @@ def test_all_parser_atlas_choices(self) -> None:
         args = parser.parse_args(["all", "/input", "-o", "/output", "--atlas", "aal"])
         assert args.atlas == ["aal"]
 
-    def test_all_parser_has_fwhm(self) -> None:
-        """Test all subparser includes --fwhm argument."""
+    def test_all_parser_has_smooth(self) -> None:
+        """Test all subparser includes --smooth argument."""
         parser = create_parser()
-        args = parser.parse_args(["all", "/input", "-o", "/output", "--fwhm", "8.0"])
-        assert args.fwhm == 8.0
+        args = parser.parse_args(["all", "/input", "-o", "/output", "--smooth", "8.0"])
+        assert args.smooth == 8.0
 
     def test_all_parser_has_start_tr(self) -> None:
         """Test all subparser includes --start-tr argument."""
@@ -203,10 +203,10 @@ def test_all_parser_task_default_none(self) -> None:
         assert args.task is None
 
     def test_all_parser_fwhm_default(self) -> None:
-        """Test all subparser --fwhm defaults to 6.0."""
+        """Test all subparser --smooth defaults to None."""
         parser = create_parser()
         args = parser.parse_args(["all", "/input", "-o", "/output"])
-        assert args.fwhm == 6.0
+        assert args.smooth is None
 
     def test_all_parser_start_tr_default(self) -> None:
         """Test all subparser --start-tr defaults to 2."""

tests/unit/cli/test_functional.py

@@ -33,6 +33,7 @@ def func_namespace(self, tmp_path: Path) -> argparse.Namespace:
             regressor=["36-parameter"],
             task=None,
             tr=None,
+            smooth=None,
             tmp_dir=None,
             func_template=None,
             func_template_mask=None,

tests/unit/cli/test_metrics.py

@@ -29,7 +29,7 @@ def base_args(tmp_path: Path) -> argparse.Namespace:
         session_label=[],
         task=None,
         atlas=["schaefer_200"],
-        fwhm=6.0,
+        smooth=None,
         regressor=["36-parameter"],
         tr=None,
         tmp_dir=None,
@@ -55,7 +55,7 @@ def test_defaults(self, base_args: argparse.Namespace) -> None:
         args = MetricsArgs.validate_namespace(base_args)
         assert args.task is None
         assert "schaefer_200" in args.atlas_files
-        assert args.smooth == 6.0
+        assert args.smooth is None
         assert args.regressor == ["36-parameter"]
         assert args.participant_label == []
         assert args.session_label == []
@@ -150,13 +150,13 @@ def test_metrics_parser_atlas_choices(self) -> None:
         )
         assert args.atlas == ["aal"]
 
-    def test_metrics_parser_has_fwhm(self) -> None:
-        """Test metrics subparser includes --fwhm argument."""
+    def test_metrics_parser_has_smooth(self) -> None:
+        """Test metrics subparser includes --smooth argument."""
         parser = create_parser()
         args = parser.parse_args(
-            ["metrics", "/input", "-o", "/output", "--fwhm", "8.0"]
+            ["metrics", "/input", "-o", "/output", "--smooth", "8.0"]
         )
-        assert args.fwhm == 8.0
+        assert args.smooth == 8.0
 
     def test_metrics_parser_has_task(self) -> None:
         """Test metrics subparser includes --task argument."""
@@ -178,11 +178,11 @@ def test_metrics_parser_task_default_none(self) -> None:
         args = parser.parse_args(["metrics", "/input", "-o", "/output"])
         assert args.task is None
 
-    def test_metrics_parser_fwhm_default(self) -> None:
-        """Test metrics subparser --fwhm defaults to 6.0."""
+    def test_metrics_parser_smooth_default(self) -> None:
+        """Test metrics subparser --smooth defaults to None."""
         parser = create_parser()
         args = parser.parse_args(["metrics", "/input", "-o", "/output"])
-        assert args.fwhm == 6.0
+        assert args.smooth is None
 
 
 class TestResolveAtlasArgs: