Drop tissue-mask transforms from longitudinal anat (Stage 4 of #301)

docs/data_dictionary.md

@@ -131,8 +131,5 @@ Produced by the `rbc longitudinal` subcommand group (`template`, `anatomical`, `
 | -------------------------------------------------- | ------ | ------------------------------------------------------------------------- | ------------------------------------------ | ---------------------------- |
 | `*_space-longitudinal_desc-brain_T1w.nii.gz`       | `T1w`  | Skull-stripped brain image aligned to the subject's longitudinal template | ANTs registration to longitudinal template | 3D NIfTI                     |
 | `*_space-longitudinal_desc-T1w_mask.nii.gz`        | `mask` | Brain mask in longitudinal template space                                 | ANTs registration to longitudinal template | 3D NIfTI, binary mask        |
-| `*_space-longitudinal_desc-csf_mask.nii.gz`        | `mask` | CSF mask in longitudinal template space                                   | ANTs registration to longitudinal template | 3D NIfTI, binary mask        |
-| `*_space-longitudinal_desc-gm_mask.nii.gz`         | `mask` | Gray matter mask in longitudinal template space                           | ANTs registration to longitudinal template | 3D NIfTI, binary mask        |
-| `*_space-longitudinal_desc-wm_mask.nii.gz`         | `mask` | White matter mask in longitudinal template space                          | ANTs registration to longitudinal template | 3D NIfTI, binary mask        |
 | `*_from-T1w_to-longitudinal_mode-image_xfm.nii.gz` | `xfm`  | Warp field mapping subject anatomy to the longitudinal template           | ANTs registration                          | 3D NIfTI, displacement field |
 | `*_from-longitudinal_to-T1w_mode-image_xfm.nii.gz` | `xfm`  | Inverse warp field mapping longitudinal template back to subject anatomy  | ANTs registration                          | 3D NIfTI, displacement field |

src/rbc/bids/longitudinal/anatomical.py

@@ -52,9 +52,6 @@ def resolve_longitudinal_anat(
         ),
         "brain": anat_q.expect(anat_df, suffix=Suffix.T1W, desc="brain"),
         "brain_mask": anat_q.find(anat_df, suffix=Suffix.MASK, desc="T1w"),
-        "csf_mask": anat_q.find(anat_df, suffix=Suffix.MASK, desc="csf"),
-        "gm_mask": anat_q.find(anat_df, suffix=Suffix.MASK, desc="gm"),
-        "wm_mask": anat_q.find(anat_df, suffix=Suffix.MASK, desc="wm"),
     }
 
 
@@ -71,21 +68,6 @@ def export_longitudinal_anat(aex: Bids, outputs: AnatomicalLongOutputs) -> None:
         suffix=Suffix.MASK,
         desc="T1w",
     )
-    aex.save(
-        _require_file(outputs.csf_mask, "csf_mask"),
-        suffix=Suffix.MASK,
-        desc="csf",
-    )
-    aex.save(
-        _require_file(outputs.gm_mask, "gm_mask"),
-        suffix=Suffix.MASK,
-        desc="gm",
-    )
-    aex.save(
-        _require_file(outputs.wm_mask, "wm_mask"),
-        suffix=Suffix.MASK,
-        desc="wm",
-    )
     aex.save(
         outputs.long_to_template_xfm,
         suffix="xfm",

src/rbc/workflows/longitudinal/anatomical.py

@@ -27,21 +27,12 @@ class AnatomicalLongOutputs(NamedTuple):
         brain: Skull-stripped T1w brain warped to longitudinal template space.
         brain_mask: Binary brain mask warped to longitudinal template space,
             or *None* if not provided.
-        csf_mask: CSF tissue mask warped to longitudinal template space,
-            or *None* if not provided.
-        gm_mask: GM tissue mask warped to longitudinal template space,
-            or *None* if not provided.
-        wm_mask: WM tissue mask warped to longitudinal template space,
-            or *None* if not provided.
         long_to_template_xfm: Longitudinal template-to-MNI152 composite warp.
         template_to_long_xfm: MNI152-to-longitudinal template composite warp.
     """
 
     brain: Path
     brain_mask: Path | None
-    csf_mask: Path | None
-    gm_mask: Path | None
-    wm_mask: Path | None
     long_to_template_xfm: Path
     template_to_long_xfm: Path
 
@@ -52,9 +43,6 @@ def longitudinal_process(
     *,
     brain: Path,
     brain_mask: Path | None = None,
-    csf_mask: Path | None = None,
-    gm_mask: Path | None = None,
-    wm_mask: Path | None = None,
     registration_template: Path = REGISTRATION_TEMPLATES.brain_1mm,
 ) -> AnatomicalLongOutputs:
     """Transform preprocessed anatomical outputs to longitudinal template space.
@@ -67,35 +55,28 @@ def longitudinal_process(
         subj_to_template_xfm: Subject-to-longitudinal-template composite warp.
         brain: Preprocessed brain image.
         brain_mask: Brain mask, if available.
-        csf_mask: CSF partial volume mask, if available.
-        gm_mask: Grey matter partial volume mask, if available.
-        wm_mask: White matter partial volume mask, if available.
         registration_template: Brain template for ANTs registration.
 
     Returns:
         :class:`AnatomicalLongOutputs` with all non-null inputs transformed to template
             space.
     """
-
-    def _xfm(val: Path | None) -> Path | None:
-        if val is None:
-            return None
-        return anat_transform(in_file=val, template=template, xfm=subj_to_template_xfm)
-
     _logger.info("Transforming anatomical outputs to longitudinal template space")
     _logger.info("Registration of longitudinal template to standard-space (ANTs)")
     transforms = ants_registration(
         in_file=template,
         registration_template=registration_template,
     )
+    brain_mask_out = (
+        anat_transform(in_file=brain_mask, template=template, xfm=subj_to_template_xfm)
+        if brain_mask is not None
+        else None
+    )
     return AnatomicalLongOutputs(
         brain=anat_transform(
             in_file=brain, template=template, xfm=subj_to_template_xfm
         ),
-        brain_mask=_xfm(brain_mask),
-        csf_mask=_xfm(csf_mask),
-        gm_mask=_xfm(gm_mask),
-        wm_mask=_xfm(wm_mask),
+        brain_mask=brain_mask_out,
         long_to_template_xfm=transforms.anat_to_template,
         template_to_long_xfm=transforms.template_to_anat,
     )

tests/unit/bids/test_longitudinal_anatomical.py

@@ -0,0 +1,227 @@
+"""Unit tests for ``rbc.bids.longitudinal.anatomical``."""
+
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
+import polars as pl
+
+from rbc.bids.longitudinal.anatomical import (
+    export_longitudinal_anat,
+    resolve_longitudinal_anat,
+)
+from rbc.context import RunContext
+from rbc.workflows.longitudinal.anatomical import AnatomicalLongOutputs
+
+if TYPE_CHECKING:
+    from pathlib import Path
+
+
+def _make_long_outputs(workdir: Path) -> AnatomicalLongOutputs:
+    """Build a populated AnatomicalLongOutputs pointing at dummy files."""
+
+    def _dummy(name: str) -> Path:
+        p = workdir / name
+        p.write_bytes(b"\x00")
+        return p
+
+    return AnatomicalLongOutputs(
+        brain=_dummy("brain.nii.gz"),
+        brain_mask=_dummy("brain_mask.nii.gz"),
+        long_to_template_xfm=_dummy("long_to_tpl.nii.gz"),
+        template_to_long_xfm=_dummy("tpl_to_long.nii.gz"),
+    )
+
+
+class TestExportLongitudinalAnat:
+    """Tests for :func:`export_longitudinal_anat`."""
+
+    def test_writes_expected_files(self, tmp_path: Path) -> None:
+        """Exports brain, brain_mask, and the two xfms under space-longitudinal."""
+        workdir = tmp_path / "work"
+        workdir.mkdir()
+        out_dir = tmp_path / "out"
+
+        ctx = RunContext(sub="01", ses="baseline", output_dir=out_dir)
+        aex = ctx.bids(datatype="anat").derive(space="longitudinal")
+
+        export_longitudinal_anat(aex, _make_long_outputs(workdir))
+
+        saved = sorted(p.name for p in out_dir.rglob("*.*"))
+        # Xfm filenames currently carry both ``space-longitudinal`` and the
+        # ``from-…_to-…`` pair, which is redundant (Jason handover #18 flags
+        # the ``from-`` workaround more broadly). We assert the current shape
+        # so regressions are caught, but if that cleanup lands the expected
+        # xfm names here should drop ``space-longitudinal_``.
+        assert saved == [
+            "sub-01_ses-baseline_space-longitudinal_desc-T1w_mask.nii.gz",
+            "sub-01_ses-baseline_space-longitudinal_desc-brain_T1w.nii.gz",
+            "sub-01_ses-baseline_space-longitudinal_from-MNI152NLin6Asym"
+            "_to-longitudinal_mode-image_xfm.nii.gz",
+            "sub-01_ses-baseline_space-longitudinal_from-longitudinal"
+            "_to-MNI152NLin6Asym_mode-image_xfm.nii.gz",
+        ]
+
+    def test_tissue_masks_not_produced(self, tmp_path: Path) -> None:
+        """No csf/gm/wm masks are written under space-longitudinal (#5)."""
+        workdir = tmp_path / "work"
+        workdir.mkdir()
+        out_dir = tmp_path / "out"
+
+        ctx = RunContext(sub="01", ses="baseline", output_dir=out_dir)
+        aex = ctx.bids(datatype="anat").derive(space="longitudinal")
+
+        export_longitudinal_anat(aex, _make_long_outputs(workdir))
+
+        names = [p.name for p in out_dir.rglob("*.*")]
+        for tissue in ("csf", "gm", "wm"):
+            assert not any(f"desc-{tissue}_mask" in n for n in names), (
+                f"Expected no space-longitudinal {tissue}_mask; got {names}"
+            )
+
+
+def _anat_row(
+    *,
+    sub: str,
+    ses: str,
+    suffix: str,
+    desc: str | None,
+    ext: str = ".nii.gz",
+    extra: list[dict[str, str]] | None = None,
+) -> dict[str, object]:
+    """Build a single BIDS-like row, including an ``extra_entities`` list."""
+    desc_part = f"_desc-{desc}" if desc else ""
+    path = f"sub-{sub}/ses-{ses}/anat/sub-{sub}_ses-{ses}{desc_part}_{suffix}{ext}"
+    return {
+        "datatype": "anat",
+        "suffix": suffix,
+        "ext": ext,
+        "sub": sub,
+        "ses": ses,
+        "desc": desc,
+        "root": "/data",
+        "path": path,
+        "extra_entities": extra or [],
+    }
+
+
+def _df(*rows: dict[str, object]) -> pl.DataFrame:
+    return pl.DataFrame(list(rows))
+
+
+class TestResolveLongitudinalAnat:
+    """Tests for :func:`resolve_longitudinal_anat`."""
+
+    def test_resolves_all_inputs(self, tmp_path: Path) -> None:
+        """Happy path: all four keys resolve to the expected paths."""
+        anat_df = _df(
+            _anat_row(sub="01", ses="baseline", suffix="T1w", desc="brain"),
+            _anat_row(sub="01", ses="baseline", suffix="mask", desc="T1w"),
+        )
+        tpl_df = _df(
+            _anat_row(sub="01", ses="longitudinal", suffix="T1w", desc=None),
+            _anat_row(
+                sub="01",
+                ses="longitudinal",
+                suffix="xfm",
+                desc=None,
+                ext=".txt",
+                extra=[
+                    {"key": "from", "value": "baseline"},
+                    {"key": "to", "value": "longitudinal"},
+                ],
+            ),
+        )
+
+        ctx = RunContext(sub="01", ses="baseline", output_dir=tmp_path)
+        anat_q = ctx.bids(datatype="anat")
+        tpl_q = anat_q.derive(ses="longitudinal")
+
+        resolved = resolve_longitudinal_anat(
+            anat_q, tpl_q, anat_df, tpl_df, ses="baseline"
+        )
+
+        assert set(resolved) == {
+            "template",
+            "subj_to_template_xfm",
+            "brain",
+            "brain_mask",
+        }
+        assert str(resolved["template"]).endswith("sub-01_ses-longitudinal_T1w.nii.gz")
+        assert str(resolved["subj_to_template_xfm"]).endswith(
+            "sub-01_ses-longitudinal_xfm.txt"
+        )
+        assert str(resolved["brain"]).endswith(
+            "sub-01_ses-baseline_desc-brain_T1w.nii.gz"
+        )
+        assert str(resolved["brain_mask"]).endswith(
+            "sub-01_ses-baseline_desc-T1w_mask.nii.gz"
+        )
+
+    def test_missing_brain_mask_is_none(self, tmp_path: Path) -> None:
+        """brain_mask is optional (``.find``) — returns None when absent."""
+        anat_df = _df(
+            _anat_row(sub="01", ses="baseline", suffix="T1w", desc="brain"),
+        )
+        tpl_df = _df(
+            _anat_row(sub="01", ses="longitudinal", suffix="T1w", desc=None),
+            _anat_row(
+                sub="01",
+                ses="longitudinal",
+                suffix="xfm",
+                desc=None,
+                ext=".txt",
+                extra=[
+                    {"key": "from", "value": "baseline"},
+                    {"key": "to", "value": "longitudinal"},
+                ],
+            ),
+        )
+
+        ctx = RunContext(sub="01", ses="baseline", output_dir=tmp_path)
+        anat_q = ctx.bids(datatype="anat")
+        tpl_q = anat_q.derive(ses="longitudinal")
+
+        resolved = resolve_longitudinal_anat(
+            anat_q, tpl_q, anat_df, tpl_df, ses="baseline"
+        )
+
+        assert resolved["brain_mask"] is None
+        assert resolved["brain"] is not None
+
+    def test_xfm_query_uses_bids_safe_label(self, tmp_path: Path) -> None:
+        """Session labels with non-alphanumerics resolve through ``bids_safe_label``.
+
+        ``pre-op`` is stored as ``from-preop`` in the xfm entity; the resolver
+        must sanitize the ses arg before querying or the xfm won't be found.
+        """
+        anat_df = _df(
+            _anat_row(sub="01", ses="pre-op", suffix="T1w", desc="brain"),
+        )
+        tpl_df = _df(
+            _anat_row(sub="01", ses="longitudinal", suffix="T1w", desc=None),
+            _anat_row(
+                sub="01",
+                ses="longitudinal",
+                suffix="xfm",
+                desc=None,
+                ext=".txt",
+                extra=[
+                    {"key": "from", "value": "preop"},
+                    {"key": "to", "value": "longitudinal"},
+                ],
+            ),
+        )
+
+        ctx = RunContext(sub="01", ses="pre-op", output_dir=tmp_path)
+        anat_q = ctx.bids(datatype="anat")
+        tpl_q = anat_q.derive(ses="longitudinal")
+
+        resolved = resolve_longitudinal_anat(
+            anat_q, tpl_q, anat_df, tpl_df, ses="pre-op"
+        )
+
+        assert resolved["subj_to_template_xfm"] is not None
+        assert str(resolved["subj_to_template_xfm"]).endswith(
+            "sub-01_ses-longitudinal_xfm.txt"
+        )

tests/unit/orchestration/test_longitudinal.py

@@ -17,6 +17,7 @@
 from rbc.context import RunContext
 from rbc.orchestration import Filters
 from rbc.orchestration.longitudinal import process_anat, process_func
+from rbc.workflows.longitudinal.anatomical import AnatomicalLongOutputs
 
 _SCHEMA = [
     "datatype",
@@ -48,17 +49,15 @@ def _func_row(sub: str, ses: str, task: str = "rest") -> tuple:
     return ("func", "bold", ".nii.gz", sub, ses, None, task, None, None, "/data", path)
 
 
-def _mock_anat_outputs() -> Mock:
+def _mock_anat_outputs() -> AnatomicalLongOutputs:
+    """Build a real AnatomicalLongOutputs so typos on missing attrs fail loudly."""
     fake = Path("fake_workdir")
-    m = Mock()
-    m.brain = fake / "brain.nii.gz"
-    m.brain_mask = fake / "brain_mask.nii.gz"
-    m.csf_mask = fake / "csf_mask.nii.gz"
-    m.gm_mask = fake / "gm_mask.nii.gz"
-    m.wm_mask = fake / "wm_mask.nii.gz"
-    m.long_to_template_xfm = fake / "long_to_template_xfm.nii.gz"
-    m.template_to_long_xfm = fake / "template_to_long_xfm.nii.gz"
-    return m
+    return AnatomicalLongOutputs(
+        brain=fake / "brain.nii.gz",
+        brain_mask=fake / "brain_mask.nii.gz",
+        long_to_template_xfm=fake / "long_to_template_xfm.nii.gz",
+        template_to_long_xfm=fake / "template_to_long_xfm.nii.gz",
+    )
 
 
 def _mock_func_outputs(*, with_bold_mask: bool = True) -> Mock:
@@ -302,7 +301,7 @@ def test_missing_required_output_raises(
         pipe_ctx = RunContext(sub="01", ses="baseline", output_dir=tmp_path)
         outputs = _mock_anat_outputs()
         if side_effect is None:
-            setattr(outputs, null_field, None)
+            outputs = outputs._replace(**{null_field: None})  # type: ignore[arg-type]
             get_patch = patch(
                 "rbc.bids.query.find_file",
                 return_value=Path("fake_workdir/file.nii.gz"),