Merge pull request #578 from effigies/fix/legacy_dtseries_json

FIX: Cordon off .dtseries.json contents

Author: effigies

niworkflows/interfaces/bids.py

@@ -653,9 +653,21 @@ def _run_interface(self, runtime):
                 }
             )
             if self._metadata:
-                sidecar = Path(self._results["out_file"][0]).parent / (
-                    "%s.json" % _splitext(self._results["out_file"][0])[0]
-                )
+                out_file = Path(self._results["out_file"][0])
+                # 1.3.x hack
+                # For dtseries, we have been generating weird non-BIDS JSON files.
+                # We can safely keep producing them to avoid breaking derivatives, but
+                # only the existing keys should keep going into them.
+                if out_file.name.endswith(".dtseries.nii"):
+                    legacy_metadata = {}
+                    for key in ("grayordinates", "space", "surface", "surface_density", "volume"):
+                        if key in self._metadata:
+                            legacy_metadata[key] = self._metadata.pop(key)
+                    if legacy_metadata:
+                        sidecar = out_file.parent / f"{_splitext(str(out_file))[0]}.json"
+                        sidecar.write_text(dumps(legacy_metadata, sort_keys=True, indent=2))
+                # The future: the extension is the first . and everything after
+                sidecar = out_file.parent / f"{out_file.name.split('.', 1)[0]}.json"
                 sidecar.write_text(dumps(self._metadata, sort_keys=True, indent=2))
                 self._results["out_meta"] = str(sidecar)
         return runtime

niworkflows/interfaces/tests/test_bids.py

@@ -1,6 +1,7 @@
 """Tests on BIDS compliance."""
 import os
 from pathlib import Path
+import json
 
 import numpy as np
 import nibabel as nb
@@ -278,6 +279,46 @@ def test_DerivativesDataSink_build_path(
         assert Path(out).relative_to(tmp_path) == Path(base) / exp
 
 
+def test_DerivativesDataSink_dtseries_json_hack(tmp_path):
+    cifti_fname = str(tmp_path / "test.dtseries.nii")
+
+    axes = (nb.cifti2.SeriesAxis(start=0, step=2, size=20),
+            nb.cifti2.BrainModelAxis.from_mask(np.ones((5, 5, 5))))
+    hdr = nb.cifti2.cifti2_axes.to_header(axes)
+    cifti = nb.Cifti2Image(np.zeros(hdr.matrix.get_data_shape(), dtype=np.float32),
+                           header=hdr)
+    cifti.nifti_header.set_intent("ConnDenseSeries")
+    cifti.to_filename(cifti_fname)
+
+    source_file = tmp_path / "bids" / "sub-01" / "func" / "sub-01_task-rest_bold.nii.gz"
+    source_file.parent.mkdir(parents=True)
+    source_file.touch()
+
+    dds = bintfs.DerivativesDataSink(
+        in_file=cifti_fname,
+        base_directory=str(tmp_path),
+        source_file=str(source_file),
+        compress=False,
+        out_path_base="",
+        space="fsLR",
+        grayordinates="91k",
+        RepetitionTime=2.0,
+    )
+
+    res = dds.run()
+
+    out_path = Path(res.outputs.out_file)
+
+    assert out_path.name == "sub-01_task-rest_space-fsLR_bold.dtseries.nii"
+    old_sidecar = out_path.with_name("sub-01_task-rest_space-fsLR_bold.dtseries.json")
+    new_sidecar = out_path.with_name("sub-01_task-rest_space-fsLR_bold.json")
+
+    assert old_sidecar.exists()
+    assert "grayordinates" in json.loads(old_sidecar.read_text())
+    assert new_sidecar.exists()
+    assert "RepetitionTime" in json.loads(new_sidecar.read_text())
+
+
 @pytest.mark.parametrize(
     "space, size, units, xcodes, zipped, fixed, data_dtype",
     [