Add compatability patch for OME-Zarr v0.3

src/ndevio/bioio_plugins/_compatibility.py

@@ -4,6 +4,21 @@
 consolidated warning when a known incompatibility is detected, so that
 downstream property accessors can fail silently without repeating noisy
 messages.
+
+OME-Zarr spec version differences handled here:
+
+- **v0.1/v0.2**: No ``axes`` field, no ``coordinateTransformations`` in
+  ``datasets`` entries. ``bioio_ome_zarr`` falls back to guessing dims
+  from shape, but ``scale``/``dimension_properties`` raise ``KeyError``.
+  We warn and let nImage fall back to ``scale=1.0`` / ``units=None``.
+
+- **v0.3**: ``axes`` is a **list of strings** (e.g. ``["t", "c", "z", "y", "x"]``),
+  but ``bioio_ome_zarr`` assumes v0.4 dict-axes (``[{"name": "z", ...}]``).
+  Attempting ``ax["name"]`` on a string raises ``TypeError``.
+  We normalise string-axes to dict-axes **in-place** on the reader metadata
+  so all downstream code works transparently.
+
+- **v0.4+**: ``axes`` is a list of dicts — no patching needed.
 """
 
 from __future__ import annotations
@@ -13,11 +28,80 @@
 
 logger = logging.getLogger(__name__)
 
+# Dimension name → OME-Zarr axis type mapping (v0.4 spec).
+_AXIS_TYPE_MAP: dict[str, str] = {
+    't': 'time',
+    'c': 'channel',
+    'z': 'space',
+    'y': 'space',
+    'x': 'space',
+}
+
 if TYPE_CHECKING:
     from bioio_ome_zarr import Reader as OmeZarrReader
 
 
-def warn_if_old_zarr_format(reader: OmeZarrReader) -> None:
+def apply_ome_zarr_compat_patches(reader: OmeZarrReader) -> None:
+    """Apply all OME-Zarr compatibility patches to *reader*.
+
+    Currently handles:
+    - v0.1/v0.2 stores (warning only — no ``coordinateTransformations``)
+    - v0.3 stores (normalise string-axes to dict-axes in-place)
+
+    Parameters
+    ----------
+    reader : OmeZarrReader
+    """
+    _normalize_v03_string_axes(reader)
+    _warn_if_no_coordinate_transforms(reader)
+
+
+def _normalize_v03_string_axes(reader: OmeZarrReader) -> None:
+    """Convert v0.3 string-axes to v0.4 dict-axes in-place.
+
+    OME-Zarr v0.3 stores ``axes`` as ``["t", "c", "z", "y", "x"]``.
+    ``bioio_ome_zarr`` expects v0.4 format: ``[{"name": "z", "type": "space"}, ...]``.
+
+    This function mutates ``reader._multiscales_metadata`` so that all
+    downstream code in ``bioio_ome_zarr`` works without modification.
+    If the axes are already dicts (v0.4+) or absent (v0.1/v0.2), this
+    is a no-op.
+
+    Parameters
+    ----------
+    reader : OmeZarrReader
+    """
+    multiscales = reader._multiscales_metadata
+    if not multiscales:
+        return
+
+    patched = False
+    for scene_meta in multiscales:
+        axes = scene_meta.get('axes', [])
+        if not axes:
+            continue
+        # v0.3: axes are strings; v0.4+: axes are dicts
+        if isinstance(axes[0], str):
+            scene_meta['axes'] = [
+                {
+                    'name': name,
+                    'type': _AXIS_TYPE_MAP.get(name.lower(), 'space'),
+                }
+                for name in axes
+            ]
+            patched = True
+
+    if patched:
+        version = multiscales[0].get('version', 'unknown (likely 0.3)')
+        logger.info(
+            'OME-Zarr compatibility: normalised v0.3 string-axes to '
+            'v0.4 dict-axes for spec version %s. Image will open '
+            'normally but axis units are unavailable in this format.',
+            version,
+        )
+
+
+def _warn_if_no_coordinate_transforms(reader: OmeZarrReader) -> None:
     """Emit one warning if *reader* is a ``bioio_ome_zarr.Reader`` for a v0.1/v0.2 store.
 
     ``bioio_ome_zarr.Reader`` unconditionally accesses ``coordinateTransformations``

src/ndevio/nimage.py

@@ -184,9 +184,11 @@ def __init__(
         # Any compatibility warnings for old formats should be emitted at this point
         # Cheaply check without imports by looking at the reader's module name
         if self.reader.__module__.startswith('bioio_ome_zarr'):
-            from .bioio_plugins._compatibility import warn_if_old_zarr_format
+            from .bioio_plugins._compatibility import (
+                apply_ome_zarr_compat_patches,
+            )
 
-            warn_if_old_zarr_format(self.reader)
+            apply_ome_zarr_compat_patches(self.reader)
 
     @property
     def reference_xarray(self) -> xr.DataArray:
@@ -370,12 +372,12 @@ def layer_scale(self) -> tuple[float, ...]:
         axis_labels = self.layer_axis_labels
 
         # Try to get scale from BioImage - may fail for array-like inputs
-        # where physical_pixel_sizes is None (AttributeError), or for old OME-Zarr formats
-        # (v0.1/v0.2) that lack 'coordinateTransformations' in their dataset
-        # metadata (introduced in v0.3) (KeyError).
+        # where physical_pixel_sizes is None (AttributeError), old OME-Zarr
+        # v0.1/v0.2 missing 'coordinateTransformations' (KeyError), or
+        # v0.3 string-axes that weren't normalised (TypeError).
         try:
             bio_scale = self.scale
-        except (AttributeError, KeyError):
+        except (AttributeError, KeyError, TypeError):
             return tuple(1.0 for _ in axis_labels)
         return tuple(
             getattr(bio_scale, dim, None) or 1.0 for dim in axis_labels
@@ -427,9 +429,9 @@ def layer_units(self) -> tuple[str | None, ...]:
 
         try:
             dim_props = self.dimension_properties
-        # Old OME-Zarr v0.1/v0.2: dimension_properties → reader.scale →
-        # _get_scale_array raises KeyError for missing 'coordinateTransformations'.
-        except (AttributeError, KeyError):
+        # Old OME-Zarr v0.1/v0.2 (KeyError), v0.3 string-axes (TypeError),
+        # or array-like inputs without dimension metadata (AttributeError).
+        except (AttributeError, KeyError, TypeError):
             return tuple(None for _ in axis_labels)
 
         def _get_unit(dim: str) -> str | None:

tests/test_bioio_plugins/test_compatibility.py

@@ -19,11 +19,12 @@ def _make_v01_multiscales(version: str = '0.1') -> list:
     return [{'version': version, 'datasets': [{'path': '0'}, {'path': '1'}]}]
 
 
-def _make_v03_multiscales() -> list:
-    """Minimal OME-Zarr >=v0.3 multiscales — has coordinateTransformations."""
+def _make_v03_string_axes_multiscales() -> list:
+    """OME-Zarr v0.3 multiscales — axes are strings, has coordinateTransformations."""
     return [
         {
             'version': '0.3',
+            'axes': ['z', 'y', 'x'],
             'datasets': [
                 {
                     'path': '0',
@@ -36,19 +37,43 @@ def _make_v03_multiscales() -> list:
     ]
 
 
-class TestWarnIfOldZarrFormat:
-    """Unit tests for warn_if_old_zarr_format."""
+def _make_v04_multiscales() -> list:
+    """Minimal OME-Zarr >=v0.4 multiscales — dict-axes and coordinateTransformations."""
+    return [
+        {
+            'version': '0.4',
+            'axes': [
+                {'name': 'z', 'type': 'space'},
+                {'name': 'y', 'type': 'space'},
+                {'name': 'x', 'type': 'space'},
+            ],
+            'datasets': [
+                {
+                    'path': '0',
+                    'coordinateTransformations': [
+                        {'type': 'scale', 'scale': [1.0, 0.5, 0.5]}
+                    ],
+                }
+            ],
+        }
+    ]
+
+
+class TestWarnIfNoCoordinateTransforms:
+    """Unit tests for _warn_if_no_coordinate_transforms."""
 
     def test_v01_emits_warning(self, caplog):
         """v0.1 metadata (no coordinateTransformations) triggers a warning."""
-        from ndevio.bioio_plugins._compatibility import warn_if_old_zarr_format
+        from ndevio.bioio_plugins._compatibility import (
+            _warn_if_no_coordinate_transforms,
+        )
 
         reader = _make_zarr_reader(_make_v01_multiscales('0.1'))
 
         with caplog.at_level(
             logging.WARNING, logger='ndevio.bioio_plugins._compatibility'
         ):
-            warn_if_old_zarr_format(reader)
+            _warn_if_no_coordinate_transforms(reader)
 
         assert len(caplog.records) == 1
         assert '0.1' in caplog.records[0].message
@@ -57,47 +82,70 @@ def test_v01_emits_warning(self, caplog):
 
     def test_v02_emits_warning(self, caplog):
         """v0.2 metadata also triggers a warning."""
-        from ndevio.bioio_plugins._compatibility import warn_if_old_zarr_format
+        from ndevio.bioio_plugins._compatibility import (
+            _warn_if_no_coordinate_transforms,
+        )
 
         reader = _make_zarr_reader(_make_v01_multiscales('0.2'))
 
         with caplog.at_level(
             logging.WARNING, logger='ndevio.bioio_plugins._compatibility'
         ):
-            warn_if_old_zarr_format(reader)
+            _warn_if_no_coordinate_transforms(reader)
 
         assert len(caplog.records) == 1
         assert '0.2' in caplog.records[0].message
 
-    def test_v03_no_warning(self, caplog):
-        """v0.3+ metadata (has coordinateTransformations) emits no warning."""
-        from ndevio.bioio_plugins._compatibility import warn_if_old_zarr_format
+    def test_v03_with_transforms_no_warning(self, caplog):
+        """v0.3 metadata (has coordinateTransformations) emits no warning."""
+        from ndevio.bioio_plugins._compatibility import (
+            _warn_if_no_coordinate_transforms,
+        )
 
-        reader = _make_zarr_reader(_make_v03_multiscales())
+        reader = _make_zarr_reader(_make_v03_string_axes_multiscales())
 
         with caplog.at_level(
             logging.WARNING, logger='ndevio.bioio_plugins._compatibility'
         ):
-            warn_if_old_zarr_format(reader)
+            _warn_if_no_coordinate_transforms(reader)
+
+        assert len(caplog.records) == 0
+
+    def test_v04_no_warning(self, caplog):
+        """v0.4 metadata emits no warning."""
+        from ndevio.bioio_plugins._compatibility import (
+            _warn_if_no_coordinate_transforms,
+        )
+
+        reader = _make_zarr_reader(_make_v04_multiscales())
+
+        with caplog.at_level(
+            logging.WARNING, logger='ndevio.bioio_plugins._compatibility'
+        ):
+            _warn_if_no_coordinate_transforms(reader)
 
         assert len(caplog.records) == 0
 
     def test_empty_multiscales_no_warning(self, caplog):
         """Empty multiscales list does not raise and emits no warning."""
-        from ndevio.bioio_plugins._compatibility import warn_if_old_zarr_format
+        from ndevio.bioio_plugins._compatibility import (
+            _warn_if_no_coordinate_transforms,
+        )
 
         reader = _make_zarr_reader([])
 
         with caplog.at_level(
             logging.WARNING, logger='ndevio.bioio_plugins._compatibility'
         ):
-            warn_if_old_zarr_format(reader)
+            _warn_if_no_coordinate_transforms(reader)
 
         assert len(caplog.records) == 0
 
     def test_unknown_version_in_warning(self, caplog):
         """When version key is missing the warning still fires with a fallback string."""
-        from ndevio.bioio_plugins._compatibility import warn_if_old_zarr_format
+        from ndevio.bioio_plugins._compatibility import (
+            _warn_if_no_coordinate_transforms,
+        )
 
         # No 'version' key, no 'coordinateTransformations'
         multiscales = [{'datasets': [{'path': '0'}]}]
@@ -106,32 +154,74 @@ def test_unknown_version_in_warning(self, caplog):
         with caplog.at_level(
             logging.WARNING, logger='ndevio.bioio_plugins._compatibility'
         ):
-            warn_if_old_zarr_format(reader)
+            _warn_if_no_coordinate_transforms(reader)
 
         assert len(caplog.records) == 1
         assert 'unknown' in caplog.records[0].message.lower()
 
 
+class TestNormalizeV03StringAxes:
+    """Unit tests for _normalize_v03_string_axes."""
+
+    def test_string_axes_normalized(self):
+        """v0.3 string-axes are converted to v0.4 dict-axes."""
+        from ndevio.bioio_plugins._compatibility import (
+            _normalize_v03_string_axes,
+        )
+
+        reader = _make_zarr_reader(_make_v03_string_axes_multiscales())
+        _normalize_v03_string_axes(reader)
+
+        axes = reader._multiscales_metadata[0]['axes']
+        assert all(isinstance(ax, dict) for ax in axes)
+        assert axes[0] == {'name': 'z', 'type': 'space'}
+        assert axes[1] == {'name': 'y', 'type': 'space'}
+        assert axes[2] == {'name': 'x', 'type': 'space'}
+
+    def test_dict_axes_untouched(self):
+        """v0.4 dict-axes are not modified."""
+        from ndevio.bioio_plugins._compatibility import (
+            _normalize_v03_string_axes,
+        )
+
+        reader = _make_zarr_reader(_make_v04_multiscales())
+        import copy
+
+        original = copy.deepcopy(reader._multiscales_metadata[0]['axes'])
+        _normalize_v03_string_axes(reader)
+
+        assert reader._multiscales_metadata[0]['axes'] == original
+
+    def test_empty_multiscales(self):
+        """No crash on empty multiscales."""
+        from ndevio.bioio_plugins._compatibility import (
+            _normalize_v03_string_axes,
+        )
+
+        reader = _make_zarr_reader([])
+        _normalize_v03_string_axes(reader)  # should not raise
+
+
 class TestNImageCompatibilityGuard:
-    """Integration tests: nImage.__init__ only calls warn_if_old_zarr_format for zarr readers."""
+    """Integration tests: nImage.__init__ calls apply_ome_zarr_compat_patches for zarr readers."""
 
     def test_non_zarr_reader_skips_check(self, resources_dir):
-        """A TIFF-backed nImage never calls warn_if_old_zarr_format."""
+        """A TIFF-backed nImage never calls apply_ome_zarr_compat_patches."""
         from ndevio import nImage
 
         with patch(
-            'ndevio.bioio_plugins._compatibility.warn_if_old_zarr_format'
+            'ndevio.bioio_plugins._compatibility.apply_ome_zarr_compat_patches'
         ) as mock_check:
             nImage(resources_dir / 'cells3d2ch_legacy.tiff')
 
         mock_check.assert_not_called()
 
     def test_zarr_reader_calls_check(self, resources_dir):
-        """A zarr-backed nImage calls warn_if_old_zarr_format exactly once."""
+        """A zarr-backed nImage calls apply_ome_zarr_compat_patches exactly once."""
         from ndevio import nImage
 
         with patch(
-            'ndevio.bioio_plugins._compatibility.warn_if_old_zarr_format'
+            'ndevio.bioio_plugins._compatibility.apply_ome_zarr_compat_patches'
         ) as mock_check:
             nImage(resources_dir / 'dimension_handling_zyx_V3.zarr')