Include axes validation in write_multiscales_metadata

- Split the axes validation logic from the axes guessing logic so it can
be re-used
- Add tests covering the scenarios of format 0.1/0.2 as well as invalid axes

ome_zarr/writer.py

@@ -40,34 +40,36 @@ def _validate_axes_names(
     if isinstance(axes, str):
         axes = list(axes)
 
-    if axes is not None:
-        if len(axes) != ndim:
-            raise ValueError("axes length must match number of dimensions")
-        # from https://github.com/constantinpape/ome-ngff-implementations/
-        val_axes = tuple(axes)
-        if ndim == 2:
-            if val_axes != ("y", "x"):
-                raise ValueError(f"2D data must have axes ('y', 'x') {val_axes}")
-        elif ndim == 3:
-            if val_axes not in [("z", "y", "x"), ("c", "y", "x"), ("t", "y", "x")]:
-                raise ValueError(
-                    "3D data must have axes ('z', 'y', 'x') or ('c', 'y', 'x')"
-                    " or ('t', 'y', 'x'), not %s" % (val_axes,)
-                )
-        elif ndim == 4:
-            if val_axes not in [
-                ("t", "z", "y", "x"),
-                ("c", "z", "y", "x"),
-                ("t", "c", "y", "x"),
-            ]:
-                raise ValueError("4D data must have axes tzyx or czyx or tcyx")
-        else:
-            if val_axes != ("t", "c", "z", "y", "x"):
-                raise ValueError("5D data must have axes ('t', 'c', 'z', 'y', 'x')")
-
+    if len(axes) != ndim:
+        raise ValueError("axes length must match number of dimensions")
+    _validate_axes(axes)
     return axes
 
 
+def _validate_axes(axes: List[str], fmt: Format = CurrentFormat()) -> None:
+
+    val_axes = tuple(axes)
+    if len(val_axes) == 2:
+        if val_axes != ("y", "x"):
+            raise ValueError(f"2D data must have axes ('y', 'x') {val_axes}")
+    elif len(val_axes) == 3:
+        if val_axes not in [("z", "y", "x"), ("c", "y", "x"), ("t", "y", "x")]:
+            raise ValueError(
+                "3D data must have axes ('z', 'y', 'x') or ('c', 'y', 'x')"
+                " or ('t', 'y', 'x'), not %s" % (val_axes,)
+            )
+    elif len(val_axes) == 4:
+        if val_axes not in [
+            ("t", "z", "y", "x"),
+            ("c", "z", "y", "x"),
+            ("t", "c", "y", "x"),
+        ]:
+            raise ValueError("4D data must have axes tzyx or czyx or tcyx")
+    else:
+        if val_axes != ("t", "c", "z", "y", "x"):
+            raise ValueError("5D data must have axes ('t', 'c', 'z', 'y', 'x')")
+
+
 def write_multiscale(
     pyramid: List,
     group: zarr.Group,
@@ -111,7 +113,7 @@ def write_multiscales_metadata(
     group: zarr.Group,
     paths: List[str],
     fmt: Format = CurrentFormat(),
-    axes: Union[str, List[str]] = None,
+    axes: List[str] = None,
 ) -> None:
     """
     Write the multiscales metadata in the group metadata
@@ -137,7 +139,11 @@ def write_multiscales_metadata(
         }
     ]
     if axes is not None:
-        multiscales[0]["axes"] = axes
+        if fmt.version in ("0.1", "0.2"):
+            LOGGER.info("axes ignored for version 0.1 or 0.2")
+        else:
+            _validate_axes(axes, fmt)
+            multiscales[0]["axes"] = axes
     group.attrs["multiscales"] = multiscales
 
 

tests/test_writer.py

@@ -178,3 +178,25 @@ def test_axes(self, axes):
         write_multiscales_metadata(self.root, ["0"], axes=axes)
         assert "multiscales" in self.root.attrs
         assert self.root.attrs["multiscales"][0]["axes"] == axes
+
+    @pytest.mark.parametrize("fmt", (FormatV01(), FormatV02()))
+    def test_axes_ignored(self, fmt):
+        write_multiscales_metadata(
+            self.root, ["0"], fmt=fmt, axes=["t", "c", "z", "y", "x"]
+        )
+        assert "multiscales" in self.root.attrs
+        assert "axes" not in self.root.attrs["multiscales"][0]
+
+    @pytest.mark.parametrize(
+        "axes",
+        (
+            [],
+            ["i", "j"],
+            ["x", "y"],
+            ["y", "x", "c"],
+            ["x", "y", "z", "c", "t"],
+        ),
+    )
+    def test_invalid_0_3_axes(self, axes):
+        with pytest.raises(ValueError):
+            write_multiscales_metadata(self.root, ["0"], fmt=FormatV03(), axes=axes)