expand testing

src/ngio/core/image_like_handler.py

@@ -2,7 +2,7 @@
 
 from zarr.store.common import StoreLike
 
-from ngio.ngff_meta import FractalImageMeta, get_ngff_image_meta_handler, PixelSize
+from ngio.ngff_meta import FractalImageMeta, PixelSize, get_ngff_image_meta_handler
 
 
 class ImageLikeHandler:

src/ngio/ngff_meta/fractal_image_meta.py

@@ -169,7 +169,7 @@ def to_ordered_list(self) -> list:
         """Return the pixel size according to the axis order."""
         return [getattr(self, axis) for axis in self.axis_order]
 
-    def change_units(self, new_unit: SpaceUnits | str) -> "PixelSize":
+    def to_units(self, new_unit: SpaceUnits | str) -> "PixelSize":
         """Return a new PixelSize object with the pixel size in the new unit.
 
         Args:
@@ -486,10 +486,10 @@ def axes_names(self) -> list[str]:
         """List of axes names in the Image."""
         names = []
         for ax in self.axes:
-            if isinstance(ax.name, str):
-                names.append(ax.name)
-            else:
+            if isinstance(ax.name, SpaceNames) or isinstance(ax.name, TimeNames):
                 names.append(ax.name.value)
+            else:
+                names.append(ax.name)
         return names
 
     @property

tests/data/meta_v04/base_ome_zarr_label_meta.json

@@ -0,0 +1,44 @@
+{
+    "multiscales": [
+        {
+            "axes": [
+                {"name": "z", "type": "space", "unit": "micrometer"},
+                {"name": "y", "type": "space", "unit": "micrometer"},
+                {"name": "x", "type": "space", "unit": "micrometer"}
+            ],
+            "datasets": [
+                {
+                    "coordinateTransformations": [
+                        {"scale": [1.0, 0.1625, 0.1625], "type": "scale"}
+                    ],
+                    "path": "0"
+                },
+                {
+                    "coordinateTransformations": [
+                        {"scale": [1.0, 0.325, 0.325], "type": "scale"}
+                    ],
+                    "path": "1"
+                },
+                {
+                    "coordinateTransformations": [
+                        {"scale": [1.0, 0.65, 0.65], "type": "scale"}
+                    ],
+                    "path": "2"
+                },
+                {
+                    "coordinateTransformations": [
+                        {"scale": [1.0, 1.3, 1.3], "type": "scale"}
+                    ],
+                    "path": "3"
+                },
+                {
+                    "coordinateTransformations": [
+                        {"scale": [1.0, 2.6, 2.6], "type": "scale"}
+                    ],
+                    "path": "4"
+                }
+            ],
+            "version": "0.4"
+        }
+    ]
+}

tests/ngff_meta/conftest.py

@@ -18,3 +18,17 @@ def ome_zarr_image_v04_path(tmpdir):
     base_ome_zarr_meta = base_ome_zarr_meta
     group.attrs.update(base_ome_zarr_meta)
     return zarr_path
+
+
+@fixture
+def ome_zarr_label_v04_path(tmpdir):
+    zarr_path = Path(tmpdir) / "test_ome_ngff_image_v04.zarr"
+
+    group = zarr.open_group(store=zarr_path, mode="w", zarr_format=2)
+
+    with open("tests/data/meta_v04/base_ome_zarr_label_meta.json") as f:
+        base_ome_zarr_meta = json.load(f)
+
+    base_ome_zarr_meta = base_ome_zarr_meta
+    group.attrs.update(base_ome_zarr_meta)
+    return zarr_path

tests/ngff_meta/test_fractal_image_meta.py

@@ -45,3 +45,33 @@ def test_modify_axis_from_metadata(self, ome_zarr_image_v04_path):
             metadata=meta_no_channel, idx=0, axis_name="c", units=None
         )
         assert meta_add_channel.axes_names == fractal_meta.axes_names
+
+    def test_pixel_size(self, ome_zarr_image_v04_path):
+        from ngio.ngff_meta import get_ngff_image_meta_handler
+
+        handler = get_ngff_image_meta_handler(
+            store=ome_zarr_image_v04_path, meta_mode="image"
+        )
+
+        pixel_size = handler.load_meta().pixel_size(level_path=0)
+        assert pixel_size.to_ordered_list() == [1.0, 0.1625, 0.1625]
+        pixel_size_nm = pixel_size.to_units("nm")
+        assert pixel_size_nm.to_ordered_list() == [1000.0, 162.5, 162.5]
+
+    def test_modify_axis_from_label_metadata(self, ome_zarr_label_v04_path):
+        from ngio.ngff_meta import get_ngff_image_meta_handler
+        from ngio.ngff_meta.utils import add_axis_to_metadata, remove_axis_from_metadata
+
+        handler = get_ngff_image_meta_handler(
+            store=ome_zarr_label_v04_path, meta_mode="label"
+        )
+
+        fractal_meta = handler.load_meta()
+
+        meta_no_channel = fractal_meta.remove_axis(axis_name="z")
+        assert meta_no_channel.axes_names == ["y", "x"]
+
+        meta_add_channel = meta_no_channel.add_axis(
+            idx=0, axis_name="z", units="micrometer", axis_type="space"
+        )
+        assert meta_add_channel.axes_names == fractal_meta.axes_names