fix some tests

src/ngio/ngff_meta/fractal_image_meta.py

@@ -652,10 +652,10 @@ def get_dataset(
         else:
             raise ValueError("get_dataset has no valid arguments.")
 
-    def get_highest_resolution(self) -> Dataset:
+    def get_highest_resolution_dataset(self) -> Dataset:
         """Get the dataset with the highest resolution."""
         return self._get_dataset_by_pixel_size(
-            PixelSize(0.0, 0.0, 0.0, SpaceUnits.um), strict=False
+            pixel_size=PixelSize(x=0.0, y=0.0, z=0.0, unit=SpaceUnits.um), strict=False
         )
 
     def scale(self, path: str | None = None, idx: int | None = None) -> list[float]:
@@ -750,7 +750,11 @@ class ImageMeta(BaseMeta):
     """Image metadata model."""
 
     def __init__(
-        self, version: str, name: str, datasets: list[Dataset], omero: Omero | None
+        self,
+        version: str,
+        name: str,
+        datasets: list[Dataset],
+        omero: Omero | None = None,
     ) -> None:
         """Initialize the ImageMeta object."""
         super().__init__(version=version, name=name, datasets=datasets)

src/ngio/ngff_meta/utils.py

@@ -193,27 +193,25 @@ def remove_axis_from_metadata(
     metadata: ImageMeta,
     *,
     axis_name: str | None = None,
-    idx: int | None = None,
 ) -> ImageMeta:
     """Remove an axis from the metadata.
 
     Args:
-        metadata: A FractalImageMeta object.
+        metadata: A ImageMeta object.
         axis_name: The name of the axis to remove.
-        idx: The index of the axis to remove.
     """
-    return metadata.remove_axis(axis_name=axis_name, idx=idx)
+    return metadata.remove_axis(axis_name=axis_name)
 
 
 def add_axis_to_metadata(
     metadata: ImageMeta | LabelMeta,
     axis_name: str,
     scale: float = 1.0,
 ) -> ImageMeta | LabelMeta:
-    """Add an axis to the FractalImageMeta or FractalLabelMeta object.
+    """Add an axis to the ImageMeta or LabelMeta object.
 
     Args:
-        metadata: A FractalImageMeta or FractalLabelMeta object.
+        metadata: A ImageMeta or LabelMeta object.
         axis_name: The name of the axis to add.
         scale: The scale of the axis
     """

tests/ngff_meta/test_fractal_image_meta.py

@@ -11,19 +11,17 @@ def test_basic_workflow(self, ome_zarr_image_v04_path):
 
         fractal_meta = handler.load_meta()
         np.testing.assert_array_equal(
-            fractal_meta.pixel_size(level_path=0).zyx,
+            fractal_meta.pixel_size(idx=0).zyx,
             [1.0, 0.1625, 0.1625],
         )
         np.testing.assert_array_equal(
-            fractal_meta.scale(level_path=0), [1.0, 1.0, 0.1625, 0.1625]
+            fractal_meta.scale(idx=0), [1.0, 1.0, 0.1625, 0.1625]
         )
         assert fractal_meta.num_levels == 5
         assert fractal_meta.levels_paths == ["0", "1", "2", "3", "4"]
-        assert fractal_meta.axes == fractal_meta.multiscale.axes
-        assert fractal_meta.datasets == fractal_meta.multiscale.datasets
-        assert fractal_meta.channel_names == ["DAPI", "nanog", "Lamin B1"]
-        assert fractal_meta.get_channel_idx_by_label("DAPI") == 0
-        assert fractal_meta.get_channel_idx_by_wavelength_id("A01_C01") == 0
+        assert fractal_meta.channel_labels == ["DAPI", "nanog", "Lamin B1"]
+        assert fractal_meta.get_channel_idx(label="DAPI") == 0
+        assert fractal_meta.get_channel_idx(wavelength_id="A01_C01") == 0
         assert fractal_meta.axes_names == ["c", "z", "y", "x"]
         assert fractal_meta.space_axes_names == ["z", "y", "x"]
         assert fractal_meta.get_highest_resolution_dataset().path == "0"
@@ -43,7 +41,7 @@ def test_modify_axis_from_metadata(self, ome_zarr_image_v04_path):
         assert meta_no_channel.axes_names == ["z", "y", "x"]
 
         meta_add_channel = add_axis_to_metadata(
-            metadata=meta_no_channel, idx=0, axis_name="c", units=None
+            metadata=meta_no_channel, axis_name="c", scale=1.0
         )
         assert meta_add_channel.axes_names == fractal_meta.axes_names
 
@@ -54,7 +52,7 @@ def test_pixel_size(self, ome_zarr_image_v04_path):
             store=ome_zarr_image_v04_path, meta_mode="image"
         )
 
-        pixel_size = handler.load_meta().pixel_size(level_path=0)
+        pixel_size = handler.load_meta().pixel_size(idx=0)
         assert pixel_size.zyx == (1.0, 0.1625, 0.1625)
 
     def test_modify_axis_from_label_metadata(self, ome_zarr_label_v04_path):
@@ -69,7 +67,5 @@ def test_modify_axis_from_label_metadata(self, ome_zarr_label_v04_path):
         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"
-        )
+        meta_add_channel = meta_no_channel.add_axis(axis_name="z", scale=1.0)
         assert meta_add_channel.axes_names == fractal_meta.axes_names