refactoring tests

src/ngio/core/image_handler.py

@@ -1,25 +1,66 @@
 """A module to handle OME-NGFF images stored in Zarr format."""
 
-from ngio.core.image_like_handler import ImageLikeHandler
+from ngio.core.image_like_handler import ImageLike
+from ngio.io import StoreOrGroup
+from ngio.ngff_meta.fractal_image_meta import ImageMeta, PixelSize
 
 
-class ImageHandler(ImageLikeHandler):
+class Image(ImageLike):
     """A class to handle OME-NGFF images stored in Zarr format.
 
     This class provides methods to access image data and ROI tables.
     """
 
-    @property
-    def channel_names(self) -> list[str]:
-        """Return the names of the channels in the image."""
-        return self.metadata.channel_names
+    def __init__(
+        self,
+        store: StoreOrGroup,
+        *,
+        path: str | None = None,
+        idx: int | None = None,
+        pixel_size: PixelSize | None = None,
+        highest_resolution: bool = False,
+        strict: bool = True,
+        cache: bool = True,
+    ) -> None:
+        """Initialize the MultiscaleHandler in read mode.
 
-    def get_channel_idx_by_label(self, label: str) -> int:
-        """Return the index of the channel with the given label."""
-        return self.metadata.get_channel_idx_by_label(label=label)
+        Note: Only one of `path`, `idx`, 'pixel_size' or 'highest_resolution'
+        should be provided.
 
-    def get_channel_idx_by_wavelength_id(self, wavelength_id: int) -> int:
-        """Return the index of the channel with the given wavelength id."""
-        return self.metadata.get_channel_idx_by_wavelength_id(
-            wavelength_id=wavelength_id
+        store (StoreOrGroup): The Zarr store or group containing the image data.
+        path (str | None): The path to the level.
+        idx (int | None): The index of the level.
+        pixel_size (PixelSize | None): The pixel size of the level.
+        highest_resolution (bool): Whether to get the highest resolution level.
+        strict (bool): Whether to raise an error where a pixel size is not found
+            to match the requested "pixel_size".
+        cache (bool): Whether to cache the metadata.
+        """
+        super().__init__(
+            store=store,
+            path=path,
+            idx=idx,
+            pixel_size=pixel_size,
+            highest_resolution=highest_resolution,
+            strict=strict,
+            meta_mode="image",
+            cache=cache,
         )
+
+    @property
+    def metadata(self) -> ImageMeta:
+        """Return the metadata of the image."""
+        return super().metadata
+
+    @property
+    def channel_labels(self) -> list[str]:
+        """Return the names of the channels in the image."""
+        return self.metadata.channel_labels
+
+    def get_channel_idx(
+        self,
+        label: str | None = None,
+        wavelength_id: str | None = None,
+    ) -> int:
+        """Return the index of the channel."""
+        return self.metadata.get_channel_idx(label=label, wavelength_id=wavelength_id)

src/ngio/core/image_like_handler.py

@@ -1,17 +1,20 @@
 """Generic class to handle Image-like data in a OME-NGFF file."""
 
+from typing import Literal
+
 import zarr
 
 from ngio.io import StoreOrGroup, open_group
 from ngio.ngff_meta import (
-    ImageMeta,
+    Dataset,
+    ImageLabelMeta,
     PixelSize,
     SpaceUnits,
     get_ngff_image_meta_handler,
 )
 
 
-class ImageLikeHandler:
+class ImageLike:
     """A class to handle OME-NGFF images stored in Zarr format.
 
     This class provides methods to access image data and ROI tables.
@@ -20,77 +23,88 @@ class ImageLikeHandler:
     def __init__(
         self,
         store: StoreOrGroup,
-        *,
-        level_path: str | int | None = None,
-        pixel_size: tuple[float, ...] | list[float] | None = None,
+        path: str | None = None,
+        idx: int | None = None,
+        pixel_size: PixelSize | None = None,
         highest_resolution: bool = False,
+        strict: bool = True,
+        meta_mode: Literal["image", "label"] = "image",
+        cache: bool = True,
     ) -> None:
-        """Initialize the MultiscaleHandler in read mode."""
+        """Initialize the MultiscaleHandler in read mode.
+
+        Note: Only one of `path`, `idx`, 'pixel_size' or 'highest_resolution'
+        should be provided.
+
+        store (StoreOrGroup): The Zarr store or group containing the image data.
+        path (str | None): The path to the level.
+        idx (int | None): The index of the level.
+        pixel_size (PixelSize | None): The pixel size of the level.
+        highest_resolution (bool): Whether to get the highest resolution level.
+        strict (bool): Whether to raise an error where a pixel size is not found
+            to match the requested "pixel_size".
+        meta_mode (str): The mode of the metadata handler.
+        cache (bool): Whether to cache the metadata.
+        """
         if not isinstance(store, zarr.Group):
             store = open_group(store=store, mode="r")
 
         self._metadata_handler = get_ngff_image_meta_handler(
-            store=store, meta_mode="image", cache=True
+            store=store, meta_mode=meta_mode, cache=cache
         )
 
         # Find the level / resolution index
-        self.level_path = self._find_level(level_path, pixel_size, highest_resolution)
+        metadata = self._metadata_handler.load_meta()
+        self._dataset = metadata.get_dataset(
+            path=path,
+            idx=idx,
+            pixel_size=pixel_size,
+            highest_resolution=highest_resolution,
+            strict=strict,
+        )
         self._group = store
 
-    def _find_level(
-        self,
-        level_path: int | str | None,
-        pixel_size: tuple[float, ...] | list[float] | None,
-        highest_resolution: bool,
-    ) -> str:
-        """Find the index of the level."""
-        args_valid = [
-            level_path is not None,
-            pixel_size is not None,
-            highest_resolution,
-        ]
-
-        if sum(args_valid) != 1:
-            raise ValueError(
-                "One and only one of level_path, pixel_size, "
-                "or highest_resolution=True can be used. "
-                f"Received: {level_path=}, {pixel_size=}, {highest_resolution=}"
-            )
-        meta = self._metadata_handler.load_meta()
-        if level_path is not None:
-            return meta.get_dataset(level_path).path
-
-        if pixel_size is not None:
-            return meta.get_dataset_from_pixel_size(pixel_size, strict=True).path
-
-        return meta.get_highest_resolution_dataset().path
-
     @property
     def group(self) -> zarr.Group:
         """Return the Zarr group containing the image data."""
         return self._group
 
     @property
-    def metadata(self) -> ImageMeta:
+    def metadata(self) -> ImageLabelMeta:
         """Return the metadata of the image."""
         return self._metadata_handler.load_meta()
 
+    @property
+    def dataset(self) -> Dataset:
+        """Return the dataset of the image."""
+        return self._dataset
+
+    @property
+    def path(self) -> str:
+        """Return the path of the dataset (relative to the root group)."""
+        return self.dataset.path
+
+    @property
+    def channel_labels(self) -> list[str]:
+        """Return the names of the channels in the image."""
+        return self.dataset.path
+
     @property
     def axes_names(self) -> list[str]:
         """Return the names of the axes in the image."""
-        return self.metadata.axes_names
+        return self.dataset.axes_names
 
     @property
     def space_axes_names(self) -> list[str]:
         """Return the names of the space axes in the image."""
-        return self.metadata.space_axes_names
+        return self.dataset.space_axes_names
 
     @property
     def space_axes_unit(self) -> SpaceUnits:
         """Return the units of the space axes in the image."""
-        return self.metadata.space_axes_unit
+        return self.dataset.space_axes_unit
 
     @property
     def pixel_size(self) -> PixelSize:
         """Return the pixel resolution of the image."""
-        return self.metadata.pixel_size(level_path=self.level_path)
+        return self.dataset.pixel_size

src/ngio/core/label_handler.py

@@ -1,35 +1,78 @@
 """A module to handle OME-NGFF images stored in Zarr format."""
 
-import zarr
 from zarr.store.common import StoreLike
 
-from ngio.core.image_like_handler import ImageLikeHandler
+from ngio.core.image_like_handler import ImageLike
+from ngio.io import StoreOrGroup
+from ngio.ngff_meta.fractal_image_meta import LabelMeta, PixelSize
 
 
-class LabelHandler(ImageLikeHandler):
+class Label(ImageLike):
     """A class to handle OME-NGFF images stored in Zarr format.
 
     This class provides methods to access image data and ROI tables.
     """
 
-    pass
+    def __init__(
+        store: StoreOrGroup,
+        *,
+        path: str | None = None,
+        idx: int | None = None,
+        pixel_size: PixelSize | None = None,
+        highest_resolution: bool = False,
+        strict: bool = True,
+        cache: bool = True,
+    ) -> None:
+        """Initialize the MultiscaleHandler in read mode.
 
+        Note: Only one of `path`, `idx`, 'pixel_size' or 'highest_resolution'
+        should be provided.
 
-class LabelGroupHandler:
+        store (StoreOrGroup): The Zarr store or group containing the image data.
+        path (str | None): The path to the level.
+        idx (int | None): The index of the level.
+        pixel_size (PixelSize | None): The pixel size of the level.
+        highest_resolution (bool): Whether to get the highest resolution level.
+        strict (bool): Whether to raise an error where a pixel size is not found
+            to match the requested "pixel_size".
+        cache (bool): Whether to cache the metadata.
+        """
+        super().__init__(
+            store,
+            path=path,
+            idx=idx,
+            pixel_size=pixel_size,
+            highest_resolution=highest_resolution,
+            strict=strict,
+            meta_mode="label",
+            cache=cache,
+        )
+
+    def metadata(self) -> LabelMeta:
+        """Return the metadata of the image."""
+        return super().metadata
+
+
+class LabelGroup:
     """A class to handle the /labels group in an OME-NGFF file."""
 
-    def __init__(self, group: zarr.Group, group_name: str = "labels") -> None:
+    def __init__(self, group: StoreLike) -> None:
         """Initialize the LabelGroupHandler."""
         self._group = group
 
+    @property
+    def group_name(self) -> str:
+        """Return the name of the group."""
+        return "labels"
+
     def list(self) -> list[str]:
         """List all labels in the group."""
         return list(self._group.array_keys())
 
-    def get(self, name: str) -> LabelHandler:
+    def get(self, name: str) -> Label:
         """Get a label from the group."""
         raise NotImplementedError("Not yet implemented.")
 
-    def write(self, name: str, data: LabelHandler) -> None:
+    def write(self, name: str, data: Label) -> None:
         """Create a label in the group."""
         raise NotImplementedError("Not yet implemented.")

src/ngio/core/ngff_image.py

@@ -4,7 +4,7 @@
 
 from zarr.store.common import StoreLike
 
-from ngio.core.image_handler import ImageHandler
+from ngio.core.image_handler import Image
 from ngio.io import open_group
 from ngio.ngff_meta import FractalImageLabelMeta, get_ngff_image_meta_handler
 
@@ -93,7 +93,7 @@ def get_image(
         level_path: str | int | None = None,
         pixel_size: tuple[float, ...] | list[float] | None = None,
         highest_resolution: bool = True,
-    ) -> ImageHandler:
+    ) -> Image:
         """Get an image handler for the given level.
 
         Args:
@@ -106,7 +106,7 @@ def get_image(
         Returns:
             ImageHandler: The image handler.
         """
-        return ImageHandler(
+        return Image(
             store=self.group,
             level_path=level_path,
             pixel_size=pixel_size,

src/ngio/ngff_meta/__init__.py

@@ -1,6 +1,21 @@
 """IO and validation of NGFF metadata."""
 
-from ngio.ngff_meta.fractal_image_meta import ImageMeta, PixelSize, SpaceUnits
+from ngio.ngff_meta.fractal_image_meta import (
+    Dataset,
+    ImageLabelMeta,
+    ImageMeta,
+    LabelMeta,
+    PixelSize,
+    SpaceUnits,
+)
 from ngio.ngff_meta.meta_handler import get_ngff_image_meta_handler
 
-__all__ = ["get_ngff_image_meta_handler", "ImageMeta", "PixelSize", "SpaceUnits"]
+__all__ = [
+    "Dataset",
+    "ImageMeta",
+    "LabelMeta",
+    "ImageLabelMeta",
+    "PixelSize",
+    "SpaceUnits",
+    "get_ngff_image_meta_handler",
+]