fix edge case in pyramid build

src/ngio/core/image_like_handler.py

@@ -423,7 +423,6 @@ def consolidate(self, order: int = 1) -> None:
                     )
                 ]
             )
-
             partial_zoom = partial(zoom, zoom=zoom_factors, order=order)
             out_image = da.map_blocks(
                 partial_zoom,
@@ -432,7 +431,7 @@ def consolidate(self, order: int = 1) -> None:
                 chunks=target_image.array.chunks,
             )
             out_image = out_image.astype(target_image.array.dtype)
+            # da.to_zarr(out_image, target_image.array, overwrite=True)
             target_image.array[...] = out_image.compute()
             # compute the transformation
-
             processed_paths.append(target_image)

src/ngio/core/label_handler.py

@@ -1,9 +1,13 @@
 """A module to handle OME-NGFF images stored in Zarr format."""
 
+from typing import Literal
+
 import zarr
 
+from ngio._common_types import ArrayLike
 from ngio.core.image_handler import Image
 from ngio.core.image_like_handler import ImageLike
+from ngio.core.roi import WorldCooROI
 from ngio.core.utils import create_empty_ome_zarr_label
 from ngio.io import StoreLike, StoreOrGroup
 from ngio.ngff_meta.fractal_image_meta import LabelMeta, PixelSize
@@ -57,6 +61,110 @@ def metadata(self) -> LabelMeta:
         """Return the metadata of the image."""
         return super().metadata
 
+    def get_data_from_roi(
+        self,
+        roi: WorldCooROI,
+        t: int | slice | None = None,
+        mode: Literal["numpy"] | Literal["dask"] = "numpy",
+        preserve_dimensions: bool = False,
+    ) -> ArrayLike:
+        """Return the label data from a region of interest (ROI).
+
+        Args:
+            roi (WorldCooROI): The region of interest.
+            t (int | slice | None): The time index or slice.
+            mode (str): The mode to return the data.
+            preserve_dimensions (bool): Whether to preserve the dimensions of the data.
+        """
+        return super().get_data_from_roi(
+            roi=roi, t=t, c=None, mode=mode, preserve_dimensions=preserve_dimensions
+        )
+
+    def set_data_from_roi(
+        self,
+        patch: ArrayLike,
+        roi: WorldCooROI,
+        t: int | slice | None = None,
+        preserve_dimensions: bool = False,
+    ) -> None:
+        """Set the label data from a region of interest (ROI).
+
+        Args:
+            roi (WorldCooROI): The region of interest.
+            patch (ArrayLike): The patch to set.
+            t (int | slice | None): The time index or slice.
+            preserve_dimensions (bool): Whether to preserve the dimensions of the data.
+        """
+        return super().set_data_from_roi(
+            patch=patch, roi=roi, t=t, c=None, preserve_dimensions=preserve_dimensions
+        )
+
+    def get_data(
+        self,
+        x: int | slice | None = None,
+        y: int | slice | None = None,
+        z: int | slice | None = None,
+        t: int | slice | None = None,
+        mode: Literal["numpy"] | Literal["dask"] = "numpy",
+        preserve_dimensions: bool = False,
+    ) -> ArrayLike:
+        """Return the label data.
+
+        Args:
+            x (int | slice | None): The x index or slice.
+            y (int | slice | None): The y index or slice.
+            z (int | slice | None): The z index or slice.
+            t (int | slice | None): The time index or slice.
+            mode (str): The mode to return the data.
+            preserve_dimensions (bool): Whether to preserve the dimensions of the data.
+        """
+        return super().get_data(
+            x=x,
+            y=y,
+            z=z,
+            t=t,
+            c=None,
+            mode=mode,
+            preserve_dimensions=preserve_dimensions,
+        )
+
+    def set_data(
+        self,
+        patch: ArrayLike,
+        x: int | slice | None = None,
+        y: int | slice | None = None,
+        z: int | slice | None = None,
+        t: int | slice | None = None,
+        preserve_dimensions: bool = False,
+    ) -> None:
+        """Set the label data in the zarr array.
+
+        Args:
+            patch (ArrayLike): The patch to set.
+            x (int | slice | None): The x index or slice.
+            y (int | slice | None): The y index or slice.
+            z (int | slice | None): The z index or slice.
+            t (int | slice | None): The time index or slice.
+            preserve_dimensions (bool): Whether to preserve the dimensions of the data.
+        """
+        return super().set_data(
+            patch=patch,
+            x=x,
+            y=y,
+            z=z,
+            t=t,
+            c=None,
+            preserve_dimensions=preserve_dimensions,
+        )
+
+    def consolidate(self) -> None:
+        """Consolidate the label group.
+
+        This method consolidates the label group by
+        filling all other pyramid levels with the data
+        """
+        return super().consolidate(order=0)
+
 
 class LabelGroup:
     """A class to handle the /labels group in an OME-NGFF file."""

src/ngio/core/utils.py

@@ -1,13 +1,14 @@
 """Utility functions for creating and manipulating images."""
 
 from typing import Any
+import math
 
 from ngio.core.image_handler import Image
 from ngio.io import StoreLike
 from ngio.ngff_meta import (
     create_image_metadata,
-    get_ngff_image_meta_handler,
     create_label_metadata,
+    get_ngff_image_meta_handler,
 )
 from ngio.ngff_meta.fractal_image_meta import (
     PixelSize,
@@ -184,7 +185,19 @@ def create_empty_ome_zarr_label(
         )
 
         # Todo redo this with when a proper build of pyramid id implemente
-        shape = [int(s / sc) for s, sc in zip(shape, scaling_factor, strict=True)]
+        _shape = []
+        for s, sc in zip(shape, scaling_factor, strict=True):
+            if math.floor(s / sc) % 2 == 0:
+                _shape.append(math.floor(s / sc))
+            else:
+                _shape.append(math.ceil(s / sc))
+        shape = list(_shape)
 
         if chunks is not None:
-            chunks = [int(c / sc) for c, sc in zip(chunks, scaling_factor, strict=True)]
+            _chunks = []
+            for c, sc in zip(chunks, scaling_factor, strict=True):
+                if math.floor(c / sc) % 2 == 0:
+                    _chunks.append(math.floor(c / sc))
+                else:
+                    _chunks.append(math.ceil(c / sc))
+            chunks = list(_chunks)

src/ngio/tables/tables_group.py

@@ -164,6 +164,6 @@ def new(
             **type_specific_kwargs,
         )
 
-        if name not in list_of_tables:
-            self._group.attrs["tables"] = [*list_of_tables, name]
+        self._group.attrs["tables"] = [*list_of_tables, name]
+
         return new_table