ngio 0.5.0b7__py3-none-any.whl → 0.5.1__py3-none-any.whl

ngio/common/_masking_roi.py

@@ -99,7 +99,14 @@ def compute_slices(segmentation: np.ndarray) -> dict[int, tuple[slice, ...]]:
 
 
 def lazy_compute_slices(segmentation: da.Array) -> dict[int, tuple[slice, ...]]:
-    """Compute slices for each label in a segmentation."""
+    """Compute slices for each label in a segmentation using lazy evaluation.
+
+    Args:
+        segmentation: The dask segmentation array.
+
+    Returns:
+        A dictionary mapping label IDs to their bounding box slices.
+    """
     global_offsets = _compute_offsets(segmentation.chunks)
     delayed_chunks = segmentation.to_delayed()  # type: ignore
 
@@ -120,12 +127,18 @@ def compute_masking_roi(
     pixel_size: PixelSize,
     axes_order: Sequence[str],
 ) -> list[Roi]:
-    """Compute a ROIs for each label in a segmentation.
+    """Compute ROIs for each label in a segmentation.
+
+    This function expects a 2D, 3D, or 4D segmentation array.
+    The axes order should match the segmentation dimensions.
 
-    This function expects a 2D or 3D segmentation array.
-    And this function expects the axes order to be 'zyx' or 'yx'.
-    Other axes orders are not supported.
+    Args:
+        segmentation: The segmentation array (2D, 3D, or 4D).
+        pixel_size: The pixel size metadata for coordinate conversion.
+        axes_order: The order of axes in the segmentation (e.g., 'zyx' or 'yx').
 
+    Returns:
+        A list of Roi objects, one for each unique label in the segmentation.
     """
     if segmentation.ndim not in [2, 3, 4]:
         raise NgioValueError("Only 2D, 3D, and 4D segmentations are supported.")

ngio/hcs/_plate.py

@@ -1,7 +1,7 @@
 """A module for handling the Plate Sequence in an OME-Zarr file."""
 
 import asyncio
-import warnings
+import logging
 from collections.abc import Sequence
 from typing import Literal
 
@@ -48,6 +48,8 @@ from ngio.utils import (
     ZarrGroupHandler,
 )
 
+logger = logging.getLogger(f"ngio:{__name__}")
+
 
 def _try_get_table_container(
     handler: ZarrGroupHandler, create_mode: bool = True
@@ -918,12 +920,10 @@ class OmeZarrPlate:
 
         """
         if check_type is not None:
-            warnings.warn(
-                "The 'check_type' argument is deprecated, and will be removed in "
-                "ngio=0.3. Use 'get_table_as' instead or one of the "
-                "type specific get_*table() methods.",
-                DeprecationWarning,
-                stacklevel=2,
+            logger.warning(
+                "The 'check_type' argument is deprecated and will be removed in "
+                "ngio=0.6. Please use 'get_table_as' instead or one of the "
+                "type specific get_*table() methods."
             )
         return self.tables_container.get(name=name, strict=False)
 
@@ -1182,9 +1182,21 @@ def _create_empty_plate_from_meta(
     meta: NgioPlateMeta,
     overwrite: bool = False,
 ) -> ZarrGroupHandler:
-    """Create an empty OME-Zarr plate from metadata."""
+    """Create an empty OME-Zarr plate from metadata.
+
+    Args:
+        store: The Zarr store or group to create the plate in.
+        meta: The plate metadata to use.
+        overwrite: Whether to overwrite an existing plate.
+
+    Returns:
+        The ZarrGroupHandler for the created plate.
+    """
     mode = "w" if overwrite else "w-"
-    group_handler = ZarrGroupHandler(store=store, cache=True, mode=mode)
+    zarr_format = 2 if meta.plate.version == "0.4" else 3
+    group_handler = ZarrGroupHandler(
+        store=store, cache=True, mode=mode, zarr_format=zarr_format
+    )
     update_ngio_plate_meta(group_handler, meta)
     return group_handler
 
@@ -1211,11 +1223,9 @@ def create_empty_plate(
         overwrite (bool): Whether to overwrite the existing plate.
     """
     if version is not None:
-        warnings.warn(
-            "The 'version' argument is deprecated, and will be removed in ngio=0.3. "
-            "Please use 'ngff_version' instead.",
-            DeprecationWarning,
-            stacklevel=2,
+        logger.warning(
+            "The 'version' argument is deprecated and will be removed in ngio=0.6. "
+            "Please use 'ngff_version' instead."
         )
         ngff_version = version
     plate_meta = NgioPlateMeta.default_init(
@@ -1268,11 +1278,9 @@ def derive_ome_zarr_plate(
         overwrite (bool): Whether to overwrite the existing plate.
     """
     if version is not None:
-        warnings.warn(
-            "The 'version' argument is deprecated, and will be removed in ngio=0.3. "
-            "Please use 'ngff_version' instead.",
-            DeprecationWarning,
-            stacklevel=2,
+        logger.warning(
+            "The 'version' argument is deprecated and will be removed in ngio=0.6. "
+            "Please use 'ngff_version' instead."
         )
         ngff_version = version
 
@@ -1333,11 +1341,9 @@ def create_empty_well(
         overwrite (bool): Whether to overwrite the existing well.
     """
     if version is not None:
-        warnings.warn(
-            "The 'version' argument is deprecated, and will be removed in ngio=0.3. "
-            "Please use 'ngff_version' instead.",
-            DeprecationWarning,
-            stacklevel=2,
+        logger.warning(
+            "The 'version' argument is deprecated and will be removed in ngio=0.6. "
+            "Please use 'ngff_version' instead."
         )
         ngff_version = version
     group_handler = ZarrGroupHandler(

ngio/images/_abstract_image.py

@@ -1,6 +1,6 @@
 """Generic class to handle Image-like data in a OME-NGFF file."""
 
-import warnings
+import logging
 from abc import ABC, abstractmethod
 from collections.abc import Mapping, Sequence
 from typing import Any, Literal
@@ -52,6 +52,13 @@ from ngio.ome_zarr_meta.ngio_specs import (
     NgffVersions,
     NgioLabelMeta,
 )
+from ngio.ome_zarr_meta.ngio_specs._axes import (
+    AxesSetup,
+    DefaultSpaceUnit,
+    DefaultTimeUnit,
+    SpaceUnits,
+    TimeUnits,
+)
 from ngio.tables import RoiTable
 from ngio.utils import (
     NgioFileExistsError,
@@ -61,6 +68,8 @@ from ngio.utils import (
 )
 from ngio.utils._zarr_utils import find_dimension_separator
 
+logger = logging.getLogger(f"ngio:{__name__}")
+
 
 class AbstractImage(ABC):
     """A class to handle a single image (or level) in an OME-Zarr image.
@@ -136,6 +145,11 @@ class AbstractImage(ABC):
         """Return the axes handler of the image."""
         return self.dataset.axes_handler
 
+    @property
+    def axes_setup(self) -> AxesSetup:
+        """Return the axes setup of the image."""
+        return self.axes_handler.axes_setup
+
     @property
     def axes(self) -> tuple[str, ...]:
         """Return the axes of the image."""
@@ -205,6 +219,47 @@ class AbstractImage(ABC):
         """Return True if the image has the given axis."""
         return self.axes_handler.has_axis(axis)
 
+    def set_axes_unit(
+        self,
+        space_unit: SpaceUnits = DefaultSpaceUnit,
+        time_unit: TimeUnits = DefaultTimeUnit,
+    ) -> None:
+        """Set the axes unit of the image.
+
+        Args:
+            space_unit (SpaceUnits): The space unit of the image.
+            time_unit (TimeUnits): The time unit of the image.
+        """
+        meta = self._meta_handler.get_meta()
+        meta = meta.to_units(space_unit=space_unit, time_unit=time_unit)
+        self._meta_handler.update_meta(meta)  # type: ignore
+
+    def set_axes_names(self, axes_names: Sequence[str]) -> None:
+        """Set the axes names of the label.
+
+        Args:
+            axes_names (Sequence[str]): The axes names to set.
+        """
+        meta = self._meta_handler.get_meta()
+        meta = meta.rename_axes(axes_names=axes_names)
+        self._meta_handler._axes_setup = meta.axes_handler.axes_setup
+        self._meta_handler.update_meta(meta)  # type: ignore
+
+    def set_name(
+        self,
+        name: str,
+    ) -> None:
+        """Set the name of the image in the metadata.
+
+        This does not change the group name or any paths.
+
+        Args:
+            name (str): The name of the image.
+        """
+        meta = self._meta_handler.get_meta()
+        meta = meta.rename_image(name=name)
+        self._meta_handler.update_meta(meta)  # type: ignore
+
     def _get_as_numpy(
         self,
         axes_order: Sequence[str] | None = None,
@@ -887,7 +942,7 @@ def abstract_derive(
     # Deprecated arguments
     labels: Sequence[str] | None = None,
     pixel_size: PixelSize | None = None,
-) -> ZarrGroupHandler:
+) -> tuple[ZarrGroupHandler, AxesSetup]:
     """Create an empty OME-Zarr image from an existing image.
 
     If a kwarg is not provided, the value from the reference image will be used.
@@ -934,19 +989,16 @@ def abstract_derive(
     """
     # TODO: remove in ngio 0.6
     if labels is not None:
-        warnings.warn(
+        logger.warning(
             "The 'labels' argument is deprecated and will be removed in "
-            "a future release.",
-            DeprecationWarning,
-            stacklevel=2,
+            "ngio=0.6. Please use 'channels_meta' instead."
         )
         channels_meta = list(labels)
     if pixel_size is not None:
-        warnings.warn(
+        logger.warning(
             "The 'pixel_size' argument is deprecated and will be removed in "
-            "a future release.",
-            DeprecationWarning,
-            stacklevel=2,
+            "ngio=0.6. Please use 'pixelsize', 'z_spacing', and 'time_spacing'"
+            "instead."
         )
         pixelsize = (pixel_size.y, pixel_size.x)
     # End of deprecated arguments handling
@@ -1012,7 +1064,7 @@ def abstract_derive(
         channels_meta=channels_meta,
     )
 
-    handler = init_image_like_from_shapes(
+    handler, axes_setup = init_image_like_from_shapes(
         store=store,
         meta_type=meta_type,
         shapes=shapes,
@@ -1023,6 +1075,7 @@ def abstract_derive(
         space_unit=ref_image.space_unit,
         axes_names=axes,
         name=name,
+        axes_setup=ref_image.axes_setup,
         channels_meta=channels_meta_,
         chunks=chunks,
         shards=shards,
@@ -1033,4 +1086,4 @@ def abstract_derive(
         ngff_version=ngff_version,
         extra_array_kwargs=extra_array_kwargs,
     )
-    return handler
+    return handler, axes_setup

ngio/images/_create_synt_container.py

@@ -85,7 +85,7 @@ def create_synthetic_ome_zarr(
     ome_zarr = create_ome_zarr_from_array(
         store=store,
         array=raw,
-        pixelsize=sample_info.xy_pixelsize,
+        pixelsize=sample_info.pixelsize,
         z_spacing=sample_info.z_spacing,
         time_spacing=sample_info.time_spacing,
         levels=levels,

ngio/images/_create_utils.py

@@ -1,6 +1,6 @@
 """Utility functions for working with OME-Zarr images."""
 
-import warnings
+import logging
 from collections.abc import Mapping, Sequence
 from typing import Any, Literal, TypeVar
 
@@ -22,6 +22,7 @@ from ngio.ome_zarr_meta.ngio_specs import (
     NgffVersions,
     SpaceUnits,
     TimeUnits,
+    build_axes_handler,
     build_canonical_axes_handler,
     canonical_axes_order,
     canonical_label_axes_order,
@@ -29,37 +30,9 @@ from ngio.ome_zarr_meta.ngio_specs import (
 from ngio.ome_zarr_meta.ngio_specs._axes import AxesSetup
 from ngio.utils import NgioValueError, StoreOrGroup, ZarrGroupHandler
 
-_image_or_label_meta = TypeVar("_image_or_label_meta", NgioImageMeta, NgioLabelMeta)
-
+logger = logging.getLogger(f"ngio:{__name__}")
 
-def _build_axes_handler(
-    *,
-    shape: tuple[int, ...],
-    axes_names: Sequence[str] | None,
-    default_channel_order: tuple[str, ...],
-    space_units: SpaceUnits | str | None = DefaultSpaceUnit,
-    time_units: TimeUnits | str | None = DefaultTimeUnit,
-    axes_setup: AxesSetup | None = None,
-    allow_non_canonical_axes: bool = False,
-    strict_canonical_order: bool = False,
-) -> AxesHandler:
-    """Compute axes names for given shape."""
-    if axes_names is None:
-        axes_names = default_channel_order[-len(shape) :]
-    # Validate length
-    if len(axes_names) != len(shape):
-        raise NgioValueError(
-            f"Number of axes names {axes_names} does not match the number of "
-            f"dimensions {shape}."
-        )
-    return build_canonical_axes_handler(
-        axes_names=axes_names,
-        space_units=space_units,
-        time_units=time_units,
-        axes_setup=axes_setup,
-        allow_non_canonical_axes=allow_non_canonical_axes,
-        strict_canonical_order=strict_canonical_order,
-    )
+_image_or_label_meta = TypeVar("_image_or_label_meta", NgioImageMeta, NgioLabelMeta)
 
 
 def _align_to_axes(
@@ -85,9 +58,9 @@ def _check_deprecated_scaling_factors(
     shape: tuple[int, ...],
 ) -> Sequence[float] | Literal["auto"]:
     if yx_scaling_factor is not None or z_scaling_factor is not None:
-        warnings.warn(
+        logger.warning(
             "The 'yx_scaling_factor' and 'z_scaling_factor' arguments are deprecated "
-            "and will be removed in future versions. Please use the 'scaling_factors' "
+            "and will be removed in ngio=0.6. Please use the 'scaling_factors' "
             "argument instead.",
             DeprecationWarning,
             stacklevel=2,
@@ -231,6 +204,38 @@ def _add_channels_meta(
     return meta
 
 
+def _build_axes_handler(
+    *,
+    shape: tuple[int, ...],
+    meta_type: type[_image_or_label_meta],
+    axes_names: Sequence[str] | None = None,
+    axes_setup: AxesSetup | None = None,
+    space_unit: SpaceUnits | str | None = None,
+    time_unit: TimeUnits | str | None = None,
+) -> AxesHandler:
+    """Build axes handler for given shape and axes names."""
+    if meta_type is NgioImageMeta:
+        canonical_axes_order_ = canonical_axes_order()
+    else:
+        canonical_axes_order_ = canonical_label_axes_order()
+    if axes_names is None:
+        axes_names = canonical_axes_order_[-len(shape) :]
+
+    if axes_setup is None:
+        return build_canonical_axes_handler(
+            axes_names=axes_names,
+            canonical_channel_order=canonical_axes_order_,
+            space_unit=space_unit,
+            time_unit=time_unit,
+        )
+    return build_axes_handler(
+        axes_names=axes_names,
+        axes_setup=axes_setup,
+        space_unit=space_unit,
+        time_unit=time_unit,
+    )
+
+
 def init_image_like(
     *,
     # Where to create the image
@@ -259,31 +264,27 @@ def init_image_like(
     extra_array_kwargs: Mapping[str, Any] | None = None,
     # internal axes configuration for advanced use cases
     axes_setup: AxesSetup | None = None,
-    allow_non_canonical_axes: bool = False,
-    strict_canonical_order: bool = False,
     # Whether to overwrite existing image
     overwrite: bool = False,
     # Deprecated arguments
     yx_scaling_factor: float | tuple[float, float] | None = None,
     z_scaling_factor: float | None = None,
-) -> ZarrGroupHandler:
+) -> tuple[ZarrGroupHandler, AxesSetup]:
     """Create an empty OME-Zarr image with the given shape and metadata."""
     shape = tuple(shape)
-    if meta_type is NgioImageMeta:
-        default_axes_order = canonical_axes_order()
-    else:
-        default_axes_order = canonical_label_axes_order()
-
     axes_handler = _build_axes_handler(
         shape=shape,
+        meta_type=meta_type,
         axes_names=axes_names,
-        default_channel_order=default_axes_order,
-        space_units=space_unit,
-        time_units=time_unit,
         axes_setup=axes_setup,
-        allow_non_canonical_axes=allow_non_canonical_axes,
-        strict_canonical_order=strict_canonical_order,
+        space_unit=space_unit,
+        time_unit=time_unit,
     )
+    if len(shape) != len(axes_handler.axes_names):
+        raise NgioValueError(
+            f"Mismatch between shape {shape} "
+            f"and number of axes {len(axes_handler.axes_names)}."
+        )
     base_scale = compute_base_scale(
         pixelsize=pixelsize,
         z_spacing=z_spacing,
@@ -327,12 +328,13 @@ def init_image_like(
     )
     meta = _add_channels_meta(meta=meta, channels_meta=channels_meta)
     # Keep this creation at the end to avoid partial creations on errors
-    return _create_image_like_group(
+    image_handler = _create_image_like_group(
         store=store,
         pyramid_builder=pyramid_builder,
         meta=meta,
         overwrite=overwrite,
     )
+    return image_handler, axes_handler.axes_setup
 
 
 def init_image_like_from_shapes(
@@ -360,28 +362,24 @@ def init_image_like_from_shapes(
     extra_array_kwargs: Mapping[str, Any] | None = None,
     # internal axes configuration for advanced use cases
     axes_setup: AxesSetup | None = None,
-    allow_non_canonical_axes: bool = False,
-    strict_canonical_order: bool = False,
     # Whether to overwrite existing image
     overwrite: bool = False,
-) -> ZarrGroupHandler:
+) -> tuple[ZarrGroupHandler, AxesSetup]:
     """Create an empty OME-Zarr image with the given shape and metadata."""
     base_shape = shapes[0]
-    if meta_type is NgioImageMeta:
-        default_axes_order = canonical_axes_order()
-    else:
-        default_axes_order = canonical_label_axes_order()
-
     axes_handler = _build_axes_handler(
         shape=base_shape,
+        meta_type=meta_type,
         axes_names=axes_names,
-        default_channel_order=default_axes_order,
-        space_units=space_unit,
-        time_units=time_unit,
         axes_setup=axes_setup,
-        allow_non_canonical_axes=allow_non_canonical_axes,
-        strict_canonical_order=strict_canonical_order,
+        space_unit=space_unit,
+        time_unit=time_unit,
     )
+    if len(base_shape) != len(axes_handler.axes_names):
+        raise NgioValueError(
+            f"Mismatch between shape {base_shape} "
+            f"and number of axes {len(axes_handler.axes_names)}."
+        )
     if levels is None:
         levels_paths = tuple(str(i) for i in range(len(shapes)))
     else:
@@ -411,9 +409,10 @@ def init_image_like_from_shapes(
     )
     meta = _add_channels_meta(meta=meta, channels_meta=channels_meta)
     # Keep this creation at the end to avoid partial creations on errors
-    return _create_image_like_group(
+    image_handler = _create_image_like_group(
         store=store,
         pyramid_builder=pyramid_builder,
         meta=meta,
         overwrite=overwrite,
     )
+    return image_handler, axes_handler.axes_setup