ngio 0.5.0__py3-none-any.whl → 0.5.0a1__py3-none-any.whl

ngio/io_pipes/_io_pipes.py

@@ -7,7 +7,7 @@ import zarr
 from dask.array import Array as DaskArray
 
 from ngio.common._dimensions import Dimensions
-from ngio.common._roi import Roi
+from ngio.common._roi import Roi, RoiPixels
 from ngio.io_pipes._ops_axes import (
     AxesOps,
     build_axes_ops,
@@ -72,7 +72,7 @@ class DataGetter(ABC, Generic[T]):
         slicing_ops: SlicingOps,
         axes_ops: AxesOps,
         transforms: Sequence[TransformProtocol] | None = None,
-        roi: Roi | None = None,
+        roi: Roi | RoiPixels | None = None,
     ) -> None:
         self._zarr_array = zarr_array
         self._slicing_ops = slicing_ops
@@ -106,7 +106,7 @@ class DataGetter(ABC, Generic[T]):
         return self._transforms
 
     @property
-    def roi(self) -> Roi:
+    def roi(self) -> Roi | RoiPixels:
         if self._roi is None:
             name = self.__class__.__name__
             raise ValueError(f"No ROI defined for {name}.")
@@ -127,7 +127,7 @@ class DataSetter(ABC, Generic[T]):
         slicing_ops: SlicingOps,
         axes_ops: AxesOps,
         transforms: Sequence[TransformProtocol] | None = None,
-        roi: Roi | None = None,
+        roi: Roi | RoiPixels | None = None,
     ) -> None:
         self._zarr_array = zarr_array
         self._slicing_ops = slicing_ops
@@ -161,7 +161,7 @@ class DataSetter(ABC, Generic[T]):
         return self._transforms
 
     @property
-    def roi(self) -> Roi:
+    def roi(self) -> Roi | RoiPixels:
         if self._roi is None:
             name = self.__class__.__name__
             raise ValueError(f"No ROI defined for {name}.")
@@ -185,7 +185,7 @@ class NumpyGetter(DataGetter[np.ndarray]):
         transforms: Sequence[TransformProtocol] | None = None,
         slicing_dict: dict[str, SlicingInputType] | None = None,
         remove_channel_selection: bool = False,
-        roi: Roi | None = None,
+        roi: Roi | RoiPixels | None = None,
     ) -> None:
         """Build a pipe to get a numpy or dask array from a zarr array."""
         slicing_ops, axes_ops = setup_io_pipe(
@@ -225,7 +225,7 @@ class DaskGetter(DataGetter[DaskArray]):
         transforms: Sequence[TransformProtocol] | None = None,
         slicing_dict: dict[str, SlicingInputType] | None = None,
         remove_channel_selection: bool = False,
-        roi: Roi | None = None,
+        roi: Roi | RoiPixels | None = None,
     ) -> None:
         """Build a pipe to get a numpy or dask array from a zarr array."""
         slicing_ops, axes_ops = setup_io_pipe(
@@ -279,7 +279,7 @@ class NumpySetter(DataSetter[np.ndarray]):
         transforms: Sequence[TransformProtocol] | None = None,
         slicing_dict: dict[str, SlicingInputType] | None = None,
         remove_channel_selection: bool = False,
-        roi: Roi | None = None,
+        roi: Roi | RoiPixels | None = None,
     ) -> None:
         """Build a pipe to get a numpy or dask array from a zarr array."""
         slicing_ops, axes_ops = setup_io_pipe(
@@ -325,7 +325,7 @@ class DaskSetter(DataSetter[DaskArray]):
         transforms: Sequence[TransformProtocol] | None = None,
         slicing_dict: dict[str, SlicingInputType] | None = None,
         remove_channel_selection: bool = False,
-        roi: Roi | None = None,
+        roi: Roi | RoiPixels | None = None,
     ) -> None:
         """Build a pipe to get a numpy or dask array from a zarr array."""
         slicing_ops, axes_ops = setup_io_pipe(

ngio/io_pipes/_io_pipes_masked.py

@@ -6,7 +6,7 @@ import zarr
 from dask.array import Array as DaskArray
 
 from ngio.common._dimensions import Dimensions
-from ngio.common._roi import Roi
+from ngio.common._roi import Roi, RoiPixels
 from ngio.io_pipes._io_pipes import (
     DaskGetter,
     DaskSetter,
@@ -57,7 +57,7 @@ def _setup_numpy_getters(
     dimensions: Dimensions,
     label_zarr_array: zarr.Array,
     label_dimensions: Dimensions,
-    roi: Roi,
+    roi: Roi | RoiPixels,
     axes_order: Sequence[str] | None = None,
     transforms: Sequence[TransformProtocol] | None = None,
     label_transforms: Sequence[TransformProtocol] | None = None,
@@ -117,7 +117,7 @@ class NumpyGetterMasked(DataGetter[np.ndarray]):
         dimensions: Dimensions,
         label_zarr_array: zarr.Array,
         label_dimensions: Dimensions,
-        roi: Roi,
+        roi: Roi | RoiPixels,
         axes_order: Sequence[str] | None = None,
         transforms: Sequence[TransformProtocol] | None = None,
         label_transforms: Sequence[TransformProtocol] | None = None,
@@ -187,7 +187,7 @@ class NumpySetterMasked(DataSetter[np.ndarray]):
         dimensions: Dimensions,
         label_zarr_array: zarr.Array,
         label_dimensions: Dimensions,
-        roi: Roi,
+        roi: Roi | RoiPixels,
         axes_order: Sequence[str] | None = None,
         transforms: Sequence[TransformProtocol] | None = None,
         label_transforms: Sequence[TransformProtocol] | None = None,
@@ -290,7 +290,7 @@ def _setup_dask_getters(
     dimensions: Dimensions,
     label_zarr_array: zarr.Array,
     label_dimensions: Dimensions,
-    roi: Roi,
+    roi: Roi | RoiPixels,
     axes_order: Sequence[str] | None = None,
     transforms: Sequence[TransformProtocol] | None = None,
     label_transforms: Sequence[TransformProtocol] | None = None,
@@ -350,7 +350,7 @@ class DaskGetterMasked(DataGetter[DaskArray]):
         dimensions: Dimensions,
         label_zarr_array: zarr.Array,
         label_dimensions: Dimensions,
-        roi: Roi,
+        roi: Roi | RoiPixels,
         axes_order: Sequence[str] | None = None,
         transforms: Sequence[TransformProtocol] | None = None,
         label_transforms: Sequence[TransformProtocol] | None = None,
@@ -418,7 +418,7 @@ class DaskSetterMasked(DataSetter[DaskArray]):
         dimensions: Dimensions,
         label_zarr_array: zarr.Array,
         label_dimensions: Dimensions,
-        roi: Roi,
+        roi: Roi | RoiPixels,
         axes_order: Sequence[str] | None = None,
         transforms: Sequence[TransformProtocol] | None = None,
         label_transforms: Sequence[TransformProtocol] | None = None,

ngio/io_pipes/_io_pipes_roi.py

@@ -3,7 +3,7 @@ from collections.abc import Sequence
 import zarr
 
 from ngio.common._dimensions import Dimensions
-from ngio.common._roi import Roi
+from ngio.common._roi import Roi, RoiPixels
 from ngio.io_pipes._io_pipes import (
     DaskGetter,
     DaskSetter,
@@ -17,7 +17,7 @@ from ngio.ome_zarr_meta.ngio_specs._pixel_size import PixelSize
 
 def roi_to_slicing_dict(
     *,
-    roi: Roi,
+    roi: Roi | RoiPixels,
     pixel_size: PixelSize,
     slicing_dict: dict[str, SlicingInputType] | None = None,
 ) -> dict[str, SlicingInputType]:
@@ -40,7 +40,7 @@ class NumpyRoiGetter(NumpyGetter):
         *,
         zarr_array: zarr.Array,
         dimensions: Dimensions,
-        roi: Roi,
+        roi: Roi | RoiPixels,
         axes_order: Sequence[str] | None = None,
         transforms: Sequence[TransformProtocol] | None = None,
         slicing_dict: dict[str, SlicingInputType] | None = None,
@@ -68,7 +68,7 @@ class DaskRoiGetter(DaskGetter):
         *,
         zarr_array: zarr.Array,
         dimensions: Dimensions,
-        roi: Roi,
+        roi: Roi | RoiPixels,
         axes_order: Sequence[str] | None = None,
         transforms: Sequence[TransformProtocol] | None = None,
         slicing_dict: dict[str, SlicingInputType] | None = None,
@@ -96,7 +96,7 @@ class NumpyRoiSetter(NumpySetter):
         *,
         zarr_array: zarr.Array,
         dimensions: Dimensions,
-        roi: Roi,
+        roi: Roi | RoiPixels,
         axes_order: Sequence[str] | None = None,
         transforms: Sequence[TransformProtocol] | None = None,
         slicing_dict: dict[str, SlicingInputType] | None = None,
@@ -124,7 +124,7 @@ class DaskRoiSetter(DaskSetter):
         *,
         zarr_array: zarr.Array,
         dimensions: Dimensions,
-        roi: Roi,
+        roi: Roi | RoiPixels,
         axes_order: Sequence[str] | None = None,
         transforms: Sequence[TransformProtocol] | None = None,
         slicing_dict: dict[str, SlicingInputType] | None = None,

ngio/io_pipes/_io_pipes_types.py

@@ -3,7 +3,7 @@ from typing import Protocol, TypeVar
 
 import zarr
 
-from ngio.common._roi import Roi
+from ngio.common._roi import Roi, RoiPixels
 from ngio.io_pipes._ops_axes import AxesOps
 from ngio.io_pipes._ops_slices import SlicingOps
 from ngio.io_pipes._ops_transforms import TransformProtocol
@@ -26,7 +26,7 @@ class DataGetterProtocol(Protocol[GetterDataType]):
     def transforms(self) -> Sequence[TransformProtocol] | None: ...
 
     @property
-    def roi(self) -> Roi: ...
+    def roi(self) -> Roi | RoiPixels: ...
 
     def __call__(self) -> GetterDataType:
         return self.get()
@@ -48,7 +48,7 @@ class DataSetterProtocol(Protocol[SetterDataType]):
     def transforms(self) -> Sequence[TransformProtocol] | None: ...
 
     @property
-    def roi(self) -> Roi: ...
+    def roi(self) -> Roi | RoiPixels: ...
 
     def __call__(self, patch: SetterDataType) -> None:
         return self.set(patch)

ngio/io_pipes/_match_shape.py

@@ -1,11 +1,10 @@
-import warnings
 from collections.abc import Sequence
 from enum import Enum
 
 import dask.array as da
 import numpy as np
 
-from ngio.utils import NgioValueError
+from ngio.utils import NgioValueError, ngio_logger
 
 
 class Action(str, Enum):
@@ -29,7 +28,7 @@ def _compute_pad_widths(
             pad_def.append((before, after))
         else:
             pad_def.append((0, 0))
-    warnings.warn(
+    ngio_logger.warning(
         f"Images have a different shape ({array_shape} vs {target_shape}). "
         f"Resolving by padding: {pad_def}",
         stacklevel=2,
@@ -76,7 +75,7 @@ def _compute_trim_slices(
         else:
             slices.append(slice(0, s))
 
-    warnings.warn(
+    ngio_logger.warning(
         f"Images have a different shape ({array_shape} vs {target_shape}). "
         f"Resolving by trimming: {slices}",
         stacklevel=2,
@@ -118,7 +117,7 @@ def _compute_rescaling_shape(
             rescaling_shape.append(s)
             factor.append(1.0)
 
-    warnings.warn(
+    ngio_logger.warning(
         f"Images have a different shape ({array_shape} vs {target_shape}). "
         f"Resolving by scaling with factors {factor}.",
         stacklevel=2,
@@ -266,11 +265,14 @@ def numpy_match_shape(
         reference_axes (Sequence[str]): The axes names of the reference shape.
         tolerance (int): The maximum number of pixels by which dimensions
             can differ when matching shapes.
+        allow_broadcast (bool): If True, allow broadcasting new dimensions to
+            match the reference shape. If False, single-dimension axes will
+            be left as is.
         pad_mode (str): The mode to use for padding. See numpy.pad for options.
         pad_values (int | float): The constant value to use for padding if
             pad_mode is 'constant'.
         allow_rescaling (bool): If True, when the array differs more than the
-            tolerance, it will be rescaled to the reference shape. If False,
+            tolerance, it will be rescalingd to the reference shape. If False,
             an error will be raised.
     """
     _check_axes(

ngio/io_pipes/_ops_slices_utils.py

@@ -1,9 +1,8 @@
-import warnings
 from collections.abc import Iterable, Iterator
 from itertools import product
 from typing import TypeAlias, TypeVar
 
-from ngio.utils import NgioValueError
+from ngio.utils import NgioValueError, ngio_logger
 
 T = TypeVar("T")
 
@@ -86,10 +85,9 @@ def check_if_regions_overlap(slices: Iterable[tuple[SlicingType, ...]]) -> bool:
             return True
 
         if it == 10_000:
-            warnings.warn(
+            ngio_logger.warning(
                 "Performance Warning check_for_overlaps is O(n^2) and may be slow for "
-                "large numbers of regions.",
-                stacklevel=2,
+                "large numbers of regions."
             )
     return False
 
@@ -191,9 +189,8 @@ def check_if_chunks_overlap(
         if si & sj:
             return True
         if it == 10_000:
-            warnings.warn(
+            ngio_logger.warning(
                 "Performance Warning check_for_chunks_overlaps is O(n^2) and may be "
-                "slow for large numbers of regions.",
-                stacklevel=2,
+                "slow for large numbers of regions."
             )
     return False

ngio/ome_zarr_meta/__init__.py

@@ -3,28 +3,22 @@
 from ngio.ome_zarr_meta._meta_handlers import (
     ImageMetaHandler,
     LabelMetaHandler,
-    LabelsGroupMetaHandler,
-    PlateMetaHandler,
-    WellMetaHandler,
-    update_ngio_image_meta,
-    update_ngio_label_meta,
-    update_ngio_labels_group_meta,
-    update_ngio_meta,
-    update_ngio_plate_meta,
-    update_ngio_well_meta,
+    find_image_meta_handler,
+    find_label_meta_handler,
+    find_plate_meta_handler,
+    find_well_meta_handler,
+    get_image_meta_handler,
+    get_label_meta_handler,
+    get_plate_meta_handler,
+    get_well_meta_handler,
 )
 from ngio.ome_zarr_meta.ngio_specs import (
     AxesHandler,
-    Channel,
-    ChannelsMeta,
-    ChannelVisualisation,
     Dataset,
-    DefaultNgffVersion,
     ImageInWellPath,
     NgffVersions,
     NgioImageMeta,
     NgioLabelMeta,
-    NgioLabelsGroupMeta,
     NgioPlateMeta,
     NgioWellMeta,
     PixelSize,
@@ -34,32 +28,27 @@ from ngio.ome_zarr_meta.ngio_specs import (
 
 __all__ = [
     "AxesHandler",
-    "Channel",
-    "ChannelVisualisation",
-    "ChannelsMeta",
     "Dataset",
-    "DefaultNgffVersion",
     "ImageInWellPath",
     "ImageMetaHandler",
+    "ImageMetaHandler",
+    "LabelMetaHandler",
     "LabelMetaHandler",
-    "LabelsGroupMetaHandler",
     "NgffVersions",
     "NgffVersions",
     "NgioImageMeta",
     "NgioLabelMeta",
-    "NgioLabelsGroupMeta",
     "NgioPlateMeta",
     "NgioWellMeta",
     "PixelSize",
-    "PlateMetaHandler",
-    "PlateMetaHandler",
-    "WellMetaHandler",
     "build_canonical_axes_handler",
+    "find_image_meta_handler",
+    "find_label_meta_handler",
+    "find_plate_meta_handler",
+    "find_well_meta_handler",
+    "get_image_meta_handler",
+    "get_label_meta_handler",
+    "get_plate_meta_handler",
+    "get_well_meta_handler",
     "path_in_well_validation",
-    "update_ngio_image_meta",
-    "update_ngio_label_meta",
-    "update_ngio_labels_group_meta",
-    "update_ngio_meta",
-    "update_ngio_plate_meta",
-    "update_ngio_well_meta",
 ]