ngio 0.2.1__py3-none-any.whl → 0.2.3__py3-none-any.whl

ngio/__init__.py

@@ -10,7 +10,14 @@ __author__ = "Lorenzo Cerrone"
 __email__ = "lorenzo.cerrone@uzh.ch"
 
 from ngio.common import ArrayLike, Dimensions, Roi, RoiPixels
-from ngio.hcs import OmeZarrPlate, create_empty_plate, open_ome_zarr_plate
+from ngio.hcs import (
+    OmeZarrPlate,
+    OmeZarrWell,
+    create_empty_plate,
+    create_empty_well,
+    open_ome_zarr_plate,
+    open_ome_zarr_well,
+)
 from ngio.images import (
     Image,
     Label,
@@ -20,24 +27,35 @@ from ngio.images import (
     open_image,
     open_ome_zarr_container,
 )
-from ngio.ome_zarr_meta.ngio_specs import AxesSetup, ImageInWellPath, PixelSize
+from ngio.ome_zarr_meta.ngio_specs import (
+    AxesSetup,
+    DefaultNgffVersion,
+    ImageInWellPath,
+    NgffVersions,
+    PixelSize,
+)
 
 __all__ = [
     "ArrayLike",
     "AxesSetup",
+    "DefaultNgffVersion",
     "Dimensions",
     "Image",
     "ImageInWellPath",
     "Label",
+    "NgffVersions",
     "OmeZarrContainer",
     "OmeZarrPlate",
+    "OmeZarrWell",
     "PixelSize",
     "Roi",
     "RoiPixels",
     "create_empty_ome_zarr",
     "create_empty_plate",
+    "create_empty_well",
     "create_ome_zarr_from_array",
     "open_image",
     "open_ome_zarr_container",
     "open_ome_zarr_plate",
+    "open_ome_zarr_well",
 ]

ngio/common/_pyramid.py

@@ -190,12 +190,16 @@ def init_empty_pyramid(
             "The shape and chunks must have the same number of dimensions."
         )
 
+    if chunks is not None:
+        chunks = [min(c, s) for c, s in zip(chunks, ref_shape, strict=True)]
+
     if len(ref_shape) != len(scaling_factors):
         raise NgioValueError(
             "The shape and scaling factor must have the same number of dimensions."
         )
 
-    root_group, _ = open_group_wrapper(store, mode=mode)
+    root_group = open_group_wrapper(store, mode=mode)
+
     for path in paths:
         if any(s < 1 for s in ref_shape):
             raise NgioValueError(

ngio/common/_roi.py

@@ -10,7 +10,7 @@ import numpy as np
 from pydantic import BaseModel, ConfigDict, Field
 
 from ngio.common._dimensions import Dimensions
-from ngio.ome_zarr_meta.ngio_specs import PixelSize, SpaceUnits
+from ngio.ome_zarr_meta.ngio_specs import DefaultSpaceUnit, PixelSize, SpaceUnits
 from ngio.utils import NgioValueError
 
 
@@ -36,7 +36,7 @@ class Roi(BaseModel):
     x: float = 0.0
     y: float = 0.0
     z: float = 0.0
-    unit: SpaceUnits = Field(SpaceUnits.micrometer, repr=False)
+    unit: SpaceUnits | str | None = Field(DefaultSpaceUnit, repr=False)
 
     model_config = ConfigDict(extra="allow")
 

ngio/hcs/__init__.py

@@ -1,5 +1,19 @@
 """OME-Zarr HCS objects models."""
 
-from ngio.hcs.plate import OmeZarrPlate, create_empty_plate, open_ome_zarr_plate
+from ngio.hcs.plate import (
+    OmeZarrPlate,
+    OmeZarrWell,
+    create_empty_plate,
+    create_empty_well,
+    open_ome_zarr_plate,
+    open_ome_zarr_well,
+)
 
-__all__ = ["OmeZarrPlate", "create_empty_plate", "open_ome_zarr_plate"]
+__all__ = [
+    "OmeZarrPlate",
+    "OmeZarrWell",
+    "create_empty_plate",
+    "create_empty_well",
+    "open_ome_zarr_plate",
+    "open_ome_zarr_well",
+]