ngio 0.2.1__tar.gz → 0.2.3__tar.gz

{ngio-0.2.1 → ngio-0.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.2.1
+Version: 0.2.3
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/lorenzocerrone/ngio
 Project-URL: repository, https://github.com/lorenzocerrone/ngio
@@ -23,7 +23,9 @@ Requires-Dist: filelock
 Requires-Dist: numpy
 Requires-Dist: ome-zarr-models
 Requires-Dist: pandas>=1.2.0
+Requires-Dist: polars
 Requires-Dist: pooch
+Requires-Dist: pyarrow
 Requires-Dist: pydantic
 Requires-Dist: requests
 Requires-Dist: xarray

{ngio-0.2.1 → ngio-0.2.3}/docs/getting_started/5_hcs.md

@@ -38,8 +38,8 @@ The `OmeZarrPlate` object provides a high-level overview of the plate, including
 === "Acquisitions"
     Show the acquisitions ids:
     ```pycon exec="true" source="console" session="hcs_plate"
-    >>> ome_zarr_plate.acquisitions_ids
-    >>> print(ome_zarr_plate.acquisitions_ids) # markdown-exec: hide
+    >>> ome_zarr_plate.acquisition_ids
+    >>> print(ome_zarr_plate.acquisition_ids) # markdown-exec: hide
     ```
 
 ## Retrieving the path to the images

{ngio-0.2.1 → ngio-0.2.3}/pyproject.toml

@@ -46,6 +46,8 @@ dependencies = [
     "xarray",
     "ome-zarr-models",
     "pooch",
+    "polars",
+    "pyarrow",
 ]
 
 # https://peps.python.org/pep-0621/#dependencies-optional-dependencies

{ngio-0.2.1 → ngio-0.2.3}/src/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-0.2.1 → ngio-0.2.3}/src/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-0.2.1 → ngio-0.2.3}/src/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-0.2.3/src/ngio/hcs/__init__.py

@@ -0,0 +1,19 @@
+"""OME-Zarr HCS objects models."""
+
+from ngio.hcs.plate import (
+    OmeZarrPlate,
+    OmeZarrWell,
+    create_empty_plate,
+    create_empty_well,
+    open_ome_zarr_plate,
+    open_ome_zarr_well,
+)
+
+__all__ = [
+    "OmeZarrPlate",
+    "OmeZarrWell",
+    "create_empty_plate",
+    "create_empty_well",
+    "open_ome_zarr_plate",
+    "open_ome_zarr_well",
+]