ngio 0.3.5__py3-none-any.whl → 0.4.0a1__py3-none-any.whl

ngio/hcs/_plate.py

@@ -1,11 +1,12 @@
-"""A module for handling the Plate Collection in an OME-Zarr file."""
+"""A module for handling the Plate Sequence in an OME-Zarr file."""
 
 import asyncio
 import warnings
-from collections.abc import Collection
+from collections.abc import Sequence
 from typing import Literal
 
-from ngio.common import (
+from ngio.images import (
+    OmeZarrContainer,
     concatenate_image_tables,
     concatenate_image_tables_as,
     concatenate_image_tables_as_async,
@@ -13,7 +14,6 @@ from ngio.common import (
     list_image_tables,
     list_image_tables_async,
 )
-from ngio.images import OmeZarrContainer
 from ngio.ome_zarr_meta import (
     ImageInWellPath,
     NgffVersions,
@@ -67,7 +67,7 @@ class MockLock:
 
 
 class OmeZarrWell:
-    """A class to handle the Well Collection in an OME-Zarr file."""
+    """A class to handle the Well Sequence in an OME-Zarr file."""
 
     def __init__(self, group_handler: ZarrGroupHandler) -> None:
         """Initialize the LabelGroupHandler.
@@ -190,7 +190,7 @@ class OmeZarrWell:
             acquisition_id (int | None): The acquisition id to filter the images.
             strict (bool): Whether to check if the acquisition id is already exists
                 in the well. Defaults to True. If False this might lead to
-                acquision in a well that does not exist at the plate level.
+                acquisition in a well that does not exist at the plate level.
         """
         return self._add_image(
             image_path=image_path,
@@ -200,11 +200,11 @@ class OmeZarrWell:
         )
 
 
-def _build_extras(paths: Collection[str]) -> list[dict[str, str]]:
+def _build_extras(paths: Sequence[str]) -> list[dict[str, str]]:
     """Build the extras for the images.
 
     Args:
-        paths (Collection[str]): The paths of the images.
+        paths (Sequence[str]): The paths of the images.
 
     Returns:
         list[dict[str, str]]: The extras for the images.
@@ -223,7 +223,7 @@ def _build_extras(paths: Collection[str]) -> list[dict[str, str]]:
 
 
 class OmeZarrPlate:
-    """A class to handle the Plate Collection in an OME-Zarr file."""
+    """A class to handle the Plate Sequence in an OME-Zarr file."""
 
     def __init__(
         self,
@@ -382,7 +382,8 @@ class OmeZarrPlate:
         """
         wells = self._group_handler.get_from_cache("wells")
         if wells is not None:
-            return wells  # type: ignore[return-value]
+            assert isinstance(wells, dict)
+            return wells
 
         def process_well(well_path):
             group_handler = self._group_handler.derive_handler(well_path)
@@ -410,7 +411,8 @@ class OmeZarrPlate:
         """
         wells = self._group_handler.get_from_cache("wells")
         if wells is not None:
-            return wells  # type: ignore[return-value]
+            assert isinstance(wells, dict)
+            return wells
 
         def process_well(well_path):
             group_handler = self._group_handler.derive_handler(well_path)
@@ -442,7 +444,8 @@ class OmeZarrPlate:
         """
         images = self._group_handler.get_from_cache("images")
         if images is not None:
-            return images  # type: ignore[return-value]
+            assert isinstance(images, dict)
+            return images
 
         paths = await self.images_paths_async(acquisition=acquisition)
 
@@ -473,7 +476,8 @@ class OmeZarrPlate:
         """
         images = self._group_handler.get_from_cache("images")
         if images is not None:
-            return images  # type: ignore[return-value]
+            assert isinstance(images, dict)
+            return images
         paths = self.images_paths(acquisition=acquisition)
 
         def process_image(image_path):
@@ -969,9 +973,9 @@ class OmeZarrPlate:
                 If 'common', return only common tables between all images.
                 If 'all', return all tables. Defaults to 'common'.
         """
-        images = self.get_images(acquisition=acquisition)
+        images = tuple(self.get_images(acquisition=acquisition).values())
         return list_image_tables(
-            images=images.values(),
+            images=images,
             filter_types=filter_types,
             mode=mode,
         )
@@ -993,15 +997,16 @@ class OmeZarrPlate:
                 If 'all', return all tables. Defaults to 'common'.
         """
         images = await self.get_images_async(acquisition=acquisition)
+        images = tuple(images.values())
         return await list_image_tables_async(
-            images=images.values(),
+            images=images,
             filter_types=filter_types,
             mode=mode,
         )
 
     def concatenate_image_tables(
         self,
-        table_name: str,
+        name: str,
         acquisition: int | None = None,
         strict: bool = True,
         index_key: str | None = None,
@@ -1010,7 +1015,7 @@ class OmeZarrPlate:
         """Concatenate tables from all images in the plate.
 
         Args:
-            table_name: The name of the table to concatenate.
+            name: The name of the table to concatenate.
             index_key: The key to use for the index of the concatenated table.
             acquisition: The acquisition id to filter the images.
             strict: If True, raise an error if the table is not found in the image.
@@ -1021,11 +1026,11 @@ class OmeZarrPlate:
                 if 'lazy', the table will be loaded as a lazy frame.
         """
         images = self.get_images(acquisition=acquisition)
-        extras = _build_extras(images.keys())
+        extras = _build_extras(tuple(images.keys()))
         return concatenate_image_tables(
-            images=images.values(),
+            images=tuple(images.values()),
             extras=extras,
-            table_name=table_name,
+            name=name,
             index_key=index_key,
             strict=strict,
             mode=mode,
@@ -1033,7 +1038,7 @@ class OmeZarrPlate:
 
     def concatenate_image_tables_as(
         self,
-        table_name: str,
+        name: str,
         table_cls: type[TableType],
         acquisition: int | None = None,
         index_key: str | None = None,
@@ -1043,7 +1048,7 @@ class OmeZarrPlate:
         """Concatenate tables from all images in the plate as a specific type.
 
         Args:
-            table_name: The name of the table to concatenate.
+            name: The name of the table to concatenate.
             table_cls: The type of the table to concatenate.
             index_key: The key to use for the index of the concatenated table.
             acquisition: The acquisition id to filter the images.
@@ -1055,11 +1060,11 @@ class OmeZarrPlate:
                 if 'lazy', the table will be loaded as a lazy frame.
         """
         images = self.get_images(acquisition=acquisition)
-        extras = _build_extras(images.keys())
+        extras = _build_extras(tuple(images.keys()))
         return concatenate_image_tables_as(
-            images=images.values(),
+            images=tuple(images.values()),
             extras=extras,
-            table_name=table_name,
+            name=name,
             table_cls=table_cls,
             index_key=index_key,
             strict=strict,
@@ -1068,7 +1073,7 @@ class OmeZarrPlate:
 
     async def concatenate_image_tables_async(
         self,
-        table_name: str,
+        name: str,
         acquisition: int | None = None,
         index_key: str | None = None,
         strict: bool = True,
@@ -1077,7 +1082,7 @@ class OmeZarrPlate:
         """Concatenate tables from all images in the plate asynchronously.
 
         Args:
-            table_name: The name of the table to concatenate.
+            name: The name of the table to concatenate.
             index_key: The key to use for the index of the concatenated table.
             acquisition: The acquisition id to filter the images.
             index_key: If a string is provided, a new index column will be created
@@ -1088,11 +1093,11 @@ class OmeZarrPlate:
                 if 'lazy', the table will be loaded as a lazy frame.
         """
         images = await self.get_images_async(acquisition=acquisition)
-        extras = _build_extras(images.keys())
+        extras = _build_extras(tuple(images.keys()))
         return await concatenate_image_tables_async(
-            images=images.values(),
+            images=tuple(images.values()),
             extras=extras,
-            table_name=table_name,
+            name=name,
             index_key=index_key,
             strict=strict,
             mode=mode,
@@ -1100,7 +1105,7 @@ class OmeZarrPlate:
 
     async def concatenate_image_tables_as_async(
         self,
-        table_name: str,
+        name: str,
         table_cls: type[TableType],
         acquisition: int | None = None,
         index_key: str | None = None,
@@ -1110,7 +1115,7 @@ class OmeZarrPlate:
         """Concatenate tables from all images in the plate as a specific type.
 
         Args:
-            table_name: The name of the table to concatenate.
+            name: The name of the table to concatenate.
             table_cls: The type of the table to concatenate.
             index_key: The key to use for the index of the concatenated table.
             acquisition: The acquisition id to filter the images.
@@ -1122,11 +1127,11 @@ class OmeZarrPlate:
                 if 'lazy', the table will be loaded as a lazy frame.
         """
         images = await self.get_images_async(acquisition=acquisition)
-        extras = _build_extras(images.keys())
+        extras = _build_extras(tuple(images.keys()))
         return await concatenate_image_tables_as_async(
-            images=images.values(),
+            images=tuple(images.values()),
             extras=extras,
-            table_name=table_name,
+            name=name,
             table_cls=table_cls,
             index_key=index_key,
             strict=strict,

ngio/images/__init__.py

@@ -1,23 +1,44 @@
 """OME-Zarr object models."""
 
-from ngio.images._image import Image, ImagesContainer
+from ngio.images._create_synt_container import create_synthetic_ome_zarr
+from ngio.images._image import ChannelSelectionModel, Image, ImagesContainer
 from ngio.images._label import Label, LabelsContainer
 from ngio.images._ome_zarr_container import (
     OmeZarrContainer,
     create_empty_ome_zarr,
     create_ome_zarr_from_array,
     open_image,
+    open_label,
     open_ome_zarr_container,
 )
+from ngio.images._table_ops import (
+    concatenate_image_tables,
+    concatenate_image_tables_as,
+    concatenate_image_tables_as_async,
+    concatenate_image_tables_async,
+    conctatenate_tables,
+    list_image_tables,
+    list_image_tables_async,
+)
 
 __all__ = [
+    "ChannelSelectionModel",
     "Image",
     "ImagesContainer",
     "Label",
     "LabelsContainer",
     "OmeZarrContainer",
+    "concatenate_image_tables",
+    "concatenate_image_tables_as",
+    "concatenate_image_tables_as_async",
+    "concatenate_image_tables_async",
+    "conctatenate_tables",
     "create_empty_ome_zarr",
     "create_ome_zarr_from_array",
+    "create_synthetic_ome_zarr",
+    "list_image_tables",
+    "list_image_tables_async",
     "open_image",
+    "open_label",
     "open_ome_zarr_container",
 ]