ngio 0.5.0__py3-none-any.whl → 0.5.0a2__py3-none-any.whl

ngio/experimental/iterators/_rois_utils.py

@@ -1,4 +1,4 @@
-from ngio import Roi
+from ngio import Roi, RoiPixels
 from ngio.images._abstract_image import AbstractImage
 
 
@@ -48,17 +48,18 @@ def grid(
         for z in range(0, z_dim, stride_z):
             for y in range(0, y_dim, stride_y):
                 for x in range(0, x_dim, stride_x):
-                    roi = Roi.from_values(
+                    roi = RoiPixels(
                         name=base_name,
-                        slices={
-                            "x": (x, size_x),
-                            "y": (y, size_y),
-                            "z": (z, size_z),
-                            "t": (t, size_t),
-                        },
-                        space="pixel",
+                        x=x,
+                        y=y,
+                        z=z,
+                        t=t,
+                        x_length=size_x,
+                        y_length=size_y,
+                        z_length=size_z,
+                        t_length=size_t,
                     )
-                    new_rois.append(roi.to_world(pixel_size=ref_image.pixel_size))
+                    new_rois.append(roi.to_roi(pixel_size=ref_image.pixel_size))
 
     return rois_product(rois, new_rois)
 

ngio/hcs/_plate.py

@@ -15,16 +15,15 @@ from ngio.images import (
     list_image_tables_async,
 )
 from ngio.ome_zarr_meta import (
-    DefaultNgffVersion,
     ImageInWellPath,
     NgffVersions,
     NgioPlateMeta,
     NgioWellMeta,
-    PlateMetaHandler,
-    WellMetaHandler,
+    find_plate_meta_handler,
+    find_well_meta_handler,
+    get_plate_meta_handler,
+    get_well_meta_handler,
     path_in_well_validation,
-    update_ngio_plate_meta,
-    update_ngio_well_meta,
 )
 from ngio.tables import (
     ConditionTable,
@@ -42,22 +41,17 @@ from ngio.tables import (
 from ngio.utils import (
     AccessModeLiteral,
     NgioCache,
-    NgioError,
     NgioValueError,
     StoreOrGroup,
     ZarrGroupHandler,
 )
 
 
-def _try_get_table_container(
-    handler: ZarrGroupHandler, create_mode: bool = True
-) -> TablesContainer | None:
+def _default_table_container(handler: ZarrGroupHandler) -> TablesContainer | None:
     """Return a default table container."""
-    try:
-        table_handler = handler.get_handler("tables", create_mode=create_mode)
+    success, table_handler = handler.safe_derive_handler("tables")
+    if success and isinstance(table_handler, ZarrGroupHandler):
         return TablesContainer(table_handler)
-    except NgioError:
-        return None
 
 
 # Mock lock class that does nothing
@@ -83,7 +77,7 @@ class OmeZarrWell:
             group_handler: The Zarr group handler that contains the Well.
         """
         self._group_handler = group_handler
-        self._meta_handler = WellMetaHandler(group_handler)
+        self._meta_handler = find_well_meta_handler(group_handler)
 
     def __repr__(self) -> str:
         """Return a string representation of the well."""
@@ -97,7 +91,7 @@ class OmeZarrWell:
     @property
     def meta(self):
         """Return the metadata."""
-        return self._meta_handler.get_meta()
+        return self._meta_handler.meta
 
     @property
     def acquisition_ids(self) -> list[int]:
@@ -143,7 +137,7 @@ class OmeZarrWell:
         Returns:
             OmeZarrContainer: The image.
         """
-        handler = self._group_handler.get_handler(image_path)
+        handler = self._group_handler.derive_handler(image_path)
         return OmeZarrContainer(handler)
 
     def _add_image(
@@ -165,7 +159,7 @@ class OmeZarrWell:
             meta = self.meta.add_image(
                 path=image_path, acquisition=acquisition_id, strict=strict
             )
-            self.meta_handler.update_meta(meta)
+            self.meta_handler.write_meta(meta)
             self.meta_handler._group_handler.clean_cache()
 
         return self._group_handler.get_group(image_path, create_mode=True)
@@ -244,7 +238,7 @@ class OmeZarrPlate:
             table_container: The tables container that contains plate level tables.
         """
         self._group_handler = group_handler
-        self._meta_handler = PlateMetaHandler(group_handler)
+        self._meta_handler = find_plate_meta_handler(group_handler)
         self._tables_container = table_container
         self._wells_cache: NgioCache[OmeZarrWell] = NgioCache(
             use_cache=self._group_handler.use_cache
@@ -265,7 +259,7 @@ class OmeZarrPlate:
     @property
     def meta(self):
         """Return the metadata."""
-        return self._meta_handler.get_meta()
+        return self._meta_handler.meta
 
     @property
     def columns(self) -> list[str]:
@@ -383,7 +377,7 @@ class OmeZarrPlate:
         if cached_well is not None:
             return cached_well
 
-        group_handler = self._group_handler.get_handler(well_path)
+        group_handler = self._group_handler.derive_handler(well_path)
         self._wells_cache.set(well_path, OmeZarrWell(group_handler))
         return OmeZarrWell(group_handler)
 
@@ -444,7 +438,7 @@ class OmeZarrPlate:
         cached_image = self._images_cache.get(image_path)
         if cached_image is not None:
             return cached_image
-        img_group_handler = self._group_handler.get_handler(image_path)
+        img_group_handler = self._group_handler.derive_handler(image_path)
         image = OmeZarrContainer(img_group_handler)
         self._images_cache.set(image_path, image)
         return image
@@ -535,7 +529,7 @@ class OmeZarrPlate:
         for image_paths in self.well_images_paths(
             row=row, column=column, acquisition=acquisition
         ):
-            group_handler = self._group_handler.get_handler(image_paths)
+            group_handler = self._group_handler.derive_handler(image_paths)
             images[image_paths] = OmeZarrContainer(group_handler)
         return images
 
@@ -564,11 +558,11 @@ class OmeZarrPlate:
                 meta = meta.add_acquisition(
                     acquisition_id=acquisition_id, acquisition_name=acquisition_name
                 )
-            self.meta_handler.update_meta(meta)
+            self.meta_handler.write_meta(meta)
             self.meta_handler._group_handler.clean_cache()
 
         well_path = self.meta.get_well_path(row=row, column=column)
-        group_handler = self._group_handler.get_handler(well_path)
+        group_handler = self._group_handler.derive_handler(well_path)
 
         if atomic:
             well_lock = group_handler.lock
@@ -583,19 +577,18 @@ class OmeZarrPlate:
                 well_meta = NgioWellMeta.default_init()
                 version = self.meta.plate.version
                 version = version if version is not None else "0.4"
-                update_ngio_well_meta(group_handler, well_meta)
-                meta_handler = WellMetaHandler(group_handler=group_handler)
+                meta_handler = get_well_meta_handler(group_handler, version=version)
             else:
-                meta_handler = WellMetaHandler(group_handler=group_handler)
-                well_meta = meta_handler.get_meta()
+                meta_handler = find_well_meta_handler(group_handler)
+                well_meta = meta_handler.meta
 
-            group_handler = self._group_handler.get_handler(well_path)
+            group_handler = self._group_handler.derive_handler(well_path)
 
             if image_path is not None:
                 well_meta = well_meta.add_image(
                     path=image_path, acquisition=acquisition_id, strict=False
                 )
-            meta_handler.update_meta(well_meta)
+            meta_handler.write_meta(well_meta)
             meta_handler._group_handler.clean_cache()
 
         if image_path is not None:
@@ -672,7 +665,7 @@ class OmeZarrPlate:
     ) -> "OmeZarrPlate":
         """Add a column to an ome-zarr plate."""
         meta, _ = self.meta.add_column(column)
-        self.meta_handler.update_meta(meta)
+        self.meta_handler.write_meta(meta)
         self.meta_handler._group_handler.clean_cache()
         return self
 
@@ -682,7 +675,7 @@ class OmeZarrPlate:
     ) -> "OmeZarrPlate":
         """Add a row to an ome-zarr plate."""
         meta, _ = self.meta.add_row(row)
-        self.meta_handler.update_meta(meta)
+        self.meta_handler.write_meta(meta)
         self.meta_handler._group_handler.clean_cache()
         return self
 
@@ -702,7 +695,7 @@ class OmeZarrPlate:
         meta = self.meta.add_acquisition(
             acquisition_id=acquisition_id, acquisition_name=acquisition_name
         )
-        self.meta_handler.update_meta(meta)
+        self.meta_handler.write_meta(meta)
         self.meta_handler._group_handler.clean_cache()
         return self
 
@@ -721,7 +714,7 @@ class OmeZarrPlate:
         with plate_lock:
             meta = self.meta
             meta = meta.remove_well(row, column)
-            self.meta_handler.update_meta(meta)
+            self.meta_handler.write_meta(meta)
             self.meta_handler._group_handler.clean_cache()
 
     def _remove_image(
@@ -742,7 +735,7 @@ class OmeZarrPlate:
         with well_lock:
             well_meta = well.meta
             well_meta = well_meta.remove_image(path=image_path)
-            well.meta_handler.update_meta(well_meta)
+            well.meta_handler.write_meta(well_meta)
             well.meta_handler._group_handler.clean_cache()
             if len(well_meta.paths()) == 0:
                 self._remove_well(row, column, atomic=atomic)
@@ -779,8 +772,7 @@ class OmeZarrPlate:
         self,
         store: StoreOrGroup,
         plate_name: str | None = None,
-        version: NgffVersions | None = None,
-        ngff_version: NgffVersions = DefaultNgffVersion,
+        version: NgffVersions = "0.4",
         keep_acquisitions: bool = False,
         cache: bool = False,
         overwrite: bool = False,
@@ -790,8 +782,7 @@ class OmeZarrPlate:
         Args:
             store (StoreOrGroup): The Zarr store or group that stores the plate.
             plate_name (str | None): The name of the new plate.
-            version (NgffVersion | None): Deprecated. Please use 'ngff_version' instead.
-            ngff_version (NgffVersion): The NGFF version to use for the new plate.
+            version (NgffVersion): The version of the new plate.
             keep_acquisitions (bool): Whether to keep the acquisitions in the new plate.
             cache (bool): Whether to use a cache for the zarr group metadata.
             overwrite (bool): Whether to overwrite the existing plate.
@@ -800,21 +791,19 @@ class OmeZarrPlate:
             ome_zarr_plate=self,
             store=store,
             plate_name=plate_name,
-            ngff_version=ngff_version,
             version=version,
             keep_acquisitions=keep_acquisitions,
             cache=cache,
             overwrite=overwrite,
         )
 
-    def _get_tables_container(self, create_mode: bool = True) -> TablesContainer | None:
+    def _get_tables_container(self) -> TablesContainer | None:
         """Return the tables container."""
-        if self._tables_container is not None:
-            return self._tables_container
-        _tables_container = _try_get_table_container(
-            self._group_handler, create_mode=create_mode
-        )
-        self._tables_container = _tables_container
+        if self._tables_container is None:
+            _tables_container = _default_table_container(self._group_handler)
+            if _tables_container is None:
+                return None
+            self._tables_container = _tables_container
         return self._tables_container
 
     @property
@@ -829,20 +818,17 @@ class OmeZarrPlate:
 
     def list_tables(self, filter_types: TypedTable | str | None = None) -> list[str]:
         """List all tables in the image."""
-        _tables_container = self._get_tables_container(create_mode=False)
-        if _tables_container is None:
-            return []
         return self.tables_container.list(filter_types=filter_types)
 
     def list_roi_tables(self) -> list[str]:
         """List all ROI tables in the image."""
-        roi = self.tables_container.list(
-            filter_types="roi_table",
-        )
         masking_roi = self.tables_container.list(
             filter_types="masking_roi_table",
         )
-        return roi + masking_roi
+        roi = self.tables_container.list(
+            filter_types="roi_table",
+        )
+        return masking_roi + roi
 
     def get_roi_table(self, name: str) -> RoiTable:
         """Get a ROI table from the image.
@@ -919,8 +905,8 @@ class OmeZarrPlate:
         """
         if check_type is not None:
             warnings.warn(
-                "The 'check_type' argument is deprecated and will be removed in "
-                "ngio=0.6. Please use 'get_table_as' instead or one of the "
+                "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,
@@ -959,25 +945,6 @@ class OmeZarrPlate:
             name=name, table=table, backend=backend, overwrite=overwrite
         )
 
-    def delete_table(self, name: str, missing_ok: bool = False) -> None:
-        """Delete a table from the group.
-
-        Args:
-            name (str): The name of the table to delete.
-            missing_ok (bool): If True, do not raise an error if the table does not
-                exist.
-
-        """
-        table_container = self._get_tables_container(create_mode=False)
-        if table_container is None and missing_ok:
-            return
-        if table_container is None:
-            raise NgioValueError(
-                f"No tables found in the image, cannot delete {name}. "
-                "Set missing_ok=True to ignore this error."
-            )
-        table_container.delete(name=name, missing_ok=missing_ok)
-
     def list_image_tables(
         self,
         acquisition: int | None = None,
@@ -1180,24 +1147,14 @@ def open_ome_zarr_plate(
 def _create_empty_plate_from_meta(
     store: StoreOrGroup,
     meta: NgioPlateMeta,
+    version: NgffVersions = "0.4",
     overwrite: bool = False,
 ) -> ZarrGroupHandler:
-    """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.
-    """
+    """Create an empty OME-Zarr plate from metadata."""
     mode = "w" if overwrite else "w-"
-    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)
+    group_handler = ZarrGroupHandler(store=store, cache=True, mode=mode)
+    meta_handler = get_plate_meta_handler(group_handler, version=version)
+    meta_handler.write_meta(meta)
     return group_handler
 
 
@@ -1205,8 +1162,7 @@ def create_empty_plate(
     store: StoreOrGroup,
     name: str,
     images: list[ImageInWellPath] | None = None,
-    version: NgffVersions | None = None,
-    ngff_version: NgffVersions = DefaultNgffVersion,
+    version: NgffVersions = "0.4",
     cache: bool = False,
     overwrite: bool = False,
 ) -> OmeZarrPlate:
@@ -1217,26 +1173,18 @@ def create_empty_plate(
         name (str): The name of the plate.
         images (list[ImageInWellPath] | None): A list of images to add to the plate.
             If None, no images are added. Defaults to None.
-        version (NgffVersion | None): Deprecated. Please use 'ngff_version' instead.
-        ngff_version (NgffVersion): The NGFF version to use for the new plate.
+        version (NgffVersion): The version of the new plate.
         cache (bool): Whether to use a cache for the zarr group metadata.
         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=0.6. "
-            "Please use 'ngff_version' instead.",
-            DeprecationWarning,
-            stacklevel=2,
-        )
-        ngff_version = version
     plate_meta = NgioPlateMeta.default_init(
         name=name,
-        ngff_version=ngff_version,
+        version=version,
     )
     group_handler = _create_empty_plate_from_meta(
         store=store,
         meta=plate_meta,
+        version=version,
         overwrite=overwrite,
     )
 
@@ -1261,8 +1209,7 @@ def derive_ome_zarr_plate(
     ome_zarr_plate: OmeZarrPlate,
     store: StoreOrGroup,
     plate_name: str | None = None,
-    version: NgffVersions | None = None,
-    ngff_version: NgffVersions = DefaultNgffVersion,
+    version: NgffVersions = "0.4",
     keep_acquisitions: bool = False,
     cache: bool = False,
     overwrite: bool = False,
@@ -1273,33 +1220,24 @@ def derive_ome_zarr_plate(
         ome_zarr_plate (OmeZarrPlate): The existing OME-Zarr plate.
         store (StoreOrGroup): The Zarr store or group that stores the plate.
         plate_name (str | None): The name of the new plate.
-        version (NgffVersion | None): Deprecated. Please use 'ngff_version' instead.
-        ngff_version (NgffVersion): The NGFF version to use for the new plate.
+        version (NgffVersion): The version of the new plate.
         keep_acquisitions (bool): Whether to keep the acquisitions in the new plate.
         cache (bool): Whether to use a cache for the zarr group metadata.
         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=0.6. "
-            "Please use 'ngff_version' instead.",
-            DeprecationWarning,
-            stacklevel=2,
-        )
-        ngff_version = version
-
     if plate_name is None:
         plate_name = ome_zarr_plate.meta.plate.name
 
     new_meta = ome_zarr_plate.meta.derive(
         name=plate_name,
-        ngff_version=ngff_version,
+        version=version,
         keep_acquisitions=keep_acquisitions,
     )
     _ = _create_empty_plate_from_meta(
         store=store,
         meta=new_meta,
         overwrite=overwrite,
+        version=version,
     )
     return open_ome_zarr_plate(
         store=store,
@@ -1330,8 +1268,7 @@ def open_ome_zarr_well(
 
 def create_empty_well(
     store: StoreOrGroup,
-    version: NgffVersions | None = None,
-    ngff_version: NgffVersions = DefaultNgffVersion,
+    version: NgffVersions = "0.4",
     cache: bool = False,
     overwrite: bool = False,
 ) -> OmeZarrWell:
@@ -1339,25 +1276,16 @@ def create_empty_well(
 
     Args:
         store (StoreOrGroup): The Zarr store or group that stores the well.
-        version (NgffVersion | None): Deprecated. Please use 'ngff_version' instead.
-        ngff_version (NgffVersion): The version of the new well.
+        version (NgffVersion): The version of the new well.
         cache (bool): Whether to use a cache for the zarr group metadata.
         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=0.6. "
-            "Please use 'ngff_version' instead.",
-            DeprecationWarning,
-            stacklevel=2,
-        )
-        ngff_version = version
     group_handler = ZarrGroupHandler(
         store=store, cache=True, mode="w" if overwrite else "w-"
     )
-    update_ngio_well_meta(
-        group_handler, NgioWellMeta.default_init(ngff_version=ngff_version)
-    )
+    meta_handler = get_well_meta_handler(group_handler, version=version)
+    meta = NgioWellMeta.default_init()
+    meta_handler.write_meta(meta)
 
     return open_ome_zarr_well(
         store=store,