ngio 0.5.0a2__py3-none-any.whl → 0.5.0a3__py3-none-any.whl

ngio/experimental/iterators/_rois_utils.py

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

ngio/hcs/_plate.py

@@ -19,11 +19,11 @@ from ngio.ome_zarr_meta import (
     NgffVersions,
     NgioPlateMeta,
     NgioWellMeta,
-    find_plate_meta_handler,
-    find_well_meta_handler,
-    get_plate_meta_handler,
-    get_well_meta_handler,
+    PlateMetaHandler,
+    WellMetaHandler,
     path_in_well_validation,
+    update_ngio_plate_meta,
+    update_ngio_well_meta,
 )
 from ngio.tables import (
     ConditionTable,
@@ -41,17 +41,22 @@ from ngio.tables import (
 from ngio.utils import (
     AccessModeLiteral,
     NgioCache,
+    NgioError,
     NgioValueError,
     StoreOrGroup,
     ZarrGroupHandler,
 )
 
 
-def _default_table_container(handler: ZarrGroupHandler) -> TablesContainer | None:
+def _try_get_table_container(
+    handler: ZarrGroupHandler, create_mode: bool = True
+) -> TablesContainer | None:
     """Return a default table container."""
-    success, table_handler = handler.safe_derive_handler("tables")
-    if success and isinstance(table_handler, ZarrGroupHandler):
+    try:
+        table_handler = handler.get_handler("tables", create_mode=create_mode)
         return TablesContainer(table_handler)
+    except NgioError:
+        return None
 
 
 # Mock lock class that does nothing
@@ -77,7 +82,7 @@ class OmeZarrWell:
             group_handler: The Zarr group handler that contains the Well.
         """
         self._group_handler = group_handler
-        self._meta_handler = find_well_meta_handler(group_handler)
+        self._meta_handler = WellMetaHandler(group_handler)
 
     def __repr__(self) -> str:
         """Return a string representation of the well."""
@@ -91,7 +96,7 @@ class OmeZarrWell:
     @property
     def meta(self):
         """Return the metadata."""
-        return self._meta_handler.meta
+        return self._meta_handler.get_meta()
 
     @property
     def acquisition_ids(self) -> list[int]:
@@ -137,7 +142,7 @@ class OmeZarrWell:
         Returns:
             OmeZarrContainer: The image.
         """
-        handler = self._group_handler.derive_handler(image_path)
+        handler = self._group_handler.get_handler(image_path)
         return OmeZarrContainer(handler)
 
     def _add_image(
@@ -159,7 +164,7 @@ class OmeZarrWell:
             meta = self.meta.add_image(
                 path=image_path, acquisition=acquisition_id, strict=strict
             )
-            self.meta_handler.write_meta(meta)
+            self.meta_handler.update_meta(meta)
             self.meta_handler._group_handler.clean_cache()
 
         return self._group_handler.get_group(image_path, create_mode=True)
@@ -238,7 +243,7 @@ class OmeZarrPlate:
             table_container: The tables container that contains plate level tables.
         """
         self._group_handler = group_handler
-        self._meta_handler = find_plate_meta_handler(group_handler)
+        self._meta_handler = PlateMetaHandler(group_handler)
         self._tables_container = table_container
         self._wells_cache: NgioCache[OmeZarrWell] = NgioCache(
             use_cache=self._group_handler.use_cache
@@ -259,7 +264,7 @@ class OmeZarrPlate:
     @property
     def meta(self):
         """Return the metadata."""
-        return self._meta_handler.meta
+        return self._meta_handler.get_meta()
 
     @property
     def columns(self) -> list[str]:
@@ -377,7 +382,7 @@ class OmeZarrPlate:
         if cached_well is not None:
             return cached_well
 
-        group_handler = self._group_handler.derive_handler(well_path)
+        group_handler = self._group_handler.get_handler(well_path)
         self._wells_cache.set(well_path, OmeZarrWell(group_handler))
         return OmeZarrWell(group_handler)
 
@@ -438,7 +443,7 @@ 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.derive_handler(image_path)
+        img_group_handler = self._group_handler.get_handler(image_path)
         image = OmeZarrContainer(img_group_handler)
         self._images_cache.set(image_path, image)
         return image
@@ -529,7 +534,7 @@ class OmeZarrPlate:
         for image_paths in self.well_images_paths(
             row=row, column=column, acquisition=acquisition
         ):
-            group_handler = self._group_handler.derive_handler(image_paths)
+            group_handler = self._group_handler.get_handler(image_paths)
             images[image_paths] = OmeZarrContainer(group_handler)
         return images
 
@@ -558,11 +563,11 @@ class OmeZarrPlate:
                 meta = meta.add_acquisition(
                     acquisition_id=acquisition_id, acquisition_name=acquisition_name
                 )
-            self.meta_handler.write_meta(meta)
+            self.meta_handler.update_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.derive_handler(well_path)
+        group_handler = self._group_handler.get_handler(well_path)
 
         if atomic:
             well_lock = group_handler.lock
@@ -577,18 +582,19 @@ class OmeZarrPlate:
                 well_meta = NgioWellMeta.default_init()
                 version = self.meta.plate.version
                 version = version if version is not None else "0.4"
-                meta_handler = get_well_meta_handler(group_handler, version=version)
+                update_ngio_well_meta(group_handler, well_meta)
+                meta_handler = WellMetaHandler(group_handler=group_handler)
             else:
-                meta_handler = find_well_meta_handler(group_handler)
-                well_meta = meta_handler.meta
+                meta_handler = WellMetaHandler(group_handler=group_handler)
+                well_meta = meta_handler.get_meta()
 
-            group_handler = self._group_handler.derive_handler(well_path)
+            group_handler = self._group_handler.get_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.write_meta(well_meta)
+            meta_handler.update_meta(well_meta)
             meta_handler._group_handler.clean_cache()
 
         if image_path is not None:
@@ -665,7 +671,7 @@ class OmeZarrPlate:
     ) -> "OmeZarrPlate":
         """Add a column to an ome-zarr plate."""
         meta, _ = self.meta.add_column(column)
-        self.meta_handler.write_meta(meta)
+        self.meta_handler.update_meta(meta)
         self.meta_handler._group_handler.clean_cache()
         return self
 
@@ -675,7 +681,7 @@ class OmeZarrPlate:
     ) -> "OmeZarrPlate":
         """Add a row to an ome-zarr plate."""
         meta, _ = self.meta.add_row(row)
-        self.meta_handler.write_meta(meta)
+        self.meta_handler.update_meta(meta)
         self.meta_handler._group_handler.clean_cache()
         return self
 
@@ -695,7 +701,7 @@ class OmeZarrPlate:
         meta = self.meta.add_acquisition(
             acquisition_id=acquisition_id, acquisition_name=acquisition_name
         )
-        self.meta_handler.write_meta(meta)
+        self.meta_handler.update_meta(meta)
         self.meta_handler._group_handler.clean_cache()
         return self
 
@@ -714,7 +720,7 @@ class OmeZarrPlate:
         with plate_lock:
             meta = self.meta
             meta = meta.remove_well(row, column)
-            self.meta_handler.write_meta(meta)
+            self.meta_handler.update_meta(meta)
             self.meta_handler._group_handler.clean_cache()
 
     def _remove_image(
@@ -735,7 +741,7 @@ class OmeZarrPlate:
         with well_lock:
             well_meta = well.meta
             well_meta = well_meta.remove_image(path=image_path)
-            well.meta_handler.write_meta(well_meta)
+            well.meta_handler.update_meta(well_meta)
             well.meta_handler._group_handler.clean_cache()
             if len(well_meta.paths()) == 0:
                 self._remove_well(row, column, atomic=atomic)
@@ -797,13 +803,14 @@ class OmeZarrPlate:
             overwrite=overwrite,
         )
 
-    def _get_tables_container(self) -> TablesContainer | None:
+    def _get_tables_container(self, create_mode: bool = True) -> TablesContainer | None:
         """Return the 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
+        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
         return self._tables_container
 
     @property
@@ -818,17 +825,20 @@ 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."""
-        masking_roi = self.tables_container.list(
-            filter_types="masking_roi_table",
-        )
         roi = self.tables_container.list(
             filter_types="roi_table",
         )
-        return masking_roi + roi
+        masking_roi = self.tables_container.list(
+            filter_types="masking_roi_table",
+        )
+        return roi + masking_roi
 
     def get_roi_table(self, name: str) -> RoiTable:
         """Get a ROI table from the image.
@@ -1153,8 +1163,7 @@ def _create_empty_plate_from_meta(
     """Create an empty OME-Zarr plate from metadata."""
     mode = "w" if overwrite else "w-"
     group_handler = ZarrGroupHandler(store=store, cache=True, mode=mode)
-    meta_handler = get_plate_meta_handler(group_handler, version=version)
-    meta_handler.write_meta(meta)
+    update_ngio_plate_meta(group_handler, meta)
     return group_handler
 
 
@@ -1283,9 +1292,7 @@ def create_empty_well(
     group_handler = ZarrGroupHandler(
         store=store, cache=True, mode="w" if overwrite else "w-"
     )
-    meta_handler = get_well_meta_handler(group_handler, version=version)
-    meta = NgioWellMeta.default_init()
-    meta_handler.write_meta(meta)
+    update_ngio_well_meta(group_handler, NgioWellMeta.default_init())
 
     return open_ome_zarr_well(
         store=store,