ngio 0.5.0b1__tar.gz → 0.5.0b2__tar.gz

{ngio-0.5.0b1 → ngio-0.5.0b2}/CHANGELOG.md

@@ -5,6 +5,7 @@
 ### Features
 - Add support for OME-NGFF v0.5
 - Move to zarr-python v3
+- API to delete labels and tables from OME-Zarr containers and HCS plates.
 
 ### API Breaking Changes
 

{ngio-0.5.0b1 → ngio-0.5.0b2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.5.0b1
+Version: 0.5.0b2
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/BioVisionCenter/ngio
 Project-URL: repository, https://github.com/BioVisionCenter/ngio

{ngio-0.5.0b1 → ngio-0.5.0b2}/src/ngio/__init__.py

@@ -37,6 +37,7 @@ from ngio.ome_zarr_meta.ngio_specs import (
     NgffVersions,
     PixelSize,
 )
+from ngio.utils import NgioSupportedStore, StoreOrGroup
 
 __all__ = [
     "AxesSetup",
@@ -47,12 +48,14 @@ __all__ = [
     "ImageInWellPath",
     "Label",
     "NgffVersions",
+    "NgioSupportedStore",
     "OmeZarrContainer",
     "OmeZarrPlate",
     "OmeZarrWell",
     "PixelSize",
     "Roi",
     "RoiSlice",
+    "StoreOrGroup",
     "create_empty_ome_zarr",
     "create_empty_plate",
     "create_empty_well",

{ngio-0.5.0b1 → ngio-0.5.0b2}/src/ngio/hcs/_plate.py

@@ -15,6 +15,7 @@ from ngio.images import (
     list_image_tables_async,
 )
 from ngio.ome_zarr_meta import (
+    DefaultNgffVersion,
     ImageInWellPath,
     NgffVersions,
     NgioPlateMeta,
@@ -778,7 +779,8 @@ class OmeZarrPlate:
         self,
         store: StoreOrGroup,
         plate_name: str | None = None,
-        version: NgffVersions = "0.4",
+        version: NgffVersions | None = None,
+        ngff_version: NgffVersions = DefaultNgffVersion,
         keep_acquisitions: bool = False,
         cache: bool = False,
         overwrite: bool = False,
@@ -788,7 +790,8 @@ 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): The version 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.
             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.
@@ -797,6 +800,7 @@ class OmeZarrPlate:
             ome_zarr_plate=self,
             store=store,
             plate_name=plate_name,
+            ngff_version=ngff_version,
             version=version,
             keep_acquisitions=keep_acquisitions,
             cache=cache,
@@ -955,6 +959,25 @@ 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,
@@ -1157,7 +1180,6 @@ 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."""
@@ -1171,7 +1193,8 @@ def create_empty_plate(
     store: StoreOrGroup,
     name: str,
     images: list[ImageInWellPath] | None = None,
-    version: NgffVersions = "0.4",
+    version: NgffVersions | None = None,
+    ngff_version: NgffVersions = DefaultNgffVersion,
     cache: bool = False,
     overwrite: bool = False,
 ) -> OmeZarrPlate:
@@ -1182,18 +1205,26 @@ 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): The version 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.
         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=0.3. "
+            "Please use 'ngff_version' instead.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+        ngff_version = version
     plate_meta = NgioPlateMeta.default_init(
         name=name,
-        version=version,
+        ngff_version=ngff_version,
     )
     group_handler = _create_empty_plate_from_meta(
         store=store,
         meta=plate_meta,
-        version=version,
         overwrite=overwrite,
     )
 
@@ -1218,7 +1249,8 @@ def derive_ome_zarr_plate(
     ome_zarr_plate: OmeZarrPlate,
     store: StoreOrGroup,
     plate_name: str | None = None,
-    version: NgffVersions = "0.4",
+    version: NgffVersions | None = None,
+    ngff_version: NgffVersions = DefaultNgffVersion,
     keep_acquisitions: bool = False,
     cache: bool = False,
     overwrite: bool = False,
@@ -1229,24 +1261,33 @@ 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): The version 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.
         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=0.3. "
+            "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,
-        version=version,
+        ngff_version=ngff_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,
@@ -1277,7 +1318,8 @@ def open_ome_zarr_well(
 
 def create_empty_well(
     store: StoreOrGroup,
-    version: NgffVersions = "0.4",
+    version: NgffVersions | None = None,
+    ngff_version: NgffVersions = DefaultNgffVersion,
     cache: bool = False,
     overwrite: bool = False,
 ) -> OmeZarrWell:
@@ -1285,14 +1327,25 @@ def create_empty_well(
 
     Args:
         store (StoreOrGroup): The Zarr store or group that stores the well.
-        version (NgffVersion): The version of the new well.
+        version (NgffVersion | None): Deprecated. Please use 'ngff_version' instead.
+        ngff_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=0.3. "
+            "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())
+    update_ngio_well_meta(
+        group_handler, NgioWellMeta.default_init(ngff_version=ngff_version)
+    )
 
     return open_ome_zarr_well(
         store=store,

{ngio-0.5.0b1 → ngio-0.5.0b2}/src/ngio/images/_label.py

@@ -182,6 +182,31 @@ class LabelsContainer:
         )
         return Label(group_handler, path, label_meta_handler)
 
+    def delete(self, name: str, missing_ok: bool = False) -> None:
+        """Delete a label from the group.
+
+        Args:
+            name (str): The name of the label to delete.
+            missing_ok (bool): If True, do not raise an error if the label does not
+                exist.
+
+        """
+        existing_labels = self.list()
+        if name not in existing_labels:
+            if missing_ok:
+                return
+            raise NgioValueError(
+                f"Label '{name}' not found in the Labels group. "
+                f"Available labels: {existing_labels}"
+            )
+
+        self._group_handler.delete_group(name)
+        existing_labels.remove(name)
+        update_meta = NgioLabelsGroupMeta(
+            labels=existing_labels, version=self.meta.version
+        )
+        self._meta_handler.update_meta(update_meta)
+
     def derive(
         self,
         name: str,

{ngio-0.5.0b1 → ngio-0.5.0b2}/src/ngio/images/_ome_zarr_container.py

@@ -674,6 +674,25 @@ class OmeZarrContainer:
             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_labels(self) -> list[str]:
         """List all labels in the image."""
         label_container = self._get_labels_container(create_mode=False)
@@ -739,6 +758,25 @@ class OmeZarrContainer:
             masking_roi_table=masking_table,
         )
 
+    def delete_label(self, name: str, missing_ok: bool = False) -> None:
+        """Delete a label from the group.
+
+        Args:
+            name (str): The name of the label to delete.
+            missing_ok (bool): If True, do not raise an error if the label does not
+                exist.
+
+        """
+        label_container = self._get_labels_container(create_mode=False)
+        if label_container is None and missing_ok:
+            return
+        if label_container is None:
+            raise NgioValueError(
+                f"No labels found in the image, cannot delete {name}. "
+                "Set missing_ok=True to ignore this error."
+            )
+        label_container.delete(name=name, missing_ok=missing_ok)
+
     def derive_label(
         self,
         name: str,

{ngio-0.5.0b1 → ngio-0.5.0b2}/src/ngio/ome_zarr_meta/__init__.py

@@ -16,6 +16,7 @@ from ngio.ome_zarr_meta._meta_handlers import (
 from ngio.ome_zarr_meta.ngio_specs import (
     AxesHandler,
     Dataset,
+    DefaultNgffVersion,
     ImageInWellPath,
     NgffVersions,
     NgioImageMeta,
@@ -31,6 +32,7 @@ from ngio.ome_zarr_meta.ngio_specs import (
 __all__ = [
     "AxesHandler",
     "Dataset",
+    "DefaultNgffVersion",
     "ImageInWellPath",
     "ImageMetaHandler",
     "LabelMetaHandler",

{ngio-0.5.0b1 → ngio-0.5.0b2}/src/ngio/ome_zarr_meta/ngio_specs/_ngio_hcs.py

@@ -62,9 +62,9 @@ class NgioWellMeta(BaseModel):
     @classmethod
     def default_init(
         cls,
-        version: NgffVersions = DefaultNgffVersion,
+        ngff_version: NgffVersions = DefaultNgffVersion,
     ) -> "NgioWellMeta":
-        well = cls(images=[], version=version)
+        well = cls(images=[], version=ngff_version)
         return well
 
     @property
@@ -217,7 +217,7 @@ class NgioPlateMeta(BaseModel):
         cls,
         images: list[ImageInWellPath] | None = None,
         name: str | None = None,
-        version: NgffVersions = DefaultNgffVersion,
+        ngff_version: NgffVersions = DefaultNgffVersion,
     ) -> "NgioPlateMeta":
         plate = cls(
             plate=PlateWithVersion(
@@ -227,9 +227,9 @@ class NgioPlateMeta(BaseModel):
                 wells=[],
                 field_count=None,
                 name=name,
-                version=version,
+                version=ngff_version,
             ),
-            version=version,
+            version=ngff_version,
         )
 
         if images is None:
@@ -503,14 +503,14 @@ class NgioPlateMeta(BaseModel):
     def derive(
         self,
         name: str | None = None,
-        version: NgffVersions | None = None,
+        ngff_version: NgffVersions | None = None,
         keep_acquisitions: bool = False,
     ) -> "NgioPlateMeta":
         """Derive the plate metadata.
 
         Args:
             name (str): The name of the derived plate.
-            version (NgffVersion | None): The version of the derived plate.
+            ngff_version (NgffVersion | None): The version of the derived plate.
                 If None, use the version of the original plate.
             keep_acquisitions (bool): If True, keep the acquisitions in the plate.
         """
@@ -522,8 +522,8 @@ class NgioPlateMeta(BaseModel):
         else:
             acquisitions = None
 
-        if version is None:
-            version = self.version
+        if ngff_version is None:
+            ngff_version = self.version
 
         return NgioPlateMeta(
             plate=PlateWithVersion(
@@ -533,7 +533,7 @@ class NgioPlateMeta(BaseModel):
                 wells=[],
                 field_count=self.plate.field_count,
                 name=name,
-                version=version,
+                version=ngff_version,
             ),
-            version=version,
+            version=ngff_version,
         )

{ngio-0.5.0b1 → ngio-0.5.0b2}/src/ngio/tables/_tables_container.py

@@ -311,6 +311,27 @@ class TablesContainer:
             backend=backend,
         )  # type: ignore[return-value]
 
+    def delete(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.
+        """
+        existing_tables = self._get_tables_list()
+        if name not in existing_tables:
+            if missing_ok:
+                return
+            raise NgioValueError(
+                f"Table '{name}' not found in the Tables group. "
+                f"Available tables: {existing_tables}"
+            )
+
+        self._group_handler.delete_group(name)
+        existing_tables.remove(name)
+        self._group_handler.write_attrs({"tables": existing_tables})
+
     def add(
         self,
         name: str,

{ngio-0.5.0b1 → ngio-0.5.0b2}/src/ngio/utils/__init__.py

@@ -17,6 +17,7 @@ from ngio.utils._fractal_fsspec_store import fractal_fsspec_store
 from ngio.utils._zarr_utils import (
     AccessModeLiteral,
     NgioCache,
+    NgioSupportedStore,
     StoreOrGroup,
     ZarrGroupHandler,
     copy_group,
@@ -29,6 +30,7 @@ __all__ = [
     "NgioError",
     "NgioFileExistsError",
     "NgioFileNotFoundError",
+    "NgioSupportedStore",
     "NgioTableValidationError",
     "NgioValidationError",
     "NgioValueError",

{ngio-0.5.0b1 → ngio-0.5.0b2}/src/ngio/utils/_zarr_utils.py

@@ -3,7 +3,7 @@
 import json
 import warnings
 from pathlib import Path
-from typing import Literal
+from typing import Literal, TypeAlias
 
 import dask.array as da
 import fsspec
@@ -26,17 +26,11 @@ AccessModeLiteral = Literal["r", "r+", "w", "w-", "a"]
 # StoreLike is more restrictive than it could be
 # but to make sure we can handle the store correctly
 # we need to be more restrictive
-NgioSupportedStore = (
-    str
-    | Path
-    | fsspec.mapping.FSMap
-    | FsspecStore
-    | MemoryStore
-    | LocalStore
-    | ZipStore
+NgioSupportedStore: TypeAlias = (
+    str | Path | fsspec.mapping.FSMap | FsspecStore | MemoryStore | dict | LocalStore
 )
-GenericStore = Store | NgioSupportedStore
-StoreOrGroup = GenericStore | zarr.Group
+GenericStore: TypeAlias = NgioSupportedStore | Store
+StoreOrGroup: TypeAlias = NgioSupportedStore | zarr.Group
 
 
 def _check_store(store) -> NgioSupportedStore:
@@ -398,6 +392,12 @@ class ZarrGroupHandler:
         self._group_cache._cache.pop(path, None)
         self._handlers_cache._cache.pop(path, None)
 
+    def delete_self(self) -> None:
+        """Delete the current group."""
+        if self.group.read_only:
+            raise NgioValueError("Cannot delete a group in read only mode.")
+        self.group.__delitem__("/")
+
     def copy_group(self, dest_group: zarr.Group):
         """Copy the group to a new store."""
         copy_group(self.group, dest_group)

{ngio-0.5.0b1 → ngio-0.5.0b2}/tests/unit/hcs/test_plate.py

@@ -1,5 +1,6 @@
 import asyncio
 from pathlib import Path
+from typing import Literal
 
 import pandas.testing as pdt
 import pytest
@@ -59,8 +60,11 @@ def test_open_real_ome_zarr_plate(cardiomyocyte_tiny_path: Path):
     assert well.get_image_acquisition_id("0") is None
 
 
-def test_create_and_edit_plate(tmp_path: Path):
-    test_plate = create_empty_plate(tmp_path / "test_plate.zarr", name="test_plate")
+@pytest.mark.parametrize("ngff_version", ["0.4", "0.5"])
+def test_create_and_edit_plate(tmp_path: Path, ngff_version: Literal["0.4", "0.5"]):
+    test_plate = create_empty_plate(
+        tmp_path / "test_plate.zarr", name="test_plate", ngff_version=ngff_version
+    )
     assert test_plate.columns == []
     assert test_plate.rows == []
     assert test_plate.acquisition_ids == []
@@ -183,6 +187,18 @@ def test_tables_api(tmp_path: Path):
         test_df,
         check_names=False,
     )
+    test_plate.delete_table("test_table")
+    assert "test_table" not in test_plate.list_tables()
+    test_plate.delete_table("test_table", missing_ok=True)
+    with pytest.raises(NgioValueError):
+        test_plate.delete_table("test_table", missing_ok=False)
+
+    test_plate = create_empty_plate(
+        tmp_path / "test_plate.zarr", name="test_plate", overwrite=True
+    )
+    with pytest.raises(NgioValueError):
+        test_plate.delete_table("non_existing_table")
+    test_plate.delete_table("non_existing_table", missing_ok=True)
 
 
 @pytest.mark.filterwarnings("ignore::anndata._warnings.ImplicitModificationWarning")

{ngio-0.5.0b1 → ngio-0.5.0b2}/tests/unit/images/test_omezarr_container.py

@@ -12,7 +12,7 @@ from ngio import (
 from ngio.images._image import ChannelSelectionModel
 from ngio.io_pipes._ops_axes import AxesOps
 from ngio.io_pipes._ops_slices import SlicingOps
-from ngio.utils import fractal_fsspec_store
+from ngio.utils import NgioValueError, fractal_fsspec_store
 
 
 class IdentityTransform:
@@ -340,3 +340,39 @@ def test_derive_copy_labels_and_tables(tmp_path: Path):
     )
     assert ome_zarr.list_labels() == derived_ome_zarr.list_labels()
     assert ome_zarr.list_tables() == derived_ome_zarr.list_tables()
+
+
+def test_delete_label_and_table(tmp_path: Path):
+    store = tmp_path / "ome_zarr.zarr"
+    ome_zarr = create_synthetic_ome_zarr(
+        store,
+        shape=(3, 20, 30),
+        levels=1,
+        axes_names=["c", "y", "x"],
+    )
+    ome_zarr.derive_label("label_to_delete")
+    assert "label_to_delete" in ome_zarr.list_labels()
+    ome_zarr.delete_label("label_to_delete")
+    assert "label_to_delete" not in ome_zarr.list_labels()
+    ome_zarr.delete_label("label_to_delete", missing_ok=True)
+    with pytest.raises(NgioValueError):
+        ome_zarr.delete_label("label_to_delete", missing_ok=False)
+
+    new_table = ome_zarr.build_image_roi_table()
+    ome_zarr.add_table("table_to_delete", new_table)
+    assert "table_to_delete" in ome_zarr.list_tables()
+    ome_zarr.delete_table("table_to_delete")
+    assert "table_to_delete" not in ome_zarr.list_tables()
+    ome_zarr.delete_table("table_to_delete", missing_ok=True)
+    with pytest.raises(NgioValueError):
+        ome_zarr.delete_table("table_to_delete", missing_ok=False)
+
+    ome_zarr = create_empty_ome_zarr(
+        store, shape=(3, 20, 30), pixelsize=0.5, overwrite=True
+    )
+    with pytest.raises(NgioValueError):
+        ome_zarr.delete_label("non_existing_label")
+    ome_zarr.delete_label("non_existing_label", missing_ok=True)
+    with pytest.raises(NgioValueError):
+        ome_zarr.delete_table("non_existing_table")
+    ome_zarr.delete_table("non_existing_table", missing_ok=True)

{ngio-0.5.0b1 → ngio-0.5.0b2}/tests/unit/utils/test_zarr_utils.py

@@ -65,6 +65,29 @@ def test_group_handler_from_group(tmp_path: Path):
     assert handler.group == group
 
 
+def test_group_handler_delete(tmp_path: Path):
+    store = tmp_path / "test_group_handler_from_group.zarr"
+    group = zarr.group(store=store, overwrite=True)
+    group.create_group("to_be_deleted")
+    handler = ZarrGroupHandler(store=group, cache=True, mode="a")
+    assert isinstance(handler.get_group("to_be_deleted"), zarr.Group)
+    handler.delete_group("to_be_deleted")
+    with pytest.raises(NgioFileNotFoundError):
+        handler.get_group("to_be_deleted")
+    assert store.exists()
+    handler.delete_self()
+    assert not store.exists()
+
+    store = tmp_path / "test_group_handler_from_group.zarr"
+    group = zarr.group(store=store, overwrite=True)
+    group.create_group("to_be_deleted")
+    handler = ZarrGroupHandler(store=group, cache=True, mode="r")
+    with pytest.raises(NgioValueError):
+        handler.delete_group("to_be_deleted")
+    with pytest.raises(NgioValueError):
+        handler.delete_self()
+
+
 def test_group_handler_read(tmp_path: Path):
     store = tmp_path / "test_group_handler_read.zarr"