ngio 0.2.2__py3-none-any.whl → 0.2.4__py3-none-any.whl

ngio/tables/v1/_roi_table.py

@@ -14,7 +14,7 @@ from pydantic import BaseModel
 
 from ngio.common import Roi
 from ngio.tables._validators import validate_columns
-from ngio.tables.backends import ImplementedTableBackends
+from ngio.tables.backends import BackendMeta, ImplementedTableBackends
 from ngio.utils import NgioValueError, ZarrGroupHandler
 
 REQUIRED_COLUMNS = [
@@ -91,12 +91,11 @@ def _rois_to_dataframe(rois: dict[str, Roi], index_key: str) -> pd.DataFrame:
     return dataframe
 
 
-class RoiTableV1Meta(BaseModel):
+class RoiTableV1Meta(BackendMeta):
     """Metadata for the ROI table."""
 
     fractal_table_version: Literal["1"] = "1"
     type: Literal["roi_table"] = "roi_table"
-    backend: str | None = None
 
 
 class RegionMeta(BaseModel):
@@ -105,12 +104,11 @@ class RegionMeta(BaseModel):
     path: str
 
 
-class MaskingRoiTableV1Meta(BaseModel):
+class MaskingRoiTableV1Meta(BackendMeta):
     """Metadata for the ROI table."""
 
     fractal_table_version: Literal["1"] = "1"
     type: Literal["masking_roi_table"] = "masking_roi_table"
-    backend: str | None = None
     region: RegionMeta | None = None
     instance_key: str = "label"
 
@@ -191,7 +189,7 @@ class _GenericRoiTableV1(Generic[_roi_meta]):
             )
             meta.backend = backend_name
 
-        if not backend.implements_dataframe:
+        if not backend.implements_pandas:
             raise NgioValueError(
                 "The backend does not implement the dataframe protocol."
             )
@@ -201,7 +199,7 @@ class _GenericRoiTableV1(Generic[_roi_meta]):
         table._meta = meta
         table._table_backend = backend
 
-        dataframe = backend.load_as_dataframe()
+        dataframe = backend.load_as_pandas_df()
         dataframe = validate_columns(
             dataframe,
             required_columns=REQUIRED_COLUMNS,
@@ -229,13 +227,18 @@ class _GenericRoiTableV1(Generic[_roi_meta]):
         """List all ROIs in the table."""
         return list(self._rois.values())
 
-    def add(self, roi: Roi | Iterable[Roi]) -> None:
-        """Append ROIs to the current table."""
+    def add(self, roi: Roi | Iterable[Roi], overwrite: bool = False) -> None:
+        """Append ROIs to the current table.
+
+        Args:
+            roi: A single ROI or a list of ROIs to add to the table.
+            overwrite: If True, overwrite existing ROIs with the same name.
+        """
         if isinstance(roi, Roi):
             roi = [roi]
 
         for _roi in roi:
-            if _roi.name in self._rois:
+            if not overwrite and _roi.name in self._rois:
                 raise NgioValueError(f"ROI {_roi.name} already exists in the table.")
             self._rois[_roi.name] = _roi
 
@@ -253,8 +256,8 @@ class _GenericRoiTableV1(Generic[_roi_meta]):
             required_columns=REQUIRED_COLUMNS,
             optional_columns=OPTIONAL_COLUMNS,
         )
-        self._table_backend.write_from_dataframe(
-            dataframe, metadata=self._meta.model_dump(exclude_none=True)
+        self._table_backend.write(
+            dataframe, metadata=self._meta.model_dump(exclude_none=True), mode="pandas"
         )
 
 

ngio/utils/_zarr_utils.py

@@ -8,7 +8,7 @@ import fsspec
 import zarr
 from filelock import BaseFileLock, FileLock
 from zarr.errors import ContainsGroupError, GroupNotFoundError
-from zarr.storage import DirectoryStore, FSStore, Store
+from zarr.storage import DirectoryStore, FSStore, MemoryStore, Store, StoreLike
 
 from ngio.utils import NgioFileExistsError, NgioFileNotFoundError, NgioValueError
 from ngio.utils._errors import NgioError
@@ -17,7 +17,9 @@ 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 | FSStore | DirectoryStore
+NgioSupportedStore = (
+    str | Path | fsspec.mapping.FSMap | FSStore | DirectoryStore | MemoryStore
+)
 GenericStore = Store | NgioSupportedStore
 StoreOrGroup = GenericStore | zarr.Group
 
@@ -48,9 +50,7 @@ def _check_group(group: zarr.Group, mode: AccessModeLiteral) -> zarr.Group:
     return group
 
 
-def open_group_wrapper(
-    store: StoreOrGroup, mode: AccessModeLiteral
-) -> tuple[zarr.Group, NgioSupportedStore]:
+def open_group_wrapper(store: StoreOrGroup, mode: AccessModeLiteral) -> zarr.Group:
     """Wrapper around zarr.open_group with some additional checks.
 
     Args:
@@ -62,18 +62,11 @@ def open_group_wrapper(
     """
     if isinstance(store, zarr.Group):
         group = _check_group(store, mode)
-        if hasattr(group, "store_path"):
-            _store = group.store_path
-        if isinstance(group.store, DirectoryStore):
-            _store = group.store.path
-        else:
-            _store = group.store
-
-        _store = _check_store(_store)
-        return group, _store
+        _check_store(group.store)
+        return group
 
     try:
-        store = _check_store(store)
+        _check_store(store)
         group = zarr.open_group(store=store, mode=mode)
 
     except ContainsGroupError as e:
@@ -84,7 +77,7 @@ def open_group_wrapper(
     except GroupNotFoundError as e:
         raise NgioFileNotFoundError(f"No Zarr group found at {store}") from e
 
-    return group, store
+    return group
 
 
 class ZarrGroupHandler:
@@ -119,27 +112,29 @@ class ZarrGroupHandler:
                 "If you want to use the lock mechanism, you should not use the cache."
             )
 
-        _group, _store = open_group_wrapper(store, mode)
+        group = open_group_wrapper(store, mode)
+        _store = group.store
 
         # Make sure the cache is set in the attrs
         # in the same way as the cache in the handler
-        _group.attrs.cache = cache
+        group.attrs.cache = cache
 
         if parallel_safe:
-            if not isinstance(_store, str | Path):
+            if not isinstance(_store, DirectoryStore):
                 raise NgioValueError(
-                    "The store needs to be a path to use the lock mechanism."
+                    "The store needs to be a DirectoryStore to use the lock mechanism. "
+                    f"Instead, got {_store.__class__.__name__}."
                 )
-            self._lock_path = f"{_store}.lock"
+            store_path = Path(_store.path) / group.path
+            self._lock_path = store_path.with_suffix(".lock")
             self._lock = FileLock(self._lock_path, timeout=10)
 
         else:
             self._lock_path = None
             self._lock = None
 
-        self._group = _group
+        self._group = group
         self._mode = mode
-        self._store = _store
         self.use_cache = cache
         self._parallel_safe = parallel_safe
         self._cache = {}
@@ -148,19 +143,23 @@ class ZarrGroupHandler:
     def __repr__(self) -> str:
         """Return a string representation of the handler."""
         return (
-            f"ZarrGroupHandler(full_path={self.full_path}, mode={self.mode}, "
+            f"ZarrGroupHandler(full_url={self.full_url}, mode={self.mode}, "
             f"cache={self.use_cache}"
         )
 
     @property
-    def store(self) -> NgioSupportedStore:
+    def store(self) -> StoreLike:
         """Return the store of the group."""
-        return self._store
+        return self.group.store
 
     @property
-    def full_path(self) -> str:
+    def full_url(self) -> str | None:
         """Return the store path."""
-        return f"{self._store}/{self._group.path}"
+        if isinstance(self.store, DirectoryStore | FSStore):
+            _store_path = str(self.store.path)
+            _store_path = _store_path.rstrip("/")
+            return f"{self.store.path}/{self._group.path}"
+        return None
 
     @property
     def mode(self) -> AccessModeLiteral:
@@ -275,17 +274,25 @@ class ZarrGroupHandler:
         self,
         path: str,
         create_mode: bool = False,
+        overwrite: bool = False,
     ) -> zarr.Group:
         """Get a group from the group.
 
         Args:
             path (str): The path to the group.
             create_mode (bool): If True, create the group if it does not exist.
+            overwrite (bool): If True, overwrite the group if it exists.
 
         Returns:
             zarr.Group: The Zarr group.
 
         """
+        if overwrite and not create_mode:
+            raise NgioValueError("Cannot overwrite a group without create_mode=True.")
+
+        if overwrite:
+            return self.create_group(path, overwrite=overwrite)
+
         group = self._obj_get(path)
         if isinstance(group, zarr.Group):
             return group
@@ -361,9 +368,15 @@ class ZarrGroupHandler:
     def derive_handler(
         self,
         path: str,
+        overwrite: bool = False,
     ) -> "ZarrGroupHandler":
-        """Derive a new handler from the current handler."""
-        group = self.get_group(path, create_mode=True)
+        """Derive a new handler from the current handler.
+
+        Args:
+            path (str): The path to the group.
+            overwrite (bool): If True, overwrite the group if it exists.
+        """
+        group = self.get_group(path, create_mode=True, overwrite=overwrite)
         return ZarrGroupHandler(
             store=group,
             cache=self.use_cache,
@@ -375,10 +388,11 @@ class ZarrGroupHandler:
     def safe_derive_handler(
         self,
         path: str,
+        overwrite: bool = False,
     ) -> tuple[bool, "ZarrGroupHandler | NgioError"]:
         """Derive a new handler from the current handler."""
         try:
-            return True, self.derive_handler(path)
+            return True, self.derive_handler(path, overwrite=overwrite)
         except NgioError as e:
             return False, e
 
@@ -393,7 +407,7 @@ class ZarrGroupHandler:
         )
         if n_skipped > 0:
             raise NgioValueError(
-                f"Error copying group to {handler.full_path}, "
+                f"Error copying group to {handler.full_url}, "
                 f"#{n_skipped} files where skipped."
             )
 

{ngio-0.2.2.dist-info → ngio-0.2.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.2.2
+Version: 0.2.4
 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-0.2.2.dist-info → ngio-0.2.4.dist-info}/RECORD

@@ -5,19 +5,19 @@ ngio/common/_axes_transforms.py,sha256=kWU0M5erNmgWBXdu5LNv-tLW3jqkT00MMYX7cz-ky
 ngio/common/_common_types.py,sha256=OkAYNSNjZkixL1MI-HPBVuXamheFBr862uJ4PvTxmhk,129
 ngio/common/_dimensions.py,sha256=UV2XulWaROb3Y2f4fv27ZkTIu-MoS53U26aDkrv-_lk,3900
 ngio/common/_masking_roi.py,sha256=-o6meGP17iTXEbkO9aGh1VX2drkc2laIcRJvCy_pRRM,4919
-ngio/common/_pyramid.py,sha256=8xTFnrKcldYXSnBqcVtH1E6hzS9_et8NdoPo8zfTCjc,7308
+ngio/common/_pyramid.py,sha256=SJzPauuduuqcm9B7nFCJhMTzIg6Knjsnp4CY4lN61Is,7411
 ngio/common/_roi.py,sha256=dq1iVT8-G_zWuxcYWJeHfviBSbPgsyKUcDL3Vg6jx6I,5122
 ngio/common/_slicer.py,sha256=AKpwXRncOmF9nhjKYma0C_41WqAgSv860beKGx-aw-0,3075
 ngio/common/_zoom.py,sha256=KsURa5VuixmpbAAY5-6obmuQV8vfiHKZqBxZDXvchpM,5473
 ngio/hcs/__init__.py,sha256=5oAYT_454WGhms97kxo8gS4_rKHtFf_x-9uu8M_VeVM,356
-ngio/hcs/plate.py,sha256=Upmq8-1zi0rWtsTVHsZYAma6EwvbgaEF54nHlcL5PBU,26219
+ngio/hcs/plate.py,sha256=zmhHXRsoc4s_-bPccYCH9rqoYg419j-T-NF-OojXRZM,30509
 ngio/images/__init__.py,sha256=DYbXAdBgPxyjBRdJrWvU0UnBRI0gUMmx9KaJ-Bucvz4,533
-ngio/images/abstract_image.py,sha256=oR0CeWUdQJkJ8bbI4kegX3xFIRcR3x5F_yaT4Z-mbag,10226
+ngio/images/abstract_image.py,sha256=8PNQPZjiDz-pcTFXSJAVw7nUr4yL_iRwqDEUTKkAnp0,10266
 ngio/images/create.py,sha256=XYn30m_2OSZeHHASYHc3eK9u_gZIYy9wo6mGdRGaq5c,9473
-ngio/images/image.py,sha256=FSlYvwOk3Fz4ywUZwWcLeCMWLMB4wQ-U0lCGYomVI-o,16108
-ngio/images/label.py,sha256=bmwWuOfZWApjttL_CspiNg-j728ODF1i2zKtKIP_u6k,10120
+ngio/images/image.py,sha256=mKLIR2DGQUWtQbf3my2fh0bEPkbbsabUoge_XJPhfWE,17824
+ngio/images/label.py,sha256=qgbBHFPGYpUR2fHf1OiXZh4sn0FgCeeWwH1F4SrOM1c,10460
 ngio/images/masked_image.py,sha256=IBo8x2jHyXBXn7ORo8fSiwBPjV_1JOTb_vatjKNxbJ0,8531
-ngio/images/ome_zarr_container.py,sha256=mEKOtZtZkJbMG02ne0pRIKtlFoi8B1QV8j9WSXDavRs,28705
+ngio/images/ome_zarr_container.py,sha256=-9bbzNtsVAjU1X_h78Lr5LOV0JXtOiWVWqmt3DFpXus,28927
 ngio/ome_zarr_meta/__init__.py,sha256=oZ8PEsWM7U0KwzpsnvVfX9k4UfuTz5sZ8B6B9eY5hyY,1193
 ngio/ome_zarr_meta/_meta_handlers.py,sha256=BLvYt5PONYrWkEb2XgEiAXR_OX9rfeX_C0eEqen0jQA,25549
 ngio/ome_zarr_meta/ngio_specs/__init__.py,sha256=05NQukZG0nNvjzf8AKWGu7PhjhQcImGSAOK3D3Bg-Js,1786
@@ -31,25 +31,27 @@ ngio/ome_zarr_meta/v04/__init__.py,sha256=dJRzzxyYc81kf-0Hip_bqvbdManaM8XTdQX2me
 ngio/ome_zarr_meta/v04/_custom_models.py,sha256=5GxiDERvLuvq4QvApcA6EiKLS6hLFX1R0R_9rSaa85A,530
 ngio/ome_zarr_meta/v04/_v04_spec_utils.py,sha256=05tEr2eEP_XVIfBMOAWLT7lzJV4KS5eYrpK8l94tn3w,15876
 ngio/tables/__init__.py,sha256=gxvNvAgLePgrngOm06H5qU50Axc6boeIs5iCfrmqTi0,609
-ngio/tables/_validators.py,sha256=RzF09YrlUSb-xdVlosuU-_BaLswtvhpduHfzLaWu2mY,6468
-ngio/tables/tables_container.py,sha256=elOTjpRuC_zsRuZmGeBWfMl2y6OLp2g6FmOe__xLsWE,9845
-ngio/tables/backends/__init__.py,sha256=NlOXmZXDA1kOCVONUyo_aqSjdMHmfqk-3xuKBLXpaUM,217
-ngio/tables/backends/_abstract_backend.py,sha256=JlaHqLjDm2uVnXFWxsHMojNeKo3leg6uauzoFMSF5O4,2256
-ngio/tables/backends/_anndata_utils.py,sha256=zo85K0bwgyQKBj8hQASfOSWugdd4BPUTyT6_tRO58fI,6917
-ngio/tables/backends/_anndata_v1.py,sha256=hhEwoBybWFDHqajOk_JEazniYmhAlCehOYTtmcYJfyY,2615
-ngio/tables/backends/_json_v1.py,sha256=9ZC0d_tMiiugm-VXDL3sRFfESzSnnY9kAtSxoXYV-dY,1910
-ngio/tables/backends/_table_backends.py,sha256=XXtnZqVDbMqFkbUkHbf9IBNz4teCouLpa5fWgEgVtfg,3269
+ngio/tables/_validators.py,sha256=7Eqln9j1tWmNakSCnryy2q39SbTuk6V31O2iMByTWWw,3363
+ngio/tables/tables_container.py,sha256=DFlz_6ts5p0lHkm6NMBtKZget30OicCYHrLbiG4xU1s,10188
+ngio/tables/backends/__init__.py,sha256=Y9MIFefwUaSmhhv5FDZFn7jBdYXDML2FovO-uK-vxgI,936
+ngio/tables/backends/_abstract_backend.py,sha256=--4qeVHs4YRo5i5XsREmDm6BxMsQ5tIqc6XZ810GJno,8776
+ngio/tables/backends/_anndata_utils.py,sha256=DBWIcR0btnH-DIvDvzlcnMXoYhhtXc9DstryiOP0Qsg,3122
+ngio/tables/backends/_anndata_v1.py,sha256=5p_8pWUkYM4rEhm7g-b2yCXt2mmyd6lFisc1ubksAio,2469
+ngio/tables/backends/_csv_v1.py,sha256=o5AGlBH3UQdXx6MP2DtMm7zmXkOwnBBzu5TKk-QgQdI,5847
+ngio/tables/backends/_json_v1.py,sha256=7ALjB2thKTxPBeYOleqn2LNuAy6erp0Nzd-GZ9Xcd4Y,3079
+ngio/tables/backends/_table_backends.py,sha256=NXdH4pxo9XWZ_YxC5RVaw4PTOg-do30c3vlIy8KG4vQ,5831
+ngio/tables/backends/_utils.py,sha256=D0zI8_b6HEBZ2ER-80JvEEh_2-aCC1kpyKJGDPBPHco,14661
 ngio/tables/v1/__init__.py,sha256=XWi6f_KbjbX45Ku-7uymJRSTVWyFAPAAEp_TXDeZV4s,314
-ngio/tables/v1/_feature_table.py,sha256=mR8BwvZfkUT42mQuS0KACW7fTqcsIl6Ckiwg-1UEGpY,5865
-ngio/tables/v1/_generic_table.py,sha256=jVW0vv0HMPXZjuP_uAvz-rPsvLQhjo3RfSa2Y9vdg1o,5679
-ngio/tables/v1/_roi_table.py,sha256=oE898CUh0ZbtnFXiM05T6VwTwRguv-aVYKkBmSx0Kj0,11296
+ngio/tables/v1/_feature_table.py,sha256=2pZEENyZAmn_Awezu8VLGq90d-J7aXd6Ry8gNNR0wAQ,6104
+ngio/tables/v1/_generic_table.py,sha256=O2fu8k_TjhWEZtJxlU3Uj7ZTZnc75vLlvjw5lweSnd8,5710
+ngio/tables/v1/_roi_table.py,sha256=zGoISSC5q0UHyc0hcxfm2xpw2W6wUocoYctdi5nMmwg,11460
 ngio/utils/__init__.py,sha256=r3nuLWgp6-cQlS4ODjYSBrfgdTLkCOVke9jKbn1NpkA,1129
 ngio/utils/_datasets.py,sha256=EdYJHIifpRou4f43dIuiKsdxe4K6FaeS4f1_e_EYrcI,1727
 ngio/utils/_errors.py,sha256=pKQ12LUjQLYE1nUawemA5h7HsgznjaSvV1n2PQU33N0,759
 ngio/utils/_fractal_fsspec_store.py,sha256=7qoGLiLi8JQFh9Ej_z5WNwQQuWrujb0f6p9nj8ocsS8,548
 ngio/utils/_logger.py,sha256=HIuqD_2ShfFGDswBddcouStbKfL0Vz_ah8cAIFGhbS8,888
-ngio/utils/_zarr_utils.py,sha256=r075cNpr-JHZ1PaDHX1KlENIGMvLf-WTTYwpODACWm4,12924
-ngio-0.2.2.dist-info/METADATA,sha256=tYJbuBZdqsie42NofiB0ALq7NhAaFn-ccwLe-QQ-bY0,5170
-ngio-0.2.2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-ngio-0.2.2.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
-ngio-0.2.2.dist-info/RECORD,,
+ngio/utils/_zarr_utils.py,sha256=qOI-HL2HsfFLCj_yxsTR-aq4oHpSqS9KR13aEIvhGDY,13593
+ngio-0.2.4.dist-info/METADATA,sha256=dzoSMNR-uED7qerei4X-ItLMcdn8U-EjUnjuFUl9aEQ,5215
+ngio-0.2.4.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+ngio-0.2.4.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
+ngio-0.2.4.dist-info/RECORD,,