ngio 0.2.3__py3-none-any.whl → 0.2.5__py3-none-any.whl

ngio/hcs/plate.py

@@ -686,6 +686,9 @@ class OmeZarrPlate:
         """List all ROI tables in the image."""
         return self.tables_container.list_roi_tables()
 
+    @overload
+    def get_table(self, name: str) -> Table: ...
+
     @overload
     def get_table(self, name: str, check_type: None) -> Table: ...
 
@@ -708,8 +711,19 @@ class OmeZarrPlate:
     ) -> GenericRoiTable: ...
 
     def get_table(self, name: str, check_type: TypedTable | None = None) -> Table:
-        """Get a table from the image."""
-        table = self.tables_container.get(name)
+        """Get a table from the image.
+
+        Args:
+            name (str): The name of the table.
+            check_type (TypedTable | None): The type of the table. If None, the
+                type is not checked. If a type is provided, the table must be of that
+                type.
+        """
+        if check_type is None:
+            table = self.tables_container.get(name, strict=False)
+            return table
+
+        table = self.tables_container.get(name, strict=True)
         match check_type:
             case "roi_table":
                 if not isinstance(table, RoiTable):
@@ -740,8 +754,6 @@ class OmeZarrPlate:
                         f"Found type: {table.type()}"
                     )
                 return table
-            case None:
-                return table
             case _:
                 raise NgioValueError(f"Unknown check_type: {check_type}")
 

ngio/images/ome_zarr_container.py

@@ -353,6 +353,9 @@ class OmeZarrContainer:
         """List all ROI tables in the image."""
         return self.tables_container.list_roi_tables()
 
+    @overload
+    def get_table(self, name: str) -> Table: ...
+
     @overload
     def get_table(self, name: str, check_type: None) -> Table: ...
 
@@ -375,8 +378,19 @@ class OmeZarrContainer:
     ) -> GenericRoiTable: ...
 
     def get_table(self, name: str, check_type: TypedTable | None = None) -> Table:
-        """Get a table from the image."""
-        table = self.tables_container.get(name)
+        """Get a table from the image.
+
+        Args:
+            name (str): The name of the table.
+            check_type (TypedTable | None): The type of the table. If None, the
+                type is not checked. If a type is provided, the table must be of that
+                type.
+        """
+        if check_type is None:
+            table = self.tables_container.get(name, strict=False)
+            return table
+
+        table = self.tables_container.get(name, strict=True)
         match check_type:
             case "roi_table":
                 if not isinstance(table, RoiTable):
@@ -407,8 +421,6 @@ class OmeZarrContainer:
                         f"Found type: {table.type()}"
                     )
                 return table
-            case None:
-                return table
             case _:
                 raise NgioValueError(f"Unknown check_type: {check_type}")
 

ngio/ome_zarr_meta/ngio_specs/_ngio_hcs.py

@@ -361,6 +361,7 @@ class NgioPlateMeta(HCSAttrs):
             acquisitions=self.plate.acquisitions,
             wells=wells,
             field_count=self.plate.field_count,
+            name=self.plate.name,
             version=self.plate.version,
         )
         return NgioPlateMeta(plate=new_plate), row_idx
@@ -398,6 +399,7 @@ class NgioPlateMeta(HCSAttrs):
             acquisitions=self.plate.acquisitions,
             wells=wells,
             field_count=self.plate.field_count,
+            name=self.plate.name,
             version=self.plate.version,
         )
         return NgioPlateMeta(plate=new_plate), column_idx
@@ -435,6 +437,7 @@ class NgioPlateMeta(HCSAttrs):
             acquisitions=plate.plate.acquisitions,
             wells=wells,
             field_count=plate.plate.field_count,
+            name=plate.plate.name,
             version=plate.plate.version,
         )
         return NgioPlateMeta(plate=new_plate)
@@ -473,6 +476,7 @@ class NgioPlateMeta(HCSAttrs):
             acquisitions=acquisitions,
             wells=self.plate.wells,
             field_count=self.plate.field_count,
+            name=self.plate.name,
             version=self.plate.version,
         )
         return NgioPlateMeta(plate=new_plate)
@@ -508,6 +512,7 @@ class NgioPlateMeta(HCSAttrs):
             acquisitions=self.plate.acquisitions,
             wells=wells,
             field_count=self.plate.field_count,
+            name=self.plate.name,
             version=self.plate.version,
         )
         return NgioPlateMeta(plate=new_plate)

ngio/tables/backends/_utils.py

@@ -53,6 +53,10 @@ def _validate_index_key_df(pandas_df: DataFrame, index_key: str | None) -> DataF
         pandas_df.index.name = index_key
         return pandas_df
 
+    if pandas_df.index.name is None:
+        pandas_df.index.name = index_key
+        return pandas_df
+
     raise NgioTableValidationError(f"Index key '{index_key}' is not found in DataFrame")
 
 

ngio/tables/tables_container.py

@@ -90,6 +90,7 @@ class ImplementedTables:
         version: str,
         handler: ZarrGroupHandler,
         backend_name: str | None = None,
+        strict: bool = True,
     ) -> Table:
         """Try to get a handler for the given store based on the metadata version."""
         _errors = {}
@@ -102,7 +103,12 @@ class ImplementedTables:
                 )
                 return table
             except Exception as e:
-                _errors[name] = e
+                if strict:
+                    raise NgioValidationError(
+                        f"Could not load table {name} from handler. Error: {e}"
+                    ) from e
+                else:
+                    _errors[name] = e
         # If no table was found, we can try to load the table from a generic table
         try:
             table = GenericTable._from_handler(
@@ -207,7 +213,9 @@ class TablesContainer:
                 filtered_tables.append(table_name)
         return filtered_tables
 
-    def get(self, name: str, backend_name: str | None = None) -> Table:
+    def get(
+        self, name: str, backend_name: str | None = None, strict: bool = True
+    ) -> Table:
         """Get a label from the group."""
         if name not in self.list():
             raise KeyError(f"Table '{name}' not found in the group.")
@@ -220,6 +228,7 @@ class TablesContainer:
             version=table_version,
             handler=table_handler,
             backend_name=backend_name,
+            strict=strict,
         )
 
     def add(

ngio/tables/v1/_roi_table.py

@@ -227,13 +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
 

{ngio-0.2.3.dist-info → ngio-0.2.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.2.3
+Version: 0.2.5
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/lorenzocerrone/ngio
 Project-URL: repository, https://github.com/lorenzocerrone/ngio

{ngio-0.2.3.dist-info → ngio-0.2.5.dist-info}/RECORD

@@ -10,21 +10,21 @@ 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=MK-HTuSyxt2dp1CuA9tvSwRc9VWEjDz4Pju-2dxXQf4,30102
+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=8PNQPZjiDz-pcTFXSJAVw7nUr4yL_iRwqDEUTKkAnp0,10266
 ngio/images/create.py,sha256=XYn30m_2OSZeHHASYHc3eK9u_gZIYy9wo6mGdRGaq5c,9473
 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=5tgUd1iq2nQOmWsIZY-kwVR1d5UV4rKlVEXTslDBCno,28520
+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
 ngio/ome_zarr_meta/ngio_specs/_axes.py,sha256=Kqe9T7LWa_9o3UWS5uzALyyNluIhXxWhDGxWY4-GIo8,16707
 ngio/ome_zarr_meta/ngio_specs/_channels.py,sha256=ufZuYuTO5PJA1vcBrNAcuZCMgIEwF57buPloTHIzB1Q,14082
 ngio/ome_zarr_meta/ngio_specs/_dataset.py,sha256=hY8ogPPxvCgVg6k02t3zUr24lasYrvnxBd1iPEigdG4,5892
-ngio/ome_zarr_meta/ngio_specs/_ngio_hcs.py,sha256=VhXfgy87z3xpzIqC4Pz5iwcoh0C47mvRiAhN0vLVSJA,17294
+ngio/ome_zarr_meta/ngio_specs/_ngio_hcs.py,sha256=uh345KQmEQtslIyMmLK9sB-NbjPYxi0Y9FuYIFhd3Rc,17465
 ngio/ome_zarr_meta/ngio_specs/_ngio_image.py,sha256=8E38Mgw-l0Ff1nkmCJIzo64G_paAVhM8xktUS_V5egY,17960
 ngio/ome_zarr_meta/ngio_specs/_pixel_size.py,sha256=5TT8250XdCKUnk3OwZeyXIMNFKOg_jx4NnoCo9RLsXI,4079
 ngio/ome_zarr_meta/v04/__init__.py,sha256=dJRzzxyYc81kf-0Hip_bqvbdManaM8XTdQX2meWyCSs,583
@@ -32,7 +32,7 @@ ngio/ome_zarr_meta/v04/_custom_models.py,sha256=5GxiDERvLuvq4QvApcA6EiKLS6hLFX1R
 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=7Eqln9j1tWmNakSCnryy2q39SbTuk6V31O2iMByTWWw,3363
-ngio/tables/tables_container.py,sha256=Jt9FNjWU9EPbb4L9pKhLIuzDcr_gCkTEoRN5Wt-vOjw,9888
+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
@@ -40,18 +40,18 @@ ngio/tables/backends/_anndata_v1.py,sha256=5p_8pWUkYM4rEhm7g-b2yCXt2mmyd6lFisc1u
 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=Q1Twe-knhg5b5LHKKSiwppT9lhCPE9-NWb6o1boD7ao,14557
+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=2pZEENyZAmn_Awezu8VLGq90d-J7aXd6Ry8gNNR0wAQ,6104
 ngio/tables/v1/_generic_table.py,sha256=O2fu8k_TjhWEZtJxlU3Uj7ZTZnc75vLlvjw5lweSnd8,5710
-ngio/tables/v1/_roi_table.py,sha256=9kVLKzXz2gGrTmPC_sR3Zc6cX5VVROHYEjOJ-0Ol08g,11248
+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=qOI-HL2HsfFLCj_yxsTR-aq4oHpSqS9KR13aEIvhGDY,13593
-ngio-0.2.3.dist-info/METADATA,sha256=8q0VoG887uE9DmawKNHljCbGcXPsqjr4_Tp8nrHAK5A,5215
-ngio-0.2.3.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-ngio-0.2.3.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
-ngio-0.2.3.dist-info/RECORD,,
+ngio-0.2.5.dist-info/METADATA,sha256=CfWGOhGP41xxTqsvNvwDeA4nT2hjeMS6yMJ4xHalXqo,5215
+ngio-0.2.5.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+ngio-0.2.5.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
+ngio-0.2.5.dist-info/RECORD,,