ngio 0.2.3__tar.gz → 0.2.5__tar.gz

{ngio-0.2.3 → ngio-0.2.5}/PKG-INFO

@@ -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 → ngio-0.2.5}/src/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-0.2.3 → ngio-0.2.5}/src/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-0.2.3 → ngio-0.2.5}/src/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-0.2.3 → ngio-0.2.5}/src/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-0.2.3 → ngio-0.2.5}/src/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-0.2.3 → ngio-0.2.5}/src/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 → ngio-0.2.5}/tests/unit/hcs/test_plate.py

@@ -61,6 +61,8 @@ def test_create_and_edit_plate(tmp_path: Path):
     test_plate.add_image(row="B", column="03", image_path="0", acquisition_id=0)
     test_plate.add_image(row="B", column="03", image_path="1", acquisition_id=0)
 
+    assert test_plate.meta.plate.name == "test_plate"
+
     with pytest.raises(NgioValueError):
         test_plate.add_image(row="B", column="03", image_path="1", acquisition_id=1)
 
@@ -106,6 +108,7 @@ def test_add_well(tmp_path: Path):
     assert test_plate.rows == ["B"]
     assert test_plate.acquisition_ids == []
     assert test_plate.wells_paths() == ["B/03"]
+    assert test_plate.meta.plate.name == "test_plate"
 
     test_plate.add_column("04")
     test_plate.add_row("C")

{ngio-0.2.3 → ngio-0.2.5}/tests/unit/tables/test_backends_utils.py

@@ -118,6 +118,17 @@ def test_normalize_pandas_df(in_df, out_df, index_key, index_type, reset_index):
     )
 
 
+def test_normalize_pandas_df_index_none():
+    """Test the normalization of a pandas DataFrame."""
+    df = normalize_pandas_df(
+        sample_pandas_df_no_index(),
+        index_key="new_index_name",
+        index_type="str",
+        reset_index=False,
+    )
+    assert df.index.name == "new_index_name"
+
+
 def test_fail_normalize_pandas_df():
     """Test the normalization of a pandas DataFrame."""
     with pytest.raises(NgioTableValidationError):
@@ -130,7 +141,7 @@ def test_fail_normalize_pandas_df():
 
     with pytest.raises(NgioTableValidationError):
         normalize_pandas_df(
-            sample_pandas_df_no_index(),
+            sample_pandas_df_str_index(),
             index_key="not_exist",
             index_type="str",
             reset_index=False,

{ngio-0.2.3 → ngio-0.2.5}/tests/unit/tables/test_roi_table_v1.py

@@ -1,10 +1,13 @@
 from pathlib import Path
 
+import pandas as pd
 import pytest
 
+from ngio.tables import RoiTable
+from ngio.tables.backends._anndata_v1 import AnnDataBackend
 from ngio.tables.tables_container import open_table, write_table
-from ngio.tables.v1._roi_table import Roi, RoiTableV1
-from ngio.utils import NgioValueError
+from ngio.tables.v1._roi_table import Roi, RoiTableV1, RoiTableV1Meta
+from ngio.utils import NgioValueError, ZarrGroupHandler
 
 
 def test_roi_table_v1(tmp_path: Path):
@@ -38,6 +41,7 @@ def test_roi_table_v1(tmp_path: Path):
     )
 
     with pytest.raises(NgioValueError):
+        # ROI name already exists
         table.add(
             roi=Roi(
                 name="roi2",
@@ -51,6 +55,20 @@ def test_roi_table_v1(tmp_path: Path):
             )
         )
 
+    table.add(
+        roi=Roi(
+            name="roi2",
+            x=0.0,
+            y=0.0,
+            z=0.0,
+            x_length=1.0,
+            y_length=1.0,
+            z_length=1.0,
+            unit="micrometer",  # type: ignore
+        ),
+        overwrite=True,
+    )
+
     write_table(store=tmp_path / "roi_table.zarr", table=table, backend="anndata_v1")
 
     loaded_table = open_table(store=tmp_path / "roi_table.zarr")
@@ -66,3 +84,32 @@ def test_roi_table_v1(tmp_path: Path):
     assert loaded_table._meta.backend == "anndata_v1"
     assert loaded_table._meta.fractal_table_version == loaded_table.version()
     assert loaded_table._meta.type == loaded_table.type()
+
+
+def test_roi_no_index(tmp_path: Path):
+    """ngio needs to support reading a table without an index. for legacy reasons"""
+    handler = ZarrGroupHandler(tmp_path / "roi_table.zarr")
+    backend = AnnDataBackend(
+        group_handler=handler,
+    )
+
+    roi_table = pd.DataFrame(
+        {
+            "x_micrometer": [0.0, 1.0],
+            "y_micrometer": [0.0, 1.0],
+            "z_micrometer": [0.0, 1.0],
+            "len_x_micrometer": [1.0, 1.0],
+            "len_y_micrometer": [1.0, 1.0],
+            "len_z_micrometer": [1.0, 1.0],
+        }
+    )
+    roi_table.index = pd.Index(["roi_1", "roi_2"])
+
+    backend.write(
+        roi_table,
+        metadata=RoiTableV1Meta().model_dump(exclude_none=True),
+    )
+
+    roi_table = RoiTable._from_handler(handler=handler)
+    assert isinstance(roi_table, RoiTable)
+    assert len(roi_table.rois()) == 2