ngio 0.1.3__py3-none-any.whl → 0.1.5__py3-none-any.whl

ngio/ngff_meta/fractal_image_meta.py

@@ -823,9 +823,7 @@ class Dataset:
             raise ValueError("Spatial axes must have a unit.")
         if return_type not in SpaceUnits.allowed_names():
             raise ValueError(f"Invalid space unit {return_type}.")
-        if isinstance(return_type, str):
-            return_type = SpaceUnits(return_type)
-        return return_type
+        return SpaceUnits(return_type)
 
     @property
     def pixel_size(self) -> PixelSize:
@@ -850,8 +848,7 @@ class Dataset:
         if len(types) == 0:
             return None
         elif len(types) == 1:
-            assert isinstance(types[0], TimeUnits)
-            return types[0]
+            return TimeUnits(types[0])
         else:
             raise ValueError("Multiple time axes found. Only one time axis is allowed.")
 

ngio/ngff_meta/v04/zarr_utils.py

@@ -110,7 +110,13 @@ def vanilla_omero_v04_to_fractal(omero04: Omero04) -> Omero:
     for channel04 in omero04.channels:
         # Convert the window to a dictionary
         label = channel04.label
-        wavelength_id = channel04.extra_fields.get("wavelength_id", label)
+
+        if "wavelength_id" in channel04.extra_fields:
+            # If the wavelength_id is present, pop it from the extra fields
+            # so that it is not added to the channel_visualisation
+            wavelength_id = channel04.extra_fields.pop("wavelength_id")
+        else:
+            wavelength_id = label
 
         if channel04.window is None:
             window04 = Window04(
@@ -161,6 +167,7 @@ def fractal_omero_to_vanilla_v04(omero: Omero) -> Omero04:
             color=channel.channel_visualisation.color,
             active=channel.channel_visualisation.active,
             window=window04,
+            wavelength_id=channel.wavelength_id,
             **channel.channel_visualisation.extra_fields,
         )
         list_channels04.append(channel04)

ngio/tables/tables_group.py

@@ -156,14 +156,17 @@ class TableGroup:
 
         list_of_tables = self._get_list_of_tables()
         self._validate_list_of_tables(list_of_tables=list_of_tables)
+
+        all_table_types = ["roi_table", "feature_table", "masking_roi_table"]
+
         if table_type is None:
             return list_of_tables
 
         else:
-            if table_type not in ["roi_table", "feature_table", "masking_roi_table"]:
+            if table_type not in all_table_types:
                 raise ValueError(
                     f"Table type {table_type} not recognized. "
-                    " Allowed values are: 'roi', 'feature', 'masking_roi'."
+                    f" Allowed values are: {all_table_types}"
                 )
             list_of_typed_tables = []
             for table_name in list_of_tables:

{ngio-0.1.3.dist-info → ngio-0.1.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.1.3
+Version: 0.1.5
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/lorenzocerrone/ngio
 Project-URL: repository, https://github.com/lorenzocerrone/ngio

{ngio-0.1.3.dist-info → ngio-0.1.5.dist-info}/RECORD

@@ -13,12 +13,12 @@ ngio/io/_zarr_array_utils.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,
 ngio/io/_zarr_group_utils.py,sha256=-cqgxQBvSqPhy5m7iXADOCji3IiEmCgc7zOLeJW5fYw,1754
 ngio/iterators/__init__.py,sha256=-jQ5h6oNftLKtiHDru8nPOrR3x8H1rMo85hzvqkhxmw,29
 ngio/ngff_meta/__init__.py,sha256=HhtHzjjk55gaHYbjiHoHRyYmOs1QZgBdWeCBb7O19Vo,560
-ngio/ngff_meta/fractal_image_meta.py,sha256=VfRBEhj1PrxF5OReiKhXhO1BAnA5NUGHyY_xZvIHwNw,43472
+ngio/ngff_meta/fractal_image_meta.py,sha256=yc97iEGj5VjaCWv0Md94b5I2p9qzx94DMu_HlyKmrmg,43353
 ngio/ngff_meta/meta_handler.py,sha256=YDqOl-UUzE-flqC2EXGbJc-ctqZsULsZzA0Xj6X7XkM,2588
 ngio/ngff_meta/utils.py,sha256=eZSlm1-XJAGiThSol8RW7a_61Crj91f9vXbBGssWnhk,7978
 ngio/ngff_meta/v04/__init__.py,sha256=zlIL9-R3fNT_mgrOxE51dGyhnJlZ1UX0uRNeEl8WuRM,239
 ngio/ngff_meta/v04/specs.py,sha256=cjdMlL8L8Sbk-cGq5J3-wgOxQ9zr3r3u2q09fDI11kM,4256
-ngio/ngff_meta/v04/zarr_utils.py,sha256=ZCheqDpuaRqxlJCn3Q6igszbvw3X_Nr4qAp-RA-NaT0,11567
+ngio/ngff_meta/v04/zarr_utils.py,sha256=02ISrsAGIXB1iLfcXPpqDljDlp0vC8Y_MyL5c016FY8,11859
 ngio/pipes/__init__.py,sha256=Ypt9bCqrk0qSg81GTBNqH5oljMg2rQPwyOWVZRKzaYg,299
 ngio/pipes/_slicer_transforms.py,sha256=UyN_aeAg-mtO9wsbqcvUIvnV5PJFTbj8AUmegMsF05k,5812
 ngio/pipes/_transforms.py,sha256=S7PqIwyf10i1cjQ-lKcJLr7YLfW2zKJKGf6DKKP3bTA,1067
@@ -27,7 +27,7 @@ ngio/pipes/data_pipe.py,sha256=SBe-3kTgbHyvFC2lVYyVZj12JazmHCx9QaTDZW1PNxU,1907
 ngio/tables/__init__.py,sha256=kedgmeeFVxBAJACoZ1yxfoyTmlmI1HCBWFhgyprbNWI,260
 ngio/tables/_ad_reader.py,sha256=OQJ3ZwS0wMedlSjz-wQuovIDBojnHRk2Qhq6FL29248,2677
 ngio/tables/_utils.py,sha256=GFOROQUubpYiZMSJ1tdqUWZGBcXAXGdf18iK2_oj8-0,10236
-ngio/tables/tables_group.py,sha256=idcdCAT517ZzoGG6fwRc-yLfBjsfAGXDwg9m-bSdWqM,8603
+ngio/tables/tables_group.py,sha256=DFSDVQz6dYdvI00sKXEeDG7FOX1vAWXiHDDVwEfxL9I,8633
 ngio/tables/v1/__init__.py,sha256=vwJwo3lSpp6feGcwbn6lWivD1MJ_A8Py7WFsL40xUs0,308
 ngio/tables/v1/_generic_table.py,sha256=sW9fIyfZZt7QJclFzgWrMFSnCk7gKTP5Kj2atIKi6oA,6084
 ngio/tables/v1/feature_tables.py,sha256=piC6_eOGOt9IyzXWYqHlR09v0z9Ywm1o8gsdEAsEWts,5892
@@ -38,7 +38,7 @@ ngio/utils/_common_types.py,sha256=ylo6RfCyKVyXPx1Mz7WAwFfz8F85R9yd2_TPlRGRUyo,1
 ngio/utils/_errors.py,sha256=rLy9LOFkaEmsSD0-nToKUrXY1ZuPfcpcGpmeHVSnTNg,583
 ngio/utils/_logger.py,sha256=zvFG-Ta3ZIJxTyY93zYoPGp2A6TTUf7mSO0zr_uFy4A,837
 ngio/utils/_pydantic_utils.py,sha256=uN5-76cjE3bvV8GvLX62fpxoRi8GOsZu6K5aynGH1bY,1711
-ngio-0.1.3.dist-info/METADATA,sha256=H75ePMg5vNzlZ2KGAmblELVRXevDwxOqMDwgJaIZpxU,5705
-ngio-0.1.3.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-ngio-0.1.3.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
-ngio-0.1.3.dist-info/RECORD,,
+ngio-0.1.5.dist-info/METADATA,sha256=foHqb5q_WPlk8-fJ2fnwBcirrAY_rbcT0NYPATqy7us,5705
+ngio-0.1.5.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+ngio-0.1.5.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
+ngio-0.1.5.dist-info/RECORD,,