ngio 0.1.2__py3-none-any.whl → 0.1.4__py3-none-any.whl

ngio/core/ngff_image.py

@@ -300,6 +300,8 @@ class NgffImage:
         store: StoreLike,
         name: str,
         overwrite: bool = True,
+        copy_labels: bool = False,
+        copy_tables: bool = False,
         **kwargs: dict,
     ) -> "NgffImage":
         """Derive a new image from the current image.
@@ -308,6 +310,10 @@ class NgffImage:
             store (StoreLike): The store to create the new image in.
             name (str): The name of the new image.
             overwrite (bool): Whether to overwrite the image if it exists
+            copy_labels (bool): Whether to copy the labels from the current image
+                to the new image.
+            copy_tables (bool): Whether to copy the tables from the current image
+                to the new image.
             **kwargs: Additional keyword arguments.
                 Follow the same signature as `create_empty_ome_zarr_image`.
 
@@ -351,4 +357,31 @@ class NgffImage:
         create_empty_ome_zarr_image(
             **default_kwargs,
         )
-        return NgffImage(store=store)
+
+        new_image = NgffImage(store=store)
+
+        if copy_tables:
+            # TODO: to be refactored when the table location is changed in the spec
+            source_tables_group = self.tables._table_group
+
+            if source_tables_group is None:
+                raise ValueError("No tables group found in the source image.")
+
+            zarr.copy(source=source_tables_group, dest=new_image.group)
+
+            # Reopen the image to get the new tables
+            new_image = NgffImage(store=store)
+
+        if copy_labels:
+            # TODO: to be refactored when the label location is changed in the spec
+            source_labels_group = self.labels._label_group
+
+            if source_labels_group is None:
+                raise ValueError("No labels group found in the source image.")
+
+            zarr.copy(source=source_labels_group, dest=new_image.group)
+
+            # Reopen the image to get the new labels
+            new_image = NgffImage(store=store)
+
+        return new_image

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/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-0.1.2.dist-info → ngio-0.1.4.dist-info}/METADATA

@@ -1,11 +1,12 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: ngio
-Version: 0.1.2
+Version: 0.1.4
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/lorenzocerrone/ngio
 Project-URL: repository, https://github.com/lorenzocerrone/ngio
 Author-email: Lorenzo Cerrone <lorenzo.cerrone@uzh.ch>
 License: BSD-3-Clause
+License-File: LICENSE
 Classifier: Development Status :: 3 - Alpha
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Programming Language :: Python :: 3

{ngio-0.1.2.dist-info → ngio-0.1.4.dist-info}/RECORD

@@ -4,7 +4,7 @@ ngio/core/dimensions.py,sha256=AyiXXwgfwe1LiJ7cNhefUVTG2GQqVzDiO0ge_KePf8Q,3722
 ngio/core/image_handler.py,sha256=2eiklMWCSZD9ajZHEwYJHB1WoQE92YTVOy7qslrtSaw,7569
 ngio/core/image_like_handler.py,sha256=_k1xs3Uct_FXKoyUDTfQwG755SmiMGlztGhsQW-OtOA,18821
 ngio/core/label_handler.py,sha256=yBWMQbhme0j4XhXcoWuNY0x3Kt_MH3aYTu6peOfWyTc,14102
-ngio/core/ngff_image.py,sha256=7gTPeU4cr51VTODeYEXAwsgXj8fW5NtWzNoLL5DUbSo,12491
+ngio/core/ngff_image.py,sha256=3C4FE9Q-wtKwLn0Cdy7sCGIvFstgZbRWbUq-pUReOG4,13757
 ngio/core/roi.py,sha256=Vn9aKNxRvJs77ZfVFMAdjOzhy2I2ctpikLcbFP5aj74,2884
 ngio/core/utils.py,sha256=Z3_nI7nLtMZT2gHFgEFtAox6fcENiFuQA5n6UuK2uDo,10170
 ngio/io/__init__.py,sha256=g7KmkgRcVBTZbVkqstl_FldUFzz66R-b__HV9hsLvtc,400
@@ -13,7 +13,7 @@ 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
@@ -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-0.1.2.dist-info/METADATA,sha256=8F1QCxbL9n5L3KJ7CkhDEhd_3WPD16vTN4IEwLRdWyE,5683
-ngio-0.1.2.dist-info/WHEEL,sha256=C2FUgwZgiLbznR-k0b_5k3Ai_1aASOXDss3lzCUsUug,87
-ngio-0.1.2.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
-ngio-0.1.2.dist-info/RECORD,,
+ngio-0.1.4.dist-info/METADATA,sha256=PjRzmV7qfMiHPuUPexCO4rLkoyKeTe6QEFBft8dPEnM,5705
+ngio-0.1.4.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+ngio-0.1.4.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
+ngio-0.1.4.dist-info/RECORD,,

{ngio-0.1.2.dist-info → ngio-0.1.4.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: hatchling 1.26.3
+Generator: hatchling 1.27.0
 Root-Is-Purelib: true
 Tag: py3-none-any