ngio 0.5.0b2__py3-none-any.whl → 0.5.0b3__py3-none-any.whl

ngio/common/_pyramid.py

@@ -273,6 +273,10 @@ class PyramidLevel(BaseModel):
                     "Shards must have the same length as shape "
                     f"({len(self.shape)}), got {len(self.shards)}"
                 )
+            normalized_shards = []
+            for dim_size, shard_size in zip(self.shape, self.shards, strict=True):
+                normalized_shards.append(min(dim_size, shard_size))
+            self.shards = tuple(normalized_shards)
         return self
 
 

ngio/images/_abstract_image.py

@@ -800,7 +800,7 @@ def abstract_derive(
     channels_meta: Sequence[str | Channel] | None = None,
     ngff_version: NgffVersions | None = None,
     # Zarr Array parameters
-    chunks: ChunksLike = "auto",
+    chunks: ChunksLike | None = None,
     shards: ShardsLike | None = None,
     dtype: str | None = None,
     dimension_separator: Literal[".", "/"] | None = None,
@@ -835,7 +835,7 @@ def abstract_derive(
         channels_meta (Sequence[str | Channel] | None): The channels metadata
             of the new image.
         ngff_version (NgffVersions | None): The NGFF version to use.
-        chunks (Sequence[int] | None): The chunk shape of the new image.
+        chunks (ChunksLike | None): The chunk shape of the new image.
         shards (ShardsLike | None): The shard shape of the new image.
         dtype (str | None): The data type of the new image.
         dimension_separator (DIMENSION_SEPARATOR | None): The separator to use for
@@ -918,7 +918,7 @@ def abstract_derive(
 
     if chunks is None:
         chunks = ref_image.zarr_array.chunks
-
+    print(chunks)
     if shards is None:
         shards = ref_image.zarr_array.shards
 

ngio/images/_image.py

@@ -613,9 +613,10 @@ class ImagesContainer:
         time_spacing: float | None = None,
         name: str | None = None,
         channels_meta: Sequence[str | Channel] | None = None,
+        channels_policy: Literal["same", "squeeze", "singleton"] | int = "same",
         ngff_version: NgffVersions | None = None,
         # Zarr Array parameters
-        chunks: ChunksLike = "auto",
+        chunks: ChunksLike | None = None,
         shards: ShardsLike | None = None,
         dtype: str = "uint16",
         dimension_separator: Literal[".", "/"] = "/",
@@ -644,8 +645,15 @@ class ImagesContainer:
             name (str | None): The name of the new image.
             channels_meta (Sequence[str | Channel] | None): The channels metadata
                 of the new image.
+            channels_policy (Literal["same", "squeeze", "singleton"] | int):
+                Possible policies:
+                - If "squeeze", the channels axis will be removed (no matter its size).
+                - If "same", the channels axis will be kept as is (if it exists).
+                - If "singleton", the channels axis will be set to size 1.
+                - If an integer is provided, the channels axis will be changed to have
+                    that size.
             ngff_version (NgffVersions | None): The NGFF version to use.
-            chunks (Sequence[int] | None): The chunk shape of the new image.
+            chunks (ChunksLike | None): The chunk shape of the new image.
             shards (ShardsLike | None): The shard shape of the new image.
             dtype (str | None): The data type of the new image.
             dimension_separator (DIMENSION_SEPARATOR | None): The separator to use for
@@ -674,6 +682,7 @@ class ImagesContainer:
             time_spacing=time_spacing,
             name=name,
             channels_meta=channels_meta,
+            channels_policy=channels_policy,
             ngff_version=ngff_version,
             chunks=chunks,
             shards=shards,
@@ -769,7 +778,7 @@ def derive_image_container(
     channels_meta: Sequence[str | Channel] | None = None,
     ngff_version: NgffVersions | None = None,
     # Zarr Array parameters
-    chunks: ChunksLike = "auto",
+    chunks: ChunksLike | None = None,
     shards: ShardsLike | None = None,
     dtype: str | None = None,
     dimension_separator: Literal[".", "/"] | None = None,
@@ -804,7 +813,7 @@ def derive_image_container(
         channels_meta (Sequence[str | Channel] | None): The channels metadata
             of the new image.
         ngff_version (NgffVersions | None): The NGFF version to use.
-        chunks (ChunksLike): The chunk shape of the new image. Defaults to "auto".
+        chunks (ChunksLike | None): The chunk shape of the new image.
         shards (ShardsLike | None): The shard shape of the new image.
         dtype (str | None): The data type of the new image.
         dimension_separator (Literal[".", "/"] | None): The separator to use for

ngio/images/_label.py

@@ -219,7 +219,7 @@ class LabelsContainer:
         channels_policy: Literal["same", "squeeze", "singleton"] | int = "squeeze",
         ngff_version: NgffVersions | None = None,
         # Zarr Array parameters
-        chunks: ChunksLike = "auto",
+        chunks: ChunksLike | None = None,
         shards: ShardsLike | None = None,
         dtype: str | None = None,
         dimension_separator: Literal[".", "/"] | None = None,
@@ -256,7 +256,7 @@ class LabelsContainer:
                 - If an integer is provided, the channels axis will be changed to have
                     that size.
             ngff_version (NgffVersions | None): The NGFF version to use.
-            chunks (Sequence[int] | None): The chunk shape of the new image.
+            chunks (ChunksLike | None): The chunk shape of the new image.
             shards (ShardsLike | None): The shard shape of the new image.
             dtype (str | None): The data type of the new image.
             dimension_separator (DIMENSION_SEPARATOR | None): The separator to use for
@@ -328,7 +328,7 @@ def derive_label(
     channels_policy: Literal["same", "squeeze", "singleton"] | int = "squeeze",
     ngff_version: NgffVersions | None = None,
     # Zarr Array parameters
-    chunks: ChunksLike = "auto",
+    chunks: ChunksLike | None = None,
     shards: ShardsLike | None = None,
     dtype: str | None = None,
     dimension_separator: Literal[".", "/"] | None = None,
@@ -359,7 +359,7 @@ def derive_label(
             - If an integer is provided, the channels axis will be changed to have that
                 size.
         ngff_version (NgffVersions | None): The NGFF version to use.
-        chunks (ChunksLike): The chunk shape of the new label. Defaults to "auto".
+        chunks (ChunksLike | None): The chunk shape of the new label.
         shards (ShardsLike | None): The shard shape of the new label.
         dtype (str | None): The data type of the new label.
         dimension_separator (Literal[".", "/"] | None): The separator to use for

ngio/images/_ome_zarr_container.py

@@ -434,7 +434,7 @@ class OmeZarrContainer:
         channels_meta: Sequence[str | Channel] | None = None,
         ngff_version: NgffVersions | None = None,
         # Zarr Array parameters
-        chunks: ChunksLike = "auto",
+        chunks: ChunksLike | None = None,
         shards: ShardsLike | None = None,
         dtype: str = "uint16",
         dimension_separator: Literal[".", "/"] = "/",
@@ -471,7 +471,7 @@ class OmeZarrContainer:
             channels_meta (Sequence[str | Channel] | None): The channels metadata
                 of the new image.
             ngff_version (NgffVersions | None): The NGFF version to use.
-            chunks (ChunksLike): The chunk shape of the new image. Defaults to "auto".
+            chunks (ChunksLike | None): The chunk shape of the new image.
             shards (ShardsLike | None): The shard shape of the new image.
             dtype (str): The data type of the new image. Defaults to "uint16".
             dimension_separator (Literal[".", "/"]): The separator to use for
@@ -503,6 +503,7 @@ class OmeZarrContainer:
             time_spacing=time_spacing,
             name=name,
             channels_meta=channels_meta,
+            channels_policy=channels_policy,
             ngff_version=ngff_version,
             chunks=chunks,
             shards=shards,
@@ -789,7 +790,7 @@ class OmeZarrContainer:
         channels_policy: Literal["same", "squeeze", "singleton"] | int = "squeeze",
         ngff_version: NgffVersions | None = None,
         # Zarr Array parameters
-        chunks: ChunksLike = "auto",
+        chunks: ChunksLike | None = None,
         shards: ShardsLike | None = None,
         dtype: str | None = None,
         dimension_separator: Literal[".", "/"] | None = None,
@@ -821,7 +822,7 @@ class OmeZarrContainer:
                     that size.
                 Defaults to "squeeze".
             ngff_version (NgffVersions | None): The NGFF version to use.
-            chunks (ChunksLike): The chunk shape of the new label. Defaults to "auto".
+            chunks (ChunksLike | None): The chunk shape of the new label.
             shards (ShardsLike | None): The shard shape of the new label.
             dtype (str | None): The data type of the new label.
             dimension_separator (Literal[".", "/"] | None): The separator to use for

{ngio-0.5.0b2.dist-info → ngio-0.5.0b3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.5.0b2
+Version: 0.5.0b3
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/BioVisionCenter/ngio
 Project-URL: repository, https://github.com/BioVisionCenter/ngio
@@ -42,6 +42,7 @@ Requires-Dist: pyqt5; extra == 'dev'
 Requires-Dist: rich; extra == 'dev'
 Requires-Dist: ruff; extra == 'dev'
 Requires-Dist: scikit-image; extra == 'dev'
+Requires-Dist: zarrs; extra == 'dev'
 Provides-Extra: docs
 Requires-Dist: griffe-typingdoc; extra == 'docs'
 Requires-Dist: markdown-exec[ansi]; extra == 'docs'

{ngio-0.5.0b2.dist-info → ngio-0.5.0b3.dist-info}/RECORD

@@ -2,7 +2,7 @@ ngio/__init__.py,sha256=kyInohhWrBs4qkbMYFIQeAiy1CDpvbSOtXB4buFocbw,1535
 ngio/common/__init__.py,sha256=F3zAHQIhwig1xUA-SpmFVRtMeOrEj926-nHWhj-wS6c,684
 ngio/common/_dimensions.py,sha256=w8PYgyWxA8hgJETjFbw5CXf7WrasCL5FbzgfL1in86M,11361
 ngio/common/_masking_roi.py,sha256=YSEZ5nv3-TqMrQ04cI70U9NGx3LSy7Z1_cbw_NE-78k,4831
-ngio/common/_pyramid.py,sha256=vPlxHUWBmfw6BtRoZeA7YNu3ft1YdAzyW1tWG8gA_to,14117
+ngio/common/_pyramid.py,sha256=JRqVm9eFyxHi1a2hCcAoTJU3L8vctRHbkVWkskyQG_U,14354
 ngio/common/_roi.py,sha256=UMr7ie7dIZ6gMcM0_AlFMev_PRKxBdzUy_1WKRZ4zQU,11403
 ngio/common/_synt_images_utils.py,sha256=B6uYOW1NyrM06YMR-csca3_YnAAkPRTbvnbLdy9tk9E,3188
 ngio/common/_zoom.py,sha256=U01c-vqXjzZkrpd9Yvs24frVfTls_xPJeeaFCGmUwYI,6727
@@ -17,13 +17,13 @@ ngio/experimental/iterators/_segmentation.py,sha256=xzotGvTn04HPeMeXZ_URnQqWco6d
 ngio/hcs/__init__.py,sha256=G8j9vD-liLeB_UeGtKYIgshWvJnUA6ks9GwjvWBLdHs,357
 ngio/hcs/_plate.py,sha256=l2a2ZMniutxRzZ88HOYwajug-svr6OanREG5mTy39x0,45773
 ngio/images/__init__.py,sha256=9Whvt7GTiCgT_vXaEEqGnDaY1-UsRk3dhLTv091F_g4,1211
-ngio/images/_abstract_image.py,sha256=PyginvViqjKNsnUBF8yX7pUI2fHDJq4QthjeQzJWzDU,31906
+ngio/images/_abstract_image.py,sha256=gvOS7Nb52pgLgtBpvu3vYxwbSocqw2w-sEsJaJVrHWE,31925
 ngio/images/_create_synt_container.py,sha256=Cvg_J0KSxK0PH8IBzlKLIcCwH2vRTuBj-nZo5uOKXXk,5182
 ngio/images/_create_utils.py,sha256=hXVbFM8D_0mZTfBAhcZiuGX2lLXSJCep8THuxpH4d4E,14374
-ngio/images/_image.py,sha256=TiKQXnzm0Mhxx6zmS4CVThcIJLV_guwjbVx7ZOd_0IU,34197
-ngio/images/_label.py,sha256=MYmYIikKyf2nDqrFd8xZ3nYR-JKe-JneUNuE1jEPHdA,15682
+ngio/images/_image.py,sha256=A2dE9O3L1dLU3gdjQrNCFUYDF_NuxTxVm8klmBfmPCc,34792
+ngio/images/_label.py,sha256=0dqLKBVibqw6scSTWxzSyxjnXLs-fhBGQzol8C5Rzok,15676
 ngio/images/_masked_image.py,sha256=YhbBzgPZMav6rX0WYue1BaxAzEIsfaQrxUIOK6ZWZcw,18848
-ngio/images/_ome_zarr_container.py,sha256=aa8l8wfZ8p0YpsdBd8ixvrdgVcdZs6RnSOpUWPE1ixU,48247
+ngio/images/_ome_zarr_container.py,sha256=mD1PEos33EfapkUVMJnSZdQiQI57cZa_bB2hdEEJQuM,48276
 ngio/images/_table_ops.py,sha256=jFv_AMqoB4JBpoWsMtZppZVW7dAOC_u-JpfNm8b33kY,15292
 ngio/io_pipes/__init__.py,sha256=arW_7GWzZs82kPNKdm_6B1sIDFV0lWwp-ZaORr9Q1FQ,2412
 ngio/io_pipes/_io_pipes.py,sha256=l85mmjj1l0uYU3qzsSHg9l8cMIEevInm_MTD-8MlXgw,10603
@@ -82,7 +82,7 @@ ngio/utils/_datasets.py,sha256=6GtxfPkjutNaeg5BHuJDBP0GudvQXHLU6mmHp_o0bGA,5650
 ngio/utils/_errors.py,sha256=pKQ12LUjQLYE1nUawemA5h7HsgznjaSvV1n2PQU33N0,759
 ngio/utils/_fractal_fsspec_store.py,sha256=RdcCFOgHexRKX9zZvJV5RI-5OPc7VOPS6q_IeRxm24I,1548
 ngio/utils/_zarr_utils.py,sha256=MVbW-a0S3iuzMaknqkliJa_lp8i6mEO4Q2YN2XxmeDw,18158
-ngio-0.5.0b2.dist-info/METADATA,sha256=r1un40xipjI7Kctjt0Gj9-B28PjO5pBSPWxOyoQjXCc,6294
-ngio-0.5.0b2.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
-ngio-0.5.0b2.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
-ngio-0.5.0b2.dist-info/RECORD,,
+ngio-0.5.0b3.dist-info/METADATA,sha256=cTOSheYJVPvHvY-3CTTSxPXudzxMzGbN98tkvpFBzbs,6331
+ngio-0.5.0b3.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+ngio-0.5.0b3.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
+ngio-0.5.0b3.dist-info/RECORD,,