ngio 0.4.4__py3-none-any.whl → 0.4.6__py3-none-any.whl

ngio/common/_pyramid.py

@@ -2,6 +2,7 @@ import math
 from collections.abc import Callable, Sequence
 from typing import Literal
 
+import dask
 import dask.array as da
 import numpy as np
 import zarr
@@ -36,9 +37,17 @@ def _on_disk_dask_zoom(
 ) -> None:
     source_array = da.from_zarr(source)
     target_array = dask_zoom(source_array, target_shape=target.shape, order=order)
-
+    # This is a potential fix for Dask 2025.11
+    # chunk_size_bytes = np.prod(target.chunks) * target_array.dtype.itemsize
+    # current_chunk_size = dask.config.get("array.chunk-size", 0)
+    #
+    #if current_chunk_size < chunk_size_bytes:
+    #    # Increase the chunk size to avoid dask potentially creating 
+    #    # corrupted chunks when writing chunks that are not multiple of the
+    #    # target chunk size
+    #    dask.config.set({"array.chunk-size": f"{chunk_size_bytes}B"})
     target_array = target_array.rechunk(target.chunks)
-    target_array.compute_chunk_sizes()
+    target_array = target_array.compute_chunk_sizes()
     target_array.to_zarr(target)
 
 
@@ -241,13 +250,11 @@ def init_empty_pyramid(
             compressor=compressor,
         )
 
-        _shape = [
+        ref_shape = [
             math.floor(s / sc) for s, sc in zip(ref_shape, scaling_factors, strict=True)
         ]
-        ref_shape = _shape
+        chunks = tuple(
+            min(c, s) for c, s in zip(new_arr.chunks, ref_shape, strict=True)
+        )
 
-        if chunks is None:
-            chunks = new_arr.chunks
-            assert chunks is not None
-        chunks = [min(c, s) for c, s in zip(chunks, ref_shape, strict=True)]
     return None

ngio/images/_image.py

@@ -875,7 +875,7 @@ def _parse_str_or_model(
             )
         elif channel_selection.mode == "wavelength_id":
             return image.get_channel_idx(
-                channel_label=str(channel_selection.identifier)
+                wavelength_id=str(channel_selection.identifier)
             )
         elif channel_selection.mode == "index":
             return int(channel_selection.identifier)

ngio/tables/_tables_container.py

@@ -359,7 +359,7 @@ ImplementedTables().add_implementation(ConditionTableV1)
 def open_tables_container(
     store: StoreOrGroup,
     cache: bool = False,
-    mode: AccessModeLiteral = "a",
+    mode: AccessModeLiteral = "r+",
     parallel_safe: bool = False,
 ) -> TablesContainer:
     """Open a table handler from a Zarr store."""
@@ -373,7 +373,7 @@ def open_table(
     store: StoreOrGroup,
     backend: TableBackend | None = None,
     cache: bool = False,
-    mode: AccessModeLiteral = "a",
+    mode: AccessModeLiteral = "r+",
     parallel_safe: bool = False,
 ) -> Table:
     """Open a table from a Zarr store."""
@@ -391,7 +391,7 @@ def open_table_as(
     table_cls: type[TableType],
     backend: TableBackend | None = None,
     cache: bool = False,
-    mode: AccessModeLiteral = "a",
+    mode: AccessModeLiteral = "r+",
     parallel_safe: bool = False,
 ) -> TableType:
     """Open a table from a Zarr store as a specific type."""

ngio/tables/v1/_roi_table.py

@@ -86,10 +86,10 @@ def _dataframe_to_rois(
 ) -> dict[str, Roi]:
     """Convert a DataFrame to a WorldCooROI object."""
     # Validate the columns of the DataFrame
-    _required_columns = set(dataframe.columns).intersection(set(required_columns))
-    if len(_required_columns) != len(required_columns):
+    _missing_columns = set(required_columns).difference(set(dataframe.columns))
+    if len(_missing_columns) != 0:
         raise NgioTableValidationError(
-            f"Could not find required columns: {_required_columns} in the table."
+            f"Could not find required columns: {_missing_columns} in the table."
         )
 
     extra_columns = set(dataframe.columns).difference(

{ngio-0.4.4.dist-info → ngio-0.4.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.4.4
+Version: 0.4.6
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/BioVisionCenter/ngio
 Project-URL: repository, https://github.com/BioVisionCenter/ngio
@@ -17,8 +17,8 @@ Classifier: Typing :: Typed
 Requires-Python: <3.14,>=3.11
 Requires-Dist: aiohttp
 Requires-Dist: anndata<0.11.4,>=0.8.0
-Requires-Dist: dask[array]
-Requires-Dist: dask[distributed]
+Requires-Dist: dask[array]<2025.11.0
+Requires-Dist: dask[distributed]<2025.11.0
 Requires-Dist: filelock
 Requires-Dist: numpy
 Requires-Dist: ome-zarr-models

{ngio-0.4.4.dist-info → ngio-0.4.6.dist-info}/RECORD

@@ -2,7 +2,7 @@ ngio/__init__.py,sha256=rEgnXuU6TCejUUGsxt4eKmjMhxjYh0fYBxWF4o5YjbE,1435
 ngio/common/__init__.py,sha256=aPSuUbdGryrxbnlWrsVNe3LZoBAWC4GijR1BNH1UwuU,612
 ngio/common/_dimensions.py,sha256=w8PYgyWxA8hgJETjFbw5CXf7WrasCL5FbzgfL1in86M,11361
 ngio/common/_masking_roi.py,sha256=ZZTXordEZoq_ADk0OzADvq-5dPOwUBSuNobzFR8fpTw,5697
-ngio/common/_pyramid.py,sha256=F5OI_mULxzMTpMeihC4Y22cjuB5GKN2jRdpwfMXJHiE,8018
+ngio/common/_pyramid.py,sha256=Wxj8RXSWWEPm5ILqvga484Hd2j3IQ4tGzHZsL5WSOuo,8446
 ngio/common/_roi.py,sha256=9fKFTHoUiP0xmxvQiFkNmIuwWg3bFuRaAx-froCSqvA,11487
 ngio/common/_synt_images_utils.py,sha256=B6uYOW1NyrM06YMR-csca3_YnAAkPRTbvnbLdy9tk9E,3188
 ngio/common/_zoom.py,sha256=U01c-vqXjzZkrpd9Yvs24frVfTls_xPJeeaFCGmUwYI,6727
@@ -20,7 +20,7 @@ ngio/images/__init__.py,sha256=9Whvt7GTiCgT_vXaEEqGnDaY1-UsRk3dhLTv091F_g4,1211
 ngio/images/_abstract_image.py,sha256=hrB9xn4MFRxnxE1d7HKnM8SXVPUGhMD9u32yBHTsFiU,18517
 ngio/images/_create.py,sha256=61cuco2jUK25WzOY-Sel9s931FtGPL2ut25L9W10bJ4,10171
 ngio/images/_create_synt_container.py,sha256=il_rr5_2KIQ5Xsskj2rb2fEm100ZErZq89aW06kn_7k,5444
-ngio/images/_image.py,sha256=GDUmBhoTj9js7rC785g3__l_xSH1oKSgx2AAAr25OSM,33053
+ngio/images/_image.py,sha256=aMJb-YDghbZIHfSzY8ZoTmScEOqNfWQzJFO2AoMCdF4,33053
 ngio/images/_label.py,sha256=Se3ZpgXDArtLHPlx9pw8Rnr5pZ_sEkmbeMh9sU63ncg,11799
 ngio/images/_masked_image.py,sha256=YhbBzgPZMav6rX0WYue1BaxAzEIsfaQrxUIOK6ZWZcw,18848
 ngio/images/_ome_zarr_container.py,sha256=UJERXEgBkwclpLaHzWqUIQc6P-TG4zYuKuxPukJGa4Y,38433
@@ -55,7 +55,7 @@ ngio/resources/20200812-CardiomyocyteDifferentiation14-Cycle1_B03/nuclei.png,sha
 ngio/resources/20200812-CardiomyocyteDifferentiation14-Cycle1_B03/raw.jpg,sha256=82lejQAIokj5w9g-qqhysDTWpHtNvJTkdURG_BjqIxQ,37743
 ngio/tables/__init__.py,sha256=_BV3sclNMLITu_J8_3DkkUrCB6Kro0HzeWLDCD1ivKM,877
 ngio/tables/_abstract_table.py,sha256=rwGa47TzbFmosucBWVfFq6JEXtgGvOdUVtU9DIelV88,8204
-ngio/tables/_tables_container.py,sha256=3xmpREaN671l40MPprnl1BD-VoOb6xfjECb5mNoMW0w,12173
+ngio/tables/_tables_container.py,sha256=jB3iVlUnJdMIBUqfuZDtPkiEI9haL19Bz-QfJ0BUwl4,12176
 ngio/tables/backends/__init__.py,sha256=MwSRXNF1rWQBFOTDA_vT3oGoNZpviVgytsL5Txnu08I,1619
 ngio/tables/backends/_abstract_backend.py,sha256=54Vh9yPfLx1NixGVfFkW4msD51nsim0zIfHRnO80Xt8,7276
 ngio/tables/backends/_anndata.py,sha256=97RWG4Hjc42JBxm-YxjHEU8HHd14NiayelKlI1PTsCo,2868
@@ -70,7 +70,7 @@ ngio/tables/v1/__init__.py,sha256=Wr1_9RZFpaN8FYMTnxT9Yjkw4AS7y9FMWailmB_uj5g,61
 ngio/tables/v1/_condition_table.py,sha256=T0Uq5BKkmMoEspt_Rx0U99Ow6S9GAMZDHqvUO5obCAM,1780
 ngio/tables/v1/_feature_table.py,sha256=n9uMHwoBh-_dlOhUXCFbmAjXFVXncNCR3SjE2qzXI68,3821
 ngio/tables/v1/_generic_table.py,sha256=1ktJHeuv7U1g5Z8PFUuTkCjOzcYMQd8xegKHKUedJB8,1240
-ngio/tables/v1/_roi_table.py,sha256=g7UpMmpf3uAfaG59WYRnimUBgiB_T1qUJRwMZpMt9cI,17099
+ngio/tables/v1/_roi_table.py,sha256=b7lwjsdCSUOCMT6Lx4hwAqGBKC25Q5bdzoK3DQWnAQM,17074
 ngio/transforms/__init__.py,sha256=JA0-Ui7skbXkm9ofN-AEhU1FTLutkMkwTdVD-310frQ,113
 ngio/transforms/_zoom.py,sha256=otyE-vxFnywUJ8U4mHjat-bNG_7_jv62ckTpqDMxyVQ,550
 ngio/utils/__init__.py,sha256=XPYh8ehC7uXNU2cFFXZAw-S3DpWpX1Yq2xGkffZv5vI,1142
@@ -79,7 +79,7 @@ ngio/utils/_errors.py,sha256=pKQ12LUjQLYE1nUawemA5h7HsgznjaSvV1n2PQU33N0,759
 ngio/utils/_fractal_fsspec_store.py,sha256=RdcCFOgHexRKX9zZvJV5RI-5OPc7VOPS6q_IeRxm24I,1548
 ngio/utils/_logger.py,sha256=N5W0a_xwze4blS1MolidBkTMbjTbg8GPguJZNun3mAE,1392
 ngio/utils/_zarr_utils.py,sha256=GUOcAx02IcfrJ5tIdKu8ChtRUUaBbkkddW5jaCCYnS8,13797
-ngio-0.4.4.dist-info/METADATA,sha256=1yjBnjq6IURXZSApn3fLn31KBRWNLhTM6J4unvUrnHg,6117
-ngio-0.4.4.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-ngio-0.4.4.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
-ngio-0.4.4.dist-info/RECORD,,
+ngio-0.4.6.dist-info/METADATA,sha256=swcrfn7bpQliiDtVbWuUOf-JMMgK6zEfkXeh9Qv8fxg,6137
+ngio-0.4.6.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+ngio-0.4.6.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
+ngio-0.4.6.dist-info/RECORD,,