ngio 0.4.3__py3-none-any.whl → 0.4.5__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/ome_zarr_meta/ngio_specs/_channels.py

@@ -102,6 +102,20 @@ def valid_hex_color(v: str) -> bool:
     return True
 
 
+def into_valid_hex_color(v: str) -> str:
+    """Convert a string into a valid hexadecimal color.
+
+    If the string is already a valid hexadecimal color, return it.
+    Otherwise, return a hexadecimal color based on the hash of the string.
+    """
+    # strip leading '#' if present
+    v = v.lstrip("#")
+    if valid_hex_color(v):
+        return v
+
+    return NgioColors.semi_random_pick(v.lower()).value
+
+
 class ChannelVisualisation(BaseModel):
     """Channel visualisation model.
 
@@ -135,13 +149,10 @@ class ChannelVisualisation(BaseModel):
         """
         if value is None:
             return NgioColors.semi_random_pick().value
-        if isinstance(value, str) and valid_hex_color(value):
-            return value
+        if isinstance(value, str):
+            return into_valid_hex_color(value)
         elif isinstance(value, NgioColors):
             return value.value
-        elif isinstance(value, str):
-            value_lower = value.lower()
-            return NgioColors.semi_random_pick(value_lower).value
         else:
             raise NgioValueError(f"Invalid color {value}.")
 
@@ -159,19 +170,6 @@ class ChannelVisualisation(BaseModel):
             data["end"] = start + 1
         return data
 
-    @model_validator(mode="after")
-    def check_model(self) -> "ChannelVisualisation":
-        """Check that the start and end values are within the min and max values."""
-        if self.start < self.min or self.start > self.max:
-            raise NgioValidationError(
-                f"Start value {self.start} is out of range [{self.min}, {self.max}]"
-            )
-        if self.end < self.min or self.end > self.max:
-            raise NgioValidationError(
-                f"End value {self.end} is out of range [{self.min}, {self.max}]"
-            )
-        return self
-
     @classmethod
     def default_init(
         cls,

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-0.4.3.dist-info → ngio-0.4.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.4.3
+Version: 0.4.5
 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-0.4.3.dist-info → ngio-0.4.5.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
@@ -40,7 +40,7 @@ ngio/ome_zarr_meta/__init__.py,sha256=tzxW2oVhfeMBVuv3XkcbOLzMnbDvUnie-AVsvSxRkd
 ngio/ome_zarr_meta/_meta_handlers.py,sha256=ctknNDT8jxwyvxQf9on5gW31H1tRRsnneO38GT2UXoE,25880
 ngio/ome_zarr_meta/ngio_specs/__init__.py,sha256=U2FqZR91Ob2N6CqKdyw-_Ll-wMgmGuPZGVRCr6wuRFY,1698
 ngio/ome_zarr_meta/ngio_specs/_axes.py,sha256=gNzxCddn53m9dlNJlV5CL-aQS-nGJrbCDGfAp5L97LY,16412
-ngio/ome_zarr_meta/ngio_specs/_channels.py,sha256=CVsbG52U31TaMdTj8XqvClUdBya2Ar3qBjDo_xhP-NM,16967
+ngio/ome_zarr_meta/ngio_specs/_channels.py,sha256=TDxIy-yVc2YaWPIFJRYnYwZbA8O5Ee_OiWppHYrEdpU,16647
 ngio/ome_zarr_meta/ngio_specs/_dataset.py,sha256=CrHnjVWBGYPqErKkHR-E2DKrE3DmGznXMkd3Y9Z4uYo,3434
 ngio/ome_zarr_meta/ngio_specs/_ngio_hcs.py,sha256=N1CGPOubwf0pvm8tiTnh-C1cOu9lToyDe3WagnEnPN4,17207
 ngio/ome_zarr_meta/ngio_specs/_ngio_image.py,sha256=XmqeffYRspBZmv8gCrfJvnykmBViWgDo2AtJJkR7OEs,15886
@@ -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-0.4.3.dist-info/METADATA,sha256=BPhEA2JyzaofdvVLPsB2O3ZGr-gr-3nPCZwJ4LOWn5A,6117
-ngio-0.4.3.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-ngio-0.4.3.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
-ngio-0.4.3.dist-info/RECORD,,
+ngio-0.4.5.dist-info/METADATA,sha256=6g28iSwZ32mHJmEmOYOFaixVkTyQa-xaCy50teScyjk,6137
+ngio-0.4.5.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+ngio-0.4.5.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
+ngio-0.4.5.dist-info/RECORD,,