ngio 0.5.0b3__py3-none-any.whl → 0.5.0b5__py3-none-any.whl

ngio/common/_masking_roi.py

@@ -1,6 +1,7 @@
 """Utilities to build masking regions of interest (ROIs)."""
 
 import itertools
+from collections.abc import Sequence
 
 import dask.array as da
 import numpy as np
@@ -115,7 +116,9 @@ def lazy_compute_slices(segmentation: da.Array) -> dict[int, tuple[slice, ...]]:
 
 
 def compute_masking_roi(
-    segmentation: np.ndarray | da.Array, pixel_size: PixelSize
+    segmentation: np.ndarray | da.Array,
+    pixel_size: PixelSize,
+    axes_order: Sequence[str],
 ) -> list[Roi]:
     """Compute a ROIs for each label in a segmentation.
 
@@ -127,6 +130,12 @@ def compute_masking_roi(
     if segmentation.ndim not in [2, 3, 4]:
         raise NgioValueError("Only 2D, 3D, and 4D segmentations are supported.")
 
+    if len(axes_order) != segmentation.ndim:
+        raise NgioValueError(
+            "The length of axes_order must match the number of dimensions "
+            "of the segmentation."
+        )
+
     if isinstance(segmentation, da.Array):
         slices = lazy_compute_slices(segmentation)
     else:
@@ -134,24 +143,11 @@ def compute_masking_roi(
 
     rois = []
     for label, slice_ in slices.items():
-        if len(slice_) == 2:
-            slices = {"y": slice_[0], "x": slice_[1]}
-        elif len(slice_) == 3:
-            slices = {"z": slice_[0], "y": slice_[1], "x": slice_[2]}
-        elif len(slice_) == 4:
-            slices = {
-                "t": slice_[0],
-                "z": slice_[1],
-                "y": slice_[2],
-                "x": slice_[3],
-            }
-        else:
-            raise ValueError("Invalid slice length.")
-
+        assert len(slice_) == len(axes_order)
+        slices = dict(zip(axes_order, slice_, strict=True))
         roi = Roi.from_values(
             name=str(label), slices=slices, label=label, space="pixel"
         )
-
         roi = roi.to_world(pixel_size=pixel_size)
         rois.append(roi)
     return rois

ngio/common/_pyramid.py

@@ -92,16 +92,7 @@ def _on_disk_coarsen(
 
     coarsening_setup = {}
     for i, s in enumerate(_scale):
-        factor = 1 / s
-        # This check is very strict, but it is necessary to avoid
-        # a few pixels shift in the coarsening
-        # We could add a tolerance
-        if factor.is_integer():
-            coarsening_setup[i] = int(factor)
-        else:
-            raise NgioValueError(
-                f"Coarsening factor must be an integer, got {factor} on axis {i}"
-            )
+        coarsening_setup[i] = int(np.round(1 / s))
 
     out_target = da.coarsen(
         aggregation_function, source_array, coarsening_setup, trim_excess=True

ngio/common/_roi.py

@@ -4,7 +4,7 @@ These are the interfaces bwteen the ROI tables / masking ROI tables and
     the ImageLikeHandler.
 """
 
-from collections.abc import Callable
+from collections.abc import Callable, Mapping
 from typing import Literal, Self
 
 from pydantic import BaseModel, ConfigDict, Field, field_validator
@@ -183,7 +183,7 @@ class Roi(BaseModel):
     @classmethod
     def from_values(
         cls,
-        slices: dict[str, float | tuple[float | None, float | None] | slice],
+        slices: Mapping[str, float | tuple[float | None, float | None] | slice],
         name: str | None,
         label: int | None = None,
         space: Literal["world", "pixel"] = "world",

ngio/images/_abstract_image.py

@@ -615,7 +615,6 @@ def _shapes_from_ref_image(
     if len(shapes) == len(paths):
         return shapes
     missing_levels = len(paths) - len(shapes)
-    print(ref_image.meta.scaling_factor())
     extended_shapes = shapes_from_scaling_factors(
         base_shape=shapes[-1],
         scaling_factors=ref_image.meta.scaling_factor(),
@@ -918,7 +917,6 @@ 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/_label.py

@@ -97,9 +97,11 @@ class Label(AbstractImage):
         meta = meta.to_units(space_unit=space_unit, time_unit=time_unit)
         self.meta_handler.update_meta(meta)
 
-    def build_masking_roi_table(self) -> MaskingRoiTable:
+    def build_masking_roi_table(
+        self, axes_order: Sequence[str] | None = None
+    ) -> MaskingRoiTable:
         """Compute the masking ROI table."""
-        return build_masking_roi_table(self)
+        return build_masking_roi_table(self, axes_order=axes_order)
 
     def consolidate(
         self,
@@ -405,8 +407,11 @@ def derive_label(
     return group_handler
 
 
-def build_masking_roi_table(label: Label) -> MaskingRoiTable:
+def build_masking_roi_table(
+    label: Label, axes_order: Sequence[str] | None = None
+) -> MaskingRoiTable:
     """Compute the masking ROI table for a label."""
-    array = label.get_as_dask(axes_order=["t", "z", "y", "x"])
-    rois = compute_masking_roi(array, label.pixel_size)
+    axes_order = axes_order or label.axes
+    array = label.get_as_dask(axes_order=axes_order)
+    rois = compute_masking_roi(array, label.pixel_size, axes_order=axes_order)
     return MaskingRoiTable(rois, reference_label=label.meta.name)

ngio/utils/_datasets.py

@@ -155,5 +155,11 @@ def download_ome_zarr_dataset(
         path=download_dir,
         processor=processor,
         progressbar=progressbar,
+        # Add User-Agent to avoid 403 errors from Zenodo
+        downloader=pooch.HTTPDownloader(
+            headers={
+                "User-Agent": f"pooch/{pooch.__version__} (https://github.com/BioVisionCenter/ngio)"
+            }
+        ),
     )
     return processor.output_file()

{ngio-0.5.0b3.dist-info → ngio-0.5.0b5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.5.0b3
+Version: 0.5.0b5
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/BioVisionCenter/ngio
 Project-URL: repository, https://github.com/BioVisionCenter/ngio
@@ -13,8 +13,9 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Classifier: Typing :: Typed
-Requires-Python: <3.14,>=3.11
+Requires-Python: <3.15,>=3.11
 Requires-Dist: aiohttp
 Requires-Dist: anndata
 Requires-Dist: dask[array]<2025.11.0

{ngio-0.5.0b3.dist-info → ngio-0.5.0b5.dist-info}/RECORD

@@ -1,9 +1,9 @@
 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=JRqVm9eFyxHi1a2hCcAoTJU3L8vctRHbkVWkskyQG_U,14354
-ngio/common/_roi.py,sha256=UMr7ie7dIZ6gMcM0_AlFMev_PRKxBdzUy_1WKRZ4zQU,11403
+ngio/common/_masking_roi.py,sha256=rWOvhT08KfxX5djvUsX6LsUVofyU0Fq5LcUmpOYElDg,4757
+ngio/common/_pyramid.py,sha256=kvtacAhJb8zcV5ungNPYRDBShgti-kxtD_4LdBpnyDw,14012
+ngio/common/_roi.py,sha256=G2KICRbxlYenbc1qmKmdxLrfJRmqYSUbeaBdEuUYW-Q,11415
 ngio/common/_synt_images_utils.py,sha256=B6uYOW1NyrM06YMR-csca3_YnAAkPRTbvnbLdy9tk9E,3188
 ngio/common/_zoom.py,sha256=U01c-vqXjzZkrpd9Yvs24frVfTls_xPJeeaFCGmUwYI,6727
 ngio/experimental/__init__.py,sha256=3pmBtHi-i8bKjTsvrOJM56ZyRX3Pv_dceCdt88-8COQ,147
@@ -17,11 +17,11 @@ 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=gvOS7Nb52pgLgtBpvu3vYxwbSocqw2w-sEsJaJVrHWE,31925
+ngio/images/_abstract_image.py,sha256=n7xIURa3QCfTuBZz-g58y0Q2maG41AL79C9Ae8I08Ko,31864
 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=A2dE9O3L1dLU3gdjQrNCFUYDF_NuxTxVm8klmBfmPCc,34792
-ngio/images/_label.py,sha256=0dqLKBVibqw6scSTWxzSyxjnXLs-fhBGQzol8C5Rzok,15676
+ngio/images/_label.py,sha256=P4m6K6xaYoE7XrpCxbxHQwJOHncXdmXY057ZUv4a76E,15856
 ngio/images/_masked_image.py,sha256=YhbBzgPZMav6rX0WYue1BaxAzEIsfaQrxUIOK6ZWZcw,18848
 ngio/images/_ome_zarr_container.py,sha256=mD1PEos33EfapkUVMJnSZdQiQI57cZa_bB2hdEEJQuM,48276
 ngio/images/_table_ops.py,sha256=jFv_AMqoB4JBpoWsMtZppZVW7dAOC_u-JpfNm8b33kY,15292
@@ -78,11 +78,11 @@ ngio/transforms/__init__.py,sha256=JA0-Ui7skbXkm9ofN-AEhU1FTLutkMkwTdVD-310frQ,1
 ngio/transforms/_zoom.py,sha256=otyE-vxFnywUJ8U4mHjat-bNG_7_jv62ckTpqDMxyVQ,550
 ngio/utils/__init__.py,sha256=d2OHQGMFPpf8-_ipuqquxtqCNGJpX5yXt34A65nScUU,1037
 ngio/utils/_cache.py,sha256=Ey9fgc_BTdMyqg6c80C0CuGDhOafln8-3e_1MQ0MFzw,1283
-ngio/utils/_datasets.py,sha256=6GtxfPkjutNaeg5BHuJDBP0GudvQXHLU6mmHp_o0bGA,5650
+ngio/utils/_datasets.py,sha256=YOV367skFA8nbKAqbyK0EsUU7E9UId_u5ButuLesrzk,5896
 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-0.5.0b3.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,,
+ngio-0.5.0b5.dist-info/METADATA,sha256=kDswYTjCsCUVZUZc2TA-tNK9CZZ4PhncumU74hE8vXc,6382
+ngio-0.5.0b5.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+ngio-0.5.0b5.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
+ngio-0.5.0b5.dist-info/RECORD,,