ngio 0.5.0b2__tar.gz → 0.5.0b4__tar.gz

{ngio-0.5.0b2 → ngio-0.5.0b4}/CHANGELOG.md

@@ -6,6 +6,7 @@
 - Add support for OME-NGFF v0.5
 - Move to zarr-python v3
 - API to delete labels and tables from OME-Zarr containers and HCS plates.
+- Allow to explicitly set axes order when building masking roi tables.
 
 ### API Breaking Changes
 
@@ -18,7 +19,10 @@
 - Internal changes to `ZarrGroupHandler` to support cleanup unused apis.
 - Remove `ngio_logger` in favor of standard warnings module.
 
-## [v0.4.6]
+## [v0.4.7]
+
+### Bug Fixes
+- Fix bug adding time axis to masking roi tables.
 
 ### Bug Fixes
 - Fix channel selection from `wavelength_id`

{ngio-0.5.0b2 → ngio-0.5.0b4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.5.0b2
+Version: 0.5.0b4
 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 → ngio-0.5.0b4}/pyproject.toml

@@ -66,6 +66,7 @@ test = [
 ]
 
 dev = [
+    "zarrs",
     "Pympler",
     "napari",
     "pyqt5",

{ngio-0.5.0b2 → ngio-0.5.0b4}/src/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-0.5.0b2 → ngio-0.5.0b4}/src/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-0.5.0b2 → ngio-0.5.0b4}/src/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-0.5.0b2 → ngio-0.5.0b4}/src/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(),
@@ -800,7 +799,7 @@ 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 +834,7 @@ 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 +917,6 @@ def abstract_derive(
 
     if chunks is None:
         chunks = ref_image.zarr_array.chunks
-
     if shards is None:
         shards = ref_image.zarr_array.shards
 

{ngio-0.5.0b2 → ngio-0.5.0b4}/src/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-0.5.0b2 → ngio-0.5.0b4}/src/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,
@@ -219,7 +221,7 @@ 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 +258,7 @@ 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 +330,7 @@ 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 +361,7 @@ 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
@@ -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-0.5.0b2 → ngio-0.5.0b4}/src/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 → ngio-0.5.0b4}/tests/unit/images/test_create.py

@@ -195,6 +195,32 @@ def test_derive_from_non_dishogeneus_shapes():
     assert lbl.shape == (4, 3, 32, 19)
 
 
+def test_create_with_sharding(tmp_path: Path):
+    store = tmp_path / "test_image_sharded.zarr"
+    ome_zarr = create_empty_ome_zarr(
+        store=store,
+        shape=(4, 3, 64, 64),
+        pixelsize=0.5,
+        chunks=(2, 1, 32, 32),
+        shards=(4, 3, 64, 64),
+        dtype="uint8",
+        levels=3,
+        overwrite=True,
+        ngff_version="0.5",
+    )
+    ome_zarr.derive_label("label_sharded")
+    img = ome_zarr.get_image(path="0")
+    assert img.zarr_array.shards is not None
+    assert img.zarr_array.chunks == (2, 1, 32, 32)
+    assert img.zarr_array.shards == (4, 3, 64, 64)
+
+    img = ome_zarr.get_image(path="2")
+    assert img.zarr_array.shards is not None
+    # Check clipping of chunks/shards at the smallest level
+    assert img.zarr_array.chunks == (2, 1, 16, 16)
+    assert img.zarr_array.shards == (4, 3, 16, 16)
+
+
 def test_fail_derive_singleton():
     store = MemoryStore()
     ome_zarr = create_empty_ome_zarr(store=store, shape=(1, 1, 64, 4), pixelsize=0.5)

{ngio-0.5.0b2 → ngio-0.5.0b4}/tests/unit/images/test_images.py

@@ -225,7 +225,6 @@ def test_zoom_virtual_axes(
     assert img2_data.shape[0] == 1  # Virtual channel axis
 
     roi = img1.build_image_roi_table().rois()[0]
-    print(roi)
     img2_roi_data = img2.get_roi_as_numpy(roi, transforms=[zoom], axes_order="czyx")
     # Roi data should match exactly except for virtual axis
     assert img1_data.shape[1:] == img2_roi_data.shape[1:]

{ngio-0.5.0b2 → ngio-0.5.0b4}/tests/unit/tables/test_backends.py

@@ -111,8 +111,6 @@ def test_csv_backend(tmp_path: Path):
 
     backend.write(test_table, metadata={"test": "test"})
     loaded_table = backend.load_as_pandas_df()
-    print(loaded_table)
-    print(test_table)
     assert loaded_table.equals(test_table), loaded_table
     meta = backend._group_handler.load_attrs()
     assert meta["test"] == "test"