Fix derive label (#117)

* fix #114

* add pillow fix #115

* update change long

Author: lorenzocerrone

CHANGELOG.md

@@ -1,5 +1,13 @@
 # Changelog
 
+## [v0.4.3]
+
+### Bug Fixes
+
+- Fix bug in deriving labels and image from OME-Zarr with non standard path names.
+- Add missing pillow dependency.
+- Update pixi workspace config.
+
 ## [v0.4.2]
 
 ### API Changes

pyproject.toml

@@ -48,6 +48,7 @@ dependencies = [
     "pooch",
     "polars",
     "pyarrow",
+    "pillow",
 ]
 
 # https://peps.python.org/pep-0621/#dependencies-optional-dependencies
@@ -186,7 +187,7 @@ source = ["ngio"]
 [tool.check-manifest]
 ignore = [".pre-commit-config.yaml", ".ruff_cache/**/*", "tests/**/*"]
 
-[tool.pixi.project]
+[tool.pixi.workspace]
 channels = ["conda-forge"]
 platforms = ["osx-arm64", "linux-64", "win-64"]
 

src/ngio/images/_image.py

@@ -801,7 +801,7 @@ def derive_image_container(
         pixelsize=pixel_size.x,
         z_spacing=pixel_size.z,
         time_spacing=pixel_size.t,
-        levels=ref_meta.levels,
+        levels=ref_meta.paths,
         yx_scaling_factor=ref_meta.yx_scaling(),
         z_scaling_factor=ref_meta.z_scaling(),
         time_unit=pixel_size.time_unit,

src/ngio/images/_label.py

@@ -318,7 +318,7 @@ def derive_label(
         pixelsize=ref_image.pixel_size.x,
         z_spacing=ref_image.pixel_size.z,
         time_spacing=ref_image.pixel_size.t,
-        levels=ref_meta.levels,
+        levels=ref_meta.paths,
         yx_scaling_factor=ref_meta.yx_scaling(),
         z_scaling_factor=ref_meta.z_scaling(),
         time_unit=ref_image.pixel_size.time_unit,

tests/unit/images/test_images.py

@@ -220,3 +220,24 @@ def test_zoom_virtual_axes(
     # Roi data should match exactly except for virtual axis
     assert img1_data.shape[1:] == img2_roi_data.shape[1:]
     img2.set_roi(roi=roi, patch=img2_roi_data, transforms=[zoom], axes_order="czyx")
+
+
+def test_derive_image_consistency(
+    tmp_path: Path,
+):
+    path1 = tmp_path / "image1.zarr"
+    ome_zarr = create_empty_ome_zarr(
+        store=path1,
+        shape=(3, 16, 16, 16),
+        axes_names="czyx",
+        xy_pixelsize=1.0,
+        levels=["s0", "s1", "s2"],
+    )
+    ome_zarr_der = ome_zarr.derive_image(tmp_path / "derived_image.zarr")
+    assert ome_zarr.channel_labels == ome_zarr_der.channel_labels
+    assert ome_zarr.levels_paths == ome_zarr_der.levels_paths
+    assert ome_zarr.space_unit == ome_zarr_der.space_unit
+    assert ome_zarr.time_unit == ome_zarr_der.time_unit
+
+    label = ome_zarr.derive_label("derived_label")
+    assert label.path == "s0"

tests/unit/images/test_omezarr_container.py

@@ -296,3 +296,18 @@ def test_get_and_squeeze(tmp_path: Path):
     image.get_as_dask(
         channel_selection=ChannelSelectionModel(identifier="0", mode="index")
     )
+
+
+def test_derive_image_and_labels(tmp_path: Path):
+    # Testing for #116
+    store = tmp_path / "ome_zarr.zarr"
+    ome_zarr = create_empty_ome_zarr(
+        store,
+        shape=(3, 20, 30),
+        xy_pixelsize=0.5,
+        levels=1,
+        axes_names=["c", "y", "x"],
+        dtype="uint8",
+    )
+    derived_ome_zarr = ome_zarr.derive_image(tmp_path / "derived.zarr")
+    _ = derived_ome_zarr.derive_label("derived_label")