Fixes #195

CHANGELOG.md

@@ -1,6 +1,9 @@
 # Changelog
 
-## [unreleased]
+## [v0.5.13]
+
+### Fix
+- Fix `derive_label` (and `OmeZarrContainer.derive_label`) rejecting an explicit `shape` that omits the channel axis. When the reference image has a `c` axis and `channels_policy` removes or overrides it (`"squeeze"`, `"singleton"`, or an integer), the up-front shape-length check failed before the channel policy was applied. The provided shape is now normalized to the reference dimensionality before pyramid computation, so a channel-less shape (e.g. `(z, y, x)` for a `(c, z, y, x)` image) is accepted. `channels_policy="same"` still requires the full shape.
 
 ### Chores
 - Harden GitHub Actions and scan workflows through `zizmor`.

src/ngio/images/_abstract_image.py

@@ -729,6 +729,31 @@ def _compute_pyramid_shapes(
     return _shapes_from_new_shape(ref_image=ref_image, shape=shape)
 
 
+def _normalize_shape_for_channel_policy(
+    ref_image: AbstractImage,
+    shape: Sequence[int] | None,
+    channels_policy: Literal["squeeze", "same", "singleton"] | int,
+) -> Sequence[int] | None:
+    """Insert a placeholder channel axis when the provided shape omits it.
+
+    For every channels_policy except "same", the channel axis is fully
+    determined by the policy ("squeeze" removes it, "singleton"/int overwrite
+    it), so the caller may pass a shape that omits the channel axis. Pyramid
+    computation requires a shape matching the reference dimensionality, so we
+    insert a placeholder channel dimension here; _apply_channel_policy then
+    removes or overwrites it. See issue #195.
+    """
+    if shape is None or channels_policy == "same":
+        return shape
+    channel_index = ref_image.axes_handler.get_index("c")
+    if channel_index is None:
+        return shape
+    if len(shape) == len(ref_image.shape) - 1:
+        c_size = ref_image.shape[channel_index]
+        return (*shape[:channel_index], c_size, *shape[channel_index:])
+    return shape
+
+
 def _check_len_compatibility(
     ref_shape: tuple[int, ...],
     chunks: ChunksLike,
@@ -1010,6 +1035,11 @@ def abstract_derive(
     # End of deprecated arguments handling
     ref_meta = ref_image.meta
 
+    shape = _normalize_shape_for_channel_policy(
+        ref_image=ref_image,
+        shape=shape,
+        channels_policy=channels_policy,
+    )
     shapes, scales = _compute_pyramid_shapes(
         shape=shape,
         ref_image=ref_image,

src/ngio/ome_zarr_meta/v05/_v05_spec.py

@@ -23,7 +23,6 @@
 from ome_zarr_models.v05.hcs import HCSAttrs as HCSAttrsV05
 from ome_zarr_models.v05.image import ImageAttrs as ImageAttrsV05
 from ome_zarr_models.v05.image_label import ImageLabelAttrs as ImageLabelAttrsV05
-from ome_zarr_models.v05.labels import Labels as Labels
 from ome_zarr_models.v05.labels import LabelsAttrs as LabelsAttrsV05
 from ome_zarr_models.v05.multiscales import Dataset as DatasetV05
 from ome_zarr_models.v05.multiscales import Multiscale as MultiscaleV05

tests/unit/images/test_create.py

@@ -161,6 +161,43 @@ def test_derive_label_channels_policy():
     assert label.dimensions.get("c") == 2
 
 
+def test_derive_label_shape_without_channel_axis():
+    # Regression test for https://github.com/BioVisionCenter/ngio/issues/195
+    # A (c, z, y, x) image should accept a label shape without the channel axis
+    # for any policy that owns the channel axis (squeeze/singleton/int).
+    store = MemoryStore()
+    ome_zarr = create_synthetic_ome_zarr(store, shape=(1, 1, 64, 64))
+
+    # Default policy is "squeeze": the channel-less shape is the saved shape.
+    label = ome_zarr.derive_label("lbl-squeeze", shape=(1, 64, 64))
+    assert "c" not in label.axes
+    assert label.shape == (1, 64, 64)
+
+    label = ome_zarr.derive_label(
+        "lbl-singleton", shape=(1, 64, 64), channels_policy="singleton"
+    )
+    assert label.dimensions.get("c") == 1
+
+    label = ome_zarr.derive_label("lbl-int", shape=(1, 64, 64), channels_policy=2)
+    assert label.dimensions.get("c") == 2
+
+    # A full-length shape with the channel axis still squeezes (no regression).
+    label = ome_zarr.derive_label("lbl-squeeze-full", shape=(1, 1, 64, 64))
+    assert "c" not in label.axes
+    assert label.shape == (1, 64, 64)
+
+    # "same" keeps the channel from the shape, so the full shape is required.
+    with pytest.raises(NgioValueError):
+        ome_zarr.derive_label("lbl-same", shape=(1, 64, 64), channels_policy="same")
+
+    # A channel-less reference image: the shape is used as-is (nothing to insert),
+    # even with a non-"same" policy like the default "squeeze".
+    no_c = create_synthetic_ome_zarr(MemoryStore(), shape=(4, 64, 64))
+    label = no_c.derive_label("lbl-no-c", shape=(4, 64, 64))
+    assert "c" not in label.axes
+    assert label.shape == (4, 64, 64)
+
+
 def test_derive_from_non_dishogeneus_shapes():
     # Yes those shapes are intentionally weird
     shapes = [