Merge pull request #23 from fractal-analytics-platform/fix_wavelength…

…_ids

fix bug in ngio when saving wavelenght ids

src/ngio/ngff_meta/v04/zarr_utils.py

@@ -110,7 +110,13 @@ def vanilla_omero_v04_to_fractal(omero04: Omero04) -> Omero:
     for channel04 in omero04.channels:
         # Convert the window to a dictionary
         label = channel04.label
-        wavelength_id = channel04.extra_fields.get("wavelength_id", label)
+
+        if "wavelength_id" in channel04.extra_fields:
+            # If the wavelength_id is present, pop it from the extra fields
+            # so that it is not added to the channel_visualisation
+            wavelength_id = channel04.extra_fields.pop("wavelength_id")
+        else:
+            wavelength_id = label
 
         if channel04.window is None:
             window04 = Window04(
@@ -161,6 +167,7 @@ def fractal_omero_to_vanilla_v04(omero: Omero) -> Omero04:
             color=channel.channel_visualisation.color,
             active=channel.channel_visualisation.active,
             window=window04,
+            wavelength_id=channel.wavelength_id,
             **channel.channel_visualisation.extra_fields,
         )
         list_channels04.append(channel04)

tests/ngff_meta/test_utils.py

@@ -22,6 +22,7 @@ def test_create_fractal_meta_with_t(self) -> None:
         )
 
         assert meta.channel_labels == ["DAPI", "nanog", "Lamin B1"]
+        assert meta.channel_wavelength_ids == ["A01_C01", "A02_C02", "A03_C03"]
         np.testing.assert_array_equal(meta.pixel_size(idx=0).zyx, [1.0, 1.0, 1.0])
         np.testing.assert_array_equal(meta.scale(idx=0), [1.0, 1.0, 1.0, 1.0, 1.0])
         np.testing.assert_array_equal(meta.pixel_size(path="2").zyx, [1.0, 4.0, 4.0])

tests/ngff_meta/test_v04.py

@@ -4,6 +4,36 @@
 
 
 class TestOMEZarrHandlerV04:
+    def test_create_image_meta(self, tmp_path):
+        from ngio.ngff_meta import create_image_metadata
+        from ngio.ngff_meta.v04.zarr_utils import (
+            fractal_ngff_image_meta_to_vanilla_v04,
+            vanilla_ngff_image_meta_v04_to_fractal,
+        )
+
+        meta = create_image_metadata(
+            on_disk_axis=("t", "c", "z", "y", "x"),
+            pixel_sizes=None,
+            xy_scaling_factor=2.0,
+            z_scaling_factor=1.0,
+            time_spacing=1.0,
+            time_units="s",
+            levels=5,
+            name="test",
+            channel_labels=["DAPI", "nanog", "Lamin B1"],
+            channel_wavelengths=["A01_C01", "A02_C02", "A03_C03"],
+            channel_visualization=None,
+            omero_kwargs=None,
+            version="0.4",
+        )
+
+        meta04 = fractal_ngff_image_meta_to_vanilla_v04(meta)
+        meta2 = vanilla_ngff_image_meta_v04_to_fractal(meta04)
+        assert meta.channel_labels == meta2.channel_labels
+        assert meta.channel_wavelength_ids == meta2.channel_wavelength_ids
+        assert meta.axes_names == meta2.axes_names
+        assert meta.scale(path="2") == meta2.scale(path="2")
+
     def test_basic_workflow(self, ome_zarr_image_v04_path):
         from ngio.ngff_meta import get_ngff_image_meta_handler
         from ngio.ngff_meta.v04.zarr_utils import NgffImageMeta04