Merge pull request #548 from fractal-analytics-platform/547-omero-cha…

…nnels-window-parameters-became-required-unintentionally-with-0120-changes Make `Channel.window` attribute optional in `lib_ngff.py`
fractal-analytics-platform · Oct 4, 2023 · 0efcf33 · 0efcf33
2 parents 3ed0b95 + 7004516
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,7 +1,8 @@
 **Note**: Numbers like (\#123) point to closed Pull Requests on the fractal-tasks-core repository.
 
-# Unreleased
+# 0.12.1
 
+* Make `Channel.window` attribute optional in `lib_ngff.py` (\#548).
 * Automate procedure for publishing package to PyPI (\#545).
 
 # 0.12.0

diff --git a/fractal_tasks_core/lib_ngff.py b/fractal_tasks_core/lib_ngff.py
@@ -33,7 +33,7 @@ class Channel(BaseModel):
     See https://ngff.openmicroscopy.org/0.4/#omero-md.
     """
 
-    window: Window
+    window: Optional[Window] = None
     label: Optional[str] = None
     family: Optional[str] = None
     color: str

diff --git a/tests/data/ngff_examples/image_no_omero_channel_window.json b/tests/data/ngff_examples/image_no_omero_channel_window.json
@@ -0,0 +1,53 @@
+{
+    "multiscales": [
+        {
+            "axes": [
+                {
+                    "name": "y",
+                    "type": "space",
+                    "unit": "micrometer"
+                },
+                {
+                    "name": "x",
+                    "type": "space",
+                    "unit": "micrometer"
+                }
+            ],
+            "datasets": [
+                {
+                    "path": 0,
+                    "coordinateTransformations": [
+                        {
+                            "type": "scale",
+                            "scale": [
+                                0.1625,
+                                0.1625
+                            ]
+                        }
+                    ]
+                }
+            ],
+            "version": "0.4"
+        }
+    ],
+    "omero": {
+        "channels": [
+            {
+                "wavelength_id": "A01_C01",
+                "label": "some-label-1",
+                "color": "00FFFF"
+            },
+            {
+                "wavelength_id": "A01_C02",
+                "label": "some-label-2",
+                "color": "00FFFF",
+                "window":{
+                    "start": 0,
+                    "end": 1,
+                    "min": 0,
+                    "max": 1
+                }
+            }
+        ]
+    }
+}
diff --git a/tests/test_unit_ngff.py b/tests/test_unit_ngff.py
@@ -118,6 +118,14 @@ def test_NgffImageMeta(ngffdata_path):
     debug(e.value)
     assert "are too small" in str(e.value)
 
+    # Load an image where not all omero channels have a window attribute
+    ngff_image_meta = _load_and_validate(
+        ngffdata_path / "image_no_omero_channel_window.json", NgffImageMeta
+    )
+    debug(ngff_image_meta.omero)
+    assert ngff_image_meta.omero.channels[0].window is None
+    assert ngff_image_meta.omero.channels[1].window is not None
+
 
 def test_ImageNgffMeta_missing_Z(ngffdata_path, caplog):
     ngff_image_meta = _load_and_validate(