Fall back to MICS cycle ID if Cycle is not present in v0 metadata

Author: MSHelm

src/spatialdata_io/readers/macsima.py

@@ -456,8 +456,12 @@ def _parse_v0_ome_metadata(ome: OME) -> dict[str, Any]:
         except (TypeError, ValueError):
             metadata["exposure"] = None
 
+    cyc = None
     if "Cycle" in ma_values:
         cyc = ma_values["Cycle"]
+    elif "MICS cycle ID" in ma_values:  # Very old formats do not have "Cycle", then use "MICS cycle ID"
+        cyc = ma_values["MICS cycle ID"]
+    if cyc:
         try:
             metadata["cycle"] = int(cyc)
         except (TypeError, ValueError):

tests/test_macsima.py

@@ -469,6 +469,34 @@ def test_parse_v0_ome_metadata_handles_missing_or_invalid_numeric_fields() -> No
     assert md["well"] is None
 
 
+def test_parse_v0_ome_metadata_falls_back_to_MICScycleID_if_no_cycle_keyword() -> None:
+    ome = OME(
+        structured_annotations=StructuredAnnotations(
+            map_annotations=[
+                MapAnnotation(
+                    value={
+                        "MICS cycle ID": "5",
+                    }
+                )
+            ]
+        ),
+    )
+
+    md = _parse_v0_ome_metadata(ome)
+    assert md["cycle"] == 5
+
+
+def test_parse_v0_ome_metadata_prefers_Cycle_over_MICScycleID_keyword() -> None:
+    ome = OME(
+        structured_annotations=StructuredAnnotations(
+            map_annotations=[MapAnnotation(value={"MICS cycle ID": "5", "Cycle": "1"})]
+        ),
+    )
+
+    md = _parse_v0_ome_metadata(ome)
+    assert md["cycle"] == 1
+
+
 def test_parse_v0_ome_metadata_bleach_cycle_appends_background() -> None:
     ome = OME(
         structured_annotations=StructuredAnnotations(