Added logic to try searching for XML metadata in other tag keys found in FIB atlas file if it's not found under the default key

Author: tieneupin

src/murfey/workflows/fib/register_atlas.py

@@ -92,10 +92,26 @@ def _parse_metadata(file: Path, visit_name: str):
     Parses through the atlas image's tags to extract the relevant metadata
     """
 
-    # Metadata is stored in the TIFF file under tag number 34683
+    # Search for the XML metadata in the tags (34683 is the default key)
     img = PIL.Image.open(file)
     tags = dict(img.tag_v2)
-    xml_metadata = ET.fromstring(str(tags.get(34683)))
+    xml_metadata = None
+    if (
+        isinstance((tag_contents := tags.get(34683)), str)
+        and "xml version" in tag_contents
+    ):
+        xml_metadata = ET.fromstring(tag_contents)
+    else:
+        logger.warning(
+            "Could not find metadata under tag key 34683, iterating through tags"
+        )
+        for key, value in tags.items():
+            if key == 34683:  # Already inspected
+                continue
+            if isinstance(value, str) and "xml version" in value:
+                xml_metadata = ET.fromstring(value)
+    if xml_metadata is None:
+        raise ValueError(f"Could not find required metadata in file {file}")
 
     # Extract key values from metadata
     return FIBAtlasMetadata(

tests/workflows/fib/test_register_atlas.py

@@ -134,6 +134,7 @@ def create_electron_snapshot_metadata(
     "test_params",
     (
         (
+            34683,  # Tag key
             "Electron Snapshot",
             "some_project",
             2000,  # Voltage
@@ -153,6 +154,7 @@ def create_electron_snapshot_metadata(
             1e-6,  # Y
         ),
         (
+            34682,  # Tag key
             "Electron Snapshot (2)",
             "another_project",
             2000,  # Voltage
@@ -176,6 +178,7 @@ def create_electron_snapshot_metadata(
 def test_parse_metadata(
     mocker: MockerFixture,
     test_params: tuple[
+        int,
         str,
         str,
         float,
@@ -198,6 +201,7 @@ def test_parse_metadata(
 ):
     # Unpack test params
     (
+        tag_key,
         image_name,
         project_name,
         voltage,
@@ -245,7 +249,9 @@ def test_parse_metadata(
         pixel_size_y,
     )
     mock_image = MagicMock()
-    mock_image.tag_v2 = {34683: xml_string}
+    tags = dict.fromkeys([*list(range(100)), *list(range(34600, 34700))], 0)
+    tags[tag_key] = xml_string
+    mock_image.tag_v2 = tags
     mocker.patch(
         "murfey.workflows.fib.register_atlas.PIL.Image.open",
         return_value=mock_image,