Include lamella number as part of site name in FIB workflow

src/murfey/util/models.py

@@ -248,6 +248,7 @@ class FIBImageMetadata(BaseModel):
     visit_name: str
     file: Path
     thumbnail_path: Path | None = None
+    lamella_number: int | None = None
     # Acceleration voltage (V)
     voltage: float
     # Beam shifts (m)
@@ -309,7 +310,10 @@ def site_name(self) -> str:
         Create a site name for the current image based on the project name
         and its slot number.
         """
-        return f"{self.project_name}--slot_{self.slot_number}"
+        site_name = f"{self.project_name}/grid_{self.slot_number}"
+        if self.lamella_number is not None:
+            site_name += f"/lamella_{self.lamella_number}"
+        return site_name
 
 
 """

src/murfey/workflows/fib/register_milling_progress.py

@@ -43,7 +43,7 @@ def _ensure_prerequisites(
 
     """
     # Construct the DataCollectionGroup and GridSquare lookup tags
-    dcg_tag = f"{project_name}--slot_{slot_number}"
+    dcg_tag = f"{project_name}/grid_{slot_number}"
 
     # Determine variables to register data collection group and atlas with
     proposal_code = "".join(char for char in visit_name.split("-")[0] if char.isalpha())

src/murfey/workflows/fib/shared.py

@@ -11,7 +11,7 @@
 import PIL.Image
 
 from murfey.util.db import ImagingSite
-from murfey.util.fib import get_slot_number
+from murfey.util.fib import get_slot_number, number_from_name
 from murfey.util.models import FIBImageMetadata
 
 
@@ -101,6 +101,13 @@ def parse_image_metadata(
                 ),  # Convert to degrees
                 rotation_offset=rotation_offset,
             )
+            # Determine the lamella number
+            try:
+                parts = file.parts
+                site_idx = parts.index("Sites") + 1
+                extracted["lamella_number"] = number_from_name(parts[site_idx])
+            except ValueError:
+                extracted["lamella_number"] = None
         case _:
             raise NotImplementedError(
                 f"Unsupported metadata format {metadata_format!r}"

tests/workflows/fib/test_fib_shared.py

@@ -5,6 +5,7 @@
 import pytest
 from pytest_mock import MockerFixture
 
+from murfey.util.fib import number_from_name
 from murfey.util.models import FIBImageMetadata
 from murfey.workflows.fib.shared import parse_image_metadata
 from tests.conftest import ExampleVisit
@@ -134,8 +135,10 @@ def create_image_metadata(
     "test_params",
     (
         (
+            "autotem",
             "Metadata",  # Tag key
             "2026-04-15-21-50-14_drift_corrected_image_Finer Milling - Electron Image.png",
+            "Lamella",  # Lamella folder
             "some_project",
             2000,  # Voltage
             0,  # Beam shift X
@@ -156,8 +159,34 @@ def create_image_metadata(
             1e-6,  # Y
         ),
         (
+            "autotem",
             "Metadata",  # Tag key
             "2026-04-16-02-39-40_drift_corrected_image_Polishing 2 - Electron Image.png",
+            "Lamella (23)",  # Lamella folder
+            "another_project",
+            2000,  # Voltage
+            0,  # Beam shift X
+            0,  # Y
+            0.003072,  # Field of view X
+            0.002048,  # Y
+            -0.003,  # Stage X
+            0.0003,  # Y
+            0.01,  # Z
+            1.833,  # Rotation
+            -75,  # Rotation offset
+            0,  # Alpha tilt
+            0,  # Beta tilt
+            2,  # Expected slot number
+            3072,  # Image size X
+            2048,  # Y
+            1e-6,  # Pixel size X
+            1e-6,  # Y
+        ),
+        (
+            "maps",
+            34683,  # Tag key
+            "Electron Snapshot.tiff",
+            "",  # Lamella folder
             "another_project",
             2000,  # Voltage
             0,  # Beam shift X
@@ -182,6 +211,8 @@ def create_image_metadata(
 def test_parse_metadata(
     mocker: MockerFixture,
     test_params: tuple[
+        str,
+        str | int,
         str,
         str,
         str,
@@ -207,8 +238,10 @@ def test_parse_metadata(
 ):
     # Unpack test params
     (
+        workflow_name,
         tag_key,
         image_name,
+        lamella_folder,
         project_name,
         voltage,
         shift_x,
@@ -229,13 +262,25 @@ def test_parse_metadata(
         pixel_size_y,
     ) = test_params
     file = (
-        visit_dir
-        / "autotem"
-        / project_name
-        / "Sites"
-        / "Lamella"
-        / "LamellaEvaluationImages"
-        / image_name
+        (
+            visit_dir
+            / "autotem"
+            / project_name
+            / "Sites"
+            / lamella_folder
+            / "LamellaEvaluationImages"
+            / image_name
+        )
+        if workflow_name == "autotem"
+        else (
+            visit_dir
+            / "maps"
+            / project_name
+            / "LayersData"
+            / "Layer"
+            / "Electron Snapshot"
+            / image_name
+        )
     )
 
     # Mock the results of opening an image file
@@ -256,9 +301,15 @@ def test_parse_metadata(
         pixel_size_x,
         pixel_size_y,
     )
-    tags = dict.fromkeys(["Metadata", "MetadataAsINI"], 0)
-    tags[tag_key] = xml_string
-    mock_image = MagicMock(text=tags)
+    tags: dict[str | int, str | int]
+    if workflow_name == "autotem":
+        tags = dict.fromkeys(["Metadata", "MetadataAsINI"], 0)
+        tags[tag_key] = xml_string
+        mock_image = MagicMock(text=tags)
+    else:
+        tags = dict.fromkeys([34682, 34683], 0)
+        tags[tag_key] = xml_string
+        mock_image = MagicMock(tag_v2=tags)
     mocker.patch(
         "murfey.workflows.fib.shared.PIL.Image.open",
         return_value=mock_image,
@@ -273,6 +324,8 @@ def test_parse_metadata(
 
     assert parsed.visit_name == visit_name
     assert parsed.file == file
+    lamella_number = number_from_name(lamella_folder) if lamella_folder else None
+    assert parsed.lamella_number == lamella_number
     assert parsed.voltage == voltage
     assert parsed.shift_x == shift_x
     assert parsed.shift_y == shift_y
@@ -289,5 +342,8 @@ def test_parse_metadata(
     assert parsed.pixel_size_x == pixel_size_x
     assert parsed.pixel_size_y == pixel_size_y
     assert parsed.slot_number == expected_slot_number
-    assert parsed.site_name == f"{project_name}--slot_{expected_slot_number}"
+    expected_site_name = f"{project_name}/grid_{expected_slot_number}"
+    if workflow_name == "autotem":
+        expected_site_name += f"/lamella_{lamella_number}"
+    assert parsed.site_name == expected_site_name
     assert parsed.pixel_size == 0.5 * (pixel_size_x + pixel_size_y)

tests/workflows/fib/test_register_milling_progress.py

@@ -414,7 +414,7 @@ def test_run_with_db(
         sm_select(MurfeyDB.DataCollectionGroup)
         .where(MurfeyDB.DataCollectionGroup.session_id == session_id)
         .where(
-            MurfeyDB.DataCollectionGroup.tag == f"{site_info['project_name']}--slot_1"
+            MurfeyDB.DataCollectionGroup.tag == f"{site_info['project_name']}/grid_1"
         )
     ).one_or_none()
     assert dcg_murfey is not None