Read whether a search map is a lamella and request hooks (#820)

* Adds a lamella column to the search map database table
* Reads lamella status from the Session.dm file when registering search maps
* Runs any hooks with the name murfey.hooks.search_map, giving ispyb id, file path, lamella status and pixel size

Author: stephen-riggs

src/murfey/client/contexts/tomo_metadata.py

@@ -150,6 +150,19 @@ def post_transfer(
                 else ""
             )
 
+            # Read the session dm to find out if this is a lamella search map or not
+            lamella = None
+            if source and (source / "Session.dm").is_file():
+                with open(source / "Session.dm") as xml:
+                    session_xml = xmltodict.parse(xml.read())
+                lamella_workflow = session_xml.get("TomographySession", {}).get(
+                    "LamellaWorkflow", None
+                )
+                if lamella_workflow:
+                    lamella = lamella_workflow == "true"
+            else:
+                logger.warning("Cannot find tomography Session.dm file")
+
             capture_post(
                 base_url=str(environment.url.geturl()),
                 router_name="session_control.tomo_router",
@@ -168,6 +181,7 @@ def post_transfer(
                     "reference_matrix": ref_matrix,
                     "stage_correction": stage_matrix,
                     "image_shift_correction": image_matrix,
+                    "lamella": lamella,
                 },
             )
 

src/murfey/util/db.py

@@ -556,41 +556,42 @@ class SearchMap(SQLModel, table=True):  # type: ignore
     session_id: int = Field(foreign_key="session.id")
     name: str
     tag: str
-    x_location: Optional[float] = None
-    y_location: Optional[float] = None
-    x_stage_position: Optional[float] = None
-    y_stage_position: Optional[float] = None
-    pixel_size: Optional[float] = None
+    lamella: bool | None = None
+    x_location: float | None = None
+    y_location: float | None = None
+    x_stage_position: float | None = None
+    y_stage_position: float | None = None
+    pixel_size: float | None = None
     image: str = ""
-    binning: Optional[float] = None
-    reference_matrix_m11: Optional[float] = None
-    reference_matrix_m12: Optional[float] = None
-    reference_matrix_m21: Optional[float] = None
-    reference_matrix_m22: Optional[float] = None
-    stage_correction_m11: Optional[float] = None
-    stage_correction_m12: Optional[float] = None
-    stage_correction_m21: Optional[float] = None
-    stage_correction_m22: Optional[float] = None
-    image_shift_correction_m11: Optional[float] = None
-    image_shift_correction_m12: Optional[float] = None
-    image_shift_correction_m21: Optional[float] = None
-    image_shift_correction_m22: Optional[float] = None
-    width: Optional[int] = None
-    height: Optional[int] = None
+    binning: float | None = None
+    reference_matrix_m11: float | None = None
+    reference_matrix_m12: float | None = None
+    reference_matrix_m21: float | None = None
+    reference_matrix_m22: float | None = None
+    stage_correction_m11: float | None = None
+    stage_correction_m12: float | None = None
+    stage_correction_m21: float | None = None
+    stage_correction_m22: float | None = None
+    image_shift_correction_m11: float | None = None
+    image_shift_correction_m12: float | None = None
+    image_shift_correction_m21: float | None = None
+    image_shift_correction_m22: float | None = None
+    width: int | None = None
+    height: int | None = None
     session: Optional[Session] = Relationship(back_populates="search_maps")
     tilt_series: List["TiltSeries"] = Relationship(
         back_populates="search_map", sa_relationship_kwargs={"cascade": "delete"}
     )
-    atlas_id: Optional[int] = Field(
+    atlas_id: int | None = Field(
         foreign_key="datacollectiongroup.dataCollectionGroupId"
     )
-    scaled_pixel_size: Optional[float] = None
-    pixel_location_x: Optional[int] = None
-    pixel_location_y: Optional[int] = None
-    scaled_height: Optional[int] = None
-    scaled_width: Optional[int] = None
-    angle: Optional[float] = None
-    quality_indicator: Optional[float] = None
+    scaled_pixel_size: float | None = None
+    pixel_location_x: int | None = None
+    pixel_location_y: int | None = None
+    scaled_height: int | None = None
+    scaled_width: int | None = None
+    angle: float | None = None
+    quality_indicator: float | None = None
     data_collection_group: Optional["DataCollectionGroup"] = Relationship(
         back_populates="search_maps"
     )

src/murfey/util/models.py

@@ -317,20 +317,21 @@ class FoilHoleParameters(BaseModel):
 
 class SearchMapParameters(BaseModel):
     tag: str
-    x_location: Optional[float] = None
-    y_location: Optional[float] = None
-    x_stage_position: Optional[float] = None
-    y_stage_position: Optional[float] = None
-    pixel_size: Optional[float] = None
-    image: Optional[str] = None
-    binning: Optional[float] = None
+    x_location: float | None = None
+    y_location: float | None = None
+    x_stage_position: float | None = None
+    y_stage_position: float | None = None
+    pixel_size: float | None = None
+    image: str | None = None
+    binning: float | None = None
     reference_matrix: Dict[str, float] = {}
     stage_correction: Dict[str, float] = {}
     image_shift_correction: Dict[str, float] = {}
-    height: Optional[int] = None
-    width: Optional[int] = None
-    height_on_atlas: Optional[int] = None
-    width_on_atlas: Optional[int] = None
+    height: int | None = None
+    width: int | None = None
+    height_on_atlas: int | None = None
+    width_on_atlas: int | None = None
+    lamella: bool | None = None
 
 
 class BatchPositionParameters(BaseModel):

src/murfey/workflows/tomo/tomo_metadata.py

@@ -1,4 +1,5 @@
 import logging
+from importlib.metadata import entry_points
 
 import numpy as np
 from sqlmodel import Session, select
@@ -40,6 +41,7 @@ def register_search_map_in_database(
     if search_map_query:
         # See if there is already a search map with this name and update if so
         search_map = search_map_query[0]
+        search_map.lamella = search_map_params.lamella or search_map.lamella
         search_map.x_stage_position = (
             search_map_params.x_stage_position or search_map.x_stage_position
         )
@@ -120,6 +122,7 @@ def register_search_map_in_database(
             name=search_map_name,
             session_id=session_id,
             tag=search_map_params.tag,
+            lamella=search_map_params.lamella,
             x_stage_position=search_map_params.x_stage_position,
             y_stage_position=search_map_params.y_stage_position,
             pixel_size=search_map_params.pixel_size,
@@ -243,6 +246,18 @@ def register_search_map_in_database(
     if close_db:
         murfey_db.close()
 
+    if search_map_hooks := entry_points(group="murfey.hooks", name="search_map"):
+        try:
+            for hook in search_map_hooks:
+                hook.load()(
+                    ispyb_id=search_map.id,
+                    image=search_map_params.image,
+                    pixel_size=search_map_params.pixel_size,
+                    lamella=search_map_params.lamella,
+                )
+        except Exception as e:
+            logger.error(f"Call to search map hook failed with {e}", exc_info=True)
+
 
 def register_batch_position_in_database(
     session_id: MurfeySessionID,