Fixes for gridsquare registration in SmartEM (#783)

Author: d-j-hatton

src/murfey/client/contexts/spa_metadata.py

@@ -84,6 +84,7 @@ def __init__(
         super().__init__("SPAMetadataContext", acquisition_software, token)
         self._basepath = basepath
         self._machine_config = machine_config
+        self._registered_squares: set[int] = set()
 
     def post_transfer(
         self,
@@ -243,39 +244,44 @@ def post_transfer(
                     },
                 )
 
-            for fh, fh_data in fh_positions.items():
-                capture_post(
-                    base_url=str(environment.url.geturl()),
-                    router_name="session_control.spa_router",
-                    function_name="register_foil_hole",
-                    token=self._token,
-                    instrument_name=environment.instrument_name,
-                    session_id=environment.murfey_session,
-                    gs_name=gs_name,
-                    data={
-                        "name": fh,
-                        "x_location": fh_data.x_location,
-                        "y_location": fh_data.y_location,
-                        "x_stage_position": fh_data.x_stage_position,
-                        "y_stage_position": fh_data.y_stage_position,
-                        "readout_area_x": fh_data.readout_area_x,
-                        "readout_area_y": fh_data.readout_area_y,
-                        "thumbnail_size_x": fh_data.thumbnail_size_x,
-                        "thumbnail_size_y": fh_data.thumbnail_size_y,
-                        "pixel_size": fh_data.pixel_size,
-                        "diameter": fh_data.diameter,
-                        "tag": visitless_source,
-                        "image": fh_data.image,
-                    },
-                )
-            if fh_positions:
-                capture_post(
-                    base_url=str(environment.url.geturl()),
-                    router_name="session_control.spa_router",
-                    function_name="register_square",
-                    token=self._token,
-                    instrument_name=environment.instrument_name,
-                    session_id=environment.murfey_session,
-                    gsid=gs_name,
-                    data={"tag": visitless_source},
-                )
+            if gs_name not in self._registered_squares:
+                for fh, fh_data in fh_positions.items():
+                    capture_post(
+                        base_url=str(environment.url.geturl()),
+                        router_name="session_control.spa_router",
+                        function_name="register_foil_hole",
+                        token=self._token,
+                        instrument_name=environment.instrument_name,
+                        session_id=environment.murfey_session,
+                        gs_name=gs_name,
+                        data={
+                            "name": fh,
+                            "x_location": fh_data.x_location,
+                            "y_location": fh_data.y_location,
+                            "x_stage_position": fh_data.x_stage_position,
+                            "y_stage_position": fh_data.y_stage_position,
+                            "readout_area_x": fh_data.readout_area_x,
+                            "readout_area_y": fh_data.readout_area_y,
+                            "thumbnail_size_x": fh_data.thumbnail_size_x,
+                            "thumbnail_size_y": fh_data.thumbnail_size_y,
+                            "pixel_size": fh_data.pixel_size,
+                            "diameter": fh_data.diameter,
+                            "tag": visitless_source,
+                            "image": fh_data.image,
+                        },
+                    )
+                if fh_positions:
+                    capture_post(
+                        base_url=str(environment.url.geturl()),
+                        router_name="session_control.spa_router",
+                        function_name="register_square",
+                        token=self._token,
+                        instrument_name=environment.instrument_name,
+                        session_id=environment.murfey_session,
+                        gsid=gs_name,
+                        data={
+                            "tag": visitless_source,
+                            "count": len(self._registered_squares) + 1,
+                        },
+                    )
+                    self._registered_squares.add(gs_name)

src/murfey/server/api/session_control.py

@@ -417,6 +417,7 @@ def register_atlas(
 
 class SquareRegistration(BaseModel):
     tag: str
+    count: int | None = None
 
 
 @spa_router.post("/sessions/{session_id}/register_square/{gsid}")
@@ -442,7 +443,9 @@ def register_square(
                 smartem_client = SmartEMAPIClient(
                     base_url=machine_config.smartem_api_url, logger=logger
                 )
-                smartem_client.gridsquare_registered(gs.smartem_uuid)
+                smartem_client.gridsquare_registered(
+                    gs.smartem_uuid, count=square_registration_data.count
+                )
     else:
         logger.info("smartem deactivated so did not register square")
 

src/murfey/workflows/spa/flush_spa_preprocess.py

@@ -11,6 +11,7 @@
     from smartem_common.schemas import (
         FoilHoleData as SmartEMFoilHoleData,
         GridSquareData as SmartEMGridSquareData,
+        GridSquareMetadata as SmartEMGridSquareMetadata,
     )
 
     SMARTEM_ACTIVE = True
@@ -154,6 +155,21 @@ def register_grid_square(
                     .where(DataCollectionGroup.tag == grid_square_params.tag)
                 ).one_or_none()
                 if dcg and dcg.smartem_grid_uuid:
+                    secured_grid_square_image_path_full_res: Path | None = None
+                    if grid_square_params.image:
+                        secured_grid_square_image_path_full_res = secure_path(
+                            Path(grid_square_params.image)
+                        )
+                        if secured_grid_square_image_path_full_res.with_suffix(
+                            ".tiff"
+                        ).is_file():
+                            secured_grid_square_image_path_full_res = (
+                                secured_grid_square_image_path_full_res.with_suffix(".tiff")
+                            )
+                        else:
+                            secured_grid_square_image_path_full_res = (
+                                secured_grid_square_image_path_full_res.with_suffix(".mrc")
+                            )
                     smartem_client = SmartEMAPIClient(
                         base_url=machine_config.smartem_api_url, logger=logger
                     )
@@ -177,6 +193,15 @@ def register_grid_square(
                             if grid_square.smartem_uuid
                             else {}
                         ),
+                        metadata=SmartEMGridSquareMetadata(
+                            atlas_node_id=0,
+                            stage_position=None,
+                            state=None,
+                            rotation=None,
+                            image_path=secured_grid_square_image_path_full_res,
+                            selected=False,
+                            unusable=False,
+                        ),
                     )
                     if grid_square.smartem_uuid:
                         smartem_client.update_gridsquare(gs_data)