Scale search map dimensions and location to be those on jpg (#635)

The size and location of the search maps we insert into ispyb are currently those on the atlas mrc. This scales them to be those on the jpg, and also scales the location of tomograms on search maps.

Also inserts an angle of 0 and handles inserting atlas pixel size when a data collection group is first made.

Something similar will probably be needed for the tomogram sizes on search maps, but that may need to be done in pato as there is an extra scaling based on pixel sizes as well.

Author: stephen-riggs

src/murfey/server/feedback.py

@@ -1982,6 +1982,7 @@ def feedback_callback(header: dict, message: dict) -> None:
                         session_id=message["session_id"],
                         tag=message.get("tag"),
                     )
+                    dcgid = murfey_dcg.id
                 else:
                     record = DataCollectionGroup(
                         sessionId=ispyb_session_id,
@@ -1999,9 +2000,14 @@ def feedback_callback(header: dict, message: dict) -> None:
                         atlas_id = murfey.server._transport_object.do_insert_atlas(
                             atlas_record
                         )["return_value"]
+                    else:
+                        atlas_id = None
                     murfey_dcg = db.DataCollectionGroup(
                         id=dcgid,
                         atlas_id=atlas_id,
+                        atlas=message.get("atlas", ""),
+                        atlas_pixel_size=message.get("atlas_pixel_size"),
+                        sample=message.get("sample"),
                         session_id=message["session_id"],
                         tag=message.get("tag"),
                     )

src/murfey/server/ispyb.py

@@ -405,13 +405,34 @@ def do_insert_search_map(
             search_map_parameters.pixel_size *= (
                 search_map_parameters.height / search_map_parameters.height_on_atlas
             )
+        search_map_parameters.height = (
+            int(search_map_parameters.height / 7.8)
+            if search_map_parameters.height
+            else None
+        )
+        search_map_parameters.width = (
+            int(search_map_parameters.width / 7.8)
+            if search_map_parameters.width
+            else None
+        )
+        search_map_parameters.x_location = (
+            int(search_map_parameters.x_location / 7.8)
+            if search_map_parameters.x_location
+            else None
+        )
+        search_map_parameters.y_location = (
+            int(search_map_parameters.y_location / 7.8)
+            if search_map_parameters.y_location
+            else None
+        )
         record = GridSquare(
             atlasId=atlas_id,
             gridSquareImage=search_map_parameters.image,
             pixelLocationX=search_map_parameters.x_location,
             pixelLocationY=search_map_parameters.y_location,
             height=search_map_parameters.height_on_atlas,
             width=search_map_parameters.width_on_atlas,
+            angle=0,
             stageLocationX=search_map_parameters.x_stage_position,
             stageLocationY=search_map_parameters.y_stage_position,
             pixelSize=search_map_parameters.pixel_size,
@@ -452,13 +473,19 @@ def do_update_search_map(
                 if search_map_parameters.image:
                     grid_square.gridSquareImage = search_map_parameters.image
                 if search_map_parameters.x_location:
-                    grid_square.pixelLocationX = search_map_parameters.x_location
+                    grid_square.pixelLocationX = int(
+                        search_map_parameters.x_location / 7.8
+                    )
                 if search_map_parameters.y_location:
-                    grid_square.pixelLocationY = search_map_parameters.y_location
+                    grid_square.pixelLocationY = int(
+                        search_map_parameters.y_location / 7.8
+                    )
                 if search_map_parameters.height_on_atlas:
-                    grid_square.height = search_map_parameters.height_on_atlas
+                    grid_square.height = int(
+                        search_map_parameters.height_on_atlas / 7.8
+                    )
                 if search_map_parameters.width_on_atlas:
-                    grid_square.width = search_map_parameters.width_on_atlas
+                    grid_square.width = int(search_map_parameters.width_on_atlas / 7.8)
                 if search_map_parameters.x_stage_position:
                     grid_square.stageLocationX = search_map_parameters.x_stage_position
                 if search_map_parameters.y_stage_position:

src/murfey/workflows/tomo/tomo_metadata.py

@@ -339,10 +339,20 @@ def register_batch_position_in_database(
             search_map.height / 2,
         ]
         tilt_series.x_location = (
-            centre_batch_pixel[0] - batch_parameters.x_beamshift / search_map.pixel_size
+            (
+                centre_batch_pixel[0]
+                - batch_parameters.x_beamshift / search_map.pixel_size
+            )
+            * 512
+            / search_map.width
         )
         tilt_series.y_location = (
-            centre_batch_pixel[1] - batch_parameters.y_beamshift / search_map.pixel_size
+            (
+                centre_batch_pixel[1]
+                - batch_parameters.y_beamshift / search_map.pixel_size
+            )
+            * 512
+            / search_map.width
         )
     else:
         logger.warning(

tests/workflows/tomo/test_tomo_metadata.py

@@ -249,8 +249,8 @@ def test_register_batch_position_update(murfey_db_session: Session):
 
     # These two should have been updated, values are known as used identity matrices
     bp_final_parameters = murfey_db_session.exec(select(TiltSeries)).one()
-    assert bp_final_parameters.x_location == 880
-    assert bp_final_parameters.y_location == 1780
+    assert bp_final_parameters.x_location == 880 * 512 / search_map.width
+    assert bp_final_parameters.y_location == 1780 * 512 / search_map.width
 
 
 def test_register_batch_position_update_skip(murfey_db_session: Session):
@@ -361,5 +361,5 @@ def test_register_batch_position_new(murfey_db_session: Session):
 
     # These two should have been updated, values are known as used identity matrices
     bp_final_parameters = murfey_db_session.exec(select(TiltSeries)).one()
-    assert bp_final_parameters.x_location == 880
-    assert bp_final_parameters.y_location == 1780
+    assert bp_final_parameters.x_location == 880 * 512 / search_map.width
+    assert bp_final_parameters.y_location == 1780 * 512 / search_map.width