Scale search map dimensions and location to be those on jpg

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