Insert tomogram positions on search maps

pyproject.toml

@@ -34,7 +34,7 @@ dependencies = [
     "graypy",
     "healpy",
     "icebreaker-em",
-    "ispyb>=11.0.3",
+    "ispyb>=11.0.5",
     "mrcfile",
     "numpy<2",
     "pillow",

recipes/em-tomo-align.json

@@ -5,7 +5,10 @@
       "dcid": "{dcid}",
       "ispyb_command": "insert_tomogram",
       "program_id": "{appid}",
-      "store_result": "ispyb_tomogram_id"
+      "store_result": "ispyb_tomogram_id",
+      "pixel_location_x": "{x_location}",
+      "pixel_location_y": "{y_location}",
+      "grid_square_id": "{search_map_id}"
     },
     "queue": "ispyb_connector",
     "service": "EMISPyB"

src/cryoemservices/util/ispyb_commands.py

@@ -616,6 +616,9 @@ def full_parameters(param):
             projXY=full_parameters("proj_xy"),
             projXZ=full_parameters("proj_xz"),
             globalAlignmentQuality=full_parameters("alignment_quality"),
+            gridSquareId=full_parameters("grid_square_id"),
+            pixelLocationX=full_parameters("pixel_location_x"),
+            pixelLocationY=full_parameters("pixel_location_y"),
         )
         tomogram_row = (
             session.query(models.Tomogram)

tests/recipes/test_recipes.py

@@ -46,6 +46,9 @@ class ISPyBParameters(BaseModel):
     status: str
     store_result: str
     tomogram_id: int
+    grid_square_id: int
+    pixel_location_x: float
+    pixel_location_y: float
 
 
 class MurfeyParameters(BaseModel):

tests/util/test_ispyb_commands.py

@@ -744,6 +744,9 @@ def mock_tomogram_parameters(p):
             "proj_xy": "/path/to/xy",
             "proj_xz": "/path/to/xz",
             "alignment_quality": 0.2,
+            "grid_square_id": 12345,
+            "pixel_location_x": 200,
+            "pixel_location_y": 400,
         }
         return tomogram_parameters[p]
 
@@ -783,6 +786,9 @@ def mock_tomogram_parameters(p):
         projXY="/path/to/xy",
         projXZ="/path/to/xz",
         globalAlignmentQuality=0.2,
+        gridSquareId=12345,
+        pixelLocationX=200,
+        pixelLocationY=400,
     )
     mock_session.add.assert_called()
     mock_session.commit.assert_called()
@@ -812,6 +818,9 @@ def mock_tomogram_parameters(p):
             "proj_xy": "/path/to/xy",
             "proj_xz": "/path/to/xz",
             "alignment_quality": 0.2,
+            "grid_square_id": 12345,
+            "pixel_location_x": 200,
+            "pixel_location_y": 400,
         }
         return tomogram_parameters[p]
 
@@ -852,6 +861,9 @@ def mock_tomogram_parameters(p):
             "projXY": "/path/to/xy",
             "projXZ": "/path/to/xz",
             "globalAlignmentQuality": 0.2,
+            "gridSquareId": 12345,
+            "pixelLocationX": 200,
+            "pixelLocationY": 400,
         }
     )
     mock_session.add.assert_not_called()