Insert tilt series start, end, length into ispyb

Author: stephen-riggs

src/murfey/client/contexts/sxt.py

@@ -66,8 +66,13 @@ def register_sxt_data_collection(
                 "image_size_x": data_collection_parameters.get("image_size_x", 0),
                 "image_size_y": data_collection_parameters.get("image_size_y", 0),
                 "magnification": data_collection_parameters.get("magnification", 0),
-                "energy": data_collection_parameters.get("energy", 0),
+                "energy": data_collection_parameters.get("energy"),
                 "voltage": 0,
+                "axis_start": data_collection_parameters.get("minimum_angle"),
+                "axis_end": data_collection_parameters.get("maximum_angle"),
+                "tilt_series_length": data_collection_parameters.get(
+                    "tilt_series_length"
+                ),
             }
             capture_post(
                 base_url=str(environment.url.geturl()),

src/murfey/server/api/workflow.py

@@ -290,12 +290,15 @@ class DCParameters(BaseModel):
     tag: str
     source: str
     magnification: float
-    total_exposed_dose: Optional[float] = None
-    c2aperture: Optional[float] = None
-    exposure_time: Optional[float] = None
-    slit_width: Optional[float] = None
+    total_exposed_dose: float | None = None
+    c2aperture: float | None = None
+    exposure_time: float | None = None
+    slit_width: float | None = None
     phase_plate: bool = False
-    energy: float = 0
+    energy: float | None = None
+    axis_start: float | None = None
+    axis_end: float | None = None
+    tilt_series_length: int | None = None
     data_collection_tag: str = ""
 
 
@@ -337,6 +340,9 @@ def start_dc(
         "exposure_time": dc_params.exposure_time,
         "slit_width": dc_params.slit_width,
         "phase_plate": dc_params.phase_plate,
+        "axis_start": dc_params.axis_start,
+        "axis_end": dc_params.axis_end,
+        "tilt_series_length": dc_params.tilt_series_length,
         "session_id": session_id,
     }
 

src/murfey/workflows/register_data_collection.py

@@ -76,6 +76,9 @@ def run(message: dict, murfey_db: SQLModelSession) -> dict[str, bool]:
                 totalExposedDose=message.get("total_exposed_dose"),
                 c2aperture=message.get("c2aperture"),
                 phasePlate=int(message.get("phase_plate", 0)),
+                axisStart=message.get("axis_start"),
+                axisEnd=message.get("axis_end"),
+                numberOfImages=message.get("tilt_series_length"),
             )
             dcid = _transport_object.do_insert_data_collection(
                 record,

tests/client/contexts/test_sxt.py

@@ -120,6 +120,9 @@ def test_sxt_context_txrm(mock_ole_file, mock_post, tmp_path):
             "magnification": 1000,
             "energy": 519,
             "voltage": 0,
+            "axis_start": -55,
+            "axis_end": 65,
+            "tilt_series_length": 5,
         },
         headers={"Authorization": "Bearer "},
     )

tests/workflows/test_register_data_collection.py

@@ -86,6 +86,9 @@ def test_run(
         "total_exposed_dose": 30,
         "c2aperture": 5,
         "phase_plate": 1,
+        "axis_start": -60,
+        "axis_end": 55,
+        "tilt_series_length": 250,
     }
     result = run(message=message, murfey_db=mock_murfey_db)
     if dcg_result is None: