Read energy and insert into ispyb

Author: stephen-riggs

src/murfey/client/contexts/sxt.py

@@ -61,11 +61,12 @@ def register_sxt_data_collection(
                 "source": str(self._basepath),
                 "tag": tilt_series,
                 "pixel_size_on_image": str(
-                    data_collection_parameters.get("pixel_size", 100)
+                    data_collection_parameters.get("pixel_size", 100) * 1e-10
                 ),
                 "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),
                 "voltage": 0,
             }
             capture_post(
@@ -177,16 +178,43 @@ def post_transfer(
                     ).tolist()
                     metadata["tilt_series_length"] = tilt_count_txrm[0]
 
+                if txrm_ole.exists("PositionInfo/AxisNames") and txrm_ole.exists(
+                    "PositionInfo/MotorPositions"
+                ):
+                    # The ImageInfo/Energy field is empty
+                    # Instead it needs extracting from the PositionInfo list
+                    axis_names = [
+                        i
+                        for i in txrm_ole.openstream("PositionInfo/AxisNames")
+                        .read()
+                        .decode("ascii")
+                        .split("\x00")
+                        if i
+                    ]
+                    axis_values = np.frombuffer(
+                        txrm_ole.openstream("PositionInfo/MotorPositions").getvalue(),
+                        np.float32,
+                    )
+                    if "Energy" in axis_names:
+                        energy_index = list(np.array(axis_names) == "Energy").index(
+                            True
+                        )
+                        metadata["energy"] = int(round(axis_values[energy_index]))
+
             if not metadata.get("has_reference", False):
                 logger.debug(f"Reference image {transferred_file} not processed")
                 return True
 
+            visit_index = transferred_file.parent.parts.index(environment.visit)
+            destination_search_dir = "/".join(
+                transferred_file.parent.parts[: visit_index + 2]
+            )
             self.register_sxt_data_collection(
                 tilt_series=transferred_file.stem,
                 data_collection_parameters=metadata,
                 file_extension=transferred_file.suffix,
                 image_directory=environment.default_destinations.get(
-                    transferred_file.parent, transferred_file.parent
+                    Path(destination_search_dir), destination_search_dir
                 ),
                 environment=environment,
             )

src/murfey/server/api/workflow.py

@@ -301,6 +301,7 @@ class DCParameters(BaseModel):
     exposure_time: Optional[float] = None
     slit_width: Optional[float] = None
     phase_plate: bool = False
+    energy: float = 0
     data_collection_tag: str = ""
 
 
@@ -327,6 +328,7 @@ def start_dc(
         "image_directory": str(rsync_basepath / dc_params.image_directory),
         "start_time": str(datetime.now()),
         "voltage": dc_params.voltage,
+        "energy": dc_params.energy,
         "pixel_size": str(float(dc_params.pixel_size_on_image) * 1e9),
         "image_suffix": dc_params.file_extension,
         "experiment_type": dc_params.experiment_type,

src/murfey/workflows/register_data_collection.py

@@ -65,6 +65,7 @@ def run(message: dict, murfey_db: SQLModelSession) -> dict[str, bool]:
                 imageDirectory=message["image_directory"],
                 imageSuffix=message["image_suffix"],
                 voltage=message["voltage"],
+                wavelength=message["energy"],
                 dataCollectionGroupId=dcgid,
                 pixelSizeOnImage=message["pixel_size"],
                 imageSizeX=message["image_size_x"],
@@ -81,7 +82,11 @@ def run(message: dict, murfey_db: SQLModelSession) -> dict[str, bool]:
                 tag=(
                     message.get("tag")
                     if message["experiment_type"] == "tomography"
-                    else ""
+                    else (
+                        message.get("tag", "").split("_angle")[0]
+                        if message["experiment_type"] == "sxt"
+                        else ""
+                    )
                 ),
             ).get("return_value", None)
             if dcid is None: