Override the tomography processing parameters with ones from web ui (#565)

Tomography processing did not allow a dose of zero, which happens if the instrument server is reconnected. This ensures that in that case the processing parameters in the `SessionProcessingParameters` table are used.

Author: stephen-riggs

src/murfey/server/__init__.py

@@ -1948,7 +1948,9 @@ def _register_bfactors(message: dict, _db=murfey_db, demo: bool = False):
 
     if message["symmetry"] != relion_params.symmetry:
         # Currently don't do anything with a symmetrised re-run of the refinement
-        logger.info(f"Recieved symmetrised structure of {message['symmetry']}")
+        logger.info(
+            f"Received symmetrised structure of {sanitise(message['symmetry'])}"
+        )
         return True
 
     if not feedback_params.hold_refine:

src/murfey/server/api/__init__.py

@@ -90,7 +90,6 @@
     MillingParameters,
     PostInfo,
     PreprocessingParametersTomo,
-    ProcessFile,
     ProcessingJobParameters,
     ProcessingParametersSPA,
     ProcessingParametersTomo,
@@ -104,6 +103,7 @@
     TiltInfo,
     TiltSeriesGroupInfo,
     TiltSeriesInfo,
+    TomoProcessFile,
     Visit,
 )
 from murfey.util.processing_params import default_spa_parameters
@@ -1210,7 +1210,10 @@ async def request_spa_preprocessing(
 
 @router.post("/visits/{visit_name}/{session_id}/tomography_preprocess")
 async def request_tomography_preprocessing(
-    visit_name: str, session_id: MurfeySessionID, proc_file: ProcessFile, db=murfey_db
+    visit_name: str,
+    session_id: MurfeySessionID,
+    proc_file: TomoProcessFile,
+    db=murfey_db,
 ):
     instrument_name = (
         db.exec(select(Session).where(Session.id == session_id)).one().instrument_name
@@ -1260,15 +1263,15 @@ async def request_tomography_preprocessing(
         if not mrc_out.parent.exists():
             mrc_out.parent.mkdir(parents=True, exist_ok=True)
 
-        processing_job_parameters = db.exec(
-            select(TomographyProcessingParameters).where(
-                TomographyProcessingParameters.pj_id == data_collection[0][2].id
+        session_processing_parameters = db.exec(
+            select(SessionProcessingParameters).where(
+                SessionProcessingParameters.session_id == session_id
             )
         ).all()
-        if processing_job_parameters:
-            proc_file.gain_ref = processing_job_parameters[0].gain_ref
-            proc_file.dose_per_frame = processing_job_parameters[0].dose_per_frame
-            proc_file.eer_fractionation_file = processing_job_parameters[
+        if session_processing_parameters:
+            proc_file.gain_ref = session_processing_parameters[0].gain_ref
+            proc_file.dose_per_frame = session_processing_parameters[0].dose_per_frame
+            proc_file.eer_fractionation_file = session_processing_parameters[
                 0
             ].eer_fractionation_file
 

src/murfey/server/demo_api.py

@@ -73,7 +73,6 @@
     GridSquareParameters,
     PostInfo,
     PreprocessingParametersTomo,
-    ProcessFile,
     ProcessingJobParameters,
     ProcessingParametersSPA,
     ProcessingParametersTomo,
@@ -86,6 +85,7 @@
     TiltInfo,
     TiltSeriesGroupInfo,
     TiltSeriesInfo,
+    TomoProcessFile,
     Visit,
 )
 from murfey.util.processing_params import default_spa_parameters
@@ -1196,7 +1196,7 @@ def flush_tomography_processing(
 
 @router.post("/visits/{visit_name}/{client_id}/tomography_preprocess")
 async def request_tomography_preprocessing(
-    visit_name: str, client_id: int, proc_file: ProcessFile, db=murfey_db
+    visit_name: str, client_id: int, proc_file: TomoProcessFile, db=murfey_db
 ):
     if not sanitise_path(Path(proc_file.path)).exists():
         log.warning(

src/murfey/util/models.py

@@ -308,13 +308,13 @@ class Token(BaseModel):
 """
 
 
-class ProcessFile(BaseModel):  # Rename to TomoProcessFile
+class TomoProcessFile(BaseModel):
     path: str
     description: str
     tag: str
     image_number: int
     pixel_size: float
-    dose_per_frame: float
+    dose_per_frame: Optional[float]
     frame_count: int
     tilt_axis: Optional[float]
     mc_uuid: Optional[int] = None
@@ -350,7 +350,7 @@ class CompletedTiltSeries(BaseModel):
 
 
 class PreprocessingParametersTomo(BaseModel):
-    dose_per_frame: float
+    dose_per_frame: Optional[float]
     frame_count: int
     tilt_axis: float
     gain_ref: Optional[str]