Restore default values

Author: stephen-riggs

src/murfey/util/config.py

@@ -76,7 +76,7 @@ class MachineConfig(BaseModel):  # type: ignore
     processing_enabled: bool = True
     process_by_default: bool = True
     gain_directory_name: str = "processing"
-    process_multiple_datasets: bool = False
+    process_multiple_datasets: bool = True
     processed_directory_name: str = "processed"
     processed_extra_directory: str = ""
     recipes: dict[str, str] = {

src/murfey/util/processing_params.py

@@ -126,13 +126,13 @@ class SPAParameters(BaseModel):
     nr_iter_2d: int = 25
     nr_iter_3d: int = 25
     nr_iter_ini_model: int = 100
-    batch_size_2d: int = 1000  # just for fun
-    nr_classes_2d: int = 10
+    batch_size_2d: int = 50000
+    nr_classes_2d: int = 50
     nr_classes_3d: int = 4
     downscale: bool = True
     do_icebreaker_jobs: bool = True
-    fraction_of_classes_to_remove_2d: float = 0.3
-    nr_picks_before_diameter: int = 2000  # just for fun
+    fraction_of_classes_to_remove_2d: float = 0.7
+    nr_picks_before_diameter: int = 10000
     bfactor_min_particles: int = 2000
 
 

src/murfey/workflows/spa/picking.py

@@ -376,7 +376,6 @@ def _check_notifications(message: dict, murfey_db: Session) -> None:
 
 
 def particles_picked(message: dict, murfey_db: Session) -> dict[str, bool]:
-    logger.debug("New picked particle!")
     movie = murfey_db.exec(
         select(Movie).where(Movie.murfey_id == message["motion_correction_id"])
     ).one()
@@ -415,15 +414,9 @@ def particles_picked(message: dict, murfey_db: Session) -> dict[str, bool]:
             == _pj_id(message["program_id"], murfey_db)
         )
     ).one()
-    logger.debug(f"{feedback_params}")
-    print(feedback_params)
     if feedback_params.estimate_particle_diameter:
-        logger.debug("use diameter")
-        print("use diameter")
         _register_picked_particles_use_diameter(message, murfey_db)
     else:
-        logger.debug("use box size")
-        print("use box size")
         _register_picked_particles_use_boxsize(message, murfey_db)
     prom.preprocessed_movies.labels(
         processing_job=_pj_id(message["program_id"], murfey_db)