Removing static imports

Author: Koldstream

src/murfey/server/api/session_info.py

@@ -176,7 +176,6 @@ def create_session(
         instrument_name=instrument_name,
         visit_end_time=visit_end_time.end_time,
     )
-    print(db)
     db.add(s)
     db.commit()
     sid = s.id

src/murfey/server/feedback.py

@@ -693,7 +693,7 @@ def _register_complete_2d_batch(message: dict, _db):
     ).one()
     _db.expunge(relion_params)
     _db.expunge(feedback_params)
-    if feedback_params.hold_class2d or feedback_params.picker_ispyb_id is None:
+    if feedback_params.hold_class2d:
         feedback_params.rerun_class2d = True
         _db.add(feedback_params)
         _db.commit()
@@ -1007,15 +1007,15 @@ def _register_class_selection(message: dict, _db):
     ).one()
     _db.expunge(feedback_params)
 
-    if feedback_params.picker_ispyb_id is None:
+    """if feedback_params.picker_ispyb_id is None:
         selection_stash = db.SelectionStash(
             pj_id=pj_id,
             class_selection_score=message["class_selection_score"] or 0,
         )
         _db.add(selection_stash)
         _db.commit()
         _db.close()
-        return
+        return"""
 
     feedback_params.class_selection_score = message.get("class_selection_score") or 0
     feedback_params.hold_class2d = False

src/murfey/util/processing_params.py

@@ -49,7 +49,7 @@ def motion_corrected_mrc(
     extra_path = machine_config.processed_extra_directory
     """
 
-    job_number = get_current_job_number(visit_name, machine_config)
+    #job_number = get_current_job_number(visit_name, machine_config)
 
     mrc_out = (
         Path(visit_name)
@@ -100,13 +100,13 @@ class SPAParameters(BaseModel):
     nr_iter_2d: int = 25
     nr_iter_3d: int = 25
     nr_iter_ini_model: int = 100
-    batch_size_2d: int = 50000
-    nr_classes_2d: int = 50
+    batch_size_2d: int = 1000 # just for fun
+    nr_classes_2d: int = 10
     nr_classes_3d: int = 4
     downscale: bool = True
     do_icebreaker_jobs: bool = True
-    fraction_of_classes_to_remove_2d: float = 0.7
-    nr_picks_before_diameter: int = 10000
+    fraction_of_classes_to_remove_2d: float = 0.3
+    nr_picks_before_diameter: int = 2000 # just for fun
     bfactor_min_particles: int = 2000
 
 

src/murfey/workflows/spa/flush_spa_preprocess.py

@@ -6,7 +6,7 @@
 from sqlalchemy.exc import NoResultFound
 from sqlmodel import Session, select
 
-from murfey.server import _transport_object
+import murfey.server
 from murfey.server.feedback import _murfey_id
 from murfey.util import sanitise, secure_path
 from murfey.util.config import get_machine_config, get_microscope
@@ -82,16 +82,16 @@ def register_grid_square(
         )
         grid_square.pixel_size = grid_square_params.pixel_size or grid_square.pixel_size
         grid_square.image = grid_square_params.image or grid_square.image
-        if _transport_object:
-            _transport_object.do_update_grid_square(grid_square.id, grid_square_params)
+        if murfey.server._transport_object:
+            murfey.server._transport_object.do_update_grid_square(grid_square.id, grid_square_params)
     except Exception:
-        if _transport_object:
+        if murfey.server._transport_object:
             dcg = murfey_db.exec(
                 select(DataCollectionGroup)
                 .where(DataCollectionGroup.session_id == session_id)
                 .where(DataCollectionGroup.tag == grid_square_params.tag)
             ).one()
-            gs_ispyb_response = _transport_object.do_insert_grid_square(
+            gs_ispyb_response = murfey.server._transport_object.do_insert_grid_square(
                 dcg.atlas_id, gsid, grid_square_params
             )
         else:
@@ -179,13 +179,13 @@ def register_foil_hole(
             foil_hole_params.thumbnail_size_y or foil_hole.thumbnail_size_y
         ) or jpeg_size[1]
         foil_hole.pixel_size = foil_hole_params.pixel_size or foil_hole.pixel_size
-        if _transport_object and gs.readout_area_x:
-            _transport_object.do_update_foil_hole(
+        if murfey.server._transport_object and gs.readout_area_x:
+            murfey.server._transport_object.do_update_foil_hole(
                 foil_hole.id, gs.thumbnail_size_x / gs.readout_area_x, foil_hole_params
             )
     except Exception:
-        if _transport_object:
-            fh_ispyb_response = _transport_object.do_insert_foil_hole(
+        if murfey.server._transport_object:
+            fh_ispyb_response = murfey.server._transport_object.do_insert_foil_hole(
                 gs.id,
                 gs.thumbnail_size_x / gs.readout_area_x if gs.readout_area_x else None,
                 foil_hole_params,
@@ -440,11 +440,11 @@ def flush_spa_preprocess(message: dict, murfey_db: Session) -> dict[str, bool]:
                 "foil_hole_id": foil_hole_id,
             },
         }
-        if _transport_object:
+        if murfey.server._transport_object:
             zocalo_message["parameters"]["feedback_queue"] = (
-                _transport_object.feedback_queue
+                murfey.server._transport_object.feedback_queue
             )
-            _transport_object.send(
+            murfey.server._transport_object.send(
                 "processing_recipe", zocalo_message, new_connection=True
             )
             murfey_db.delete(f)

src/murfey/workflows/spa/picking.py

@@ -6,7 +6,7 @@
 from sqlmodel import Session, select
 
 import murfey.server.prometheus as prom
-from murfey.server import _transport_object
+import murfey.server
 from murfey.server.feedback import (
     _app_id,
     _flush_class2d,
@@ -83,13 +83,14 @@ def _register_picked_particles_use_diameter(message: dict, _db: Session):
         particle_diameter = relion_params.particle_diameter
 
         if feedback_params.picker_ispyb_id is None:
-            if not _transport_object:
+            if not murfey.server._transport_object:
                 feedback_params.picker_ispyb_id = 1000
             else:
                 assert feedback_params.picker_murfey_id is not None
-                feedback_params.picker_ispyb_id = _transport_object.do_buffer_lookup(
+                """feedback_params.picker_ispyb_id = murfey.server._transport_object.do_buffer_lookup(
                     message["program_id"], feedback_params.picker_murfey_id
-                )
+                )"""
+
                 if feedback_params.picker_ispyb_id is not None:
                     _flush_class2d(message["session_id"], message["program_id"], _db)
             _db.add(feedback_params)
@@ -152,11 +153,11 @@ def _register_picked_particles_use_diameter(message: dict, _db: Session):
                     },
                     "recipes": ["em-spa-extract"],
                 }
-                if _transport_object:
+                if murfey.server._transport_object:
                     zocalo_message["parameters"]["feedback_queue"] = (
-                        _transport_object.feedback_queue
+                        murfey.server._transport_object.feedback_queue
                     )
-                    _transport_object.send(
+                    murfey.server._transport_object.send(
                         "processing_recipe", zocalo_message, new_connection=True
                     )
         else:
@@ -192,11 +193,11 @@ def _register_picked_particles_use_diameter(message: dict, _db: Session):
                 },
                 "recipes": ["em-spa-extract"],
             }
-            if _transport_object:
+            if murfey.server._transport_object:
                 zocalo_message["parameters"]["feedback_queue"] = (
-                    _transport_object.feedback_queue
+                    murfey.server._transport_object.feedback_queue
                 )
-                _transport_object.send(
+                murfey.server._transport_object.send(
                     "processing_recipe", zocalo_message, new_connection=True
                 )
 
@@ -252,11 +253,11 @@ def _register_picked_particles_use_boxsize(message: dict, _db: Session):
         )
     ).one()
 
-    if feedback_params.picker_ispyb_id is None and _transport_object:
+    if feedback_params.picker_ispyb_id is None and murfey.server._transport_object:
         assert feedback_params.picker_murfey_id is not None
-        feedback_params.picker_ispyb_id = _transport_object.do_buffer_lookup(
+        """feedback_params.picker_ispyb_id = murfey.server._transport_object.do_buffer_lookup(
             message["program_id"], feedback_params.picker_murfey_id
-        )
+        )"""
         if feedback_params.picker_ispyb_id is not None:
             _flush_class2d(message["session_id"], message["program_id"], _db)
         _db.add(feedback_params)
@@ -302,11 +303,11 @@ def _register_picked_particles_use_boxsize(message: dict, _db: Session):
         },
         "recipes": ["em-spa-extract"],
     }
-    if _transport_object:
+    if murfey.server._transport_object:
         zocalo_message["parameters"]["feedback_queue"] = (
-            _transport_object.feedback_queue
+            murfey.server._transport_object.feedback_queue
         )
-        _transport_object.send("processing_recipe", zocalo_message, new_connection=True)
+        murfey.server._transport_object.send("processing_recipe", zocalo_message, new_connection=True)
     _db.close()
 
 
@@ -319,8 +320,8 @@ def _request_email(
     config = get_machine_config(instrument_name=session.instrument_name)[
         session.instrument_name
     ]
-    if _transport_object:
-        _transport_object.send(
+    if murfey.server._transport_object:
+        murfey.server._transport_object.send(
             config.notifications_queue,
             {
                 "groupId": dcg_id,
@@ -427,6 +428,7 @@ 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()
@@ -439,9 +441,15 @@ 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)