Stop passing so many parameters around

Author: stephen-riggs

src/murfey/client/contexts/spa.py

@@ -108,27 +108,9 @@ class SPAModularContext(Context):
             "Dose Per Frame [e- / Angstrom^2 / frame] (after EER grouping if relevant)",
             default=1,
         ),
-        ProcessingParameter(
-            "estimate_particle_diameter",
-            "Use crYOLO to Estimate Particle Diameter",
-            default=True,
-        ),
-        ProcessingParameter(
-            "particle_diameter", "Particle Diameter (Angstroms)", default=None
-        ),
-        ProcessingParameter("use_cryolo", "Use crYOLO Autopicking", default=True),
         ProcessingParameter("symmetry", "Symmetry Group", default="C1"),
         ProcessingParameter("eer_fractionation", "EER Fractionation", default=20),
-        ProcessingParameter(
-            "mask_diameter", "Mask Diameter (2D classification)", default=190
-        ),
-        ProcessingParameter("boxsize", "Box Size", default=256),
-        ProcessingParameter("downscale", "Downscale Extracted Particles", default=True),
-        ProcessingParameter(
-            "small_boxsize", "Downscaled Extracted Particle Size (pixels)", default=128
-        ),
         ProcessingParameter("gain_ref", "Gain Reference"),
-        ProcessingParameter("gain_ref_superres", "Unbinned Gain Reference"),
     ]
     metadata_params = [
         ProcessingParameter("voltage", "Voltage"),
@@ -283,29 +265,11 @@ def gather_metadata(
         metadata["image_size_x"] = str(int(metadata["image_size_x"]) * binning_factor)
         metadata["image_size_y"] = str(int(metadata["image_size_y"]) * binning_factor)
         metadata["motion_corr_binning"] = 1 if binning_factor_xml == 2 else 2
-
-        metadata["use_cryolo"] = (
-            self.data_collection_parameters.get("use_cryolo") or True
-        )
-        metadata["symmetry"] = self.data_collection_parameters.get("symmetry") or "C1"
-        metadata["mask_diameter"] = (
-            self.data_collection_parameters.get("mask_diameter") or 190
-        )
-        metadata["boxsize"] = self.data_collection_parameters.get("boxsize") or 256
-        metadata["downscale"] = self.data_collection_parameters.get("downscale") or True
-        metadata["small_boxsize"] = (
-            self.data_collection_parameters.get("small_boxsize") or 128
-        )
+        metadata["symmetry"] = (environment.symmetry if environment else None) or "C1"
         metadata["eer_fractionation"] = (
-            self.data_collection_parameters.get("eer_fractionation") or 20
-        )
+            environment.eer_fractionation if environment else None
+        ) or 20
         metadata["source"] = str(self._basepath)
-        metadata["particle_diameter"] = (
-            self.data_collection_parameters.get("particle_diameter") or 0
-        )
-        metadata["estimate_particle_diameter"] = (
-            self.data_collection_parameters.get("estimate_particle_diameter") or True
-        )
         return metadata
 
     def _position_analysis(

src/murfey/client/instance_environment.py

@@ -50,6 +50,7 @@ class MurfeyInstanceEnvironment(BaseModel):
     dose_per_frame: Optional[float] = None
     gain_ref: Optional[Path] = None
     symmetry: Optional[str] = None
+    eer_fractionation: Optional[int] = None
     superres: bool = False
     murfey_session: Optional[int] = None
     samples: Dict[Path, SampleInfo] = {}
@@ -72,3 +73,4 @@ def clear(self):
         self.dose_per_frame = None
         self.gain_ref = None
         self.symmetry = None
+        self.eer_fractionation = None

src/murfey/server/api/instrument.py

@@ -178,6 +178,7 @@ async def pass_proc_params_to_instrument_server(
         dose_per_frame=proc_params.dose_per_frame,
         gain_ref=session.current_gain_ref,
         symmetry=proc_params.symmetry,
+        eer_fractionation=proc_params.eer_fractionation,
     )
     db.add(session_processing_parameters)
     db.commit()

src/murfey/server/feedback.py

@@ -2242,11 +2242,6 @@ def feedback_callback(header: dict, message: dict) -> None:
                     motion_corr_binning=message["motion_corr_binning"],
                     eer_fractionation_file=message["eer_fractionation_file"],
                     symmetry=message["symmetry"],
-                    particle_diameter=message["particle_diameter"],
-                    downscale=message["downscale"],
-                    boxsize=message["boxsize"],
-                    small_boxsize=message["small_boxsize"],
-                    mask_diameter=message["mask_diameter"],
                 )
                 feedback_params = db.SPAFeedbackParameters(
                     pj_id=collected_ids[2].id,