Rename tomo preprocessing params to just processing params

Author: stephen-riggs

src/murfey/client/analyser.py

@@ -24,7 +24,7 @@
 from murfey.client.tui.forms import FormDependency
 from murfey.util import Observer, get_machine_config_client
 from murfey.util.mdoc import get_block
-from murfey.util.models import PreprocessingParametersTomo, ProcessingParametersSPA
+from murfey.util.models import ProcessingParametersSPA, ProcessingParametersTomo
 
 logger = logging.getLogger("murfey.client.analyser")
 
@@ -65,7 +65,7 @@ def __init__(
         self._environment = environment
         self._force_mdoc_metadata = force_mdoc_metadata
         self.parameters_model: (
-            Type[ProcessingParametersSPA] | Type[PreprocessingParametersTomo] | None
+            Type[ProcessingParametersSPA] | Type[ProcessingParametersTomo] | None
         ) = None
 
         self.queue: queue.Queue = queue.Queue()
@@ -183,7 +183,7 @@ def _find_context(self, file_path: Path) -> bool:
                 if not self._context:
                     logger.info("Acquisition software: tomo")
                     self._context = TomographyContext("tomo", self._basepath)
-                    self.parameters_model = PreprocessingParametersTomo
+                    self.parameters_model = ProcessingParametersTomo
                 return True
 
             # Files with these suffixes belong to the serial EM tomography workflow
@@ -207,7 +207,7 @@ def _find_context(self, file_path: Path) -> bool:
                 ):
                     return False
                 self._context = TomographyContext("serialem", self._basepath)
-                self.parameters_model = PreprocessingParametersTomo
+                self.parameters_model = ProcessingParametersTomo
                 return True
         return False
 

src/murfey/client/multigrid_control.py

@@ -438,7 +438,7 @@ def _start_dc(self, json, from_form: bool = False):
                 eer_fractionation_file = eer_response.json()["eer_fractionation_file"]
                 json.update({"eer_fractionation_file": eer_fractionation_file})
             capture_post(
-                f"{self._environment.url.geturl()}/sessions/{self._environment.murfey_session}/tomography_preprocessing_parameters",
+                f"{self._environment.url.geturl()}/sessions/{self._environment.murfey_session}/tomography_processing_parameters",
                 json=json,
             )
             capture_post(

src/murfey/client/tui/app.py

@@ -504,7 +504,7 @@ def _start_dc(self, json, from_form: bool = False):
                 eer_fractionation_file = eer_response.json()["eer_fractionation_file"]
                 json.update({"eer_fractionation_file": eer_fractionation_file})
             requests.post(
-                f"{self.app._environment.url.geturl()}/sessions/{self.app._environment.murfey_session}/tomography_preprocessing_parameters",
+                f"{self.app._environment.url.geturl()}/sessions/{self.app._environment.murfey_session}/tomography_processing_parameters",
                 json=json,
             )
             capture_post(

src/murfey/client/tui/screens.py

@@ -57,7 +57,7 @@
 from murfey.client.rsync import RSyncer
 from murfey.client.tui.forms import FormDependency
 from murfey.util import capture_post, get_machine_config_client, posix_path, read_config
-from murfey.util.models import PreprocessingParametersTomo, ProcessingParametersSPA
+from murfey.util.models import ProcessingParametersSPA, ProcessingParametersTomo
 
 log = logging.getLogger("murfey.tui.screens")
 
@@ -463,7 +463,7 @@ def compose(self):
     def _write_params(
         self,
         params: dict | None = None,
-        model: PreprocessingParametersTomo | ProcessingParametersSPA | None = None,
+        model: ProcessingParametersTomo | ProcessingParametersSPA | None = None,
     ):
         if params:
             try:
@@ -473,9 +473,9 @@ def _write_params(
             for k in analyser._context.user_params + analyser._context.metadata_params:
                 self.app.query_one("#info").write(f"{k.label}: {params.get(k.name)}")
             self.app._start_dc(params)
-            if model == PreprocessingParametersTomo:
+            if model == ProcessingParametersTomo:
                 requests.post(
-                    f"{self.app._environment.url.geturl()}/sessions/{self.app._environment.murfey_session}/tomography_preprocessing_parameters",
+                    f"{self.app._environment.url.geturl()}/sessions/{self.app._environment.murfey_session}/tomography_processing_parameters",
                     json=params,
                 )
             elif model == ProcessingParametersSPA:
@@ -1156,9 +1156,7 @@ def on_input_changed(self, event):
     def on_button_pressed(self, event):
         if self.app._multigrid and self.app._processing_enabled:
             if self._context == TomographyContext:
-                valid = validate_form(
-                    self._user_params, PreprocessingParametersTomo.Base
-                )
+                valid = validate_form(self._user_params, ProcessingParametersTomo.Base)
             else:
                 valid = validate_form(self._user_params, ProcessingParametersSPA.Base)
             if not valid:

src/murfey/server/__init__.py

@@ -190,10 +190,10 @@ def get_job_ids(tilt_series_id: int, appid: int) -> JobIDs:
     )
 
 
-def get_tomo_preproc_params(dcg_id: int, *args) -> db.TomographyPreprocessingParameters:
+def get_tomo_preproc_params(dcg_id: int, *args) -> db.TomographyProcessingParameters:
     results = murfey_db.exec(
-        select(db.TomographyPreprocessingParameters).where(
-            db.TomographyPreprocessingParameters.dcg_id == dcg_id
+        select(db.TomographyProcessingParameters).where(
+            db.TomographyProcessingParameters.dcg_id == dcg_id
         )
     ).one()
     return results
@@ -2537,11 +2537,11 @@ def feedback_callback(header: dict, message: dict) -> None:
                 .where(db.ProcessingJob.recipe == "em-tomo-preprocess")
             ).one()
             if not murfey_db.exec(
-                select(func.count(db.TomographyPreprocessingParameters.dcg_id)).where(
-                    db.TomographyPreprocessingParameters.dcg_id == collected_ids[0].id
+                select(func.count(db.TomographyProcessingParameters.dcg_id)).where(
+                    db.TomographyProcessingParameters.dcg_id == collected_ids[0].id
                 )
             ).one():
-                params = db.TomographyPreprocessingParameters(
+                params = db.TomographyProcessingParameters(
                     dcg_id=collected_ids[0].id,
                     pixel_size=float(message["pixel_size_on_image"]) * 10**10,
                     voltage=message["voltage"],

src/murfey/server/api/__init__.py

@@ -88,9 +88,9 @@
     GridSquareParameters,
     MillingParameters,
     PostInfo,
-    PreprocessingParametersTomo,
     ProcessingJobParameters,
     ProcessingParametersSPA,
+    ProcessingParametersTomo,
     RegistrationMessage,
     RsyncerInfo,
     RsyncerSource,
@@ -613,9 +613,9 @@ def post_foil_hole(
     return register_foil_hole(session_id, gs_name, foil_hole_params, db)
 
 
-@router.post("/sessions/{session_id}/tomography_preprocessing_parameters")
+@router.post("/sessions/{session_id}/tomography_processing_parameters")
 def register_tomo_preproc_params(
-    session_id: MurfeySessionID, proc_params: PreprocessingParametersTomo, db=murfey_db
+    session_id: MurfeySessionID, proc_params: ProcessingParametersTomo, db=murfey_db
 ):
     session_processing_parameters = db.exec(
         select(SessionProcessingParameters).where(

src/murfey/server/demo_api.py

@@ -57,7 +57,7 @@
     SPARelionParameters,
     Tilt,
     TiltSeries,
-    TomographyPreprocessingParameters,
+    TomographyProcessingParameters,
 )
 from murfey.util.models import (
     ClientInfo,
@@ -71,9 +71,9 @@
     GainReference,
     GridSquareParameters,
     PostInfo,
-    PreprocessingParametersTomo,
     ProcessingJobParameters,
     ProcessingParametersSPA,
+    ProcessingParametersTomo,
     RegistrationMessage,
     RsyncerInfo,
     RsyncerSource,
@@ -477,9 +477,9 @@ def register_spa_proc_params(
     db.commit()
 
 
-@router.post("/sessions/{session_id}/tomography_preprocessing_parameters")
+@router.post("/sessions/{session_id}/tomography_processing_parameters")
 def register_tomo_preproc_params(
-    session_id: MurfeySessionID, proc_params: PreprocessingParametersTomo, db=murfey_db
+    session_id: MurfeySessionID, proc_params: ProcessingParametersTomo, db=murfey_db
 ):
     log.info(
         f"Registering tomography preprocessing parameters {sanitise(proc_params.tag)}, {sanitise(proc_params.tilt_series_tag)}"
@@ -500,11 +500,11 @@ def register_tomo_preproc_params(
         .where(ProcessingJob.recipe == "em-tomo-preprocess")
     ).one()
     if not db.exec(
-        select(func.count(TomographyPreprocessingParameters.dcg_id)).where(
-            TomographyPreprocessingParameters.dcg_id == collected_ids[0].id
+        select(func.count(TomographyProcessingParameters.dcg_id)).where(
+            TomographyProcessingParameters.dcg_id == collected_ids[0].id
         )
     ).one():
-        params = TomographyPreprocessingParameters(
+        params = TomographyProcessingParameters(
             dcg_id=collected_ids[0].id,
             pixel_size=proc_params.pixel_size_on_image,
             dose_per_frame=proc_params.dose_per_frame,

src/murfey/util/db.py

@@ -378,7 +378,7 @@ class DataCollectionGroup(SQLModel, table=True):  # type: ignore
         back_populates="data_collection_group",
         sa_relationship_kwargs={"cascade": "delete"},
     )
-    tomography_preprocessing_parameters: List["TomographyPreprocessingParameters"] = (
+    tomography_processing_parameters: List["TomographyProcessingParameters"] = (
         Relationship(
             back_populates="data_collection_group",
             sa_relationship_kwargs={"cascade": "delete"},
@@ -493,7 +493,7 @@ class SelectionStash(SQLModel, table=True):  # type: ignore
     )
 
 
-class TomographyPreprocessingParameters(SQLModel, table=True):  # type: ignore
+class TomographyProcessingParameters(SQLModel, table=True):  # type: ignore
     dcg_id: int = Field(primary_key=True, foreign_key="datacollectiongroup.id")
     pixel_size: float
     dose_per_frame: float
@@ -504,7 +504,7 @@ class TomographyPreprocessingParameters(SQLModel, table=True):  # type: ignore
     motion_corr_binning: int = 1
     gain_ref: Optional[str] = None
     data_collection_group: Optional[DataCollectionGroup] = Relationship(
-        back_populates="tomography_preprocessing_parameters"
+        back_populates="tomography_processing_parameters"
     )
 
 

src/murfey/util/models.py

@@ -349,7 +349,7 @@ class CompletedTiltSeries(BaseModel):
     rsync_source: str
 
 
-class PreprocessingParametersTomo(BaseModel):
+class ProcessingParametersTomo(BaseModel):
     dose_per_frame: Optional[float]
     frame_count: int
     tilt_axis: float