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Remove the need for a picker id during classification #764

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0622932
Remove the need for a picker id during classification
stephen-riggs Mar 23, 2026
ca56aa1
Update test to remove picker id
stephen-riggs Mar 23, 2026
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31 changes: 1 addition & 30 deletions src/murfey/server/feedback.py
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Original file line number Diff line number Diff line change
Expand Up @@ -353,7 +353,6 @@ def _release_2d_hold(message: dict, _db):
"nr_classes": default_spa_parameters.nr_classes_2d,
"do_icebreaker_jobs": default_spa_parameters.do_icebreaker_jobs,
"class2d_fraction_of_classes_to_remove": default_spa_parameters.fraction_of_classes_to_remove_2d,
"picker_id": feedback_params.picker_ispyb_id,
"class_uuids": _2d_class_murfey_ids(
first_class2d.particles_file, message["program_id"], _db
),
Expand Down Expand Up @@ -431,7 +430,6 @@ def _release_3d_hold(message: dict, _db):
"mask_diameter": relion_params.mask_diameter or 0,
"do_initial_model": False if feedback_params.initial_model else True,
"initial_model_file": feedback_params.initial_model,
"picker_id": feedback_params.picker_ispyb_id,
"class_uuids": _3d_class_murfey_ids(
class3d_params.particles_file, _app_id(pj_id, _db), _db
),
Expand Down Expand Up @@ -517,7 +515,6 @@ def _release_refine_hold(message: dict, _db):
"symmetry": relion_params.symmetry,
"node_creator_queue": machine_config.node_creator_queue,
"nr_iter": default_spa_parameters.nr_iter_3d,
"picker_id": feedback_params.picker_ispyb_id,
"refined_class_uuid": _refine_murfey_id(
refine_dir=refine_params.refine_dir,
tag=refine_params.tag,
Expand Down Expand Up @@ -589,13 +586,6 @@ def _register_incomplete_2d_batch(message: dict, _db):
feedback_params.hold_class2d = True
relion_options = dict(relion_params)
other_options = dict(feedback_params)
if other_options["picker_ispyb_id"] is None:
logger.info("No ISPyB particle picker ID yet")
feedback_params.hold_class2d = False
_db.add(feedback_params)
_db.commit()
_db.expunge(feedback_params)
return
_db.add(feedback_params)
_db.commit()
_db.expunge(feedback_params)
Expand Down Expand Up @@ -629,7 +619,6 @@ def _register_incomplete_2d_batch(message: dict, _db):
"batch_is_complete": False,
"particle_diameter": relion_options["particle_diameter"],
"combine_star_job_number": -1,
"picker_id": other_options["picker_ispyb_id"],
"nr_iter": default_spa_parameters.nr_iter_2d,
"batch_size": default_spa_parameters.batch_size_2d,
"nr_classes": default_spa_parameters.nr_classes_2d,
Expand Down Expand Up @@ -693,7 +682,7 @@ 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()
Expand Down Expand Up @@ -791,7 +780,6 @@ def _register_complete_2d_batch(message: dict, _db):
"mask_diameter": relion_params.mask_diameter or 0,
"combine_star_job_number": feedback_params.star_combination_job,
"autoselect_min_score": 0,
"picker_id": feedback_params.picker_ispyb_id,
"class_uuids": class_uuids,
"class2d_grp_uuid": class2d_grp_uuid,
"nr_iter": default_spa_parameters.nr_iter_2d,
Expand Down Expand Up @@ -866,7 +854,6 @@ def _register_complete_2d_batch(message: dict, _db):
"mask_diameter": relion_params.mask_diameter or 0,
"combine_star_job_number": feedback_params.star_combination_job,
"autoselect_min_score": feedback_params.class_selection_score or 0,
"picker_id": feedback_params.picker_ispyb_id,
"class_uuids": class_uuids,
"class2d_grp_uuid": class2d_grp_uuid,
"nr_iter": default_spa_parameters.nr_iter_2d,
Expand Down Expand Up @@ -957,7 +944,6 @@ def _flush_class2d(
"mask_diameter": relion_params.mask_diameter or 0,
"combine_star_job_number": feedback_params.star_combination_job,
"autoselect_min_score": feedback_params.class_selection_score or 0,
"picker_id": feedback_params.picker_ispyb_id,
"class_uuids": _2d_class_murfey_ids(
saved_message.particles_file, _app_id(pj_id, _db), _db
),
Expand Down Expand Up @@ -1007,16 +993,6 @@ def _register_class_selection(message: dict, _db):
).one()
_db.expunge(feedback_params)

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

feedback_params.class_selection_score = message.get("class_selection_score") or 0
feedback_params.hold_class2d = False
_flush_class2d(
Expand Down Expand Up @@ -1284,7 +1260,6 @@ def _register_3d_batch(message: dict, _db):
"particle_diameter": relion_options["particle_diameter"],
"mask_diameter": relion_options["mask_diameter"] or 0,
"do_initial_model": True,
"picker_id": other_options["picker_ispyb_id"],
"class_uuids": {i + 1: m for i, m in enumerate(class_uuids)},
"class3d_grp_uuid": class3d_grp_uuid,
"nr_iter": default_spa_parameters.nr_iter_3d,
Expand Down Expand Up @@ -1325,7 +1300,6 @@ def _register_3d_batch(message: dict, _db):
"mask_diameter": relion_options["mask_diameter"] or 0,
"do_initial_model": False,
"initial_model_file": other_options["initial_model"],
"picker_id": other_options["picker_ispyb_id"],
"class_uuids": _3d_class_murfey_ids(
class3d_params.particles_file, _app_id(pj_id, _db), _db
),
Expand Down Expand Up @@ -1534,7 +1508,6 @@ def _register_refinement(message: dict, _db):
db.ClassificationFeedbackParameters.pj_id == pj_id_params
)
).one()
other_options = dict(feedback_params)

if feedback_params.hold_refine:
# If waiting then save the message
Expand Down Expand Up @@ -1626,7 +1599,6 @@ def _register_refinement(message: dict, _db):
"symmetry": relion_options["symmetry"],
"node_creator_queue": machine_config.node_creator_queue,
"nr_iter": default_spa_parameters.nr_iter_3d,
"picker_id": other_options["picker_ispyb_id"],
"refined_class_uuid": _refine_murfey_id(
refine_dir=refine_params.refine_dir,
tag=refine_params.tag,
Expand Down Expand Up @@ -1761,7 +1733,6 @@ def _register_bfactors(message: dict, _db):
"particle_diameter": relion_options["particle_diameter"],
"mask_diameter": relion_options["mask_diameter"] or 0,
"node_creator_queue": machine_config.node_creator_queue,
"picker_id": feedback_params.picker_ispyb_id,
"refined_grp_uuid": bfactor_params.refined_grp_uuid,
"refined_class_uuid": bfactor_params.refined_class_uuid,
"session_id": message["session_id"],
Expand Down
13 changes: 0 additions & 13 deletions src/murfey/util/db.py
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Original file line number Diff line number Diff line change
Expand Up @@ -317,9 +317,6 @@ class ProcessingJob(SQLModel, table=True): # type: ignore
auto_proc_programs: List["AutoProcProgram"] = Relationship(
back_populates="processing_job", sa_relationship_kwargs={"cascade": "delete"}
)
selection_stash: List["SelectionStash"] = Relationship(
back_populates="processing_job", sa_relationship_kwargs={"cascade": "delete"}
)
particle_sizes: List["ParticleSizes"] = Relationship(
back_populates="processing_job", sa_relationship_kwargs={"cascade": "delete"}
)
Expand Down Expand Up @@ -371,15 +368,6 @@ class PreprocessStash(SQLModel, table=True): # type: ignore
foil_hole: Optional["FoilHole"] = Relationship(back_populates="preprocess_stashes")


class SelectionStash(SQLModel, table=True): # type: ignore
id: Optional[int] = Field(default=None, primary_key=True)
class_selection_score: float
pj_id: int = Field(foreign_key="processingjob.processingJobId")
processing_job: Optional[ProcessingJob] = Relationship(
back_populates="selection_stash"
)


class TomographyProcessingParameters(SQLModel, table=True): # type: ignore
dcg_id: int = Field(
primary_key=True, foreign_key="datacollectiongroup.dataCollectionGroupId"
Expand Down Expand Up @@ -692,7 +680,6 @@ class ClassificationFeedbackParameters(SQLModel, table=True): # type: ignore
initial_model: str
next_job: int
picker_murfey_id: Optional[int] = Field(default=None, foreign_key="murfeyledger.id")
picker_ispyb_id: Optional[int] = None
processing_job: Optional[ProcessingJob] = Relationship(
back_populates="classification_feedback_parameters"
)
Expand Down
63 changes: 0 additions & 63 deletions src/murfey/workflows/spa/picking.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,9 +9,7 @@
from murfey.server import _transport_object
from murfey.server.feedback import (
_app_id,
_flush_class2d,
_pj_id,
_register_class_selection,
)
from murfey.util.config import get_machine_config
from murfey.util.db import (
Expand All @@ -24,7 +22,6 @@
NotificationValue,
ParticleSizes,
ProcessingJob,
SelectionStash,
Session as MurfeySession,
SPARelionParameters,
)
Expand Down Expand Up @@ -74,40 +71,8 @@ def _register_picked_particles_use_diameter(message: dict, _db: Session):
select(SPARelionParameters).where(SPARelionParameters.pj_id == pj_id)
).one()
relion_options = dict(relion_params)
feedback_params = _db.exec(
select(ClassificationFeedbackParameters).where(
ClassificationFeedbackParameters.pj_id == pj_id
)
).one()

particle_diameter = relion_params.particle_diameter

if feedback_params.picker_ispyb_id is None:
if not _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(
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)
_db.commit()
selection_stash = _db.exec(
select(SelectionStash).where(SelectionStash.pj_id == pj_id)
).all()
for s in selection_stash:
_register_class_selection(
{
"session_id": s.session_id,
"class_selection_score": s.class_selection_score or 0,
},
_db=_db,
)
_db.delete(s)
_db.commit()

if not particle_diameter:
# If the diameter has not been calculated then find it
picking_db = _db.exec(
Expand Down Expand Up @@ -246,34 +211,6 @@ def _register_picked_particles_use_boxsize(message: dict, _db: Session):
relion_params = _db.exec(
select(SPARelionParameters).where(SPARelionParameters.pj_id == pj_id)
).one()
feedback_params = _db.exec(
select(ClassificationFeedbackParameters).where(
ClassificationFeedbackParameters.pj_id == pj_id
)
).one()

if feedback_params.picker_ispyb_id is None and _transport_object:
assert feedback_params.picker_murfey_id is not None
feedback_params.picker_ispyb_id = _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)
_db.commit()
selection_stash = _db.exec(
select(SelectionStash).where(SelectionStash.pj_id == pj_id)
).all()
for s in selection_stash:
_register_class_selection(
{
"session_id": s.session_id,
"class_selection_score": s.class_selection_score or 0,
},
_db=_db,
)
_db.delete(s)
_db.commit()

# Send the message to extraction with the box sizes
zocalo_message: dict = {
Expand Down
2 changes: 0 additions & 2 deletions src/murfey/workflows/tomo/picking.py
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Original file line number Diff line number Diff line change
Expand Up @@ -135,7 +135,6 @@ def _register_picked_tomogram_use_diameter(message: dict, murfey_db: Session):
"autoproc_program_id": _app_id(pj_id, murfey_db),
"batch_size": default_tomo_parameters.batch_size_2d,
"nr_classes": default_tomo_parameters.nr_classes_2d,
"picker_id": None,
"class2d_grp_uuid": class2d_grp_uuid,
"class_uuids": class_uuids,
"next_job": feedback_params.next_job,
Expand Down Expand Up @@ -177,7 +176,6 @@ def _register_picked_tomogram_use_diameter(message: dict, murfey_db: Session):
"autoproc_program_id": _app_id(pj_id, murfey_db),
"batch_size": default_tomo_parameters.batch_size_2d,
"nr_classes": default_tomo_parameters.nr_classes_2d,
"picker_id": None,
"class2d_grp_uuid": class2d_grp_uuid,
"class_uuids": class_uuids,
"next_job": feedback_params.next_job,
Expand Down
3 changes: 0 additions & 3 deletions tests/workflows/tomo/test_tomo_picking.py
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Original file line number Diff line number Diff line change
Expand Up @@ -222,7 +222,6 @@ def test_picked_tomogram_run_class2d_with_diameter(
"autoproc_program_id": 0,
"batch_size": 5000,
"nr_classes": 5,
"picker_id": None,
"class2d_grp_uuid": 6,
"class_uuids": {str(i): i for i in range(1, 6)},
"next_job": 9,
Expand Down Expand Up @@ -312,7 +311,6 @@ def test_picked_tomogram_run_class2d_estimate_diameter(
"autoproc_program_id": 0,
"batch_size": 5000,
"nr_classes": 5,
"picker_id": None,
"class2d_grp_uuid": 12,
"class_uuids": {str(i): i + 6 for i in range(1, 6)},
"next_job": 9,
Expand All @@ -336,7 +334,6 @@ def test_picked_tomogram_run_class2d_estimate_diameter(
"autoproc_program_id": 0,
"batch_size": 5000,
"nr_classes": 5,
"picker_id": None,
"class2d_grp_uuid": 18,
"class_uuids": {str(i): i + 12 for i in range(1, 6)},
"next_job": 11,
Expand Down
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