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Wrongly indented code on initial models #745

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Merged
stephen-riggs merged 5 commits into from
Feb 16, 2026
Merged

Wrongly indented code on initial models #745

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280155b
If atlas not in visit, determine expected path
stephen-riggs Feb 13, 2026
cc72af3
Do not crash analyser if dcg fails
stephen-riggs Feb 13, 2026
399c7a9
Add rescaled initial model to database if it exists
stephen-riggs Feb 13, 2026
1995f40
Not supposed to be on this branch
stephen-riggs Feb 16, 2026
7e1f7d3
next job is not needed
stephen-riggs Feb 16, 2026
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55 changes: 27 additions & 28 deletions src/murfey/server/feedback.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1090,7 +1090,7 @@ def _downscaled_box_size(
raise ValueError(f"Box size is too large: {box_size}")


def _resize_intial_model(
def _resize_initial_model(
downscaled_box_size: int,
downscaled_pixel_size: float,
input_path: Path,
Expand Down Expand Up @@ -1203,7 +1203,7 @@ def _register_3d_batch(message: dict, _db):
/ f"{provided_initial_model.stem}_rescaled_{pj_id}{provided_initial_model.suffix}"
)
if not rescaled_initial_model_path.is_file():
_resize_intial_model(
_resize_initial_model(
*_downscaled_box_size(
relion_options["particle_diameter"],
relion_options["angpix"],
Expand All @@ -1213,33 +1213,32 @@ def _register_3d_batch(message: dict, _db):
machine_config.external_executables,
machine_config.external_environment,
)
feedback_params.initial_model = str(rescaled_initial_model_path)
other_options["initial_model"] = str(rescaled_initial_model_path)
next_job = feedback_params.next_job
class3d_dir = (
f"{class3d_message['class3d_dir']}{(feedback_params.next_job + 1):03}"
)
feedback_params.next_job += 1
_db.add(feedback_params)
_db.commit()
feedback_params.initial_model = str(rescaled_initial_model_path)
other_options["initial_model"] = str(rescaled_initial_model_path)
class3d_dir = (
f"{class3d_message['class3d_dir']}{(feedback_params.next_job + 1):03}"
)
feedback_params.next_job += 1
_db.add(feedback_params)
_db.commit()

class3d_grp_uuid = _murfey_id(message["program_id"], _db)[0]
class_uuids = _murfey_id(message["program_id"], _db, number=4)
class3d_params = db.Class3DParameters(
pj_id=pj_id,
murfey_id=class3d_grp_uuid,
particles_file=class3d_message["particles_file"],
class3d_dir=class3d_dir,
batch_size=class3d_message["batch_size"],
)
_db.add(class3d_params)
_db.commit()
_murfey_class3ds(
class_uuids,
class3d_message["particles_file"],
message["program_id"],
_db,
)
class3d_grp_uuid = _murfey_id(message["program_id"], _db)[0]
class_uuids = _murfey_id(message["program_id"], _db, number=4)
class3d_params = db.Class3DParameters(
pj_id=pj_id,
murfey_id=class3d_grp_uuid,
particles_file=class3d_message["particles_file"],
class3d_dir=class3d_dir,
batch_size=class3d_message["batch_size"],
)
_db.add(class3d_params)
_db.commit()
_murfey_class3ds(
class_uuids,
class3d_message["particles_file"],
message["program_id"],
_db,
)

if feedback_params.hold_class3d:
# If waiting then save the message
Expand Down