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Correct smartem foil hole position registration #852

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Merged
d-j-hatton merged 2 commits into from
Aug 4, 2026
Merged

Correct smartem foil hole position registration #852

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91fcce1
the ispyb insert function for foil holes mutates the data so the smar…
d-j-hatton Aug 4, 2026
8770d8c
stop mutation of foil hole data in ispyb insert function
d-j-hatton Aug 4, 2026
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22 changes: 13 additions & 9 deletions src/murfey/server/ispyb.py
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -335,27 +335,31 @@ def do_insert_foil_hole(
scale_factor: Optional[float],
foil_hole_parameters: FoilHoleParameters,
):
pixel_size = foil_hole_parameters.pixel_size
diameter = foil_hole_parameters.diameter
x_location = foil_hole_parameters.x_location
y_location = foil_hole_parameters.y_location
if (
foil_hole_parameters.thumbnail_size_x is not None
and foil_hole_parameters.readout_area_x is not None
and foil_hole_parameters.pixel_size is not None
and pixel_size is not None
):
foil_hole_parameters.pixel_size *= (
pixel_size *= (
foil_hole_parameters.readout_area_x
/ foil_hole_parameters.thumbnail_size_x
)
if scale_factor:
foil_hole_parameters.diameter = (
diameter = (
int(foil_hole_parameters.diameter * scale_factor)
if foil_hole_parameters.diameter
else None
)
foil_hole_parameters.x_location = (
x_location = (
int(foil_hole_parameters.x_location * scale_factor)
if foil_hole_parameters.x_location
else None
)
foil_hole_parameters.y_location = (
y_location = (
int(foil_hole_parameters.y_location * scale_factor)
if foil_hole_parameters.y_location
else None
Expand All @@ -364,12 +368,12 @@ def do_insert_foil_hole(
gridSquareId=grid_square_id,
foilHoleLabel=foil_hole_parameters.name,
foilHoleImage=foil_hole_parameters.image,
pixelLocationX=foil_hole_parameters.x_location,
pixelLocationY=foil_hole_parameters.y_location,
diameter=foil_hole_parameters.diameter,
pixelLocationX=x_location,
pixelLocationY=y_location,
diameter=diameter,
stageLocationX=foil_hole_parameters.x_stage_position,
stageLocationY=foil_hole_parameters.y_stage_position,
pixelSize=foil_hole_parameters.pixel_size,
pixelSize=pixel_size,
)
try:
with ISPyBSession() as db:
Expand Down
108 changes: 56 additions & 52 deletions src/murfey/workflows/spa/flush_spa_preprocess.py
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Original file line number Diff line number Diff line change
Expand Up @@ -252,6 +252,61 @@ def register_foil_hole(
.where(FoilHole.grid_square_id == gsid)
.where(FoilHole.session_id == session_id)
).all()

fh_smartem_uuid = None

# do this first as the data gets mutated by the ispyb insert function
if SMARTEM_ACTIVE and gs.smartem_uuid:
try:
murfey_session = murfey_db.exec(
select(MurfeySession).where(MurfeySession.id == session_id)
).one()
machine_config = get_machine_config(
instrument_name=murfey_session.instrument_name
)[murfey_session.instrument_name]
if machine_config.smartem_api_url:
smartem_client = SmartEMAPIClient(
base_url=machine_config.smartem_api_url, logger=logger
)
fh_data = SmartEMFoilHoleData(
id=str(foil_hole_params.name),
gridsquare_id=str(gs.name),
gridsquare_uuid=gs.smartem_uuid,
x_location=(
int(foil_hole_params.x_location)
if foil_hole_params.x_location is not None
else None
),
y_location=(
int(foil_hole_params.y_location)
if foil_hole_params.y_location is not None
else None
),
x_stage_position=foil_hole_params.x_stage_position,
y_stage_position=foil_hole_params.y_stage_position,
diameter=(
int(foil_hole_params.diameter)
if foil_hole_params.diameter is not None
else None
),
**(
{"uuid": foil_hole_query[0].smartem_uuid}
if foil_hole_query and foil_hole_query[0].smartem_uuid
else {}
),
)
if foil_hole_query and foil_hole_query[0].smartem_uuid:
smartem_client.update_foilhole(fh_data)
fh_smartem_uuid = foil_hole_query[0].smartem_uuid
else:
responses = smartem_client.create_gridsquare_foilholes(
gs.smartem_uuid, [fh_data]
)
if responses:
fh_smartem_uuid = responses[0].uuid
except Exception:
logger.warning("Failed to register foil hole with smartem", exc_info=True)

if foil_hole_query:
# Foil hole already exists in the murfey database
foil_hole = foil_hole_query[0]
Expand Down Expand Up @@ -311,61 +366,10 @@ def register_foil_hole(
image=str(secured_foil_hole_image_path),
)
fh_id = foil_hole.id
foil_hole.smartem_uuid = fh_smartem_uuid
murfey_db.add(foil_hole)
murfey_db.commit()

if SMARTEM_ACTIVE and gs.smartem_uuid:
try:
murfey_session = murfey_db.exec(
select(MurfeySession).where(MurfeySession.id == session_id)
).one()
machine_config = get_machine_config(
instrument_name=murfey_session.instrument_name
)[murfey_session.instrument_name]
if machine_config.smartem_api_url:
smartem_client = SmartEMAPIClient(
base_url=machine_config.smartem_api_url, logger=logger
)
fh_data = SmartEMFoilHoleData(
id=str(foil_hole_params.name),
gridsquare_id=str(gs.name),
gridsquare_uuid=gs.smartem_uuid,
x_location=(
int(foil_hole_params.x_location)
if foil_hole_params.x_location is not None
else None
),
y_location=(
int(foil_hole_params.y_location)
if foil_hole_params.y_location is not None
else None
),
x_stage_position=foil_hole_params.x_stage_position,
y_stage_position=foil_hole_params.y_stage_position,
diameter=(
int(foil_hole_params.diameter)
if foil_hole_params.diameter is not None
else None
),
**(
{"uuid": foil_hole.smartem_uuid}
if foil_hole.smartem_uuid
else {}
),
)
if foil_hole.smartem_uuid:
smartem_client.update_foilhole(fh_data)
else:
responses = smartem_client.create_gridsquare_foilholes(
gs.smartem_uuid, [fh_data]
)
if responses:
foil_hole.smartem_uuid = responses[0].uuid
murfey_db.add(foil_hole)
murfey_db.commit()
except Exception:
logger.warning("Failed to register foil hole with smartem", exc_info=True)

murfey_db.close()
return fh_id

Expand Down