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Fixes for gridsquare registration in SmartEM #783

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Merged
d-j-hatton merged 1 commit into from
Apr 15, 2026
Merged

Fixes for gridsquare registration in SmartEM #783

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78 changes: 42 additions & 36 deletions src/murfey/client/contexts/spa_metadata.py
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Original file line number Diff line number Diff line change
Expand Up @@ -84,6 +84,7 @@ def __init__(
super().__init__("SPA_metadata", acquisition_software, token)
self._basepath = basepath
self._machine_config = machine_config
self._registered_squares: set[int] = set()

def post_transfer(
self,
Expand Down Expand Up @@ -243,39 +244,44 @@ def post_transfer(
},
)

for fh, fh_data in fh_positions.items():
capture_post(
base_url=str(environment.url.geturl()),
router_name="session_control.spa_router",
function_name="register_foil_hole",
token=self._token,
instrument_name=environment.instrument_name,
session_id=environment.murfey_session,
gs_name=gs_name,
data={
"name": fh,
"x_location": fh_data.x_location,
"y_location": fh_data.y_location,
"x_stage_position": fh_data.x_stage_position,
"y_stage_position": fh_data.y_stage_position,
"readout_area_x": fh_data.readout_area_x,
"readout_area_y": fh_data.readout_area_y,
"thumbnail_size_x": fh_data.thumbnail_size_x,
"thumbnail_size_y": fh_data.thumbnail_size_y,
"pixel_size": fh_data.pixel_size,
"diameter": fh_data.diameter,
"tag": visitless_source,
"image": fh_data.image,
},
)
if fh_positions:
capture_post(
base_url=str(environment.url.geturl()),
router_name="session_control.spa_router",
function_name="register_square",
token=self._token,
instrument_name=environment.instrument_name,
session_id=environment.murfey_session,
gsid=gs_name,
data={"tag": visitless_source},
)
if gs_name not in self._registered_squares:
for fh, fh_data in fh_positions.items():
capture_post(
base_url=str(environment.url.geturl()),
router_name="session_control.spa_router",
function_name="register_foil_hole",
token=self._token,
instrument_name=environment.instrument_name,
session_id=environment.murfey_session,
gs_name=gs_name,
data={
"name": fh,
"x_location": fh_data.x_location,
"y_location": fh_data.y_location,
"x_stage_position": fh_data.x_stage_position,
"y_stage_position": fh_data.y_stage_position,
"readout_area_x": fh_data.readout_area_x,
"readout_area_y": fh_data.readout_area_y,
"thumbnail_size_x": fh_data.thumbnail_size_x,
"thumbnail_size_y": fh_data.thumbnail_size_y,
"pixel_size": fh_data.pixel_size,
"diameter": fh_data.diameter,
"tag": visitless_source,
"image": fh_data.image,
},
)
if fh_positions:
capture_post(
base_url=str(environment.url.geturl()),
router_name="session_control.spa_router",
function_name="register_square",
token=self._token,
instrument_name=environment.instrument_name,
session_id=environment.murfey_session,
gsid=gs_name,
data={
"tag": visitless_source,
"count": len(self._registered_squares) + 1,
},
)
self._registered_squares.add(gs_name)
5 changes: 4 additions & 1 deletion src/murfey/server/api/session_control.py
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Original file line number Diff line number Diff line change
Expand Up @@ -415,6 +415,7 @@ def register_atlas(

class SquareRegistration(BaseModel):
tag: str
count: int | None = None


@spa_router.post("/sessions/{session_id}/register_square/{gsid}")
Expand All @@ -440,7 +441,9 @@ def register_square(
smartem_client = SmartEMAPIClient(
base_url=machine_config.smartem_api_url, logger=logger
)
smartem_client.gridsquare_registered(gs.smartem_uuid)
smartem_client.gridsquare_registered(
gs.smartem_uuid, count=square_registration_data.count
)
else:
logger.info("smartem deactivated so did not register square")

Expand Down
25 changes: 25 additions & 0 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 @@ -11,6 +11,7 @@
from smartem_common.schemas import (
FoilHoleData as SmartEMFoilHoleData,
GridSquareData as SmartEMGridSquareData,
GridSquareMetadata as SmartEMGridSquareMetadata,
)

SMARTEM_ACTIVE = True
Expand Down Expand Up @@ -154,6 +155,21 @@ def register_grid_square(
.where(DataCollectionGroup.tag == grid_square_params.tag)
).one_or_none()
if dcg and dcg.smartem_grid_uuid:
secured_grid_square_image_path_full_res: Path | None = None
if grid_square_params.image:
secured_grid_square_image_path_full_res = secure_path(
Path(grid_square_params.image)
)
if secured_grid_square_image_path_full_res.with_suffix(
".tiff"
).is_file():
secured_grid_square_image_path_full_res = (
secured_grid_square_image_path_full_res.with_suffix(".tiff")
)
else:
secured_grid_square_image_path_full_res = (
secured_grid_square_image_path_full_res.with_suffix(".mrc")
)
smartem_client = SmartEMAPIClient(
base_url=machine_config.smartem_api_url, logger=logger
)
Expand All @@ -177,6 +193,15 @@ def register_grid_square(
if grid_square.smartem_uuid
else {}
),
metadata=SmartEMGridSquareMetadata(
atlas_node_id=0,
stage_position=None,
state=None,
rotation=None,
image_path=secured_grid_square_image_path_full_res,
selected=False,
unusable=False,
),
)
if grid_square.smartem_uuid:
smartem_client.update_gridsquare(gs_data)
Expand Down
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