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Merged
stephen-riggs merged 2 commits into from
Sep 15, 2026
Merged

Convert grid square registration to workflow #884

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2d2cbf7
Convert grid square registration to workflow
stephen-riggs Sep 11, 2026
4276008
Add workflow to pyproject
stephen-riggs Sep 11, 2026
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1 change: 1 addition & 0 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -126,6 +126,7 @@ TomographyMetadataContext = "murfey.client.contexts.tomo_metadata:TomographyMeta
"spa.ctf_estimated" = "murfey.workflows.spa.ctf_estimation:ctf_estimated"
"spa.flush_spa_preprocess" = "murfey.workflows.spa.flush_spa_preprocess:flush_spa_preprocess"
"spa.motion_corrected" = "murfey.workflows.spa.motion_correction:motion_corrected"
"spa.register_grid_square" = "murfey.workflows.spa.register_grid_square:run"
"spa.smartem_atlas" = "murfey.workflows.spa.smartem_atlas:smartem_atlas"
"sxt.process_tilt_series" = "murfey.workflows.sxt.process_sxt_tilt_series:run"
"sxt.register_roi" = "murfey.workflows.sxt.sxt_metadata:run"
Expand Down
12 changes: 10 additions & 2 deletions src/murfey/server/api/session_control.py
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Expand Up @@ -72,7 +72,6 @@
from murfey.workflows.spa.atlas import atlas_jpg_from_mrc
from murfey.workflows.spa.flush_spa_preprocess import (
register_foil_hole as _register_foil_hole,
register_grid_square as _register_grid_square,
)
from murfey.workflows.tomo.tomo_metadata import (
register_batch_position_in_database,
Expand Down Expand Up @@ -457,7 +456,16 @@ def register_grid_square(
grid_square_params: GridSquareParameters,
db=murfey_db,
):
return _register_grid_square(session_id, gsid, grid_square_params, db)
if murfey.server._transport_object:
murfey.server._transport_object.send(
murfey.server._transport_object.feedback_queue,
{
"register": "spa.register_grid_square",
"session_id": session_id,
"gsid": gsid,
"grid_square_params": grid_square_params.model_dump(),
},
)


@spa_router.post("/sessions/{session_id}/grid_square/{gs_name}/foil_hole")
Expand Down
192 changes: 2 additions & 190 deletions src/murfey/workflows/spa/flush_spa_preprocess.py
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Expand Up @@ -3,17 +3,12 @@
from typing import Optional

from PIL import Image
from sqlalchemy import desc
from sqlalchemy.exc import NoResultFound
from sqlmodel import Session, select

try:
from smartem_backend.api_client import SmartEMAPIClient
from smartem_common.schemas import (
FoilHoleData as SmartEMFoilHoleData,
GridSquareData as SmartEMGridSquareData,
GridSquareMetadata as SmartEMGridSquareMetadata,
)
from smartem_common.schemas import FoilHoleData as SmartEMFoilHoleData

from murfey.util.config import get_smartem_keycloak_client

Expand Down Expand Up @@ -51,194 +46,11 @@
grid_square_data,
grid_square_from_file,
)
from murfey.workflows.spa.register_grid_square import register_grid_square

logger = logging.getLogger("murfey.workflows.spa.flush_spa_preprocess")


def register_grid_square(
session_id: int,
gsid: int,
grid_square_params: GridSquareParameters,
murfey_db: Session,
):
# Calculate scaled down version of the image for registration to ISPyB first
if grid_square_params.x_location is not None:
grid_square_params.x_location_scaled = int(grid_square_params.x_location / 7.8)
if grid_square_params.y_location is not None:
grid_square_params.y_location_scaled = int(grid_square_params.y_location / 7.8)
if grid_square_params.height is not None:
grid_square_params.height_scaled = int(grid_square_params.height / 7.8)
if grid_square_params.width is not None:
grid_square_params.width_scaled = int(grid_square_params.width / 7.8)

if grid_square_params.sample is not None:
dcg = murfey_db.exec(
select(DataCollectionGroup)
.where(DataCollectionGroup.session_id == session_id)
.where(DataCollectionGroup.sample == grid_square_params.sample)
.order_by(desc(DataCollectionGroup.id))
).first()
else:
dcg = murfey_db.exec(
select(DataCollectionGroup)
.where(DataCollectionGroup.session_id == session_id)
.where(DataCollectionGroup.tag == grid_square_params.tag)
.order_by(desc(DataCollectionGroup.id))
).first()
grid_square_query = murfey_db.exec(
select(GridSquare)
.where(GridSquare.name == gsid)
.where(GridSquare.tag == dcg.tag)
.where(GridSquare.session_id == session_id)
).all()
if grid_square_query:
# Grid square already exists in the murfey database
grid_square = grid_square_query[0]
grid_square.x_location = grid_square_params.x_location or grid_square.x_location
grid_square.y_location = grid_square_params.y_location or grid_square.y_location
grid_square.x_stage_position = (
grid_square_params.x_stage_position or grid_square.x_stage_position
)
grid_square.y_stage_position = (
grid_square_params.y_stage_position or grid_square.y_stage_position
)
grid_square.readout_area_x = (
grid_square_params.readout_area_x or grid_square.readout_area_x
)
grid_square.readout_area_y = (
grid_square_params.readout_area_y or grid_square.readout_area_y
)
grid_square.thumbnail_size_x = (
grid_square_params.thumbnail_size_x or grid_square.thumbnail_size_x
)
grid_square.thumbnail_size_y = (
grid_square_params.thumbnail_size_y or grid_square.thumbnail_size_y
)
grid_square.pixel_size = grid_square_params.pixel_size or grid_square.pixel_size
grid_square.image = grid_square_params.image or grid_square.image
if murfey.server._transport_object:
murfey.server._transport_object.do_update_grid_square(
grid_square.id, grid_square_params
)
else:
# No existing grid square in the murfey database
if murfey.server._transport_object:
dcg = murfey_db.exec(
select(DataCollectionGroup)
.where(DataCollectionGroup.session_id == session_id)
.where(DataCollectionGroup.tag == grid_square_params.tag)
).one()
gs_ispyb_response = murfey.server._transport_object.do_insert_grid_square(
dcg.atlas_id, gsid, grid_square_params
)
else:
# mock up response so that below still works
gs_ispyb_response = {"success": False, "return_value": None}
secured_grid_square_image_path = secure_path(Path(grid_square_params.image))
if secured_grid_square_image_path and secured_grid_square_image_path.is_file():
jpeg_size = Image.open(secured_grid_square_image_path).size
else:
jpeg_size = (0, 0)
grid_square = GridSquare(
id=(
gs_ispyb_response["return_value"]
if gs_ispyb_response["success"]
else None
),
name=gsid,
session_id=session_id,
tag=grid_square_params.tag,
x_location=grid_square_params.x_location,
y_location=grid_square_params.y_location,
x_stage_position=grid_square_params.x_stage_position,
y_stage_position=grid_square_params.y_stage_position,
readout_area_x=grid_square_params.readout_area_x,
readout_area_y=grid_square_params.readout_area_y,
thumbnail_size_x=grid_square_params.thumbnail_size_x or jpeg_size[0],
thumbnail_size_y=grid_square_params.thumbnail_size_y or jpeg_size[1],
pixel_size=grid_square_params.pixel_size,
image=str(secured_grid_square_image_path),
)
murfey_db.add(grid_square)
murfey_db.commit()

if SMARTEM_ACTIVE:
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:
if 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,
keycloak_client=keycloak_client,
)
gs_data = SmartEMGridSquareData(
gridsquare_id=str(gsid),
grid_uuid=dcg.smartem_grid_uuid,
center_x=(
int(grid_square_params.x_location)
if grid_square_params.x_location is not None
else None
),
center_y=(
int(grid_square_params.y_location)
if grid_square_params.y_location is not None
else None
),
size_width=grid_square_params.width,
size_height=grid_square_params.height,
**(
{"uuid": grid_square.smartem_uuid}
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)
else:
response = smartem_client.create_grid_gridsquare(gs_data)
grid_square.smartem_uuid = response.uuid
murfey_db.add(grid_square)
murfey_db.commit()
except Exception:
logger.warning("Failed to register grid square with smartem", exc_info=True)

murfey_db.close()


def register_foil_hole(
session_id: int,
gs_name: int,
Expand Down
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