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Simplify FIB atlas registration workflow #903

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Merged
tieneupin merged 2 commits into from
Sep 25, 2026
Merged

Simplify FIB atlas registration workflow #903

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4685f80
Let 'feedback_callback' handle raised exceptions and database connect…
tieneupin Sep 24, 2026
f84c22a
Use new 'register_dcg' function instead of loading the entry point
tieneupin Sep 24, 2026
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163 changes: 54 additions & 109 deletions src/murfey/workflows/fib/register_atlas.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,4 @@
import logging
import traceback
from importlib.metadata import entry_points
from pathlib import Path
from typing import Any, cast
Expand All @@ -16,6 +15,7 @@
parse_image_metadata,
populate_fib_imaging_site_entry,
)
from murfey.workflows.register_data_collection_group import register_dcg

logger = logging.getLogger("murfey.workflows.fib.register_atlas")

Expand Down Expand Up @@ -153,23 +153,14 @@ def _register_dcg_and_atlas(
"atlas_pixel_size": atlas_pixel_size,
"sample": metadata.slot_number,
}
if entry_point_result := entry_points(
group="murfey.workflows", name="data_collection_group"
):
(workflow,) = entry_point_result
# Register grid square
_ = workflow.load()(
message=dcg_message,
murfey_db=murfey_db,
dcg_entry = register_dcg(
message=dcg_message,
murfey_db=murfey_db,
)
if not dcg_entry:
raise RuntimeError(
f"Could not register DataCollectionGroup entry for {imaging_site.image_path}"
)
else:
logger.warning("No workflow found for 'data_collection_group'")
dcg_entry = murfey_db.exec(
select(MurfeyDB.DataCollectionGroup)
.where(MurfeyDB.DataCollectionGroup.session_id == session_id)
.where(MurfeyDB.DataCollectionGroup.tag == imaging_site.site_name)
).one()

imaging_site.dcg_id = dcg_entry.id
imaging_site.dcg_name = dcg_entry.tag
murfey_db.add(imaging_site)
Expand All @@ -185,101 +176,55 @@ def run(
message: dict[str, Any],
murfey_db: Session,
):
# Outer try-finally block to ensure database connection closes
try:
try:
# Validate incoming message
fib_info = FIBAtlasRegistrationInfo(**message)
except Exception:
logger.error("Could not validate incoming message", exc_info=True)
return {"success": False, "requeue": False}
# Validate incoming message
fib_info = FIBAtlasRegistrationInfo(**message)

try:
# Load visit information
murfey_session = murfey_db.exec(
select(MurfeyDB.Session).where(
MurfeyDB.Session.id == fib_info.session_id
)
).one()
visit_name = murfey_session.visit
instrument_name = murfey_session.instrument_name
except Exception:
logger.error(
"Exception encountered while querying Murfey database", exc_info=True
)
return {"success": False, "requeue": False}

try:
# Load the machine config
machine_config = get_machine_config(instrument_name)[instrument_name]
rotation_offset: float = cast(
float, machine_config.calibrations.get("rotation_offset", 0)
)
# Load visit information
murfey_session = murfey_db.exec(
select(MurfeyDB.Session).where(MurfeyDB.Session.id == fib_info.session_id)
).one()
visit_name = murfey_session.visit
instrument_name = murfey_session.instrument_name

# Extract metadata from Electron Snapshot image
metadata = FIBImageMetadata(
visit_name=visit_name,
file=fib_info.atlas_file,
**parse_image_metadata(
fib_info.atlas_file,
rotation_offset=rotation_offset,
),
)
except Exception:
logger.error(
f"Error extracting metadata from file {fib_info.atlas_file}",
exc_info=True,
)
return {"success": False, "requeue": False}
# Load the machine config
machine_config = get_machine_config(instrument_name)[instrument_name]
rotation_offset: float = cast(
float, machine_config.calibrations.get("rotation_offset", 0)
)

try:
# Make a thumbnail of the image and update metadata accordingly
metadata.thumbnail_path = _make_thumbnail(
file=metadata.file,
metadata=metadata,
visit_name=visit_name,
)
except Exception:
logger.warning(
f"Error creating thumbnail of file {fib_info.atlas_file}", exc_info=True
)
# Extract metadata from Electron Snapshot image
metadata = FIBImageMetadata(
visit_name=visit_name,
file=fib_info.atlas_file,
**parse_image_metadata(
fib_info.atlas_file,
rotation_offset=rotation_offset,
),
)

try:
# Register imaging site in Murfey, or update existing one
fib_imaging_site = _register_fib_imaging_site(
fib_info.session_id, metadata, murfey_db
)
logger.info(
f"Registered FIB atlas image {fib_info.atlas_file} "
f"for slot {metadata.slot_number} in Murfey database"
)
except Exception:
logger.error(
"Error registering FIB atlas image "
f"{fib_info.atlas_file} in Murfey database",
exc_info=True,
)
return {"success": False, "requeue": False}
# Make a thumbnail of the image and update metadata accordingly
metadata.thumbnail_path = _make_thumbnail(
file=metadata.file,
metadata=metadata,
visit_name=visit_name,
)

try:
# Register data collection group and atlas in ISPyB
_register_dcg_and_atlas(
session_id=fib_info.session_id,
instrument_name=murfey_session.instrument_name,
visit_name=murfey_session.visit,
imaging_site=fib_imaging_site,
metadata=metadata,
murfey_db=murfey_db,
)
except Exception:
# Log error but allow workflow to proceed
logger.error(
"Error registering data collection group for FIB workflow "
f"for {metadata.site_name!r}: \n"
f"{traceback.format_exc()}"
)
return {"success": False, "requeue": True}
return {"success": True, "requeue": False}
# Register imaging site in Murfey, or update existing one
fib_imaging_site = _register_fib_imaging_site(
fib_info.session_id, metadata, murfey_db
)
logger.info(
f"Registered FIB atlas image {fib_info.atlas_file} "
f"for slot {metadata.slot_number} in Murfey database"
)

finally:
murfey_db.close()
# Register data collection group and atlas in ISPyB
_register_dcg_and_atlas(
session_id=fib_info.session_id,
instrument_name=murfey_session.instrument_name,
visit_name=murfey_session.visit,
imaging_site=fib_imaging_site,
metadata=metadata,
murfey_db=murfey_db,
)
return {"success": True, "requeue": False}
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