rahix/openflexure-microscope-server
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

More complete testing of code that runs stitching subprocess.

Browse source
This commit is contained in:
Julian Stirling 2025-08-04 00:55:21 +01:00
parent cf74ea1351
commit d7a7ac4c7d
5 changed files with 126 additions and 37 deletions
Download patch file Download diff file Expand all files Collapse all files

2
src/openflexure_microscope_server/scan_directories.py
View file

@ -58,7 +58,7 @@ class ScanData(BaseModel):
max_dist: int
dx: int
dy: int
autofocus_range: int
autofocus_dz: int
autofocus_on: bool
start_time: datetime
skip_background: bool

29
src/openflexure_microscope_server/things/smart_scan.py
View file

@ -101,7 +101,6 @@ class SmartScanThing(lt.Thing):
self._ongoing_scan: Optional[scan_directories.ScanDirectory] = None
# TODO see if starting position can go into ScanData
self._starting_position: Optional[Mapping[str, int]] = None
self._capture_thread: Optional[ErrorCapturingThread] = None
self._scan_images_taken: Optional[int] = None
# TODO Scan data is a dict during refactoring, should become a dataclass
self._scan_data: Optional[scan_directories.ScanData] = None
@ -138,7 +137,6 @@ class SmartScanThing(lt.Thing):
# TODO check if metadata_getter this can be removed without error?
self._metadata_getter = metadata_getter
self._csm = csm
self._capture_thread = None
self._scan_images_taken = 0
# Set _scan_data to None. This is needed just in case an exception is raised
@ -171,7 +169,6 @@ class SmartScanThing(lt.Thing):
self._cam = None
self._metadata_getter = None
self._csm = None
self._capture_thread = None
self._ongoing_scan = None
self._scan_images_taken = None
self._scan_data = None
@ -347,10 +344,6 @@ class SmartScanThing(lt.Thing):
scan should be stitched and whether the microscope should return to the
starting x,y,z position.
"""
# Used to check if finally was reached via exception (except
# cancel by user)
scan_successful = True
try:
self._cam.start_streaming(main_resolution=(3280, 2464))
self._scan_data = self._collect_scan_data()
@ -370,13 +363,11 @@ class SmartScanThing(lt.Thing):
self._save_final_scan_data(scan_result="success")
except lt.exceptions.InvocationCancelledError:
scan_successful = False
# Reset the cancel event so it can be thrown again
self._cancel.clear()
self._scan_logger.info("Stopping scan because it was cancelled.")
self._save_final_scan_data(scan_result="cancelled by user")
except scan_directories.NotEnoughFreeSpaceError as e:
scan_successful = False
self._save_final_scan_data(scan_result=str(e))
self._scan_logger.error(
f"Stopping scan to avoid filling up the disk: {e}",
@ -384,7 +375,6 @@ class SmartScanThing(lt.Thing):
)
raise e
except Exception as e:
scan_successful = False
self._save_final_scan_data(scan_result=str(e))
self._scan_logger.error(
f"The scan stopped because of an error: {e} "
@ -397,21 +387,7 @@ class SmartScanThing(lt.Thing):
# Start streaming in the default resolution again as soon as possible
self._cam.start_streaming()
if self._capture_thread:
# If the capture thread had an error, we capture it here
try:
self._capture_thread.join()
except Exception as e:
# If the scan has already ended due to an exception,
# ignore any exceptions. If it appeared to be successful,
# log the error.
if scan_successful:
self._scan_logger.error(
"The scan appears to have completed successfully, however "
f"the final capture raised the following error: {e}."
"Attempting to stitch and archive images.",
exc_info=e,
)
# This is what happens if the scan completes successfully or the
# user cancels it.
@ -508,7 +484,8 @@ class SmartScanThing(lt.Thing):
self._scan_logger.info("Waiting for background processes to finish...")
self._preview_stitcher.wait()
if self._preview_stitcher is not None:
self._preview_stitcher.wait()
if self._scan_data.stitch_automatically:
self._scan_logger.info("Stitching final image (may take some time)...")