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Merge branch 'cancel-scan-early-bugfix' into 'v3'

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Fix error trying to purge empty scans if current scan has no images

Closes #563

See merge request openflexure/openflexure-microscope-server!398
This commit is contained in:
Joe Knapper 2025-09-26 09:33:21 +00:00
commit 3deb5a4897
2 changed files with 5 additions and 12 deletions
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6
src/openflexure_microscope_server/things/smart_scan.py
View file

@ -179,6 +179,9 @@ class SmartScanThing(lt.Thing):
# Ensure any PreviewStitcher created cannot be reused. # Ensure any PreviewStitcher created cannot be reused.
self._preview_stitcher = None self._preview_stitcher = None
# Remove any scan folders containing zero images.
self.purge_empty_scans(logger=logger)
@_scan_running @_scan_running
def _check_background_and_csm_set(self) -> None: def _check_background_and_csm_set(self) -> None:
"""Before starting a scan, check that background and camera-stage-mapping are set. """Before starting a scan, check that background and camera-stage-mapping are set.
@ -386,9 +389,6 @@ class SmartScanThing(lt.Thing):
self._return_to_starting_position() self._return_to_starting_position()
self._perform_final_stitch() self._perform_final_stitch()
# Remove any scan folders containing zero images
self.purge_empty_scans(logger=self._scan_logger)
@_scan_running @_scan_running
def _main_scan_loop(self) -> None: def _main_scan_loop(self) -> None:
"""Run the main loop of the scan. """Run the main loop of the scan.

11
tests/test_smart_scan.py
View file

@ -331,9 +331,8 @@ def test_save_final_scan_data(scan_thing_mocked_for_scan_data):
def scan_thing_mocked_for_run_scan(scan_thing_mocked_for_scan_data, mocker): def scan_thing_mocked_for_run_scan(scan_thing_mocked_for_scan_data, mocker):
"""Return a scan_thing mocked so _run_scan works. """Return a scan_thing mocked so _run_scan works.
main_scan_loop(), _return_to_starting_position(), _perform_final_stitch(), and main_scan_loop(), _return_to_starting_position(), and _perform_final_stitch() are
purge_empty_scans() are Mocks Mocks and _cam is a MockCameraThing
_cam is a MockCameraThing
""" """
scan_thing = scan_thing_mocked_for_scan_data scan_thing = scan_thing_mocked_for_scan_data
scan_thing._cam = MockCameraThing() scan_thing._cam = MockCameraThing()
@ -341,7 +340,6 @@ def scan_thing_mocked_for_run_scan(scan_thing_mocked_for_scan_data, mocker):
mocker.patch.object(scan_thing, "_main_scan_loop") mocker.patch.object(scan_thing, "_main_scan_loop")
mocker.patch.object(scan_thing, "_return_to_starting_position") mocker.patch.object(scan_thing, "_return_to_starting_position")
mocker.patch.object(scan_thing, "_perform_final_stitch") mocker.patch.object(scan_thing, "_perform_final_stitch")
mocker.patch.object(scan_thing, "purge_empty_scans")
return scan_thing return scan_thing
@ -373,7 +371,6 @@ def check_run_scan(scan_thing, caplog, expected_exception=None):
"main_scan_loop_calls": scan_thing._main_scan_loop.call_count, "main_scan_loop_calls": scan_thing._main_scan_loop.call_count,
"return_to_start_calls": scan_thing._return_to_starting_position.call_count, "return_to_start_calls": scan_thing._return_to_starting_position.call_count,
"perform_final_stitch_calls": scan_thing._perform_final_stitch.call_count, "perform_final_stitch_calls": scan_thing._perform_final_stitch.call_count,
"purge_empty_scans_calls": scan_thing.purge_empty_scans.call_count,
"save_scan_data_calls": scan_thing._ongoing_scan.save_scan_data.call_count, "save_scan_data_calls": scan_thing._ongoing_scan.save_scan_data.call_count,
} }
return final_scan_data.scan_result, caplog.records, calls return final_scan_data.scan_result, caplog.records, calls
@ -391,7 +388,6 @@ def test_run_scan(scan_thing_mocked_for_run_scan, caplog):
"main_scan_loop_calls": 1, "main_scan_loop_calls": 1,
"return_to_start_calls": 1, "return_to_start_calls": 1,
"perform_final_stitch_calls": 1, "perform_final_stitch_calls": 1,
"purge_empty_scans_calls": 1,
"save_scan_data_calls": 2, "save_scan_data_calls": 2,
} }
assert calls == expected_calls_numbers assert calls == expected_calls_numbers
@ -417,7 +413,6 @@ def test_run_scan_err_in_main_loop(scan_thing_mocked_for_run_scan, caplog, mocke
"main_scan_loop_calls": 1, "main_scan_loop_calls": 1,
"return_to_start_calls": 0, "return_to_start_calls": 0,
"perform_final_stitch_calls": 0, "perform_final_stitch_calls": 0,
"purge_empty_scans_calls": 0,
"save_scan_data_calls": 2, "save_scan_data_calls": 2,
} }
assert calls == expected_calls_numbers assert calls == expected_calls_numbers
@ -443,7 +438,6 @@ def test_run_scan_cancelled(scan_thing_mocked_for_run_scan, caplog, mocker):
"main_scan_loop_calls": 1, "main_scan_loop_calls": 1,
"return_to_start_calls": 1, "return_to_start_calls": 1,
"perform_final_stitch_calls": 1, "perform_final_stitch_calls": 1,
"purge_empty_scans_calls": 1,
"save_scan_data_calls": 2, "save_scan_data_calls": 2,
} }
assert calls == expected_calls_numbers assert calls == expected_calls_numbers
@ -469,7 +463,6 @@ def test_run_scan_fill_disk(scan_thing_mocked_for_run_scan, caplog, mocker):
"main_scan_loop_calls": 1, "main_scan_loop_calls": 1,
"return_to_start_calls": 0, "return_to_start_calls": 0,
"perform_final_stitch_calls": 0, "perform_final_stitch_calls": 0,
"purge_empty_scans_calls": 0,
"save_scan_data_calls": 2, "save_scan_data_calls": 2,
} }
assert calls == expected_calls_numbers assert calls == expected_calls_numbers