Julian Stirling
06632f195e
Spelling corrections and docstring improvements
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Co-authored by Joe Knapper <jaknapper@hotmail.com>
2025-04-14 15:46:27 +00:00
Julian Stirling
7f46bc2d9b
Fixing capture_thread variable and autofocus logic
2025-04-14 11:27:25 +01:00
Julian Stirling
a0b6dbdfce
Add weay to access a copy of the data from a ScanPlanner
2025-04-14 11:27:25 +01:00
Julian Stirling
91073535a8
More tests for scan planners
2025-04-14 11:27:25 +01:00
Julian Stirling
842e196f9b
Add some basic tests, and do minor fixes based on tests and MyPy
2025-04-14 11:27:25 +01:00
Julian Stirling
1f66e8bc7a
Enormous refactor of the scan code, was hard to find an intermediate working place to commit
2025-04-14 11:27:25 +01:00
Julian Stirling
cddb49c9f7
Clean up code as I remove bare excepts
2025-04-14 11:27:25 +01:00
Julian Stirling
2c171026be
Still tidying the start end end of the scan code
2025-04-14 11:27:25 +01:00
Julian Stirling
797f3bcb60
Collecting scan parameters into dictionary that will become a dataclass
2025-04-14 11:27:25 +01:00
Julian Stirling
7665d45e09
Make the coverage report touch all files
2025-04-11 23:29:32 +01:00
Julian Stirling
1c871749b0
Remove module level noqa from background detect.
2025-04-11 12:32:32 +01:00
Julian Stirling
4eeff35e2d
Fixes to naming to make basic lint checks pass
2025-04-11 12:29:14 +01:00
Julian Stirling
b7c472bb24
fix comment on number of zeros padding the scan name
2025-04-10 22:39:22 +01:00
Julian Stirling
31c768c12a
Move @_scan_running decorator out of class and tidy as suggested in review
2025-04-10 22:14:56 +01:00
Julian Stirling
e030eb576b
Add @scan_running decorator for scans to try to access to the scan logger for methods not called by the scan
2025-04-10 17:52:12 +01:00
Julian Stirling
26e265f026
Fixes from review (mostly spellings)
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Co authored by:
* Joe Knapper <jaknapper@hotmail.com>
* Beth Probert <beth_probert@outlook.com>
2025-04-10 16:35:49 +00:00
Julian Stirling
840c527cc2
Remove unused Stitching Thing
2025-04-10 13:53:51 +01:00
Julian Stirling
a5d55c95b8
Further tidying of scan directory variables
2025-04-10 13:24:11 +01:00
Julian Stirling
90cfce146d
Fix default scan name
2025-04-10 11:46:16 +01:00
Julian Stirling
040373ef88
Run check background aonly fter scan variables are stored
2025-04-10 11:45:57 +01:00
Julian Stirling
83d2930d1f
Fix capture error handing
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The error handling for capture needs to still send the aquired event
or it will lock forever. On getting the errors to work there
were some other minor issues in how the errors were called.
2025-04-09 23:52:47 +01:00
Julian Stirling
70e7a21a29
Starting to refactor smart scan to rely on class variables
2025-04-09 22:55:35 +01:00
Julian Stirling
ff1184d453
Handle errors in capture thread
2025-04-09 22:45:18 +01:00
Joe Knapper
1d5d67f35a
Split out background detect into a new file
2025-04-09 17:25:19 +01:00
Joe Knapper
f4db9b6e52
Removed commented out code and unused functions
2025-04-09 15:32:13 +01:00
jaknapper
a5d1f1e965
Removed commented out code
2025-04-09 15:11:26 +01:00
jaknapper
e28a160b22
Ruff formatting adding commas
2025-04-09 14:59:20 +01:00
jaknapper
8d14aee27c
Breaking out capture and save code into three seperate methods
2025-04-09 13:20:06 +01:00
jaknapper
9c2ab977c5
Removed imports and variable to pass Ruff linting
2025-04-08 19:07:23 +01:00
jaknapper
574aa1c6c0
Only grab a JPEG from the stream to get scanning working
2025-04-08 17:52:55 +01:00
Joe Knapper
d4247235e3
Merge branch 'csm-return-to-start' into 'v3'
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CSM always returns to start on error
See merge request openflexure/openflexure-microscope-server!227
2025-04-08 12:49:38 +00:00
Joe Knapper
e4ef8b2717
Merge branch 'consistent-logging' into 'v3'
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Stop uvicorn.run disabling existing loggers
Closes #284
See merge request openflexure/openflexure-microscope-server!228
2025-04-08 11:31:33 +00:00
jaknapper
b340da488e
Use the UV channels only to determine if an area is background or sample
2025-04-08 11:14:17 +01:00
Julian Stirling
1493f51212
Purge all windows line endings and add check to formatter.
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Also changes python version in pyproject.toml as it is incorrect
2025-04-08 10:51:26 +01:00
Julian Stirling
3a47151694
Serve logfile and logs for UI seperately
2025-04-07 23:45:19 +01:00
Julian Stirling
70d9e2f758
Add custom log handler for sending logs to UI
2025-04-07 23:16:00 +01:00
jaknapper
33c74741fe
Fixed import and re-raise cancelled error
2025-04-07 15:46:20 +01:00
Joe Knapper
a506625e40
Treat cancellation and other errors differently
2025-04-07 14:22:43 +01:00
Joe Knapper
9995e5b3bb
Import custom Mapping error from camera_stage_mapping
2025-04-07 14:18:07 +01:00
Julian Stirling
dd0b30df51
Stop uvicorn.run disabling existing loggers
2025-04-06 15:26:39 +01:00
jaknapper
67443ff939
Capture ValueErrors, which covers most CSM errors, not all Exceptions
2025-04-03 13:52:04 +01:00
jaknapper
46d513d9e6
Catch cancelled and other errors in single line
2025-04-02 18:25:35 +01:00
Joe Knapper
79b396a66f
CSM always returns to start on error
2025-04-02 17:54:12 +01:00
Julian Stirling
32f2a7ce70
Fix spurious line endings, don't allow ruff-format to fail anymore
2025-04-02 14:25:22 +01:00
Richard Bowman
83e10b125b
Fix return type annotation for autofocus
2024-12-18 14:23:58 +00:00
Richard Bowman
9fd8fc37f1
Formatted with Ruff
2024-12-03 06:46:08 +00:00
Richard Bowman
27aec769a2
Linter fixes
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NB I have permitted bare except: blocks in smart_scan. This should be reverted.
2024-12-03 06:43:45 +00:00
Richard Bowman
57177c6a56
Sped up camera and got CSM passing
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Using lower resolution helps speed it up, and skipping CSM settling time makes a big difference.
2024-12-03 06:35:16 +00:00
Richard Bowman
1e7069b375
Add more tests, speed up dummy stage
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I've sped up the stage motion, to run tests in a more reasonable time.
CSM doesn't yet calibrate in the test - I suspect debugging of capture_array
is needed.
2024-12-03 00:16:26 +00:00
Richard Bowman
bccb1ee923
Stub class for camera protocol
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As with the previous commit, this adds a concrete stub Thing to enable
DirectThingClient generation, so we
can depend on the camera.
2024-11-29 12:53:42 +00:00
