rahix/openflexure-microscope-server
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747 commits

Author SHA1 Message Date
Julian Stirling
7f8fb623ef Remove deps from stage_measure 2025-12-16 17:27:22 +00:00
Julian Stirling
189e82e8dc Remove deps from autofocus 2025-12-16 17:27:22 +00:00
Julian Stirling
4a327cc901 Remove deps from camera_stage_mapping 2025-12-16 16:24:04 +00:00
Julian Stirling
4a72521531 Remove deps from system thing 2025-12-16 14:57:13 +00:00
Julian Stirling
426178ba31 Remove dependencies from stages 2025-12-16 14:57:12 +00:00
Julian Stirling
4b845fcf18 Remove dependencies from camera 2025-12-16 14:22:31 +00:00
Julian Stirling
ddc81f9c17 Apply suggestions from code review of branch update-for-labthings0.0.12 
Co-authored-by: Richard Bowman <richard.bowman@cantab.net>
 2025-12-16 13:32:57 +00:00
Julian Stirling
a67afdf21f Fix bug in simulation frame timing which may be affecting integration test 2025-12-16 13:32:57 +00:00
Julian Stirling
942e9e5024 Fix type for ROM calibrated_range 2025-12-16 13:32:57 +00:00
Julian Stirling
baf0ff9a11 Updating for changes related to NotConnectedToServerErrors 2025-12-15 17:18:30 +00:00
Julian Stirling
dec90f5b6b Update legacy_api.py test_sangaboard and test_server_cli so tests pass for labthings-fastapi 0.0.12 2025-12-14 20:53:33 +00:00
Julian Stirling
cfbb7cf7f9 Start fixing tests. This involves further blocking portal changes. 
This will need PR 225 of labthings-fastapi to be merged to run.
 2025-12-14 19:21:06 +00:00
Julian Stirling
9ef417971f Remove a load more /names/ 2025-12-14 18:23:33 +00:00
Julian Stirling
e7f669cb56 No blocking portals 2025-12-14 18:23:33 +00:00
Julian Stirling
ca3f339cbe Simulation camera get dummy stage from thing_slot 2025-12-14 18:23:33 +00:00
Julian Stirling
c318fddf89 Update fastapi_endpoint to endpoint 2025-12-14 18:23:33 +00:00
Julian Stirling
5d3aa71b4f Update things to have thing_server_interface, and further fixes to properties 2025-12-14 18:23:27 +00:00
Julian Stirling
5eea78cac7 update action, property, and setting syntax for labthings-fastapi 0.0.12 2025-12-14 18:23:26 +00:00
Julian Stirling
bbbfaf8602 Get fallback server working again 2025-12-14 11:33:03 +00:00
Julian Stirling
7bc4c514a6 Autofix import order 2025-12-02 16:26:15 +00:00
Joe Knapper
99afe89c10 Merge branch 'scanning-stability' into 'v3' 
Improve the stability of scanning

Closes #599 and #600

See merge request openflexure/openflexure-microscope-server!434
 2025-12-02 15:47:03 +00:00
Julian Stirling
38c596fb49 Merge branch 'Sanga-firmware-check' into 'v3' 
Log an error if the sangaboard firmware is below v1.0.4

Closes #623

See merge request openflexure/openflexure-microscope-server!447
 2025-12-02 15:14:50 +00:00
Julian Stirling
dd7c135fa8 Fix comment in sangaboard firmware check 2025-12-02 14:36:10 +00:00
Julian Stirling
240b7d1ba5 Use semver library for checking sangaboard firmware version. 2025-12-02 11:55:56 +00:00
Julian Stirling
797dda3514 Add failing unit test for sangaboard version before v1 2025-12-02 11:00:41 +00:00
Julian Stirling
5017fea9d1 A couple of final edits suggested in review 2025-12-02 09:57:25 +00:00
Julian Stirling
9b58f4d59e Apply suggestions from code review of branch scanning-stability 
Co-authored-by: Joe Knapper <joe.knapper@glasgow.ac.uk>
 2025-12-02 09:57:25 +00:00
Julian Stirling
2749a1818c Add unit tests for ChannelDeviationLUV background detector 2025-12-02 09:57:25 +00:00
Julian Stirling
e5d2ebbb79 Add tests for checking stack result 2025-12-02 09:57:24 +00:00
Julian Stirling
573330dede Add tests for z_stack 2025-12-02 09:57:24 +00:00
Julian Stirling
b9c58b70c9 Looping autofocus errors on failure to find focus. Test looping autofocus algorithm 2025-12-02 09:57:24 +00:00
Julian Stirling
aa704239ed Modify background detect check to check for all squares having no std. As LUV appears insensitive to low colour noise 2025-12-02 09:57:24 +00:00
Julian Stirling
1f2099e46f Add minimum standard deviations for ColourChannelDetectLUV 2025-12-02 09:57:24 +00:00
Julian Stirling
a2a6d870e2 Make turing point check in z-stack optional 2025-12-02 09:57:24 +00:00
Julian Stirling
873968877b Log warning rather than error if the named background detector doesn't exist to prevent not booting if detectors change 2025-12-02 09:57:24 +00:00
Julian Stirling
79c94c96ed Set channel minima and error if any LUV channels have std==0 2025-12-02 09:57:24 +00:00
Julian Stirling
38b8c5baa5 Apply suggestions from code review of branch scanning-stability 
Co-authored-by: Joe Knapper <joe.knapper@glasgow.ac.uk>
 2025-12-02 09:57:24 +00:00
Julian Stirling
23f87869ac Add a new background detector based on an 8x8 grid 2025-12-02 09:57:24 +00:00
Julian Stirling
cf92d4f3ac Make autofocus considerably stricter, forcing a parabolic fit, and only one turning point 
Background can still pass this much stricter check
 2025-12-02 09:57:24 +00:00
Julian Stirling
dabb195b08 Ensure smart stack exits and saves on failure only if check background is false 2025-12-02 09:57:24 +00:00
jaknapper
70e052fa21 Check the firmware and log relevant messages 2025-12-01 18:08:25 +00:00
Julian Stirling
ed9076a115 Log an error if the sangaboard firmware is below v1.0.4 2025-12-01 14:21:56 +00:00
Julian Stirling
dfe7fb6c42 Stop scan planner plots erroring if there are no secondary locations 2025-11-28 12:00:35 +00:00
Julian Stirling
90be139575 Update scan planners so secondary locations are imaged first and don't affect later planning 2025-11-28 09:53:24 +00:00
Julian Stirling
f3c79b746f Fix RGB vs BGR issue for opencv camera 2025-11-11 18:12:37 +00:00
Julian Stirling
3ecc41720d Merge branch 'recentre-with-rom-methods' into 'v3' 
Recentre using RangeOfMotionThing methods

Closes #499 and #573

See merge request openflexure/openflexure-microscope-server!429
 2025-11-11 17:49:08 +00:00
Julian Stirling
614fd8b9e9 Apply suggestions from code review of branch recentre-with-rom-methods 
Co-authored-by: Richard Bowman <richard.bowman@cantab.net>
 2025-11-11 17:15:20 +00:00
Julian Stirling
ed9b8ff01d Adjust algorithm to start checks for centre after first 5 mendium sized moves & improve logging. 2025-11-11 12:51:04 +00:00
Julian Stirling
b8742b449c Apply suggestions from code review of branch recentre-with-rom-methods 
Co-authored-by: Joe Knapper <joe.knapper@glasgow.ac.uk>
 2025-11-11 12:37:09 +00:00
Julian Stirling
8a4e6390c7 Apply suggestions from code review of branch temperature-ccm 
Co-authored-by: Joe Knapper <joe.knapper@glasgow.ac.uk>
 2025-11-11 11:20:08 +00:00