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232 commits

Author SHA1 Message Date
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
5375e9578b Update version for alpha 4 release and update changelog 2025-12-08 15:07:14 +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
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
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
a15f23bec2 Add unit tests for captureing images in a stack 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
13e065a44d Add test for the outer smart stack algorithm 2025-12-02 09:57:24 +00:00
Julian Stirling
a5d5ba4af8 Update scan planner test pickles 2025-11-28 12:00:35 +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
cd53024c4f Update the scan test helpers so it is easier to save and plot 2025-11-28 09:52:09 +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
b0b755f19b Update unit tests for algorithmic change to recentre 2025-11-11 17:13:52 +00:00
Julian Stirling
982c55905c Update default exposure in picam and defaul LST values in tuning files, and set default colour gains from LST 2025-11-11 11:20:08 +00:00
Julian Stirling
13d3871059 Add testing for loading the tuning files in the normal test suite now not tied to picamera 2025-11-11 11:20:08 +00:00
Julian Stirling
ec16cc17f8 Update tuning file utils for our own tuning files. 2025-11-11 11:20:07 +00:00
Julian Stirling
f7d03d8c00 Fix confusion between (x,y) image coordinates and (y,x) matrix indicies 2025-11-05 13:19:28 +00:00
Julian Stirling
dcf4b0b383 Split the logic for deciding how to move in recentre from the moves and the main loop 2025-11-05 11:43:25 +00:00
Julian Stirling
7f0e7c52f9 Test everything remainign in recentre except the main algorithm for an axis 2025-11-05 00:36:43 +00:00
Julian Stirling
a5a372b6c0 Split out matix calculations from CSM, and continue testing recentre 2025-11-05 00:15:30 +00:00
Julian Stirling
c659a556cc Update stage_measure test data to be more parabolic and add turning point test 2025-11-04 18:54:15 +00:00
Julian Stirling
b09aa7b5b8 First interation of a recentre algoritm build on ROM test methods 2025-11-04 18:54:15 +00:00
Julian Stirling
cd5d74b5e6 Add tests for not reading ongoing scan data 2025-11-04 18:50:17 +00:00
Julian Stirling
e4cb48eb6d Stricter rules on pytest.raises, requiring match for generic error types 
Closes #560
 2025-10-28 17:20:40 +00:00
Julian Stirling
adf9736fab Add testing for patching json files 2025-10-27 15:07:45 +00:00
Julian Stirling
9e9764e196 Implement JSON Merge Patch from IETF RFC 7396 2025-10-27 15:07:43 +00:00
Julian Stirling
418a6b5364 Merge branch 'calibration-wizard-refactor' into 'v3' 
Refactor Calibration Wizard

Closes #578

See merge request openflexure/openflexure-microscope-server!415
 2025-10-27 14:15:05 +00:00
Julian Stirling
94c9a0e7dd Merge branch 'rom_test_only' into 'v3' 
Adding automatic range of motion measurements

See merge request openflexure/openflexure-microscope-server!335
 2025-10-27 12:18:31 +00:00
Julian Stirling
df979eb3cf Add checks for new calibration required property to tests 2025-10-26 15:47:41 +00:00
Julian Stirling
08046ff657 Clarify behaviour of overloads, and better error checking of _move_and_measure inputs 2025-10-24 17:27:43 +01:00
Julian Stirling
ba8a4ca744 Apply suggestions from code review of branch rom_test_only 
Co-authored-by: Beth Probert <beth_probert@outlook.com>
 2025-10-24 14:05:07 +00:00
Julian Stirling
b8eb1907c3 Modify range of motion _move_back_until_motion_detected to move in SMALL_STEP steps 
This will carry on until at least 1.5x BIG_STEP in total motion. If
no motion is detected then something is up.
 2025-10-21 14:40:18 +01:00
Julian Stirling
7f657ae853 No error on parasitic motion after small step checking for stage movement, use background detect 2025-10-20 23:02:08 +01:00
Julian Stirling
72c35c302c Adjust CSM Thing to allow calculation of stage coords from img coords and use this in stage measure 
Using this stops the z-axis being flipped when the off diagonal elements of the CSM are different
signs.
 2025-10-20 22:20:19 +01:00
Julian Stirling
ff606ff10d Apply spelling corrections and variable renaming from code review of branch improve-scan-planning 
Co-authored-by: Joe Knapper <joe.knapper@glasgow.ac.uk>
 2025-10-20 18:26:20 +01:00
Julian Stirling
635375a012 Fix assumption that CSM was a numpy array not a list 2025-10-20 16:40:41 +01:00
Julian Stirling
f781e6b674 Image intermediate locations between sample and background 2025-10-19 21:29:11 +01:00
Julian Stirling
39a04df5be Objects for scan locations allowing more sophisitcated tracking. 
This commit updates the scan planners to allow more sophisticated
tracking of past positions. Currently it still checks that
the algorithm is unchanged from past behaviour.
 2025-10-19 19:55:36 +01:00
Julian Stirling
b314ced4f7 Final Range of motion tests 2025-10-17 17:31:34 +01:00
Julian Stirling
30217a4c38 Add tests for initial moves at start of ROM test 2025-10-17 15:19:06 +01:00
Julian Stirling
95f5bbb16c Ensure ROM z-predict returns an integer and add more tests. 2025-10-17 15:19:06 +01:00
Julian Stirling
3d49cbf921 Adding even more ROM tests 2025-10-17 15:19:06 +01:00
Julian Stirling
664c7de5f8 Add more ROM tests 2025-10-17 15:19:06 +01:00
Julian Stirling
50d6298c06 Start updating ROM tests for new structure 2025-10-17 15:19:06 +01:00