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Author SHA1 Message Date
Julian Stirling
368c980c77 Pin fastapi-version until upstream issue in LabThings is fixed 2025-12-08 16:06:24 +00:00
Julian Stirling
5375e9578b Update version for alpha 4 release and update changelog 2025-12-08 15:07:14 +00:00
Julian Stirling
6d74a68eca Bump stitching version to v0.2.2 2025-12-08 14:37:13 +00:00
Joe Knapper
32ec08d4f4 Merge branch 'bump-stitching-0.2.1' into 'v3' 
Bump required stitching version to 0.2.1

See merge request openflexure/openflexure-microscope-server!448
 2025-12-03 12:50:13 +00:00
Julian Stirling
c3cb8436dc Bump required stitching version 2025-12-03 11:14:47 +00:00
Julian Stirling
13eb50877d Merge branch 'isort' into 'v3' 
Formalise import sorting rules and enforce

See merge request openflexure/openflexure-microscope-server!438
 2025-12-02 17:46:43 +00:00
Julian Stirling
42413c6b00 Update picamera zip 2025-12-02 17:10:27 +00:00
Julian Stirling
7bc4c514a6 Autofix import order 2025-12-02 16:26:15 +00:00
Julian Stirling
98cdb276d8 Add ruff isort rules with custom group for our own external packages 2025-12-02 16:25:11 +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
d482a4cb36 Update picamera coverage info 2025-12-02 10:15:25 +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
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
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
3ebc4578d3 Show which background detector is active in GUI 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
d3bd921db2 Merge branch 'visit-secondary-locations-first' into 'v3' 
Visit secondary locations first

See merge request openflexure/openflexure-microscope-server!444
 2025-12-01 16:31:24 +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
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
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
cd53024c4f Update the scan test helpers so it is easier to save and plot 2025-11-28 09:52:09 +00:00
Joe Knapper
23989977c2 Merge branch 'manual-config' into 'v3' 
Configuration for manual microscope

See merge request openflexure/openflexure-microscope-server!439
 2025-11-13 14:42:29 +00:00
Julian Stirling
11e9374dfa Merge branch 'consolidate-action-button' into 'v3' 
Consolidate action buton to just a button

Closes #535

See merge request openflexure/openflexure-microscope-server!437
 2025-11-13 12:12:31 +00:00
Julian Stirling
fe77908253 Make the findOngoingActions function plural to match what happens 2025-11-13 11:51:03 +00:00
Julian Stirling
8333165307 Merge branch '569-release-checklist' into 'v3' 
Resolve "Release Checklist"

Closes #569

See merge request openflexure/openflexure-microscope-server!440
 2025-11-12 16:10:30 +00:00
Beth Probert
7df1fea643 Fix typo 2025-11-12 15:32:18 +00:00
Beth Probert
560f863c47 Apply suggestions from code review of branch 569-release-checklist 
Co-authored-by: Julian Stirling <julian@julianstirling.co.uk>
 2025-11-12 15:29:15 +00:00
Beth Probert
1311cc103e Responding to comment on branching. 2025-11-12 11:27:02 +00:00
Beth Probert
f128caedff Apply suggestions from code review of branch 569-release-checklist 
Co-authored-by: Julian Stirling <julian@julianstirling.co.uk>
 2025-11-12 11:10:44 +00:00
Julian Stirling
f3c79b746f Fix RGB vs BGR issue for opencv camera 2025-11-11 18:12:37 +00:00
Julian Stirling
abb2698687 Add config json for manual microscope 2025-11-11 18:12:37 +00:00