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469 commits

Author SHA1 Message Date
Julian Stirling
2e6ba73345 Apply suggestions from code review of branch yet-another-smart-scan-refactor 
Co-authored-by: Joe Knapper <joe.knapper@glasgow.ac.uk>
 2025-08-06 17:27:26 +01:00
Julian Stirling
6739a84d7c Apply suggestions from code review of branch yet-another-smart-scan-refactor 
Co-authored-by: Joe Knapper <joe.knapper@glasgow.ac.uk>
 2025-08-06 17:27:26 +01:00
Julian Stirling
f9fcdf628b Squash final todos for SmartScan refactor 2025-08-06 17:27:26 +01:00
Julian Stirling
7d83aadf8d Squash some TODOs 2025-08-06 17:27:26 +01:00
Julian Stirling
4e9b07c78f Consolidate information into ScanData, remove ad-hoc differences for specific error in _run_scan 2025-08-06 17:27:26 +01:00
Julian Stirling
82691a6b78 Tweak error reporting in _run_scan and add a lot more testing for _run_scan 2025-08-06 17:27:26 +01:00
Julian Stirling
d7a7ac4c7d More complete testing of code that runs stitching subprocess. 2025-08-06 17:27:26 +01:00
Julian Stirling
cf74ea1351 More complete testing of code that runs stitching subprocess. 2025-08-06 17:27:26 +01:00
Julian Stirling
7569c7d6b2 Add validation checks to prevent arbitrary code execution via stitching. 2025-08-06 17:27:26 +01:00
Julian Stirling
a632ddee92 Add unit tests for generated stitching commands. 2025-08-06 17:27:26 +01:00
Julian Stirling
573fc20dec Add new tests new scan directory function and for scan data serialisation 2025-08-06 17:27:26 +01:00
Julian Stirling
6ceb1a9845 Pull stitching out of SmartScanThing 2025-08-06 17:27:26 +01:00
Julian Stirling
f449bcdd78 Turn scan_data into a BaseModel with validation for custom formatting 2025-08-06 17:27:26 +01:00
Julian Stirling
73beb2b09d Merge branch 'fix-movements' into 'v3' 
Fix movements axes

Closes #498

See merge request openflexure/openflexure-microscope-server!338
 2025-08-06 15:50:08 +00:00
Julian Stirling
0921a73a81 Merge branch 'simulation-scanning' into 'v3' 
Scanning in simulation

Closes #395

See merge request openflexure/openflexure-microscope-server!344
 2025-08-06 13:11:14 +00:00
Julian Stirling
b672c3c2a7 Clarify docstring for Simulation start_streaming 2025-08-06 13:24:25 +01:00
Julian Stirling
cbd2f9e0e3 Add check that _lock is a lock in requires_lock 2025-08-05 23:13:11 +01:00
Julian Stirling
9be9097246 Make scan directory manager thread safe 2025-08-05 23:13:11 +01:00
Joe Knapper
c7dd269c01 Apply suggestions from code review of branch fix-movements 
Co-authored-by: Julian Stirling <julian@julianstirling.co.uk>
 2025-08-05 13:09:59 +00:00
Julian Stirling
f3c8add398 Make axis inversion robust agains UI sending positions as strings 2025-08-05 08:30:54 +01:00
Julian Stirling
4eca6c3f54 Fix docstring formatting 2025-08-05 08:30:54 +01:00
Julian Stirling
dacf219ea1 Change from axis direction set by ints to set by bools. Add a lot more tests. 2025-08-05 08:30:54 +01:00
Julian Stirling
58e3b5dcbd Start adding stage test and apply fixes to base class 2025-08-05 08:30:54 +01:00
Julian Stirling
7e5a455b75 Complete refactor so that child stages only work in hardware reference frame and BaseStage handles conversion 2025-08-05 08:30:54 +01:00
Julian Stirling
b373931c1a Start to refactor into having an internal and external coordinates for stages to handle inversion 2025-08-05 08:30:54 +01:00
jaknapper
ee9362ce48 Invert x by default 2025-08-05 08:30:54 +01:00
jaknapper
35fbef67e4 axis direction server setting and action to invert each axis 2025-08-05 08:30:54 +01:00
Julian Stirling
8ce06991f9 Small tweaks to simulation camera to get scanning working. 2025-08-05 08:28:10 +01:00
Julian Stirling
7231e1cf5b Apply suggestions from code review of branch camera-and-bg-detect-setting-customisation 2025-08-04 22:44:40 +00:00
Julian Stirling
cde6d0c9b3 Save settings when detector settings updated 2025-07-31 21:10:52 +01:00
Julian Stirling
33413a591a Complete UI for arbitrary dectector settings. Required better method for invoking actions. 
Error handling was fixed in the process of getting the above correct.
 2025-07-31 20:56:55 +01:00
Julian Stirling
92d15d921b Display background detector settings built automatically from schema 2025-07-31 20:56:55 +01:00
Julian Stirling
e7e3a08210 Camera settings exposed in UI defined by server. 2025-07-31 20:56:55 +01:00
Julian Stirling
3651013440 Generalise server specified action buttons. 2025-07-31 20:56:55 +01:00
Julian Stirling
0794d4777f Camera calibration buttons specified by server. Simulation has option to remove sample 2025-07-31 20:56:55 +01:00
Joe Knapper
c00c027ab1 Apply suggestions from code review of branch img-name 
Co-authored-by: Julian Stirling <julian@julianstirling.co.uk>
 2025-07-31 14:52:21 +00:00
jaknapper
df918bf286 Prepend images with img_ 2025-07-31 13:53:57 +01:00
Julian Stirling
931a570b43 Merge branch 'purge-recentre' into 'v3' 
Remove auto-recentre stage

Closes #486

See merge request openflexure/openflexure-microscope-server!339
 2025-07-30 09:05:10 +00:00
jaknapper
10a49db9c9 Remove autorecentre 2025-07-29 18:29:15 +01:00
Julian Stirling
38f4a745c3 Fix bug with setting exposure time on load, add associated test 2025-07-29 14:05:12 +01:00
Julian Stirling
b90b02cf7d Better fix for exposure drift with more complete testing. Also fix return value for capture_to_memory 2025-07-29 12:11:45 +01:00
Julian Stirling
376780ea28 Stop exposure walking on camera reload, reset CCM on full calibration 2025-07-28 14:43:48 +01:00
Julian Stirling
547704fdc0 Merge branch 'bg_detect_in_camera' into 'v3' 
Refactor background detect to allow switching algorithms

See merge request openflexure/openflexure-microscope-server!327
 2025-07-28 09:21:43 +00:00
Julian Stirling
c17d7af1ab Apply suggestions from code review of branch bg_detect_in_camera 2025-07-27 19:26:05 +00:00
Julian Stirling
8e133a978d Clean up LUV background detect calculation 2025-07-27 10:32:33 +01:00
Julian Stirling
238d022342 Apply suggestions from code review of branch bg_detect_in_camera 
Co-authored-by: Beth Probert <beth_probert@outlook.com>
 2025-07-26 16:45:06 +01:00
Joe Knapper
b4eaf48785 Merge branch 'Stitch-all' into 'v3' 
Stitch all scans button, and refresh scan tab when closing modals

See merge request openflexure/openflexure-microscope-server!330
 2025-07-25 17:20:03 +00:00
Joe Knapper
d6f1502593 Apply suggestions from code review of branch Stitch-all 
Co-authored-by: Julian Stirling <julian@julianstirling.co.uk>
 2025-07-25 16:42:27 +00:00
jaknapper
7ac77c3e89 Stitch all scans button, and refresh scan tab when closing modals 2025-07-25 16:52:37 +01:00
Julian Stirling
cc05ab4b5f Finish basic tests of background detect 2025-07-25 11:55:20 +01:00