rahix/openflexure-microscope-server
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573 commits

Author SHA1 Message Date
Julian Stirling
4450fda945 Merge branch 'simulation_wrap' into 'v3' 
Make simulation image wrap to prevent errors when moving out of range.

Closes #513

See merge request openflexure/openflexure-microscope-server!380
 2025-08-27 16:13:24 +00:00
Julian Stirling
5515d55e6d Merge branch 'error-types' into 'v3' 
Tweak a few error types.

Closes #320

See merge request openflexure/openflexure-microscope-server!376
 2025-08-27 13:47:26 +00:00
Julian Stirling
c31fffad5b Make simulation image wrap to prevent errors when moving out of range. 2025-08-26 16:03:56 +01:00
Julian Stirling
9257c4489e Apply suggestions from code review of branch prevent-broken-frames-ending-scans 
Co-authored-by: Beth Probert <beth_probert@outlook.com>
 2025-08-21 18:05:46 +01:00
Julian Stirling
dade26cde1 Tweak a few error types. 2025-08-21 16:11:30 +01:00
Julian Stirling
6fa4e4dc64 Add a grab_as_array camera method that grabs from the stream but catches broken jpegs and retries 2025-08-21 13:35:21 +01:00
Julian Stirling
0a9b6be9bd Raise error if tuning algorithm cannot be returned, unless explicityly asked not to 2025-08-21 12:44:57 +01:00
Julian Stirling
fdae0b9226 Add get_tuning_algo method to StreamingPiCamera2 2025-08-20 14:53:53 +01:00
Julian Stirling
ab0bece70b Deepcopy default tuning file so it isn't affected by calibration. 2025-08-20 14:51:19 +01:00
Joe Knapper
c2980dc988 Merge branch 'typehint-autofocus' into 'v3' 
Typehints and better variable names for autofocus

Closes #271

See merge request openflexure/openflexure-microscope-server!367
 2025-08-15 10:30:36 +00:00
Joe Knapper
f383365cf7 Apply suggestions from code review of branch typehint-autofocus 
Co-authored-by: Julian Stirling <julian@julianstirling.co.uk>
 2025-08-15 10:30:29 +00:00
Joe Knapper
bd115e0023 Change all CameraDeps to CameraClients 2025-08-15 10:16:36 +00:00
Joe Knapper
504b81fef6 Typehints and better variable names for autofocus 2025-08-14 14:51:03 +01:00
Julian Stirling
af93db7de8 Merge branch 'let-preview-stitch-cancel' into 'v3' 
Allow preview to cancel!

See merge request openflexure/openflexure-microscope-server!359
 2025-08-13 15:18:13 +00:00
Julian Stirling
05644456e0 Allow preview to cancel! 2025-08-12 16:41:55 +01:00
Julian Stirling
6142a267db Add flake8 bugbear checks 2025-08-12 13:09:43 +01:00
Julian Stirling
cd311f08bf Update stiching to differentiate bwtween stitchers that use a thread and those that block 2025-08-06 17:47:33 +01:00
Julian Stirling
5f092835ac Apply suggestions from code review of branch yet-another-smart-scan-refactor 2025-08-06 17:27:26 +01:00
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
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
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
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
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
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