rahix/openflexure-microscope-server
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499 commits

Author SHA1 Message Date
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
99652eca41 Merge branch 'log-oom-error' into 'v3' 
Custom sigkill error

See merge request openflexure/openflexure-microscope-server!351
 2025-08-15 12:13:25 +00:00
Julian Stirling
46802db308 Merge branch 'check-static-files' into 'v3' 
Check static files exist or throw a useful error

See merge request openflexure/openflexure-microscope-server!368
 2025-08-15 11:22:41 +00:00
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
7b2a4cc3f6 Merge branch 'camera-deps' into 'v3' 
Change all CameraDeps to CameraClients

Closes #483

See merge request openflexure/openflexure-microscope-server!366
 2025-08-15 10:16:36 +00:00
Joe Knapper
bd115e0023 Change all CameraDeps to CameraClients 2025-08-15 10:16:36 +00:00
Julian Stirling
3289221c6b Add unit tests for all of serving static files. Update docs in src to clarify behaviour 2025-08-15 11:01:43 +01:00
Julian Stirling
44e24f42a6 Check webapp is available or give useful error 2025-08-15 09:21:38 +01:00
Julian Stirling
bfdbbb9ad2 Merge branch 'request-no-cache' into 'v3' 
Request no cache

See merge request openflexure/openflexure-microscope-server!361
 2025-08-14 19:59:58 +00:00
Joe Knapper
504b81fef6 Typehints and better variable names for autofocus 2025-08-14 14:51:03 +01:00
Julian Stirling
98c023032c Allow fonts to cache 2025-08-14 14:45:20 +01:00
Joe Knapper
1e368aef81 Apply suggestions from code review of branch log-oom-error 
Co-authored-by: Julian Stirling <julian@julianstirling.co.uk>
 2025-08-14 14:09:54 +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
jaknapper
025e6b1fba Request no caching for static files like webapp 2025-08-12 18:47:02 +01:00
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
jaknapper
7cedd31ff4 Default tile size 8192 2025-08-08 10:43:54 +01:00
jaknapper
279055108f Set final stitch tile size to 4096px 2025-08-07 18:30:14 +01:00
jaknapper
4d32152427 Custom Memory error changed to generic sigkill 2025-08-07 18:10:02 +01:00
jaknapper
feec53aa1f Custom out of memory error 2025-08-07 17:56:34 +01:00
Julian Stirling
dbdf254154 Fix CLI arg for FinalStitcher, and a docstring typo. 2025-08-07 15:20:14 +01:00
Julian Stirling
5caae613dc Apply suggestions from code review of branch yet-another-smart-scan-refactor 
Co-authored-by: Beth Probert <beth_probert@outlook.com>
 2025-08-07 13:55:47 +00:00
Julian Stirling
7727d0a51d Update language in BaseStitcher to clarify that the stitching uses subprocess not threading 2025-08-07 12:06:58 +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
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