rahix/openflexure-microscope-server
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266 commits

Author SHA1 Message Date
jaknapper
e8c4103bb0 Remove unneeded logging 2025-06-17 14:34:42 +01:00
jaknapper
f363ec0eff Docstring for test_stack 2025-06-17 14:34:42 +01:00
jaknapper
dbb65d55b5 Use scan autofocus dz 2025-06-17 14:34:42 +01:00
jaknapper
cdd603d751 Capture the full stack requested 2025-06-17 14:34:42 +01:00
jaknapper
0671f2d1be Backlash correction as global, more comments 2025-06-17 14:34:42 +01:00
jaknapper
712f524414 Looping autofocus on failed smart stack 2025-06-17 14:34:42 +01:00
jaknapper
3e164102f6 A stack that tests whether the sharpest image is towards the middle 2025-06-17 14:34:42 +01:00
Julian Stirling
1c54d25212 Add ruff checking for unnecessary comprehensions 2025-06-10 16:07:49 +01:00
Julian Stirling
2050c2dc7c Add return checker, needed 4 fixes 2025-06-10 16:07:48 +01:00
Julian Stirling
3f0564f253 Turning on more lint checkers, warning for cameras that ignore resolution setting 2025-06-10 16:07:48 +01:00
Joe Knapper
ae2ec1864f Merge branch 'config-scan-dir' into 'v3' 
Add scan directory to json config

Closes #393

See merge request openflexure/openflexure-microscope-server!283
 2025-06-09 13:42:27 +00:00
Chish36
7eed48ed26 Swapped the order of CSM so y axis is completed first 2025-06-09 13:39:06 +00:00
Julian Stirling
3a1c3bb026 Ensure server and config vars always defined before fallback server is started 2025-06-06 12:42:21 +01:00
Julian Stirling
b45f5651ab Add scan directory to json config 2025-06-06 12:21:51 +01:00
Joe Knapper
08d1371569 Apply 1 suggestion(s) to 1 file(s) 
Co-authored-by: Julian Stirling <julian@julianstirling.co.uk>
 2025-06-06 10:25:34 +00:00
Joe Knapper
69db7b4041 Apply 2 suggestion(s) to 1 file(s) 
Co-authored-by: Julian Stirling <julian@julianstirling.co.uk>
 2025-06-05 17:09:37 +00:00
Joe Knapper
41f6c8879a RATIO as a global, better naming and splitting of generate_image() 2025-06-05 15:03:26 +01:00
Joe Knapper
2db895a1fc Defocus and realign simulation axes 2025-06-05 12:09:01 +01:00
Julian Stirling
16317bf94c Merge branch 'fix-simulation' into 'v3' 
Simulation fixes

See merge request openflexure/openflexure-microscope-server!279
 2025-06-05 10:35:53 +00:00
Joe Knapper
c919f8a19f Logging config based on default uvicorn settings 2025-06-03 14:48:13 +01:00
Julian Stirling
4ef74c42c3 Configure log folder in json file 2025-06-03 14:05:58 +01:00
jaknapper
a499d9230c Switch to updated "preview stitch" mode in stitching 2025-05-23 16:28:22 +01:00
jaknapper
cc3620d2ed Stitch with dzi by default, and check for dzi available in scans() 2025-05-23 16:28:21 +01:00
jaknapper
efe2127afb Mount scans to app on startup 2025-05-23 16:28:21 +01:00
Julian Stirling
fe1696df28 Fix error in purge_empty_scans if the images dir hadn't been created 2025-05-23 12:49:46 +01:00
Julian Stirling
70f4304b2e Fix bug where .jpg files are not counted in scan list (only .jpeg) 2025-05-23 11:45:26 +01:00
jaknapper
b812c6be35 Settling time as global, settle before taking first image in stack 2025-05-21 15:41:49 +01:00
Julian Stirling
6332c8b647 Merge branch 'openflexure-stitching-from-pip' into 'v3' 
Import openflexure-stitching from pip

See merge request openflexure/openflexure-microscope-server!270
 2025-05-21 10:00:48 +00:00
jaknapper
44f2435ea4 Removed stitching path as kwarg for scanning 2025-05-21 10:30:42 +01:00
Julian Stirling
c793620fcd Merge branch 'cleanup_empty_scans' into 'v3' 
Added purge_empty_scans() method

Closes #370

See merge request openflexure/openflexure-microscope-server!257
 2025-05-20 18:26:00 +00:00
Joe Knapper
6c8c8bf358 Apply 1 suggestion(s) to 1 file(s) 
Co-authored-by: Julian Stirling <julian@julianstirling.co.uk>
 2025-05-20 17:04:48 +00:00
jaknapper
4a44dceac6 More clear variable name, use _delete_scan to avoid calling fastapi-endpoint in loops 2025-05-20 16:36:57 +01:00
Joe Knapper
a563c634a3 Update serve static files to serve correct directory and to add docstrings 2025-05-15 16:30:37 +00:00
jaknapper
d4b3508b77 Clean up of serve_static_files 2025-05-15 14:10:15 +01:00
jaknapper
19d72bef1c Error handling in _delete_scan(), which is now handled in GUI main.js 2025-05-14 16:11:02 +01:00
Joe Knapper
1468a90c60 Merge branch 'scan_tab' into 'v3' 
Scan tab updates

See merge request openflexure/openflexure-microscope-server!260
 2025-05-14 11:53:19 +00:00
jaknapper
99e52bcb2f Formatting and fixing wrong variable in loop 2025-05-14 12:23:01 +01:00
Joe Knapper
251b0ca770 Apply 1 suggestion(s) to 1 file(s) 
Co-authored-by: Julian Stirling <julian@julianstirling.co.uk>
 2025-05-14 10:26:37 +00:00
jaknapper
3eea4bbaf6 Log each line individually to ensure line breaks 2025-05-13 17:08:09 +01:00
jaknapper
69260d1973 stitch available property, allowing GUI to only stitch when needed 2025-05-13 15:51:11 +01:00
jaknapper
a77c0f6f9d Updated wrong path to file 2025-05-13 15:28:16 +01:00
Joe Knapper
b5893bc29c Apply 1 suggestion(s) to 1 file(s) 
Co-authored-by: Julian Stirling <julian@julianstirling.co.uk>
 2025-05-13 12:34:50 +00:00
jaknapper
56edddd195 Data filename as global 2025-05-13 13:03:34 +01:00
jaknapper
1952e05284 Scan result in data json 2025-05-13 13:00:04 +01:00
jaknapper
9734bba23b Inputs renamed to data where appropriate 2025-05-13 12:45:55 +01:00
jaknapper
0e3c71b958 Removed from finally block 2025-05-13 12:39:04 +01:00
jaknapper
3a45c68ef3 Try Except around deleting scans to check for PermissionErrors 2025-05-13 12:23:01 +01:00
jaknapper
845c21c68a Move update data outside of finally block 2025-05-13 11:46:56 +01:00
jaknapper
272f050905 Move update data outside of finally block 2025-05-13 11:32:03 +01:00
jaknapper
4234c92fed Better formatting of duration as datetime timedelta without microseconds 2025-05-13 11:10:27 +01:00