jaknapper
a1784941fe
Ruff formatting and removing all capturing from smart_scan
2025-06-23 11:17:45 +01:00
jaknapper
603b9c7d16
Functional z stack Thing
2025-06-23 11:17:45 +01:00
jaknapper
a001da0bcb
Restore closest_focus_site function
2025-06-20 15:01:09 +01:00
Joe Knapper
d1ed7ec797
Apply suggestions from code review of branch fast-stack
2025-06-20 11:26:58 +00:00
Joe Knapper
006d3b2a7b
Apply suggestions from code review of branch fast-stack
...
Co-authored-by: Beth Probert <beth_probert@outlook.com>
2025-06-20 11:23:14 +00:00
jaknapper
ce33b94aab
Capture as a Raw dependency to use methods that aren't actions
2025-06-20 12:19:07 +01:00
Julian Stirling
cdf23bc403
Add a timeout when shutting down the server.
...
The browser needs to be closed for graceful shutdown. If the browser
is left open the microscope may never shut down as it is waiting on
the uvicorn process to finish. This causes potential SD card issues.
This forces the server to force shutdown if it doesn't exit gracefully in
2 seconds.
2025-06-19 16:25:43 -04:00
jaknapper
6cf2f4d8c3
Typehints and docstrings in z_stack
2025-06-19 14:58:16 +01:00
jaknapper
00321d761d
Update docstring for nearby focus site
2025-06-19 14:57:27 +01:00
jaknapper
6acfbaefd6
Split up z stack function
2025-06-18 18:36:21 +01:00
jaknapper
c0677858a1
Scan planner finds lowest neighbour, not most recent
2025-06-18 15:40:21 +01:00
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)
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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)
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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'
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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'
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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'
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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'
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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
