rahix/openflexure-microscope-server
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1118 commits

Author SHA1 Message Date
Julian Stirling
573330dede Add tests for z_stack 2025-12-02 09:57:24 +00:00
Julian Stirling
b9c58b70c9 Looping autofocus errors on failure to find focus. Test looping autofocus algorithm 2025-12-02 09:57:24 +00:00
Julian Stirling
aa704239ed Modify background detect check to check for all squares having no std. As LUV appears insensitive to low colour noise 2025-12-02 09:57:24 +00:00
Julian Stirling
1f2099e46f Add minimum standard deviations for ColourChannelDetectLUV 2025-12-02 09:57:24 +00:00
Julian Stirling
a2a6d870e2 Make turing point check in z-stack optional 2025-12-02 09:57:24 +00:00
Julian Stirling
873968877b Log warning rather than error if the named background detector doesn't exist to prevent not booting if detectors change 2025-12-02 09:57:24 +00:00
Julian Stirling
79c94c96ed Set channel minima and error if any LUV channels have std==0 2025-12-02 09:57:24 +00:00
Julian Stirling
38b8c5baa5 Apply suggestions from code review of branch scanning-stability 
Co-authored-by: Joe Knapper <joe.knapper@glasgow.ac.uk>
 2025-12-02 09:57:24 +00:00
Julian Stirling
23f87869ac Add a new background detector based on an 8x8 grid 2025-12-02 09:57:24 +00:00
Julian Stirling
cf92d4f3ac Make autofocus considerably stricter, forcing a parabolic fit, and only one turning point 
Background can still pass this much stricter check
 2025-12-02 09:57:24 +00:00
Julian Stirling
dabb195b08 Ensure smart stack exits and saves on failure only if check background is false 2025-12-02 09:57:24 +00:00
jaknapper
70e052fa21 Check the firmware and log relevant messages 2025-12-01 18:08:25 +00:00
Julian Stirling
ed9076a115 Log an error if the sangaboard firmware is below v1.0.4 2025-12-01 14:21:56 +00:00
Julian Stirling
dfe7fb6c42 Stop scan planner plots erroring if there are no secondary locations 2025-11-28 12:00:35 +00:00
Julian Stirling
90be139575 Update scan planners so secondary locations are imaged first and don't affect later planning 2025-11-28 09:53:24 +00:00
Julian Stirling
f3c79b746f Fix RGB vs BGR issue for opencv camera 2025-11-11 18:12:37 +00:00
Julian Stirling
3ecc41720d Merge branch 'recentre-with-rom-methods' into 'v3' 
Recentre using RangeOfMotionThing methods

Closes #499 and #573

See merge request openflexure/openflexure-microscope-server!429
 2025-11-11 17:49:08 +00:00
Julian Stirling
614fd8b9e9 Apply suggestions from code review of branch recentre-with-rom-methods 
Co-authored-by: Richard Bowman <richard.bowman@cantab.net>
 2025-11-11 17:15:20 +00:00
Julian Stirling
ed9b8ff01d Adjust algorithm to start checks for centre after first 5 mendium sized moves & improve logging. 2025-11-11 12:51:04 +00:00
Julian Stirling
b8742b449c Apply suggestions from code review of branch recentre-with-rom-methods 
Co-authored-by: Joe Knapper <joe.knapper@glasgow.ac.uk>
 2025-11-11 12:37:09 +00:00
Julian Stirling
8a4e6390c7 Apply suggestions from code review of branch temperature-ccm 
Co-authored-by: Joe Knapper <joe.knapper@glasgow.ac.uk>
 2025-11-11 11:20:08 +00:00
Julian Stirling
5c56c1e851 Apply suggestions from code review of branch temperature-ccm 
Co-authored-by: Richard Bowman <richard.bowman@cantab.net>
 2025-11-11 11:20:08 +00:00
Julian Stirling
f432247446 Fix typos during refactor caught by CI 2025-11-11 11:20:08 +00:00
Julian Stirling
982c55905c Update default exposure in picam and defaul LST values in tuning files, and set default colour gains from LST 2025-11-11 11:20:08 +00:00
Julian Stirling
13d3871059 Add testing for loading the tuning files in the normal test suite now not tied to picamera 2025-11-11 11:20:08 +00:00
Julian Stirling
6763845e38 Let the tuning file utils handle lens shading table manipulation. 2025-11-11 11:20:08 +00:00
Julian Stirling
ec16cc17f8 Update tuning file utils for our own tuning files. 2025-11-11 11:20:07 +00:00
Julian Stirling
f74a51866a Adjust tuning files to have adaptive algorithms turned off. 2025-11-11 11:20:07 +00:00
Julian Stirling
01a883e95c Reset CCM resets to the CCM in the default tuning file. 2025-11-11 11:20:07 +00:00
Julian Stirling
cec6f4af73 Load tuning files in without using Picamera2 2025-11-11 11:20:07 +00:00
Julian Stirling
a2900b0c16 Move tuning files into vc4 folder in case we support pisp (Pi5) later and update README 2025-11-11 11:20:07 +00:00
jaknapper
1b14990b76 Stop overwriting CCM in full recalibrate 
Fix typo
 2025-11-11 11:20:06 +00:00
jaknapper
ac08462405 Attempt to load custom tuning file first 
Most likely want to be in try except
 2025-11-11 11:20:06 +00:00
jaknapper
e3a7252d78 Example custom tuning files 
imx219 has been tested briefly

imx477 untested, based on imx219 with custom ccm
 2025-11-11 11:20:06 +00:00
jaknapper
b47413100e README walking through the settings in the tuning file, and initial thoughts 2025-11-11 11:20:06 +00:00
Julian Stirling
f7d03d8c00 Fix confusion between (x,y) image coordinates and (y,x) matrix indicies 2025-11-05 13:19:28 +00:00
Julian Stirling
dcf4b0b383 Split the logic for deciding how to move in recentre from the moves and the main loop 2025-11-05 11:43:25 +00:00
Julian Stirling
a5a372b6c0 Split out matix calculations from CSM, and continue testing recentre 2025-11-05 00:15:30 +00:00
Julian Stirling
b09aa7b5b8 First interation of a recentre algoritm build on ROM test methods 2025-11-04 18:54:15 +00:00
Julian Stirling
8b7de05a9c Building a recentre action with ROM methods 2025-11-04 18:54:15 +00:00
Julian Stirling
ff70e44858 Don't read json data of ongoing scans 2025-11-04 18:50:17 +00:00
Julian Stirling
46e9070a33 Rename ScanListData to ScanListInfo as it containts ScanInfo not ScanData objects 2025-11-04 18:50:17 +00:00
Julian Stirling
7d583dcf94 Apply suggestions from code review of branch dont-mutate-tuning-files 
Co-authored-by: Joe Knapper <joe.knapper@glasgow.ac.uk>
 2025-10-29 13:08:10 +00:00
Julian Stirling
ee2ef848b1 Add native implementation of find_tuning_algo 2025-10-29 13:08:10 +00:00
Julian Stirling
815b112069 Update the picamera tuning file utilities to not modify the dictionaries in place 2025-10-29 13:08:10 +00:00
Julian Stirling
2bc315f85d Update picamera cal docstring now white balance isn't its own method. 2025-10-28 14:00:02 +00:00
jaknapper
ba3f7f6cf5 Remove unused code, add comments 2025-10-28 14:00:01 +00:00
jaknapper
506693f653 Set colour gains directly from Lens Shading Table 2025-10-28 13:58:53 +00:00
Julian Stirling
adf9736fab Add testing for patching json files 2025-10-27 15:07:45 +00:00
Julian Stirling
c7e4160a08 Implement patching base labthings configuration files 2025-10-27 15:07:45 +00:00