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Author SHA1 Message Date
Julian Stirling
4071b81d5f Add script to generate thing descriptions and openapi json 2026-02-12 16:35:48 +00:00
Julian Stirling
ec810f3a64 Remove old historic sphinx docs 2026-02-12 16:07:16 +00:00
Joe Knapper
52c592e35c Merge branch 'More-workflow-layers' into 'v3' 
More workflow layers

Closes #628

See merge request openflexure/openflexure-microscope-server!469
 2026-02-12 13:49:51 +00:00
Julian Stirling
2a38375040 Consolidate moves_between and total_moves_between into 1 function with switchable metrics 2026-02-12 11:00:03 +00:00
jaknapper
8081dc9426 Split moves_between to support Manhattan or Chebyshev distance 2026-02-11 15:13:47 +00:00
jaknapper
d0f55786ce Test raster scan planner and z estimate from raster and snake 2026-02-11 15:13:17 +00:00
Julian Stirling
511b37176e Add clarifying docstring 2026-02-11 11:03:08 +00:00
Julian Stirling
5d5bae7f79 Apply suggestions from code review of branch More-workflow-layers 
Co-authored-by: Joe Knapper <joe.knapper@glasgow.ac.uk>
 2026-02-11 11:03:08 +00:00
Julian Stirling
af5c8f01da Update scan_planner module docstring 2026-02-11 11:03:08 +00:00
Julian Stirling
351a66a42c Cleaning up workflows and fixing tests. 2026-02-11 11:03:08 +00:00
Julian Stirling
86fa48fb9b Update select_nearby_focus_site to use moves between 2026-02-11 11:03:07 +00:00
Julian Stirling
9e477a26d8 Simplify planners a little to consolidate snake and raster 2026-02-11 10:39:30 +00:00
Julian Stirling
1221b6ca02 Apply suggestions from code review of branch More-workflow-layers 
Co-authored-by: Joe Knapper <joe.knapper@glasgow.ac.uk>
 2026-02-10 16:40:11 +00:00
Julian Stirling
0e5f9f46ca Fix docstring error 2026-02-10 16:37:32 +00:00
Julian Stirling
15798d9b7d Further layering of the classes for scan workflows 2026-02-10 16:02:18 +00:00
jaknapper
1f01717a1b Fix UI workflow test as order changed 2026-02-10 14:24:41 +00:00
jaknapper
f1845c3039 RectangleWorkflow as a baseclass 2026-02-10 14:05:38 +00:00
jaknapper
6294cde471 Fully subclass Rectangle basescanner for raster and snake 2026-02-09 19:35:19 +00:00
Joe Knapper
fb7a8b4959 Prettier on slideScanContent 2026-02-09 18:48:49 +00:00
Joe Knapper
1a0dd71f30 Intermediate level RectangleScan class for all three scanners 2026-02-09 18:48:49 +00:00
Joe Knapper
3beb8e1147 Auto-populate workflow dropdown 2026-02-09 18:48:49 +00:00
Joe Knapper
0177596fb6 Add raster scan, with generic typing to allow subclassed settings 2026-02-09 18:48:49 +00:00
Julian Stirling
9ab5a461c0 Merge branch 'snake-scan' into 'v3' 
SnakeScan as a scan planner

See merge request openflexure/openflexure-microscope-server!464
 2026-02-09 17:10:12 +00:00
jaknapper
383fc31f22 Add snake-scan to full config 2026-02-09 16:10:29 +00:00
Joe Knapper
eb88e1f1c0 Apply suggestions from code review of branch snake-scan 
Co-authored-by: Julian Stirling <julian@julianstirling.co.uk>
 2026-02-09 16:05:49 +00:00
Joe Knapper
1c17b27c05 Apply suggestions from code review of branch snake-scan 
Co-authored-by: Julian Stirling <julian@julianstirling.co.uk>
 2026-02-09 16:05:22 +00:00
Joe Knapper
7413aa57f8 Docstring and typehints suggestions from @julianstirling 2026-02-09 15:08:53 +00:00
Joe Knapper
f230eef2dc New scan workflow for snake scans, move next pos into scan baseclass 
Update tests that were testing wrong method, update all to new select_nearby_focus_site
 2026-02-09 13:19:10 +00:00
Joe Knapper
e59d5e82d8 mypy fix for coords list 2026-02-09 13:09:09 +00:00
Joe Knapper
b4957e0420 SnakeScan as a scan planner 2026-02-09 13:09:07 +00:00
Julian Stirling
663a18a38f Merge branch 'scan-workflows' into 'v3' 
Implement ScanWorkflows allowing multiple scanning methods

Closes #641, #566, #371, and #333

See merge request openflexure/openflexure-microscope-server!462
 2026-02-06 15:21:09 +00:00
Julian Stirling
83c111e71f Update picamera coverage zip 2026-02-06 14:19:57 +00:00
Julian Stirling
cf941b1d11 Fix unit tests for scan workflows 2026-02-06 13:50:47 +00:00
Julian Stirling
8f30f08bdf Apply suggestions from code review of branch scan-workflows 
Co-authored-by: Joe Knapper <joe.knapper@glasgow.ac.uk>
 2026-02-06 13:28:30 +00:00
Julian Stirling
504a47cbf8 Add some property tests for scanning 2026-01-18 23:37:10 +01:00
Julian Stirling
b26dda60a4 More tests and assoicated bugfixes 2026-01-18 23:19:44 +01:00
Julian Stirling
eb93342d9f Add test of logic for selecting worflow. 2026-01-18 14:23:18 +00:00
Julian Stirling
b22fcf4b88 Complete testing of HistoScanWorkflow 2026-01-16 18:16:50 +00:00
Julian Stirling
1bc6b9e0c4 Add a number of extra tests to ScanWorkflows 2026-01-16 17:02:07 +00:00
Julian Stirling
57b20782a0 Further fixes after introducing scan workflow selection 2026-01-16 13:04:23 +00:00
Julian Stirling
23426ae12c Reorder scan workflow title and blurb in scan tab 2026-01-16 12:25:55 +00:00
Julian Stirling
21b779a4a5 Dynamic UI for scan workflows 2026-01-16 12:18:54 +00:00
Julian Stirling
2a3a54b936 Get unit tests passing with Scan Workflows 2026-01-16 09:28:15 +00:00
Julian Stirling
c82523dd5b Start updating unit tests after refactoring into ScanWorkflows 2026-01-16 09:28:15 +00:00
Julian Stirling
11ef1217e0 Docstrings and tweaks of ScanWorflow refactor 2026-01-16 09:28:15 +00:00
Julian Stirling
c938560f00 Docstrings and final tweaks of ScanWorflow refactor 2026-01-15 21:59:53 +00:00
Julian Stirling
665622a802 First working interation of ScanWorkflows. Needs a tidy 2026-01-15 20:59:53 +00:00
Julian Stirling
adab5bae24 Start smart stack parameters in scan workflow 2026-01-15 16:05:02 +00:00
Julian Stirling
54ed78c832 Create aquisition routines for scan workflows, remove background detector from base ScanWorkflow class 2026-01-15 14:53:47 +00:00
Julian Stirling
b6343362b2 Start splitting ScanData into workflow specific data. 2026-01-15 12:59:06 +00:00