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1017 commits

Author SHA1 Message Date
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
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
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
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
Julian Stirling
5ce74cad8a A start to implementing ScanWorkflow 2026-01-15 12:59:06 +00:00
Julian Stirling
ca46439269 Rename "active_detector" for background detecor. Improve thing selector coercion 2026-01-14 15:10:13 +00:00
Julian Stirling
6b97d2da44 Fix unit tests for background detectors as Things 2026-01-14 10:05:04 +00:00
Julian Stirling
3e8874188e Get UI working for background detector things 2026-01-14 10:05:04 +00:00
Julian Stirling
44860bf777 Continue turning background detectors back into Things 2026-01-14 10:05:04 +00:00
Julian Stirling
6a1ad573d9 Start turning background detectors back into things 2026-01-14 10:05:04 +00:00
Julian Stirling
ad53f72a60 Bugfox, stop saving scans into log folder 2026-01-13 18:03:13 +00:00
Joe Knapper
9df3fd6360 Merge branch 'fast-sim' into 'v3' 
Simulation Camera Improvements

Closes #638

See merge request openflexure/openflexure-microscope-server!458
 2026-01-13 14:15:35 +00:00
Julian Stirling
0bba613a4b Apply suggestions from code review of branch fast-sim 
Co-authored-by: Joe Knapper <joe.knapper@glasgow.ac.uk>
 2026-01-13 11:45:32 +00:00
Julian Stirling
51d6bdb991 Fully generate simulation sample canvas before setting to class attribute 2026-01-13 11:34:49 +00:00
Julian Stirling
4c557612fb Apply suggestions from code review of branch fast-sim 
Co-authored-by: Richard Bowman <richard.bowman@cantab.net>
Co-authored-by: Joe Knapper <joe.knapper@glasgow.ac.uk>
 2026-01-12 17:41:51 +00:00
Julian Stirling
ec29a1999f Update how stitching is called in Windows 2026-01-12 16:20:22 +00:00
Julian Stirling
0abbd827fd Remove exception block from simulation that only silence errors and errors that are impossible to reach 2026-01-12 16:17:11 +00:00
Julian Stirling
8f52841f67 Add tests for new simulated camera poperites that update the canvas 2026-01-12 16:17:11 +00:00
Julian Stirling
fa89f24477 Type fixing for simulation camera 2026-01-12 16:17:11 +00:00
Julian Stirling
fc3ca8cbe7 Slightly increase glyph shape so that blob cannot touch edge 2026-01-12 16:17:10 +00:00
Julian Stirling
980af66548 Let lists of colours be set for simulation sample. 2026-01-12 16:17:10 +00:00
Julian Stirling
11379d8fa7 Allow colour to be set for simulation sample. 2026-01-12 16:17:10 +00:00
Julian Stirling
7b9f4aa202 Expose sample density and sample repeat for simulation camera to the UI in camera settings rather than as init options 2026-01-12 16:17:10 +00:00
Julian Stirling
159e2d14ab Unify canvas and sample shape for simulation, set flag for if repeating. 2026-01-12 16:17:10 +00:00
Julian Stirling
99f7802195 Create sprites upsampled, before downsampling so they hhave a smoother edge interpolation 2026-01-12 16:17:10 +00:00
Julian Stirling
fa249a0f24 Calculate simulation images downsampled for speed 2026-01-12 16:17:10 +00:00
Julian Stirling
06cab8a6a4 Use type[] not Type[] in typehints, and add clarification comment. 2026-01-12 15:28:10 +00:00
Julian Stirling
560ca6e9fe Tweak a docstring as the variables out of date 2026-01-12 15:28:10 +00:00
Julian Stirling
3db83534e8 Update for how Labthings-Fastapi 0.0.14 impements the fallback server 2026-01-09 17:43:11 +00:00
Julian Stirling
c1ad445517 Fix some final type issues in Autofocus 2026-01-09 15:18:06 +00:00
Julian Stirling
141ccc06c1 Some minor type fixes 2026-01-09 15:18:05 +00:00
Julian Stirling
58aa3df587 Fix a number of issues with camera_stage_mapping 2026-01-09 15:18:05 +00:00
Julian Stirling
18e89aa148 More typing fixes 2026-01-09 15:18:05 +00:00
Julian Stirling
8890590551 Type fix stitching 2026-01-09 15:18:05 +00:00
Julian Stirling
2e03ad28c4 Type fix scan directories 2026-01-09 15:18:05 +00:00
Julian Stirling
2701576a2c Properly type the generic Background Detector class 2026-01-09 15:18:05 +00:00