rahix/openflexure-microscope-server
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1118 commits

Author SHA1 Message Date
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
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