rahix/openflexure-microscope-server
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions
4390 commits 1 branch 0 tags 24 MiB
Commit graph

989 commits

Author SHA1 Message Date
Joe Knapper
2e1066477e Add parser.path to html sanitiser, fixing tests 2026-03-11 10:24:40 +00:00
Julian Stirling
c4d0c0e9da Explicit header, text and bullet blocks rather than one HTML block in ui spec 2026-03-10 15:25:37 +00:00
Julian Stirling
85ebfef44a Improve and test html sanitisation 2026-03-10 15:25:37 +00:00
Julian Stirling
0bfec5d046 Apply suggestions from code review of branch dynamic-ui 
Co-authored-by: Joe Knapper <joe.knapper@glasgow.ac.uk>
 2026-03-10 15:25:37 +00:00
Julian Stirling
eccf26851e Reintroduce recactive button state for background detect 2026-03-10 15:25:37 +00:00
Julian Stirling
4da05b1869 Move background detect settings into SlideScan 2026-03-10 15:25:37 +00:00
Julian Stirling
bfef998300 Move more of scan workflow UI into the server 2026-03-10 15:25:37 +00:00
Julian Stirling
ca21ab03c6 Tidy up server specified interface 2026-03-10 15:25:37 +00:00
Julian Stirling
9f2cde2275 Implement recursive Interface in vue 2026-03-10 15:25:36 +00:00
Julian Stirling
a11f9b7f62 Start making a structure for general UI specification 2026-03-10 15:25:36 +00:00
Joe Knapper
2e99e4c4c2 Merge branch '523-improve-validation-checks' into 'v3' 
Improve Validation Checks

Closes #523

See merge request openflexure/openflexure-microscope-server!524
 2026-03-09 19:19:18 +00:00
Beth Probert
6d66dd0ed8 Change make_path_safe to is_path_safe and update tests to reflect this 2026-03-09 15:45:32 +00:00
Beth Probert
f50b3d5cfa Allow spaces in linux paths 2026-03-09 14:29:24 +00:00
Beth Probert
968237bec0 Ruff checks 2026-03-09 14:02:15 +00:00
Beth Probert
fc437f529c Merge branch '523-improve-validation-checks' of https://gitlab.com/openflexure/openflexure-microscope-server into 523-improve-validation-checks 2026-03-09 13:54:45 +00:00
Beth Probert
f67699fbc8 Raise warnings if there are unsafe file path elements rather than coercing file paths. Stitching still raises an error if your file name is unsafe 2026-03-09 13:54:43 +00:00
Beth Probert
14b3e5a627 Apply suggestions from code review of branch 523-improve-validation-checks 
Co-authored-by: Julian Stirling <julian@julianstirling.co.uk>
 2026-03-07 18:17:43 +00:00
Joe Knapper
25c733a0c3 Apply suggestions from code review of branch check-setting-validation 
Co-authored-by: Julian Stirling <julian@julianstirling.co.uk>
 2026-03-07 18:14:22 +00:00
Joe Knapper
c9cc4e8468 Apply suggestions from code review of branch check-setting-validation 
Co-authored-by: Julian Stirling <julian@julianstirling.co.uk>
 2026-03-07 18:14:22 +00:00
Joe Knapper
99b9b0f3d6 Add limits to noise level, sample density and downsample 2026-03-07 18:14:22 +00:00
Joe Knapper
06f12973f4 Add limits to background detect and settling time settings 2026-03-07 18:14:22 +00:00
Beth Probert
349485d43b Remove multi-underscores from allowed names 2026-03-06 15:52:50 +00:00
Beth Probert
2c2f97cb56 Force file names to be lower case to avoid Windows issues around case sensitivity when checking if a file already exists. Path names can be uppercase as these will be defined on a users system and pre-exist. Files are created by us so we can force sanitation 2026-03-06 15:37:01 +00:00
Julian Stirling
011fc5a795 Fix spellings found as codespell updates 2026-03-06 15:06:53 +00:00
Beth Probert
35f7adcf07 Codespell 2026-03-06 14:16:42 +00:00
Beth Probert
4395d4001c Allow relative imports with two dots at start of path. Update unit tests. 2026-03-06 14:13:00 +00:00
Beth Probert
e5429d6cda Change make_path_safe to allow single dot relative imports, but no dots anywhere else. Added new unit tests for this. 2026-03-06 14:07:07 +00:00
Beth Probert
35efba19b8 Use pytest parametrize for better coverage of forbidden commands and reserved names 2026-03-05 13:55:05 +00:00
Beth Probert
48f6e1b369 Allow python and python3 as stitching commands. They are allowed. Move stitching tests into one file 2026-03-05 13:35:21 +00:00
Beth Probert
98e71207c5 Add forbidden windows commands to stitching and utilities to check for file name sanitation. Unit tests also added 2026-03-05 13:03:17 +00:00
Joe Knapper
84f3032022 Update docstrings to explain lower brightness 2026-03-04 20:52:49 +00:00
jaknapper
e324014a81 Increase target exposure to 40% 2026-03-04 20:52:49 +00:00
Joe Knapper
75ca73f148 Decrease target brightness for both cameras as its pre-gamma 2026-03-04 20:52:49 +00:00
Julian Stirling
7e4ec53d78 Update how the application configuration is read for LabThings 0.0.17 2026-03-04 17:22:03 +00:00
Julian Stirling
45903f92a6 Create and mount application level data direcory rather than just a scan directory 2026-03-04 17:22:03 +00:00
jaknapper
7ca94497c7 Remove link from basecamera docstring 2026-03-03 15:32:59 +00:00
jaknapper
3020ab59f4 Fix typing for gamma_curve 2026-03-03 14:21:28 +00:00
jaknapper
b716013ef2 Fixed tuning file gamma key to gamma_curve 2026-03-03 14:03:17 +00:00
jaknapper
0173cf912f Add gamma_curve to metadata 2026-03-03 13:59:43 +00:00
Joe Knapper
5019884175 Camera metadata includes subclass name, and test 2026-03-03 13:23:30 +00:00
Julian Stirling
ac9852a7ad Merge branch 'less-stack-coersion' into 'v3' 
Do less coersion for stacks now labthings validates settings.

See merge request openflexure/openflexure-microscope-server!516
 2026-03-03 10:02:05 +00:00
Julian Stirling
0fdcb9b623 Merge branch 'equal-offsets' into 'v3' 
Allow histo scans with equal dx and dy

See merge request openflexure/openflexure-microscope-server!517
 2026-03-02 22:56:53 +00:00
Julian Stirling
1dce732a9a Always log dx and dy steps for Histoscan 2026-03-02 20:53:16 +00:00
Joe Knapper
c09164a4e3 Apply suggestions from code review of branch equal-offsets 
Co-authored-by: Julian Stirling <julian@julianstirling.co.uk>
 2026-03-02 20:47:12 +00:00
Joe Knapper
5a79e4ffd3 Allow histo scans with equal dx and dy 2026-03-02 19:24:20 +00:00
Julian Stirling
d7b4457a55 Do less coersion for stacks now labthings validates settings. 2026-03-02 18:19:11 +00:00
Julian Stirling
d4fbcb6d61 Apply suggestions from code review of branch backlash-in-stage 
Co-authored-by: Joe Knapper <joe.knapper@glasgow.ac.uk>
 2026-03-02 14:40:27 +00:00
Julian Stirling
9ab7e50773 Apply suggestions from code review of branch backlash-in-stage 
Co-authored-by: Joe Knapper <joe.knapper@glasgow.ac.uk>
 2026-03-02 14:40:27 +00:00
Julian Stirling
0527990282 Use backlash compensation in smart scan and autofocus 2026-03-02 14:40:25 +00:00
Julian Stirling
c2b784e606 Add stage backlash correction 2026-03-02 14:37:21 +00:00