rahix/openflexure-microscope-server
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368 commits

Author SHA1 Message Date
Julian Stirling
a0065931e4 Merge branch 'include-sangaboard' into 'v3' 
Move SangaboardThing into repo

See merge request openflexure/openflexure-microscope-server!311
 2025-07-03 14:27:38 +00:00
Julian Stirling
544ede0bf9 Apply suggestions from code review of branch include-sangaboard 
Co-authored-by: Beth Probert <beth_probert@outlook.com>
 2025-07-03 14:57:48 +01:00
Julian Stirling
222a0c973d Remove old sangaboard abort_move action as moves are not cancelled with a cancel hook 2025-07-03 13:16:25 +01:00
Julian Stirling
e7cf0c3f24 Allow stiching to be cancelled after a scan complete 
Closes #417
 2025-07-02 18:13:48 +01:00
Julian Stirling
5e6aeb9bbf Move SangaboardThing into repo 2025-07-02 16:42:38 +01:00
Julian Stirling
ffd958f823 Remove test Thing that is is never used. 2025-07-02 14:33:23 +01:00
Julian Stirling
2e18c2017a Apply suggestions from code review of branch download-stitched-image 
Co-authored-by: Beth Probert <beth_probert@outlook.com>
 2025-07-02 09:39:33 +00:00
Julian Stirling
7295b86cf6 Split up ScanDirectory._find_files into seperate functions 2025-07-01 19:45:45 +01:00
Julian Stirling
254305a7a5 Clarify whether name or path is returned in scan directory functions 2025-07-01 19:21:56 +01:00
Julian Stirling
3671d52499 Do not zip DZI files, or their associated tiles 2025-07-01 09:04:14 +01:00
Julian Stirling
daf2cee481 Add tests and correct stitch path 2025-06-30 23:03:54 +01:00
jaknapper
ff43deae36 Download stitched image of scan (if present) 
* Docstring for download stitch
* use global STITCH_SUFFIX
 2025-06-30 20:18:48 +01:00
Julian Stirling
51f9df995d More changes suggested in review, generally docstring issues. 2025-06-30 17:25:58 +01:00
Julian Stirling
ad838e8643 Apply suggestions from code review of branch split-scan-dir-operations 
Co-authored-by: Beth Probert <beth_probert@outlook.com>
 2025-06-30 17:25:58 +01:00
Julian Stirling
7f0745d772 Add some more scan_directories tests 2025-06-28 23:59:35 +01:00
Julian Stirling
7193ec34f5 Starting to test more smart scan functionality using mocked Thing Dependencies 2025-06-27 21:06:16 +01:00
Julian Stirling
3aa9b9100a Add a number of tests for scan directories and fix bugs 2025-06-27 21:06:16 +01:00
Julian Stirling
1267d881b9 Start writing tests for smart scan 
Focusing on methods that don't start the whole scan.
 2025-06-27 21:06:16 +01:00
Julian Stirling
32f78a4cff Trying to make a distinction between file directory operations for scans and scanning code 
This started as a small change and spiralled out of control it needs good unit tests and testing
before considering to merge
 2025-06-27 21:06:16 +01:00
Julian Stirling
0d2f324324 Split creation of scan directory information into class with small testable methods 2025-06-27 21:06:16 +01:00
Julian Stirling
8002600fcf Apply suggestions from code review of branch fast-stack 
Co-authored-by: Joe Knapper <joe.knapper@glasgow.ac.uk>
 2025-06-27 16:40:18 +00:00
Julian Stirling
9a92fd478a Final docstring and testing updates based on code review 2025-06-27 16:54:28 +01:00
Julian Stirling
46f3d21632 Apply suggestions from code review of branch fast-stack 
Co-authored-by: Beth Probert <beth_probert@outlook.com>
 2025-06-27 11:52:53 +01:00
Julian Stirling
fc6c13f40e Apply suggestions from code review of branch fast-stack 
Co-authored-by: Beth Probert <beth_probert@outlook.com>
 2025-06-27 10:41:53 +00:00
Julian Stirling
73e54b802b Stop smart stack infinietly looping 2025-06-27 01:29:26 +01:00
Julian Stirling
e90ff73499 Move smart stack specific scan planning logic to SmartSpiral 2025-06-27 01:08:55 +01:00
Julian Stirling
2ce2f998fa add tests for helper classes defined by fast stack 2025-06-27 00:34:51 +01:00
Julian Stirling
05af5e7548 Write unit teasts for CameraMemoryBuffer and fix minor issues found 2025-06-26 22:49:09 +01:00
Julian Stirling
2aea6a2569 Docstrings and stop using Pydantic for ScanParameters 2025-06-26 19:46:25 +01:00
Julian Stirling
43d5f2fdfe Change capture_resolution to save resolution, because it is used for saving not capture 2025-06-26 19:00:52 +01:00
Julian Stirling
6a87805b47 Fixing a number of issues from the merge and refactor. 2025-06-26 18:29:12 +01:00
Julian Stirling
61dd5e4958 Compete first (untested) pass of trying to make fast stack compatible with new memory captures 2025-06-26 17:43:11 +01:00
Julian Stirling
fda0a6e1ab Merge branch 'v3' into fast-stack, with conflict resolution but not fully 
working yet
 2025-06-26 11:50:24 +01:00
Joe Knapper
378998d230 Merge branch 'jpeg-capture-in-stacking' into 'v3' 
2MP from 8MP capturing

Closes #364, #413, #298, #303, #288, #358, and #433

See merge request openflexure/openflexure-microscope-server!251
 2025-06-25 17:57:51 +00:00
Joe Knapper
b49aecb802 Apply suggestions from code review of branch jpeg-capture-in-stacking 2025-06-25 17:32:05 +00:00
Julian Stirling
761957d7fb Clarify exposure variables in docstring 2025-06-25 17:53:43 +01:00
Julian Stirling
0389ab760a Apply suggestions from code review of branch jpeg-capture-in-stacking 
Co-authored-by: Joe Knapper <joe.knapper@glasgow.ac.uk>
 2025-06-25 16:52:23 +00:00
Julian Stirling
ee8c58c99f Docstrings, typehints, and clarifications in PiCamera and its utils 2025-06-25 17:36:11 +01:00
Julian Stirling
83e0e08ccc Apply suggestions from code review of branch jpeg-capture-in-stacking 
Co-authored-by: Beth Probert <beth_probert@outlook.com>
 2025-06-25 15:12:28 +00:00
Julian Stirling
ce5b5b781c Add typehints and docstrings as suggested in review 2025-06-25 15:55:48 +01:00
Julian Stirling
0933ece63a Apply suggestions from code review of branch jpeg-capture-in-stacking 
Co-authored-by: Beth Probert <beth_probert@outlook.com>
 2025-06-25 15:39:36 +01:00
Julian Stirling
2d49bf2061 Remove duplicate exposure property from picamera thing 2025-06-25 10:21:54 +01:00
Julian Stirling
8a4ad49c03 Apply suggestions from code review of branch jpeg-capture-in-stacking 
Co-authored-by: Richard Bowman <richard.bowman@cantab.net>
 2025-06-25 09:17:32 +00:00
Julian Stirling
4e78f3d104 Fix exposure time adjusting when setting the same value and add test 
Closes #433
 2025-06-24 17:01:16 +01:00
Julian Stirling
be07966631 Remove the overwriting of internal globals, requires removing future annoations 2025-06-24 10:18:30 +01:00
jaknapper
11c8f47e20 Rename central image to sharpest 2025-06-23 18:13:46 +01:00
jaknapper
7c3a9ad01f Copy sharpest image from stack, not the most average sharpness! 2025-06-23 18:08:27 +01:00
Julian Stirling
febb0d2690 Clarify white balance code. 2025-06-23 17:49:35 +01:00
Julian Stirling
cdae90013a Modify comment for clarity in the function that copies the lens shading algorithm 2025-06-23 16:24:40 +00:00
Julian Stirling
afea1e3658 Create function for flattening and rounding array and converting to a list 2025-06-23 17:22:28 +01:00