rahix/openflexure-microscope-server
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244 commits

Author SHA1 Message Date
jaknapper
52b58241cc Added copy_sharpest_image to autofocus 2025-06-23 11:19:23 +01:00
jaknapper
d39bcbaf5c Moved streaming changing to inner loop 2025-06-23 11:19:23 +01:00
jaknapper
0d32983b62 Only undershoot z stack if image count > 1, settle before first capture 2025-06-23 11:19:23 +01:00
jaknapper
744ec28f93 Get images as a PIL image from camera, use resizing and saving as settling time in stack 2025-06-23 11:19:20 +01:00
jaknapper
dbed1c6971 Default resize in stitching for scan tab stitching 2025-06-23 11:17:46 +01:00
jaknapper
9f2a131f1e Swap stream for scan, target_resolution as arg 2025-06-23 11:17:46 +01:00
jaknapper
f5c1ff2621 Ruff formating 2025-06-23 11:17:46 +01:00
jaknapper
17f3bbe646 Low res stream during scanning for instant high res captures 2025-06-23 11:17:46 +01:00
jaknapper
a9fdd0ea3e Wait params in captures, multiple attempts to capture 2025-06-23 11:17:46 +01:00
jaknapper
de7ffb9d1e Stream_name and capture_method args updated 2025-06-23 11:17:46 +01:00
jaknapper
8bc0573ab1 Capture_array can now use "full" stream 2025-06-23 11:17:46 +01:00
jaknapper
9d1385231d Rename jpeg_array to highres_array 2025-06-23 11:17:46 +01:00
jaknapper
132efa8033 Options for capture method, default downsampling of correlations 2025-06-23 11:17:45 +01:00
jaknapper
26163dc97e Added a new way to capture full res JPEGs, need to do a comparison of results 2025-06-23 11:17:45 +01:00
jaknapper
ab33de7ccd Capture a jpeg to disk 2025-06-23 11:17:45 +01:00
jaknapper
d8878e40da Stacking in autofocus with temp capture Thing 2025-06-23 11:17:45 +01:00
jaknapper
46458ca8a1 Create a stack folder and copy the middle image to image_dir 2025-06-23 11:17:45 +01:00
jaknapper
a1784941fe Ruff formatting and removing all capturing from smart_scan 2025-06-23 11:17:45 +01:00
jaknapper
603b9c7d16 Functional z stack Thing 2025-06-23 11:17:45 +01:00
Julian Stirling
1c54d25212 Add ruff checking for unnecessary comprehensions 2025-06-10 16:07:49 +01:00
Julian Stirling
2050c2dc7c Add return checker, needed 4 fixes 2025-06-10 16:07:48 +01:00
Julian Stirling
3f0564f253 Turning on more lint checkers, warning for cameras that ignore resolution setting 2025-06-10 16:07:48 +01:00
Joe Knapper
ae2ec1864f Merge branch 'config-scan-dir' into 'v3' 
Add scan directory to json config

Closes #393

See merge request openflexure/openflexure-microscope-server!283
 2025-06-09 13:42:27 +00:00
Chish36
7eed48ed26 Swapped the order of CSM so y axis is completed first 2025-06-09 13:39:06 +00:00
Julian Stirling
b45f5651ab Add scan directory to json config 2025-06-06 12:21:51 +01:00
Joe Knapper
08d1371569 Apply 1 suggestion(s) to 1 file(s) 
Co-authored-by: Julian Stirling <julian@julianstirling.co.uk>
 2025-06-06 10:25:34 +00:00
Joe Knapper
69db7b4041 Apply 2 suggestion(s) to 1 file(s) 
Co-authored-by: Julian Stirling <julian@julianstirling.co.uk>
 2025-06-05 17:09:37 +00:00
Joe Knapper
41f6c8879a RATIO as a global, better naming and splitting of generate_image() 2025-06-05 15:03:26 +01:00
Joe Knapper
2db895a1fc Defocus and realign simulation axes 2025-06-05 12:09:01 +01:00
jaknapper
a499d9230c Switch to updated "preview stitch" mode in stitching 2025-05-23 16:28:22 +01:00
jaknapper
cc3620d2ed Stitch with dzi by default, and check for dzi available in scans() 2025-05-23 16:28:21 +01:00
Julian Stirling
fe1696df28 Fix error in purge_empty_scans if the images dir hadn't been created 2025-05-23 12:49:46 +01:00
Julian Stirling
70f4304b2e Fix bug where .jpg files are not counted in scan list (only .jpeg) 2025-05-23 11:45:26 +01:00
jaknapper
b812c6be35 Settling time as global, settle before taking first image in stack 2025-05-21 15:41:49 +01:00
Julian Stirling
6332c8b647 Merge branch 'openflexure-stitching-from-pip' into 'v3' 
Import openflexure-stitching from pip

See merge request openflexure/openflexure-microscope-server!270
 2025-05-21 10:00:48 +00:00
jaknapper
44f2435ea4 Removed stitching path as kwarg for scanning 2025-05-21 10:30:42 +01:00
Julian Stirling
c793620fcd Merge branch 'cleanup_empty_scans' into 'v3' 
Added purge_empty_scans() method

Closes #370

See merge request openflexure/openflexure-microscope-server!257
 2025-05-20 18:26:00 +00:00
Joe Knapper
6c8c8bf358 Apply 1 suggestion(s) to 1 file(s) 
Co-authored-by: Julian Stirling <julian@julianstirling.co.uk>
 2025-05-20 17:04:48 +00:00
jaknapper
4a44dceac6 More clear variable name, use _delete_scan to avoid calling fastapi-endpoint in loops 2025-05-20 16:36:57 +01:00
jaknapper
19d72bef1c Error handling in _delete_scan(), which is now handled in GUI main.js 2025-05-14 16:11:02 +01:00
Joe Knapper
1468a90c60 Merge branch 'scan_tab' into 'v3' 
Scan tab updates

See merge request openflexure/openflexure-microscope-server!260
 2025-05-14 11:53:19 +00:00
jaknapper
99e52bcb2f Formatting and fixing wrong variable in loop 2025-05-14 12:23:01 +01:00
Joe Knapper
251b0ca770 Apply 1 suggestion(s) to 1 file(s) 
Co-authored-by: Julian Stirling <julian@julianstirling.co.uk>
 2025-05-14 10:26:37 +00:00
jaknapper
3eea4bbaf6 Log each line individually to ensure line breaks 2025-05-13 17:08:09 +01:00
jaknapper
69260d1973 stitch available property, allowing GUI to only stitch when needed 2025-05-13 15:51:11 +01:00
jaknapper
a77c0f6f9d Updated wrong path to file 2025-05-13 15:28:16 +01:00
Joe Knapper
b5893bc29c Apply 1 suggestion(s) to 1 file(s) 
Co-authored-by: Julian Stirling <julian@julianstirling.co.uk>
 2025-05-13 12:34:50 +00:00
jaknapper
56edddd195 Data filename as global 2025-05-13 13:03:34 +01:00
jaknapper
1952e05284 Scan result in data json 2025-05-13 13:00:04 +01:00
jaknapper
9734bba23b Inputs renamed to data where appropriate 2025-05-13 12:45:55 +01:00