Joe Knapper
c18667c973
Update pickles
2025-04-15 16:38:11 +01:00
Joe Knapper
b414697cfb
Update testing for multiple sample shapes
2025-04-15 16:35:52 +01:00
jaknapper
7373424fcf
Ruff formatting
2025-04-15 10:40:45 +01:00
jaknapper
ec25ae7126
Add a scan path planner that prioritises shorter moves
2025-04-14 18:49:35 +01:00
Julian Stirling
be64d4c5e0
Merge branch 'further-scan-refactor' into 'v3'
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Further scan refactor
See merge request openflexure/openflexure-microscope-server!242
2025-04-14 16:07:37 +00:00
Julian Stirling
06632f195e
Spelling corrections and docstring improvements
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Co-authored by Joe Knapper <jaknapper@hotmail.com>
2025-04-14 15:46:27 +00:00
Julian Stirling
bd411db5ea
Relax line length when linting (increased checker)
2025-04-14 11:27:25 +01:00
Julian Stirling
7f46bc2d9b
Fixing capture_thread variable and autofocus logic
2025-04-14 11:27:25 +01:00
Julian Stirling
2ced848695
Add functionality for testing the scan planner on a given sample shape
2025-04-14 11:27:25 +01:00
Julian Stirling
a0b6dbdfce
Add weay to access a copy of the data from a ScanPlanner
2025-04-14 11:27:25 +01:00
Julian Stirling
91073535a8
More tests for scan planners
2025-04-14 11:27:25 +01:00
Julian Stirling
842e196f9b
Add some basic tests, and do minor fixes based on tests and MyPy
2025-04-14 11:27:25 +01:00
Julian Stirling
1f66e8bc7a
Enormous refactor of the scan code, was hard to find an intermediate working place to commit
2025-04-14 11:27:25 +01:00
Julian Stirling
cddb49c9f7
Clean up code as I remove bare excepts
2025-04-14 11:27:25 +01:00
Julian Stirling
2c171026be
Still tidying the start end end of the scan code
2025-04-14 11:27:25 +01:00
Julian Stirling
797f3bcb60
Collecting scan parameters into dictionary that will become a dataclass
2025-04-14 11:27:25 +01:00
Joe Knapper
19a4724eb9
Merge branch 'more-linting' into 'v3'
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Add some extra rules to ruff, also add a more complete ruff config that fails
See merge request openflexure/openflexure-microscope-server!241
2025-04-14 09:02:28 +00:00
Julian Stirling
7665d45e09
Make the coverage report touch all files
2025-04-11 23:29:32 +01:00
Julian Stirling
1c871749b0
Remove module level noqa from background detect.
2025-04-11 12:32:32 +01:00
Julian Stirling
4eeff35e2d
Fixes to naming to make basic lint checks pass
2025-04-11 12:29:14 +01:00
Julian Stirling
e4cfcc76a7
Add some extra rules to ruff, also add a more complete ruff config that fails
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Over time we can enable more rules for `ruff check`
2025-04-11 11:56:55 +01:00
Julian Stirling
5ab0a62964
Merge branch 'refactor-scanning' into 'v3'
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Refactor scanning
See merge request openflexure/openflexure-microscope-server!240
2025-04-10 22:05:40 +00:00
Julian Stirling
b7c472bb24
fix comment on number of zeros padding the scan name
2025-04-10 22:39:22 +01:00
Julian Stirling
31c768c12a
Move @_scan_running decorator out of class and tidy as suggested in review
2025-04-10 22:14:56 +01:00
Julian Stirling
e030eb576b
Add @scan_running decorator for scans to try to access to the scan logger for methods not called by the scan
2025-04-10 17:52:12 +01:00
Julian Stirling
26e265f026
Fixes from review (mostly spellings)
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Co authored by:
* Joe Knapper <jaknapper@hotmail.com>
* Beth Probert <beth_probert@outlook.com>
2025-04-10 16:35:49 +00:00
Julian Stirling
840c527cc2
Remove unused Stitching Thing
2025-04-10 13:53:51 +01:00
Julian Stirling
a5d55c95b8
Further tidying of scan directory variables
2025-04-10 13:24:11 +01:00
Julian Stirling
90cfce146d
Fix default scan name
2025-04-10 11:46:16 +01:00
Julian Stirling
040373ef88
Run check background aonly fter scan variables are stored
2025-04-10 11:45:57 +01:00
Julian Stirling
83d2930d1f
Fix capture error handing
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The error handling for capture needs to still send the aquired event
or it will lock forever. On getting the errors to work there
were some other minor issues in how the errors were called.
2025-04-09 23:52:47 +01:00
Julian Stirling
70e7a21a29
Starting to refactor smart scan to rely on class variables
2025-04-09 22:55:35 +01:00
Julian Stirling
ff1184d453
Handle errors in capture thread
2025-04-09 22:45:18 +01:00
Julian Stirling
5dd23f6ef4
Merge branch 'scanning-cleanup' into 'v3'
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Scanning cleanup
See merge request openflexure/openflexure-microscope-server!239
2025-04-09 17:13:59 +00:00
Joe Knapper
1d5d67f35a
Split out background detect into a new file
2025-04-09 17:25:19 +01:00
Joe Knapper
f4db9b6e52
Removed commented out code and unused functions
2025-04-09 15:32:13 +01:00
jaknapper
a5d1f1e965
Removed commented out code
2025-04-09 15:11:26 +01:00
jaknapper
e28a160b22
Ruff formatting adding commas
2025-04-09 14:59:20 +01:00
jaknapper
8d14aee27c
Breaking out capture and save code into three seperate methods
2025-04-09 13:20:06 +01:00
Joe Knapper
6ec7487001
Merge branch 'inverse_colours' into 'v3'
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Inverse colours
See merge request openflexure/openflexure-microscope-server!236
2025-04-09 11:08:59 +00:00
jaknapper
9c2ab977c5
Removed imports and variable to pass Ruff linting
2025-04-08 19:07:23 +01:00
jaknapper
52532a90d7
More spacing below buttons
2025-04-08 18:41:11 +01:00
jaknapper
4fa2813e6a
More spacing and nicer dark mode colours
2025-04-08 18:30:40 +01:00
jaknapper
574aa1c6c0
Only grab a JPEG from the stream to get scanning working
2025-04-08 17:52:55 +01:00
Joe Knapper
d4247235e3
Merge branch 'csm-return-to-start' into 'v3'
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CSM always returns to start on error
See merge request openflexure/openflexure-microscope-server!227
2025-04-08 12:49:38 +00:00
Joe Knapper
bf82f37c47
Dependency bump for camera_stage_mapping to 0.1.8
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Returns the errors we expect
2025-04-08 12:09:15 +00:00
Joe Knapper
e4ef8b2717
Merge branch 'consistent-logging' into 'v3'
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Stop uvicorn.run disabling existing loggers
Closes #284
See merge request openflexure/openflexure-microscope-server!228
2025-04-08 11:31:33 +00:00
Joe Knapper
2cffe21727
Merge branch 'background-UV' into 'v3'
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Use the UV channels only to determine if an area is background or sample
Closes #300
See merge request openflexure/openflexure-microscope-server!211
2025-04-08 10:30:17 +00:00
Julian Stirling
a4390255db
Merge branch 'reorder_tabs' into 'v3'
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Reorder tabs
See merge request openflexure/openflexure-microscope-server!231
2025-04-08 10:27:18 +00:00
jaknapper
b340da488e
Use the UV channels only to determine if an area is background or sample
2025-04-08 11:14:17 +01:00
