jaknapper
fbbb3decdc
Ruff formatting
2025-05-01 13:16:48 +00:00
jaknapper
b8ddab1ed8
Remove correlation only stitching, now covered by preview stitch
2025-05-01 13:16:48 +00:00
Julian Stirling
3adc34c30b
Merge branch 'dont-test-focus-change' into 'v3'
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Remove focus_change_acceptable test
Closes #342
See merge request openflexure/openflexure-microscope-server!249
2025-04-23 11:28:05 +00:00
Joe Knapper
c4dc357cf3
Apply 1 suggestion(s) to 1 file(s)
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Co-authored-by: Julian Stirling <julian@julianstirling.co.uk>
2025-04-23 10:57:56 +00:00
Joe Knapper
283a10c560
Always move back to expected focus after failed autofocus
2025-04-23 09:15:54 +00:00
Julian Stirling
0ac455bf89
Merge branch 'autofocus-at-start' into 'v3'
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Looping autofocus at the start of the scan
See merge request openflexure/openflexure-microscope-server!247
2025-04-23 08:10:21 +00:00
jaknapper
3bcc71304e
Fixed focused path tracking, move to estimated focus before autofocus
2025-04-22 14:33:27 +01:00
jaknapper
7cb1a3980e
Remove focus_change_acceptable test, autofocus from centre
2025-04-17 17:20:40 +01:00
jaknapper
5d8a1073b2
Remove focus_change_acceptable
2025-04-17 17:02:39 +01:00
Julian Stirling
257d700333
Merge branch 'shorter-move-spiral-path' into 'v3'
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Add a scan path planner that prioritises shorter moves
See merge request openflexure/openflexure-microscope-server!245
2025-04-17 15:37:52 +00:00
Joe Knapper
07cbef0536
Reimplement tie breaking by distance between
2025-04-17 10:25:40 +01:00
jaknapper
c895383a83
Remove repeated moves_from_centre() code
2025-04-17 10:12:12 +01:00
jaknapper
c18472dc8a
Add the import info for ScanPlanner
2025-04-17 09:56:23 +01:00
Joe Knapper
041106ebea
Only open pickle file if planner was successfully generated
2025-04-17 08:48:14 +00:00
Joe Knapper
1248c2b7c8
Remove unneeded third sort key
2025-04-17 08:47:24 +00:00
Joe Knapper
871cab72f4
Apply 5 suggestion(s) to 2 file(s)
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Co-authored-by: Julian Stirling <julian@julianstirling.co.uk>
2025-04-17 08:43:51 +00:00
jaknapper
2741123cf9
Looping autofocus at the start of the scan
2025-04-16 18:47:47 +01:00
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
