Joe Knapper
a1be3e518f
Apply 2 suggestion(s) to 1 file(s)
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Co-authored-by: Julian Stirling <julian@julianstirling.co.uk>
2025-05-01 14:14:34 +00:00
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
jaknapper
5ca4c824aa
Remove producing thumbnail (to be added to stitching repo)
2025-04-23 14:28:41 +01:00
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
jaknapper
91057f164a
Thumbnails and accurate durations in scan-list tab
2025-04-22 19:02:29 +01:00
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
jaknapper
2741123cf9
Looping autofocus at the start of the scan
2025-04-16 18:47:47 +01:00
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
7f46bc2d9b
Fixing capture_thread variable and autofocus logic
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
Julian Stirling
4eeff35e2d
Fixes to naming to make basic lint checks pass
2025-04-11 12:29:14 +01:00
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
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
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
jaknapper
9c2ab977c5
Removed imports and variable to pass Ruff linting
2025-04-08 19:07:23 +01:00
jaknapper
574aa1c6c0
Only grab a JPEG from the stream to get scanning working
2025-04-08 17:52:55 +01:00
jaknapper
b340da488e
Use the UV channels only to determine if an area is background or sample
2025-04-08 11:14:17 +01:00
Julian Stirling
1493f51212
Purge all windows line endings and add check to formatter.
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Also changes python version in pyproject.toml as it is incorrect
2025-04-08 10:51:26 +01:00
Julian Stirling
32f2a7ce70
Fix spurious line endings, don't allow ruff-format to fail anymore
2025-04-02 14:25:22 +01:00
Richard Bowman
9fd8fc37f1
Formatted with Ruff
2024-12-03 06:46:08 +00:00
Richard Bowman
27aec769a2
Linter fixes
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NB I have permitted bare except: blocks in smart_scan. This should be reverted.
2024-12-03 06:43:45 +00:00
Richard Bowman
a0fbbc3e40
Convert Stage to a Protocol
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The Stage is now implemented as a runtime-checkable Protocol.
Part of this led to the realisation that we can't create a DirectThingClient
based on a Protocol, only on a concrete Thing. While it might be
a good idea to address that in LabThings in due course, for now
we work around it by creating both a Protocol and a stub class. The stub class implements the protocol, and
can be used to declare a dependency.
2024-11-29 12:53:04 +00:00
Richard Bowman
adbb805556
Formal Protocol for camera interface
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I've now split the base camera code into a runtime-checkable Protocol
and a concrete base class (which is optional). This removes the requirement
for cameras to subclass `openflexure_microscope.things.camera.Camera`
and instead uses duck typing that should
work both statically and dynamically.
As part of this, I've moved the commonly-used dependencies
on the camera inside `openflexure_microscope.things.camera` for consistency, and to make it easy to update them if it changes in the future.
2024-11-29 11:26:38 +00:00
Richard Bowman
1ba799de22
Migrate to new Blob type and update imports
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This now uses the latest version of labthings-fastapi.
2024-11-28 17:35:56 +00:00
Richard Bowman
2268425bf3
Depend only on generic Camera and Stage
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I've now defined parent classes for camera and stage, and depend only on those. This allows
proper typing while enabling the actual hardware
classes to be swapped.
The interfaces definitely aren't final - this is a first
draft, largely to enable me to test out the concept
of a configuration server.
2024-08-09 02:41:39 +01:00
Joe Knapper
4ea3b5b623
Increase minimum fraction coverage - makes stitching much more reliable
2024-05-30 11:42:25 +00:00
jaknapper
f08840f0e8
Zip a stitched image with the scan name in the filename
2024-03-05 13:38:24 +00:00
jaknapper
43cf7e837a
Produce tiff as property
2024-02-21 14:42:52 +00:00
jaknapper
169df15fd1
More restricted range
2024-02-21 14:04:07 +00:00
Joe Knapper
6031280a19
Merge branch 'changes-into-saturation-fix' into verify-focus
2024-02-20 14:17:25 +00:00
