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498 commits

Author SHA1 Message Date
Julian Stirling
26e265f026 Fixes from review (mostly spellings) 
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 
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
Joe Knapper
d4247235e3 Merge branch 'csm-return-to-start' into 'v3' 
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
e4ef8b2717 Merge branch 'consistent-logging' into 'v3' 
Stop uvicorn.run disabling existing loggers

Closes #284

See merge request openflexure/openflexure-microscope-server!228
 2025-04-08 11:31:33 +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
Julian Stirling
1493f51212 Purge all windows line endings and add check to formatter. 
Also changes python version in pyproject.toml as it is incorrect
 2025-04-08 10:51:26 +01:00
Julian Stirling
3a47151694 Serve logfile and logs for UI seperately 2025-04-07 23:45:19 +01:00
Julian Stirling
70d9e2f758 Add custom log handler for sending logs to UI 2025-04-07 23:16:00 +01:00
jaknapper
33c74741fe Fixed import and re-raise cancelled error 2025-04-07 15:46:20 +01:00
Joe Knapper
a506625e40 Treat cancellation and other errors differently 2025-04-07 14:22:43 +01:00
Joe Knapper
9995e5b3bb Import custom Mapping error from camera_stage_mapping 2025-04-07 14:18:07 +01:00
Julian Stirling
dd0b30df51 Stop uvicorn.run disabling existing loggers 2025-04-06 15:26:39 +01:00
jaknapper
67443ff939 Capture ValueErrors, which covers most CSM errors, not all Exceptions 2025-04-03 13:52:04 +01:00
jaknapper
46d513d9e6 Catch cancelled and other errors in single line 2025-04-02 18:25:35 +01:00
Joe Knapper
79b396a66f CSM always returns to start on error 2025-04-02 17:54:12 +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
83e10b125b Fix return type annotation for autofocus 2024-12-18 14:23:58 +00:00
Richard Bowman
9fd8fc37f1 Formatted with Ruff 2024-12-03 06:46:08 +00:00
Richard Bowman
27aec769a2 Linter fixes 
NB I have permitted bare except: blocks in smart_scan. This should be reverted.
 2024-12-03 06:43:45 +00:00
Richard Bowman
57177c6a56 Sped up camera and got CSM passing 
Using lower resolution helps speed it up, and skipping CSM settling time makes a big difference.
 2024-12-03 06:35:16 +00:00
Richard Bowman
1e7069b375 Add more tests, speed up dummy stage 
I've sped up the stage motion, to run tests in a more reasonable time.

CSM doesn't yet calibrate in the test - I suspect debugging of capture_array
is needed.
 2024-12-03 00:16:26 +00:00
Richard Bowman
bccb1ee923 Stub class for camera protocol 
As with the previous commit, this adds a concrete stub Thing to enable
DirectThingClient generation, so we
can depend on the camera.
 2024-11-29 12:53:42 +00:00
Richard Bowman
a0fbbc3e40 Convert Stage to a Protocol 
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
2e2e877d75 JPEGBlob class definition 
Static type checking is easier if JPEGBlob is declared as a class, rather than
being created with a function.
 2024-11-29 12:19:05 +00:00
Richard Bowman
adbb805556 Formal Protocol for camera interface 
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 
This now uses the latest version of labthings-fastapi.
 2024-11-28 17:35:56 +00:00
Richard Bowman
868aa0598c Simulation mode 
I successfully calibrated and used the camera-stage mapping.
 2024-11-02 00:10:25 +00:00
Richard Bowman
2019234ad1 Close OpenCV camera cleanly 2024-08-09 02:50:39 +01:00
Richard Bowman
2268425bf3 Depend only on generic Camera and Stage 
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
Richard Bowman
aa49cfcba3 Search the package for static files 
This isn't foolproof: a zipped package will break it.
If that's something we want to support, we might
need to extract the folder to a temp location.
 2024-08-09 02:39:04 +01:00
Richard Bowman
e3e248c46e Move server config to a config file 
Currently this is "just" a LabThings config file.
 2024-08-09 01:51:11 +01:00
Richard Bowman
b7f9f6cbaf Fix import from LabThings 2024-08-09 01:50:46 +01:00
Richard Bowman
5279dffe6a Dummy stage class 2024-08-09 01:12:16 +01:00
Richard Bowman
3f92ed8266 Add a stub OpenCV-based camera 
This allows the server to run on a laptop, to some extent. I've not tested if this will make the whole
web app work properly.

As StreamingPiCamera2 is hardcoded in various places, this certainly doesn't make cameras totally
interchangeable - but it is a step towards that.
 2024-08-09 00:52:31 +01:00
Richard Bowman
c32b44d1a6 Refactor server into submodule 2024-08-09 00:49:24 +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