Commit graph

2592 commits

Author SHA1 Message Date
Richard Bowman
a54c972891 Merge branch 'new_things' into 'v3'
Scanning and recentring

See merge request openflexure/openflexure-microscope-server!162
2023-12-14 15:19:02 +00:00
jaknapper
1d50dcb3f8 Scanning and centring things 2023-12-14 15:08:43 +00:00
Richard Bowman
d0eb9fa2c1 Format/comment improvements 2023-12-13 16:35:13 +00:00
Richard Bowman
3b2fd29fb0 Log to a file and make it visible via the API 2023-12-13 01:54:42 +00:00
Richard Bowman
3059683186 Enable logging
`logging.basicConfig` doesn't work when run via `uvicorn`.
I now explicitly get the root logger and set its level to INFO,
which means we now see logs on the terminal.
2023-12-13 00:51:41 +00:00
Richard Bowman
94e1619056 Use safer metadata dependency
Retrieving metadata pre-action risks stale metadata being
returned if DirectThingClients are used. I've switched to
the safer callable dependency, which is guaranteed to be fresh.
2023-12-12 23:40:12 +00:00
Richard Bowman
d9711522d5 Detect static directories
Simplified code and removed hard-coded list of static dirs.
2023-12-12 22:55:50 +00:00
Richard Bowman
753514c24b Added v2 API routes and hard-coded static files to support Connect
Connect looks for /routes and /api/v2/streams/snapshot
These are now present and working.

I've also hard coded the static files directory - fixing this
properly is a work in progress.
2023-12-11 23:59:11 +00:00
Richard Bowman
60f854b7db Return None if calibration matrix is missing
Previously, we raised an exception (and thus HTTP error
code) if the CSM matrix was requested and not yet set.
Now, we just return None, and I've added a (not-network-exposed)
function that will raise an HTTPException if it's missing.
2023-12-01 21:29:14 +00:00
Richard Bowman
a6e8c7ab93 Return HTTP error properly if CSM is uncalibrated 2023-12-01 02:18:28 +00:00
Richard Bowman
e5e5be7369 Added settings manager to store arbitrary metadata 2023-11-29 23:38:28 +00:00
Richard Bowman
b6ed55caba Fixed module docstring 2023-11-29 23:38:12 +00:00
Richard Bowman
b9605fa2a0 Added module docstring 2023-11-29 23:37:54 +00:00
Richard Bowman
20a7fd52b1 Reinstate move_and_measure 2023-11-28 23:47:53 +00:00
Richard Bowman
291bbde9cf Don't raise an exception if thing_state called before calibration
It's helpful to raise an exception if we access the calibration
before it's been set - but thing state should not raise exceptions,
just return an empty dict if the data is not there yet.
2023-11-28 21:06:42 +00:00
Richard Bowman
27c74bff6e Add shutdown/restart actions 2023-11-02 21:18:59 +00:00
Richard Bowman
7bbc105fc6 Expose last calibration and thing_state 2023-11-02 20:29:22 +00:00
Richard Bowman
92ba79ef7a Improved docstrings 2023-11-02 10:27:27 +00:00
Richard Bowman
6eefa4f25b Add image resolution to CSM metadata
The camera stage mapper should now note the resolution
used when it was last calibrated - this is helpful for tiling,
because we may need to scale it if the images recorded are
a different resolution from the images used for calibration.

This addresses https://gitlab.com/openflexure/microscope-extensions/camera-stage-mapping/-/issues/11
2023-11-02 10:05:54 +00:00
Richard Bowman
4caba58d6c Revert to Sangaboard, rather than proscan 2023-11-01 18:02:16 +00:00
Richard Bowman
796622b802 Relax scipy version 2023-10-31 22:28:47 +00:00
Richard Bowman
b9804cdc2d Serve static web app at / 2023-09-06 11:56:20 +01:00
Richard Bowman
da711a7d8c linter fixes 2023-09-04 22:08:27 +01:00
Richard Bowman
799dc7f522 WIP: update webapp to use new backend
This is still very much WIP, but I now have fast
autofocus, stage moves, image streaming, and click-to-move.
2023-09-04 22:00:56 +01:00
Richard Bowman
e82acf2941 Add thing_state metadata 2023-09-04 11:43:32 +01:00
Richard Bowman
63d7a6eb4d WIP: camera stage mapping
This still has some bugs, mostly related to numpy and serialisation.
2023-08-31 19:37:09 +01:00
Richard Bowman
6e04618051 Autofocus module!
Currently only has fast_autofocus, and there
may be some work to do on timing, but it works :)

Getting timestamps from the camera rather than
time.time() would be ideal, but it would take some thought to tie that up with
the encoder.

I'm using a low-res stream, as it seems impossible to
turn the bitrate control of the MJPEG stream off,
at least within the picamera2 API.
2023-08-30 21:34:06 +01:00
Richard Bowman
081654533f First images on labthings-fastapi
We now have very basic camera and stage support.
2023-08-29 17:02:16 +01:00
Richard Bowman
ac45423739 Merge branch 'sangaboard-v4' into 'master'
Support latest sangaboard firmware

See merge request openflexure/openflexure-microscope-server!154
2023-04-12 07:23:15 +00:00
Richard Bowman
7abdbdde4a Add full list of server prerequisites
The server needs various packages installed on
the system. This list is lifted from the SD card
builder repository.
2023-04-06 21:27:51 +01:00
Richard Bowman
a95baee25f Fix lxml and update README
lxml requires an apt-installed package to work.
I've also mentioned in README that Pipfile
is now pi-specific.
2023-04-06 16:03:20 +01:00
Richard Bowman
d0aad6633c Redo CI to run on armv6
I've refactored the CI substantially, using the
new `extends` keyword to tidy it up a lot.
I have also changed from running the Python
tests on Python:3.7 to using a Raspberry Pi
OS from the Balena project.

This means we are now ONLY locking
dependencies for the Pi, and we are no longer
expecting the Pipfile to work on non-arm
systems.
2023-04-06 15:20:48 +01:00
Richard Bowman
fdafeca446 Only consider piwheels in Pipfile
Including both piwheels and pypi in Pipfile caused hash mismatches,
which caused installation to fail. I've removed pypi, but this may
break installation on other platforms.

I may need to duplicate Pipfile and Pipfile.lock, one for Pi and
one for non-Pi platforms.

I can confim this commit installed successfully on a Pi.
2023-04-03 22:03:57 +01:00
Richard Bowman
12fd9a5f4a Mention dependencies in readme 2023-04-03 20:38:57 +01:00
Richard Bowman
62eef8f8e1 Re-lock dependencies on a Raspberry Pi
I couldn't install this on a Pi, because it incorrectly chose
versions of e.g. numpy that did not exist in binary form for the
pi. I re-locked dependencies with:

`PIP_ONLY_BINARY=":all:" pipenv lock --dev`

This forced the use of wheels, and not only completed but did so
in ~10 minutes.
2023-04-03 20:32:52 +01:00
Richard Bowman
3f9c3447de Fixed typos in comments spotted in code review 2023-03-23 13:31:25 +00:00
Richard Bowman
d948d3f04d Merge branch 'Update-WoT-links' into 'sangaboard-v4'
Update swagger with links to WoT documentation

See merge request openflexure/openflexure-microscope-server!155
2023-03-22 10:37:47 +00:00
Richard Bowman
1f558bbeb7 OpenAPI Validation Fixes
OpenAPI validation seems to have become stricter about checking for None defaults
in parameters that don't allow None. I have
modified two things as a result:

1. StageTypeProperty (used to pick between SangaStage and SangaDeltaStage)
now defaults to SangaStage (which is the
original behaviour anyway)
2. It is now allowed to pass x,y,z=None when making a move - this is the same as
not passing the respective argument, so the
function already correctly handled this case.
2023-03-22 08:58:04 +00:00
Richard Bowman
4b73fd82f6 Format fix 2023-03-21 15:11:24 +00:00
Richard Bowman
824248583d Add !154 to changelog 2023-03-21 15:05:22 +00:00
Joe Knapper
f6691cbc11 Update openapi.py with live links to WoT documentation 2023-03-21 15:05:21 +00:00
Richard Bowman
8e50a90fb2 Explicitly mark arguments as optional
mypy now considers implicitly Optional arguments
to be errors - I have made them now explicitly
Optional, which passes.
2023-03-21 15:04:49 +00:00
Richard Bowman
ba62bdf867 Update pysangaboard to 0.3.3 2023-03-21 12:51:03 +00:00
Richard Bowman
f2f00b0d11 Update w3c schema to 2020 format
The `thing-context` definition used a 2019 draft of how to specify a
tuple (where `items` set the mandatory items and `additionalItems`
set the rest).  These have been renamed to `prefixItems` and `items`
respectively, and I have applied this change.  Schema now validates
again :)
2022-08-09 13:33:10 +01:00
Richard Bowman
80d026d778 Downgrade markupsafe so jinja2 still works 2022-08-09 13:18:07 +01:00
Richard Bowman
106b50d333 Format fixes from black 2022-08-09 13:17:45 +01:00
Richard Bowman
9dbb083ee7 More Marshmallow argument updates 2022-08-09 13:16:10 +01:00
Richard Bowman
e22f36b308 Start explicit metadata argument for marshmallow
A side effect of re-locking dependencies is having a newer marshmallow.
This deprecates having `description=` as a keyword, and puts it in a
separate metadata arg instead.

This commit is the start of my search-and-replaceing to update to the new
format.
2022-08-09 12:52:57 +01:00
Richard Bowman
78ef9c531b Format fixes from black 2022-08-09 09:37:03 +01:00
Richard Bowman
5404521458 Use different names for unused variables
mypy flagged too many assignments to `_` which this commit fixes.
2022-08-09 09:36:25 +01:00