Commit graph

2730 commits

Author SHA1 Message Date
Joe Knapper
d1908eb29a Run stitching thing with appropriate overlap setting 2024-01-13 13:38:39 +00:00
jaknapper
d369105111 Fixed log link 2024-01-12 17:15:09 +02:00
jaknapper
c4e02d9087 Maximum lateral range and minimum autofocus range 2024-01-11 20:38:47 +00:00
Richard Bowman
e611840aca Save microscope id as a string
UUIDs don't serialise to JSON, so I'm now saving it as a plain
string and reconstructing a UUID object when it's returned.

Returning a UUID seems clearer than returning a string.
2024-01-11 19:53:08 +00:00
Richard Bowman
a279831c41 Reordered cleanup operations for robustness
I now define the variables needed in the finally: block at
the very start, so I can test if they are None.

I've reordered the final move so it can happen as we are awaiting the background processes. I've added exception handling so this won't cause problems with the lock.
2024-01-11 16:39:06 +00:00
Richard Bowman
606ee9bcc2 Return hostname using a v2 URL for Connect compatibility 2024-01-11 16:20:49 +00:00
Richard Bowman
074b9c67f8 Serialise microscope ID to string
UUID objects don't serialise with `json.dumps` and thus cause
errors when we try to embed `thing_state` into images.
2024-01-11 15:58:42 +00:00
Richard Bowman
f51d6ced71 Add hostname and microscope ID to metadata
It's often helpful to tell if images came from the same
microscope - this metadata should answer that question.
2024-01-11 14:48:08 +00:00
Richard Bowman
924cce649a Autofocus tweaks for smart scan
We've removed the initial double-autofocus (we just do a
single looping autofocus at the start), and now only do 3 retries rather than 5 if the focus is rejected.
2024-01-11 14:15:54 +00:00
Richard Bowman
20efaa2799 Appearance tweaks
actionLogDisplay had white-on-white text in dark mode: I've fixed color to be black now.

added a title for the mini stream display during scans
2024-01-11 14:08:32 +00:00
Richard Bowman
13f39d5303 Merge branch 'integrated-stitching' into 'v3'
Run `openflexure-stitch` on the server

See merge request openflexure/openflexure-microscope-server!169
2024-01-11 14:01:02 +00:00
Richard Bowman
a965d04047 Move raw images folder inside images folder
This ensures images.zip contains everything - a neater solution
for this is TBD.
2024-01-11 13:56:24 +00:00
Richard Bowman
f4c4206a53 Return an empty scans list if the folder is missing 2024-01-11 13:40:47 +00:00
Richard Bowman
6b6946ec60 Cope with an empty scan list 2024-01-11 13:37:57 +00:00
Richard Bowman
d96dbdd546 Only stringify boolean values when setting properties
My workaround to the axios bug that makes `false` values not work
2024-01-11 13:37:57 +00:00
Richard Bowman
ba86c37292 Swap background detection from argument to property
For consistency, I've made background detection a property.
2024-01-11 03:21:50 +00:00
Richard Bowman
f26230efb6 Swap background detect from argument to property
I've added boolean support to PropertyControl. This required
working around a bug in axios, that ignored `false` when sent
as the body of a request.
2024-01-11 03:01:33 +00:00
Richard Bowman
3de7aa2fb2 Don't invoke stitching from the front-end
Stitching is now done automatically in a sub process by the
server. This is much cleaner - and all we need to do is poll for
file updates.

I've also styled the log display slightly better.
2024-01-11 01:51:17 +00:00
Richard Bowman
9a2b830ff5 Fix completed event 2024-01-11 01:50:01 +00:00
Richard Bowman
6b466c80a9 Add polling for preview stitched images 2024-01-11 01:50:01 +00:00
Richard Bowman
717cf7657c Combine stitcher and smart scan Things
I'm now running stitching in subprocesses during the scan.
This seems to be working well - I'm using multiple CPU
cores and getting images out. However, the only way to
avoid circular dependencies was to combine the Things.

I'm still getting not-infrequent memory allocation errors from the camera, which may or may not be related.
2024-01-11 01:49:24 +00:00
Richard Bowman
b5fbcc85b5 Succeed immediately if the stitched image is up to date
To save some CPU cycles, we will return immediately if the
images don't look newer than the stitch. NB this does mean
that the stitched image will be repeatedly transferred, as its
URL will change each time it's re-requested.

Alternatively, we could fail with an error, which may be more efficient, at the expense of being uglier.
2024-01-10 23:17:16 +00:00
Richard Bowman
00a4b38a83 Prevent scans from filling the SD card 2024-01-10 21:07:25 +00:00
Richard Bowman
8fb70bf43a Make latest_scan_name a property 2024-01-10 20:51:50 +00:00
Richard Bowman
9ce52c2845 Added a Thing to run stitching as Actions 2024-01-10 20:51:49 +00:00
Richard Bowman
b6b1fd06bf Merge branch 'refactor-task-submitter' into 'v3'
Refactor task submitter

See merge request openflexure/openflexure-microscope-server!168
2024-01-10 20:49:10 +00:00
Richard Bowman
7c88704059 Only show scrollbar if needed 2024-01-10 20:48:22 +00:00
Richard Bowman
215bfb5121 Leave scan log open until closed
The log/progress view is now closed explicitly, rather than disappearing as soon as the scan is over.
2024-01-10 20:46:06 +00:00
Richard Bowman
f03e0188e4 Fix a typo when reacting to an existing invocation
checkExistingTasks was looking up the task's `self` link by
checking for `rel=self`, which failed. I have corrected this
to `rel="self"` - `self` would have evaluated to `undefined`.
2024-01-10 20:46:06 +00:00
Richard Bowman
81540ebc45 Linter fixes 2024-01-10 20:46:06 +00:00
Richard Bowman
29177d7214 Scroll to the bottom when status messages appear
The log viewer was scrolling to the bottom when new logs
appeared, but not when the status updated. This meant that the status update may have been invisible. I now scroll
when the status changes too, which should fix the problem.
2024-01-10 20:46:06 +00:00
Richard Bowman
46444770f3 Improved styling and synchronisation 2024-01-10 20:46:06 +00:00
Richard Bowman
53644a691b Refactored taskSubmitter to enable bits to be re-used 2024-01-10 20:46:06 +00:00
Richard Bowman
cf075c6261 Merge branch 'v3-log' into 'v3'
Restored old log path

See merge request openflexure/openflexure-microscope-server!167
2024-01-10 19:53:53 +00:00
Joe Knapper
1464d7d553 Restored old log path 2024-01-10 18:33:08 +00:00
Joe Knapper
ddfce7dcff Success and warning alerts in webapp 2024-01-10 18:29:43 +00:00
jaknapper
6d622c1bf8 Avoid negative dx/dy and allow for float CSM image resolution 2024-01-10 15:38:34 +00:00
jaknpper
d219e32bc8 Option to run scan without background detect in webapp and Thing 2024-01-09 20:24:51 +00:00
Joe Knapper
89dae7ba80 Button for not-smart scan and better positioned navigate buttons 2024-01-09 16:46:13 +00:00
Joe Knapper
090f447d26 Thing properties for autofocus dz, overlap and range limit 2024-01-08 19:33:24 +00:00
Richard Bowman
9a3e870d21 Remove unused taskId data
taskSubmitter's "taskId"  data member was usually incorrect and
wasn't necessary - it is removed.
2024-01-08 17:35:06 +00:00
Richard Bowman
d615522712 Raw images and better cancellation
Cancelling a smart scan now resets position to the starting point.

a "raw images" folder now includes images without resampling.
2024-01-08 17:25:31 +00:00
Richard Bowman
26f5b1955e Reset position to starting point when CSM is cancelled
NB there's a confusing feature, where stage.move will
fail after the task has been cancelled, because it is cancellable.
For now, we can work around it by passing `block_cancellation` but
this may want to be solved more generally in LabThings
2024-01-08 17:24:18 +00:00
Richard Bowman
552fde45ed Improve logging commands
use logging.exception instead of setting exc_info.
2024-01-08 16:43:28 +00:00
Richard Bowman
7eeee89b23 Error messages if background detect fails. 2024-01-08 16:40:07 +00:00
Richard Bowman
ec61019d76 Improve modal progress dialog
I've tidied up the UI a bit here:
* The modal box stays open and must be explicitly closed.
  Pretty much everywhere we want to use this, it would be nice
  to see the final confirmation it's worked - so I have removed
  the line that closes it after the task completes.
* The progress bar no longer animates after the task has
  finished (logic previously didn't consider that state as the
  bar wasn't visible except while it was running).
* A helpful message is printed when the task completes or is
  cancelled.
2024-01-08 16:24:43 +00:00
Richard Bowman
c0d25b194c Format fixes/disable warnings
My v-html use is OK as the  HTML is sanitized.
2024-01-08 16:24:43 +00:00
jaknapper
4445990966 Check we have a background set before starting scan 2024-01-08 16:21:57 +00:00
Joe Knapper
125bae9c6d Merge branch 'spiral_path' into 'v3'
Pseudo spiral scan path and fixed dx-dy inversion

See merge request openflexure/openflexure-microscope-server!166
2024-01-08 16:10:17 +00:00
jaknapper
ae68a1b319 Pseudo spiral scan path and fixed dx-dy inversion 2024-01-08 16:01:54 +00:00