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.
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.
The update to pylint means we were failing because open()
doesn't specify the encoding everywhere. I have now specified utf-8
everywhere. This was patchy before, and is default behaviour on the
Pi. There's a slim chance it will cause some issues on Windows, but
that shouldn't affect anyone outside the developers.
I've also ignored a couple of new spurious warnings, and explicitly
ignored some unused variables.
I have:
* Moved the autofocus and focus-prediction code into a
new `FocusManager` class. This hopefully keeps the logic relating to
axial motion in one place.
* Moved set-up code relating to autofocus and background detection
into separate functions.
* Changed the scan path from a ragged list-of-lists to a one dimensional
list. I've left the old 2D function and added a new 1D function that
calls it and coverts, so it's not a breaking change.
The actual sequence of moves executed, and the accompanying logic, is
unchanged from the previous commit. I've tested this a couple of times,
on my microscope with actual hardware.
I don't think it's necessary to test more widely as this is only a
refactoring change, not an algorithm change.
The shift from 2D to 1D scan path was one I initially decided against,
because I was trying to keep the new code as small as possible, and
avoid refactoring what's already there. Since I'm doing that anyway,
I have taken the opportunity to eliminate the concept of scan
"lines".
The old behaviour was to always use the position of the last point
as the starting point for the next autofocus. There was an exception
to this for raster scans, where the big jump used the first point
of the last line instead. The new behaviour always uses the closest
point, which reproduces this behaviour without the need for a hard
coded exception.
If the "fast" scan axis (y) has a longer step size than the "slow"
scan axis (x), we may base the autofocus off the previous row, rather
than the previous point in the current row. I don't see that this
should be any less reliable than the current behaviour, and is
arguably better. It's also unlikely to be noticed, because our
default scan settings have longer spacing in X. I think the
reduced complexity of the code is definitely worth the small
chance of changing some edge-case behaviour.
The primary change here is that there's now an option
to skip autofocus if the background detect plugin says
the current image is background.
I have also overhauled the way it picks the next Z position
based on Joe's code; instead of just using the last point, it will
pick the closest point where we have a successful autofocus
recorded. This will usually be the last point, except for raster
scans where it neatly reproduces the behaviour of the old code
but without needing to treat it as a special case (when we jump
back to the start of a line, it will use the z position of the start
of the previous line, rather than the end of the previous line).
This does represent a minor change to previous behaviour, but
it should not break anything that isn't already broken, i.e. it might
cause slightly odd behaviour if autofocus gives random results -
but probably indistinguishable from the current behaviour.
taskSubmitter ended up in a confused state if the initial POST request
encountered an error.
I've updated `startPolling` to return a Promise, and moved the
error handling code to the top level.
This doesn't change anything for the case where we get a non-error
response to the POST request, but means that e.g. 400 errors
get caught and displayed properly.
The action wrapper was using an unbound function - it
now passes the extension object as self.
We were incorrectly passing endpoint names as positional arguments -
this is fixed and I now use a keyword argument.
If missing=None, we need to specify allow_None=False
in order to generate valid OpenAPI.
This may also be fixed by an upstream change in LabThings.
Also, OneOf was being used incorrectly in StageTypeProperty.
Given that it changes the "capture" button from
single image acquisition to a long running scan,
I think it's less confusing if the "scan capture" setting
is not remembered across page refreshes.
