Stage widget #142

tlambert03 · 2022-03-09T01:38:30Z

creating a new General purpose StageDevice Widget

tlambert03 · 2022-03-09T02:03:30Z

still very much WIP, but managed to get rid of 1400 lines of code (including the UI file, and icon svgs) and have this so far:

tlambert03 · 2022-03-10T01:17:18Z

this is getting closer to ready for a critical eye @fdrgsp. Particularly we want to check whether most of the logic in main_window has been preserved (though it's all removed from main_window now). might be worth checking this on a real scope. Currently, it's rather generic, so it's also likely something specific to (e.g.) autofocus may have been lost.

Couple minor aesthetic issues remaining, but looking decent:

ianhi · 2022-03-14T19:41:57Z

micromanager_gui/_gui_objects/_xyz_stages.py

+
+    def _on_cfg_loaded(self):
+        self._clear()
+        if dev := self._mmc.getXYStageDevice():


I think we should provide an object for generic StageWidgets and then a subclass that follows the default stage widget. Like what I did in #150 (in spirit if not in implementation)

that's primarily what this PR is doing. See micromanager_gui/_core_widgets/_stage_widget.py

this file here is just for the few things that are special about napari micromanager (like the QCollapsible). hence why it's in gui_objects :)

and this one arranges the generic stage widget into a multi widget. That could also happen in core, but the primary widget here is class StageWidget(QWidget) in that other file

ah indeed - I scanned too quickly sorry!

ianhi · 2022-03-14T20:49:06Z

One test failure will be fixed with a rebase - other one looks real

ianhi · 2022-03-14T20:56:38Z

Renders squashed for me when I run the dev script:

gets fixed if i toggle the qcollapsible on and off - but broken on opening

tlambert03 · 2022-03-14T21:08:39Z

gets fixed if i toggle the qcollapsible on and off - but broken on opening

yep, this needs https://github.com/napari/superqt/pull/72 to be released

ianhi · 2022-03-14T21:15:48Z

micromanager_gui/_core_widgets/_stage_widget.py

+        if self._snap_on_click:
+            self._mmc.snap()


Either there needs to be a change in core to have this stop live mode - or there there needs to be acheck here of if a sequence is running. This can result in this error:

untimeError Traceback (most recent call last) File ~/Documents/oss/micro/napari-micromanager/micromanager_gui/_core_widgets/_stage_widget.py:207, in StageWidget._on_click(self=<micromanager_gui._core_widgets._stage_widget.StageWidget object>) 205 btn: QPushButton = self.sender() 206 xmag, ymag = self.BTNS[f"{PREFIX}.{btn.text()}"][-2:] --> 207 self._move_stage(self._scale(xmag), self._scale(ymag)) xmag = 2 ymag = 0 self = <micromanager_gui._core_widgets._stage_widget.StageWidget object at 0x7f5d33328ee0> File ~/Documents/oss/micro/napari-micromanager/micromanager_gui/_core_widgets/_stage_widget.py:218, in StageWidget._move_stage(self=<micromanager_gui._core_widgets._stage_widget.StageWidget object>, x=20, y=0) 216 self._mmc.waitForDevice(self._device) 217 if self._snap_on_click: --> 218 self._mmc.snap() self = <micromanager_gui._core_widgets._stage_widget.StageWidget object at 0x7f5d33328ee0> self._mmc = <CMMCorePlus at 0x7f5d3326cd10> File ~/mambaforge/envs/pymm/lib/python3.10/site-packages/pymmcore_plus/core/_mmcore_plus.py:648, in CMMCorePlus.snap(self=<CMMCorePlus>, fix=True, *args=()) 629 def snap(self, *args, fix=True) -> np.ndarray: 630 """ 631 snap and return an image. 632 (...) 646 img : np.ndarray 647 """ --> 648 self.snapImage() self = <CMMCorePlus at 0x7f5d3326cd10> 649 img = self.getImage() 650 self.events.imageSnapped.emit(img) File ~/mambaforge/envs/pymm/lib/python3.10/site-packages/wrapt/decorators.py:469, in synchronized.<locals>._synchronized(wrapped=<bound method CMMCorePlus.snapImage of <CMMCorePlus>>, instance=<CMMCorePlus>, args=(), kwargs={}) 463 @decorator 464 def _synchronized(wrapped, instance, args, kwargs): 465 # Execute the wrapped function while the original supplied 466 # lock is held. 468 with lock: --> 469 return wrapped(*args, **kwargs) wrapped = <bound method CMMCorePlus.snapImage of <CMMCorePlus at 0x7f5d3326cd10>> args = () kwargs = {} File ~/mambaforge/envs/pymm/lib/python3.10/site-packages/pymmcore_plus/core/_mmcore_plus.py:553, in CMMCorePlus.snapImage(self=<CMMCorePlus>) 551 @synchronized(lock) 552 def snapImage(self) -> None: --> 553 return super().snapImage() RuntimeError: This operation can not be executed while sequence acquisition is running.

to reproduce that error:

launch

start live mode

trying moving stage

I love this "snap_after_stage_moves" function but I think we can remove it for now and see how to add it back once the stage, the snap and the live button widgets are merged. Do you agree?

micromanager_gui/_core_widgets/_stage_widget.py

ianhi · 2022-03-14T21:20:54Z

I think there needs to be a UI element showing the difference between a single arrow move vs a double arrow move. As it stands I'm not actually sure of the difference.

ianhi · 2022-03-14T21:22:49Z

I think there needs to be a UI element showing the difference between a single arrow move vs a double arrow move. As it stands I'm not actually sure of the difference.

Ahh I see this in the tooltip so less urgent - but still it was not immediately obvious. I think MM behavior of allowing you to set two values is pretty nice. One for fine adjust, and one for something like moving a field of view over

codecov · 2022-04-21T22:10:17Z

Codecov Report

Merging #142 (8abf461) into main (318724a) will increase coverage by 0.90%.
The diff coverage is 86.21%.

@@            Coverage Diff             @@
##             main     #142      +/-   ##
==========================================
+ Coverage   80.66%   81.56%   +0.90%     
==========================================
  Files          24       25       +1     
  Lines        2100     2268     +168     
==========================================
+ Hits         1694     1850     +156     
- Misses        406      418      +12

Impacted Files	Coverage Δ
micromanager_gui/_core_widgets/_device_widget.py	`89.77% <0.00%> (ø)`
micromanager_gui/_gui_objects/_xyz_stages.py	`68.05% <67.60%> (-20.04%)`	⬇️
micromanager_gui/_core_widgets/_stage_widget.py	`91.24% <91.24%> (ø)`
micromanager_gui/_gui_objects/_mm_widget.py	`96.90% <100.00%> (+0.06%)`	⬆️
micromanager_gui/main_window.py	`69.44% <100.00%> (+0.07%)`	⬆️

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tlambert03

I'm ok with this whenever you guys are. We can follow up with autofocus stuff in another PR. @fdrgsp, do you feel like this is complete as is? or want more time with it?

(thanks again for taking this over the finish line!!)

ianhi · 2022-04-28T02:50:25Z

We can follow up with autofocus stuff in another PR

I'd vote for merging sooner as this will fix issues I have with a z stage that doesn't have z in the name so the value doesn't update on main :(

I'm ok with this whenever you guys are.

Trying this out again since I last did I'm I do have one thing I dont love. There no longer seems to be a way to have the stage controls be part of the main controls layout - it's now triggered by a button:

and that leaves you with a floating stage controls:

I'm not sure exactly what is meant to be in "Light Sources" but I'm not sure it should be given equal screen space to the XYZ stage. Overall the layout in hte main widget and light source stuff feels like a bit of feature creep. Could this PR be limited to just the new stage widget and then those other things get considered in followups?

micromanager_gui/_core_widgets/_stage_widget.py

fdrgsp · 2022-04-28T04:19:00Z

@tlambert03

I'm ok with this whenever you guys are. We can follow up with autofocus stuff in another PR. @fdrgsp, do you feel like this is complete as is? or want more time with it?

You can have look, I think this is complete!

However I'm not sure it will work well if there is an autofocus device in the cfg (e.g. Nikon PFS)...these devices in micromanager have 2 "modules", one of which is considered as a Z-Stage device. A stage widget will therefore be generated for these devices as well and I'm not sure if there will be any error (maybe when trying to move the stage through the control buttons...)

fdrgsp · 2022-04-28T04:24:03Z

There no longer seems to be a way to have the stage controls be part of the main controls layout - it's now triggered by a button

@ianhi I think it does not matter much at the moment. I believe we can discuss about the gui "structure" once all the widgets will be ready (in a widget package). What do you think?

ianhi · 2022-04-28T04:36:46Z

@ianhi I think it does not matter much at the moment.

I've been using this to do experiments and definitely like this much less so it matters to me at least :). This is would be a decrease in usefulness to me and I would probably run a local branch re-integrating it instead of running off main.

I believe we can discuss about the gui "structure" once all the widgets will be ready (in a widget package). What do you think?

Totally agree, but that's also why I think changes like this should not be included in PRs like this one. Improving the widget and changing the UI layout are really orthogonal to each other so lumping them into one PR can make keeping track of things a bit confusing. I'd rather that we should determine the overall plan and implement it wholesale and consistently across all components.

ianhi · 2022-04-28T16:51:59Z

Thanks for being flexible @fdrgsp - really appreciate it :)

I'm now noticing an issue wiht the QCollapsibles - which may be an issue from superqt (so heads up @tlambert03 )
(I'm running superqt HEAD)

Stages don't fully collapse
If you collapse the tab above then the stage section goes wild

tlambert03 · 2022-04-28T16:53:06Z

yeah, I noticed that too. it is in superqt. and it came from the fix in https://github.com/napari/superqt/pull/72

:/

ianhi · 2022-04-28T16:56:26Z

That aside everything looks fine on the demo cam. I will try to try this out a real scope today or tomorrow (pending availability). Should we wait until that's fixed in superqt, or can we forge ahead assuming that superqt will be fixed before it's next release?

ianhi · 2022-04-28T18:59:40Z

Ok! I tried this out on a real scope and have the following notes:

The ordering of stage widgets isn't the same between scopes. We should maybe consider first sorting by stage type, then by name. On the TE2000 I got XY last rather than first. This isn't a big issue, but it owuld be nice to be consistent between scopes

important There is no way to trigger the polling on the Z or autofocus widgets
- For me the device drivers dont have callbacks, which means that these never update.

fdrgsp · 2022-04-28T19:30:18Z

The ordering of stage widgets isn't the same between scopes.

At the moment the order depends on the device name (alphabetical order). But I made the widgets draggable, so you can manually change the position. Do you think we need to do something different?

There is no way to trigger the polling on the Z or autofocus widgets

I will add the poll checkbox also to the z stages:)

ianhi · 2022-04-28T19:32:05Z

But I made the widgets draggable,

oooh neat. We should try to make that more discoverable. I would never have figured that out if you hadn't told me.

ianhi

This is a good user experience and a nice improvement! Can we merge and the iterate more (autofocus etc) in future PRs?

fdrgsp · 2022-04-29T13:18:32Z

@ianhi I added a line of code and now we always display the XY stages first and then the Z stages (widgets still draggable).

ianhi · 2022-04-29T16:50:40Z

@ianhi I added a line of code and now we always display the XY stages first and then the Z stages (widgets still draggable).

🤩

tlambert03 added 4 commits March 8, 2022 16:02

wip

1aad859

wip

f27d7cd

remove arrow icons

7a279e0

update styles

bce14d7

tlambert03 added 3 commits March 9, 2022 18:49

style

c06b6af

more refinements, remove from main window

64b5743

minor

686d22f

minor reorg

451bae1

ianhi reviewed Mar 14, 2022

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micromanager_gui/_core_widgets/_stage_widget.py Outdated Show resolved Hide resolved

fdrgsp mentioned this pull request Mar 17, 2022

Snap button widget #147

Merged

fdrgsp added 6 commits April 21, 2022 15:25

stage and illumination wdg buttons

9be0273

Merge remote-tracking branch 'upstream/main' into stage-widget

3072dc5

layout, description and snap_on_click

7bee0c9

snap_checkbox

42d4359

self._step = QDoubleSpinBox()

273c661

fix test

706e202

fdrgsp added 4 commits April 22, 2022 09:09

test

0bd5893

update test

8716507

_create_widget() and waitForDevice()

642879e

update test Z stage

f68200a

tlambert03 marked this pull request as ready for review April 28, 2022 00:01

tlambert03 commented Apr 28, 2022

View reviewed changes

ianhi reviewed Apr 28, 2022

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micromanager_gui/_core_widgets/_stage_widget.py Outdated Show resolved Hide resolved

fdrgsp added 2 commits April 27, 2022 23:57

minor update

c353bc3

mm_widget rename obj_wdg

ddb533a

fix _on_system_cfg name

b74246f

fdrgsp changed the title ~~[WIP] Stage widget~~ Stage widget Apr 28, 2022

fdrgsp added 2 commits April 28, 2022 00:27

add_mm_objectives_widget

6448ae2

_stage_wdg in create_gui

24aaa78

fdrgsp added 3 commits April 28, 2022 01:10

revert gui

af2f27d

Merge remote-tracking branch 'upstream/main' into stage-widget

fd86dab

remove events connection

638c383

poll QCheckBox for Z Stages

f074fbc

ianhi approved these changes Apr 29, 2022

View reviewed changes

fdrgsp added 2 commits April 29, 2022 08:50

add XY stages before Z

a36fac2

remove print

8abf461

tlambert03 merged commit e411f45 into main May 2, 2022

tlambert03 deleted the stage-widget branch May 2, 2022 19:56

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