Map active layer to current ij window

[gselzer]

When we are running in interactive mode, it would be nice to have better support for original ImageJ plugins when the ImageJ UI is not shown. To that end, if ImageJ is enabled but the ImageJ UI is not visible, we can set the active ImagePlus to the active napari layer, to mimic the GUI components needed.

The current improvements allow you to call an inplace PlugIn taking one input, and synchronize the output back into the active napari layer.

There are, at time of writing, some open questions/bugs, that make this a draft PR:

1. The Gaussian Blur... command can cause napari-imagej to hang on shutdown. A stacktrace dump shows a non-daemon thread pool is still active, so it may be coming from here
2. We need to figure out how to close all of the relevant Java-side images when we perform something like this. How do we ensure that all created ImageDisplays/ImagePluses created through this code path are deleted after we're done? Otherwise, the created images can affect the execution of other ImageJ functionality?
3. How do we replicate this functionality for multiple input ImagePluses? @ctrueden mentioned something about proxies, but I'm naive about this.

This would close #203

[ctrueden]

@ctrueden mentioned something about proxies, but I'm naive about this.

Unfortunately, you can only make a Proxy of an interface, and ImagePlus is not an interface.

My current thinking is that, maybe, we could always wrap all napari image layers into Java (to Dataset and then via the legacy map to ImagePlus as well), whenever any Java-side functionality is invoked from the napari-imagej widget. However, these wrapped images should not be shown, but merely exist hidden, even while in interactive mode, until they are explicitly shown via some code path. (e.g. the user clicks the "transfer to ImageJ" button, or a script calls ui.show(dataset) or imp.show()). I am skeptical that this idea would actually work in practice—I have some concerns, e.g. "what about when the user runs a plugin via the ImageJ GUI? should that also proactively sync napari layers before execution? it could..."—but maybe it's worth a shot?

[codecov-commenter]

Codecov Report

Patch coverage: 61.72% and project coverage change: -0.77 ⚠️

Comparison is base (6e48793) 89.81% compared to head (d5eabbe) 89.05%.

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Additional details and impacted files

@@            Coverage Diff             @@
##             main     #205      +/-   ##
==========================================
- Coverage   89.81%   89.05%   -0.77%     
==========================================
  Files          45       47       +2     
  Lines        4242     4421     +179     
==========================================
+ Hits         3810     3937     +127     
- Misses        432      484      +52     

Impacted Files	Coverage Δ
src/napari_imagej/utilities/_module_utils.py	77.08% <58.20%> (-6.32%)	⬇️
src/napari_imagej/java.py	81.85% <78.57%> (-0.22%)	⬇️

... and 7 files with indirect coverage changes

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[gselzer]

So, while this works great in limited scenarios, there are too many issues with original ImageJ plugins running in the napari UI that I'm doing to dismiss this effort, in favor of #207.