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Add callback mechanism for GUI mode #301

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Add callback mechanism for GUI mode #301

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@elevans elevans commented Mar 4, 2024

Update

Update I wanted to preserve the original text (below) for this PR as its relevant to the goals (i.e. create a better experience for macOS users). With the awesome work that @ctrueden has done with jaunch we now have a way to actually support interactive mode on macOS. This PR introduces the following new elements and also paves the way for interactive mode on macOS via jaunch.

This PR adds:

  • A "global gateway" which enables other projects to hook into a already running instance of imagej (e.g. napari-imagej).
  • A callback mechanism which enables users to register functions with when_imagej_starts(). This can enable some GUI related workflows on macOS (a kind of limited psuedo-interactive mode). See notebook 5 section 5.2 for the relevant documentation. This callback mechanism is not compatible with napari.
  • An override flag to the main init method. This flag will enable users/developers to bypass initialization checks/blocks we've put in place to stop unsupported/application breaking behavior -- mainly interactive mode on macOS. To test interactive mode on macOS:
    • Install/setup jaunch.
    • Modify jaunch's fiji.py file. Add the override=True flag to ij = imagej.init(app_dir, mode="interactive") on line 72.
    • Jaunch Fiji with ./fiji-macos-universal -i --python.

Some other relevant information: Based on what I now understand about Python's threading system and some experimentation on macOS/Linux with jaunch, Python will always think its in a main thread. There is no way (from what I gather) to know if a particular Python instance was started with/in a pthread. Instead, threads that are spawned from an already running instance, say in a function that creates threads, are identified as "non-main" thread. This is obvious, but it would have been cool if there was a way to know about how the current instance was started.

Original text

Until we can find a true interactive mode for macOS (see #298) this callback mechanism gives macOS users the ability to run their desired Python functions before the REPL is locked by the AppHelper.runConsoleEventLoop().

Here's how you register a callback with PyImageJ:

import imagej

# register a function that takes no params
imagej.when_imagej_starts(lambda: func())

# register an ImageJ function (if a parameter is present, assume its ij)
imagej.when_imagej_starts(lambda ij: ij.RoiManager.getRoiManager())

# initialize ImageJ in GUI mode
ij = imagej.init(mode='gui')

Unfortunately this callback strategy doesn't work with napari. Registering the callback lambda: napari.Viewer() results in this segfault:

(pyimagej) loci@dyn-144-92-48-223 Documents % python test.py
WARNING: package sun.awt.X11 not in java.desktop
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by net.imagej.legacy.IJ1Helper (file:/Users/loci/.jgo/net.imagej/imagej/RELEASE/28b74e6959b0634f2a8e10c27afe06e7039fb4a0dc582d9746d028ba40e5bd04/imagej-legacy-1.2.1.jar) to method com.apple.eawt.Application.getApplication()
WARNING: Please consider reporting this to the maintainers of net.imagej.legacy.IJ1Helper
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGILL (0x4) at pc=0x00007ff8116c90c2, pid=2487, tid=42247
#
# JRE version: OpenJDK Runtime Environment Zulu11.70+15-CA (11.0.22+7) (build 11.0.22+7-LTS)
# Java VM: OpenJDK 64-Bit Server VM Zulu11.70+15-CA (11.0.22+7-LTS, mixed mode, tiered, compressed oops, g1 gc, bsd-amd64)
# Problematic frame:
# C  [libdispatch.dylib+0x50c2]  _dispatch_assert_queue_fail+0x66
#
# No core dump will be written. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# An error report file with more information is saved as:
# /Users/loci/Documents/hs_err_pid2487.log
#
# If you would like to submit a bug report, please visit:
#   http://www.azul.com/support/
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#
zsh: abort      python test.py
(pyimagej) loci@dyn-144-92-48-223 Documents % 

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codecov bot commented Mar 4, 2024

Codecov Report

Attention: Patch coverage is 78.39506% with 35 lines in your changes missing coverage. Please review.

Project coverage is 77.48%. Comparing base (a173d5a) to head (a833767).
Report is 14 commits behind head on main.

Files Patch % Lines
src/imagej/__init__.py 43.33% 17 Missing ⚠️
tests/test_legacy.py 68.57% 11 Missing ⚠️
tests/test_fiji.py 12.50% 7 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #301      +/-   ##
==========================================
- Coverage   77.81%   77.48%   -0.33%     
==========================================
  Files          16       17       +1     
  Lines        2010     2034      +24     
==========================================
+ Hits         1564     1576      +12     
- Misses        446      458      +12     

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@elevans elevans force-pushed the global-gateway branch 3 times, most recently from 15e8366 to dbb930c Compare May 10, 2024 16:32
@elevans elevans force-pushed the global-gateway branch 3 times, most recently from 884c7df to 3f0188b Compare May 28, 2024 02:13
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elevans commented Jun 10, 2024

Just fyi all PyImageJ builds will fail for python 3.12 until labeling=0.1.14 no longer pins pillow <10 in the conda-feedstock recipe. See this issue.

Edit: This is no longer an issue with labeling 0.1.14's release.

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In general, I'm excited about these changes @elevans!

I'm a bit wary about that new override parameter on the initialization function, though - let's discuss below.

src/imagej/__init__.py Show resolved Hide resolved
conftest.py Outdated Show resolved Hide resolved
src/imagej/__init__.py Outdated Show resolved Hide resolved
ctrueden and others added 8 commits July 15, 2024 10:17
Otherwise, there is no way to access it from other threads.

This may be useful for scenarios like napari-imagej, where access to
Python scripting is available from threads other than the blocked one.
This is an internal variable, not intended as public API.
It doesn't need to be "ij_wrapper" or "ij_fixture".
It's OK to be ij!
This test checks that functions registered via
when_imagej_starts get called as part of imagej.init.
This commit adds section 5.2 to the "Convenience methods of
PyImageJ" that describes how to use the when_image_starts
callback mechanism.
This commit introduces a check to determine if the current
running thread is the main thread. If True, then we continue to block
interactive mode on macOS (it is not possible to share the main thread
with GUI event loop needed for the ImageJ GUI). If False, then the
current thread is *not* the main thread (e.g. a jaunched session) and
interactive mode for macOS can proceed.
@elevans elevans force-pushed the global-gateway branch 2 times, most recently from fda4992 to d0eed46 Compare July 15, 2024 15:45
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elevans commented Jul 15, 2024

Thanks @gselzer for your review! It made it sooo much better! I addressed all your comments. Ready to merge?

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I love the new changes!

...unfortunately, I requested a couple new things 😅

tests/test_callbacks.py Outdated Show resolved Hide resolved
src/imagej/__init__.py Outdated Show resolved Hide resolved
src/imagej/__init__.py Outdated Show resolved Hide resolved
Use a more descriptive attribute name and value for
when_imagej_starts() test.
This commit adds the pthread library loading exception to
the logger and assumes that the current thread is the main
thread if no pthread library is found.
tests/test_callbacks.py Outdated Show resolved Hide resolved
src/imagej/__init__.py Outdated Show resolved Hide resolved
The default here should be None, not True, otherwise
this test does not actually test for the `_testing`
attribute value.
This commit improves how we clean up the gateway once the UI
is closed in gui mode. Although it is highly unlikely, it is possible
for a user to run into a NameError when deleting the gateway if a user
enters gui mode but is NOT on macos and successfully exits the gui
without crashing the session (see next below, this requires some playing
around). This is resolved by assigning the gateway to None, ensuring
there is *something* to delete if no gateway object is assigned.

This commit also adds an additional check for a running JVM instance
when in gui mode on non-macos systems. This prevents a
`jpype._core.JVMNotRunning: Java Virtual Machine is not running`
error that is produced when the imagej ui visbility is polled but
is no longer available because the JVM has been shut down via
gui interactions.
@elevans elevans requested a review from ctrueden October 17, 2024 17:20
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3 participants