Certain RankFilters() operations never report system exit, hang indefinitely

[jaredbrewer]

I have recently been working with both pyimagej and FIJI/ImageJ and have identified an issue that is common to both and persists regardless of how I run it.

PyImageJ script:

import imagej, scyjava

ij = imagej.init("sc.fiji:fiji", mode = "interactive")

imp = ij.IJ.openImage("http://imagej.net/images/Rat_Hippocampal_Neuron.zip")
ij.IJ.run(imp, "Despeckle", "stack")
ij.IJ.saveAs(imp, "Tiff", "Rat_Hippocampal_Neuron_processed.tif")

I would note that the preferred (at least to me) RankFilters = scyjava.jimport("ij.plugin.filter.RankFilters"); RankFilters.rank(imp.getProcessor(), 1.0, 4) does not work due to challenges with translating python int/float values to a correct Java double

Jython version:

from ij import IJ, ImagePlus
from ij.plugin.filter import RankFilters
import sys

imp = IJ.openImage("http://imagej.net/images/Rat_Hippocampal_Neuron.zip")
RankFilters().rank(imp.getProcessor(), 1.0, 4)
# IJ.run(imp, "Despeckle", "stack") # Also does not work...
IJ.saveAs(imp, "Tiff", "Rat_Hippocampal_Neuron_processed.tif")

Run with Fiji.app/ImageJ-linux64 --ij2 --headless --run script.py

I would note that I am running both contexts with Xvfb, which works fine with almost any other kind of operation I can think of performing.

If anybody has any insight on this topic or if this is truly a bug, that would be appreciated. Running on the latest versions of everything.

[jaredbrewer]

I note the existence of this related issue: imagej/ImageJ#118

I gather that this issue is the result of unterminated threads created by the threadPoolExecutor in the JVM. I would consider this to be suboptimal behavior for use in a non-interactive environment.