CellProfiler-plugins icon indicating copy to clipboard operation
CellProfiler-plugins copied to clipboard

the predict plugin does not run in gui

Open karhohs opened this issue 7 years ago • 5 comments

The predict plugin that incorporates ilastik into a module does not work when running a pipeline from the gui. There is no error displayed. Instead, the program just hangs.

However, the predict plugin does work in headless mode and also in test-mode within the gui.

karhohs avatar Aug 17 '17 16:08 karhohs

I suspect this has something to do with CellProfiler's handling of threading ("workers") interfering with the subprocess call. I notice that when I hit "Stop Analysis" it seems that ilastik finally gets called. Setting maximum workers to 1 has no effect.

Note this only seems to affect Windows.

mcquin avatar Nov 14 '17 17:11 mcquin

A CellProfiler forum thread has additional discussion regarding this issue: http://forum.cellprofiler.org/t/cp3-0-0-hangs-in-analysis-mode-with-custom-plugin-running-subprocess-call/6322/3

karhohs avatar Jul 11 '18 16:07 karhohs

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/predict-py-in-cellprofiler/43715/2

imagesc-bot avatar Oct 07 '20 11:10 imagesc-bot

Has anyone found a work around for this? Happy to help fix the bug if I can. Thanks.

muddywellyboots avatar Oct 07 '20 12:10 muddywellyboots

Still looking for a workaround. Has anyone had any luck?

matthewjamesthomas avatar Apr 29 '21 22:04 matthewjamesthomas