Calling an imageJ1 .class plugin

#1

Hi,
I am trying to call the “Fit Polynomial” plugin that is available in ImageJ1, via the ImageJ macro node.

I tried copy/pasting the class file in the plugin folder used for ImageJ1 by KNIME, or first wrapping the class in a jar and then putting it into this folder but I dont manage to have it running.

WARN  ImageJ Macro         0:158      ImageJ Macro Error: null
WARN  ImageJ Macro         0:158      Problem occured in rowA02.tif : The specified macro has thrown an error while execution. Make sure that the used plugins are available in the selected IJ1 plugin folder! See KNIME Log for details! Missing cell has been inserted
WARN  ImageJ Macro         0:158      1 errors occurred while executing! See console log for details.

Are there some conditions on plugins to work ?

Attached the class (renamed to txt to be able to upload) and jar (renamed to zip) files.
and the line of macro code in the ImageJ node
run("Fit Polynomial", "x=2 y=2 mixed=0 shift");

FitPolynomial.zip (4,9 Ko)
Fit_Polynomial.txt (7,2 Ko)

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#2

Hi @l.thomas,

The best way is to point your KNIME-AP to an installation of ImageJ that has this plugin installed, (in the ImageJ1 integration settings page). This ensures all required dependencies are available.
https://imagej.nih.gov/ij/plugins/polynomial-fit/index.html Is that the plugin you are trying to run? I am not sure it will work as in headless mode, as it pops a gui dialog in the middle of its runtime.

It might be necessary to port this plugin to ImageJ2 first, to make it work correctly in KNIME-AP.

best,
Gabriel

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#3

Thanks for the quick reply.
I dont have more luck with the full ImageJ and it’s not this particular plugin, it’s the one shipped with ImageJ (Plugin>Filter>Fit Polynomial) which is not shipped with Fiji though, but it could be a similar GUI issue indeed.

Something to try at a hackathon eventually :wink:

Otherwise I think Cell Profiler has a similar one that I could call in KNIME too

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