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RT @haesleinhuepf: Hi #BioImageAnalysis #SciTweeps, how many image and/or data analysis books do you own? 📚🙃 If you have a favorite book,…
About 7 hours, 31 mins ago by: Kota Miura (@cmci_)

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RT @ahklemm: TissUUmaps 3.1 is here! 🥳 Try it out, take a tour, join our webinar ! #bioimageanalysis #TissUUmaps Webinar: https://t.co/Xzj
About 7 hours, 31 mins ago by: Kota Miura (@cmci_)

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RT @TheSquishyLab: Excited to release our latest work, led by @hbozhao in collaboration with our friend Andrej Košmrlj! In this preprint…
About 3 days, 13 hours ago by: Kota Miura (@cmci_)

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Though there is a plugin solution by Niko (https://t.co/vBqvTMSRPw ) another solution can be to add new org.scijava… https://t.co/EENzESBAxv
About 3 days, 17 hours ago by: Kota Miura (@cmci_)

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I mostly have used print, IJ.log, and System.out.println in my Jython script for logging but recently encountered… https://t.co/3LTrUG9ucM
About 3 days, 17 hours ago by: Kota Miura (@cmci_)

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RT @JCellBiol: Image-based pooled whole-genome #CRISPRi screening for subcellular phenotypes, developed by @gil_kanfer @youle_rj @LabYoule
About 3 days, 21 hours ago by: Kota Miura (@cmci_)
documents:20190416ijmacro_passingarguments

Passing stdout to ImageJ / Fiji

In case you want to pass stdout to ImageJ macro headlessly, use getArgument.

For example, create a test macro like this and save it as test.ijm:

tt = getArgument();
print(tt);

Then the bash command for passing stdout to this macro headlessly is:

echo "hello" | (read arg; fiji --headless -macro test.ijm "$arg")

There could be more sophisticated ways, but the command above does work. For the command “fiji” to work, it should be set in your .profile or .bash_profile

alias fiji='/Applications/Fiji.app/Contents/MacOS/ImageJ-macosx'
… you need to change the path above according to the place where your Fiji resides.

The command could also be

echo "hello" | (read arg; fiji -batch test.ijm "$arg")

but it's slower somehow.

documents/20190416ijmacro_passingarguments.txt · Last modified: 2019/04/16 12:46 by kota