====== Passing stdout to ImageJ / Fiji ======


In case you want to pass stdout to ImageJ macro headlessly, use [[https://imagej.nih.gov/ij/developer/macro/functions.html#getArgument|getArgument]]. 

For example, create a test macro like this and save it as test.ijm:
<sxh>
tt = getArgument();
print(tt);
</sxh>

Then the bash command for passing stdout to this macro headlessly is:
<sxh>
echo "hello" | (read arg; fiji --headless -macro test.ijm "$arg")
</sxh>

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

The command could also be
<sxh>
echo "hello" | (read arg; fiji -batch test.ijm "$arg")
</sxh>

but it's slower somehow.