Posted by
Jerome Mutterer-3 on
May 22, 2018; 7:20am
URL: http://imagej.273.s1.nabble.com/run-a-Fiji-imageJ-script-from-terminal-on-a-macOS-to-process-images-tp5020694p5020696.html
Hi,
You could pass the desired directory to your macro as an argument:
/Users/jmutterer/Downloads/Fiji.app/Contents/MacOS/ImageJ-macosx --headless
-macro ~/Desktop/test.ijm /Users/jmutterer/Desktop/myDir/
will print: /Users/jmutterer/Desktop/myDir/
using this example macro:
// test.ijm
dir=getArgument();
print (dir);
The argument is a string, so you can't use tilde expansion, which is a
system feature, you'll have to use full path.
(unless you include something like dir = replace (dir, '~', exec ('echo
~')); )
Jerome
2018-05-22 1:18 GMT+02:00 Yao <
[hidden email]>:
> I need to run a Fiji(imageJ) script from terminal on a macOS. Using the
> code
> below.
>
> /Applications/Fiji.app/Contents/MacOS/ImageJ-macosx --headless -macro
> ~/desktop/testing.ijm.ijm
> And the Fiji script I need to run is
>
> dir = getDirectory("Where I need help");
> run("Image Sequence...", "open=dir");
> path=dir+"needsave.avi";
> run("AVI... ", "compression=JPEG frame=5 save=&path");
> close();
> However I want the directory to be the current location in terminal. For
> example:
>
> MYs-MBP:~ csh;
> [MYs-MBP:~] cd desktop/test/test2
> [MYs-MBP:~/desktop/test/test2]
> /Applications/Fiji.app/Contents/MacOS/ImageJ-macosx --headless -macro
> ~/desktop/testing.ijm.ijm
> and therefore I will process everything in test2 by using the Fiji script I
> write.
>
> I tried to use getDirectory("current"), but it kept saying no image, while
> "desktop/test/test2" is the right place.
>
>
>
> --
> Sent from:
http://imagej.1557.x6.nabble.com/>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
--
Jerome Mutterer
CNRS - Institut de biologie moléculaire des plantes
12, rue du Général Zimmer
67084 Strasbourg Cedex
www.ibmp.cnrs.fr
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