Re: run a Fiji(imageJ) script from terminal on a macOS to process images.

Posted by Curtis Rueden on May 22, 2018; 2:48pm
URL: http://imagej.273.s1.nabble.com/run-a-Fiji-imageJ-script-from-terminal-on-a-macOS-to-process-images-tp5020694p5020697.html

Note that this question was also posted on the ImageJ Forum here:

   http://forum.imagej.net/t/set-imagej-directory-from-terminal/11060

For the archives: you can get the current working directory from a macro as
follows:

   cwd = call("java.lang.System.getProperty", "user.dir");

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Mon, May 21, 2018 at 6:18 PM, Yao <[hidden email]> wrote:

> 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
>

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