0

I am trying to write a macro for ImageJ that processes the images in the specified folder through the OrientationJ Vector Field plugin, and then saves the outputted results tables into a separate folder. The issue is that when I run the macro, the OrientationJ Vector Field's dialogue box pops up however the results are not saved anywhere. I am not sure what I am doing incorrectly, and it would be much appreciated if someone could help me. The code for my macro is shown below, thanks.

dir1 = getDirectory("Choose Source Directory ");
dir2 = getDirectory("Choose Destination Directory ");
list = getFileList(dir1);
setBatchMode(true);
for (i=0; i<list.length; i++) {
    showProgress(i+1, list.length);
    filename = dir1 + list[i];
    if (endsWith(filename, "tif")) {
        open(filename);
        run("8-bit");
        run("OrientationJ Vector Field");
        run("OrientationJ Vector Field", "tensor=2.0 gradient=0 radian=on vectorgrid=50 vectorscale=80.0 vectortype=0 vectoroverlay=off vectortable=on ");
        saveAs("Results", dir2+list[i]+".csv");
        close();
    }
 }
Charlie M.
  • 1
  • 2

2 Answers2

0

Did you try using another ImageJ-plugin, such as "Orientations_"? https://www.gluender.de/Miscellanea/MiscTexts/UtilitiesText.html#Gl-2020-1 ImageJ-Macro call: run( "Orientations ", "local diameter=16 indicator" );

Dharman
  • 30,962
  • 25
  • 85
  • 135
Herbie
  • 143
  • 5
  • Thanks for the response. I don't want to use a different plugin since OrientationJ is my preferred orientation analysis tool. Do you know how to get the macro to save the .csv results? I have seen online that there are others with similar issues, but haven't seen a solution yet. – Charlie M. Nov 29 '21 at 15:43
  • If you have the table displayed use: nme = Table.title; path = "/Users/yourName/Downloads/"; Table.save( path+nme+".csv" ); – Herbie Nov 29 '21 at 16:34
0

Update: Issue has been resolved by manually updating OrientationJ to 2.0.5 (from May 2020). In the older versions, the vector field did not work from a macro. The latest version can be found on the OrientationJ website: http://bigwww.epfl.ch/demo/orientationj/

Fiji does not have the latest version of O.J. included and so the latest version needs to manually be installed.

Charlie M.
  • 1
  • 2