How can I solve an exception error for Batch image analysis using ImageJ - imagej

Question

I am fairly new at ImageJ, but i managed beforehand to analyze aprox 720 images using the Batch->Macro feature, without any issues (I used the directionality plugin).
Now after a couple of days I am trying to use the Color Profiler plugin, which works perfectly fine when doing individual images, but when I use the same batch macro feature it gives me an Exception error for each image (I will attach the whole error).
Would you know a way to solve this issue?
I tried doing it both in classical ImageJ and also the FIJI version, but it seems to give the same issue.

Answer 1

I can replicate the problem and it seems as if the plugin needs to actually display the image which is not the case with batch processing. I didn't investigate the source code of this rather old plugin, but here is an ImageJ-macro that should do what you want (with some flickering):
//imagej-macro "batchColorProfiler" (Herbie G., 07. Jan. 2023)
requires( "1.54a" );
close("*");
run("Set Measurements...", " redirect=None decimal=2");
Dialog.create("Define input and output folder.");
Dialog.addDirectory("Where are your images?", getDir("file"));
Dialog.addDirectory("Where to store the plots and results?", getDir("file"));
Dialog.show();
in=Dialog.getString();
out=Dialog.getString();
f=getFileList(in);
for ( i=0; i<f.length; i++ ) {
if ( endsWith(f[i], "tif") ) {
path=in+f[i];
open(path);
cp(File.getNameWithoutExtension(path),out);
}
}
exit();
//
function cp(nme,dir) {
makeLine( 0, 20, 200, 120 ); // selection
run("Color Profiler");
IJ.renameResults(nme+"_results");
Table.save(dir+nme+"_results.csv");
close(nme+"_results"); // close table
nme=getTitle();
save(dir+nme+".tif");
close(); // close plot
close(getTitle()); // close image
}
//imagej-macro "batchColorProfiler" (Herbie G., 07. Jan. 2023)
Paste the macro code to an empty macro window
(Plugins >> New >> Macro) and run it.