How can I stop ImageJ's Non-Local Means denoising algorithm from making all the edges in an image orange?

Question

My code for running the ImageJ plugin is as follows:

import ij.IJ;
import ij.ImagePlus;
import ij.io.FileSaver;
import ij.plugin.PlugIn;


public class Test implements PlugIn {

public static void main(String[] args) {

    Test test = new Test();
    test.run("Denoise.ijm");

}

@Override
public void run(String arg0) {
    String directory = "C:\\Users\\Speedy Octopus\\Desktop\\10Cover Shots\\10.JPG";

    ImagePlus imp = IJ.openImage(directory);
    FileSaver fileSaver = new FileSaver(imp);

    System.setProperty("plugins.dir", "C:\\Users\\Speedy Octopus\\Downloads\\ij150-win-java8\\ImageJ\\plugins");
    IJ.run(imp, "Non-local Means Denoising", "sigma=5 smoothing_factor=1");
    fileSaver.saveAsJpeg("C:\\Users\\Speedy Octopus\\Desktop\\10Cover Shots\\10edited.JPG");
}
}

After running the remove noise macro, all of the edges of my images are turned orange. how can I stop this from happening?

Edit: This also happens when I use the actual ImageJ.jar program

Answer 1

I needed to split the channels first, there is a bug in the plugin when working with a composite.

I ended up fixing it working with the following code in my run method:

    ImagePlus imp = IJ.openImage(directory);
    FileSaver fileSaver = new FileSaver(imp);

    System.setProperty("plugins.dir", LocalMethods.readFile("NonLocalMeansDir").get(0));

    ImagePlus[] channels = ChannelSplitter.split(imp);
    String[] channelTitles = new String[3];
    for (int i = 0; i < channels.length; i++) {
        ImagePlus channel = channels[i];
        channelTitles[i] = channel.getTitle();
        IJ.run(channel, "Non-local Means Denoising", "sigma=5 smoothing_factor=1");
    }
    IJ.run(imp, "Merge Channels...", "c1=[" + imp.getTitle() +  " (" + channelTitles[0] + ") " + "] c2=[" + imp.getTitle() +  " (" + channelTitles[1] + ") " + "] c3=[" + imp.getTitle() +  " (" + channelTitles[2] + ") " + "] create");
    IJ.saveAs("jpeg", directory);