59 lines (46 with data), 1.9 kB

/*
 * Transform histogram of an image to match another image
 *
 * EXAMPLE:
 * >> ~/Applications/Fiji.app/ImageJ-linux64 --java-home /usr/lib/jvm/java-8-openjdk-amd64 \
        --headless histogram-matching.bsh \
        deformed-bridge.png bridge.png histogram-matched-deformed-bridge.png
 *
 * Copyright (C) 2019 Ignacio Arganda-Carreras <ignacio.arganda@ehu.eus>
 */

import ij.IJ;
import histogram2.HistogramMatcher;
import ij.process.StackStatistics;
import ij.ImageStack;
import ij.ImagePlus;

if( bsh.args.length < 3 )
{
	IJ.log( "histogram-matching.bsh" );
	IJ.log( "USAGE: histogram-matching.bsh referenceImage imageToTransform outputImage" );
	IJ.log( "       'referenceImage' path to reference image" );
	IJ.log( "       'imageToTransform' path to the image to transform" );
	IJ.log( "       'outputImage' path to output image file to be created (with the histogram transformed)" );
	return;
}

referenceImage = new ImagePlus( bsh.args[ 0 ] );
imageToTransform = new ImagePlus( bsh.args[ 1 ] );
outputImage = new File( bsh.args[ 2 ] );

stats1 = new StackStatistics( imageToTransform );
stats2 = new StackStatistics( referenceImage );

hist1 = stats1.histogram; // ip1.getHistogram();
hist2 = stats2.histogram; // ip2.getHistogram();

matcher = new HistogramMatcher();
newHist = matcher.matchHistograms(hist1, hist2);

//ip1.applyTable(newHist);
//imageToTransform.setProcessor(ip1);

is = new ImageStack( imageToTransform.getWidth(), imageToTransform.getHeight() );

boolean isStack = imageToTransform.getImageStackSize() > 1;

for( n=1; n<=imageToTransform.getImageStackSize(); n++)
{
	ip = imageToTransform.getImageStack().getProcessor( n );
	ip.applyTable(newHist);
	label = isStack ? imageToTransform.getImageStack().getSliceLabel( n ) : "";
	is.addSlice( label, ip );
}

imageToTransform.setStack( is );

IJ.save( imageToTransform, outputImage.getAbsolutePath() );