if you still need here is an implementation of one normalization method
You must compile the plugin before use.
To use the plugin:
1.- Open a stack or sequence
2.- select a good ilumination frame to use as reference
3.- run the plugin
The plugin
import ij.IJ;
import ij.ImagePlus;
import ij.ImageStack;
import ij.plugin.filter.PlugInFilter;
import ij.process.FloatStatistics;
import ij.process.ImageProcessor;
import utils.IOUtils;
/**
*
* @author <a ref ="
[hidden email]"> Zian Fanti Gutierrez<a/>
* @version 0.1
*/
public class Normalize_Ilumination_1 implements PlugInFilter {
private ImagePlus imp;
private int currentFrame;
public int setup(String arg0, ImagePlus imp) {
if (imp == null)
IJ.noImage();
this.imp = imp;
currentFrame = imp.getCurrentSlice();
return DOES_8G;
}
public void run(ImageProcessor ip) {
ImagePlus out = new ImagePlus(IOUtils.windowName("Normalized
Ilumination"),
normalizeIlumination(imp.getImageStack(), currentFrame));
out.show("Normalize Ilumination Done");
}
/**
* Return a new <code>ImageStack</code> with the normalized
ilumination. The
* return stack is generated from original <code>stack</code>
*
* @param referenceIndex, the index of the frame in the original
<code>stack</code>
* which is used as reference frame.
* @return Return a new <code>ImageStack</code> with the normalized
ilumination.
*
* @Article RICHARD, J., RADKE, SRINIVAS, A., OMAR, A.K. and
BADRINATH, R., 2005,
* Image Change Detection Algorithms: A Systematic Survey, IEEE
Transactions
* on Image Processing, 14(3), pp.294-307.
*/
public ImageStack normalizeIlumination(ImageStack stack, int
referenceIndex) {
int size = stack.getSize();
int width = stack.getWidth();
int height = stack.getHeight();
if (size == 1) {
return stack;
}
ImageStack resultStack = new ImageStack(width, height);
double factor = 0;
if (referenceIndex < 0 || referenceIndex > size) {
throw new NullPointerException();
} else {
ImageProcessor tmpImage = null;
ImageProcessor referenceImage =
stack.getProcessor(referenceIndex).convertToFloat();
FloatStatistics stats = new FloatStatistics(referenceImage);
double RIstdv = stats.stdDev;
double RIMean = stats.mean;
double tmpSTDV = 0;
double tmpMean = 0;
for (int i = 1; i <= size; i++) {
tmpImage = stack.getProcessor(i).convertToFloat();
stats = new FloatStatistics(tmpImage);
tmpSTDV = stats.stdDev;
tmpMean = stats.mean;
//calculate normalizated image
factor = ((RIMean * tmpSTDV) - (tmpMean * RIstdv)) / tmpSTDV;
double f1 = RIstdv / tmpSTDV;
tmpImage.multiply(f1);
tmpImage.add(factor);
resultStack.addSlice("normalized" + i,
tmpImage.convertToByte(false));
IJ.showProgress(i, size);
}
}
return resultStack;
}
}
Locked
