TrakEM2 image Normalization script error

Posted by Ashwin on Jul 17, 2013; 9:03pm
URL: http://imagej.273.s1.nabble.com/TrakEM2-image-Normalization-script-error-tp5004014.html

Hi all,

I am trying to normalize images in a trakEM2 project to a fixed mean and Std. Here is what I have so far;


import ij.*;
import ij.process.*;
import ij.plugin.filter.*;
import ij.measure.Measurements;
import ini.trakem2.display.*;


// parameters
newVar = 44.0;
newMean = 144.0;

p = Display.getFront().getActive();
imp = p.getImagePlus();
ip = imp.getProcessor();

stats = ImageStatistics.getStatistics( ip, Measurements.MEAN + Measurements.STD_DEV, null);

fp = ip.convertToFloat();

        // subtract mean
        fp.subtract(stats.mean);
       
        // divide by std dev
        fp.multiply(1.0 / stats.stdDev);

        // multiply by the new variance
        fp.multiply( newVar );

        // add the new mean
        fp.add( newMean );

        // convert to byte
        ip = fp.convertToByte( false );

imp.setProcessor( ip );

At the end of the script the selected image does not update to the new values. In the BeanShell interpreter, I do not get any errors either. But the image remains the same. I checked to see if ip is actually getting updated to the new values and it is. I am not sure why this is happening.

Could someone help with this?

Thanks,
Ashwin