BeanShell05-3.bsh

/**
 * BeanShell05-3.bsh
 * IJ BAR: https://github.com/tferr/Scripts#scripts
 * *************************************************
 * 5.3 Scripting using BAR libs III
 * *************************************************
 */

// <<Enough with this silly SMA method. I need some real
// math. I want... a Gaussian fitted to all my profiles!>>
// OK! That will be easy. Here is what we have to do:
//
//   1. Create a method for the new functionality
//   2. Place it in a lib
//   3. Instruct Smoothed_Plot_Profile.bsh to use the new
//      method


// STEP 1:
// I propose using the built-in CurveFitter of ImageJ1
// (but go ahead and use one of Fiji's third-party
// libraries if you prefer otherwise). Something like:

/** This method returns a gaussian fit from X,Y data */
double[] getGaussian(double[]xvalues, double[] yvalues) {
	import ij.measure.CurveFitter;	// http://javadoc.imagej.net/ImageJ1/index.html?ij/measure/CurveFitter.html
	cf = new CurveFitter(xvalues, yvalues);
	cf.doFit(CurveFitter.GAUSSIAN);
	fittedValues = new double[xvalues.length];
	for (i=0; i<xvalues.length; i++)
		fittedValues[i] = cf.f(xvalues[i]);
	return fittedValues;
}

// STEP 2:
// Now, let's create a shiny new lib. In the future, BAR
// will have a command for this, but meanwhile we'll do
// it the old fashion way:
// We will added to the existing BARlib.bsh file, right
// below the SMA method (getSimpleMovingAverage()).
// Cannot find it BARlib.bsh? Don't worry press <<Run>>
// and I'll open it for you:
import bar.Utils;
Utils.openScript(Utils.getLibDir(), "BARlib.bsh");