average-0masked-stack.bsh

import ij.*;
import ij.process.*;

stack = IJ.getImage().getStack();
ip = IJ.getImage().getProcessor().createProcessor( stack.getWidth(), stack.getHeight() );
imp = new ImagePlus( "masked mean", ip );
imp.show();

for ( x = 0; x < stack.getWidth(); ++x )
{
	for ( y = 0; y < stack.getHeight(); ++y )
	{
		double s = 0;
		int n = 0;
		for ( z = 0; z < stack.getSize(); ++z )
		{
			float v = stack.getProcessor( z + 1 ).getf( x, y );
			if ( v > 0 )
			{
				s += v;
				++n;
			}
		}
		if ( n > 0 )
		s /= n;
		ip.set( x, y, ( int )Math.round( s ) );
	}
	imp.updateAndDraw();
}