Convert-TWS-probabilities-to-segmentation.bsh

import ij.IJ;
import ij.ImagePlus;
import ij.ImageStack;
import ij.process.FloatProcessor;

// assume probability image as the currently selected one
probs = IJ.getImage();

// read image dimensions
width = probs.getWidth();
height = probs.getHeight();
nSlices = probs.getNSlices();
nClasses = probs.getNChannels();

// create stack to store segmentation
segmentation = new ImageStack( width, height );

// for each slice
for( s = 1; s <= nSlices; s++ )
{
	probs.setSlice( s );
	probStack = probs.getImageStack();

	segSlice = new FloatProcessor( width, height );
	
	for( x=0; x<width; x++ )
	  for( y=0; y<height; y++ )
	  {
	  	max = 0f;
	  	cIndex = 0;
	  	// select class with higher probability
	  	for( c=0; c<nClasses; c++ )
	  		if( probStack.getVoxel( x, y, c ) > max )
	  		{
	  			max = probStack.getVoxel( x, y, c );
	  			cIndex = c;
	  		}
	  	segSlice.setf( x, y, (float) cIndex );
	  }
	  segmentation.addSlice( "", segSlice ); 
}

// create and display segmentation image
result = new ImagePlus( "Thresholded probabilities", segmentation );
result.show();