import java.math.*;
import java.util.*;

import neuroml.meta.*;
import neuroml.util.*;
import neuroml.morph.*;

import static java.lang.Math.*;

/**
 * This class calculates the total membrane surface area
 * of a set of segments belonging to a group named "dendrite_group".
 * 
 * @author mschachter
 *
 */
public class SACalculator
{	
	/**
	 * Compute the total membrane surface area for all the segments
	 * for a specified Morphology in a given region.
	 * 
	 * @param morph The Morphology
	 * @param groupName The group to tally the total SA of.
	 * @return The total membrane surface area (um^2)
	 * @throws Exception If something goes wrong.
	 */
	public static double computeTotalSA(Morphology morph, String groupName) throws Exception
	{			
		//get cell (index 0) from cell list
		Cell mossCell = morph.getCellList().get(0);
		
		//get list of cables
		List<Cable> cbls = mossCell.getCableList();
		
		//re-organize the cable list into a Map for easy lookup by id
		Map<BigInteger, Cable> cblMap = new HashMap<BigInteger, Cable>();
		for (Cable c : cbls)  cblMap.put(c.getId(), c);
		
		double totalSA = 0;
		
		//get list of segments, compute surface area of each
		//and add to the total
		List<Segment> segList = mossCell.getSegmentList();
		Point prox, dist;
		Cable c;
		double len;
		List<String> groups;
		for (Segment s : segList) {
			
			//make sure cable exists
			if (!cblMap.containsKey(s.getCable()))
				throw new Exception("Cable " + s.getCable().toString() + " not found!");
			
			//get associated cable and groups it belongs in
			c = cblMap.get(s.getCable());			
			groups = c.getGroup();
			
			//only add to total if the cable is in the right group
			if (groups.contains(groupName)) {				
				prox = s.getProximal();
				dist = s.getDistal();
				
				//compute length of segment
				len = sqrt( pow(abs(prox.getX()-dist.getX()), 2) +
							pow(abs(prox.getY()-dist.getY()), 2) +
							pow(abs(prox.getZ()-dist.getZ()), 2) );
				
				//add surface area to total
				totalSA += PI*.5*(prox.getDiameter() + dist.getDiameter())*
							sqrt(.5*(prox.getDiameter() - dist.getDiameter()) + pow(len,2));
			}
		}		
		return totalSA;
	}
	
	
	public static void main(String args[])
	{
		try {			
			//create NeuroMLConverter instance
			NeuroMLConverter nc = new NeuroMLConverter();
			
			//read morphology from file
			Morphology morph = nc.xmlToMorphology("MossyCell.xml");
			
			//compute the total surface area of the segments
			//that belong to the group "dendrite_group"
			double totalSA = SACalculator.computeTotalSA(morph, "dendrite_group");		
			System.err.println("Total membrane surface area: " + totalSA + " um^2");
		} catch (Exception e) {
			e.printStackTrace(System.err);
		}
	}
	
}