function A = convexpoly(XY,CXY);
% This routine accepts one or more matrices each with 2 columns (for
% x,y coordinates) and then computes convex polygons around them. 
% It computes the area of each polygon, creates a plot of it (or them)
% and computes the area of overlap of the any subset of polygons.
% Rulon Clark, Martin Schlaepfer, and Jack Bradbury. Cornell University,
% December 2000.
dyp=50;
np=17;
tp=['ko';'ro';'bo';'go';'mo';'co';'k+';'r+';'b+';'g+';'m+';'c+';'k*';'r*';'b*';'g*';'m*';'c*'];
tc=['k';'r';'b';'g';'m';'c'];
A=[];
NH=nargin;       				% Determines whether 1 or multiple files submitted
if NH==1
   	d1x=XY(:,1);    			%pulls out the x coordinates of matrix
   	d1y=XY(:,2);				%pulls out y coordinates of matrix
   	c1=convhull(d1x,d1y);		%pulls out the points on the periphery of the mcp
	cx=d1x(c1);
	cy=d1y(c1);
   	figure('NumberTitle','off','Name','Minimum Convex Polygon')
   	hold on
   	plot(d1x,d1y,'bo');          %plots the points on the figure
   	plot(cx,cy,'b');   %plots the lines connecting the points in c1
	xlabel('X axis');
   	ylabel('Y axis');
	hold off
   	A(1)=polyarea(cx,cy);
   	tx=num2str(A(1));
	disp(' ');
   	tx=['Area of minimum convex polygon: ' tx];
   	disp(tx);
   	disp(' ');
else
	[n,m]=size(XY);			 % Begin multi-input overlap routines
	NM=max(size(CXY));       % Get number of additional animals provided
	NN=NM+1;
	CH=cell(NN,1);
	disp(' ');
	dopts=1;
	rsp=input('1. Include points in plots (1) or not (2): ','s');
	if (rsp=='2')
		dopts=0;
	end
	disp('2. Area of minimum convex polygons: ');
	tx1=' File ';
	for i=1:NN
		tx=num2str(i);
		if (i==1)
			txlb=[tx1 tx];
			XY1=XY;
			figure('NumberTitle','off','Name','Minimum Convex Polygons');
			nfigs=1;
			hold on;
		else
			XY1=CXY{(i-1)};
			tx2=[tx1 tx];
			txlb=char(txlb,tx2);
		end
		dx=XY1(:,1);
		dy=XY1(:,2);
		c=convhull(dx,dy);         	% Find indices of hull coordinates
		cx=dx(c);
		cy=dy(c);
		A(i)=polyarea(cx,cy);      	% Store area of each polygon
		tx=['  ' txlb(i,:) ': ' num2str(A(i))];
		disp(tx);
		p=[cx cy];       	        % Get hull coordinates for this polygon
		CH{i}=p;				   	% Store polygon coordinates in cell array
		j=mod(i,6);
		k=mod(i,18);
		if (dopts==1)
			plot(dx,dy,tp(k,:));			%plots the points on the figure
		end
   		plot(p(:,1),p(:,2),tc(j));	%plots the lines connecting the points in p
	end
	xlabel('x axis');
	ylabel('y axis');
	disp(' ');
	input('   Click mouse to place UL of legend and hit <return>..');
	pt=get(gca,'CurrentPoint');
	pt=pt(1,1:2);
	ppt=pt;
	yl=get(gca,'YLim');
	legdy=(yl(2)-yl(1))/dyp;
	for j=1:NN
		tf=text(pt(1),pt(2),txlb(j,:));
		set(tf,'Color',tc(mod(j,6)));
		R=get(tf,'Extent');
		pt(2)=R(2)-legdy;
	end
	hold off
	xrange=get(gca,'XLim');
	yrange=get(gca,'YLim');
	disp(' ');
	disp('3. Overlap computations:');
	more=1;
	while (more==1)
		vv=[];
		ff=[];
		tfx='   Overlap for Files ';
		disp('   Select files to include (1) or exclude (2): ');
		nf=0;
		for i=1:NN
			tq=['     ' txlb(i,:) ': '];         
			rsp=input(tq,'s');
			if (rsp=='1')
				nf=nf+1;
				vv(nf)=i;
			end
		end
		disp(' ');
		tfx=[tfx ':'];
		OP=[];
		if (nf>1)
			OP=CH{vv(1)};
			tx=num2str(vv(1));
			tx=['Overlap for Files ' tx ', '];
			for i=2:nf
				j=vv(i);
				tx1=num2str(j);
				if (i<nf)
					tx=[tx tx1 ', '];
				else
					tx=[tx tx1];
				end
				if (~isempty(OP))
					ax=[];
					ay=[];
					DP=CH{j};
					in1=isinpoly(OP(:,1),OP(:,2),DP(:,1),DP(:,2));
					n1=find(in1==0);
					in2=isinpoly(DP(:,1),DP(:,2),OP(:,1),OP(:,2));
					n2=find(in2==0);
					if (isempty(n1))
						OP=OP;        % no change since OP inside DP
					elseif (isempty(n2))
						OP=DP;        % DP entirely inside OP thus DP is overlap
					else
						[ax ay]=polyints(OP(:,1),OP(:,2),DP(:,1),DP(:,2));
						OP=[ax ay];   % OP is fraction overlap between polygons
					end
				end
			end
			if (~isempty(OP))
				c=convhull(OP(:,1),OP(:,2));
				cx=OP(c,1);
				cy=OP(c,2);
				Area=polyarea(cx,cy);
				k=mod((NN+1),6);
				figure('NumberTitle','off','Name',tx');
				hold on
				nfigs=nfigs+1;
				wp=get(gcf,'Position');
				wp(1)=wp(1)+((nfigs-1)*np);
				wp(2)=wp(2)-((nfigs-1)*np);
				set(gca,'Xlim',xrange,'YLim',yrange);
				set(gcf,'Position',wp);
				tx=num2str(Area);
				disp('    Results:');
				tx=['     Overlap Area: ' tx];
				disp(tx);
				pt=ppt;
				for i=1:nf
					j=vv(i);
					k=mod(j,6);
					tf=text(pt(1),pt(2),txlb(j,:));
					set(tf,'Color',tc(k));
					R=get(tf,'Extent');
					pt(2)=R(2)-legdy;
					p=CH{j};
   					plot(p(:,1),p(:,2),tc(k));
					tx=num2str(100*Area/A(j));
					tlb=num2str(j);
					tx=['     Overlap % File' tlb ': ' tx];
					disp(tx);
				end
				k=mod((j+1),6);
				fill(cx,cy,tc(k));
				hold off
			else
				disp(' ');
				disp('   No overlap for these files.');
				disp(' ');
			end		
		end
		disp(' ');
		rsp=input('   Do another combination (1) or quit (2): ','s');
		if (rsp=='2')
			more=0;
		end
	end
end
disp(' ');