Index: /issm/trunk-jpl/src/m/mesh/meshintersect2d.m
===================================================================
--- /issm/trunk-jpl/src/m/mesh/meshintersect2d.m	(revision 25630)
+++ /issm/trunk-jpl/src/m/mesh/meshintersect2d.m	(revision 25630)
@@ -0,0 +1,89 @@
+function indices=meshintersect2d(x,y,xs,ys,varargin)
+%MESHINTERSECT - return indices (into x,y) of common values between (x,y) and (xs,ys). 
+%  i.e: x(index)=xs; y(index)=ys;
+%
+
+
+	%process options: 
+	options=pairoptions(varargin{:});
+
+	%retrieve tolerance: 
+	maxtol=getfieldvalue(options,'maxtol',100000); %100 km.
+	tolincrement=getfieldvalue(options,'tolincrement',10);
+	force=getfieldvalue(options,'force',0);
+
+	%go through lats,longs and find within tolerance, the index of the corresponding value in lat,long: 
+	indices=zeros(length(xs),1);
+	
+	for i=1:length(xs),
+		tolerance=0;
+		distance=sqrt((x-xs(i)).^2+(y-ys(i)).^2);
+
+		s=find(distance==0); 
+		if ~isempty(s), 
+			if length(s)>1,
+
+				%we have two vertices that are coincident! Not good. 
+				for j=1:length(s),
+					hold on;plot(x(s(j)),y(s(j)),'c.','MarkerSize',40)
+				end
+				disp(['Vertex ' num2str(i) ' of input mesh coincides with the following output mesh vertices ']);
+				s
+				if force,
+					indices(i)=s(1);
+				else
+					error('');
+				end
+			else
+				indices(i)=s;
+			end
+		else
+
+			%we could not find a 0 distance, find the lowest tolerance that generates a find: 
+			count=1;
+			while isempty(s),
+				if count>1000,
+					disp(['could not find a vertex matching vertex ' num2str(i) ' of input mesh!']);
+					disp('Might think about changing tolerance increment');
+					error('');
+				end
+				tolerance=tolerance+tolincrement;
+				s=find(distance<tolerance);
+				count=count+1;
+			end
+			if tolerance>maxtol, 
+				disp(['found matching vertices ' num2str(s) ' in output mesh for input mesh vertex ' num2str(i) ]);
+				disp(' however, these vertices are farther that the max tolerance allowed!');
+				error('');
+			end
+
+			%recover minimum distance: 
+			sf=distance(s);
+			pos=find(sf==min(sf)); 
+			s=s(pos);
+			indices(i)=s;
+		end
+	end
+
+	if(~isempty(find(indices==0))) error('issue with transition vector having one empty slot'); end;
+
+
+%		if length(s)>1,
+%			for j=1:length(s),
+%				hold on;plot3(x(s(j)),y(s(j)),z(s(j)),'c.','MarkerSize',40)
+%			end
+%			if force,
+%				indices(i)=s(1);
+%			else
+%				distance(s)
+%				error(sprintf('one or more vertices on the global mesh were duplicated (offset %i)',i));
+%			end
+%		elseif isempty(s),
+%			plot(distance);
+%			min(distance);
+%			i
+%			error('cannot find concurrent vertics!');
+%		else
+%			indices(i)=s;
+%		end
+