layersurf.m

function [face,labels]=layersurf(elem,varargin)
%
% face=layersurf(elem, opt)
%    or
% [face,labels]=layersurf(elem,'option1',value1,'option2',value2,...)
%
% process a multi-layered tetrahedral mesh, like a brain mesh, to extract
% the layer surface meshes with one enclosed by another
%
% author: Qianqian Fang (q.fang at neu.edu)
%
% input:
%    elem: an Nx5 integer array, representing the tetrahedral mesh element
%         list. The first 4 columns represent the tetrahedral element node
%         indices; the last column represents tissue labels.
%    opt: (optional) a struct or pairs of names/values to provide
%         additional options; accepted options include
%         'order': ['>='] or '=', '<=' . if set to '>=' (default), the 
%             outmost layer has the lowest label count; if '<=', innermost 
%             is lowest; if '=', surface of each label is extracted
%             individually - meaning that inner surfaces will have two
%             duplicates
%         'innermost': [0] or an array of labels. The labels defined in
%             this list will be treated as the innermost regions, and its
%             boundary will be extracted using the '==' test (order='=').
%             by default; label 0 is assumed to be innermost (i.e. nothing
%             is enclosed inside).
%         'unique': [0] or 1. if 1, remove duplicated triangles; if 0, keep
%             all triangles.
%         'occurence': ['first'] or 'last'. if 'first', the unique operator
%             keeps a duplicated triangle with the lowest label number; 
%             otherwise, a repeated triange keeps the highest label number.
%
% output:
%    vol: a 2-D or 3-D array of the same type/size of the input arrays. The
%         label for each voxel is determined by the index to the highest
%         value in TPM of the same voxel. If a voxel is a background voxel
%         - i.e. zeros for all TPMs, it stays 0
%    names: a cell array storing the names of the labels (if input is a
%         struct), the first string is the name for label 1, and so on
%
% -- this function is part of brain2mesh toolbox (http://mcx.space/brain2mesh)
%    License: GPL v3 or later, see LICENSE.txt for details
%

opt=varargin2struct(varargin{:});
outsideislower=jsonopt('order','>=',opt);
dounique=jsonopt('unique',false,opt);
innermost=jsonopt('innermost',0,opt);
occurence=jsonopt('occurence','first',opt);

labels = sort(unique(elem(:,5)));
face = [];
for i = 1:length(labels)
    if(strcmp(outsideislower,'>=') && ~ismember(labels(i),innermost))
        newface=volface(elem(elem(:,5)>=labels(i),1:4));
    elseif(strcmp(outsideislower,'<=') && ~ismember(labels(i),innermost))
        newface=volface(elem(elem(:,5)<=labels(i),1:4));
    else
        newface=volface(elem(elem(:,5)==labels(i),1:4));
    end
    newface(:,4)=labels(i);
    face = [face; newface];
end

if(dounique)
    face(:,1:3) = sort(face(:,1:3),2);
    [uniqface, idx]= unique(face(:,1:3),'rows',occurence);
    face=[uniqface, face(idx,end)];
end