readnirfast.m

function nirfastmesh = readnirfast(filestub)
%
% nirfastmesh=readnirfast(v,f,filestub)
%
% load a group of mesh files saved in the NIRFAST format
%
% author: Qianqian Fang, <q.fang at neu.edu>
%
% input:
%      filestub: output file stub, output will include multiple files
%          filestub.node: node file
%          filestub.elem: element file to store the surface or tet mesh
%          filestub.param: parameter file
%          filestub.region: node label file
%          filestub.excoef: extinction coeff list
%
% output:
%      nirfastmesh.nodes: node list, 3 columns
%      nirfastmesh.elements: element list, 3 or 4 columns integers
%      nirfastmesh.bndvtx: boundary flag for each node, 1: on the boundary
%      nirfastmesh.region: node segmentation labels
%      nirfastmesh.dimension: dimension of the mesh
%      nirfastmesh.excoef: extinction coeff list
%      nirfastmesh.excoefheader: extinction coeff list field names
%      nirfastmesh.type: the header of the .param file
%      nirfastmesh.prop: optical property list (non-standard, need further processing)
%
%   format definition see http://www.dartmouth.edu/~nir/nirfast/tutorials/NIRFAST-Intro.pdf
%
% example:
%    [node,face,elem]=meshabox([0 0 0],[10 10 10],0.3,1);
%    savenirfast(node,elem,'test', [], ones(size(node)), 'user');
%    mymesh=readnirfast('test')
%    plotmesh([mymesh.nodes mymesh.bndvtx], mymesh.elements,'x>5')
%
% -- this function is part of iso2mesh toolbox (http://iso2mesh.sf.net)
%

fname = [filestub, '.node'];
if (~exist(fullfile(pwd, fname), 'file'))
    error([fname ' could not be found']);
end
nirfastmesh.nodes = load(fname);

nirfastmesh.bndvtx = nirfastmesh.nodes(:, 1);
nirfastmesh.nodes(:, 1) = [];

fname = [filestub, '.elem'];
if (~exist(fullfile(pwd, fname), 'file'))
    error([fname ' could not be found']);
end
nirfastmesh.elements = load(fname);
nirfastmesh.dimension = size(nirfastmesh.elements, 2) - 1;

fname = [filestub, '.region'];
if (exist(fullfile(pwd, fname), 'file'))
    nirfastmesh.region = load(fname);
end

fname = [filestub, '.excoef'];
fid = fopen(fname, 'rb');
if (fid >= 0)
    linenum = 0;
    textheader = {};
    while (~feof(fid))
        oneline = fgetl(fid);
        linenum = linenum + 1;
        [data, count] = sscanf(oneline, '%f');
        if (count > 1)
            params = fscanf(fid, repmat('%f ', 1, count), inf);
            params = reshape(params, length(params) / count, count);
            params(2:end + 1, :) = params;
            params(1, :) = data(:)';
            nirfastmesh.excoef = params;
            nirfastmesh.excoefheader = textheader;
            break
        else
            textheader{end + 1} = oneline;
        end
    end
    fclose(fid);
end

fname = [filestub, '.param'];
fid = fopen(fname, 'rb');
if (fid >= 0)
    linenum = 0;
    params = [];
    while (~feof(fid))
        oneline = fgetl(fid);
        if (linenum == 0)
            nirfastmesh.type = oneline;
        end
        linenum = linenum + 1;
        [data, count] = sscanf(oneline, '%f');
        if (count > 1)
            params = fscanf(fid, repmat('%f ', 1, count), inf);
            params = reshape(params, length(params) / count, count);
            params(2:end + 1, :) = params;
            params(1, :) = data(:)';
            nirfastmesh.prop = params;
            break
        end
    end
    fclose(fid);
end