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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
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