readnirfast

 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)

0001 function nirfastmesh=readnirfast(filestub)
0002 %
0003 % nirfastmesh=readnirfast(v,f,filestub)
0004 %
0005 % load a group of mesh files saved in the NIRFAST format
0006 %
0007 % author: Qianqian Fang, <q.fang at neu.edu>
0008 %
0009 % input:
0010 %      filestub: output file stub, output will include multiple files
0011 %          filestub.node: node file
0012 %          filestub.elem: element file to store the surface or tet mesh
0013 %          filestub.param: parameter file
0014 %          filestub.region: node label file
0015 %          filestub.excoef: extinction coeff list
0016 %
0017 % output:
0018 %      nirfastmesh.nodes: node list, 3 columns
0019 %      nirfastmesh.elements: element list, 3 or 4 columns integers
0020 %      nirfastmesh.bndvtx: boundary flag for each node, 1: on the boundary
0021 %      nirfastmesh.region: node segmentation labels
0022 %      nirfastmesh.dimension: dimension of the mesh
0023 %      nirfastmesh.excoef: extinction coeff list
0024 %      nirfastmesh.excoefheader: extinction coeff list field names
0025 %      nirfastmesh.type: the header of the .param file
0026 %      nirfastmesh.prop: optical property list (non-standard, need further processing)
0027 %
0028 %   format definition see http://www.dartmouth.edu/~nir/nirfast/tutorials/NIRFAST-Intro.pdf
0029 %
0030 % example:
0031 %    [node,face,elem]=meshabox([0 0 0],[10 10 10],0.3,1);
0032 %    savenirfast(node,elem,'test', [], ones(size(node)), 'user');
0033 %    mymesh=readnirfast('test')
0034 %    plotmesh([mymesh.nodes mymesh.bndvtx], mymesh.elements,'x>5')
0035 %
0036 % -- this function is part of iso2mesh toolbox (http://iso2mesh.sf.net)
0037 %
0038 
0039 fname=[filestub,'.node'];
0040 if(~exist(fullfile(pwd,fname),'file'))
0041     error([fname ' could not be found']);
0042 end
0043 nirfastmesh.nodes=load(fname);
0044 
0045 nirfastmesh.bndvtx=nirfastmesh.nodes(:,1);
0046 nirfastmesh.nodes(:,1)=[];
0047 
0048 fname=[filestub,'.elem'];
0049 if(~exist(fullfile(pwd,fname),'file'))
0050     error([fname ' could not be found']);
0051 end
0052 nirfastmesh.elements=load(fname);
0053 nirfastmesh.dimension=size(nirfastmesh.elements,2)-1;
0054 
0055 fname=[filestub,'.region'];
0056 if(exist(fullfile(pwd,fname),'file'))
0057     nirfastmesh.region=load(fname);
0058 end
0059 
0060 fname=[filestub,'.excoef'];
0061 fid=fopen(fname,'rt');
0062 if(fid>=0)
0063     linenum=0;
0064     textheader={};
0065     while(~feof(fid))
0066         oneline=fgetl(fid);
0067         linenum=linenum+1;
0068         [data, count]=sscanf(oneline,'%f');
0069         if(count>1)
0070             params=fscanf(fid,repmat('%f ',1,count),inf);
0071             params=reshape(params,length(params)/count, count);
0072             params(2:end+1,:)=params;
0073             params(1,:)=data(:)';
0074             nirfastmesh.excoef=params;
0075             nirfastmesh.excoefheader=textheader;
0076             break;
0077         else
0078             textheader{end+1}=oneline;
0079         end
0080     end
0081     fclose(fid);
0082 end
0083 
0084 fname=[filestub,'.param'];
0085 fid=fopen(fname,'rt');
0086 if(fid>=0)
0087     linenum=0;
0088     params=[];
0089     while(~feof(fid))
0090         oneline=fgetl(fid);
0091         if(linenum==0)
0092             nirfastmesh.type=oneline;
0093         end
0094         linenum=linenum+1;
0095         [data, count]=sscanf(oneline,'%f');
0096         if(count>1)
0097             params=fscanf(fid,repmat('%f ',1,count),inf);
0098             params=reshape(params,length(params)/count, count);
0099             params(2:end+1,:)=params;
0100             params(1,:)=data(:)';
0101             nirfastmesh.prop=params;
0102             break;
0103         end
0104     end
0105     fclose(fid);
0106 end