mesh_emse2matlab

 mesh_emse2matlab - Convert EMSE mesh (.wfr) to matlab format

 USEAGE: [vertices,faces,edges,meshtype] = mesh_emse2matlab(file,[options])

 All values returned are in meters.  With the returned structures, 
 create a vertex & face matrix:
 
   vertex_matrix = [vertices.x; vertices.y; vertices.z]';
   face_matrix = [faces.vertex1;faces.vertex2;faces.vertex3]';

 These can be input to the patch command:

    Hpatch = patch('Vertices',vertex_matrix,'Faces',face_matrix,...
                   'EdgeColor',[.6 .6 .6],'FaceColor',[0.9 0.9 0.9]);

 See the patch and light commands to colour this object.
 
 'options' ... a cell array of strings.  By default it contains
 options = {'vertex','face','edge'}.  By default, this routine
 reads all available data from the emse file.  If 'options' is given
 and it doesn't contain one of these strings, that data will not be
 read or returned.

 meshtype is: 'unknown','scalp','outer skull','inner skull', or 'cortex'

0001 function [vertex,face,edge,mesh] = mesh_emse2matlab(file,options)
0002 
0003 % mesh_emse2matlab - Convert EMSE mesh (.wfr) to matlab format
0004 %
0005 % USEAGE: [vertices,faces,edges,meshtype] = mesh_emse2matlab(file,[options])
0006 %
0007 % All values returned are in meters.  With the returned structures,
0008 % create a vertex & face matrix:
0009 %
0010 %   vertex_matrix = [vertices.x; vertices.y; vertices.z]';
0011 %   face_matrix = [faces.vertex1;faces.vertex2;faces.vertex3]';
0012 %
0013 % These can be input to the patch command:
0014 %
0015 %    Hpatch = patch('Vertices',vertex_matrix,'Faces',face_matrix,...
0016 %                   'EdgeColor',[.6 .6 .6],'FaceColor',[0.9 0.9 0.9]);
0017 %
0018 % See the patch and light commands to colour this object.
0019 %
0020 % 'options' ... a cell array of strings.  By default it contains
0021 % options = {'vertex','face','edge'}.  By default, this routine
0022 % reads all available data from the emse file.  If 'options' is given
0023 % and it doesn't contain one of these strings, that data will not be
0024 % read or returned.
0025 %
0026 % meshtype is: 'unknown','scalp','outer skull','inner skull', or 'cortex'
0027 %
0028 
0029 % $Revision: 1.1 $ $Date: 2004/11/12 01:32:35 $
0030 
0031 % Licence:  GNU GPL, no implied or express warranties
0032 % History:  10/98 Abbas Kouzani (egazk@flinders.edu.au)
0033 %           09/01 Darren.Weber_at_radiology.ucsf.edu
0034 %                 - created function, rather than script
0035 %                 - added functionality to handle different
0036 %                   minor revisions.
0037 %           03/02 Darren.Weber_at_radiology.ucsf.edu
0038 %                 - optimised fscanf processes for matlab, the
0039 %                   function now operates in less than 1/2 time,
0040 %                   especially for revision 3 data.
0041 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0042 
0043 if ~exist('options','var'),
0044     options = {'vertex','face','edge'};
0045 end
0046 
0047 [path,name,ext] = fileparts(file);
0048 file = fullfile(path,[name ext]);
0049 
0050 [fid,msg] = fopen(file,'r');
0051 if ~isempty(msg), error(msg); end
0052 
0053 tic;
0054 
0055 % Read prolog
0056 version   =fscanf(fid,'%f',1);
0057 file_type =fscanf(fid,'%f',1);
0058 minor_rev =fscanf(fid,'%f',1);
0059 
0060 fprintf('...WFR Version = %d, Minor_Revision = %d, File-Type = %d\n',...
0061     version,minor_rev,file_type);
0062 
0063 if ~(file_type==8000 | file_type==4000)
0064     S=sprintf('Could not convert WFR file type: %d',file_type);
0065     error(S);
0066 end
0067 
0068 % Read header (format depends on minor revision)
0069 if(minor_rev==3)
0070     type      =fscanf(fid,'%f',1);
0071 else
0072     radius    =fscanf(fid,'%f',1);
0073     vertex_no =fscanf(fid,'%d',1);
0074     face_no   =fscanf(fid,'%d',1);
0075     edge_no   =fscanf(fid,'%d',1);
0076     
0077     fprintf('...Radius = %f meters\n',radius);
0078     %...Vertices = %d\n...Patches = %d\n...Edges = %d\n',...
0079     %    vertex_no,face_no,edge_no);
0080 
0081     if(minor_rev==1), type = 0;
0082     else,             type = fscanf(fid,'%f',1);
0083     end
0084 end
0085 
0086 if(minor_rev==1)
0087     mesh = 'unknown';
0088 else
0089     switch type
0090         case 0,             mesh = 'unknown';
0091         case { 64,  40},    mesh = 'scalp';
0092         case {128,  80},    mesh = 'outer skull';
0093         case {256, 100},    mesh = 'inner skull';
0094         case {512, 200},    mesh = 'cortex';
0095         otherwise,          mesh = 'unknown';
0096     end
0097 end
0098 
0099 fprintf('...Mesh type: %s\n',mesh);
0100 
0101 % Read data (format depends on minor revision)
0102 vertex = struct([]);
0103 face = struct([]);
0104 edge = struct([]);
0105 
0106 if(minor_rev==3)
0107     
0108     % Read the whole file
0109     fprintf('...Reading Minor Revision 3 Data File');
0110     Tmp = fscanf(fid,'%s%f%f%f',[4,inf]);
0111     fprintf('...done\n');
0112     
0113     % Vertices
0114     if(max(strcmp('vertex',options)) > 0),
0115         fprintf('...Creating Vertices Struct');
0116         % first get the numeric code for 'v'
0117         vcode = Tmp(1,1);
0118         % now find all columns of Tmp with vcode in 1st row
0119         vindex = find(Tmp(1,:) == vcode);
0120         
0121         tmp = Tmp(2:4,vindex);
0122         tmp = num2cell(tmp);
0123         vertex = struct(...
0124             'index', [1:length(vindex)],...
0125             'x',     tmp( 1,:),...
0126             'y',     tmp( 2,:),...
0127             'z',     tmp( 3,:));
0128         clear tmp;
0129         fprintf('...done\n');
0130     else
0131         fprintf('...Skipping Vertices Struct\n');
0132     end
0133     
0134     % Faces
0135     if(max(strcmp('face',options)) > 0),
0136         fprintf('...Creating Faces Struct');
0137         % first get the numeric code for 't'
0138         tcode = Tmp(1,length(vindex)+1);
0139         % now find all columns of Tmp with tcode in 1st row
0140         tindex = find(Tmp(1,:) == tcode);
0141         
0142         % matlab vertex indices start at one,
0143         % not zero, so we add one to these emse values
0144         tmp = Tmp(2:4,tindex) + 1;
0145         
0146         tmp = num2cell(tmp);
0147         face = struct(...
0148             'index',   [1:length(tindex)],...
0149             'vertex1', tmp( 1,:),...
0150             'vertex2', tmp( 2,:),...
0151             'vertex3', tmp( 3,:));
0152         clear tmp;
0153         fprintf('...done\n');
0154     else
0155         fprintf('...Skipping Faces Struct\n');
0156     end
0157     
0158     % Edges
0159     fprintf('...No edges for minor revision 3\n');
0160     clear Tmp;
0161     
0162 elseif(minor_rev~=4)
0163     % minor revision 1 & 2 format
0164     disp('...Reading Minor Revision 1 or 2 Data');
0165     if(max(strcmp('vertex',options)) > 0),
0166         fprintf('...Reading %d Vertices',vertex_no);
0167         
0168         tmp = zeros(13,vertex_no);
0169         tmp = fscanf(fid,'%d%x%d%d%g%g%g%g%g%g%g%g%g',[13,vertex_no]);
0170         
0171         tmp(1,:) = tmp(1,:) + 1;
0172         tmp      = num2cell(tmp);
0173         vertex   = struct(...
0174             'index',        tmp( 1,:),...
0175             'address',      tmp( 2,:),...
0176             'channel_index',tmp( 3,:),...
0177             'x',            tmp( 5,:),...
0178             'y',            tmp( 6,:),...
0179             'z',            tmp( 7,:),...
0180             'xnormal',      tmp( 9,:),...
0181             'ynormal',      tmp(10,:),...
0182             'znormal',      tmp(11,:),...
0183             'potential',    tmp(12,:),...
0184             'curvature',    tmp(13,:));
0185         clear tmp;
0186         fprintf('...done\n');
0187     else
0188         fprintf('...Skipping %d Vertices\n',vertex_no);
0189         tmp = zeros(13,vertex_no);
0190         tmp = fscanf(fid,'%d%x%d%d%g%g%g%g%g%g%g%g%g',[13,vertex_no]);
0191         clear tmp;
0192     end
0193     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0194     if(max(strcmp('face',options)) > 0),
0195         fprintf('...Reading %d Faces',face_no);
0196         
0197         tmp = zeros(18,face_no);
0198         tmp = fscanf(fid,'%d%x%g%g%g%g%g%g%g%g%g%g%x%x%x%x%x%x',[18,face_no]);
0199         tmp(1,:) = tmp(1,:) + 1;
0200         tmp      = num2cell(tmp);
0201         face     = struct(...
0202             'index',        tmp( 1,:),...
0203             'address',      tmp( 2,:),...
0204             'solid_angle',  tmp( 3,:),...
0205             'magnitude',    tmp( 4,:),...
0206             'potential',    tmp( 5,:),...
0207             'area',         tmp( 6,:),...
0208             'center_x',     tmp( 7,:),...
0209             'center_y',     tmp( 8,:),...
0210             'center_z',     tmp( 9,:),...
0211             'normal_x',     tmp(10,:),...
0212             'normal_y',     tmp(11,:),...
0213             'normal_z',     tmp(12,:),...
0214             'vertex1',      tmp(13,:),...
0215             'vertex2',      tmp(14,:),...
0216             'vertex3',      tmp(15,:),...
0217             'edge1',        tmp(16,:),...
0218             'edge2',        tmp(17,:),...
0219             'edge3',        tmp(18,:));
0220         clear tmp;
0221         fprintf('...done\n');
0222         
0223         % In minor rev4, the face vertex and edges
0224         % refer to the vertex.address field, so this
0225         % is corrected here.  Not sure how to avoid 'for'
0226         fprintf('...Converting Face vertices from address to index (this takes a while)');
0227         for i=1:face_no,
0228             face(i).vertex1 = find([vertex.address] == face(i).vertex1);
0229             face(i).vertex2 = find([vertex.address] == face(i).vertex2);
0230             face(i).vertex3 = find([vertex.address] == face(i).vertex3);
0231         end
0232         fprintf('...done\n');
0233         if(max(strcmp('edge',options)) > 0),
0234             fprintf('...Converting Face edges from address to index (this takes a while)');
0235             for i=1:face_no,
0236                 face(i).edge1 = find([vertex.address] == face(i).edge1);
0237                 face(i).edge2 = find([vertex.address] == face(i).edge2);
0238                 face(i).edge3 = find([vertex.address] == face(i).edge3);
0239             end
0240             fprintf('...done\n');
0241         end
0242     else
0243         disp('...Skipping Faces');
0244         tmp = zeros(18,face_no);
0245         tmp = fscanf(fid,'%d%x%g%g%g%g%g%g%g%g%g%g%x%x%x%x%x%x',[18,face_no]);
0246         clear tmp;
0247     end
0248     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0249     if(max(strcmp('edge',options)) > 0),
0250         fprintf('...Reading %d Edges',edge_no);
0251         
0252         tmp = zeros(4,edge_no);
0253         tmp = fscanf(fid,'%d%x%x%x',[4,edge_no]);
0254         
0255         tmp(1,:) = tmp(1,:) + 1;
0256         tmp      = num2cell(tmp);
0257         edge     = struct(...
0258             'index',        tmp(1,:),...
0259             'address',      tmp(2,:),...
0260             'vertex1',      tmp(3,:),...
0261             'vertex2',      tmp(4,:));
0262         clear tmp;
0263         fprintf('...done\n');
0264         fprintf('...Converting Edge vertices from address to index (this takes a while)');
0265         for i=1:edge_no,
0266             edge(i).vertex1 = find([vertex.address] == edge(i).vertex1);
0267             edge(i).vertex2 = find([vertex.address] == edge(i).vertex2);
0268         end
0269         fprintf('...done\n');
0270     else
0271         disp('...Skipping Edges');
0272         %for i=1:edge_no,
0273         %    tmp=fscanf(fid,'%*d',1);
0274         %    tmp=fscanf(fid,'%*x',3);
0275         %end
0276     end
0277 else
0278     % minor revision 4 format
0279     disp('...Reading Minor Revision 4 Data');
0280     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0281     if(max(strcmp('vertex',options)) > 0),
0282         fprintf('...Reading %d Vertices',vertex_no);
0283         
0284         index = meshgrid(1:1:vertex_no,1);
0285         index = num2cell(index);
0286         
0287         tmp = zeros(11,vertex_no);
0288         tmp = fscanf(fid,'%d%d%g%g%g%d%g%g%g%g%g',[11,vertex_no]);
0289         
0290         tmp      = num2cell(tmp);
0291         vertex   = struct(...
0292             'index',        index,...
0293             'channel_index',tmp( 1,:),...
0294             'x',            tmp( 3,:),...
0295             'y',            tmp( 4,:),...
0296             'z',            tmp( 5,:),...
0297             'xnormal',      tmp( 7,:),...
0298             'ynormal',      tmp( 8,:),...
0299             'znormal',      tmp( 9,:),...
0300             'potential',    tmp(10,:),...
0301             'curvature',    tmp(11,:));
0302         clear tmp index;
0303         fprintf('...done\n');
0304     else
0305         disp('...Skipping Vertices');
0306         tmp = zeros(11,vertex_no);
0307         tmp = fscanf(fid,'%d%d%g%g%g%d%g%g%g%g%g',[11,vertex_no]);
0308     end
0309     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0310     if(max(strcmp('face',options)) > 0),
0311         fprintf('...Reading %d Faces',face_no);
0312         
0313         index = meshgrid(1:1:face_no,1);
0314         index = num2cell(index);
0315         
0316         tmp = zeros(16,face_no);
0317         tmp = fscanf(fid,'%g%g%g%g%g%g%g%g%g%g%d%d%d%d%d%d',[16,face_no]);
0318         
0319         tmp(11:16,:) = tmp(11:16,:) + 1;
0320         
0321         tmp      = num2cell(tmp);
0322         face     = struct(...
0323             'index',        index,...
0324             'solid_angle',  tmp( 1,:),...
0325             'magnitude',    tmp( 2,:),...
0326             'potential',    tmp( 3,:),...
0327             'area',         tmp( 4,:),...
0328             'center_x',     tmp( 5,:),...
0329             'center_y',     tmp( 6,:),...
0330             'center_z',     tmp( 7,:),...
0331             'normal_x',     tmp( 8,:),...
0332             'normal_y',     tmp( 9,:),...
0333             'normal_z',     tmp(10,:),...
0334             'vertex1',      tmp(11,:),...
0335             'vertex2',      tmp(12,:),...
0336             'vertex3',      tmp(13,:),...
0337             'edge1',        tmp(14,:),...
0338             'edge2',        tmp(15,:),...
0339             'edge3',        tmp(16,:));
0340         clear tmp index;
0341         fprintf('...done\n');
0342     else
0343         disp('...Skipping Faces');
0344         tmp = zeros(16,face_no);
0345         tmp = fscanf(fid,'%g%g%g%g%g%g%g%g%g%g%d%d%d%d%d%d',[16,face_no]);
0346     end
0347     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0348     if(max(strcmp('edge',options)) > 0),
0349         fprintf('...Reading %d Edges',edge_no);
0350         
0351         index = meshgrid(1:1:edge_no,1);
0352         address = num2cell(index * 0);
0353         index = num2cell(index);
0354         
0355         tmp = zeros(2,edge_no);
0356         tmp = fscanf(fid,'%d%d',[2,edge_no]);
0357         tmp = tmp + 1;
0358         tmp = num2cell(tmp);
0359         
0360         edge = struct(...
0361             'index',   index,...
0362             'address', address,...
0363             'vertex1', tmp(1,:),...
0364             'vertex2', tmp(2,:));
0365         clear tmp index address;
0366         fprintf('...done\n');
0367     else
0368         fprintf('...Skipping Edges\n');
0369         %tmp=fscanf(fid,'%*d',2*edge_no);
0370     end
0371 end
0372 
0373 fclose(fid);
0374 t=toc;
0375 fprintf('...done (%5.2f sec)\n',t);
0376 
0377 return