mk_thorax_model

MK_THORAX_MODEL FEM models of the thorax

 MK_THORAX_MODEL provides a shorthand to predefined thorax FEMs and 
 for using contributed models with PLACE_ELEC_ON_SURF. You may be asked
 to download missing files. 

 MK_THORAX_MODEL(shapestr,elec_pos, elec_shape, maxh) where:
  shapestr    - a string specifying the underlying model.
                Run MK_THORAX_MODEL('list_shapes') for a list.
  elec_pos    - a vector specifying electrode positions.
                See PLACE_ELEC_ON_SURF for details.
  elec_shape  - a vector specifying electrode shapes.
                See PLACE_ELEC_ON_SURF for details.
  This usage returns a fwd_model structure.

 MK_THORAX_MODEL(modelstr) provides quick access to predefined models.
 Run MK_THORAX_MODEL('list') for a list. This usage returns either a 
 fwd_model or an image structure.

 MK_THORAX_MODEL('list_shapes') lists available thorax shapes without 
  electrodes.

 MK_THORAX_MODEL('list') lists available predefined models.

0001 function out = mk_thorax_model(str, elec_pos, elec_shape, maxh)
0002 %MK_THORAX_MODEL FEM models of the thorax
0003 %
0004 % MK_THORAX_MODEL provides a shorthand to predefined thorax FEMs and
0005 % for using contributed models with PLACE_ELEC_ON_SURF. You may be asked
0006 % to download missing files.
0007 %
0008 % MK_THORAX_MODEL(shapestr,elec_pos, elec_shape, maxh) where:
0009 %  shapestr    - a string specifying the underlying model.
0010 %                Run MK_THORAX_MODEL('list_shapes') for a list.
0011 %  elec_pos    - a vector specifying electrode positions.
0012 %                See PLACE_ELEC_ON_SURF for details.
0013 %  elec_shape  - a vector specifying electrode shapes.
0014 %                See PLACE_ELEC_ON_SURF for details.
0015 %  This usage returns a fwd_model structure.
0016 %
0017 % MK_THORAX_MODEL(modelstr) provides quick access to predefined models.
0018 % Run MK_THORAX_MODEL('list') for a list. This usage returns either a
0019 % fwd_model or an image structure.
0020 %
0021 % MK_THORAX_MODEL('list_shapes') lists available thorax shapes without
0022 %  electrodes.
0023 %
0024 % MK_THORAX_MODEL('list') lists available predefined models.
0025 %
0026 
0027 %
0028 % See also: PLACE_ELEC_ON_SURF, MK_LIBRARY_MODEL
0029 
0030 % (C) 2015-2016 Bartlomiej Grychtol. License: GPL version 2 or 3
0031 % $Id: mk_thorax_model.m 5903 2019-02-05 11:08:03Z aadler $
0032 
0033 if nargin>0 && ischar(str) 
0034    switch(str)
0035       case 'UNIT_TEST';
0036          do_unit_test; return;
0037       case 'list_shapes'
0038          out = list_basic_shapes; return;
0039       case 'list'
0040          out = list_predef_models; return;
0041    end
0042 end
0043 if ismember(str,list_predef_models)
0044    out = build_predef_model(str);
0045    return
0046 end
0047 
0048 if ~ismember(str, list_basic_shapes)
0049    error('Shape str "%s" not understood.',str);
0050 end
0051 
0052 
0053 
0054 out = build_basic_model(str);
0055 if nargin > 1
0056    out = place_elec_on_surf(out,elec_pos,elec_shape,[],maxh);
0057    out = fix_boundary(out);
0058 end
0059 
0060 end
0061 
0062 function ls = list_basic_shapes
0063    ls = {'male','female'};
0064 end
0065 
0066 function out = build_basic_model(str)
0067 switch(str)
0068    case {'male', 'female'}
0069       out = remesh_at_model(str);
0070 end
0071 end
0072 
0073 function out = remesh_at_model(str)
0074    tmpnm  = tempname;
0075    
0076    stlfile = [tmpnm '.stl'];
0077    volfile = [tmpnm '.vol'];
0078    
0079    contrib = 'at-thorax-mesh'; file =  sprintf('%s_t_mdl.mat',str);
0080    load(get_contrib_data(contrib,file));
0081    if strcmp(str,'male')
0082       fmdl.nodes = fmdl.nodes - 10; % center the model
0083    end
0084    fmdl = fix_boundary(fmdl);
0085    STL.vertices = fmdl.nodes;
0086    STL.faces    = fmdl.boundary;
0087    stl_write(STL,stlfile);
0088    opt.stloptions.yangle = 55;
0089    opt.stloptions.edgecornerangle = 5;
0090    opt.meshoptions.fineness = 6;
0091    opt.options.meshsize = 30;
0092    opt.options.minmeshsize = 10;
0093    opt.stloptions.resthsurfcurvfac = 2;
0094    opt.stloptions.resthsurfcurvenable = 1;
0095    opt.stloptions.chartangle = 30;
0096    opt.stloptions.outerchartangle = 90;
0097    ng_write_opt(opt);
0098    call_netgen(stlfile,volfile);
0099    out=ng_mk_fwd_model(volfile,[],[],[],[]);
0100    delete(stlfile);
0101    delete(volfile);
0102    delete('ng.opt');
0103    
0104    out = rmfield(out,...
0105       {'mat_idx','np_fwd_solve','boundary_numbers'});
0106    
0107 end
0108 
0109 function mdl = fix_boundary(mdl)
0110     opt.elem2face  = 1;
0111     opt.boundary_face = 1;
0112     opt.inner_normal = 1;
0113     mdl = fix_model(mdl,opt);
0114     flip = mdl.elem2face(logical(mdl.boundary_face(mdl.elem2face).*mdl.inner_normal));
0115     mdl.faces(flip,:) = mdl.faces(flip,[1 3 2]);
0116     mdl.normals(flip,:) = -mdl.normals(flip,:);
0117     mdl.boundary = mdl.faces(mdl.boundary_face,:);
0118 end
0119 
0120 function ls = list_predef_models
0121    ls = {'adult_male_grychtol2016a_1x32'
0122          'adult_male_grychtol2016a_2x16'};
0123 end
0124 
0125 function out = build_predef_model(str)
0126    switch str
0127       case 'adult_male_grychtol2016a_1x32'
0128          out = mk_thorax_model_grychtol2016a('1x32_ring');
0129          
0130       case 'adult_male_grychtol2016a_2x16'
0131          out = mk_thorax_model_grychtol2016a('2x16_planar');
0132    end
0133 end
0134 
0135 
0136 function do_unit_test
0137    subplot(121)
0138    show_fem(mk_thorax_model('male'));
0139    
0140    subplot(122)
0141    show_fem(mk_thorax_model('female'));
0142    
0143 end