mk_library_model

MK_LIBRARY_MODEL - FEM models based on library shapes 

 MK_LIBRARY_MODEL(shape,elec_pos,elec_shape,maxsz,nfft) where:
   shape -  a cell array of strings and
     shape{1} is the shape_library model used
          (run shape_libary('list') to get a list
     shape{2} is the the boundary. If absent, 'boundary' is assumed.
     shape{3..} are strings specifying additional inclusions (such as
     lungs)
   elec_pos - a vector specifying electrode positions. See
     NG_MK_EXTRUDED_MODEL for details. To use the electrode positions
     stored in the 'electrode' field in the shape_libary, specify elec_pos
     as 'original'
   elec_shape - a vector specifying electrode shapes. See
     NG_MK_EXTRUDED_MODEL for details.
   maxsz - maximum FEM size (default: course mesh)
   nfft  - number of points to create along the boundary (default: 50)

 QUICK ACCESS TO COMMON MODELS:
   MK_LIBRARY_MODEL(str) where str is a single string specifying a model.
   Use MK_LIBRARY_MODEL('list') to obtain a list of available models.

0001 function out = mk_library_model(shape,elec_pos,elec_shape,maxsz,nfft)
0002 %MK_LIBRARY_MODEL - FEM models based on library shapes
0003 %
0004 % MK_LIBRARY_MODEL(shape,elec_pos,elec_shape,maxsz,nfft) where:
0005 %   shape -  a cell array of strings and
0006 %     shape{1} is the shape_library model used
0007 %          (run shape_libary('list') to get a list
0008 %     shape{2} is the the boundary. If absent, 'boundary' is assumed.
0009 %     shape{3..} are strings specifying additional inclusions (such as
0010 %     lungs)
0011 %   elec_pos - a vector specifying electrode positions. See
0012 %     NG_MK_EXTRUDED_MODEL for details. To use the electrode positions
0013 %     stored in the 'electrode' field in the shape_libary, specify elec_pos
0014 %     as 'original'
0015 %   elec_shape - a vector specifying electrode shapes. See
0016 %     NG_MK_EXTRUDED_MODEL for details.
0017 %   maxsz - maximum FEM size (default: course mesh)
0018 %   nfft  - number of points to create along the boundary (default: 50)
0019 %
0020 % QUICK ACCESS TO COMMON MODELS:
0021 %   MK_LIBRARY_MODEL(str) where str is a single string specifying a model.
0022 %   Use MK_LIBRARY_MODEL('list') to obtain a list of available models.
0023 
0024 % (C) 2011 Bartlomiej Grychtol. License: GPL version 2 or version 3
0025 % $Id: mk_library_model.html 2819 2011-09-07 16:43:11Z aadler $
0026 
0027 if ischar(shape)
0028     switch shape
0029         case 'LIBRARY_PATH'
0030             switch nargin
0031                 case 1
0032                     out = get_path;
0033                 case 2
0034                     set_path(elec_pos);
0035             end
0036         case 'list'
0037             out = list_predef_model_strings;
0038         case 'UNIT_TEST'
0039             out = do_unit_test; return;
0040         otherwise
0041             out = predef_model(shape);
0042     end
0043 else
0044     if ~iscell(shape) 
0045         shape = {shape, 'boundary'}; 
0046     elseif numel(shape) == 1
0047         shape{2} = 'boundary';
0048     end
0049     fname = make_filename(shape,elec_pos,elec_shape,maxsz);
0050     fname = [get_path '/' fname '.mat'];
0051     if exist(fname,'file')
0052         eidors_msg('MK_LIBRARY_MODEL: Using stored model');
0053         load(fname);
0054         out = fmdl;
0055     else
0056        s_shape = split_var_strings(shape(2:end));
0057        shapes = shape_library('get',shape{1},s_shape(1,:));
0058        if ~iscell(shapes), shapes = {shapes}; end
0059        %apply any indeces specified
0060        for i = 1:numel(shapes)
0061            eval(['shapes{i} = shapes{i}' s_shape{2,i} ';']);
0062        end
0063        if ischar(elec_pos) && strcmp(elec_pos,'original')
0064           el = shape_library('get',shape{1},'electrodes');
0065           electh= atan2(el(:,2),el(:,1))*180/pi;
0066           elec_pos = [electh,0.5*ones(size(electh))];
0067        end
0068        if nargin < 5
0069            nfft = 50;
0070        end
0071        [fmdl, mat_idx] = ng_mk_extruded_model({1,shapes,[4,nfft],maxsz},...
0072            elec_pos,elec_shape);
0073        fmdl.mat_idx = mat_idx;
0074        save(fname,'fmdl');
0075        out = fmdl;
0076     end
0077 end
0078 
0079 %%%%%
0080 % Lists predefined models (append when adding)
0081 function out = list_predef_model_strings
0082 out = {
0083     'adult_male_16el';
0084     'adult_male_32el';
0085     'adult_male_16el_lungs';
0086     'adult_male_32el_lungs';
0087     'cylinder_16x1el_coarse';
0088     'cylinder_16x1el_fine';
0089     'cylinder_16x1el_vfine';   
0090     'cylinder_16x2el_coarse';
0091     'cylinder_16x2el_fine';
0092     'cylinder_16x2el_vfine';
0093     'neonate_16el';
0094     'neonate_32el';
0095     'neonate_16el_lungs';
0096     'neonate_32el_lungs';
0097     'pig_23kg_16el';
0098     'pig_23kg_32el';
0099     'pig_23kg_16el_lungs';
0100     'pig_23kg_32el_lungs';
0101     };
0102 
0103 %%%%%
0104 % Use predefined model
0105 function out = predef_model(str)
0106 switch str
0107     case 'adult_male_16el'
0108         out = mk_library_model({'adult_male','boundary'},...
0109             [16 1 0.5],[0.05],0.08);
0110     case 'adult_male_32el'
0111         out = mk_library_model({'adult_male','boundary'},...
0112             [32 1 0.5],[0.05],0.08);
0113     case 'adult_male_16el_lungs'
0114         out = mk_library_model({'adult_male','boundary','left_lung','right_lung'},...
0115             [16 1 0.5],[0.05],0.08);
0116     case 'adult_male_32el_lungs'
0117         out = mk_library_model({'adult_male','boundary','left_lung','right_lung'},...
0118             [32 1 0.5],[0.05],0.08);
0119         
0120     case 'cylinder_16x1el_coarse'
0121         out = ng_mk_cyl_models([10,15],[16,5],[0.5,0,0.18]);
0122     case 'cylinder_16x1el_fine'  
0123         out = ng_mk_cyl_models([10,15,1.1],[16,5],[0.5,0,0.15]);
0124     case 'cylinder_16x1el_vfine' 
0125         out = ng_mk_cyl_models([10,15,0.8],[16,5],[0.5,0,0.08]);
0126     case 'cylinder_16x2el_coarse' 
0127         out = ng_mk_cyl_models([30,15],[16,10,20],[0.5,0,0.18]);
0128     case 'cylinder_16x2el_fine'  
0129         out = ng_mk_cyl_models([30,15,1.5],[16,10,20],[0.5,0,0.15]);
0130     case 'cylinder_16x2el_vfine' 
0131         out = ng_mk_cyl_models([30,15,0.8],[16,10,20],[0.5,0,0.08]);
0132         
0133         
0134     case 'neonate_16el'
0135         out = mk_library_model({'neonate','boundary'},[16 1 0.5],0.1,0.08,49);
0136     case 'neonate_32el'
0137         out = mk_library_model({'neonate','boundary'},[32 1 0.5],0.07,0.08,49);
0138     case 'neonate_16el_lungs'
0139         out = mk_library_model({'neonate','boundary','left_lung','right_lung'},[16 1 0.5],0.1,0.08,49);
0140     case 'neonate_32el_lungs'
0141         out = mk_library_model({'neonate','boundary','left_lung','right_lung'},[32 1 0.5],0.07,0.08,49);
0142         
0143     case 'pig_23kg_16el'
0144         out = mk_library_model({'pig_23kg','boundary'},...
0145             [16 1 0.5],[0.05],0.08);
0146     case 'pig_23kg_32el'
0147         out = mk_library_model({'pig_23kg','boundary'},...
0148             [32 1 0.5],[0.05],0.08);
0149     case 'pig_23kg_16el_lungs'
0150         out = mk_library_model({'pig_23kg','boundary','lungs(1:2:end,:)'},...
0151             [16 1 0.5],[0.05],0.08);
0152     case 'pig_23kg_32el_lungs'
0153         out = mk_library_model({'pig_23kg','boundary','lungs(1:2:end,:)'},...
0154             [32 1 0.5],[0.05],0.08);    case 'pig_23kg_16el'
0155         out = mk_library_model({'pig_23kg','boundary'},...
0156             [16 1 0.5],[0.05],0.08);
0157     case 'pig_23kg_32el'
0158         out = mk_library_model({'pig_23kg','boundary'},...
0159             [32 1 0.5],[0.05],0.08);
0160     case 'pig_23kg_16el_lungs'
0161         out = mk_library_model({'pig_23kg','boundary','lungs(1:2:end,:)'},...
0162             [16 1 0.5],[0.05],0.08);
0163     case 'pig_23kg_32el_lungs'
0164         out = mk_library_model({'pig_23kg','boundary','lungs(1:2:end,:)'},...
0165             [32 1 0.5],[0.05],0.08);
0166     otherwise
0167         error('No such model');
0168 end
0169 %give the model a name
0170 out.name = str;
0171 
0172 
0173 function str = make_filename(shape, elec_pos, elec_shape, maxsz)
0174 %at this point, shape is a cell array of strings e.g. {'pig_23kg','lungs')
0175 str = shape{1};
0176 shape(1) = []; %remove the first element
0177 shape = sort(shape); %sort the others
0178 for i = 1:numel(shape)
0179     str = [str '_' shape{i}];
0180 end
0181 str = [str '_EP'];
0182 for i = 1:numel(elec_pos)
0183     str = [str '_' num2str(elec_pos(i))];
0184 end
0185 str = [str '_ES'];
0186 if ischar(elec_shape)
0187     str = [str '_' elec_shape];
0188 else
0189     for i = 1:numel(elec_shape)
0190         str = [str '_' num2str(elec_shape(i))];
0191     end
0192 end
0193 if ~isempty(maxsz)
0194     str = [str '_maxsz_' num2str(maxsz)];
0195 end
0196 
0197 %remove colons
0198 str = strrep(str,':','-');
0199 
0200 function clean = split_var_strings(strc)
0201 for i = 1:numel(strc)
0202     [clean{1,i} clean{2,i}] = strtok(strc{i},'([{');
0203 end
0204 
0205 
0206 function out = get_path
0207 global eidors_objects
0208 out = eidors_objects.model_cache;
0209 
0210 function set_path(val)
0211 global eidors_objects
0212 eidors_objects.model_cache = val;
0213 %if folder doesn't exist, create it
0214 if ~exist(val,'dir')
0215     mkdir(val);
0216 end
0217 
0218 function out = do_unit_test
0219 models = mk_library_model('list');
0220 for i = 1:numel(models)
0221     mdl = mk_library_model(models{i});
0222     img = mk_image(mdl,1);
0223     try   n = numel(mdl.mat_idx); catch n =1; end
0224     if n >1
0225         for j = 2:n
0226             img.elem_data(mdl.mat_idx{j}) = 0.25;
0227         end
0228     end
0229     figure
0230     show_fem(img,[0,1,0]);
0231     title(models{i},'Interpreter','none');
0232 end
0233 
0234 
0235 out = mk_library_model({'pig_23kg','boundary','lungs(1:2:end,:)'},[32 1 0.5],[0.05],0.08);
0236