show_3d_slices

 show_3d_slices(img, z_cuts, x_cuts, y_cuts, any_cuts)
 Show a 3d view of an object with many slices through it
  z_cuts = planes in z to do a cut
  x_cuts = planes in x to do a cut
  y_cuts = planes in y to do a cut
  any_cuts = cut planes intercepts as Nx3 matrix (see mdl_slice_mapper)
 Default show 2 z_cuts and 1 x and 1 y cut

 h = show_3d_slices(...) returns a cell array of handles to the individual
 slices { z_slices, x_slices, y_slices, any_slices }

 See also: mdl_slices_mesher

0001 function h = show_3d_slices(img, varargin);
0002 % show_3d_slices(img, z_cuts, x_cuts, y_cuts, any_cuts)
0003 % Show a 3d view of an object with many slices through it
0004 %  z_cuts = planes in z to do a cut
0005 %  x_cuts = planes in x to do a cut
0006 %  y_cuts = planes in y to do a cut
0007 %  any_cuts = cut planes intercepts as Nx3 matrix (see mdl_slice_mapper)
0008 % Default show 2 z_cuts and 1 x and 1 y cut
0009 %
0010 % h = show_3d_slices(...) returns a cell array of handles to the individual
0011 % slices { z_slices, x_slices, y_slices, any_slices }
0012 %
0013 % See also: mdl_slices_mesher
0014 
0015 % (C) 2007-2012 Andy Adler & Bartlomiej Grychtol.
0016 % License: GPL version 2 or version 3
0017 % $Id: show_3d_slices.m 5990 2019-06-27 12:41:33Z aadler $
0018 
0019 % BUGS: for 2D images, large electrodes are not correctly shown (AA, jun 2019)
0020 
0021 if ischar(img) && strcmp(img,'UNIT_TEST'); do_unit_test; return; end
0022 
0023 ok= 0;
0024 try; if strcmp(img.type, 'image');
0025    ok = 1;
0026 end; end
0027 if ~ok; 
0028    error('EIDORS: show_3d_slices requires image as first parameter');
0029 end
0030 if size(img.fwd_model.elems,2) == 3; %show_3d_slices requires volume model
0031    img = fake_3d_model( img );
0032 end
0033 
0034 %multi-parametrization
0035 img = data_mapper(img);
0036 
0037 qfi = warning('query','EIDORS:FirstImageOnly');
0038 % Get data and to c2f mapping if required
0039 elem_data = get_img_data(img);
0040 % check size
0041 if size(elem_data,2) > 1
0042    q = warning('query','backtrace');
0043    warning('backtrace','off');
0044    warning('EIDORS:FirstImageOnly','show_3d_slices only shows first image');
0045    warning('backtrace',q.state);
0046    warning('off','EIDORS:FirstImageOnly');
0047 end
0048 
0049 % need to make sure boundary is just the outside
0050 img.fwd_model.boundary = find_boundary(img.fwd_model);
0051 
0052 
0053 [jnk,ref_lev,max_scale] = scale_for_display( elem_data);
0054 try 
0055     img.calc_colours.ref_level; 
0056 catch
0057     img.calc_colours.ref_level = ref_lev;
0058 end
0059 try
0060     img.calc_colours.clim;
0061 catch
0062     img.calc_colours.clim = max_scale;
0063 end
0064 try 
0065     np = img.calc_colours.npoints;
0066 catch
0067     np = calc_colours('npoints');
0068 end
0069 %  show_fem(img.fwd_model);
0070 [x_cuts, y_cuts, z_cuts, any_cuts] = get_cuts(img,varargin{:});
0071 
0072 hz = []; hy = []; hx = []; ha = [];
0073 for i= 1:length(z_cuts)
0074     hz(i) = show_slice(img,[inf inf z_cuts(i)]);
0075     hold on
0076 end
0077 
0078 for i= 1:length(x_cuts)
0079     hx(i) = show_slice(img,[x_cuts(i) inf inf]);
0080     hold on
0081 end
0082 
0083 for i= 1:length(y_cuts)
0084     hy(i) = show_slice(img,[inf y_cuts(i) inf]);
0085     hold on
0086 end
0087 
0088 for i= 1:size(any_cuts,1)
0089     ha(i) = show_slice(img,any_cuts(i,:));
0090     hold on
0091 end
0092 hold off
0093 
0094 if nargout > 0
0095    h = {hz,hx,hy,ha};
0096 end
0097 
0098 warning(qfi.state,'EIDORS:FirstImageOnly');
0099 
0100 function h = show_slice(img, level)
0101     slc = mdl_slice_mesher(img,level);
0102     try slc.calc_colours = img.calc_colours; end
0103     h = show_fem(slc);
0104 
0105 % create an extruded 3D model of height
0106 function img = fake_3d_model( img );
0107   fmdl = img.fwd_model;
0108   fnodes = fmdl.nodes;
0109   felems = fmdl.elems;
0110   maxd = max( max(fnodes) - min(fnodes) );
0111   upd = 0.1*maxd; % up and down from zero
0112   Nn = num_nodes(fmdl);
0113   Ne = num_elems(fmdl);
0114   fmdn = fmdl;
0115   fmdn.nodes =[[fnodes,-upd+0*fnodes(:,1)];
0116                [fnodes,+upd+0*fnodes(:,1)]];
0117   for i=1:num_elecs(fmdl)
0118      eni = fmdn.electrode(i).nodes;
0119      fmdn.electrode(i).nodes = [eni(:);eni(:)+Nn]';
0120      if isempty(eni) && isfield(fmdn.electrode(i),'faces')
0121         eni = unique(fmdn.electrode(i).faces);
0122         fmdn.electrode(i).nodes = [eni(:);eni(:)+Nn]';
0123      end
0124   end
0125   if isfield(fmdn.electrode,'faces'); % Horrible we need to code it like this
0126      fmdn.electrode = rmfield(fmdn.electrode,'faces');
0127   end
0128   % Doesn't need to be a conformal model, don't worry about adjacency
0129   fmdn.elems =[[felems(:,[1,2,3]), felems(:,[1    ])+Nn];
0130                [felems(:,[  2,3]), felems(:,[1,2  ])+Nn];
0131                [felems(:,[    3]), felems(:,[1,2,3])+Nn]];
0132   ed= img.elem_data;
0133   if isfield(fmdl,'coarse2fine');
0134      c2f = fmdl.coarse2fine;
0135      fmdn.coarse2fine = [c2f;c2f;c2f]; 
0136      img.fwd_model = fmdn;
0137   else
0138      img = mk_image(fmdn,[ed;ed;ed]);
0139   end
0140 
0141     
0142 function [x_cuts, y_cuts, z_cuts, any_cuts] =  get_cuts(img, varargin)
0143    mdl_max= max(img.fwd_model.nodes);
0144    mdl_min= min(img.fwd_model.nodes);
0145    any_cuts = [];
0146    if nargin==1;
0147       % Default show 2 z_cuts and 1 x and 1 y cut
0148        x_cuts= linspace(mdl_min(1), mdl_max(1), 3); x_cuts([1,3])=[];
0149        y_cuts= linspace(mdl_min(2), mdl_max(2), 3); y_cuts([1,3])=[];
0150        z_cuts= linspace(mdl_min(3), mdl_max(3), 4); z_cuts([1,4])=[];
0151    elseif nargin==2;
0152        z_cuts= varargin{1};
0153        x_cuts= [];
0154        y_cuts= [];
0155    elseif nargin==3;
0156        z_cuts= varargin{1};
0157        x_cuts= varargin{2};
0158        y_cuts= [];
0159    elseif nargin==4;
0160        z_cuts= varargin{1};
0161        x_cuts= varargin{2};
0162        y_cuts= varargin{3};
0163    elseif nargin==5;
0164        z_cuts= varargin{1};
0165        x_cuts= varargin{2};
0166        y_cuts= varargin{3};
0167        any_cuts= varargin{4};
0168    else 
0169        error('too many inputs');
0170    end
0171    
0172 
0173 
0174 function do_unit_test
0175    imdl = mk_common_model('n3r2',[16,2]);
0176    img = mk_image(imdl,1); vh= fwd_solve(img);
0177    load datacom.mat A B;
0178    img.elem_data(A) = 1.2;
0179    img.elem_data(B) = 0.8;
0180    vi = fwd_solve(img);
0181    imgr = inv_solve(imdl, vh, vi);
0182    imgr.calc_colours.npoints =64;
0183    show_3d_slices(img);
0184    calc_colours('transparency_thresh', 0.25);
0185    show_3d_slices(imgr,[1.5,2],[],[]);
0186 
0187    subplot(4,4,1);  show_3d_slices(imgr,[1,2],0,0.5);
0188    subplot(4,4,2);  show_3d_slices(img ,[1,2],0,0.5);
0189    cuts = [inf, -2.5, 1.5; inf, 10, 1.5];
0190    subplot(4,4,3);  show_3d_slices(img ,[],[],[],cuts );
0191    
0192    imgr.calc_colours.transparency_thresh = -1;
0193    img.calc_colours.transparency_thresh = -1;
0194    subplot(4,4,4);  show_3d_slices(imgr,[1,2],0.3,0.7);
0195    subplot(4,4,5);  
0196    show_fem(img.fwd_model);
0197    hold on
0198    show_3d_slices(img ,[1,2],0.3,0.7);
0199    axis off
0200 
0201    subplot(4,4,6);  
0202    img.elem_data = img.elem_data*[0,1];
0203    img.get_img_data.frame_select = 2;
0204    show_3d_slices(img ,[1],[],[]);
0205    
0206    view(10,18);
0207 
0208 
0209    subplot(4,4,7);
0210    imgs = img;        ed = img.elem_data(:,1);
0211    imgs.elem_data= [1;1.2;0.8]*[1];
0212    imgs.fwd_model.coarse2fine = [ed == img.elem_data(1),
0213                                  ed == img.elem_data(2),
0214                                  ed == img.elem_data(3)];
0215    show_3d_slices(img,[1,2],0,0.7);
0216   
0217    subplot(4,4,8);
0218    show_3d_slices(img,[1],[],[],[1,1,1]);
0219 
0220 
0221    subplot(4,4,9);  
0222    vopt.imgsz = [10,10,10];
0223    % Build a model that has a c2f. This one isn't very good,
0224    % because of transpose, but that's OK for the test
0225    [img.fwd_model,tmp] = mk_voxel_volume(imdl.fwd_model,vopt);
0226    img.fwd_model.coarse2fine = (tmp.coarse2fine * ...
0227                       img.fwd_model.coarse2fine')';
0228    show_3d_slices(img,[1,2],0,0.5);
0229 
0230    subplot(4,4,10);
0231    fmdl = getfield(mk_common_model('a2C2',4),'fwd_model');
0232    fmdl.mat_idx{1} = 1:4;
0233    fmdl = mat_idx_to_electrode(fmdl,{1});
0234    img= mk_image(fmdl,1);
0235    show_3d_slices(img,[0])
0236    
0237    subplot(4,4,11);
0238    img.fwd_model.electrode(1).faces=[28,29;29,30;30,31];
0239    show_3d_slices(img,[0])
0240 
0241    subplot(4,4,12)
0242 % Without C2f
0243    imdl = mk_common_model('a2c0',8); img= mk_image(imdl);
0244    img.elem_data([10,12]) = 1.1;
0245    show_3d_slices(img,[0],[0.2],[0]);
0246 
0247 
0248    subplot(4,4,13)
0249 % With C2f
0250    ed = img.elem_data;
0251    img.fwd_model.coarse2fine = [ed==1, ed> 1];
0252    img.elem_data= [1;1.1];
0253    show_3d_slices(img,[0],[0.2],[0]);
0254 
0255    subplot(4,4,14)
0256 % With internal electrode
0257    extra={'ball','solid ball = sphere(0.5,0.5,1;0.1);'};
0258    fmdl= ng_mk_cyl_models(2,[4,1],[0.2],extra); 
0259    fmdl.mat_idx_to_electrode.nodes_electrode = true;
0260    fmdl= mat_idx_to_electrode(fmdl,{2});
0261    show_3d_slices(mk_image(fmdl,1),[1.0],[0.5],[0.5]);
0262     
0263    subplot(4,4,15)
0264 % With internal electrode
0265    extra={'ball','solid ball = sphere(0.5,0.5,1;0.1);'};
0266    fmdl= ng_mk_cyl_models(2,[4,1],[0.2],extra); 
0267    fmdl.mat_idx_to_electrode.nodes_electrode = false;
0268    fmdl= mat_idx_to_electrode(fmdl,{2});
0269    show_3d_slices(mk_image(fmdl,1),[1.0],[0.5],[0.5]);