/
ea_add_overlay_singlefile.m
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ea_add_overlay_singlefile.m
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function cuts=ea_add_overlay(boundboxmm,cuts,tracor,options)
% This function overlays atlas data over 2d-slice views to be exported by
% LEAD-DBS. The function is called from ea_writeplanes.m
% __________________________________________________________________________________
% Copyright (C) 2014 Charite University Medicine Berlin, Movement Disorders Unit
% Andreas Horn
set(0,'CurrentFigure',cuts)
try
set(cuts,'GraphicsSmoothing','on')
end
% load/generate atlas_index.mat
if ~isfield(options,'atlases') % atlases structure can be handed down directly within options struct.
if ~exist([ea_space(options,'atlases'),options.atlasset,filesep,'atlas_index.mat'],'file')
atlases=ea_genatlastable([],ea_space(options,'atlases'),options);
else
load([ea_space(options,'atlases'),options.atlasset,filesep,'atlas_index.mat']);
atlases=ea_genatlastable(atlases,ea_space(options,'atlases'),options);
end
else
atlases=options.atlases;
end
for atlas=1:length(atlases.names)
for side=detsides(atlases.types(atlas))
planemm=[boundboxmm{1}(:),boundboxmm{2}(:),boundboxmm{3}(:)];
%planemm=round(planemm);
try
thresh=ea_detthresh(atlases,atlas,atlases.XYZ{atlas,side}.val);
catch % fibertracts
thresh=0.5;
end
atlmm=atlases.XYZ{atlas,side}.mm(:,1:3);
%ratlmm=round(atlmm);
try
atlvx=atlases.XYZ{atlas,side}.vx;
atlval=atlases.XYZ{atlas,side}.val;
catch % fibertracts
atlvx=round(atlmm);
for dim=1:3
atlvx(:,dim)=atlvx(:,dim)-min(atlvx(:,dim));
end
atlval=ones(size(atlmm,1),1);
end
atlhts=atlmm(:,ea_intersecdim(tracor));
planehts=planemm(:,ea_intersecdim(tracor));
dists=abs(atlhts-planehts(1));
try
dists=dists<abs(atlases.XYZ{atlas,side}.dims(ea_intersecdim(tracor)))*3;
catch % fibertracts
dists=dists<1*2.5;
end
if any(dists) % only if intersection exists plot the atlas.
xyatl=atlvx(dists,ea_planesdim(tracor));
xyatlmm=atlmm(dists,ea_planesdim(tracor));
valatl=atlval(dists);
for d=1:2
[~,minix]=min(xyatl(:,d));
[~,maxix]=max(xyatl(:,d));
try
atlbb(d,:)=[xyatlmm(minix,d);xyatlmm(maxix,d)];
catch
keyboard
end
end
xyatl(:,1)=xyatl(:,1)-min(xyatl(:,1))+1;
xyatl(:,2)=xyatl(:,2)-min(xyatl(:,2))+1;
slice=zeros(max(xyatl(:,1)),max(xyatl(:,2)));
slice(sub2ind(size(slice),xyatl(:,1),xyatl(:,2)))=valatl;
if ~any(size(slice)==1) % exception for problems with onedimensional slices
slice=interp2(slice,3);
slice(slice<thresh)=0;
slice=slice';
maxcolor=64;
try
if ischar(options.colormap)
jetlist = eval(options.colormap);
else
jetlist = options.colormap;
end
catch
try
jetlist=atlases.colormap;
catch
try
jetlist=eval(atlases.colormap);
catch
jetlist=jet;
end
end
end
atlases.colormap=jetlist;
try % see if there is explicit color information for this atlas
atlasc=squeeze(jetlist(round(atlases.colors(atlas)),:)); % color for toggle button icon
catch
atlases.colors(atlas)=atlas*(maxcolor/length(atlases.names));
atlasc=squeeze(jetlist(round(atlases.colors(atlas)),:)); % color for toggle button icon
end
colorf=zeros(size(slice,1),size(slice,2),3);
colorf(:,:,1)=atlasc(1);
colorf(:,:,2)=atlasc(2);
colorf(:,:,3)=atlasc(3);
%% color_overlay:
if options.d2.col_overlay
set(0,'CurrentFigure',cuts)
cof = image(colorf);
set(cof,'XData',linspace(atlbb(1,1),atlbb(1,2)),'YData',linspace(atlbb(2,1),atlbb(2,2)));
slice=slice./max(slice(:));
slice=slice*options.d2.atlasopacity;
set(cof, 'AlphaData', slice)
end
%% contour overlay:
if options.d2.con_overlay
if any(slice(:));
try
bw=bwconncomp(slice);
catch % no image toolbox available.
bw=ea_conncomp(logical(slice));
end
for cp=1:length(bw.PixelIdxList)
slice(:)=0;
slice(bw.PixelIdxList{cp})=1;
[c] = contourc(ea_zeroframe(slice),1);
c=c(:,2:end);
[~,yy]=find(c<1);
c(:,yy)=[];
dd=sum(abs(diff(c'))');
ix=[];
if any(dd>3) % detect jumps in contour (=inner holes)
ix=find(dd>3);
ix=[ix,size(c,2)];
end
cscale=c;
for dim=1:2
cscale(dim,:)=((c(dim,:)/size(slice',dim))*(atlbb(dim,2)-atlbb(dim,1)))+atlbb(dim,1);
end
set(0,'CurrentFigure',cuts)
if isempty(ix)
warning('off')
plot(cscale(1,:),cscale(2,:),'color',options.d2.con_color);
warning('on')
else
startPoint=1;
for plots=1:length(ix) % this happens if contour has an "inner hole"
plot(cscale(1,startPoint:ix(plots)),cscale(2,startPoint:ix(plots)),'color',options.d2.con_color);
startPoint=ix(plots)+1;
end
end
end
end
end
if options.d2.lab_overlay
if any(slice(:));
centr=mean(xyatlmm(valatl>thresh,:));%ea_centroid(logical(slice));
an=ea_underscore2space(atlases.names{atlas}(1:find(atlases.names{atlas}=='.')-1));
try
set(0,'CurrentFigure',cuts)
text(centr(1),centr(2),an,'color',options.d2.con_color,'VerticalAlignment','middle','HorizontalAlignment','center');
catch
end
end
end
end
end
end
end
function sides=detsides(opt)
switch opt
case 1 % left hemispheric atlas
sides=1;
case 2 % right hemispheric atlas
sides=2;
case 3
sides=1:2;
case 4
sides=1:2;
case 5
sides=1; % midline
end
function in=ea_intersecdim(tracor)
switch tracor
case 1
in=3;
case 2
in=2;
case 3
in=1;
end
function pl=ea_planesdim(tracor)
switch tracor
case 1
pl=[1,2];
case 2
pl=[1,3];
case 3
pl=[2,3];
end
function fslice=ea_zeroframe(slice)
fslice=zeros(size(slice)+[2,2]);
fslice(2:end-1,2:end-1)=slice;