function varargout = metchgui(varargin)
% alldata = metchgui(node,elem,points,pface) or metchgui(volume,points,pface)
%
% A GUI to register a point cloud to a mesh or volumetric image
%
% author: Qianqian Fang <q.fang at neu.edu>
% date: 12/16/2008
%
% parameters:
% node: node coordinate of the surface mesh (nn x 3)
% elem: element list of the surface mesh (3 columns for
% triangular mesh, 4 columns for cubic surface mesh)
% points: the coordinates (3 columns for x/y/z) of the
% point cloud which you want to register
% pface:trianglular surface defined on the point cloud.
% pface is optional; if presents, metch will display
% a surface object instead of a point cloud.
%
% the input can also be two parameters in form of metchgui(volume,points),
% where volume is a 3D image (array).
%
% outputs:
% alldata: a structrure containing all processing outputs
% the fields include:
% .node: the input node
% .elem: the input surface mesh elements
% .volume: if the input volumetric image
% .A0: the affine rotation for selected point pairs (after Initialize)
% .b0: the affine translation for selected point pairs (after Initialize)
% .A: the affine rotation for the point cloud (after Optimize)
% .b: the affine translation for the point cloud (after Optimize)
% .points: the input point cloud
% .pointsinit: the point cloud after initialization
% .pointsopt: the point cloud after optimization
% .pointsproj: the point cloud after projecting to the surface
% .initplot: the handle to the point cloud plot after init
% .optplot: the handle to the point cloud plot after optimization
% .projplot: the handle to the point cloud plot after projection
%
% If user supplys an output variable, the GUI will not return until the
% user hits the "close" button or close the window; if user does not
% supply any output, the call will return immediately; any data user
% intends to save, he has to click on "Save Session" button and provides
% a mat-file file name. A single structure named "metchsession" will be
% stored in this file.
%
% example: (meshasphere/meshunitsphere are defined in iso2mesh http://iso2mesh.sf.net)
%
% [noderef,faceref,elemref]=meshunitsphere(0.08,10);
% [no,fc]=removeisolatednode(noderef(:,1:3),faceref(:,1:3));
% [node,face,elem]=meshasphere([10 20 15],3,0.5,10);
% [no2,fc2]=removeisolatednode(node(:,1:3),face(:,1:3));
% alldata = metchgui(no,fc,no2);
% % or alldata = metchgui(no,fc,no2,fc2);
%
% Please find more information at http://iso2mesh.sf.net/cgi-bin/index.cgi?metch
%
% this function is part of "metch" toobox, see COPYING for license
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @metchgui_OpeningFcn, ...
'gui_OutputFcn', @metchgui_OutputFcn, ...
'gui_LayoutFcn', [] , ...
'gui_Callback', []);
if nargin && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
if nargout
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}, 'hasoutput');
else
gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT
% --- Executes just before metchgui is made visible.
function metchgui_OpeningFcn(hObject, eventdata, handles, varargin)
handles.hasoutput=0;
if(isempty(varargin))
fprintf(1,'Metch GUI must be called with parameters:\nFormat: alldata = metchgui(node,elem,points,pface);\n');
close(handles.MetchGUI);
return;
end
if(ischar(varargin{end}) && strcmp(varargin{end},'hasoutput'))
handles.hasoutput=1;
varargin(end)=[];
end
handles.output = hObject;
set(handles.btAddMeshPt,'userdata',[handles.axMesh,handles.btAddMeshPt,handles.btAddCloudPt]);
set(handles.btAddCloudPt,'userdata',[handles.axMesh,handles.btAddCloudPt,handles.btAddMeshPt]);
% if uses supplied 2 input variables, assume a volume image and a point cloud
if(isnumeric(varargin{1}) && length(size(varargin{1}))==3)
vol=varargin{1};
pt=varargin{2};
dat.volume=vol;
dat.points=pt;
slice=round(size(vol,3)/2);
hs=imagesc(vol(:,:,slice),'parent',handles.axMesh);
set(handles.slPos,'max',size(vol,3),'min',1,'value',slice);
if(length(varargin)>=3)
pface=varargin{3};
dat.pface=pface;
trisurf(pface(:,1:3),pt(:,1),pt(:,2),pt(:,3),'parent',handles.axPoints);
else
%plot3(pt(:,1),pt(:,2),pt(:,3),'.','parent',handles.axPoints);
ptcolor=(pt-repmat(min(pt),size(pt,1),1))./repmat(max(pt)-min(pt),size(pt,1),1);
drawnow;
scatter3(pt(:,1),pt(:,2),pt(:,3),3,ptcolor,'filled');
end
set(handles.MetchGUI,'userdata',dat);
axis(handles.axMesh,'equal');
axis(handles.axPoints,'equal');
axis(handles.axMesh,'off');
grid(handles.axPoints,'on');
%axis(handles.axPoints,'off');
set(handles.axMesh,'tag','axMesh');
set(handles.axPoints,'tag','axPoints');
set(handles.slPos,'visible','on');
set(handles.lbZPos,'visible','on');
rotate3d(handles.axPoints,'on');
rotate3d(gcf,'on');
end
% if uses supplied 3 input variables, assume a surface mesh and a point cloud/surface
if(length(varargin)>=3 && length(size(varargin{1}))==2)
node=varargin{1};
elem=varargin{2};
pt=varargin{3};
dat.node=node;
dat.elem=elem;
dat.points=pt;
if(length(varargin)>=4)
pface=varargin{4};
dat.pface=pface;
end
set(handles.MetchGUI,'userdata',dat);
drawinit(handles,dat)
end
guidata(hObject, handles);
if(handles.hasoutput)
uiwait(handles.MetchGUI);
end
%---------------------------------------------------------------------------
function drawinit(handles,dat)
node=dat.node;
elem=dat.elem;
pt=dat.points;
hs=trisurf(elem,node(:,1),node(:,2),node(:,3),'parent',handles.axMesh);
%set(hs,'linestyle','none');
%set(hs,'facecolor','b','facealpha',0.8);
%plot3(pt(:,1),pt(:,2),pt(:,3),'.','parent',handles.axPoints);
if(~isfield(dat,'pface'))
ptcolor=(pt-repmat(min(pt),size(pt,1),1))./repmat(max(pt)-min(pt),size(pt,1),1);
drawnow;
scatter3(pt(:,1),pt(:,2),pt(:,3),3,ptcolor,'filled');
else
trisurf(dat.pface,pt(:,1),pt(:,2),pt(:,3),'parent',handles.axPoints);
end
%hold(handles.axPoints,'on');
%plot3(pt(5:7,1),pt(5:7,2),pt(5:7,3),'ro','parent',handles.axPoints);
axis(handles.axMesh,'equal');
axis(handles.axPoints,'equal');
axis(handles.axMesh,'off');
%axis(handles.axPoints,'off');
set(handles.axMesh,'tag','axMesh');
set(handles.axPoints,'tag','axPoints');
rotate3d(handles.axPoints,'on');
rotate3d(handles.axMesh,'on');
rotate3d(gcf,'on');
%---------------------------------------------------------------------------
function varargout = metchgui_OutputFcn(hObject, eventdata, handles)
if(length(handles) && isfield(handles,'output') && isfield(handles,'hasoutput') && handles.hasoutput)
handles.output=get(handles.MetchGUI,'userdata');
varargout{1} =handles.output;
close(handles.MetchGUI);
end
%---------------------------------------------------------------------------
function lbMesh_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
%---------------------------------------------------------------------------
function lbPoints_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
%---------------------------------------------------------------------------
function edit1_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
%---------------------------------------------------------------------------
function edit2_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
%---------------------------------------------------------------------------
function edit3_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
%---------------------------------------------------------------------------
function isSelect_Callback(hObject, eventdata, handles)
if(get(hObject,'Value'))
datacursormode(gcf,'on');
set(datacursormode(gcf),'UpdateFcn',@myupdatefcn)
else
datacursormode(gcf,'off');
rotate3d(gcf,'on');
end
%---------------------------------------------------------------------------
% the respond function when there is a data-tip to popup
%---------------------------------------------------------------------------
function txt=myupdatefcn(empt,event_obj)
pos = get(event_obj,'Position');
idx= get(event_obj,'DataIndex');
if(length(pos)==3)
txt = {['x: ',num2str(pos(1))],...
['y: ',num2str(pos(2))],['z: ',num2str(pos(3))],['index:', num2str(idx)]};
elseif(length(pos)==2)
txt = {['x: ',num2str(pos(1))],['y: ',num2str(pos(2))]};
end
targetup=get(get(event_obj,'Target'),'parent');
set(targetup,'userdata',struct('pos',pos,'idx',idx));
if(targetup==findobj('tag','axMesh'))
set(findobj('tag','btAddMeshPt'),'enable','on');
set(findobj('tag','btAddCloudPt'),'enable','off');
elseif(targetup==findobj('tag','axPoints'))
set(findobj('tag','btAddMeshPt'),'enable','off');
set(findobj('tag','btAddCloudPt'),'enable','on');
end
%---------------------------------------------------------------------------
function bInit_Callback(hObject, eventdata, handles)
mapto=get(handles.lbMesh,'userdata');
mapfrom=get(handles.lbPoints,'userdata');
maptoidx=get(handles.txMapTo,'userdata');
mapfromidx=get(handles.txMapFrom,'userdata');
if(length(mapto)<4 | length(mapfrom)<4)
msgbox('You have to select >3 points from the point cloud plot and corresponding points from the mesh','Error','error');
return;
end
[A,b]=affinemap(mapfrom,mapto)
dat=get(handles.MetchGUI,'userdata');
dat.A0=A;
dat.b0=b;
newpt=(A*dat.points'+repmat(b(:),1,size(dat.points,1)))';
dat.pointsinit=newpt;
hold(handles.axMesh,'on');
if(isfield(dat,'initplot'))
delete dat.initplot;
dat.initplot=0;
end
dat.initplot=plot3(newpt(:,1),newpt(:,2),newpt(:,3),'r.','parent',handles.axMesh);
dat.fromidx=mapfromidx;
dat.toidx=maptoidx;
set(handles.MetchGUI,'userdata',dat);
%---------------------------------------------------------------------------
function axPoints_ButtonDownFcn(hObject, eventdata, handles)
if(get(handles.btSelect,'value')==1)
pp=getCursorInfo(datacursormode(gcf));
str=[get(handles.lbPoints,'string');mat2str(pp.Position)];
set(handles.lbPoints,'string',str);
end
%---------------------------------------------------------------------------
function addselectedpt(pos,idx,lb)
if(isempty(get(lb,'value')))
set(lb,'value',1);
end
listpt=get(lb,'string');
listpt{end+1}=[num2str(idx) ':' mat2str(pos)];
set(lb,'string',listpt);
set(lb,'userdata',[get(lb,'userdata');pos]);
%---------------------------------------------------------------------------
function btAddMeshPt_Callback(hObject, eventdata, handles)
dat=get(handles.axMesh,'userdata');
dat0=get(handles.MetchGUI,'userdata');
if(isfield(dat0,'volume'))
dat.pos(:,3)=get(handles.slPos,'value');
end
if(isfield(dat,'pos'))
addselectedpt(dat.pos,dat.idx,handles.lbMesh);
set(handles.txMapTo,'userdata',[get(handles.txMapTo,'userdata');dat.idx]);
dat0.mapto=get(handles.lbMesh,'userdata');
dat0.maptoidx=get(handles.txMapTo,'userdata');
set(handles.MetchGUI,'userdata',dat0);
else
msgbox('No point was selected. Please click on "Select" and select a point on the mesh or point cloud','Error','error');
return;
end
%---------------------------------------------------------------------------
function btAddCloudPt_Callback(hObject, eventdata, handles)
dat=get(handles.axPoints,'userdata');
dat0=get(handles.MetchGUI,'userdata');
if(isfield(dat,'pos'))
addselectedpt(dat.pos,dat.idx,handles.lbPoints);
set(handles.txMapFrom,'userdata',[get(handles.txMapFrom,'userdata');dat.idx]);
dat0.mapfrom=get(handles.lbPoints,'userdata');
dat0.mapfromidx=get(handles.txMapFrom,'userdata');
set(handles.MetchGUI,'userdata',dat0);
else
msgbox('No point was selected. Please click on "Select" and select a point on the mesh or point cloud','Error','error');
return;
end
%---------------------------------------------------------------------------
function btOptimize_Callback(hObject, eventdata, handles)
dat=get(handles.MetchGUI,'userdata');
if(isfield(dat,'A0') && isfield(dat,'b0')& isfield(dat,'node')& isfield(dat,'elem')& ...
isfield(dat,'pointsinit')& isfield(dat,'toidx')& isfield(dat,'fromidx'))
pmask=-1*ones(size(dat.pointsinit,1),1);
pmask(dat.fromidx)=dat.toidx;
if(isfield(dat,'A') && isfield(dat,'b'))
[Anew,bnew,posnew]=regpt2surf(dat.node,dat.elem,dat.points,pmask,dat.A,dat.b,ones(12,1),20);
else
[Anew,bnew,posnew]=regpt2surf(dat.node,dat.elem,dat.points,pmask,dat.A0,dat.b0,ones(12,1),20);
end
dat.A=Anew;
dat.b=bnew;
dat.pointsopt=posnew;
if(isfield(dat,'optplot') && dat.optplot)
delete dat.optplot;
dat.optplot=0;
end
dat.optplot=plot3(posnew(:,1),posnew(:,2),posnew(:,3),'g+','parent',handles.axMesh);
else
msgbox('You have to select 4 points and click "Initialize" button first','Error','error');
return;
end
set(handles.MetchGUI,'userdata',dat);
%---------------------------------------------------------------------------
function slPos_Callback(hObject, eventdata, handles)
dat=get(handles.MetchGUI,'userdata');
if(isfield(dat,'volume'))
hold(handles.axMesh,'off');
imagesc(dat.volume(:,:,round(get(hObject,'value'))),'parent',handles.axMesh);
set(handles.axMesh,'tag','axMesh');
set(handles.lbZPos,'string',num2str(round(get(hObject,'value'))));
end
set(handles.MetchGUI,'userdata',dat);
%---------------------------------------------------------------------------
function slPos_CreateFcn(hObject, eventdata, handles)
if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor',[.9 .9 .9]);
end
%--------------------------------------------------------------------------
function btProj_Callback(hObject, eventdata, handles)
dat=get(handles.MetchGUI,'userdata');
if(isfield(dat,'pointsopt'))
if(isfield(dat,'projplot') && dat.projplot)
delete dat.projplot;
dat.projplot=0;
end
nv=nodesurfnorm(dat.node,dat.elem);
[d2surf,cn]=dist2surf(dat.node,nv,dat.pointsopt);
[dat.pointsproj dat.elemid dat.weight]=proj2mesh(dat.node,dat.elem,dat.pointsopt,nv,cn);
hold(handles.axMesh,'on');
dat.projplot=plot3(dat.pointsproj(:,1),dat.pointsproj(:,2),dat.pointsproj(:,3),'c.','parent',handles.axMesh);
else
msgbox('You have to first select 4 points, then click "Initialize" and "Optimize" button','Error','error');
return;
end
set(handles.MetchGUI,'userdata',dat);
%--------------------------------------------------------------------------
function btSaveRes_Callback(hObject, eventdata, handles)
[filename, pathname] = uiputfile('*.mat', 'Save Metch Workspace as');
mapto=get(handles.lbMesh,'userdata');
mapfrom=get(handles.lbPoints,'userdata');
maptoidx=get(handles.txMapTo,'userdata');
mapfromidx=get(handles.txMapFrom,'userdata');
metchsession=get(handles.MetchGUI,'userdata');
if(~isempty(mapto)) metchsession.mapto=mapto; end
if(~isempty(mapfrom)) metchsession.mapfrom=mapfrom; end
if(~isempty(maptoidx)) metchsession.maptoidx=maptoidx; end
if(~isempty(mapfromidx)) metchsession.mapfromidx=mapfromidx; end
fname=[pathname filename];
save(fname,'metchsession');
%--------------------------------------------------------------------------
function btLoadSession_Callback(hObject, eventdata, handles)
[filename, pathname] = uigetfile('*.mat', 'Load Metch Workspace from');
fname=[pathname filename];
load(fname);
handle.output=metchsession;
cla(handles.axMesh);
cla(handles.axPoints);
drawinit(handles,metchsession.node,metchsession.elem,metchsession.points);
%--------------------------------------------------------------------------
function btPlotResults_Callback(hObject, eventdata, handles)
function btClose_Callback(hObject, eventdata, handles)
guidata(hObject,handles);
uiresume;
function btHelp_Callback(hObject, eventdata, handles)
helpmsg={
'Metch GUI: A mesh/volume registration toolbox',
'',
'Author: Qianqian Fang <q.fang at neu.edu>',
' Martinos Center for Biomedical Imaging',
' Charlestown, MA 02129, USA',
'',
'== Description of the workflow ==',
'',
' 1. when the GUI pops up, it will display the mesh and the points,',
' you can rotate both plots so that you can identify the matching ',
' features',
' 2. switch on "Select" mode, then, click on a land-mark point on the point',
' plot, when a data-tip shows up, click "Add Selected" button',
' 3. click on the corresponding position on the mesh, and click',
' "Add Selected" ',
' 4. repeat the above for at least 4 point pairs (you can select more);',
' if you want to change views, switch off "Select" box and rotate;',
' after rotation, switch on "Select" box again',
' 5. click "Initialize": this will create the initial mapping using the',
' selected point pairs',
' 6. click "Optimize": this will fit the surface with the whole point cloud',
' 7. click "Proj2Mesh": this will project the fitted point clouds onto the',
' mesh',
' 8. you can quit the GUI by hit "Close", your results will be saved to reg',
' 9. close the window '};
helpdlg(helpmsg);
