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report3dmodel.m
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function report3dmodel(varargin)
% REPORT3DMODEL
% Functions for doing 3D model reports
% Moved out from segment_main by Nisse Lundahl
%GUI to show 3D display of segmentation.
% TODO
% - get longaxismotion corrected
% - rvendo may be improperly sampled radially. This should be fixed in
% checkconsistancy.
% - -clean up persistants...
% Check if possible not to use grid
global DATA SET
if nargin > 0 && isequal(varargin{1},'rotated')
report3dmodelrotated;
return
end
if nargin==0
%------------------------------------------ No input arguments => setup
init;
else
gui = DATA.GUI.Report3DModel;
%Input arguments start different callbacks
switch varargin{1}
case 'play'
DATA.StartFrame = gui.t;
DATA.StartTime = now;
while ~gui.closing && get(gui.handles.playtogglebutton,'value')
gui.t = segment('getframenumber');
pause(0.5*SET(gui.no).BeatTime/SET(gui.no).TSize);
report3dmodel('update');
end
case 'radialvel'
if get(gui.handles.radialvelradiobutton,'value')
gui.handles.radvel = calcfunctions('calcradialvelocity',gui.no);
else
set(DATA.Handles.endosurf,...
'Cdata',repmat(97,size(EndoX,1),size(EndoX,3)));
end
report3dmodel('update');
case 'prev'
i=find(gui.t==gui.indTn);
if (i==1)
gui.t=gui.indTn(end);
else
gui.t=gui.indTn(i-1);
end
report3dmodel('update');
case 'next'
i=find(gui.t==gui.indTn);
if (i==length(gui.indTn))
gui.t=gui.indTn(1);
else
gui.t=gui.indTn(i+1);
end
report3dmodel('update');
case 'dias'
gui.t=SET(gui.no).EDT;
report3dmodel('update');
case 'sys'
gui.t=SET(gui.no).EST;
report3dmodel('update');
case 'close'
gui.closing=true;
pause(0.5)
%pause(0.5*SET(gui.no).BeatTime/SET(gui.no).TSize);
%Close the windows
try
delete(4);
catch %#ok<CTCH>
%Do nothing if failed
end
try
delete(gui.fig);
catch %#ok<CTCH>
%Do nothing if failed
end
DATA.GUI.Report3DModel = [];
case 'update'
%--- Refresh the display
if (gui.closing)
try
set(gui.handles.playtogglebutton,'value',0);
catch %#ok<CTCH>
end
return;
end
%try
%Update endosurf
if get(gui.handles.endocheckbox,'value')
set(DATA.Handles.endosurf,...
'visible','on',...
'Xdata',squeeze(gui.EndoX(:,gui.t,:)),... %EH:
'Ydata',squeeze(gui.EndoY(:,gui.t,:)),... %EH:
'Zdata',gui.EndoZ,...
'Alphadata',mygetvalue(gui.handles.endoslider)*ones(size(gui.EndoZ)));
if get(gui.handles.radialvelradiobutton,'value')
%97 = 64+1+32
set(DATA.Handles.endosurf,...
'Cdata',97+(32/DATA.MaxRadialVel)*squeeze(gui.handles.radvel(:,t,ind)));
end
else
try
set(DATA.Handles.endosurf,'visible','off');
catch %#ok<CTCH>
end
end
%Update episurf
if get(gui.handles.epicheckbox,'value')
set(DATA.Handles.episurf,...
'visible','on',...
'Xdata',squeeze(gui.EpiX(:,gui.t,:)),... %EH:
'Ydata',squeeze(gui.EpiY(:,gui.t,:)),... %EH:
'Zdata',gui.EpiZ,...
'Alphadata',mygetvalue(gui.handles.epislider)*ones(size(gui.EpiZ)));
else
try
set(DATA.Handles.episurf,'visible','off');
catch %#ok<CTCH>
end
end
%Update RVendo surf
if get(gui.handles.rvendocheckbox,'value')
set(DATA.Handles.rvendosurf,...
'visible','on',...
'Xdata',squeeze(gui.RVEndoX(:,gui.t,:)),... %EH:
'Ydata',squeeze(gui.RVEndoY(:,gui.t,:)),... %EH:
'Zdata',gui.RVEndoZ,...
'Alphadata',mygetvalue(gui.handles.rvendoslider)*ones(size(gui.RVEndoZ)));
else
try
set(DATA.Handles.rvendosurf,'visible','off');
catch %#ok<CTCH>
end
end
%Update RVepi surf
if get(gui.handles.rvepicheckbox,'value')
set(DATA.Handles.rvepisurf,...
'visible','on',...
'Xdata',squeeze(gui.RVEpiX(:,gui.t,:)),... %EH:
'Ydata',squeeze(gui.RVEpiY(:,gui.t,:)),... %EH:
'Zdata',gui.RVEpiZ,...
'Alphadata',mygetvalue(gui.handles.rvepislider)*ones(size(gui.RVEpiZ)));
else
try
set(DATA.Handles.rvepisurf,'visible','off');
catch %#ok<CTCH>
end
end
%Update annotation points
if mygetvalue(gui.handles.annotationpointscheckbox)
set(DATA.Handles.annotationpoints3d, ...
'visible','on', ...
'XData',gui.PointX, ...
'YData',gui.PointY, ...
'ZData',gui.PointZ);
else
try
set(DATA.Handles.annotationpoints3d,'visible','off');
catch %#ok<CTCH>
end
end
%Update measurements
if mygetvalue(gui.handles.measurementscheckbox)
for mloop = 1:numel(gui.MeasureX)
set(DATA.Handles.measurements3d(mloop), ...
'visible','on', ...
'XData',gui.MeasureX{mloop}, ...
'YData',gui.MeasureY{mloop}, ...
'ZData',gui.MeasureZ{mloop});
end
else
try
set(DATA.Handles.measurements3d,'visible','off');
catch %#ok<CTCH>
end
end
%Update scar
if mygetvalue(gui.handles.scarcheckbox)
set(DATA.Handles.scar3d, ...
'visible','on', ...
'XData',gui.ScarX, ...
'YData',gui.ScarY, ...
'ZData',gui.ScarZ);
else
try
set(DATA.Handles.scar3d,'visible','off');
catch %#ok<CTCH>
end
end
%Update short axis slice
if get(gui.handles.shortslicescheckbox,'value')
slice = 1+SET(gui.no).ZSize-round(mygetvalue(gui.handles.shortsliceslider));
%the most basal should give z=0
z = repmat(...
(SET(gui.no).SliceThickness+SET(gui.no).SliceGap)*(slice-gui.basalslice),...
SET(gui.no).XSize,SET(gui.no).YSize);
set(DATA.Handles.lvcutshort,'Zdata',-z);
set(DATA.Handles.lvcutshort,'visible','on',...
'CDATA',1+(63*double(squeeze(SET(gui.no).IM(:,:,gui.t,slice)))));
else
set(DATA.Handles.lvcutshort,'visible','off');
end
%Update long-axis slice
if get(gui.handles.longslicescheckbox,'value')
z = max(min(SET(gui.no).YSize*mygetvalue(gui.handles.longsliceslider),SET(gui.no).YSize),1);
set(DATA.Handles.lvcutlong,...
'visible','on',...
'Ydata',repmat(SET(gui.no).ResolutionY*z,[SET(gui.no).XSize SET(gui.no).ZSize]),...
'Cdata',1+(63*double(squeeze(SET(gui.no).IM(:,round(z),gui.t,:)))));
else
set(DATA.Handles.lvcutlong,'visible','off');
end
if DATA.Record
drawnow;
DATA.MovieFrame = mygetframe(4);
export('exportmovierecorder_Callback','newframe');
end
%catch
%Did not manage to update correctly, give it up!
% report3dmodel('close');
%end
end
end
%----------------------------
function report3dmodelrotated
%----------------------------
%Display 3D model of rotated image stacks.
global SET NO
fig = figure(88);
clf;
hold on;
stateandicon = viewfunctions('iconson',{'hidelv','hiderv'});
state = [stateandicon{:,1}];
if state(1)
if ~isempty(SET(NO).EndoX)
rotatedplothelper(...
SET(NO).EndoX,...
SET(NO).EndoY,...
'r-');
end
if ~isempty(SET(NO).EpiX)
rotatedplothelper(...
SET(NO).EpiX,...
SET(NO).EpiY,...
'g-');
end
end
if state(2)
if ~isempty(SET(NO).RVEndoX)
rotatedplothelper(...
SET(NO).RVEndoX,...
SET(NO).RVEndoY,...
'm-');
end
if ~isempty(SET(NO).RVEpiX)
rotatedplothelper(...
SET(NO).RVEpiX,...
SET(NO).RVEpiY,...
'c-');
end
end
ind = find(SET(NO).Point.T==SET(NO).CurrentTimeFrame);
for loop=1:length(ind)
[x,y,z] = calcfunctions('cyl2cart',...
SET(NO).Point.X(ind(loop)),...
SET(NO).Point.Y(ind(loop)),...
SET(NO).Point.Z(ind(loop)),...
SET(NO).ZSize,...
SET(NO).RotationCenter);
plot3(x,y,z,'r*');
end
axis image off;
hold off;
set(fig,'Numbertitle','off','Name','3D visualization of rotated stacks.');
cameratoolbar(fig,'show');
%------------------------------------------
function rotatedplothelper(xc,yc,linecolor)
%------------------------------------------
%Helper function to display segmentation in rotated image stacks.
global SET NO
tf = SET(NO).CurrentTimeFrame;
xmin = 1e10;
xmax = -1e10;
for zloop=1:SET(NO).ZSize
xmin = min(min(xc(:,tf,zloop)),xmin);
xmax = max(max(xc(:,tf,zloop)),xmax);
end
xrange = linspace(xmin,xmax,20);
for zloop=1:SET(NO).ZSize
%drawcontour
[x,y,z] = calcfunctions('cyl2cart',...
xc(:,tf,zloop),...
yc(:,tf,zloop),...
zloop,...
SET(NO).ZSize,... %Number of slices
SET(NO).RotationCenter); %Rotation center
plot3(x,y,z,linecolor);
end
%---Draw_lines
for loop=1:length(xrange)
%Loop over rows
r = [];
slice = [];
for zloop=1:SET(NO).ZSize
xt = xc(:,tf,zloop);
yt = yc(:,tf,zloop);
%Find indices that crosses
ind = find(...
((xt(2:end)>xrange(loop))&(xt(1:(end-1))<xrange(loop)))|...
((xt(2:end)<xrange(loop))&(xt(1:(end-1))>xrange(loop))));
for iloop=1:length(ind)
if yt(ind(iloop))>SET(NO).RotationCenter
r = [r yt(ind(iloop))-SET(NO).RotationCenter]; %#ok<AGROW>
slice = [slice zloop]; %#ok<AGROW>
else
r = [r SET(NO).RotationCenter-yt(ind(iloop))]; %#ok<AGROW>
slice = [slice zloop+SET(NO).ZSize]; %#ok<AGROW>
end
end
end
%--- "Sort it"
while ~isempty(slice)
drawr = [];
drawslice = [];
nextslice = min(slice); %Start with first slice
while any(slice==nextslice)
%Find maximum radius at nextslice
[~,ind] = max(r.*(slice==nextslice));
%Add to list of lines to draw
drawr = [drawr r(ind)]; %#ok<AGROW>
drawslice = [drawslice slice(ind)]; %#ok<AGROW>
%Remove taken point from list
logim = true(size(r));
logim(ind) = false;
r = r(logim);
slice = slice(logim);
%Continue along the slices
nextslice = nextslice+1;
end
%--- Plot the line section
if length(drawr)>1
%Upsample it
drawr = interp1(drawr,linspace(1,length(drawr),length(drawr)*10),'pchip');
drawslice = interp1(drawslice,linspace(1,length(drawslice),length(drawslice)*10),'linear');
%Make it go around
if 1==1
if ...
isequal(drawslice(1),1)&&...
isequal(drawslice(end),SET(NO).ZSize*2)
drawslice = [drawslice linspace(0,1,10)]; %#ok<AGROW>
drawr = [drawr interp1([drawr(end) drawr(1)],linspace(1,2,10))]; %#ok<AGROW>
end
end
angle = (drawslice-1)*pi/SET(NO).ZSize;
x = drawr.*sin(angle)+SET(NO).RotationCenter;
y = drawr.*cos(angle)+SET(NO).RotationCenter;
z = repmat(xrange(loop),size(x));
plot3(x,y,z,linecolor);
end
end
end %Loop over rows
%------------
function init
%------------
%initiating the 3D model interface
global DATA SET NO
if SET(NO).Rotated
report3dmodelrotated;
return;
end
if SET(NO).ZSize<2
myfailed('Need to have more than one slice for viewing 3D-model.',DATA.GUI.Segment);
return;
end
if isempty(SET(NO).EndoX) || all(isnan(SET(NO).EndoX(:)))
myfailed('No LV endocardium available.',DATA.GUI.Segment);
return;
end
tempnos=NO;
imissingle=classcheckim(tempnos);%checks so that SET(tempnos).IM is single and can also convert from int16 to singel if user wants
if not(imissingle)
return;
end
%Initialize
if SET(NO).TSize>1
if isequal(SET(NO).EDT,SET(NO).EST)
mywarning('Warning, end-diastole occurs at the same time as end-systole. Use autodetect under edit menu.',DATA.GUI.Segment);
end
end
% segment('checkconsistency',1:SET(NO).TSize,1:SET(NO).ZSize);
doepi = ~isempty(SET(NO).EpiX) && ~all(isnan(SET(NO).EpiX(:)));
dorvendo = ~isempty(SET(NO).RVEndoX) && ~all(isnan(SET(NO).RVEndoX(:)));
dorvepi = ~isempty(SET(NO).RVEpiX) && ~all(isnan(SET(NO).RVEpiX(:)));
dopoints = ~isempty(SET(NO).Point.X);
domeasures = ~isempty(SET(NO).Measure);
doscar = ~isempty(SET(NO).Scar);
%Check data
ind = any(~isnan(SET(NO).EndoX(1,:,:)),2);
if doepi
ind = ind|any(~isnan(SET(NO).EpiX(1,:,:)),2);
end
if dorvendo
ind = ind|any(~isnan(SET(NO).RVEndoX(1,:,:)),2);
end
if dorvepi
ind = ind|any(~isnan(SET(NO).RVEpiX(1,:,:)),2);
end
nslices = sum(ind);
if (size(SET(NO).EndoX,2)>1)
indT=(sum(~isnan(SET(NO).EndoX(1,:,:)),3)>0);
else
indT=1;
end
indTn=find(indT);
t=indTn(1);
fendo=find(any(~isnan(SET(NO).EndoX(1,:,:)),2));
if doepi
fepi = find(any(~isnan(SET(NO).EpiX(1,:,:)),2));
end
if dorvendo
frvendo = find(any(~isnan(SET(NO).RVEndoX(1,:,:)),2));
end
if dorvepi
frvepi = find(any(~isnan(SET(NO).RVEpiX(1,:,:)),2));
end
if ((1+fendo(end)-fendo(1))~=length(fendo)) ||...
(doepi&&((1+fepi(end)-fepi(1))~=length(fepi))) ||...
(dorvendo &&((1+frvendo(end)-frvendo(1))~=length(frvendo))) || ...
(dorvepi &&((1+frvepi(end)-frvepi(1))~=length(frvepi)))
myfailed('There are gaps in the segmentation, continuous segmentation required.',DATA.GUI.Segment);
return
end
%longaxis = SET(NO).Longaxis-1; %=>mm
%Create plot figure
plotfig = figure(4);
setupicon(plotfig);
set(plotfig,'units','pixels','position',[193 200 500 500]);
set(plotfig,'renderer','opengl',...
'Name','3D model',...
'numbertitle','off',...
'menubar','none',...
'CloseRequestFcn',sprintf('report3dmodel(''close'')'));
%This CloseRequestFcn is set within guide for plotmodel.fig
%Open GUI
gui = mygui('plotmodel.fig');
DATA.GUI.Report3DModel = gui;
% Use system color scheme for figure:
set(gui.fig,'Color',DATA.GUISettings.BackgroundColor); %get(0,'defaultUicontrolBackgroundColor'));
gui.closing=false;
%Which one is the most basal slice
% if nslices>1
% gui.basalslice = find(ind);
% gui.basalslice = gui.basalslice(1);
% gui.numslice = nslices;
% else
% gui.basalslice = 1;
% gui.numslice = 0;
% end
gui.numslices=nslices;
gui.basalslice=1;
gui.t = t;
gui.indTn = indTn;
gui.no = NO;
%Modify GUI components
temp = get(gui.fig,'units');
set(gui.fig,'units','pixels');
set(gui.fig,'position',[700 200 300 500]);
set(gui.fig,'units',temp);
set(gui.handles.shortsliceslider,...
'min',1,...
'max',SET(NO).ZSize,...
'value',1, ...
'SliderStep',1/(SET(NO).ZSize-1)*[1 1]);
set(gui.handles.longsliceslider,...
'min',1/(SET(NO).XSize-1),...
'max',1,...
'value',1/2, ...
'SliderStep',1/(SET(NO).XSize-1)*[1 1]);
set(gui.handles.shortslicescheckbox,'value',1);
set(gui.handles.longslicescheckbox,'value',1);
set(gui.handles.endocheckbox,'value',1);
load Icons.mat
set(gui.handles.previcon,'CData',icon.prev);
set(gui.handles.playtogglebutton,'CData',icon.play);
set(gui.handles.nexticon,'CData',icon.next);
set(gui.handles.playtogglebutton,'value',0);
set(gui.handles.nexticon,'value',0);
set(gui.handles.previcon,'value',0);
if ~all(indT)
set(gui.handles.playtogglebutton,'enable','off');
end
if isempty(find(gui.indTn==SET(NO).EST, 1))
set(gui.handles.systolebutton,'enable','off');
end
if isempty(find(gui.indTn==SET(NO).EDT, 1))
set(gui.handles.diastolebutton,'enable','off');
end
if (size(gui.indTn)==1)
set(gui.handles.playtogglebutton,'enable','off');
set(gui.handles.nexticon,'enable','off');
set(gui.handles.previcon,'enable','off');
set(gui.handles.diastolebutton,'enable','off');
set(gui.handles.systolebutton,'enable','off');
end
if ~doepi
set(gui.handles.epicheckbox,'enable','off');
else
set(gui.handles.epicheckbox,'value',1);
end
if ~dorvendo
set(gui.handles.rvendocheckbox,'enable','off');
else
set(gui.handles.rvendocheckbox,'value',1);
end
if ~dorvepi
set(gui.handles.rvepicheckbox,'enable','off');
else
set(gui.handles.rvepicheckbox,'value',1);
end
if ~dopoints
set(gui.handles.annotationpointscheckbox,'enable','off');
else
set(gui.handles.annotationpointscheckbox,'value',1);
end
if ~domeasures
set(gui.handles.measurementscheckbox,'enable','off');
else
set(gui.handles.measurementscheckbox,'value',1);
end
if ~doscar
set(gui.handles.scarcheckbox,'enable','off');
else
set(gui.handles.scarcheckbox,'value',1);
end
if nslices<=2
%No slices => disable them
set(gui.handles.endocheckbox,'value',0);
set(gui.handles.epicheckbox,'value',0);
set(gui.handles.rvendocheckbox,'value',0);
set(gui.handles.rvepicheckbox,'value',0);
set([...
gui.handles.endocheckbox ...
gui.handles.epicheckbox...
gui.handles.rvendocheckbox...
gui.handles.rvepicheckbox],'enable','off');
end
if nslices>2
gui.EndoX = SET(NO).ResolutionX*SET(NO).EndoX;
gui.EndoY = SET(NO).ResolutionY*SET(NO).EndoY;
gui.EndoZ = repmat((1-(1:SET(NO).ZSize))*(SET(NO).SliceThickness+SET(NO).SliceGap),...
[DATA.NumPoints 1]);
if doepi
gui.EpiX = SET(NO).ResolutionX*SET(NO).EpiX;
gui.EpiY = SET(NO).ResolutionY*SET(NO).EpiY;
gui.EpiZ = repmat((1-(1:SET(NO).ZSize))*(SET(NO).SliceThickness+SET(NO).SliceGap),...
[DATA.NumPoints 1]);
end
%--- Code to upsample contours in Z. Prettier when working, but causes
%many problems, notably when aligning LV with RV. To work, one needs to
%interpolate RV as well, and keep track of the zslices that are releveant
%for each. /JU
% %Prepare for endocardium
% tempxendo = SET(NO).ResolutionX*SET(NO).EndoX(:,:,ind);
% tempyendo = SET(NO).ResolutionY*SET(NO).EndoY(:,:,ind);
%
% if doepi
% tempxepi = SET(NO).ResolutionX*SET(NO).EpiX(:,:,ind);
% tempyepi = SET(NO).ResolutionY*SET(NO).EpiY(:,:,ind);
% end
% if dorv
% tempxrvendo = SET(NO).ResolutionX*SET(NO).RVEndoX(:,:,ind);
% tempyrvendo = SET(NO).ResolutionY*SET(NO).RVEndoY(:,:,ind);
% end
%
% newzsize = max(16,nslices); %Number of planes to resample it to.
% EndoX = zeros(...
% size(SET(NO).EndoX,1),...
% size(SET(NO).EndoX,2),...
% newzsize);
% EndoY = EndoX;
% EndoZ = zeros(SET(NO).TSize,newzsize); %sum(ind) is number of planes segmented.
% if doepi
% EpiX = zeros(...
% size(SET(NO).EpiX,1),...
% size(SET(NO).EpiX,2),...
% newzsize);
% EpiY = EpiX;
% EpiZ = EndoZ;
% end
% if dorv
% RVEndoX = zeros(...
% size(SET(NO).RVEndoX,1),...
% size(SET(NO).RVEndoX,2),...
% newzsize);
% RVEndoY = EndoX;
% RVEndoZ = EndoZ;
% end
% for tloop=gui.indTn
% %Find correct factor
%
% %temp2 below was NaN'ing when not all timeframes have been segmented
% %ESV/EDV are not defined unless segmentation has Sys/Dias time
% %calculations. Going [0..1] works.
% if (SET(NO).TSize==1) || ...
% any(isnan([SET(NO).EDV SET(NO).ESV SET(NO).LVV(tloop)]))
% newind = linspace(0,1,newzsize);
% else
% temp = (longaxis/(SET(NO).SliceThickness+SET(NO).SliceGap))/nslices;
% %temp=>0..1 normalized over nslices number of slices to remove
% temp2 = (1-(SET(NO).LVV(tloop)-SET(NO).ESV)/(SET(NO).EDV-SET(NO).ESV));
% %temp2=>0 at EDT, temp2=>1 at EST
% temp = temp*temp2;
% newind = linspace(temp,1,newzsize);
% end
% %Resample endocardium
% EndoX(:,tloop,:) = interp1(...
% linspace(0,1,nslices)',...
% squeeze(tempxendo(:,tloop,:))',...
% newind')';
% EndoY(:,tloop,:) = interp1(...
% linspace(0,1,nslices)',...
% squeeze(tempyendo(:,tloop,:))',...
% newind')';
% if doepi
% %Resample epicardium
% EpiX(:,tloop,:) = interp1(...
% linspace(0,1,nslices)',...
% squeeze(tempxepi(:,tloop,:))',...
% newind')';
% EpiY(:,tloop,:) = interp1(...
% linspace(0,1,nslices)',...
% squeeze(tempyepi(:,tloop,:))',...
% newind')';
% end
% if dorv
% %Resample RV endocardium
% RVEndoX(:,tloop,:) = interp1(...
% linspace(0,1,nslices)',...
% squeeze(tempxrvendo(:,tloop,:))',...
% newind')';
% RVEndoY(:,tloop,:) = interp1(...
% linspace(0,1,nslices)',...
% squeeze(tempyrvendo(:,tloop,:))',...
% newind')';
% end
% EndoZ(tloop,:) = newind*...
% sum(ind)*(SET(NO).SliceThickness+SET(NO).SliceGap);
% EpiZ(tloop,:) = newind*...
% sum(ind)*(SET(NO).SliceThickness+SET(NO).SliceGap);
% RVEndoZ(tloop,:) = newind*...
% sum(ind)*(SET(NO).SliceThickness+SET(NO).SliceGap);
% end
% clear tempxendo tempyendo tempxepi tempyepi;
%--------------
%--- Prepare RV
%--------------
if dorvendo
%RVEndoX RVEndoY RVEndoZ
%--- Create RV EndoZ, EpiZ
%gui.RVEndoZ = repmat(-(1:SET(NO).ZSize)*(SET(NO).SliceThickness+SET(NO).SliceGap),...
% [DATA.NumPoints 1]); %Changed 2020-07-26 after bug-report
gui.RVEndoZ = repmat((1-(1:SET(NO).ZSize))*(SET(NO).SliceThickness+SET(NO).SliceGap),...
[DATA.NumPoints 1]);
%--- Create RV EndoX, EndoY, EpiX, EpiY
gui.RVEndoX = SET(NO).ResolutionX*SET(NO).RVEndoX;
gui.RVEndoY = SET(NO).ResolutionY*SET(NO).RVEndoY;
if 1==1
%--- Fix with contours to re-allign them with a distant point.
for tloop=1:SET(NO).TSize
%Find center.
tempx = gui.RVEndoX(:,tloop,:);
tempx = tempx(:);
tempx = tempx(~isnan(tempx));
meanx = mean(tempx);
tempy = gui.RVEndoY(:,tloop,:);
tempy = tempy(:);
tempy = tempy(~isnan(tempy));
meany = mean(tempy);
%find point furthest away.
dist = sqrt((tempx-meanx).^2+(tempy-meany).^2);
[~,ind]=max(dist);
if isempty(tempx)
px = NaN;
py = NaN;
else
px = tempx(ind);
py = tempy(ind);
end
for zloop=1:SET(NO).ZSize
xr = gui.RVEndoX(:,tloop,zloop);
yr = gui.RVEndoY(:,tloop,zloop);
%Find point closest to cursor
[~,inda] = min(abs(complex(px-xr,py-yr)));
gui.RVEndoX(1:(DATA.NumPoints-inda+1),tloop,zloop) = xr(inda:end);
gui.RVEndoY(1:(DATA.NumPoints-inda+1),tloop,zloop) = yr(inda:end);
gui.RVEndoX((DATA.NumPoints+1-inda):end,tloop,zloop) = xr(1:inda);
gui.RVEndoY((DATA.NumPoints+1-inda):end,tloop,zloop) = yr(1:inda);
end
end
end
end
if dorvepi
%RVEndoX RVEndoY RVEndoZ
%--- Create RVEndoZ
%gui.RVEpiZ = repmat(-(1:SET(NO).ZSize)*(SET(NO).SliceThickness+SET(NO).SliceGap),...
% [DATA.NumPoints 1]); %Fixed 2020-07-26 after bug report.
gui.RVEpiZ = repmat((1-(1:SET(NO).ZSize))*(SET(NO).SliceThickness+SET(NO).SliceGap),...
[DATA.NumPoints 1]);
%--- Create EndoX, EndoY
gui.RVEpiX = SET(NO).ResolutionX*SET(NO).RVEpiX;
gui.RVEpiY = SET(NO).ResolutionY*SET(NO).RVEpiY;
if 1==1
%--- Fix with contours to re-allign them with a distant point.
for tloop=1:SET(NO).TSize
%Find center.
tempx = gui.RVEpiX(:,tloop,:);
tempx = tempx(:);
tempx = tempx(~isnan(tempx));
meanx = mean(tempx);
tempy = gui.RVEpiY(:,tloop,:);
tempy = tempy(:);
tempy = tempy(~isnan(tempy));
meany = mean(tempy);
%find point furthest away.
dist = sqrt((tempx-meanx).^2+(tempy-meany).^2);
[~,ind]=max(dist);
if isempty(tempx)
px = NaN;
py = NaN;
else
px = tempx(ind);
py = tempy(ind);
end
for zloop=1:SET(NO).ZSize
xr = gui.RVEpiX(:,tloop,zloop);
yr = gui.RVEpiY(:,tloop,zloop);
%Find point closest to cursor
[~,inda] = min(abs(complex(px-xr,py-yr)));
gui.RVEpiX(1:(DATA.NumPoints-inda+1),tloop,zloop) = xr(inda:end);
gui.RVEpiY(1:(DATA.NumPoints-inda+1),tloop,zloop) = yr(inda:end);
gui.RVEpiX((DATA.NumPoints+1-inda):end,tloop,zloop) = xr(1:inda);
gui.RVEpiY((DATA.NumPoints+1-inda):end,tloop,zloop) = yr(1:inda);
end
end
end
end
%Prepare annotation points
if dopoints
gui.PointX = SET(NO).ResolutionX*SET(NO).Point.X;
gui.PointY = SET(NO).ResolutionY*SET(NO).Point.Y;
gui.PointZ = (SET(NO).SliceThickness + SET(NO).SliceGap) * ...
(-SET(NO).Point.Z + 1);
end
%Prepare measurements
if domeasures
gui.MeasureX = cellfun(@(x)(SET(NO).ResolutionX*x), ...
{SET(NO).Measure.X},'UniformOutput',false);
gui.MeasureY = cellfun(@(x)(SET(NO).ResolutionY*x), ...
{SET(NO).Measure.Y},'UniformOutput',false);
gui.MeasureZ = cellfun(@(x)((SET(NO).SliceThickness + SET(NO).SliceGap) * ...
(-x + 1)),{SET(NO).Measure.Z},'UniformOutput',false);
end
%Prepare scar data
if doscar
ScarX = [];
ScarY = [];
ScarZ = [];
for z = 1:SET(NO).ZSize
scarcontour = contourc(double(SET(NO).Scar.Result(:,:,z)),1);
defcol = 1;
while defcol < size(scarcontour,2)
numpoints = scarcontour(2,defcol);
ScarX = [ScarX scarcontour(2,defcol+(1:numpoints))]; %#ok<AGROW>
ScarY = [ScarY scarcontour(1,defcol+(1:numpoints))]; %#ok<AGROW>
ScarZ = [ScarZ z*ones(1,numpoints)]; %#ok<AGROW>
defcol = defcol + numpoints + 1;
end
end
gui.ScarX = SET(NO).ResolutionX*ScarX;
gui.ScarY = SET(NO).ResolutionY*ScarY;
gui.ScarZ = (SET(NO).SliceThickness + SET(NO).SliceGap) * (-ScarZ+1);
end
%----- Check if need to add apex, currently disabled.
if nslices==-1 %was>3
gui.EndoX(:,:,end+1) = mean(mean(gui.EndoX(:,:,1)));
gui.EndoY(:,:,end+1) = mean(mean(gui.EndoY(:,:,1)));
gui.EndoZ(:,end+1) = gui.EndoZ(:,end)+(SET(NO).SliceThickness+SET(NO).SliceGap);
if doepi
gui.EpiX(:,:,end+1) = mean(mean(gui.EpiX(:,:,1)));
gui.EpiY(:,:,end+1) = mean(mean(gui.EpiY(:,:,1)));
gui.EpiZ(:,end+1) = gui.EpiZ(:,end)+(SET(NO).SliceThickness+SET(NO).SliceGap);
end
if dorvendo
gui.RVEndoX(:,:,end+1) = mean(mean(gui.RVEndoX(:,:,1)));
gui.RVEndoY(:,:,end+1) = mean(mean(gui.RVEndoY(:,:,1)));
gui.RVEndoZ(:,end+1) = gui.RVEndoZ(:,end)+(SET(NO).SliceThickness+SET(NO).SliceGap);
end
if dorvepi
gui.RVEpiX(:,:,end+1) = mean(mean(gui.RVEpiX(:,:,1)));
gui.RVEpiY(:,:,end+1) = mean(mean(gui.RVEpiY(:,:,1)));
gui.RVEpiZ(:,end+1) = gui.RVEpiZ(:,end)+(SET(NO).SliceThickness+SET(NO).SliceGap);
end
end
end
%------- Draw
%Create endocardium
DATA.Handles.endosurf = surf(...
squeeze(gui.EndoX(:,t,:)),... %EH:
squeeze(gui.EndoY(:,t,:)),... %EH:
gui.EndoZ,... %ZData
'FaceAlpha','flat',...
'AlphaDataMapping','none',...
'AlphaData',ones([size(gui.EndoX,1) size(gui.EndoX,3)]),...
'FaceColor','red');
%32*ones(size(EndoX,1),size(EndoX,3)));
%'facecolor','red');
hold on; %Add more things :-)
%Create epicardium
if doepi
DATA.Handles.episurf = surf(...
squeeze(gui.EpiX(:,t,:)),... %EH:
squeeze(gui.EpiY(:,t,:)),... %EH:
gui.EpiZ,... %ZData
'FaceAlpha','flat',...
'AlphaDataMapping','none',...
'AlphaData',repmat(0.5,[size(gui.EpiX,1) size(gui.EpiX,3)]),...
'FaceColor','green');
end
if dorvendo
DATA.Handles.rvendosurf = surf(...
squeeze(gui.RVEndoX(:,t,:)),... %EH:
squeeze(gui.RVEndoY(:,t,:)),... %EH:
gui.RVEndoZ,...
'FaceAlpha','flat',...
'AlphaDataMapping','none',...
'AlphaData',repmat(0.5,size(gui.RVEndoZ)),...
'FaceColor','magenta');
hold on;
end
if dorvepi
DATA.Handles.rvepisurf = surf(...
squeeze(gui.RVEpiX(:,t,:)),... %EH:
squeeze(gui.RVEpiY(:,t,:)),... %EH:
gui.RVEpiZ,...
'FaceAlpha','flat',...
'AlphaDataMapping','none',...
'AlphaData',repmat(0.5,size(gui.RVEpiZ)),...
'FaceColor','cyan');
hold on;
end
%Create annotation points
if dopoints
DATA.Handles.annotationpoints3d = plot3(...
gui.PointX, ...
gui.PointY, ...
gui.PointZ, ...
'bo');
hold on
end
%Create measurements
if domeasures
DATA.Handles.measurements3d = zeros(1,numel(gui.MeasureX));
for mloop = 1:size(gui.MeasureX,2)
DATA.Handles.measurements3d(mloop) = plot3(...
gui.MeasureX{mloop}, ...
gui.MeasureY{mloop}, ...
gui.MeasureZ{mloop}, ...
'w');
end
hold on
end
%Create scar
if doscar
DATA.Handles.scar3d = plot3(...
gui.ScarX, ...
gui.ScarY, ...
gui.ScarZ, ...
'y.');
% DATA.Handles.scarsurf = surf(...
% gui.ScarX,...
% gui.ScarY,...
% gui.ScarZ,...
% 'FaceAlpha','flat',...
% 'AlphaDataMapping','none',...
% 'AlphaData',repmat(0.5,[size(gui.EpiX,1) size(gui.EpiX,3)]),...
% 'FaceColor','yellow');
end
%------------------------------------
%--- Prepare for short axis slice cut
%------------------------------------
[x,y] = ndgrid(SET(NO).ResolutionX*(1:SET(NO).XSize),...
SET(NO).ResolutionY*(1:SET(NO).YSize));
z = repmat((SET(NO).SliceThickness+SET(NO).SliceGap)*(SET(NO).CurrentSlice-1),SET(NO).XSize,SET(NO).YSize);
DATA.Handles.lvcutshort = surf(...