function varargout = PCA_gui(varargin)
% PCA_GUI Application M-file for PCA_gui.fig
% FIG = PCA_GUI launch PCA_gui GUI.
% PCA_GUI('callback_name', ...) invoke the named callback.
% Last Modified by GUIDE v2.0 30-May-2002 14:02:29
if nargin == 0 % LAUNCH GUI
fig = openfig(mfilename,'reuse');
% Use system color scheme for figure:
set(fig,'Color',get(0,'defaultUicontrolBackgroundColor'));
% Generate a structure of handles to pass to callbacks, and store it.
handles = guihandles(fig);
guidata(fig, handles);
if nargout > 0
varargout{1} = fig;
end
elseif ischar(varargin{1}) % INVOKE NAMED SUBFUNCTION OR CALLBACK
try
if (nargout)
[varargout{1:nargout}] = feval(varargin{:}); % FEVAL switchyard
else
feval(varargin{:}); % FEVAL switchyard
end
catch
disp(lasterr);
end
end
%| ABOUT CALLBACKS:
%| GUIDE automatically appends subfunction prototypes to this file, and
%| sets objects' callback properties to call them through the FEVAL
%| switchyard above. This comment describes that mechanism.
%|
%| Each callback subfunction declaration has the following form:
%| <SUBFUNCTION_NAME>(H, EVENTDATA, HANDLES, VARARGIN)
%|
%| The subfunction name is composed using the object's Tag and the
%| callback type separated by '_', e.g. 'slider2_Callback',
%| 'figure1_CloseRequestFcn', 'axis1_ButtondownFcn'.
%|
%| H is the callback object's handle (obtained using GCBO).
%|
%| EVENTDATA is empty, but reserved for future use.
%|
%| HANDLES is a structure containing handles of components in GUI using
%| tags as fieldnames, e.g. handles.figure1, handles.slider2. This
%| structure is created at GUI startup using GUIHANDLES and stored in
%| the figure's application data using GUIDATA. A copy of the structure
%| is passed to each callback. You can store additional information in
%| this structure at GUI startup, and you can change the structure
%| during callbacks. Call guidata(h, handles) after changing your
%| copy to replace the stored original so that subsequent callbacks see
%| the updates. Type "help guihandles" and "help guidata" for more
%| information.
%|
%| VARARGIN contains any extra arguments you have passed to the
%| callback. Specify the extra arguments by editing the callback
%| property in the inspector. By default, GUIDE sets the property to:
%| <MFILENAME>('<SUBFUNCTION_NAME>', gcbo, [], guidata(gcbo))
%| Add any extra arguments after the last argument, before the final
%| closing parenthesis.
% --------------------------------------------------------------------
% LoadIma button Callback
% --------------------------------------------------------------------
function varargout = LoadImaButton_Callback(h, eventdata, handles, varargin)
% select the desired file names
%[FilesSelected, dir_path] = dir_gui;
[FilesSelected, dir_path] = uigetfiles('*.ima*','Select PET ima files');
pause(2);
handles.FileNames = sortrows(FilesSelected');
handles.dirname = dir_path;
guidata(handles.PCA_figure1,handles);
set(handles.ImaListbox,'String',handles.FileNames,...
'Value',1);
output ='no';
% loading the files
num_of_files = size(handles.FileNames,1);
for i=1:num_of_files
filelist(i).name = char(handles.FileNames(i));
end
filelist = filelist';filename=[];jobinfo=1;
%[handles.imaVOL, handles.scaninfo handles.fileheader] = loadvaxima128(filename,jobinfo,filelist,handles.dirname);
[handles.imaVOL, handles.scaninfo handles.fileheader] = loadvaxima(filename,jobinfo,filelist,handles.dirname);
if handles.scaninfo.imfm(1) ~= 128
imaVOLtmp = zeros(128,128,size(handles.imaVOL,3),'uint16');
for i=1 :size(handles.imaVOL,3);
imaVOLtmp(:,:,i) = imresize(handles.imaVOL(:,:,i),[128 128]);
end
handles.imaVOL = [];
handles.imaVOL = imaVOLtmp;
imaVOLtmp = [];
handles.scaninfo.imfm = [128, 128];
end
%handles.imaVOL = uint16(imaVOL); imaVOL =[];
handles.num_of_petslices = 15;
imsize=size(handles.imaVOL,1);
num_of_slice = size(handles.imaVOL,3);
%
% Generate the time scales
%
handles.Frames = handles.scaninfo.Frames;
scan_start = 0;
% for j=1 : handles.Frames
% if j>1
% scan_start(j) = scan_start(j-1) + handles.scaninfo(j-1).mtm/60;
% tissue_ts(j) = scan_start(j) + (handles.scaninfo(j).mtm/60)/2;
% else
% tissue_ts(j) = (handles.scaninfo(j).mtm/60)/2;
% end
% FrameLengths(j) = (handles.scaninfo(j).mtm/60);
% end
handles.tissue_ts = handles.scaninfo.tissue_ts/60;
handles.FrameLengths = handles.scaninfo.frame_lengths/60;
guidata(handles.PCA_figure1,handles);
%
% Ha ez mr nem az elso fjlbetlts, akkor trlni kell a 3D maszkolshoz
% hasznlt korbbi handles.sumimg mezot.
%
if isfield(handles,'sumimg')
handles = rmfield(handles,'sumimg');
guidata(handles.PCA_figure1,handles);
end
% --------------------------------------------------------------------
% StartSum button Callback
% --------------------------------------------------------------------
function varargout = StartSumButton_Callback(h, eventdata, handles, varargin)
%
% Sum the last N frames and generate a montage from the slices
%
N = str2double(get(handles.SumNEdit,'String'));
NofSlice = handles.num_of_petslices;
imsize = 128;
if N<1 | N> handles.Frames
disp('Az N rtke nem megfelelo az sszegzshez');beep;
return
end
imaind = [];
sumimg = zeros(imsize,imsize,NofSlice);imagesummed =zeros(imsize,imsize);
for i = 1 :NofSlice
slicetmp = handles.imaVOL(:,:,[i+(handles.Frames-N)*NofSlice: NofSlice : i+(handles.Frames-1)*NofSlice]);
%slicetmp = imaVOL(:,:,[i : 15 : i+(handles.Frames-1)*15]);
imagesummed(:) =0;
for fr = 1 : N
imagesummed = imagesummed + double(slicetmp(:,:,fr))*handles.FrameLengths(handles.Frames-N+fr);
end
sumimg(:,:,i) = imagesummed/sum(handles.FrameLengths(handles.Frames-N+1:handles.Frames));
end
for i=1:NofSlice
imaind = cat(4,imaind,fliplr(sumimg(:,:,i)));
end
fh = figure(1);
map=colormap(spectral);
hm = montage(imaind,map);
set(hm,'CDataMapping','scaled');
set(gca,'position',[0 0 1 1]);
hc = colorbar; set(hc,'position',[0.88 0 0.075 1]);
title(['Double click on the slice you want to use for PCA.',...
' PET ID (brn): ', num2str(handles.scaninfo(1).brn) ]);
%
% User input for desired slice number to use for mask area
% in the transaxial slice
%
pause(1);
disp('Double click on the slice you want to use for PCA.');
[xin,yin] = getpts(figure(1)); x=xin(1);y=yin(1);
FigRes = get(gca,'PlotBoxAspectRatio');
col_num = fix(x/(FigRes(1)/4))+1;row_num = fix(y/(FigRes(1)/4))+1;SliceNumber = (row_num-1)*4+col_num;
close(fh);
handles.SelSliceNumber = SliceNumber;
handles.sumimg = sumimg;
handles.frameforsum = 0;
guidata(handles.PCA_figure1,handles);
set(handles.FrameForSumEdit,'String',num2str(handles.frameforsum));
axes(handles.ImaAxes);
%set(handles.ImaAxes,'Visible','off');
map=colormap(spectral);
imagesc(sumimg(:,:,SliceNumber));
set(handles.ImaAxes,'Yticklabel',{});
set(handles.ImaAxes,'Xticklabel',{});
% --------------------------------------------------------------------
% StartPCA button Callback
% --------------------------------------------------------------------
function varargout = PCAStartButton_Callback(h, eventdata, handles, varargin)
Frame0 = str2double(get(handles.Frame0Edit,'String'));
Frames = handles.Frames;
sumimg = handles.sumimg;
SliceNumber = handles.SelSliceNumber;
tissue_ts = handles.tissue_ts;
imsize = 128;
imgt = zeros(imsize*imsize,Frames-Frame0);
zpx = [];
SelROIYes = get(handles.SelROICheckbox,'Value');
% Ha mr lteznek PCA brk, akkor azokat trlni kell
if isfield(handles,'fh')
for i=1 : size(handles.fh,2)
if ishandle(handles.fh(i))
delete(handles.fh(i));
end
end
handles = rmfield(handles,'fh');
guidata(handles.PCA_figure1,handles);
end
if SelROIYes
disp('Define the ROI mask for PCA.');beep;
BW = roipoly;
zpx = find(BW==0);
end
%
if size(zpx,1) > 1
for i=Frame0:Frames
imgt(:,i-Frame0+1)= reshape(handles.imaVOL(:,:,SliceNumber+(i-1)*15),imsize*imsize,1);
imgt(zpx,i-Frame0+1) = 0;
end
else
for i=Frame0:Frames
imgt(:,i-Frame0+1)= reshape(handles.imaVOL(:,:,SliceNumber+(i-1)*15),imsize*imsize,1);
end
end
px = find(sumimg(:,:,SliceNumber) > mean(mean(sumimg(:,:,SliceNumber))));
imgt_masked=imgt(px,:);
cov_img=cov(imgt_masked);
[V,D] = eig(cov_img);
DD1=diag(D);
handles.fh(1) = figure('Position',[10 600 400 300]);
semilogy([Frame0:Frames],DD1,'*g');
xlabel(['Factor serial number']);
ylabel(['Relative weigth of the factors']);
handles.fh(2) = figure('Position',[420 600 400 300]);
hold on;
plot(tissue_ts(Frame0:Frames),V(:,Frames-Frame0+1),'b-');
plot(tissue_ts(Frame0:Frames),V(:,Frames-Frame0),'g-');
plot(tissue_ts(Frame0:Frames),V(:,Frames-Frame0-1),'y-');
legend('1.factor','2.factor','3.factor');
xlabel(['time [min]']);
ylabel(['Scale of Factors [arb. unit]']);
handles.fh(3) = figure('Position',[10 40 400 300]);
imagesc(reshape(imgt*V(:,size(V,1)),128,128));colorbar;
title(['Factor Image 1.']);
handles.fh(4) = figure('Position',[420 40 400 300]);
imagesc(reshape(imgt*V(:,size(V,1)-1),128,128));colorbar;
title(['Factor Image 2.']);
handles.fh(5) = figure('Position',[830 40 400 300]);
imagesc(reshape(imgt*V(:,size(V,1)-2),128,128));colorbar;
title(['Factor Image 3.']);
guidata(handles.PCA_figure1,handles);
% --------------------------------------------------------------------
% SliceForwardButton Callback
% --------------------------------------------------------------------
function varargout = SliceForwardButton_Callback(h, eventdata, handles, varargin)
if ~isfield(handles,'SelSliceNumber')
return;
end
Frames = handles.Frames;
sumimg = handles.sumimg;
SliceNumber = handles.SelSliceNumber;
current_frame = handles.frameforsum;
NofSlice = handles.num_of_petslices;
if current_frame < Frames
current_frame = current_frame +1;
axes(handles.ImaAxes);
map=colormap(spectral);
imagesc(handles.imaVOL(:,:,SliceNumber+(current_frame-1)*NofSlice));
handles.frameforsum = current_frame;
set(handles.FrameForSumEdit,'String',num2str(handles.frameforsum));
elseif current_frame == Frames
current_frame = 0;
axes(handles.ImaAxes);
map=colormap(spectral);
imagesc(sumimg(:,:,SliceNumber));
handles.frameforsum = current_frame;
set(handles.FrameForSumEdit,'String',num2str(handles.frameforsum));
elseif current_frame == 0
axes(handles.ImaAxes);
map=colormap(spectral);
imagesc(handles.imaVOL(:,:,SliceNumber));
handles.frameforsum = 1;
set(handles.FrameForSumEdit,'String',num2str(handles.frameforsum));
end
set(handles.ImaAxes,'Yticklabel',{});
set(handles.ImaAxes,'Xticklabel',{});
guidata(handles.PCA_figure1,handles);
% --------------------------------------------------------------------
% SliceBackwardButton Callback
% --------------------------------------------------------------------
function varargout = SliceBackwardButton_Callback(h, eventdata, handles, varargin)
if ~isfield(handles,'SelSliceNumber')
return
end
Frames = handles.Frames;
sumimg = handles.sumimg;
SliceNumber = handles.SelSliceNumber;
current_frame = handles.frameforsum;
NofSlice = handles.num_of_petslices;
if current_frame > 1
current_frame = current_frame -1;
axes(handles.ImaAxes);
map=colormap(spectral);
imagesc(handles.imaVOL(:,:,SliceNumber+(current_frame-1)*NofSlice));
handles.frameforsum = current_frame;
set(handles.FrameForSumEdit,'String',num2str(handles.frameforsum));
elseif current_frame == 1
current_frame = 0;
axes(handles.ImaAxes);
map=colormap(spectral);
imagesc(sumimg(:,:,SliceNumber));
handles.frameforsum = current_frame;
set(handles.FrameForSumEdit,'String',num2str(handles.frameforsum));
elseif current_frame == 0
current_frame = Frames;
axes(handles.ImaAxes);
map=colormap(spectral);
imagesc(handles.imaVOL(:,:,SliceNumber+(Frames-1)*NofSlice));
handles.frameforsum = current_frame;
set(handles.FrameForSumEdit,'String',num2str(handles.frameforsum));
end
set(handles.ImaAxes,'Yticklabel',{});
set(handles.ImaAxes,'Xticklabel',{});
guidata(handles.PCA_figure1,handles);
% --------------------------------------------------------------------
% 3DPCAStart button Callback
% --------------------------------------------------------------------
function varargout = PCA3DStartButton_Callback(h, eventdata, handles, varargin)
imsize=128;
NumOfSlice = handles.num_of_petslices;
Frame0 = str2double(get(handles.Frame0Edit,'String'));
Frames = handles.Frames;
tissue_ts = handles.tissue_ts;
% Ha mr lteznek PCA brk, akkor azokat trlni kell
if isfield(handles,'fh')
for i=1 : 2
if ishandle(handles.fh(i))
delete(handles.fh(i));
end
end
handles = rmfield(handles,'fh');
guidata(handles.PCA_figure1,handles);
end
% Ha mg nincs sumimg akkor ltre kell hozni
if ~isfield(handles,'sumimg')
N=4; %az utols N frame sszegzse
sumimg = zeros(imsize,imsize,NumOfSlice);imagesummed =zeros(imsize,imsize);
for i = 1 :NumOfSlice
slicetmp = handles.imaVOL(:,:,[i+(handles.Frames-N)*NumOfSlice: NumOfSlice : i+(handles.Frames-1)*NumOfSlice]);
%slicetmp = imaVOL(:,:,[i : 15 : i+(handles.Frames-1)*15]);
imagesummed(:) =0;
for fr = 1 : N
imagesummed = imagesummed + double(slicetmp(:,:,fr))*handles.FrameLengths(handles.Frames-N+fr);
end
sumimg(:,:,i) = imagesummed/sum(handles.FrameLengths(handles.Frames-N+1:handles.Frames));
end
handles.sumimg = sumimg;
guidata(handles.PCA_figure1,handles);
else
sumimg = handles.sumimg;
end
% elokszlet a 3DPCA-hoz
% setting up the progression bar
info.color=[1 0 0];
info.title='3DPCA progress';
info.size=1;
info.pos='topleft';
p=progbar(info);
progbar(p,0);
imgt = uint16(zeros(imsize*imsize*NumOfSlice,Frames-Frame0));
for i=Frame0:Frames
imgt(:,i-Frame0+1)= handles.imaVOL([imsize*imsize*NumOfSlice*(i-1)+1:imsize*imsize*NumOfSlice*i])';
progbar(p,round(i*100/(Frames-Frame0)));drawnow;
end
px = find(sumimg(:) > mean(mean(sumimg(:))));
pxz = find(sumimg(:) < mean(mean(sumimg(:))));
imgt(pxz,:) = 0;
imgt_masked=imgt(px,:);
% start PCA main part
cov_img=cov(double(imgt_masked));
[V,D] = eig(cov_img);
DD1=diag(D);
% end PCA main part
close(p);
handles.fh(1) = figure('Position',[10 600 400 300]);
semilogy([Frame0:Frames],DD1,'*g');
xlabel(['Factor serial number']);
ylabel(['Relative weigth of the factors']);
handles.fh(2) = figure('Position',[420 600 400 300]);
hold on;
plot(tissue_ts(Frame0:Frames),V(:,Frames-Frame0+1),'b-');
plot(tissue_ts(Frame0:Frames),V(:,Frames-Frame0),'g-');
plot(tissue_ts(Frame0:Frames),V(:,Frames-Frame0-1),'y-');
legend('1.factor','2.factor','3.factor');
xlabel(['time [min]']);
ylabel(['Scale of Factors [arb. unit]']);
retval = pca3d_gui(imgt,V,imsize,NumOfSlice,Frame0,handles.dirname,handles.scaninfo(1),handles.fileheader);
guidata(handles.PCA_figure1,handles);
% --------------------------------------------------------------------
% Exit(Close) button Callback
% --------------------------------------------------------------------
function varargout = ExitButton_Callback(h, eventdata, handles, varargin)
delete(handles.PCA_figure1);
% --------------------------------------------------------------------
