Merge pull request #19 from ThFriedrich/peak_finder_2

Peak finder 2, compatibility fix, minor improvements

Author: Thomas Friedrich

functions/PeakFinding/tfm_PeakFinder2.m

@@ -15,7 +15,11 @@
     % License: Open Source under GPLv3
     % Contact: sandra.vanaert@uantwerpen.be
     %--------------------------------------------------------------------------
-    global thr d_min sigma xy hpf gr_cm cdat_0
+    global thr d_min sigma xy hpf gr_cm cdat_0 ver
+    % Determine Matlab version for compatibility
+    ver = version('-release');
+    ver = str2double(ver(1:4));
+
     obs = obj.obs;
     [ny,nx] = size(obs);
 
@@ -53,7 +57,9 @@
         cdat = cdat_0;
         cdat(1:32) = sin(linspace(0,pi,32));
         imagesc(hpf.par.wb,cdat); axis off; colormap(gr_cm); caxis([0 1]);
-        hpf.par.wb.Toolbar = [];
+        if ver >= 2019
+            hpf.par.wb.Toolbar = [];
+        end
 
         % Info panel
         hpf.help.pan = uipanel('Parent',hpf.par.pan,'units','normalized','Position',[0.62 0.3 0.38-br 0.6],'ShadowColor',[0 0 0],'ForegroundColor',[0 0 0],'HighlightColor',[0.95 0.95 0.95],'BackgroundColor',[0.8 0.8 0.8]);
@@ -71,21 +77,15 @@
         est_lim_s = mean(nx,ny)*0.1;
         SliderSi = uicontrol('Parent',hpf.par.pan,'Style','slider','units','normalized','Position',[br 0.38 0.2 0.15],'Min',3,'Max',est_lim_s);
         uicontrol('Parent',hpf.par.pan,'Style','text','String','Estimated Radius (px):','units','normalized','Position',[br 0.8 0.2 0.15],'FontSize',10,'HorizontalAlignment','left','BackgroundColor',[0.8 0.8 0.8]);
-%         uicontrol('Parent',hpf.par.pan,'Style','text','units','normalized','Position',[br 0.27 0.01 0.1],'String',num2str(3,0),'BackgroundColor',[0.8 0.8 0.8],'HorizontalAlignment','right');
-%         uicontrol('Parent',hpf.par.pan,'Style','text','units','normalized','Position',[0.2 0.27 0.01 0.1],'String',num2str(est_lim_s,1),'BackgroundColor',[0.8 0.8 0.8],'HorizontalAlignment','left');
 
         %Threshold
         SliderTh = uicontrol('Parent',hpf.par.pan,'Style','slider','units','normalized','Position',[br+0.2 0.38 0.2 0.15],'Min',0,'Max',1);
         uicontrol('Parent',hpf.par.pan,'Style','text','String','Threshold value:','units','normalized','Position',[br+0.2 0.8 0.2 0.15],'FontSize',10,'HorizontalAlignment','left','BackgroundColor',[0.8 0.8 0.8]);
-%         uicontrol('Parent',hpf.par.pan,'Style','text','units','normalized','Position',[br+0.2 0.27 0.01 0.1],'String','0','BackgroundColor',[0.8 0.8 0.8],'HorizontalAlignment','right');
-%         uicontrol('Parent',hpf.par.pan,'Style','text','units','normalized','Position',[0.4 0.27 0.01 0.1],'String','1','BackgroundColor',[0.8 0.8 0.8],'HorizontalAlignment','left');
 
         %Peak Distance
-        est_lim_d = mean(nx,ny)*0.1;
+        est_lim_d = mean(nx,ny)*0.2;
         SliderDm = uicontrol('Parent',hpf.par.pan,'Style','slider','units','normalized','Position',[br+0.4 0.38 0.2 0.15],'Min',0,'Max',est_lim_d);
         uicontrol('Parent',hpf.par.pan,'Style','text','String','Minimum Distance (px):','units','normalized','Position',[br+0.4 0.8 0.2 0.15],'FontSize',10,'HorizontalAlignment','left','BackgroundColor',[0.8 0.8 0.8]);
-%         uicontrol('Parent',hpf.par.pan,'Style','text','units','normalized','Position',[br+0.4 0.27 0.01 0.1],'String','0','BackgroundColor',[0.8 0.8 0.8],'HorizontalAlignment','right');
-%         uicontrol('Parent',hpf.par.pan,'Style','text','units','normalized','Position',[0.6 0.27 0.01 0.1],'String','1','BackgroundColor',[0.8 0.8 0.8],'HorizontalAlignment','left');
 
     %    Textboxes   %
     %%%%%%%%%%%%%%%%%%
@@ -236,7 +236,9 @@ function deleteFigure(hObject,~)
     function waitbar_out()
         hpf.par.wb.Children.CData = cdat_0;
         set(hpf.par.wb,'visible','off')
-        hpf.par.wb.Colormap = gr_cm;
+        if ver >= 2019
+            hpf.par.wb.Colormap = gr_cm;
+        end
         drawnow;
     end
 
@@ -247,17 +249,18 @@ function waitbar_out()
         timerDat.n_tick = 1;
         timerObject = timer('TimerFcn',@tick,...
                             'ExecutionMode','fixedRate',...
-                            'Period',0.01,...
+                            'Period',0.05,...
                             'UserData', timerDat);
         start(timerObject);
 
         function tick(timerObj,event)
-
              timerData = get(timerObj, 'UserData');
              im = timerData.im_dat;
-             im = circshift(im,timerData.n_tick,2);
+             im = circshift(im,timerData.n_tick*5,2);
              timerData.axes.Children.CData = im; 
-             timerData.axes.Colormap = gr_cm;
+             if ver >= 2019
+                timerData.axes.Colormap = gr_cm;
+             end
              timerData.n_tick = timerData.n_tick + 1;
              set(timerObj, 'UserData', timerData);
              drawnow

functions/PeakFinding/tfm_find_peaks_2d.m

@@ -21,9 +21,10 @@
 % License: Open Source under GPLv3
 % Contact: sandra.vanaert@uantwerpen.be
 %--------------------------------------------------------------------------
-   
+
     % Avoide negative values
     img = img+min(img(:));
+    img = img/max(img(:));
 
     % This ratio corresponds roughly to the the visual column radius
     sigma = sigma/3;
@@ -38,6 +39,7 @@
 
     % Apply Wiener filter
     d = wiener2(d,[nkr_w nkr_w]);
+    d = real(d);
 
     % Apply Median filter to compensate salt/pepper-like artefacts
     d = medfilt2(d,[nkr_m nkr_m],'symmetric');
@@ -46,27 +48,28 @@
     d = fcn_anscombe_inv(d);
 
     d = max(min(img(:)), d);
-    
+ 
     % Signal to noise ratio
     psnr = (var(d(:))/var(img(:)-d(:)));
     alpha = 1/psnr;
 
     % Perform deconvolution with gaussian, according to:
-    % Van Dyck, D. (2012). Basics of Image Processing and Analysis. p. 74. https://doi.org/10.5281/zenodo.51511
+    % Van Dyck, D. (2012). Basics of Image Processing and Analysis. p. 74. https://doi.org/10.5281/zenodo.51511  
     [ny, nx] = size(d);
     [gx,gy]=fcn_real_space_2_F_space(nx,ny);
     H = fcn_gauss_2d_fourier_space(gx,gy,sigma);
     Y = conj(H)./(abs(H).^2+(alpha));
-
-    d_deconv = fftshift(ifft2(fft2(ifftshift(d)).*ifftshift(Y)));
+    
+    d_deconv = fcn_conv2D(d,Y);
     d_deconv = real(d_deconv);
+    
 
-    se = strel('disk',round(5*sigma));
+    se = strel('disk',round(4*sigma));
     img_o = imtophat(d_deconv,se);
 
     sc = max(img_o(:));
     img_o = img_o/sc;
-    
+  
     if nargout > 1
         xy = fcn_local_max(img_o,pk_min,d_min);
     else
@@ -180,5 +183,34 @@
     end
     img_o = max(0, a*x.^2+e+ix.*(b+ix.*(c+ix*d)));
 
+
+end
+ 
+function im_o = fcn_conv2D(im1, im2)
+    n_pix_border = 30;
+
+    im1_pad = fcn_smooth_borders(im1,n_pix_border);
+    im2_pad = fcn_smooth_borders(im2,n_pix_border);
+
+    im_o = fftshift(ifft2(fft2(ifftshift(im1_pad)).*ifftshift(im2_pad)));
+    im_o = im_o(n_pix_border+1:end-n_pix_border,n_pix_border+1:end-n_pix_border);
+
 end
- 
+
+function im_o = fcn_smooth_borders(img,n_pix_border)
+
+    img_pad = padarray(img,[n_pix_border n_pix_border],'symmetric');
+
+    [ny, nx] = size(img_pad);
+    [X, Y] = meshgrid(0:nx-1, 0:ny-1);
+
+    dxf = nx-(abs(X-nx/2)+(nx/2));
+    dyf = ny-(abs(Y-ny/2)+(ny/2));
+
+    df = min(cat(3,dxf,dyf),[],3);
+    df = df./n_pix_border;
+    df(df>=1) = 1;
+
+    im_o = img_pad.*df;
+
+end