initial commit

+utils/follow_feature.m

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+%%% Following a feature
+for ii = 1:numel(object)
+    obj{ii} = angle(object{ii});
+end
+pixsize = p.dx_spec(1)*1e6; % Microns
+
+%Inputs
+% obj       Is a cell with different objects
+% pixsize   Pixel size
+
+% Create useful arrays
+for ii = 1:numel(object)
+    axisx{ii} = ([1:size(obj{ii},2)]-floor(object_size(2)/2)+1)*pixsize;
+    axisy{ii} = ([1:size(obj{ii},1)]-floor(object_size(1)/2)+1)*pixsize;
+    xind {ii} = [1:size(obj{ii},2)];
+    yind{ii}  = [1:size(obj{ii},1)];  
+end
+
+
+%% Feature characteristics
+f.sigma = 1.5; % Feature width in real units
+f.contrast = -1;
+
+sigma_ind = f.sigma/pixsize;  % Feature width in pixels
+
+figure(1)
+% imagesc(axisx{1},axisy{1},obj{1});
+imagesc(obj{1});
+axis xy equal tight
+colormap bone
+xlabel('\mum')
+[xinp,yinp] = ginput(1);
+xinp = round(xinp);
+yinp = round(yinp);
+
+x1 = xind{1}(abs(xind{1}-xinp)<2*sigma_ind);
+y1 = yind{1}(abs(yind{1}-yinp)<2*sigma_ind);
+x2 = x1;
+y2 = y1;
+
+for ii = 1:3
+    [X Y] = meshgrid(xind{ii},yind{ii});
+    ref = f.contrast*exp(-((X-xinp).^2+(Y-yinp).^2)/(2*sigma_ind^2));
+    x1 = xind{1}(abs(xind{1}-xinp)<2*sigma_ind);
+    y1 = yind{1}(abs(yind{1}-yinp)<2*sigma_ind);
+    x2 = x1;
+    y2 = y1;
+    [subim1, subim2, delta, deltafine, regionsout] = registersubimages_2(obj{1}, ref, x1, y1, x2, y2, 10, 1, 1);
+    % delta is (y,x) correction
+    xinp = xinp - delta(2);
+    yinp = yinp - delta(1);
+    xposobjind(ii) = xinp;
+    yposobjind(ii) = yinp;
+end
+
+%%
+ii = 3;
+figure(2)
+% imagesc(axisx{1},axisy{1},ref);
+% imagesc(ref);
+imagesc(obj{ii});
+axis xy equal tight
+colormap bone
+hold on;
+plot(xposobjind(ii),yposobjind(ii),'ow')
+hold off;
+xlabel('pixels')