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kymo_example.m

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+addpath('/useful functions/');
+velocity= importdata('./kymo_ex_data/resultats.mat');
+
+dxpix   = 0.955;        % Pixel size in um
+dttime  = 5;               % Time step in minutes
+vscale  = (dxpix/dttime);
+
+xlag    = velocity.XEul;
+ylag    = velocity.YEul;
+ulag    = vscale*velocity.UEul;
+vlag    = vscale*velocity.VEul;
+
+% xlag = velocity.XEul;
+% ylag = velocity.YEul;
+% ulag = velocity.UEul;
+% vlag = velocity.VEul;
+
+tstart  = 1;
+tend    = 189;
+
+%% Load mask
+ImgName     = './kymo_ex_data/cns_binar.tif';
+
+%%
+xmin = nanmin(xlag);
+xmax = nanmax(xlag);
+
+dx_slide = 10;
+dx_count = 50;
+
+xtab = xmin:dx_slide:xmax;
+
+for tt = tstart:tend
+    disp(['On time ',num2str(tt),' of ',num2str(tend)])
+
+    image_binar = imread(ImgName,tt);
+    [y,x] = ndgrid(1:size(image_binar,1),1:size(image_binar,2));
+
+    xlag_temp = xlag(:,tt);
+    ylag_temp = ylag(:,tt);
+    ulag_temp = ulag(:,tt);
+    vlag_temp = vlag(:,tt);
+
+    index_x = 1;
+
+    for xx = xtab
+
+        indices_temp = find((xlag_temp-(xx-dx_count/2)).*(xlag_temp-(xx+dx_count/2))<0);        % IS THIS THE PROBLEM
+        xlag_temp_xx = xlag_temp(indices_temp);
+        ylag_temp_xx = ylag_temp(indices_temp);
+        ulag_temp_xx = ulag_temp(indices_temp);
+        vlag_temp_xx = vlag_temp(indices_temp);
+
+        xlag_temp_xx_cns = NaN*ones(size(xlag_temp_xx));
+        ylag_temp_xx_cns = NaN*ones(size(ylag_temp_xx));
+        ulag_temp_xx_cns = NaN*ones(size(ulag_temp_xx));
+        vlag_temp_xx_cns = NaN*ones(size(vlag_temp_xx));
+
+        for ll = 1:size(xlag_temp_xx,1)
+
+            if image_binar(ylag_temp_xx(ll),xlag_temp_xx(ll)) == 255                      % IS THIS THE PROBLEM
+                xlag_temp_xx_cns(ll) = xlag_temp_xx(ll);
+                ylag_temp_xx_cns(ll) = ylag_temp_xx(ll);
+                ulag_temp_xx_cns(ll) = ulag_temp_xx(ll);
+                vlag_temp_xx_cns(ll) = vlag_temp_xx(ll);
+            end  
+        end
+
+        xmean(tt,index_x) = nanmean(xlag_temp_xx_cns);
+        ymean(tt,index_x) = nanmean(ylag_temp_xx_cns);
+        umean(tt,index_x) = nanmean(ulag_temp_xx_cns);
+        vmean(tt,index_x) = nanmean(vlag_temp_xx_cns);
+
+        xstd(tt,index_x) = nanstd(xlag_temp_xx_cns);
+        ystd(tt,index_x) = nanstd(ylag_temp_xx_cns);
+        ustd(tt,index_x) = nanstd(ulag_temp_xx_cns);
+        vstd(tt,index_x) = nanstd(vlag_temp_xx_cns);
+
+        index_x= index_x+1;
+    end
+
+end
+
+umean_smooth = tsmovavg_sham_gaussian_matrix(umean,[1 3 5 7 9 11 13 11 9 7 5 3 1],2);
+umean_div = NaN*ones(size(umean_smooth));
+
+for ll = 2:size(umean,2)-1
+%     umean_div(:,ll) = (umean_smooth(:,ll+1)-umean_smooth(:,ll-1))/(2*dx_slide*dxpix);
+    umean_div(:,ll) = (umean(:,ll+1)-umean(:,ll-1))/(2*dx_slide*dxpix);
+end
+
+%%
+
+umean_smooth1   = umean_smooth + umean - umean;
+
+%% Kymograph
+
+time_involution = 1;
+% dt  = 10;
+min_velocity = -0.3;
+max_velocity = 0.3;
+kymo_t = NaN*ones(size(umean));
+kymo_x = NaN*ones(size(umean));
+
+for tt = 1:size(umean,1)
+    kymo_t(tt,:) = (tt-time_involution)*dttime;
+end
+
+for xx = 1:size(umean,2)
+    kymo_x(:,xx) = xtab(xx);
+end
+figure
+% subplot(2,1,1)
+hold on
+
+g = surf(kymo_x,kymo_t,umean);
+scatter3(100,0,1000,2,[0 0 0],'filled')
+scatter3(100,600,1000,2,[0 0 0],'filled')
+scatter3(500,0,1000,2,[0 0 0],'filled')
+scatter3(500,600,1000,2,[0 0 0],'filled')
+set(g, 'edgecolor','none')
+% plot([kymo_x(1,20),kymo_x(1,20)],[1,600],'k-','LineWidth',4)
+view(2)
+set(gca,'FontSize',20)
+h = colorbar;
+colormap(fire)
+caxis([min_velocity max_velocity])
+hold off