added navigation movies

supplemental/movie/animateCell.m

@@ -27,7 +27,7 @@
 
 disp(sum(sum(position(121,:,1:5:100,1))==0))
 disp(sum(sum(position(121,:,1:5:100,2))==0))
-for runind = 1:5:100 %[126,136,137,141,148,156,159]
+for runind = 1:5:10 %[126,136,137,141,148,156,159]
     flag = 0;
     initp = posUnif(1,:,runind);
     coord = combvec(xlimit,ylimit)' + initp;
@@ -110,4 +110,5 @@
     end
 end
 
+movie2gif(vidfile, 'sin.gif', 'LoopCount', 0, 'DelayTime', 0)
 close(vidfile)

supplemental/movie/simple_gradient.m

@@ -0,0 +1,105 @@
+clear all;
+close all;
+
+%animate cell
+load(which("tissue_300by900_grad_localization_feedback.mat"),...
+                'param', 'recC', 'recF', 'posScheme','posUnif','m',...
+                'move_rate')
+
+%% panel F snapshots
+ylimit = -70:70;
+xlimit = -49:19;
+fconc = param.fcount;
+s = param.mean_cell_radius;
+nstep = 240;
+nrun = size(recC,3);
+position = cat(4,posScheme,posUnif);
+
+fname = "uniform";
+if isfile(strcat(fname,".mp4"))
+    fname = strcat(fname,"-1",".mp4");
+end
+vidfile = VideoWriter(fname,'MPEG-4');
+vidfile.FrameRate = 20;
+vidfile.Quality = 100;
+open(vidfile);
+load('TissueColormap')
+
+disp(find(sum(position(90,:,:,2))==0))
+for runind = [30,68,45]
+    flag = 0;
+    initp = posUnif(1,:,runind);
+    coord = combvec(xlimit,ylimit)' + initp;
+    envtissue = reshape(arrayfun(fconc,coord(:,1),coord(:,2)),...
+        length(xlimit),length(ylimit))';
+%     tiledlayout(1,2,'TileSpacing','compact','padding','compact');
+%     a=nexttile;
+%     b=nexttile;
+%     tiles = [a,b];
+    set(gcf, 'Position',  [100, 100, 14*(max(xlimit)-min(xlimit)),...
+                                     6*(max(ylimit)-min(ylimit))])
+    if sum(position(121,:,runind,1))==0
+        schemeStatus = 'Completed < 1hr';
+        stopScheme = find(sum(position(:,:,runind,1),2)==0,1);
+    else
+        schemeStatus = 'Failed';
+        stopScheme = nstep;
+    end
+    if sum(position(121,:,runind,2))==0
+        unifStatus = 'Completed < 1hr';
+        stopUnif = find(sum(position(:,:,runind,2),2)==0,1);
+    else
+        unifStatus = 'Failed';
+        stopUnif = nstep;
+    end
+    for ii = 1:nstep
+        for jj = 2:2
+            colormap(TissueColormap);
+            imagesc(envtissue)
+            colorbar()
+            cellcenter = position(ii,:,runind,jj);
+            if isequal(cellcenter,[0,0]) && isequal(unifStatus,'Fail')
+                flag=1;
+                break
+            end
+            if isequal(position(ii,:,runind,2),[0,0])
+                flag=1;
+                break
+            end
+            if(jj == 1)
+                status = schemeStatus;
+                receptor = recF(ii,:,runind)';
+            else
+                status = unifStatus;
+                receptor = mean(recF(10,:,runind));
+            end
+            angle = linspace(0,2*pi*(1-1/m),m);
+            cellcenter = cellcenter - initp - [min(xlimit),min(ylimit)];
+            cellsurf = cellcenter+(s+receptor/10).*[cos(angle)',sin(angle)'];  
+            circle = cellcenter + s.*[cos(angle)',sin(angle)']; 
+
+            %plotting
+            hold on
+            fill(cellsurf(:,1),cellsurf(:,2),[17 17 17]/18,'Linewidth',1)
+            fill(circle(:,1),circle(:,2),[17 17 17]/18,'Linewidth',1,...
+                'Facecolor','#0072BD')
+            hold off
+            set(gca,'fontsize',14)
+            if jj==1 && ii>stopScheme
+                timestr = append(num2str(move_rate*stopScheme/60,'%3.2f')," min");
+            else
+                timestr = append(num2str(move_rate*ii/60,'%3.2f')," min");
+            end
+            text(45,8,timestr,'FontSize',23,'Color','white');
+            pbaspect([max(xlimit)-min(xlimit),max(ylimit)-min(ylimit),1])
+%             set(gcf,'position',[10,10,492*2,276*2])
+        end
+        frame = getframe(gcf);
+        writeVideo(vidfile, frame);
+        if(flag==1)
+            break
+        end
+    end
+end
+
+close(vidfile)