Create .gif without displaying each frame

Trying to create a .gif with hundreds of frames. Matlab pops up each window which takes a while so the whole process is mentally long.

Can you plot and save the gif in the background? code below, good luck if you read all of it, thanks.

h = figure('position', [100 300 600 600]);

      plot3(recon_CuRvEkiller(:,1),recon_CuRvEkiller(:,2),recon_CuRvEkiller(:,3),'b');
      hold on
      plot3(recon_CuRvEdroso(:,1), recon_CuRvEdroso(:,2),recon_CuRvEdroso(:,3),'r');%plot3([recon_CuRvEkiller(i,1) recon_CuRvEdroso(i,1)], [recon_CuRvEkiller(i,2) recon_CuRvEdroso(i,2)], [recon_CuRvEkiller(i,3) recon_CuRvEdroso(i,3)],'-k');
      hold on
      axis equal
      grid on
      set(gca, 'XColor', [.4 .4 .4], 'YColor', [.4 .4 .4], 'ZColor', [.4 .4 .4],...
          'XTickLabel',[],'YTickLabel',[],'ZTickLabel',[]); % hides the ticks on x-axis

      %now pause and ask the user to choose viewing angle
      h = msgbox('chose correct viewing angle by rotating figure');
      timeout = 600;
      uiwait(h,timeout)
      %%4. Now change the viewing angle until we are happy wiht it and run this cell
      [az,el] = view;
      mainfolder = pwd;
      mkdir('Plotting_recon+vectors'); %this makes a new folder
      cd([pwd '\Plotting_recon+vectors']); %this moves us to the new folder
      save 'az' 'az'
      save 'el' 'el'
      cd(mainfolder)
      save 'view' 'az' 'el'
      close all
      %%5. THIS IS preparing the 6. PLOTING OF THE HEADING with LOS and 7. with LOS_neuraldelay_fixed_frames.
      %UNCOMMENT parts of this section if you want to save each snap as a TIFF

      %5.
      %skipframe = 1; % set this to 1 if we want to render each frame
      %-----------------------------------------------------------------------
      %uncomment this
      %mkdir('traj_snaps'); %this makes a new folder
      %------------------------------------------------------------------------
      %Before we plot, we must find teh min and min xyz values.
      %Calculate max values for xyz of the extended vectors and locations
      vectorkill = VeLoCiTy_norm_killer_ext'+recon_CuRvEkiller;
      vectordroso = VeLoCiTy_norm_droso_ext'+recon_CuRvEdroso;

      %find max.
      maxPOINT(1,1:3) = max(vectorkill,[],1);
      maxPOINT(2,1:3) = max(vectordroso,[],1);
      maxPOINT(3,1:3) = max(recon_CuRvEkiller,[],1);
      maxPOINT(4,1:3) = max(recon_CuRvEdroso,[],1);
      maxPOINTFINAL(1,1:3) = max(maxPOINT,[],1);

      %finmin
      minPOINT(1,1:3) = min(vectorkill,[],1);
      minPOINT(2,1:3) = min(vectordroso,[],1);
      minPOINT(3,1:3) = min(recon_CuRvEkiller,[],1);
      minPOINT(4,1:3) = min(recon_CuRvEdroso,[],1);
      minPOINTFINAL(1,1:3) = min(minPOINT,[],1);

      bit= 10;
      xmin  =  minPOINTFINAL(1,1)-bit ;
      ymin  = minPOINTFINAL(1,2)-bit;
      zmin  = minPOINTFINAL(1,3)-bit;

      xmax =  maxPOINTFINAL(1,1) +bit ;
      ymax =  maxPOINTFINAL(1,2)+bit;
      zmax =  maxPOINTFINAL(1,3)+bit;
      load distance_analysis rendertype_volume
      %6. Set up the movie for normal LOS

          gif_fps = 15;
          % Define string variable that holds the filename of your movie
          snap_traj = 'snap_traj.gif';

          for i  =  1:killer_catchframe-Killer_1stmovingframe;
              % Define a variable that holds the frames per second your "movie" should have

              h = figure('Position', [20 40 1600 900],'color','w');
              set(gca, 'XColor', [.4 .4 .4], 'YColor', [.4 .4 .4], 'ZColor', [.4 .4 .4],...
                  'XTickLabel',[],'YTickLabel',[],'ZTickLabel',[]); % hides the ticks on x-axis
              cc=hsv(size(recon_CuRvEkiller,1));

          xlim([xmin xmax])
          ylim([ymin ymax])
          zlim([zmin zmax])
          %------------------------------------------------------------------------------------
          %%paste in here the view axes results!
          view([az el]); %this needs to be changed depending on the trajectory
          hold on
          axis equal
          %-------------------------------------------------------------------------------------
            % get(gca);

             quiver3(recon_CuRvEdroso(i,1),recon_CuRvEdroso(i,2),recon_CuRvEdroso(i,3)...
                  ,VeLoCiTy_norm_droso_ext(1,i),VeLoCiTy_norm_droso_ext(2,i),...
                  VeLoCiTy_norm_droso_ext(3,i),0,'m','LineWidth',1.5,'MaxHeadSize',5) ; % the '0' turns off auto-scaling
              hold on;

              quiver3(recon_CuRvEkiller(i,1),recon_CuRvEkiller(i,2),recon_CuRvEkiller(i,3)...
                  ,VeLoCiTy_norm_killer_ext(1,i),VeLoCiTy_norm_killer_ext(2,i),...
                  VeLoCiTy_norm_killer_ext(3,i),0,'c','LineWidth',1.5,'MaxHeadSize',5) ; % the '0' turns off auto-scaling
              hold on;

              %this plots the LOS
              quiver3(recon_CuRvEkiller(i,1),recon_CuRvEkiller(i,2),recon_CuRvEkiller...
                  (i,3), LOS_vec(i,1), LOS_vec(i,2),LOS_vec(i,3),0,'--k','LineWidth',1,'ShowArrowHead','off');%'LineStyle','--','ShowArrowHead','off)
              grid on
              hold on;

              if  strcmp(rendertype_volume, 'yes')==1

                  % where (a,b,c) is center of the sphere,
                  %where xc,yc,zc is the center of the ellipsoid. 

                  adroso = recon_CuRvEdroso(:,1);
                  bdroso = recon_CuRvEdroso(:,2);
                  cdroso = recon_CuRvEdroso(:,3);

                  akiller = recon_CuRvEkiller(:,1);
                  bkiller = recon_CuRvEkiller(:,2);
                  ckiller = recon_CuRvEkiller(:,3);

                  %[x,y,z] = ellipsoid(xc,yc,zc,xr,yr,zr,n)
                 % xr,yr,zr

                  %and r is the rahdius (i.e bead size/2
                  rdroso = preysize_number_droso/2;
                  rkiller = preysize_number_killer/2;%create a unit vector sphere.

                  [x,y,z] = sphere(100);

                  %get(gca);

                  if i== 1

                      surf((rdroso*x)+adroso(i,1), (rdroso*y)+bdroso(i,1), (rdroso*z)+cdroso(i,1), 'FaceColor', 'r', 'EdgeColor', 'r', 'clipping', 'off');
                      axis manual
                      hold on

                      surf ((rkiller*x)+ akiller(i,1), (rkiller*y)+bkiller(i,1), (rkiller*z)+ckiller(i,1), 'FaceColor', 'b', 'EdgeColor', 'b','clipping', 'off' );
                      axis manual
                      hold on

                  else
                      %you can turn this into different colors by uncommented
                      %the text next to lines
                      surf((rdroso*x)+adroso(i,1), (rdroso*y)+bdroso(i,1), (rdroso*z)+cdroso(i,1),'clipping', 'off','FaceColor','r','EdgeColor','r'); %cc(i,:)
                      axis manual
                      hold on

                      surf ((rkiller*x)+ akiller(i,1), (rkiller*y)+bkiller(i,1), (rkiller*z)+ckiller(i,1),'clipping', 'off','FaceColor','b','EdgeColor', 'b');
                      axis manual
                      hold on
                  end

                  %light('Position',[1 0 0],'Style','infinite');
              else
                  %this plots the trajectories (smooth ones)
                  plot3(recon_CuRvEkiller(:,1),recon_CuRvEkiller(:,2),recon_CuRvEkiller(:,3),'b');
                  hold on

                  plot3(recon_CuRvEdroso(:,1), recon_CuRvEdroso(:,2),recon_CuRvEdroso(:,3),'r');%plot3([recon_CuRvEkiller(i,1) recon_CuRvEdroso(i,1)], [recon_CuRvEkiller(i,2) recon_CuRvEdroso(i,2)], [recon_CuRvEkiller(i,3) recon_CuRvEdroso(i,3)],'-k');
                  hold on

              end

              %-----------------------------------------------------------------------
              %uncoment this
              %this saves it as tiff.
              %saveas(h,[pwd '\Traj_snaps\' 'Frame_' int2str(i) '.tiff' ]);
              %------------------------------------------------------------------------
              drawnow;
                  pause(0.3)

              %    % Take a "screenshot" of the figure fh
              frame = getframe(h);
              % Turn screenshot into image
              im = frame2im(frame);
              % Turn image into indexed image (the gif format needs this)
              [imind,cm] = rgb2ind(im,256);
              % If first loop iteration: Create the file, else append to it

              if i == 1;
                  imwrite(imind,cm,snap_traj,'gif', 'Loopcount',inf);
              else
                  imwrite(imind,cm,snap_traj,'gif','WriteMode','append','DelayTime',1/gif_fps);
              end
              close all
          end

[Geoff Hayes]

Tom - what do you mean by Matlab pops up each window which takes a while? What window are you referring to - that for the frame which you are writing to the animated gif?

Or are you asking for an alternative to the above so that each frame is not displayed?

[Tom]

Hi - to clarify: Matlab creates each frame of the gif in turn, and closes and loads each new frame which takes time. can't it plot each frame within the same figure window?

i'd like to be able to create each frame and append it to the gif in the background without it being visible

I'm sorry i can't ask a more direct question as I don't really know that much about matlab image creation.

here is a video to show what the windows are doing: Video

Answer 1

[Geoff Hayes]

Tom - your for loop looks something like

...

 snap_traj = 'snap_traj.gif';
 for i  =  1:killer_catchframe-Killer_1stmovingframe;

     % Define a variable that holds the frames per second your "movie" should have
     h = figure('Position', [20 40 1600 900],'color','w');
     set(gca, 'XColor', [.4 .4 .4], 'YColor', [.4 .4 .4], 'ZColor', [.4 .4 .4],...
              'XTickLabel',[],'YTickLabel',[],'ZTickLabel',[]); % hides the ticks on x-axis
     cc=hsv(size(recon_CuRvEkiller,1));
     xlim([xmin xmax])
     ylim([ymin ymax])
     zlim([zmin zmax])

     % other stuff

     if i == 1;
         imwrite(imind,cm,snap_traj,'gif', 'Loopcount',inf);
     else
         imwrite(imind,cm,snap_traj,'gif','WriteMode','append','DelayTime',1/gif_fps);
     end
     close all
 end

The call to figure creates a new figure, and the close all, closes it. Try removing the close all and put the creation of the figure outside of the for loop as

 ...

 snap_traj = 'snap_traj.gif';

 % create the figure
 h = figure('Position', [20 40 1600 900],'color','w');

 for i  =  1:killer_catchframe-Killer_1stmovingframe;

     % clear the axes
     cla(gca,'reset');

     set(gca, 'XColor', [.4 .4 .4], 'YColor', [.4 .4 .4], 'ZColor', [.4 .4 .4],...
              'XTickLabel',[],'YTickLabel',[],'ZTickLabel',[]); % hides the ticks on x-axis

     % other stuff

     if i == 1;
         imwrite(imind,cm,snap_traj,'gif', 'Loopcount',inf);
     else
         imwrite(imind,cm,snap_traj,'gif','WriteMode','append','DelayTime',1/gif_fps);
     end

 end

The above is very similar to what you had, with just a couple of lines changed. Note the addition of cla(gca,'reset') as the first line in the for loop which clears the current axes (see cla for details). That should remove all graphics handles from the previous iteration. You may notice some flickering but at least a new figure won't be opened and closed each time.

[Tom]

Hi - thanks for the help; on the right track, now each frame is rewritten in the window rather than each window being reloaded.

unfortunately, it no longer appends the gif; ie the output is now a single frame gif. i can't see why that would be?

snap_traj = 'snap_traj.gif';

h = figure('Position', [20 40 1600 900],'color','w');

          for i  =  1:killer_catchframe-Killer_1stmovingframe;
              % Define a variable that holds the frames per second your "movie" should have
             % clear the axes
             cla(gca,'reset');
  %             h = figure('Position', [20 40 1600 900],'color','w');
              set(gca, 'XColor', [.4 .4 .4], 'YColor', [.4 .4 .4], 'ZColor', [.4 .4 .4],...
                  'XTickLabel',[],'YTickLabel',[],'ZTickLabel',[]); % hides the ticks on x-axis
              cc=hsv(size(recon_CuRvEkiller,1));

          xlim([xmin xmax])
          ylim([ymin ymax])
          zlim([zmin zmax])
          %------------------------------------------------------------------------------------
          %%paste in here the view axes results!
          view([az el]); %this needs to be changed depending on the trajectory
          hold on
          axis equal
          %-------------------------------------------------------------------------------------
            % get(gca);

             quiver3(recon_CuRvEdroso(i,1),recon_CuRvEdroso(i,2),recon_CuRvEdroso(i,3)...
                  ,VeLoCiTy_norm_droso_ext(1,i),VeLoCiTy_norm_droso_ext(2,i),...
                  VeLoCiTy_norm_droso_ext(3,i),0,'m','LineWidth',1.5,'MaxHeadSize',5) ; % the '0' turns off auto-scaling
              hold on;

              quiver3(recon_CuRvEkiller(i,1),recon_CuRvEkiller(i,2),recon_CuRvEkiller(i,3)...
                  ,VeLoCiTy_norm_killer_ext(1,i),VeLoCiTy_norm_killer_ext(2,i),...
                  VeLoCiTy_norm_killer_ext(3,i),0,'c','LineWidth',1.5,'MaxHeadSize',5) ; % the '0' turns off auto-scaling
              hold on;

              %this plots the LOS
              quiver3(recon_CuRvEkiller(i,1),recon_CuRvEkiller(i,2),recon_CuRvEkiller...
                  (i,3), LOS_vec(i,1), LOS_vec(i,2),LOS_vec(i,3),0,'--k','LineWidth',1,'ShowArrowHead','off');%'LineStyle','--','ShowArrowHead','off)
              grid on
              hold on;

              if  strcmp(rendertype_volume, 'yes')==1

                  % where (a,b,c) is center of the sphere,
                  %where xc,yc,zc is the center of the ellipsoid. 

                  adroso = recon_CuRvEdroso(:,1);
                  bdroso = recon_CuRvEdroso(:,2);
                  cdroso = recon_CuRvEdroso(:,3);

                  akiller = recon_CuRvEkiller(:,1);
                  bkiller = recon_CuRvEkiller(:,2);
                  ckiller = recon_CuRvEkiller(:,3);

                  %[x,y,z] = ellipsoid(xc,yc,zc,xr,yr,zr,n)
                 % xr,yr,zr

                  %and r is the rahdius (i.e bead size/2
                  rdroso = preysize_number_droso/2;
                  rkiller = preysize_number_killer/2;%create a unit vector sphere.

                  [x,y,z] = sphere(100);

                  %get(gca);

                  if i== 1

                      surf((rdroso*x)+adroso(i,1), (rdroso*y)+bdroso(i,1), (rdroso*z)+cdroso(i,1), 'FaceColor', 'r', 'EdgeColor', 'r', 'clipping', 'off');
                      axis manual
                      hold on

                      surf ((rkiller*x)+ akiller(i,1), (rkiller*y)+bkiller(i,1), (rkiller*z)+ckiller(i,1), 'FaceColor', 'b', 'EdgeColor', 'b','clipping', 'off' );
                      axis manual
                      hold on

                  else
                      %you can turn this into different colors by uncommented
                      %the text next to lines
                      surf((rdroso*x)+adroso(i,1), (rdroso*y)+bdroso(i,1), (rdroso*z)+cdroso(i,1),'clipping', 'off','FaceColor','r','EdgeColor','r'); %cc(i,:)
                      axis manual
                      hold on

                      surf ((rkiller*x)+ akiller(i,1), (rkiller*y)+bkiller(i,1), (rkiller*z)+ckiller(i,1),'clipping', 'off','FaceColor','b','EdgeColor', 'b');
                      axis manual
                      hold on
                  end

                  %light('Position',[1 0 0],'Style','infinite');
              else
                  %this plots the trajectories (smooth ones)
                  plot3(recon_CuRvEkiller(:,1),recon_CuRvEkiller(:,2),recon_CuRvEkiller(:,3),'b');
                  hold on

                  plot3(recon_CuRvEdroso(:,1), recon_CuRvEdroso(:,2),recon_CuRvEdroso(:,3),'r');%plot3([recon_CuRvEkiller(i,1) recon_CuRvEdroso(i,1)], [recon_CuRvEkiller(i,2) recon_CuRvEdroso(i,2)], [recon_CuRvEkiller(i,3) recon_CuRvEdroso(i,3)],'-k');
                  hold on

              end

              %-----------------------------------------------------------------------
              %uncoment this
              %this saves it as tiff.
              %saveas(h,[pwd '\Traj_snaps\' 'Frame_' int2str(i) '.tiff' ]);
              %------------------------------------------------------------------------
              drawnow;

              %    % Take a "screenshot" of the figure fh
              frame = getframe;
              % Turn screenshot into image
              im = frame2im(frame);
              % Turn image into indexed image (the gif format needs this)
              [imind,cm] = rgb2ind(im,256);
              % If first loop iteration: Create the file, else append to it

              if i == 1;
                  imwrite(imind,cm,snap_traj,'gif', 'Loopcount',inf);
              else
                  imwrite(imind,cm,snap_traj,'gif','WriteMode','append','DelayTime',0);
              end
  %            % close all
          end

[Geoff Hayes]

Tom - are you sure that the output image is just the single frame (is it first or last) or is it multiple copies of the same frame? If you put a breakpoint in the else block of your final if statement, does the code reach that breakpoint and try to append the image? I see from the above that you have removed set the DelayTime to be zero instead of 1/15. Why the change and could that be the reason your are only seeing one image (since there are zero seconds between each frame)?