I am trying to make a movie in matlab.
for i=1:runs;
for k=1:NO_TIMES
B = 0;
[conf dom_size] = conf_update_massmedia(time(k),conf);
shortconf=conf(1:N);
for j=1:N;
sigma(j,1:N) = conf(1+(j-1)*N:j*N);
end
figure(1)
imagesc(sigma);
colorbar;
set(gcf,'PaperPositionMode','auto');
F(k)=getframe(gcf);
end
end
movie2avi(F,'B=0.avi','Compression','none')
So my problem is that i only get a movie from the last run of the loop, i have tried to move the code for the figure around, but nothing seems to work, is there anyone who are able to help?
Pall
As #tmpearce mentioned, the problem is because of overwriting the F matrix.
I suggest you to:
Initialized your F matrix.
Always indent you code to make it readable (see here for example).
This is one of the million solutions:
f_ind = 1; % Frame index.
F = zeros(runs * NO_TIMES, 1); % initialization of Frames matrix.
figure; % remove figure(1) from your inner loop haowever.
for i = 1:runs;
for k = 1:NO_TIMES
% ...
F(f_ind)=getframe(gcf);
f_ind = f_ind + 1;
end
end
movie2avi is a little outdated and struggles on various operating systems. A better option is using the VideoWriter command:
vidObj = VideoWriter('B=0.avi');
vidObj.FrameRate=23;
open(vidObj);
for i=1:runs;
for k=1:NO_TIMES
B = 0;
[conf dom_size] = conf_update_massmedia(time(k),conf);
shortconf=conf(1:N);
for j=1:N;
sigma(j,1:N) = conf(1+(j-1)*N:j*N);
end
figure(1)
imagesc(sigma);
colorbar;
set(gcf,'PaperPositionMode','auto');
F=getframe(gcf);
writeVideo(vidObj,F);
end
end
close(vidObj);
Related
This is part of the code the makes the video:
k = 10000;
j = 1;
v = VideoWriter('myVideo.avi');
open(v)
while j < k
axis([0 5 0 1000]);
plot(0:dr:R, u_sol_matrix(:,j))
frame = getframe(gcf);
writeVideo(v,frame);
j = j + 50;
% pause(0.01)
end
close(v)
Now, given a matrix u_sol_matrix, where every column represents a solution for a PDE at a certain time point, I plot the solutions and the by the getframe command capture these plots and make a movie out of it.
The problem is that the axis keeps changing as the plot keeps adjusting to the solution. I want the axis to be constant. How do I get this to work? I have tried adding axis but this does not work apparently.
k = 10000;
j = 1;
v = VideoWriter('myVideo.avi');
open(v)
while j < k
fig = figure(); % Explicitly create figure
plot(0:dr:R, u_sol_matrix(:,j))
axis([0 5 0 1000]); % first plot, then change axis
frame = getframe(gcf);
writeVideo(v,frame);
close(fig) % close figure explicitly.
j = j + 50;
% pause(0.01)
end
close(v)
Flipping the figure creation and setting axis limits should do the trick. When you call axis without an open figure, MATLAB creates one, only to overwrite it if you don't call hold on, thus changing the limits to whatever the plot "needs" to fit.
Like Adriaan answered, you just have to flip the order of plotting and setting axis limits to make this work.
However, when creating animations, it is faster to first initialize a figure and the graphics objects (i.e. lines, scatter points, etc.), and later update the data in a loop.
k = 10000;
j = 1;
v = VideoWriter('myVideo.avi');
open(v)
% some test data
x = 10;
y = sin(1:k);
% init a figure and plot handles
fig = figure(1);
p = plot(x, y(1), 'o'); % create line object, and store the handle
axis([9 11 -1 1]) % axis limits for test data
% update data during animation
while j < k
p.XData = x; % update X and Y data properties of line object
p.YData = y(j);
frame = getframe(gcf);
writeVideo(v,frame);
j = j + 50;
pause(0.01)
end
close(v)
Since you don't have to create a new line primitive each loop iteration, this will save a lot of time. You only have to adjust the X and Y data properties of the already existing line, which has considerable less overhead.
Suppose I have a 5x5 matrix.
The elements of the matrix change (are refreshed) every second.
I would like to be able to display the matrix (not as a colormap but with the actual values in a grid) in realtime and watch the values in it change as time progresses.
How would I go about doing so in MATLAB?
A combination of clc and disp is the easiest approach (as answered by Tim), here's a "prettier" approach you might fancy, depending on your needs. This is not going to be as quick, but you might find some benefits, such as not having to clear the command window or being able to colour-code and save the figs.
Using dispMatrixInFig (code at the bottom of this answer) you can view the matrix in a figure window (or unique figure windows) at each stage.
Example test code:
fig = figure;
% Loop 10 times, pausing for 1sec each loop, display matrix
for i=1:10
A = rand(5, 5);
dispMatrixInFig(A,fig)
pause(1)
end
Output for one iteration:
Commented function code:
function dispMatrixInFig(A, fig, strstyle, figname)
%% Given a figure "fig" and a matrix "A", the matrix is displayed in the
% figure. If no figure is supplied then a new one is created.
%
% strstyle is optional to specify the string display of each value, for
% details see SPRINTF. Default is 4d.p. Can set to default by passing '' or
% no argument.
%
% figname will appear in the title bar of the figure.
if nargin < 2
fig = figure;
else
clf(fig);
end
if nargin < 3 || strcmp(strstyle, '')
strstyle = '%3.4f';
end
if nargin < 4
figname = '';
end
% Get size of matrix
[m,n] = size(A);
% Turn axes off, set origin to top left
axis off;
axis ij;
set(fig,'DefaultTextFontName','courier', ...
'DefaultTextHorizontalAlignment','left', ...
'DefaultTextVerticalAlignment','bottom', ...
'DefaultTextClipping','on');
fig.Name = figname;
axis([1, m-1, 1, n]);
drawnow
tmp = text(.5,.5,'t');
% height and width of character
ext = get(tmp, 'Extent');
dy = ext(4);
wch = ext(3);
dwc = 2*wch;
dx = 8*wch + dwc;
% set matrix values to fig positions
x = 1;
for i = 1:n
y = 0.5 + dy/2;
for j = 1:m
y = y + 1;
text(x,y,sprintf(strstyle,A(j,i)));
end
x = x + dx;
end
% Tidy up display
axis([1-dwc/2 1+n*dx-dwc/2 1 m+1]);
set(gca, 'YTick', [], 'XTickLabel',[],'Visible','on');
set(gca,'XTick',(1-dwc/2):dx:x);
set(gca,'XGrid','on','GridLineStyle','-');
end
I would have thought you could achieve this with disp:
for i=1:10
A = rand(5, 5);
disp(A);
end
If you mean that you don't want repeated outputs on top of each other in the console, you could include a clc to clear the console before each disp call:
for i=1:10
A = rand(5, 5);
clc;
disp(A);
end
If you want to display your matrix on a figure it is quite easy. Just make a dump matrix and display it. Then use text function to display your matrix on the figure. For example
randMatrix=rand(5);
figure,imagesc(ones(20));axis image;
hold on;text(2,10,num2str(randMatrix))
If you want to do it in a for loop and see the numbers change, try this:
for i=1:100;
randMatrix=rand(5);
figure(1),clf
imagesc(ones(20));axis image;
hold on;text(2,10,num2str(randMatrix));
drawnow;
end
I have written a while loop in Matlab that is supposed to send each value in an array from Matlab to arduino at a specified time interval using a tic toc delay in Matlab and then read values and store them in a variable and graph them.
The output of the while-loop slows down with each successive iteration.
I increased the buffersize which helped it a lot, but it still slows down too much. Is there another way to increase the speed to print the values on time. I have included another tic toc and graph to show the execution speed here is the code:
max = 80;
min = 40;
amp = (max-min)/2;
offset = amp + min;
btime = 5;
bpm = 12;
spb = 60/bpm;
sapb = spb/.05;
tosd = sapb*bpm*btime;
time1 = btime*60;
x = linspace(0,time1,tosd)';
x1 = amp*sin(x*(2*pi/20)) + offset;
pause(1);
fprintf(handles.UltraM,(['<P' num2str(offset) '>']))
pause(5);
y = [];
i = 1;
figure(1);
hold on;
title('Pressure Data');
xlabel('Data Number');
ylabel('Analog Voltage (0-1023)');
t1 = [];
figure(2);
hold on;
title('Time to execute task');
xlabel('iteration number');
ylabel('time taken');
while (i<=length(x))
t2 = tic;
t = tic;
fprintf(handles.UltraM,(['<P' num2str(x1(i)) '>']));
%disp((['<P' num2str(x1(i)) '>']));
y(i) = fscanf(handles.UltraM,'%d');
figure(1);
hold on;
plot(i, y(i), 'b*');
drawnow;
hold off;
while toc(t) < 0.05
continue
end
t1(i) = toc(t2);
figure(2);
hold on;
plot(i,t1(i),'b*');
drawnow;
hold off;
i = i + 1;
end
After a bit of back and forth I think I know what you're trying to achieve and what stands in your way.
I have edited your code to make it slightly more fast and readable. Most of the time the operations take just slightly above 0.05 seconds, and at several time points it can take about 5 milliseconds longer than expected. Your millage may vary of course. Since I do not have an arduino, I cannot know if there is a bottle neck there. You should also try profiling your code using the builtin Matlab profiler (it's very useful) to see what exactly slows your code down.
The main thing I found to slow your code is that you used the plot function to add one point at a time to your figure. Each time you call this function, it creates a new graphics object. After a few hundred of those, things get sluggish. Instead you should simply update the already plotted data and redraw it using drawnow.
In short, the solution is this:
1) Initialize you plot with a single point and save the graphics handle for later use:
p1 = plot(0,0,'b*');
2) Then, inside the loop, once your data arrays have been updated, replace the data in your existing plot with the new arrays.
set(p1, 'XData', 1:i, 'YData', y(1:i));
3) Redraw the plots to reflect the latest update.
drawnow;
drawnow will eventually slow down your code also since it has to redraw increasingly large plots at every iteration. To make things work faster, you might want to refresh your plot after a longer interval. For example, the following will refresh every 10 iterations:
if rem(i,10) == 0
drawnow;
end
Full code below. Let me know if you have any more issues.
max = 80;
min = 40;
amp = (max-min)/2;
offset = amp + min;
btime = 5;
bpm = 12;
spb = 60/bpm;
sapb = spb/.05;
tosd = sapb*bpm*btime;
time1 = btime*60;
x = linspace(0,time1,tosd)';
x1 = amp*sin(x*(2*pi/20)) + offset;
pause(1);
%fprintf(handles.UltraM,(['<P' num2str(offset) '>']))
disp(['<P' num2str(offset) '>']); % replacing with disp (I don't have an arduino)
pause(5);
%y = []; % unnecessary here, preallocated before loop
figure(1);
p1 = plot(0,0,'b*'); % plotting one dot to create an object, data will be overwritten
hold on;
title('Pressure Data');
xlabel('Data Number');
ylabel('Analog Voltage (0-1023)');
%t1 = []; % unnecessary here, preallocated before loop
figure(2);
p2 = plot(0,0,'b*'); % plotting one dot to create an object, data will be overwritten
hold on;
title('Time to execute task');
xlabel('iteration number');
ylabel('time taken');
% preallocate t1 and y arrays for faster operation
t1 = zeros(size(x));
y = zeros(size(x));
i = 1; % moved closer to loop beginning for better readability
while i <= length(x) % parentheses unnecessary in Matlab
t2 = tic;
t = tic;
%fprintf(handles.UltraM,(['<P' num2str(x1(i)) '>']));
disp((['<P' num2str(x1(i)) '>'])); % replacing with disp (I don't have an arduino)
%y(i) = fscanf(handles.UltraM,'%d');
y(i) = randn; % replacing with random number (I don't have an arduino)
%figure(1); % unnecessary
%hold on; % unnecessary
%plot(i, y(i), 'b*');
% replacing the above with a slightly faster version
set(p1, 'XData', 1:i, 'YData', y(1:i));
%drawnow; % first one is annecessary
%hold off; % unnecessary
while toc(t) < 0.05
continue
end
t1(i) = toc(t2);
%figure(2); % unnecessary
%hold on; % unnecessary
%plot(i,t1(i),'b*');
% replacing the above with a slightly faster version
set(p2, 'XData', 1:i, 'YData', t1(1:i));
if rem(i,10) == 0 % refreshing every 10 iterations
drawnow;
end
%hold off; % unnecessary
i = i + 1;
end
ANSWER TO PREVIOUS VERSION OF QUESTION
You can vectorize your loop by replacing it entirely with the following two statements:
% vectorizing num-to-string conversion
y4 = cellstr(strcat('<P',num2str(x1), '>'));
% deleting all spaces
y4 = cellfun(#(u) u(~isspace(u)), y4, 'UniformOutput', false)
This small adjustment makes your program run x4 faster on my PC.
Displaying/printing the results could also be done using the cellfun iterator: cellfun(#disp, y4)
% read image
I = imread(im);
H = zeros(256,1);
% m = width, n = height
[m,n] = size(I);
% loop for checking values
for GrayValue = 0:255
for i = 1:m
for j = 1:n
if I(i,j) == GrayValue % read each pixel coordinate
H(GrayValue+1) = H(GrayValue+1)+1;
end
end
end
end
This function it go get image file as im and will show a histogram of values count in the image. How can i reduce the time taken to execute this MATLAB function. It is similar to imhist() . But I want to make a similar imhist() function. I cannot figure out to remove which loop.
Obligatory bsxfun solution:
H=sum(bsxfun(#eq,I(:),0:255))
And a method that might be easier to understand. This just replaces your two inner loops with a search.
I=randi(256,50,50)-1;
H=zeros(256,1);
G=zeros(256,1);
for GrayValue=0:255
[ii,jj]=find(I==GrayValue);
G(GrayValue+1)=length(ii);
end
Assuming I to be a grayscale image, you can use histc to get H -
H = sum(histc(I,0:255),2)
Thus, the complete code would be -
% read image
I = imread(im);
H = sum(histc(I,0:255),2)
If you were looking for a little less-advanced code, you can avoid one nested loop -
% read image
I = imread(im);
H = zeros(256,1);
% loop for checking values
for GrayValue = 0:255
for i = 1:numel(I)
if I(i) == GrayValue % read each pixel coordinate
H(GrayValue+1) = H(GrayValue+1)+1;
end
end
end
I am creating figures in a for loop. The figure is a 2D mesh plot, which is supposed to be updated every iteration. The value to be plotted in a 200x200 array.
My problem is: It seems the calculation is running every iteration, but the plot is always the first one created, no matter I just plot or save to file.
Here is my code:
x = 1:200;
y = x;
for i = 1:100000
c = calculate(stuff, c); % value to be created, nothing to do with x and y
h = figure;
mesh(x,y,c);
saveas(h, sprintf('FIG%d.jpg',i);
drawnow; % did not work with or without this command
close(h);
end
First, thank you for all your inputs and suggestions! I didn't expect to get so many help within such a short time!
Then, I can answer some of the confusions here.
To Daniel: yes the c is changing. The program is calculating c based on its previous value. And there is sufficient step for c to change.
To R.Schifini: I tried pause(.1) but it didn't help unfortunately
To Andrew: thanks for pointing it. The complete program is attached now. And as to Daniel, the program calculate the value of c based on its previous values.
To The-Duck: I tried clf(h, 'reset') but unfortunately it didn't help.
Complete code:
Main program: please refer to wikipedia for the physical equation if you are interested
http://en.wikipedia.org/wiki/Cahn%E2%80%93Hilliard_equation
% Program to calculate composition evolution for nucleation and growth
% by solving Cahn-Hilliard equation - Time dependent non-linear
% differential equation
% Parameter
sig = 0.1; % J/m^2
delta = 10E-9; % m
D = 1E-9; %m^2/s
A = 10*sig/delta; % J/m
K = 3*sig*delta; % J/m^3
M = D/(2*A); % m^2/s
N = 200; % mesh size
dt = 1E-12; %s
h = delta/10;
% Rng control
r = -1+2.*rand(N);
beta = 1E-3;
n = 10000;
% initialization
c0 = zeros(200);
c0 = c0+ 0.1+beta.*r;
c = c0;
x = h.*linspace(-N/2,N/2,N);
y=x;
% Iteration
for i = 1:n
LP_c = laplacian(c,h);
d_f = A*(4*(c.^3)-6*(c.^2)+2*c);
sub = d_f - (2*K)*LP_c;
LP_RHS = laplacian(sub,h);
RHS = M*LP_RHS;
c = c + dt.*RHS;
% Save image every 2000 steps
% if ( i==1000 || i==10000 || i==100000)
% h = mesh(x,y,c);
% pause(.1);
% saveas(h, sprintf('FIG%d.jpg',i));
% clf(h,'reset');
% end
end
%h = figure;
mesh(x,y,c);
Laplacian function:
function LP_c = laplacian(c,h)
v1 = circshift(c,[0 -1]);
v2 = circshift(c,[0 1]);
v3 = circshift(c,[-1 0]);
v4 = circshift(c,[1 0]);
LP_c = (v1+v2+v3+v4-4.*c)./(h^2);
end
Result:
You can see the commented part in main program is for plotting periodically. They all give the same plots for each iteration. I tried the current OR version, also tried if ( mod(i,2000) == 0) to plot more pics. There is no difference. Shown:
However, if I comment out the periodic plotting, just run the program for different values of n, I got different plots, and they obey physical laws (evolving structure), shown in time order
Therefore I excluded the possibility that c might not update itself. It has to be some misuse of the plotting function of matlab. Or maybe some memory issue?
An interesting point I discovered during edition session: If I put the command h = figure in front of the loop and plot after the loop end, like this:
h = figure;
% Iteration
for i = 1:n
LP_c = laplacian(c,h);
d_f = A*(4*(c.^3)-6*(c.^2)+2*c);
sub = d_f - (2*K)*LP_c;
LP_RHS = laplacian(sub,h);
RHS = M*LP_RHS;
c = c + dt.*RHS;
end
mesh(x,y,c);
It seems all value of c calculated during the loop will overlap and give a figure shown below: I guess this indicates some facts about the plotting function of matlab, but I am not sure
Btw, can I answer directly to each comment and high light the new added section in my post? Sorry I am not as familiar with Stack Overlow as I should have :)
I ran your routine and with the following changes it works for me:
% Iteration
for i = 1:n
LP_c = laplacian(c,h);
d_f = A*(4*(c.^3)-6*(c.^2)+2*c);
sub = d_f - (2*K)*LP_c;
LP_RHS = laplacian(sub,h);
RHS = M*LP_RHS;
c = c + dt.*RHS;
% Save image every 2000 steps
if ( mod(i,2000)==0)
h1 = mesh(x,y,c);
drawnow;
saveas(h1, sprintf('FIG%d.jpg',i));
end
end
The main change is the figure handle variable from h to h1. Why? You are already using variable h in your equations.
Regards,