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How to create movies on each generation of a for loop in Matlab plot
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Closed 9 years ago.
I have the following code:
figure;
contour(X1,X2,f);
hold on
plot(top(1:size(top,1)), 'rx');
EDIT
figure;
for i = 1: G
contour(X1,X2,f);
hold on
plot(top(1:size(top,1)), 'rx');
end
NB: G is the maximum generation.
This is supposed to plot contours of sphere superimposed with selected individuals. In each iteration of the individuals, the best individuals is selected and these going on until the global optimum is reached. I need to show this in a movie form as shown in this below:
When you runs each stage of the iteration is indicated in the slides attached. This is what i am trying to do. Any idea please?
OK, I am just copying and pasting now, from here.
However I added FrameRate (per second) since you might want to use (or ask) it later.
writerObj = VideoWriter('Your_video.avi');
writerObj .FrameRate = 1; % 1 frames per second animation.
open(writerObj);
fig_h = figure;
for i = 1: G
contour(X1,X2,f);
hold on
plot(top(1:size(top,1)), 'rx');
frame = getframe(fig_h); % or frame = getframe; since getframe gets gcf.
writeVideo(writerObj, frame);
end
close(writerObj);
Now you will have a Your_video.avi file in your working directory.
If VideoWriter is not supported by your matlab, you could use use avifile same as mentioned in this answer (or in mathwork documentaion example here) like this:
aviobj = avifile('Your_video.avi','compression','None', 'fps', 1);
fig_h = figure;
for i = 1:G
contour(X1,X2,f);
hold on
plot(top(1:size(top,1)), 'rx');
frame = getframe(fig_h); % or frame = getframe; since getframe gets gcf.
aviobj = addframe(aviobj, frame);
end
aviobj = close(aviobj);
EDIT
A problem may occur as pointed out by this question also, which is the captured frame is a constant image. If you are running Matlab on windows, this problem may be caused by conjunction of windows in with certain graphics drivers, and may be solved as mentioned in this answer.
Related
I'm trying to write a code in Image J that will:
Open all images in separate windows that contains "488" within a folder
Use look up tables to convert images to green and RGB color From ImageJ, the commands are: run("Green"); and run("RGB Color");
Adjust the brightness and contrast with defined values for Min and Max (same values for each image).
I know that the code for that is:
//run("Brightness/Contrast..."); setMinAndMax(value min, value max); run("Apply LUT");
Save each image in the same, original folder , in Tiff and with the same name but finishing with "processed".
I have no experience with Java and am very bad with coding. I tried to piece something together using code I found on stackoverflow and on the ImageJ website, but kept getting error codes. Any help is much appreciated!
I don't know if you still need it, but here is an example.
output_dir = "C:/Users/test/"
input_dir = "C:/Users/test/"
list = getFileList(input_dir);
listlength = list.length;
setBatchMode(true);
for (z = 0; z < listlength; z++){
if(endsWith(list[z], 'tif')==true ){
if(list[z].contains("488")){
title = list[z];
end = lengthOf(title)-4;
out_path = output_dir + substring(title,0,end) + "_processed.tif";
open(input_dir + title);
//add all the functions you want
run("Brightness/Contrast...");
setMinAndMax(1, 15);
run("Apply LUT");
saveAs("tif", "" + out_path + "");
close();
};
run("Close All");
}
}
setBatchMode(false);
I think it contains all the things you need. It opens all the images (in specific folder) that ends with tif and contains 488. I didn't completely understand what you want to do with each photo, so I just added your functions. But you probably won't have problems with adding more/different since you can get them with macro recorder.
And the code is written to open tif files. If you have tiff just be cerful that you change that and also change -4 to -5.
It is very critical to learn the start time of each frame of a video.
I need to determine the starting point manually ( for example 848 here) by using below matlab code:
v = VideoReader('video1.avi','CurrentTime',848);
while hasFrame(v)
video_frame = readFrame(v);
counter=counter+1;
if counter==1
imshow(video_frame)
imhist(video_frame(:,:,1))
end
end
What I want is to distinguish some video frame from the others by using histogram. At the end my aim is to reach the exact showing time of the distinguished frames.
After editting:
This is frame histogram outputs:
Histogram size of the some frames are different from the previous one, do you know the reason?
difference=[difference sum(abs(histcounts(video_frame)-histcounts(lastframe)))];
Because of the taking the difference of the I had remove the different histogram sized frames but it causes missing some frames.
i havent found an video example that looks like what you discribe. please condsider always to have an example.
This example code calculates the differences in the histcounts. please notice that waitforbuttonpressis in the loop so you have to click for each frame while testing or remove it when the video is too long. Does this works on your file?
v = VideoReader('sample.avi','CurrentTime',1);
figure1=figure('unit','normalized','Position',[0.2 0.2 0.4 0.6]);
axes1=subplot(3,1,1);
axes2=subplot(3,1,2);
axes3 = subplot(3,1,3);
counter=0;
difference=[];
video_frame=readFrame(v);
while hasFrame(v)
lastframe=video_frame;
video_frame = readFrame(v);
counter=counter+1;
imshow(video_frame,'Parent',axes1);
[a,b]=histcounts(video_frame(:,:,1));
plot(b(1:end-1),a,'Parent',axes2);
difference=[difference sum(abs(histcounts(video_frame,0:255)-histcounts(lastframe,0:255)))];
bar(1:counter,difference,'Parent',axes3);
waitforbuttonpress
end
[~,onedistinguished]=max(difference);
%defining a threshold like every value that is bigger 4000
multidistinguished=find(difference>4000);
disp(['majorly changed at: ' num2str(distinguished)]);
I am using matlab 2013a software for my project.
I face a problem while splitting video into individual frames.
I want to know how to get frames at a specific intervals from video.. i.e., i want to grab frames at the rate of one frame per second(frame/sec) .My input video has 50 frames/sec. In the code I have used step() to slice the video into frames.
The following is my code , basically a face detection code(detects multiple faces in a video) . This code captures every frame in the video(i.e 50fp approx) and processes it. I want to process frames at the rate of 1 fps. Please help me.
clear classes;
videoFileReader = vision.VideoFileReader('C:\Users\Desktop\project\05.mp4');
**videoFrame = step(videoFileReader);**
faceDetector = vision.CascadeObjectDetector(); % Finds faces by default
tracker = MultiObjectTrackerKLT;
videoPlayer = vision.VideoPlayer('Position',[200 100 fliplr(frameSize(1:2)+30)]);
bboxes = [];
while isempty(bboxes)
**framergb = step(videoFileReader);**
frame = rgb2gray(framergb);
bboxes = faceDetector.step(frame);
end
tracker.addDetections(frame, bboxes);
frameNumber = 0;
keepRunning = true;
while keepRunning
**framergb = step(videoFileReader);**
frame = rgb2gray(framergb);
if mod(frameNumber, 10) == 0
bboxes = 2 * faceDetector.step(imresize(frame, 0.5));
if ~isempty(bboxes)
tracker.addDetections(frame, bboxes);
end
else
% Track faces
tracker.track(frame);
end
end
%% Clean up
release(videoPlayer);
But this actually considers every frame. I want to grab 1fps.
It cannot be done directly in Matlab 2013a, because the video access library does not provide the feature you want. Writing the necessary code to implement an efficient frame skipping routine is not really possible using just Matlab code (you would need to look inside the video libraries)
Working around it, you have two basic options:
Do as little work as possible on frames that you do not want to process.
Where you currently have
framergb = step(videoFileReader);
Instead do something like
for i=1:49,
step(videoFileReader);
end
framergb = step(videoFileReader);
(NB this does not allow for going beyond end of input)
Pre-process your file with a tool like ffmpeg, and reduce the frame-rate before you use Matlab.
The ffmpeg command might look something like this:
ffmpeg -i 05.mp4 -r 1 05_at_1fps.mp4
I’m trying to animate a Mayavi pipeline volume:
src = mlab.pipeline.volume(mlab.pipeline.scalar_field(data),vmin=.1*np.max(data),vmax=.2*np.max(data))
that is combined in the pipeline by another dataset represented as a cut plane.
However, I can’t get the volume visualization to update - only the first frame shows up. The animation is stepping through the data correctly (I get different values of the np.max(data[t]) below) but nothing in the visualization changes.
My understanding is that mlab_source_set should re-render correctly, and there’s nothing on the web anywhere that describes this (as far as I can tell).
The animation looks like:
#mlab.show
#mlab.animate(delay=250,ui=True)
def anim(src,data,tax,fig):
"""Animate."""
t = 0
nt = len(tax)
while 1:
vmin = .1*np.max(data[t])
vmax = .2*np.max(data[t])
print 'animation t = ',tax[t],', max = ',np.max(data[t])
src.mlab_source.set(scalar = mlab.pipeline.scalar_field(data[t]), vmin=vmin,vmax=vmax)
t = mod(t+1,nt)
yield
Any thoughts?
I have a load of data in 100 .sdf files (labelled 0000.sdf to 0099.sdf), each of which contain a still image, and I'm trying to produce a .gif from these images.
The code I use to plot the figure are (in the same directory as the sdf files):
q = GetDataSDF('0000.sdf');
imagesc(q.data');
I've attempted to write a for loop that would plot the figure and then save it with the same filename as the sdf file but to no avail, using:
for a = 1:100
q=GetDataSDF('0000.sdf');
fh = imagesc(q.dist_fn.x_px.Left.data');
frm = getframe( fh );
% save as png image
saveas(fh, 'current_frame_%02d.jpg');
end
EDIT: I received the following errors when trying to run this code:
Error using hg.image/get
The name 'Units' is not an accessible property for an instance of class 'image'.
Error in getframe>Local_getRectanglesOfInterest (line 138)
if ~strcmpi(get(h, 'Units'), 'Pixels')
Error in getframe (line 56)
[offsetRect, absoluteRect, figPos, figOuterPos] = ...
Error in loop_code (line 4)
frm = getframe( fh );
How do I save these files using a for loop, and how do I then use those files to produce a movie?
The reason for the error is that you pass an image handle to getframe, but this function excpects a figure handle.
Another problem is that you always load the same file, and that you saveas will not work for gifs. (For saving figures as static images, maybe print is the better option?)
I tried to modify my own gif-writing loop so that it works with your data. I'll try to be extra explicit in the comments, since you seem to be starting out. Remember, you can always use help name_of_command to display a short Matlab help.
% Define a variable that holds the frames per second your "movie" should have
gif_fps = 24;
% Define string variable that holds the filename of your movie
video_filename = 'video.gif';
% Create figure 1, store the handle in a variable, you'll need it later
fh = figure(1);
for a = 0:99
% Prepare file name so that you loop over the data
q = GetDataSDF(['00' num2str(a,'%02d') 'sdf']);
% Plot image
imagesc(q.dist_fn.x_px.Left.data');
% Force Matlab to actually do the plot (it sometimes gets lazy in loops)
drawnow;
% Take a "screenshot" of the figure fh
frame = getframe(fh);
% 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 a == 0;
imwrite(imind,cm,video_filename,'gif', 'Loopcount',inf);
else
imwrite(imind,cm,video_filename,'gif','WriteMode','append','DelayTime',1/gif_fps);
end
end
One more note: When the size of the data is the same for each plot, it makes sense to only use the plot(or in this case, imagesc) command once, and in later loop iterations replace it with a set(ah,'Ydata',new_y_data) (or in this case set(ah,'CData',q.dist_fn.x_px.Left.data'), where ah is a handle of the plot axes (not the plot figure!). This is orders of magnitude faster than creating a whole new plot in each loop iteration. The downside is that the scaling (here, the color-scaling) will be the same for each plot. But in every case that I have worked on so far, that was actually desirable.