plotting intensity over time

I have 135 images, taken one after another. I want to plot the intensity of each pixel (let's say 25 x 25 pixels) as a function of time. How can I do that?

Answer 1

[Thomas]

Eg:

s=rand(3,3,10);   % 10 images of size 3x3 in a 3d matrix s

pixel1(1,:)=s(1,1,:);  % pixel 1,1 from each matrix into variable pixel1

plot(pixel1)  % plot pixel1

Hope this helps

Answer 2

[Image Analyst]

A plot of 625 curves (one curve for each of the 25 by 25 pixels) showing the pixel intensity as a function of image number (time the photo was taken) won't be very informative because it will be too cluttered. Why don't you take the mean of the 25 by 25 region and then plot only that one curve? Or else make the frames into a movie with the im2frame() function. I have demos for all that if you're interested.

[Jenna]

I was hoping to have 625 separate graphs, although I am not planning on actually looking at all of them, only at the ones in the most actively changing region. I am interested in the demos, just in case. Thanks.

[Image Analyst]

You really don't want 625 plots on your screen at the same time, do you? You'd barely be able to see them!

Here's the demo:

% Demo macro to extract frames and get frame means from an avi movie
% and save individual frames to separate image files.
% Also computes the mean gray value of the color channels.
clc;    % Clear the command window.
close all;  % Close all figures (except those of imtool.)
imtool close all;  % Close all imtool figures.
clear;  % Erase all existing variables.
workspace;  % Make sure the workspace panel is showing.
fontSize = 14;

% Change the current folder to the folder of this m-file.
% (The line of code below is from Brett Shoelson of The Mathworks.)
if(~isdeployed)
  cd(fileparts(which(mfilename)));
end

% Open the rhino.avi demo movie that ships with MATLAB.
folder = fullfile(matlabroot, '\toolbox\images\imdemos');
movieFullFileName = fullfile(folder, 'rhinos.avi');
% Check to see that it exists.
if ~exist(movieFullFileName, 'file')
  strErrorMessage = sprintf('File not found:\n%s\nYou can choose a new one, or cancel', movieFullFileName);
  response = questdlg(strErrorMessage, 'File not found', 'OK - choose a new movie.', 'Cancel', 'OK - choose a new movie.');
  if strcmpi(response, 'OK - choose a new movie.')
    [baseFileName, folderName, FilterIndex] = uigetfile('*.avi');
    if ~isequal(baseFileName, 0)
      movieFullFileName = fullfile(folderName, baseFileName);
    else
      return;
    end
  else
    return;
  end
end

try
  videoObject = VideoReader(movieFullFileName)
  % Determine how many frames there are.
  numberOfFrames = videoObject.NumberOfFrames;
  vidHeight = videoObject.Height;
  vidWidth = videoObject.Width;
  
  numberOfFramesWritten = 0;
  % Prepare a figure to show the images in the upper half of the screen.
  figure;
  %   screenSize = get(0, 'ScreenSize');
  % Enlarge figure to full screen.
  set(gcf, 'units','normalized','outerposition',[0 0 1 1]);
  
  % Ask user if they want to write the individual frames out to disk.
  promptMessage = sprintf('Do you want to save the individual frames out to individual disk files?');
  button = questdlg(promptMessage, 'Save individual frames?', 'Yes', 'No', 'Yes');
  if strcmp(button, 'Yes')
    writeToDisk = true;
    
    % Extract out the various parts of the filename.
    [folder, baseFileName, extentions] = fileparts(movieFullFileName);
    % Make up a special new output subfolder for all the separate
    % movie frames that we're going to extract and save to disk.
    % (Don't worry - windows can handle forward slashes in the folder name.)
    folder = pwd;   % Make it a subfolder of the folder where this m-file lives.
    outputFolder = sprintf('%s/Movie Frames from %s', folder, baseFileName);
    % Create the folder if it doesn't exist already.
    if ~exist(outputFolder, 'dir')
      mkdir(outputFolder);
    end
  else
    writeToDisk = false;
  end
  
  % Loop through the movie, writing all frames out.
  % Each frame will be in a separate file with unique name.
  meanGrayLevels = zeros(numberOfFrames, 1);
  meanRedLevels = zeros(numberOfFrames, 1);
  meanGreenLevels = zeros(numberOfFrames, 1);
  meanBlueLevels = zeros(numberOfFrames, 1);
  for frame = 1 : numberOfFrames
    % Extract the frame from the movie structure.
    thisFrame = read(videoObject, frame);
    
    % Display it
    hImage = subplot(2, 2, 1);
    image(thisFrame);
    caption = sprintf('Frame %4d of %d.', frame, numberOfFrames);
    title(caption, 'FontSize', fontSize);
    drawnow; % Force it to refresh the window.
    
    % Write the image array to the output file, if requested.
    if writeToDisk
      % Construct an output image file name.
      outputBaseFileName = sprintf('Frame %4.4d.png', frame);
      outputFullFileName = fullfile(outputFolder, outputBaseFileName);
      
      % Stamp the name and frame number onto the image.
      % At this point it's just going into the overlay,
      % not actually getting written into the pixel values.
      text(5, 15, outputBaseFileName, 'FontSize', 20);
      
      % Extract the image with the text "burned into" it.
      frameWithText = getframe(gca);
      % frameWithText.cdata is the image with the text
      % actually written into the pixel values.
      % Write it out to disk.
      imwrite(frameWithText.cdata, outputFullFileName, 'png');
    end
    
    % Calculate the mean gray level.
    grayImage = rgb2gray(thisFrame);
    meanGrayLevels(frame) = mean(grayImage(:));
    
    % Calculate the mean R, G, and B levels.
    meanRedLevels(frame) = mean(mean(thisFrame(:, :, 1)));
    meanGreenLevels(frame) = mean(mean(thisFrame(:, :, 2)));
    meanBlueLevels(frame) = mean(mean(thisFrame(:, :, 3)));
    
    % Plot the mean gray levels.
    hPlot = subplot(2, 2, 2);
    hold off;
    plot(meanGrayLevels, 'k-', 'LineWidth', 2);
    hold on;
    plot(meanRedLevels, 'r-');
    plot(meanGreenLevels, 'g-');
    plot(meanBlueLevels, 'b-');
    grid on;
    
    % Put title back because plot() erases the existing title.
    title('Mean Gray Levels', 'FontSize', fontSize);
    if frame == 1
      xlabel('Frame Number');
      ylabel('Gray Level');
      % Get size data later for preallocation if we read
      % the movie back in from disk.
      [rows columns numberOfColorChannels] = size(thisFrame);
    end
    
    % Update user with the progress.  Display in the command window.
    if writeToDisk
      progressIndication = sprintf('Wrote frame %4d of %d.', frame, numberOfFrames);
    else
      progressIndication = sprintf('Processed frame %4d of %d.', frame, numberOfFrames);
    end
    disp(progressIndication);
    % Increment frame count (should eventually = numberOfFrames
    % unless an error happens).
    numberOfFramesWritten = numberOfFramesWritten + 1;
    
    % Now let's do the differencing
    alpha = 0.5;
    if frame == 1
      Background = thisFrame;
    else
      % Change background slightly at each frame
      %       Background(t+1)=(1-alpha)*I+alpha*Background
      Background = (1-alpha)* thisFrame + alpha * Background;
    end
    % Display the changing/adapting background.
    subplot(2, 2, 3);
    imshow(Background);
    title('Adaptive Background', 'FontSize', fontSize);
    % Calculate a difference between this frame and the background.
    differenceImage = thisFrame - uint8(Background);
    % Threshold with Otsu method.
    grayImage = rgb2gray(differenceImage); % Convert to gray level
    thresholdLevel = graythresh(grayImage); % Get threshold.
    binaryImage = im2bw( grayImage, thresholdLevel); % Do the binarization
    % Plot the binary image.
    subplot(2, 2, 4);
    imshow(binaryImage);
    title('Binarized Difference Image', 'FontSize', fontSize);
  end
  
  % Alert user that we're done.
  if writeToDisk
    finishedMessage = sprintf('Done!  It wrote %d frames to folder\n"%s"', numberOfFramesWritten, outputFolder);
  else
    finishedMessage = sprintf('Done!  It processed %d frames of\n"%s"', numberOfFramesWritten, movieFullFileName);
  end
  disp(finishedMessage); % Write to command window.
  uiwait(msgbox(finishedMessage)); % Also pop up a message box.
  
  % Exit if they didn't write any individual frames out to disk.
  if ~writeToDisk
    return;
  end
  
  % Ask user if they want to read the individual frames from the disk,
  % that they just wrote out, back into a movie and display it.
  promptMessage = sprintf('Do you want to recall the individual frames\nback from disk into a movie?\n(This will take several seconds.)');
  button = questdlg(promptMessage, 'Recall Movie?', 'Yes', 'No', 'Yes');
  if strcmp(button, 'No')
    return;
  end
  
  % Read the frames back in from disk, and convert them to a movie.
  % Preallocate recalledMovie, which will be an array of structures.
  % First get a cell array with all the frames.
  allTheFrames = cell(numberOfFrames,1);
  allTheFrames(:) = {zeros(vidHeight, vidWidth, 3, 'uint8')};
  % Next get a cell array with all the colormaps.
  allTheColorMaps = cell(numberOfFrames,1);
  allTheColorMaps(:) = {zeros(256, 3)};
  % Now combine these to make the array of structures.
  recalledMovie = struct('cdata', allTheFrames, 'colormap', allTheColorMaps)
  for frame = 1 : numberOfFrames
    % Construct an output image file name.
    outputBaseFileName = sprintf('Frame %4.4d.png', frame);
    outputFullFileName = fullfile(outputFolder, outputBaseFileName);
    % Read the image in from disk.
    thisFrame = imread(outputFullFileName);
    % Convert the image into a "movie frame" structure.
    recalledMovie(frame) = im2frame(thisFrame);
  end
  % Get rid of old image and plot.
  delete(hImage);
  delete(hPlot);
  % Create new axes for our movie.
  subplot(1, 3, 2);
  axis off;  % Turn off axes numbers.
  title('Movie recalled from disk', 'FontSize', fontSize);
  % Play the movie in the axes.
  movie(recalledMovie);
  % Note: if you want to display graphics or text in the overlay
  % as the movie plays back then you need to do it like I did at first
  % (at the top of this file where you extract and imshow a frame at a time.)
  msgbox('Done with this demo!');
  
catch ME
  % Some error happened if you get here.
  stError = lasterror;
  strErrorMessage = sprintf('Error extracting movie frames from:\n\n%s\n\nError: %s\n\n)', movieFullFileName, stError.message);
  uiwait(msgbox(strErrorMessage));
end

[Hazmi Mazlaini]

this code is for the mean value for the whole area of the frames.

can you help me, if i want to plot a graph of the total red intensity over time in just a certain area of the frame?

[Image Analyst]

What area? Do you have bounding rows and columns? Or an irregular mask shape?

[Hazmi Mazlaini]

I have video of a whole face, but only want to plot a graph of total redness in forehead as an example

[laurent jalabert]

I guess you can define a ROI (rectangular for example) and crop the image there, then average the pixel intensities inside this ROI (it will become a vector9 and then plot versus time.