Averaging in a uint 8 image pixel array

Hello,

I am trying to extract the pixel values (of an intensity image-so all R,G,B are the same) over a series of frames (video). I can extract information from a single pixel image(x,y) and plot it over time, but I want do this but with an area of pixels with their average value. I cannot figure out how to get the image pixel matrix, a 480x640 uint 8, into a form where I can do so. I have tried converting with num2cell and cell2mat and cat, but with no avail. Any tips?

I promise to also start helping people once I get better at some of these things.

Answer 1

[Matt J]

Using MAT2TILES, available here you can do things like this:

Img=uint8(rand(16)); %Fake  image
C=mat2tiles(Img,[8,8]), %Split into 8x8 tiles

AreaMeans=cellfun(@(c)mean(c(:)),C) %Means of each tile

[Jean]

Thanks! I think this will be good

Answer 2

[Image Analyst]

Here's a demo that does exactly that. I've posted it many times before.

% Demo macro to extract frames and get frame means from an avi movie
% and save individual frames to separate image files.
% Then rebuilds a new movie by recalling the saved images from disk.
% Also computes the mean gray value of the color channels
% And detects the difference between a frame and the previous frame.
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.
  strErrorMessage = sprintf('Error extracting movie frames from:\n\n%s\n\nError: %s\n\n)', movieFullFileName, ME.message);
  uiwait(msgbox(strErrorMessage));
end

[Jean]

THanks this is great. For extracting information from a certain part of an image, however, I woudl have to create a smaller version of the video just to get that part's information, correct? Also, I believe my .avi files are too large...will this work with .mp4 or .mov (for mac)?

Answer 3

[Jan]

This can be solved by FEX: BlockMean:

% Average over two rows and 3 columns:
img   = randi([0, 255], 16, 'uint8');
block = BlockMean(img, 2, 3);

[Jean]

Thanks, does the 2, 3 correspond to some portioning of the image frame or actual pixel values?

[Jan]

As the help text of the function, the description on the linked page and the comment in the posted code explain, "2,3" means that the average is built over blocks of 2 rows and 3 columns. As result for a 16x16 matrix you get a 8x5 matrix and the last column of the input matrix is ignored, because 16 is not a multiple of 3.