MATLAB: Averaging in a uint 8 image pixel array

averageimage processingImage Processing Toolboxpixeluint8

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 480×640 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.

Best Answer

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

Related Solutions

MATLAB: Converting video to frames

Try this demo. That is one of the things it does:

% 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, and convert them to a movie.
      % I don't know of any way to preallocate recalledMovie.
      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

MATLAB: How to save individual movie frames from a video

Here's a complete working demo for you:

% 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.)
workspace;  % Make sure the workspace panel is showing.
fontSize = 14;
% 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, and convert them to a movie.
      % I don't know of any way to preallocate recalledMovie.
      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

Best Answer

Related Solutions

MATLAB: Converting video to frames

MATLAB: How to save individual movie frames from a video

Related Question