Averaging in a uint 8 image pixel array

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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.

Accepted Answer

Matt J
Matt J on 5 Jul 2013
Edited: Matt J on 5 Jul 2013
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

More Answers (2)

Image Analyst
Image Analyst on 5 Jul 2013
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
  1 Comment
Jean
Jean on 7 Jul 2013
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)?

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Jan
Jan on 5 Jul 2013
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);
  2 Comments
Jean
Jean on 7 Jul 2013
Thanks, does the 2, 3 correspond to some portioning of the image frame or actual pixel values?
Jan
Jan on 7 Jul 2013
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.

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