Help me to optimize this code to perform better Image Processing

I am working on a Computer Vision project which involves analyzing and exporting Pixel intensities of RGB over a Region of Interest from a frame. Please look into the code i have attached here and suggest me some best ways to optimize this code. It's taking me a minimum of 5 seconds to maximum of 7 seconds per frame, to analyze and export desired data.

​

path='/Users/sathwikchowda/Desktop/morselab/matlab-testing/videos/1Hz-Transmission.avi';
video_files = dir(fullfile(path,'*.avi'));
movieFullFileName = fullfile(path,video_files.name);
​
tic
 videoObject = VideoReader(movieFullFileName);
    % Determine how many frames there are.
    numberOfFrames = videoObject.NumFrames;
    %numberOfFrames = 1000; % <-------------------------------- For changing number of frames
    vidHeight = videoObject.Height;
    vidWidth = videoObject.Width;
    numberOfFramesWritten = 0;
    
     % 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);
    bits = zeros(numberOfFrames,1);
    
    
    
    thisFrame = read(videoObject, 1);
    imshow(thisFrame, []);
    axis on;
    set(gcf, 'Position', get(0,'Screensize')); % Maximize figure.
    
    
    h_rect = imrect();% this helps us to draw over the frame
    % Rectangle position is given as [x, y, width, height]
    pos_rect = h_rect.getPosition();
    % Round off so the coordinates can be used as indices
    pos_rect = round(pos_rect);
    disp(pos_rect)
    
    
for frame = 1 : numberOfFrames
        
        
        % Extract the frame from the movie structure.
        thisFrame = read(videoObject, frame);
        thisFrame = imcrop(thisFrame,pos_rect);
​
        
        
 
        % 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)));
        
        %THRESHOLD
        threshold = mean(meanBlueLevels);
        
        
        
       
        Levels = table(meanRedLevels,meanBlueLevels,meanGreenLevels,meanGrayLevels, 'VariableNames',{'Red-Pixel-Intensity','Blue-Pixel-Intensity','Green-Pixel-Intensity','Gray-Levels'});
        writetable(Levels,'5Hz-PI-info.csv');
        type 5Hz-PI-info.csv
        
        % bit-stream to csv file
        if (meanBlueLevels(frame) ~=0)
            if (meanBlueLevels(frame) >= threshold )
                bits = 1;
            else
                bits = 0;
            end
            
 %          dlmwrite('5Hz-binary.csv', bits, '-append')
            writematrix(bits,'5Hz-binary.csv','WriteMode','append')             
            T3 = table(pos_rect(1),pos_rect(2),pos_rect(3),pos_rect(4),'VariableNames',{'X-coordinates','Y-coordinates','Width','Height'});
            writetable(T3,'5Hz-ROI-position-coordinates.csv');
            type 5Hz-ROI-position-coordinates.csv
        end
        progressIndication = sprintf('Processed frame %4d of %d.', frame, numberOfFrames);
        disp(progressIndication)
            
            
​
            
end
toc
​

Answer 1

[Jan]

The command mean(X) is surprisingly much slower than sum(X)/numel(X). So replace:

mean(mean(thisFrame(:, :, 1)))

by

sum(thisFrame(:, :, 1), 'all') / (pos_rect(3)*pos_rect(4))

Why do you create a new file '5Hz-PI-info.csv' in each iteration only to type its contents to the screen? This is a pure waste of time, isn't it? The same with '5Hz-ROI-position-coordinates.csv', which is written repeatedly, although it contains the same values in each iteration. I assume this unneeded disk access wastes the most time in your code. Simply omit it. If you simply want to display the contents of the table, use

disp(Levels)

It will not matter the speed, but the clarity of the code to simplify

progressIndication = sprintf('Processed frame %4d of %d.', frame, numberOfFrames);
disp(progressIndication)        

to

fprintf('Processed frame %4d of %d.', frame, numberOfFrames);

I assume this is a bug:

bits = zeros(numberOfFrames,1);
for frame = 1 : numberOfFrames
...
     bits = 1;

Do you mean:

     bits(frame) = 1;     

By the way: A simplification of:

if (meanBlueLevels(frame) >= threshold )
    bits(frame) = 1;
else
    bits(frame) = 0;
end

is

bits(frame) = (meanBlueLevels(frame) >= threshold);