Putting the whole process in the loop

attempt2

clc;
clear;

% Start with importing the video
vidObj = VideoReader('/Users/DarkSector/Desktop/vid.avi');

% Once loaded lets get the first frame and choose an ROI on it
frame1 = read(vidObj, 1);

% now let's show the image and select the ROI on it
imshow(frame1)
roiRect = imrect;

% get the position of the rectangle as well
roiPosition = roiRect.getPosition();

%masked = createMask(roiRect, frame1);

%imshow(frame1)


% figure(1);
% subplot(1,3,1);
% plot(red_channel);
% 
% subplot(1,3,2);
% plot(blue_channel);
% 
% subplot(1,3,3);
% plot(green_channel);

for frame = 1:vidObj.NumberOfFrames-145
    % Take frame and apply mask
    % crop frame
    % separate frame into three different channels
    % append frame to individual channel array
    
    % create frame object
    frameObj = read(vidObj, frame);
    
    % Create the mask
    roiMask = createMask(roiRect);    
    
    % Apply the mask on all 3 dimensions/ all channels
    mask_3chan = repmat(roiMask, [1,1,3]);
    
    % Set all other pixels to 0
    frameObj(~mask_3chan) = 0;
    
    % if we are not using the rest of the pixels, 
    % might as well remove
    % them and crop the image.
    % No reason to store dummy data
    frameObj = imcrop(frameObj, roiPosition);
    
    red_channel = frameObj;
    blue_channel = frameObj;
    green_channel = frameObj;
    %extract the red channel
    red_channel = red_channel(:,:,1);
    %extract the blue channel
    blue_channel= blue_channel(:,:,2);
    %extract the green channel
    green_channel= green_channel(:,:,2);
    
    redArray = cat(3, red_channel);
    blueArray = cat(3, blue_channel);
    greenArray = cat(3, green_channel);
            
end