MATLAB: Processing and Saving multiple images to the same file

image analysisimage processingimage segmentation

Hi, I'm having trouble with processing several images and saving it to the same file. I have 120 images of the image attached (.tif format and 16bit) and I applied a mask on the white semicircles using a code. My problem is that I'm not sure how to apply the mask to each image and save them in the same file. When I used the following code, it only applied the mask to one image and produced 120 copies of it. Is there a way use the for loop to apply the mask for each processed image and then save each image? 
% Specify the folder where the files are
myFolder = 'C:\Users\ellizafeisol\Desktop\DATA\UNF2501';
% Check to make sure that folder actually exists.  Warn user if it doesn't.
if ~isfolder(myFolder)
    errorMessage = sprintf('Error: The following folder does not exist:\n%s\nPlease specify a new folder.', myFolder);
    uiwait(warndlg(errorMessage));
    myFolder = uigetdir(); % Ask for a new one.
    if myFolder == 0
         % User clicked Cancel
         return;
    end
end
% Get a list of all files in the folder with the desired file name pattern.
filePattern = fullfile(myFolder, '*.tif'); % Change to whatever pattern required.
theFiles = dir(filePattern);
numberofImages = length(theFiles);
for k = 1 : numberofImages
    baseFileName = theFiles(k).name;
    fullFileName = fullfile(theFiles(k).folder, baseFileName);
    % Process all images in the file
    imageArray = imread(fullFileName);
    %Gray Image
    g = double(imageArray);
    grayImages = mat2gray(g); 
    % Threshold Values
    imagesToThreshold = g;
    startingLowThreshold = 0;
    startingHighThreshold = 34500; 
    % Binarize the image.
    binaryImage = (imagesToThreshold > startingLowThreshold) & (imagesToThreshold < startingHighThreshold);
    binaryImage = imfill(binaryImage, 'holes');
    mask = bwareafilt(binaryImage, 4);
  %Mask the images
    Output=grayImages.*mask;
    drawnow; % Force display to update immediately.
    
    for k= 1 : numberofImages  %k be numbers of images in the folder
    h = Output; 
	imwrite(h,sprintf('MASK_0%d.tif',k)); % will create mask1, mask2,...
    end 
end

Best Answer

Hi Elliza,
From the code I see that you have used the for loop to traverse through the images. Since the first for loop is for traversing, I don’t see the necessity of second for loop. Indeed, what it is doing is changing the value of k to numberofImages and hence when you come back to outer for loop the condition of k<= numberofImages is already is fullfilled and thus your code is only outputting same images numberofImages times. You may change the for loop with something like below. 
for k = 1 : numberofImages 
    baseFileName = theFiles(k).name; 
    fullFileName = fullfile(theFiles(k).folder, baseFileName); 
    % Process all images in the file 
    imageArray = imread(fullFileName); 
    %Gray Image 
    g = double(imageArray); 
    grayImages = mat2gray(g);  
    % Threshold Values 
    imagesToThreshold = g; 
    startingLowThreshold = 0; 
    startingHighThreshold = 34500;  
    % Binarize the image. 
    binaryImage = (imagesToThreshold > startingLowThreshold) & (imagesToThreshold < startingHighThreshold); 
    binaryImage = imfill(binaryImage, 'holes'); 
    mask = bwareafilt(binaryImage, 4); 
    %Mask the images 
    Output=grayImages.*mask; 
    drawnow; % Force display to update immediately. 
    imwrite(Output,sprintf('MASK_0%d.tif',k)); % will create mask1, mask2,... 
end
This will make sure every image is read and mask is calculated.
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