reading images from different folders

i have five folders,each containing 1000 images .i want to take each images from these folders (ie.first images from all folders and then second images etc)and find the average of these images like(if a,b,c,d,e,are first five images from five folders ,then e =a/10+/10+c/10+d/10+e/10) and stored the resultant images(averaged ) in a resultant forlder

[Walter Roberson]

What is the "first" image of a folder? Do the images have the same name in each of the folders, or is the name in the other folders computable by knowing the name in one of the folders?

I ask because the order of files in a folder is poorly defined.

[Mathieu NOE]

see this post

that might help you

trying to average some tiff's images - MATLAB Answers - MATLAB Central (mathworks.com)

Answer 1

[Mathieu NOE]

hello

maybe this ?

I created some "input" folders where the images are stored (those folders are supposed to have "in" in their names , change to your definition)

I also assumed :

• tif images (but you can change that as well)
• there is already an existing "out" folder to store the resulting images

my code also uses this Fex submission that you need to download and install in your path :

Natural-Order Filename Sort - File Exchange - MATLAB Central (mathworks.com)

%NB : data files are not searched inside the main folder (yourpath) but in
% all subfolders (dirnames)
% if S is empty that means no data file (matching the file filter is in the searched subfolder)

%% define path
yourpath = pwd; % or your specific path
list=dir(yourpath);  %get info of files/folders in current directory
isfile=~[list.isdir]; %determine index of files vs folders
dirnames={list([list.isdir]).name}; % directories names (including . and ..)
dirnames=dirnames(~(strcmp('.',dirnames)|strcmp('..',dirnames))); % remove . and .. directories names from list

% "in" folders 
dirnames_in  = dirnames(contains(dirnames,'in'));

% output directory 
out_dir = fullfile(yourpath,'\out'); % from current directory to sub directory \out

%% Loop on each folder
for ci = 1:length(dirnames_in) % 
    
    fileDir = char(dirnames_in(ci)); % current directory name
    S = dir(fullfile(fileDir,'*.tif')); % get list of data files in directory according to name structure '*.tif' 
    S = natsortfiles(S); % sort file names into natural order (what matlab does not) , see FEX : 
               %(https://fr.mathworks.com/matlabcentral/fileexchange/47434-natural-order-filename-sort)
               
    %% Loop inside folder
    for k = 1:length(S) % read data 
        tmp{ci,k} = imread(fullfile(fileDir, S(k).name));  
    end
    
end

%% do summation along  folders 
[m,n] = size(tmp);

for k = 1:n % loop over images files
    
    out = double(tmp{1,k}); % first image of k th folder, need to convert to double to avoid saturation during summation process
    for ci = 2:m % loop over folders (same image)
        out = out + double(tmp{ci,k});  % need to convert to double to avoid saturation during summation process
    end
    image_avg{k} = uint8(out/m); % here we divide by m to have the average and convert back to int format
    
    figure(k),imagesc(image_avg{k});
    axis equal
    % save to out folder
    filename = ['out_' num2str(k,4) '.tif'];
    imwrite(image_avg{k},fullfile(out_dir,filename));
end

[Mathieu NOE]

hello again

do you mind accepting my answer (if it has fullfiled your expectations ) ? tx

Answer 2

[Image Analyst]

See attached demo. Adapt as needed.