How to loop through all files in subfolders in a main folder?

Hello,

I have a main folder and several subfolders in it. Each subfolder has several files within them. I want to create a loop in such a manner that the code would open a subfolder, do what I want it to do and then move to the next one.

Thanks in advance

Answer 1

[Stephen23]

https://www.mathworks.com/help/matlab/import_export/process-a-sequence-of-files.html

D = 'full path to the main folder';
S = dir(fullfile(D,'*'));
N = setdiff({S([S.isdir]).name},{'.','..'}); % list of subfolders of D.
for ii = 1:numel(N)
    T = dir(fullfile(D,N{ii},'*')); % improve by specifying the file extension.
    C = {T(~[T.isdir]).name}; % files in subfolder.
    for jj = 1:numel(C)
        F = fullfile(D,N{ii},C{jj})
        % do whatever with file F.
    end
end

[Gopika Rajan]

Thanks a million. I have had a look at several answers, but this was the easiest one. The code worked perfectly as I desired.

Cheers!

[Suhas Nuggehalli Sampathkumar]

I was using files with extension .zfr in different sub folders. I used this loop to convert those files to .txt. Thank you

[AUWAL ABUBAKAR]

Good day and thank you Stephen for the code. It is exctaly what i was looking for.

Please is there any way I can perform the analysis seperate for each sub folder first, then combine the results from each subfolder together later?

For example; I extracted 10 values from each subfolder (containg 10 text files). I would like to calculate the mean value (M) of each sub folder so that I can have M1, M2, M3 .... M20. then calculate the standard deviation of the values M1...M20.

Thanks

[Royi Avital]

What about sub of sub of sub of sub folders?

[Emu]

I'm trying to modify this code but it is finding only the subfolders and not the files, what am I doing wrong?

S = dir(fullfile(RawECGDir,'*'));

visits = setdiff({S([S.isdir]).name},{'.','..'}); % list of subfolders of D.

for ii = 1:numel(visits)

T = dir(fullfile(RawECGDir,visits{ii},'*','C_ecg.cvs')); % improve by specifying the file extension.

C = {T(~[T.isdir]).name}; % files in subfolder.

for jj = 1:numel(C)

file = fullfile(RawECGDir,visits{ii},C{jj});

% do whatever with file F.

end

end

[Image Analyst]

@Emu, try this very well commented demo. Adapt it (from *.bmp) to whatever file extension you want, like .CSV.

% Code to list all sub-folders under some top-level folder.
% function scansubfolders()
clc;
clearvars;
close all;
workspace;
% Ask user to locate some top-level folder.
start_path = pwd;
topLevelFolder = uigetdir(start_path)
if topLevelFolder == 0
    return; % User clicked Cancel button.
end
% Generate list of all subfolders.
allSubFolders = dir(fullfile(topLevelFolder, '**/*')); % All files and folders.
allSubFolders = allSubFolders([allSubFolders.isdir]); % Extract only the folders.
allSubFolders = unique({allSubFolders.folder}); % Throw out duplicates.
% Now we have a list of all folders and subfolders as a cell array.
% Optional: display them in the command window.
disp('Here are the subfolders:');
allSubFolders

% Display BMP files from each subfolder.
for k = 1 : length(allSubFolders)
    % Get the name of this subfolder:
    thisFolder = allSubFolders{k};
    fprintf('Now processing folder #%d of %d : "%s".\n', k, length(allSubFolders), thisFolder); % Print to command window what folder we're processing.
    % Get the file pattern for the files that we want to process.
    filePattern = [thisFolder, '\*.bmp'];
    % Find out names of files with this file pattern in this folder.
    filesInThisFolder = dir(filePattern); % Cell array
    if ~isempty(filesInThisFolder) % If there are files in this folder, do this:
        numFiles = numel(filesInThisFolder); % Store the number of files in this one subfolder.
        % If there are any files, display and process them all.
        for fileNumber = 1 : numFiles
            fullFileName = fullfile(thisFolder, filesInThisFolder(fileNumber).name);
            fprintf(1, 'About to process #%d of %d in this folder : "%s".\n', fileNumber, numFiles, fullFileName);
            % For example, maybe we want to process the file by reading it in as and image and display it.
            % You can process it however you want though.
            imageArray = imread(fullFileName);
            imshow(imageArray);
            title(filesInThisFolder(fileNumber).name);
            drawnow;
            % Optional : Ask user if they want to continue and process the next file.
            if fileNumber ~= numFiles
                promptMessage = sprintf('Done with #%d of %d in this folder.\nDo you want to Continue with file #%d,\nor Cancel to abort?', fileNumber, numFiles, fileNumber+1);
                button = questdlg(promptMessage, 'Continue', 'Continue', 'Cancel', 'Continue');
                if contains(button, 'Cancel')
                    % User wants to quit.
                    return;
                end
            end
        end
    else
        fprintf('    Skipping folder #%d because there are no files in it with our pattern.\n', k); % Print to command window what folder we're processing.
    end
end
uiwait(helpdlg('Check out the command window for the folder and file names.'));

[Emu]

Awesome thank you !

[Jason Sebek]

I used this and https://www.mathworks.com/matlabcentral/answers/5304-get-list-of-subclasses to map out class/subclass structure of a bunch of files. Thank you!