How to loop through a specific file in various subfolders inside a main folder?

I have a main folder containing several subfolders in it, named in a logical way (eg. damage1_case20; damage2_case20; (...); damagei_case20). Each subfolder has several files within them, all sharing the same name between subfolders. My goal is to create a loop in a way that the code would open one subfolder (starting with damage1_case20), open a specific file inside that subfolder (eg. calculation.mat), do what I want it to do to that file, save the new version of the file (eg. calculation_fix.mat) inside that subfolder, then move on to the next subfolder (which would be damage2_case20) and repeat the proccess until the end (damagei_case20).

[Stephen23]

Whatever you do, avoid using slow and hard-to-debug CD in your code!

The simple approach is to get DIR to do most of of this task as possible.

Answer 1

[Bjorn Gustavsson]

For this I (sometimes) do this type of thing:

proj_root_dir = '/full/path/to/project';
data_dirs = {'damage1_case20','damage2_case20','damage3_case20'}; % etc, etc
% or I programmatically extract the data-directories with dir.
file2process = 'calculation.mat';
for iD = 1:numel(data_dirs)
  cd(proj_root_dir)
  cd(data_dirs{iD})
  try
    results = process_datafile(file2process)
    [~,fnm,ext] = fileparts(file2process);
    fnm2save = [fnm,'_fix',ext]; % this save-part might be better
    save(fnm2save,'results');    % inside the processing-function
                                 % but you get the idea
  catch
    disp(['something dodgy happened processing file: ',fullfile(data_dirs{iD},file2process)])
  end
end

HTH

[Vítor]

Thank you so much!!

Answer 2

[Image Analyst]

Try this robust and well commented demo:

% Finds all the subfolders under a top level folder and then for each subfolder, processes the files within that folder.
% NOTE: this does not process files in the top level folder.  It only processes files in subfolders of the top level folder.
clc;    % Clear the command window.
workspace;  % Make sure the workspace panel is showing.
format compact;
% Define input folder.
% CHANGE THIS FOLDER NAME!!!!!!
topLevelFolder = pwd;
% Check to see that the folder exists.
if ~isfolder(topLevelFolder)
    errorMessage = sprintf('Error: The following input folder does not exist:\n%s', topLevelFolder);
    uiwait(warndlg(errorMessage));
    return;
end

% Get a list of files to process.
filePattern = fullfile(topLevelFolder, '*.*'); % All files in topLevelFolder ONLY.
fileList = dir(filePattern);
% Get only files with the "isdir" flag set.  These will be subfolders.
subFolders = fileList([fileList.isdir]);
% Get a cell array of the subfolder names
allSubFolderNames = fullfile(topLevelFolder, {subFolders.name})'
% Get rid of system folders . and ..
systemFolderIndexes = endsWith(allSubFolderNames, '\.') | endsWith(allSubFolderNames, '\..')
subFolders(systemFolderIndexes) = []; % Delete those items by setting equal to null.
% Count how many subfolders we have.
numFolders = length(subFolders);
fprintf('Found %d subfolders inside "%s".\n', numFolders, topLevelFolder)
% If you want you can get a cell array of the subfolder names
allSubFolderNames = fullfile(topLevelFolder, {subFolders.name})'

% Do the processing.
for k = 1 : numFolders
    % Get the full path of this one subfolder..
    fullSubFolderName = allSubFolderNames{k};
    fprintf(1, '\nNow processing folder #%d of %d: "%s".\n', ...
        k, numFolders, fullSubFolderName);
    % Now get a list of files within this subfolder.
    fileList = dir(fullSubFolderName);
    % Get a list of files only -- not . and .. and not any subfolders of this subfolder.
    filesInSubFolder = fileList(~[fileList.isdir]);
    % Count the number of files in this subfolder.
    numFiles = numel(filesInSubFolder);
    for k2 = 1 : numFiles
        thisBaseFileName = filesInSubFolder(k2).name;
        thisFullFileName = fullfile(fullSubFolderName, thisBaseFileName);
        fprintf('    Processing file #%d of %d : "%s".\n', k2, numFiles, thisBaseFileName)
        % Now do whatever you want with thisFullFileName
        % such as opening it, copying or moving it somewhere, or whatever.
    end
end
message = sprintf('Done processing %d files in %d subfolders of \n"%s".', ...
    numFiles * numFolders, numFolders, topLevelFolder);
uiwait(msgbox(message, 'modal'));

In the innermost loop you can open the mat file, change the variables, create a new output filename, and save it.

Answer 3

[Stephen23]

The simple robust MATLAB approach is to get DIR to do most of the heavy lifting. It is very easy for DIR to loop over subfolders and to avoid dot-directory names and to list only the file you want from each subfolder:

P = 'absolute or relative path to where the subfolders are';
S = dir(fullfile(P,'damage*_case20','calculation.mat'));
for k = 1:numel(S)
    F = fullfile(S(k).folder,S(k).name);
    D = load(F);
    % do whatever with the imported file data D
    [Q,N,E] = fileparts(F);
    F = fullfile(Q,sprintf('%s',N,'_fix',E));
    save(F,'-struct',D)
end