Use a for loop to find files in subdirectories for own function, and then extract data from .csv file

I have nearly 700 folders, which all contain 3 files that I need for a pre-defined function that my lab uses (basically Dice and Jaccard calculations for image processing).

My directory looks somewhat like this:

• PID000001
• PID000001_Hipp.nii.gz
• PID000001_Hipp2.nii.gz
• PID000001_ICV.nii.gz
• PID000002
• PID000002_Hipp.nii.gz
• PID000002_Hipp2.nii.gz
• PID000002_ICV.nii.gz

and so on.

The function looks like:

function(inputfile1, inputfile2, inputfile3, output.csv)
% A single example would be like
validate_segmentation_results('PID000001_Hipp.nii.gz', 'PID0000001_Hipp2.nii.gz', 'PID0000001_ICV.nii.gz', 'PID000001_dat.csv')
% where the first 3 are the input files, and the last is the output file

I need to create a for loop that says for each subfolder, search for the files that have _Hipp, _Hipp2 and _ICV in their names, and use them in the function as inputfile1, inputfile2 and inputfile3 respesctively. This should then create a .csv file in every subfolder. I believe it should look something like this (based on a previous loop I have had help with):

% First describe the path using dir and save to a variable name.
files = dir('R:\path\where\subfolders\are');

% Next, loop through all the subdirectories and perform validation function 
for i in 1:length(files)
    % Create variable that contains a list of all the subdirectores i.
    PID_1 = files{i};
    PID_1name = {PID_1.name}
    % Identify which files contain 'Hipp', 'Hipp2' and 'ICV' in names.
    % Perform validation function
    validate_segmentation_results() % this is the function with 3 inputs and 1 output.
end

% Finally, loop through all the directories to find the output file. 
% The output file is in long format i.e. varname in col1, value in col2.
% Transform this to wide format i.e. varname on row1, value in row2.
for j in 1:length(files)
    % Create variable that contains a list of all the subdirectories j
    PID_2 = files{j};
    PID_2name = {PID_2.name};
    % Identify which files end in '.txt' in file names.
    % Use fid to open the files, then transform the data from long to wide.

end

However before the end, I get stuck. I know I should be using something akin to regular expression, but there are gaps in the code because I don't know what I should be typing. Please help!

Answer 1

[Mathieu NOE]

Hello

I would suggest this code to find the files in each folder

then you can introduce your own processing of the identified files (for each folder)

%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

%% Loop on each subfolder
for ci = 1:length(dirnames) % 
    
    fileDir = char(dirnames(ci)) % current directory name
    S = dir(fullfile(fileDir,'*.gz')); % get list of data files in directory 
    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 in specified sheet
        currentFilename = S(k).name;
        
        if contains(currentFilename,'_Hipp.')
            filename1 = currentFilename
        end
        if contains(currentFilename,'_Hipp2.')
            filename2 = currentFilename
        end        
        if contains(currentFilename,'_ICV.')
            filename3 = currentFilename
        end
    end
    
    %% Your  own code for filename1,filename2,filename3
        
end

[Mathieu NOE]

hello

Problem solved ?