Moving files in matlab

Hey,

I'm new to matlab. I've made the basic tutorial and tried searching at google, but couldn't find any answers to my question.

I have a folder named DTI_scans. In this folder i have a lot of other folders (somehwere near 100) like 1002, 1003, 1004, etc. And in those folders i have one folder called DATA and alot of other files. In this data folder ('//DTI_scans/1005/DATA') i have again some files, but what I need to do in this DATA folder is to copy a file named 'data.nii' to a folder called DTI_network. I have to do this for every folder in DTI_scans (those 'numbered' folders). I'm having a bit trouble with this.

In the DTI_network folder, I also have to copy those data.nii files into the same 'numbered folders' as they originate from. So the data.ii file from 'DTI_scans\1005\Data' has to be copied to 'DTI_network\1005'.

I hope i've explained everything clearly. Could someone help me with this? Or put me in the right direction. I can't do this with movefile function right? Thanks for reading.

[Rik]

Why do you think you can't do that with movefile? You just need to do it in a loop. (Hint: find all the folder names with dir and enough asterisks)

[Ibrahim Arslan]

Hey Rik,

thanks for your answer.

Is something like this good? Can you tell if I'm in the right direction?(I found it at http://matlab.wikia.com/wiki/FAQ#How_can_I_process_a_sequence_of_files.3F)

myFolder = 'umcms\onderzoek$\STUDIE\STUDIE - studie data\DTI_scans';

filePattern = fullfile(myFolder, 'data.nii');

theFiles = dir(filePattern);

savepath = 'umcms\onderzoek$\STUDIE\STUDIE - studie data\DTI_Network'

for k = 1 : length(theFiles)

baseFileName = theFiles(k).name;

fullFileName = fullfile(myFolder, baseFileName);

fprintf(1, 'Now reading %s\n', fullFileName);

Or do i have to use dir.

BTW, I have to copy the files, not move it.

Answer 1

[Jan]

"//DTI_scans/1005/DATA" is a strange UNC path. Usually you have "//Host/Folder/" fixed, because this is the published path. The flexible part "1005" should appear at least one level deeper. I'm not sure if this causes troubles.

Which Matlab version are you using? Modern versions can obtain a list of files in subfolders also:

FileList = dir('//DTI_scans/**/data.nii');
for iFile = 1:numel(FileList)
  inFolder  = FileList(iFile).folder;
  inFolder  = strrep(inFolder, '/', '\');  % Avoid confusions
  parts     = strsplit(inFolder, '\');
  outFolder = fullfile('DTI_Network', parts(end-1));
  movefile(fullfile(inFolder, 'data.nii'), fullfile(outFolder, 'data.nii'));
end

Something like this will solve the problem: Find the files at first, then process them one by one in a loop. Split the folder name to extract the needed parts and use them to create the output folder. Then movefile can work as wanted.

[Ibrahim Arslan]

Hey Jan,

Thanks for your answer. I'm using matlab at work. I have matlab R2014b.

My apologies. the path '//DTI_scans/..' isn't complete. It is: '\\umcms\onderzoek$\STUDIE\STUDIE - studie data\DTI_scans' I copied this from windows explorer.

The data.nii file are in the subfolders, like this:

\\umcms\nonderzoek$\STUDIE\STUDIE- studie data\DTI_scans\1003\Data\data.nii

I have to move the files to '\\umcms\onderzoek$\STUDIE\STUDIE - studie data\DTI_Network'

I tried using your code with the correct paths. It gave me this error:

Reference to non-existent field 'folder'.

BTW, I have to copy the files, not move it.

[Jan]

The .folder field and /**/ was introduced in modern Matlab versions. Sorry. Look in the FileExchange for "recursive dir" to find many solutions to obtain a list of file names in subfolders.

[Ibrahim Arslan]

Ah, that's unfortunate.

I've tried to search for the recursive dir and found this: https://nl.mathworks.com/matlabcentral/fileexchange/32226-recursive-directory-listing-enhanced-rdir

But I don't know if I can install this at work.

Isn't there another way to obtain the lists of file names in subfolders? And is the rest of the code correct for matlab 2014?

I've to copy the files btw, not move it.

[Rik]

Almost every entry in the FEX is a function (this one is no exception), which means you can simply download it and use it.

As for copying instead of moving: the function copyfile should do the trick there.

[Jan]

@Ibrahim: Of course I could write a small tool for a recursive search of files. This needs a few lines only. But the authors of the FEX submissions have done this already. So simply copy the source codes provided in the FileExchange. You can "install" this at your work exactly as if you would copy&paste code posted in the forum.

You could write a recursive search by your own also. Just try it, it is not hard. Well, I can't hold it out and give you an example:

function Files = FindFiles(Folder, Pattern)
% Get matching files in current folder:
List  = dir(fullfile(Folder, Pattern));
Files = cellfun(@(s) fullfile(Folder, s), ...
    {List(~[List.isdir]).name}, 'UniformOutput', 0);

% Get folders in current folder:
List    = dir(Folder);
Folders = {List([List.isdir]).name};
Folders(strcmp(Folders, '.') | strcmp(Folders, '..')) = [];
for k = 1:numel(Folders)  % Loop over all folders:
  % Call this function recursively for subfolders:
  Files = cat(2, Files, ...
              FindFiles(fullfile(Folder, Folders{k}), Pattern));
end

Now I've added my own 2 cent to the other 137 solutions published on the MathWorks pages. :-)

Then:

FileList = FindFiles('//DTI_scans/', 'data.nii');
FileList = strrep(FileList, '/', '\');  ??? Maybe
for k = 1:numel(FileList)
  inFolder  = fileparts(FileList{k});
  parts     = strsplit(inFolder, '\');
  outFolder = fullfile('DTI_Network', parts(end-1));  % ***
  copyfile(FileList{k}, fullfile(outFolder, 'data.nii'));
end

Please replace the output folder at * correctly by a full path.