running a script in different folders

Hi all,

I have been working on a piece of code that will automatically process multiple files in a folder automatically

saveFolder=''%save folder for data
FolderLength = ''
File_Struct = dir(fullfile(FolderLength, '*.mat'))
File_Path = cell(size(File_Struct,1), 1);
for k = 1 : 1 : size (File_Struct,1)
    File_Path {k} = fullfile(File_Struct(k).folder, File_Struct(k).name); 
    fprintf(1, 'Now reading %s\n', File_Path {k});
    load(File_Path {k}); %this is changed

   Data1 = ProcessData1(Data);
   Data2 = ProcessData2(Data);
save(fullfile(saveFolder, sprintf('psData_%d.mat', k)),'Data')

I have a folder which has 3 subfolders, each has 10 files. The code above is running the functions on each subfolder indivisually (10 files).

I know that

'**/*.mat'

will process all files in a main folder, but I want to define the subfolders and corresponding save folders somehow, then ask matlab to go over each subfolder --> process data using the above code--> then save to 1 of the 3 save folders.

I tried to use different methods like changing the directory or definining the multiple subfolder like:

mainfolder={'path for 1st subfolder','path for 2nd subfolder','path for 3rd subfolder'}
for i=mainfolder
    cd=(mainfolder{1})
saveFolder=''%save folder for data
FolderLength = ''
File_Struct = dir(fullfile(FolderLength, '*.mat'))
File_Path = cell(size(File_Struct,1), 1);
for k = 1 : 1 : size (File_Struct,1)
    File_Path {k} = fullfile(File_Struct(k).folder, File_Struct(k).name); 
    fprintf(1, 'Now reading %s\n', File_Path {k});
    load(File_Path {k}); %this is changed

   Data1 = ProcessData1(Data);
   Data2 = ProcessData2(Data);
save(fullfile(saveFolder, sprintf('psData_%d.mat', k)),'Data')

cd=(mainfolder{2})
saveFolder2=''%save folder for data
   Data1 = ProcessData1(Data);
   Data2 = ProcessData2(Data);
save(fullfile(saveFolder2, sprintf('psData_%d.mat', k)),'Data')
cd=(mainfolder{3})
saveFolder3=''%save folder for data
   Data1 = ProcessData1(Data);
   Data2 = ProcessData2(Data);
save(fullfile(saveFolder3, sprintf('psData_%d.mat', k)),'Data')

end
end

, but it did not work. Any hint would be appreciated

Answer 1

[Image Analyst]

Use sprintf() inside the loop to create a specified saveFolder. Something like

Try this code, which has a number of improvements to improve robustness:

inputFolder = pwd % Wherever...
filePattern = fullfile(inputFolder, '*.mat')
File_Struct = dir(filePattern)
numberOfFiles = length(File_Struct);
for k = 1 : numberOfFiles
	thisFolder = File_Struct(k).folder;
	fullInputFileName = fullfile(thisFolder, File_Struct(k).name);
	fprintf('%4d of %4d : Now reading input %s\n', k, numberOfFiles, fullInputFileName);
	str = load(fullInputFileName);
	if isfield(str, 'Data')
		Data = str.Data;
		Data1 = ProcessData1(Data);
		Data2 = ProcessData2(Data);
		% Make up the sub-folder name somehow.  Adapt as needed to make it whatever it needs to  be.
		newSubFolder = sprintf('%d', k);
		outputFolder = fullfile(inputFolder, newSubFolder);
		if ~isfolder(outputFolder)
			% Make output folder if it does not exist.
			mkdir(outputFolder);
		end
		% Now that we have the subfolder name, make up the new base file name of the mat file.
		baseFileName = sprintf('psData_%d Data', k);
		fullOutputFileName = fullfile(outputFolder, baseFileName);
		fprintf('     Saving output %s.\n', fullOutputFileName);
		% Save Data into a new mat file.
		save(fullOutputFileName, 'Data')
	else
		fprintf('     !!!! Data variable not found inSaving output %s.\n', fullInputFileName);
	end
end

Adapt as needed.