How to run a code (in series) in different folders?

Hi. In my current folder ('C:\Run\Analysis'), I have a MATLAB file S4.m which contains a few functions to be run. The input files (in .txt format) required to run this code are in 3 different subfolders (i.e., F1, F2, F3). I need to loop my code so that it first gets .txt files from subfolder F1, run the necessary functions, save the output files then proceed to get the .txt files from subfolder F2, and so on. I read the available answers but couldn't solve the issue.

Any help will be appreciated. Thank you.

[Stephen23]

"How to run a code (in series) in different folders?"

Do not run the code in different folders.

Run the code in one folder (preferable one which contains no data files), and provide it with the absolute/relative filepaths of the data files that you want to process. Use FULLFILE.

[Image Analyst]

@M Yousaf What about @Stephen23's comment and @Star Strider's Answer did not allow you to solve the issue? Basically you stay in the same "current folder" and just make a list of the subfolders, and loop over them creating new filenames in the loop. It seems like the code @Star Strider gave you could be easily modified for your folder names. What did you actually try? You forgot to attach Star's code that you tried. Did you modify it? If so how? We can't see your code obviously.

[M Yousaf]

@Stephen23 That's exactly what I am trying to do but in vain.

[M Yousaf]

@Image Analyst Hi. Thank you for responding. Well, I couldn't know how to integrate @Star Strider's code into mine. That is why I posted my entire code to seek more help. Please see my latest comment. You can find my code there.

Answer 1

[Star Strider]

Probably the easiest way would be to create ‘S4’ as a function and go from there.

Example —

pwd

ans = '/users/mss.system.tmzz7'

A = randi(10, 5)

A = 5x5

4 3 6 1 6 7 4 9 2 7 9 6 7 4 7 5 1 4 2 2 7 7 2 10 6

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writematrix(A, fullfile(pwd,'F1'))
B = randi([11 20], 5)

B = 5x5

19 18 11 14 18 19 20 12 12 12 12 15 16 12 12 16 11 18 18 12 17 19 13 14 14

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writematrix(B, fullfile(pwd,'F2'))
C = randi([21 30], 5)

C = 5x5

21 26 28 24 24 24 28 22 25 30 22 28 29 29 23 21 27 21 23 24 28 29 26 23 22

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writematrix(C, fullfile(pwd,'F3'))

Dirs = ["F1","F2","F3"];
for k = 1:3
    fullpath = fullfile(pwd,Dirs(k))
    data = readmatrix(fullpath)
    % data = readmatrix(fullfile(pwd,Dirs(k)))                    % Single Line Version
    [result1{k},result2{k}] = S4(data);
end

fullpath = "/users/mss.system.tmzz7/F1"

data = 5x5

4 3 6 1 6 7 4 9 2 7 9 6 7 4 7 5 1 4 2 2 7 7 2 10 6

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fullpath = "/users/mss.system.tmzz7/F2"

data = 5x5

19 18 11 14 18 19 20 12 12 12 12 15 16 12 12 16 11 18 18 12 17 19 13 14 14

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fullpath = "/users/mss.system.tmzz7/F3"

data = 5x5

21 26 28 24 24 24 28 22 25 30 22 28 29 29 23 21 27 21 23 24 28 29 26 23 22

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result1

result1 = 1x3 cell array
    {[128]}    {[374]}    {[627]}

result2

result2 = 1x3 cell array
    {[7.5880e+15]}    {[1.4539e+29]}    {[8.1687e+34]}

function [out1, out2] = S4(in)
    out1 = sum(in, 'all');
    out2 = prod(in, 'all');
end

That iis the approach I would use.

.

[M Yousaf]

@Star Strider Thank you for your answer. Pardon my ignorance but I couldn't understand the solution. If it is not too much to ask, can you please guide me on what should I add at the beginning/end of my code. I am attaching here my entire code which I run in MATLAB.

	    ImageList={}; % Usually I put as ImageList = {'Image1.txt','Image2.txt'}
            AcceptTol={};
            for iter=1:length(ImageList)
            nSteps=getNSteps(ImageList{iter});
            [counter,currTol]=doAnalysis(ImageList{iter},nSteps);
            AcceptTol(iter,1:3)={ImageList{iter},counter,currTol};
            disp(ImageList{iter});
            disp(['Counter:' num2str(counter)]);
            disp(['Tol:' num2str(currTol)]);
            end

            function [counter,currTol]=doAnalysis(Image,nSteps)
            OK=1; % Image contains all files e.g., Image1.txt, Image2.txt, ...
            TolIncr=1e-3; 
            currTol=1e-4;
            counter=0;
            while(OK~=1)
            if exist('result.txt','file')~=1
            delete('result.txt');
            end
            fid=fopen('Imagery.tcl');
            txtData='';
            tline=fgetl(fid);
            while ischar(tline)
            txtData=strjoin({txtData,tline},'\n');
            tline=fgetl(fid);
            end
            fclose(fid);
            counter=counter+1;
            if counter==1
            currTol=1e-4;
            elseif counter==2
            currTol=5e-4;
            elseif counter==3
            currTol=1e-3;
            else
            currTol=currTol+TolIncr;
            end
            txtData=replace(txtData,'{TOLERANCE}',num2str(currTol));
            txtData=replace(txtData,'{Image}',Image);
            txtData=replace(txtData,'{nSteps}',num2str(nSteps));
            fid=fopen('Imagery_Temp.tcl','w');
            fprintf(fid,'%s\n',txtData);
            fclose(fid);
            system('program1.exe S4.tcl');
            fid=fopen('result.txt','r');
            OK=fscanf(fid,'%d');
            end
            end
            function nSteps=getNSteps(fname)
            fid=fopen(fname);
            nSteps=0;
            txtData='';
            tline=fgetl(fid);
            while ischar(tline)
            nSteps=nSteps+1;
            txtData=strjoin({txtData,tline},'\n');
            tline=fgetl(fid);
            end
            end

[M Yousaf]

Folder F1 has the following files: Image1.txt, Image2.txt, Image3.txt

Folder F2 has the following files: Image1.txt, Image2.txt, Image3.txt

Folder F3 has the following files: Image1.txt, Image2.txt, Image3.txt

The file names in all folders are same but the contents are different.

[Steven Lord]

So you don't have code in different folders, you have data in different folders?

If you have the folder names and file names in different arrays, assemble them using the fullfile function.

directoryName = fullfile(matlabroot, 'toolbox', 'matlab', 'general')

directoryName = '/MATLAB/toolbox/matlab/general'

fileName = 'bench.dat';
fullName = fullfile(directoryName, fileName)

fullName = '/MATLAB/toolbox/matlab/general/bench.dat'

Here's one way you can use that full name:

fid = fopen(fullName, 'rt');
firstLine = fgetl(fid)

firstLine = 'MATLAB(R) Benchmark Data.'

fclose(fid);

[Star Strider]

I would use a loop to return the complete paths to each text file, aggregatee them in ‘ImageList’ and then present tthatt to your funciton.

I am not certain what your code is doing, however this seems to work with iit —

pwd

ans = '/users/mss.system.jrszq'

[status,msg]  = mkdir(fullfile(pwd,'F1'));
[status,msg]  = mkdir(fullfile(pwd,'F2'));
[status,msg]  = mkdir(fullfile(pwd,'F3'));

A = randi(10, 5);
writematrix(A, fullfile(pwd,'F1','image1.txt'))

B = randi([11 20], 5);
writematrix(B, fullfile(pwd,'F2','image2.txt'))

C = randi([21 30], 5);
writematrix(C, fullfile(pwd,'F3','image3.txt'))

Dirs = ["F1","F2","F3"];
for k = 1:3                                                     % Retrieve File Paths For All Subdirectories
    fullpath = fullfile(pwd,Dirs(k),"image"+k+".txt");
    ImageList{k} = fullpath
end

ImageList = 1x1 cell array
    {["/users/mss.system.jrszq/F1/image1.txt"]}

ImageList = 1x2 cell array
    {["/users/mss.system.jrszq/F1/image1.txt"]}    {["/users/mss.system.jrszq/F2/image2.txt"]}

ImageList = 1x3 cell array
    {["/users/mss.system.jrszq/F1/image1.txt"]}    {["/users/mss.system.jrszq/F2/image2.txt"]}    {["/users/mss.system.jrszq/F3/image3.txt"]}

            
            % ImageList={}; % Usually I put as ImageList = {'Image1.txt','Image2.txt'}
            % AcceptTol={};
            for iter=1:length(ImageList)
            nSteps=getNSteps(ImageList{iter});
            [counter,currTol]=doAnalysis(ImageList{iter},nSteps);
            AcceptTol(iter,1:3)={ImageList{iter},counter,currTol};
            disp(ImageList{iter});
            disp(['Counter:' num2str(counter)]);
            disp(['Tol:' num2str(currTol)]);
            end

/users/mss.system.jrszq/F1/image1.txt

Counter:0

Tol:0.0001

/users/mss.system.jrszq/F2/image2.txt

Counter:0

Tol:0.0001

/users/mss.system.jrszq/F3/image3.txt

Counter:0

Tol:0.0001

            function [counter,currTol]=doAnalysis(Image,nSteps)
            OK=1; % Image contains all files e.g., Image1.txt, Image2.txt, ...
            TolIncr=1e-3; 
            currTol=1e-4;
            counter=0;
            while(OK~=1)
            if exist('result.txt','file')~=1
            delete('result.txt');
            end
            fid=fopen('Imagery.tcl');
            txtData='';
            tline=fgetl(fid);
            while ischar(tline)
            txtData=strjoin({txtData,tline},'\n');
            tline=fgetl(fid);
            end
            fclose(fid);
            counter=counter+1;
            if counter==1
            currTol=1e-4;
            elseif counter==2
            currTol=5e-4;
            elseif counter==3
            currTol=1e-3;
            else
            currTol=currTol+TolIncr;
            end
            txtData=replace(txtData,'{TOLERANCE}',num2str(currTol));
            txtData=replace(txtData,'{Image}',Image);
            txtData=replace(txtData,'{nSteps}',num2str(nSteps));
            fid=fopen('Imagery_Temp.tcl','w');
            fprintf(fid,'%s\n',txtData);
            fclose(fid);
            system('program1.exe S4.tcl');
            fid=fopen('result.txt','r');
            OK=fscanf(fid,'%d');
            end
            end
            function nSteps=getNSteps(fname)
            fid=fopen(fname);
            nSteps=0;
            txtData='';
            tline=fgetl(fid);
            while ischar(tline)
            nSteps=nSteps+1;
            txtData=strjoin({txtData,tline},'\n');
            tline=fgetl(fid);
            end
            end

My iimporovement to it simply pulls the relevant paths and fiile names from the various directories, then saves them to a cell array that your code then uses to so what ever it is that you want iit to do.

You may have to tweak it to work with your files and directories, however this simulation seems to work.

.