how to solve the fopen error?

Hi all,

I've done the below code to read .txt files and extracting columns from each one. the error appears just from the second to the rest of files. Could anyone help me with this?

thank you

 Error using fgets
 Invalid file identifier. Use fopen to generate a valid file identifier.

 Error in RUV_readFile (line 21)
    line = fgets(file1);

 clc
 clear all
 close all

 %read file line by line 

 %loop over the files from list
 %open each file and loop over the lines, 
 files_str = fileread('foldername/files.txt');
 list = splitlines(files_str);

 for k=1:length(list)
    filename = list{k}; %index cell array of filenames using k 
    disp(filename);
    file1 = fopen(strcat('foldername',filename));
    filemat = [];
    line = fgets(file1);
    while ischar(line)
       if isempty(strfind(line,'%')) %if line doesn't contains %
           vec = str2num(line); %convert line string to vector
           filemat = [filemat;vec]; %fill matric from vectors in file
       end
 %        disp(line)
       line = fgets(file1);
    end

       fclose(file1);  
       cols = filemat(:,1:4);
       save(strcat('output/',filename), 'cols', '-ascii')

 end

[Guillaume]

As commented by Stephen, you're using a very inefficient way to read what appear to be a text file of numbers. textscan or even easier readtable could read it all in one go.

In addition,

• use fullfile instead of strcat to build path names. It's a lot more reliable
• Do you really have a folder called foldername? It's very unusual and I suspect the original intent of the code was to have an arbitrary folder whose name would be stored in a variable called foldername. In which case, the variable name should not be enclosed in quotes

file_str = fileread(fullfile(foldername, 'files.txt'));  %NOT 'foldername'

is the usual pattern.

• similarly, are the text files you're trying all named foldernamesomething. Because that's exactly what you're trying to open. Normal code would be:

file1 = fopen(fullfile(foldername, filename)); %NOT 'foldername', filename

[Stephen23]

@Guillaume: thank you for the detailed explanation. It was remiss of me to not explain as much as you did.

@Lina Eyouni: you should read the MATLAB documentation, which shows just how simple this should be:

https://www.mathworks.com/help/matlab/import_export/process-a-sequence-of-files.html

https://www.mathworks.com/help/matlab/import_export/ways-to-import-text-files.html

[Lilya]

Thanks Guillaume I am applying this now but without the apostrophes, it gives me an error. but I am working now with reading it from the links above. the other thing that I would like to clarify is the folder name. the name above is just to show the case because mine here is too long. I apologize.

thank you once again

Answer 1

[Stephen23]

1. Use fullfile instead of the rather inappropriate strcat.
2. Return the second output of fopen and check this using assert.

[file1,msg] = fopen(fullfile('foldername',filename));
assert(file1>=3,msg)

[Lilya]

Thank you Mr. Stephen. Could you please clarify this 'second output'? Do you mean line=fgets(file1)

Thank you once again

[Stephen23]

@Lina Eyouni: exactly like I show in my answer, the second output of fopen is very useful for diagnosing why fopen cannot open a file. It is trivial to add an assert using this message.

[Lilya]

Got it. Thank you SO much!

[Lilya]

I get (empty char array)

[Stephen23]

Please show exactly what this outputs:

[file1,msg] = fopen(fullfile('foldername',filename))

[Lilya]

file1 = 20 msg = 0*0 empty char array

[Stephen23]

Then you have no problem. If the first output is >=3 then fopen successfully opened the file.

Note that you should replace ischar:

while ischar(line)

with feof:

while ~feof(file1)

Also note that this:

    line = fgets(file1);
    while ischar(line)
       if isempty(strfind(line,'%')) %if line doesn't contains %
           vec = str2num(line); %convert line string to vector
           filemat = [filemat;vec]; %fill matric from vectors in file
       end
 %        disp(line)
       line = fgets(file1);
    end

is a very inefficient way to read numeric data into MATLAB. You have not described what format the files have, but you should really consider using the inbuilt functions for reading numeric data:

https://www.mathworks.com/help/matlab/standard-file-formats.html

[Lilya]

Ok. I will try with this now. Thank you so much for your response and help