Error using contains - First argument must be a string array...

Hello!

I am at my wits end trying to get this code to work.

I am basically trying to take some data from a .txt file and transpose it into a 3 column tab delimited matrix.

The error I receive is:

"Error using contains (line 39)
First argument must be a string array, character vector, or cell array of character vectors.

Error in read_logfiles (line 53)
            while (~contains(oneline,'Target Condition:'))oneline = fgetl(datafid); end"

The information I'm asking it to look at is definitely a string that says "Parnter" "Stranger" or "Friend"

So, for instance, one of these in the .txt file I'm asking it to read would look like "Target Condition: Stranger"

This script was given to me by my lab director with little instruction other than to make it work.

I apologize for posting the entire script like this but I'm really not sure what the problem is.

Any help would really be appreciated!

% 1. Read in 3 e-prime text logfiles for one subject. 
% 2. Output 9 onset files (3 conditions * 1 runs).
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

EXP_DIR = 'E:/Matlab1';

if length(subject==4) subject = subject(2:end); end
subject_dir = fullfile(EXP_DIR,sprintf('s%s',subject));
ONS_SAVE_DIR = subject_dir;
if ~exist('data_dir','var') data_dir=fullfile(subject_dir,'logfiles'); end
DATADIR = fullfile(EXP_DIR,'data');  
DATAFILE_PRE = {'CRT1-142'};
DATAFILE_SUF = '-1.txt';

num_runs = 1;
files_to_read = num_runs;
trials_per_file = 8;

%onsets are in seconds from the beginning of run (starting after the 10s
%fixation)
event_onset_list = zeros(3, trials_per_file * 6); %X events per trial: EVENT1, EVENT2, EVENT3, etc.
weights_list = ones(3, trials_per_file * 6);
%condition_list = zeros(3, trials_per_file * X);
duration_list = zeros(3, trials_per_file * 6);
Friend_mask = false(3, trials_per_file * 6);
Stranger_mask = false(3, trials_per_file * 6);
Partner_mask = false(3, trials_per_file * 6);
for ifile = 1:files_to_read
    trialnum = 0;
    seconds_from_start = 0;
    %open file (convert to ascii first)
    if ~exist(fullfile(DATADIR,[DATAFILE_PRE{ifile} subject DATAFILE_SUF]),'file') 
        error(sprintf('cannot find file %s',fullfile(DATADIR,[DATAFILE_PRE{ifile} subject DATAFILE_SUF])));
    end
    unicode2ascii(fullfile(DATADIR,[DATAFILE_PRE{ifile} subject DATAFILE_SUF]),fullfile(DATADIR,[DATAFILE_PRE{ifile} subject 'ascii' DATAFILE_SUF]));
    datafid = fopen(fullfile(DATADIR,[DATAFILE_PRE{ifile} subject 'ascii' DATAFILE_SUF]),'rt');

      oneline = fgetl(datafid);
      while ischar(oneline)
          oneline = fgetl(datafid);
          if ~ischar(oneline) break; end 
          if trialnum >= trials_per_file
              break;
          end
          if contains(oneline,'LogFrame Start')  %first line of each trial
              %get condition
              while (~contains(oneline,'Target Condition:')) oneline = fgetl(datafid); end
              splitline = split(':',oneline);
              condition = strtok(splitline{2});
              %get jitter
              while (~contains(oneline,'FixMS:')) oneline = fgetl(datafid); end
              splitline = split(':',oneline);
              jitter = str2num(strtok(splitline{2}))/1000;

              %fill in vectors
              event_onset_list(ifile,trialnum*6+1) = seconds_from_start;
              event_onset_list(ifile,trialnum*6+2) = seconds_from_start+2.5;
              event_onset_list(ifile,trialnum*6+3) = seconds_from_start+2.5;
              event_onset_list(ifile,trialnum*6+4) = seconds_from_start+2.5;
              event_onset_list(ifile,trialnum*6+5) = seconds_from_start+2.5;
              event_onset_list(ifile,trialnum*6+6) = seconds_from_start+2.5;
              duration_onset_list(ifile,trialnum*6+1) = 2.5;
              duration_onset_list(ifile,trialnum*6+2) = 2.5;
              duration_onset_list(ifile,trialnum*6+3) = 2.5;
              duration_onset_list(ifile,trialnum*6+4) = 2.5;
              duration_onset_list(ifile,trialnum*6+5) = 2.5;
              duration_onset_list(ifile,trialnum*6+6) = 2.5;
              seconds_from_start = seconds_from_start + 10 + jitter;
              switch (condition)
                  case 'Friend'
                      Stranger_mask(ifile,trialnum*6+1) = true;
                      Partner_mask(ifile,trialnum*6+1) = true;
                  case 'Partner'
                      Friend_mask(ifile,trialnum*6+1) = true;
                      Stranger_mask(ifile,trialnum*6+1) = true;
                  case 'Stranger'
                      Friend_mask(ifile,trialnum*6+1) = true;
                      Partner_mask(ifile,trialnum*6+1) = true;
                  otherwise
                      error('unknown condition');
              end
              trialnum = trialnum + 1;
          end %
      end % while get line loop
      fclose(datafid);
  end %for ifile

% now write the onset files, 1 per condition per run
for irun = 1:num_runs
    %write onset in seconds, duration in seconds, weight=1 with tabs
    %separating each
    %Regressor1
    outfilename = fullfile(EXP_DIR,'onset_files',sprintf('s%s',subject),sprintf('s%s_run%d_Friend.txt',subject,irun));
    Mwrite = [ event_onset_list(irun,Friend_mask(irun,:))' duration_onset_list(irun,Friend_mask(irun,:))' weights_list(irun,Friend_mask(irun,:))'];
    dlmwrite(outfilename,Mwrite,'\t');
    %regressor2
    outfilename = fullfile(EXP_DIR,'onset_files',sprintf('s%s',subject),sprintf('s%s_run%d_Stranger.txt',subject,irun));
    Mwrite = [ event_onset_list(irun,Stranger_mask(irun,:))' duration_onset_list(irun,Stranger_mask(irun,:))' weights_list(irun,Stranger_mask(irun,:))'];
    dlmwrite(outfilename,Mwrite,'\t');
    %regressor3
    outfilename = fullfile(EXP_DIR,'onset_files',sprintf('s%s',subject),sprintf('s%s_run%d_Partner.txt',subject,irun));
    Mwrite = [ event_onset_list(irun,Partner_mask(irun,:))' duration_onset_list(irun,Partner_mask(irun,:))' weights_list(irun,Partner_mask(irun,:))'];
    dlmwrite(outfilename,Mwrite,'\t');
end % for irun = 1:nruns

Answer 1

[Walter Roberson]

You forgot to test for end of file while doing that fgetl() loop.

[Sid Hatfield]

Thank you so much for your help!

I amended this bit of the code from what I understand on the info in the documentation.

    if contains(oneline,'LogFrame Start')  %first line of each trial
            %get condition
            while (~contains(oneline,'Target Condition:'))oneline = fgetl(datafid); end
            splitline = split(':',oneline);
            condition = strtok(splitline{2});
            %get jitter
            while (~contains(oneline,'FixMS:'))oneline = fgetl(datafid); end
            splitline = split(':',oneline);
            jitter = str2num(strtok(splitline{2}))/1000;
            while ~feof (datafid); end

I am receiving a different error now though that insists my file identifier is invalid. "datafid" is what I've used throughout the script and I haven't received this error before, did I attempt to implement ~feof incorrectly by chance?

Thanks again for any help! This project was just kind of dumped in my lap and I'm trying my best.

The "new" error(s) read as follows:

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

Error in fgetl (line 32) [tline,lt] = fgets(fid);

Error in read_logfiles (line 44) oneline = fgetl(datafid);

[Walter Roberson]

Your eof test is not doing anything useful there, and you did not fix your end of file problem. You need to change

while (~contains(oneline,'FixMS:')) oneline = fgetl(datafid); end

to something like

got_eof = false;
while (~contains(oneline,'FixMS:'))
   oneline = fgetl(datafid);
   if ~ischar(oneline)
     got_eof = true;
     break;
   end
 end
 if got_eof
   break;
 end

[Image Analyst]

Attach one of your .txt files if you want more help.

[Sid Hatfield]

Thanks again!

This moved me past me issue I was having, but of course, I now have another. The script is written in a way such that is one of the three conditions I have identified are not found (Friend, Stranger, or Partner) it returns an "unknown condition" error, which is what is happening, although I know for certain the input file has these exact terms.

I have attached my input file as requested. Here is my current script with the above changes applied. It is entirely possible that I haven't applied the change recommended above properly.

function [] = read_logfiles(subject)

% 1. Read in 3 e-prime text logfiles for one subject. 
% 2. Output 9 onset files (3 conditions * 1 runs).

EXP_DIR = 'E:/Matlab1';

if length(subject==4) subject = subject(2:end); end
subject_dir = fullfile(EXP_DIR,sprintf('s%s',subject));
ONS_SAVE_DIR = subject_dir;
if ~exist('data_dir','var') data_dir=fullfile(subject_dir,'logfiles'); end
DATADIR = fullfile(EXP_DIR,'data');  
DATAFILE_PRE = {'CRT1-142'};
DATAFILE_SUF = '-1.txt';

num_runs = 1;
files_to_read = num_runs;
trials_per_file = 8;

%onsets are in seconds from the beginning of run (starting after the 10s
%fixation)
event_onset_list = zeros(3, trials_per_file * 6); %X events per trial: EVENT1, EVENT2, EVENT3, etc.
weights_list = ones(3, trials_per_file * 6);
%condition_list = zeros(3, trials_per_file * 6);
duration_list = zeros(3, trials_per_file * 6);
Friend_mask = false(3, trials_per_file * 6);
Stranger_mask = false(3, trials_per_file * 6);
Partner_mask = false(3, trials_per_file * 6);
for ifile = 1:files_to_read
    trialnum = 0;
    seconds_from_start = 0;
    %open file (convert to ascii first)
    if ~exist(fullfile(DATADIR,[DATAFILE_PRE{ifile} subject DATAFILE_SUF]),'file') 
        error(sprintf('cannot find file %s',fullfile(DATADIR,[DATAFILE_PRE{ifile} subject DATAFILE_SUF])));
    end
    unicode2ascii(fullfile(DATADIR,[DATAFILE_PRE{ifile} subject DATAFILE_SUF]),fullfile(DATADIR,[DATAFILE_PRE{ifile} subject 'ascii' DATAFILE_SUF]));
    datafid = fopen(fullfile(DATADIR,[DATAFILE_PRE{ifile} subject 'ascii' DATAFILE_SUF]),'rt');

      oneline = fgetl(datafid);
      while ischar(oneline)
          oneline = fgetl(datafid);
          if ~ischar(oneline) break; end 
          if trialnum >= trials_per_file
              break;
          end

          if contains(oneline,'LogFrame Start')  %first line of each trial
              %get condition
              got_eof = false;
              while (~contains(oneline, 'TargetCondition:'))
                  oneline = fgetl(datafid);

                  if ~ischar(oneline)
                      got_eof = true;
                      break;
                  end
                  splitline = split(':',oneline);
                  condition = strtok(splitline{2});

                  %get jitter
                    got_eof = false;
              while (~contains(oneline, 'FixMS:'))
                  oneline = fgetl(datafid);

                  if ~ischar(oneline)
                      got_eof = true;
                      break;
                  end
             splitline = split(':',oneline);
             jitter = str2num(strtok(splitline{2}))/1000;

              %fill in vectors
              event_onset_list(ifile,trialnum*6+1) = seconds_from_start;
              event_onset_list(ifile,trialnum*6+2) = seconds_from_start+2.5;
              event_onset_list(ifile,trialnum*6+3) = seconds_from_start+2.5;
              event_onset_list(ifile,trialnum*6+4) = seconds_from_start+2.5;
              event_onset_list(ifile,trialnum*6+5) = seconds_from_start+2.5;
              event_onset_list(ifile,trialnum*6+6) = seconds_from_start+2.5;
              duration_onset_list(ifile,trialnum*6+1) = 2.5;
              duration_onset_list(ifile,trialnum*6+2) = 2.5;
              duration_onset_list(ifile,trialnum*6+3) = 2.5;
              duration_onset_list(ifile,trialnum*6+4) = 2.5;
              duration_onset_list(ifile,trialnum*6+5) = 2.5;
              duration_onset_list(ifile,trialnum*6+6) = 2.5;
              seconds_from_start = seconds_from_start + 10 + jitter;

              switch(condition)
                  case 'Friend'
                      Stranger_mask(ifile,trialnum*6+1) = true;
                      Partner_mask(ifile,trialnum*6+1) = true;
                  case 'Partner'
                      Friend_mask(ifile,trialnum*6+1) = true;
                      Stranger_mask(ifile,trialnum*6+1) = true;
                  case 'Stranger'
                      Friend_mask(ifile,trialnum*6+1) = true;
                      Partner_mask(ifile,trialnum*6+1) = true;
                  otherwise
                      error('unknown condition');
              end
              trialnum = trialnum + 1;
          end %
       fclose(datafid);
      end
  end 
      end
  end %for ifile
  % now write the onset files, 1 per condition per run
  for irun = 1:num_runs
      %write onset in seconds, duration in seconds, weight=1 with tabs
      %separating each
      %Regressor1
      outfilename = fullfile(EXP_DIR,'onset_files',sprintf('s%s',subject),sprintf('s%s_run%d_Friend.txt',subject,irun));
      Mwrite = [ event_onset_list(irun,Friend_mask(irun,:))' duration_onset_list(irun,Friend_mask(irun,:))' weights_list(irun,Friend_mask(irun,:))'];
      dlmwrite(outfilename,Mwrite,'\t');
      %regressor2
      outfilename = fullfile(EXP_DIR,'onset_files',sprintf('s%s',subject),sprintf('s%s_run%d_Stranger.txt',subject,irun));
      Mwrite = [ event_onset_list(irun,Stranger_mask(irun,:))' duration_onset_list(irun,Stranger_mask(irun,:))' weights_list(irun,Stranger_mask(irun,:))'];
      dlmwrite(outfilename,Mwrite,'\t');
      %regressor3
      outfilename = fullfile(EXP_DIR,'onset_files',sprintf('s%s',subject),sprintf('s%s_run%d_Partner.txt',subject,irun));
      Mwrite = [ event_onset_list(irun,Partner_mask(irun,:))' duration_onset_list(irun,Partner_mask(irun,:))' weights_list(irun,Partner_mask(irun,:))'];
      dlmwrite(outfilename,Mwrite,'\t');
  end % for irun = 1:nruns

[Walter Roberson]

When I look at that, it appears to me you did not end the while for the ~contains properly. Your previous code had

while (~contains(oneline,'FixMS:')) oneline = fgetl(datafid); end

which would skip over all lines until it found one with FixMS: , and that was a problem only because you might encounter EOF.

Your replacement code is of the form

while (~contains(oneline,'FixMS:')) oneline = fgetl(datafid);
  if ~ischar(oneline); break; end
  ... do a bunch of things
  end
end

which does the stuff even if the replacement line was not FixMS: