How to extract data selection from multiple .txt files and plot one graph?

Hello everyone,

I have multiple .txt files like the one (please, check the .txt file enclosed). The data of interest is these two specific columns "Zreal" and "Zimag" (it can be seen in the image below):

I've created to scripts. One named 'read_gamry_data' and the other 'nyquist_gamry'.

Here is the code 'read_gamry_data'

% EDIT: adding function call so errors are displayed here (CL)
data = read_gamry_data('Sample Potentiostatic EIS.txt')

data =

  0x1 empty cell array

function [data] = read_gamry_data(fname)
%READ_GAMRY_DATA Gets the data matrices in the file "fname" and
%stores them into the cell "data"
%get all lines of the file
stra = {};
fid=fopen(fname,'r');
sl = fgetl(fid);
while ischar(sl)
    stra{end+1,1}=strtrim(sl);
    sl = fgetl(fid);
end
fclose(fid);
%get the EIS data from the gamry .txt files
strid_dataset = 'ZCURVE';
id_start = [];
data = cell(length(id_start),1);
for y = 1:length(id_start)
    for z = id_start(y):id_end(y)
        if strcmp(strid_dataset,stra{z}(1:min(length(stra{z}),length(strid_dataset))))
            %read data matrix
            rstart = z+3;
            rend = rstart;
            while rend<=id_end(y) && length(split(stra{rend}))>1
                rend = rend+1;
            end
            rend = rend-1;
            break;    
        end
    end
    data{y}=zeros(rend-rstart+1,length(split(stra{rstart})));
    for z = rstart:rend
        data{y}(z-rstart+1,:)=(sscanf(stra{z},'%f'))';
    end
end
end % added this CL

and here is the code of 'nyquist_gamry' script. Before just plotting, I need to correct the data by the area, so I tried:

clear all;close all;

dir_files = 'EIS'

area = (pi/4)*1.5^2

fname = dir(fullfile(dir_files,'*.txt'));

for a = 1:length(fname)

data{a} = read_gamry_data(strcat(dir_files,'/', fname{a}));

data{a}{1}(:,1:2) = area.*data{a}{1}(:,1:2);

plotgraph(1,data{a}{1}(:,1),-data{a}{1}(:,2))

hold on

end

xlabel('Z_{real}(\Omega.cm^2)', 'FontSize', 12)

ylabel('-Z_{imag}(\Omega.cm^2)','FontSize', 12)

set(gca,"dataaspectratio",[1,1,1])

I constantly having errors, especially saying that my index is not supported. Can anyone try to run it and see if you can help me with? I would like to hear any suggestion from you all.

Kindly

Leandro

[Cris LaPierre]

I edited your code so that it could be run here. The sample file does not generate any errors, but the final result is also empty, so yout code is not properly loading the data..

Please share the full error message (all the red text).

Answer 1

[Cris LaPierre]

The indexing error suggests something is wrong with how your code handles multiple files. As for loading the data, if your files all share the exact same formatting, you can just use readtable.

data = readtable('Sample Potentiostatic EIS.txt','numHeaderLines',96)

data = 81x11 table
    Pt    Time       Freq       Zreal      Zimag      Zsig     Zmod       Zphz           Idc           Vdc       IERange
    __    ____    __________    ______    ________    ____    ______    _________    ___________    _________    _______

     0      7     1.0001e+06    198.38    -0.30052     1      198.38    -0.086796      9.714e-07    -0.000675       9   
     1      8     7.9439e+05    199.27     0.44131     1      199.27      0.12689    -5.0535e-07    -0.000702       9   
     2     10     6.3098e+05    199.49     0.85197     1       199.5      0.24469     1.8085e-06    -0.000656       9   
     3     11     5.0123e+05    199.52      0.8388     1      199.52      0.24088     7.9994e-07    -0.000629       9   
     4     12     3.9811e+05     199.5     0.64289     1       199.5      0.18463    -3.8204e-07     -0.00063       9   
     5     14     3.1627e+05     199.5     0.34671     1       199.5     0.099577     2.9806e-07    -0.000603       9   
     6     15      2.512e+05     199.7    0.097624     1       199.7     0.028009     4.0072e-06    -0.000576       9   
     7     16     1.9955e+05    199.63    -0.17299     1      199.63    -0.049651     1.8076e-07    -0.000565       9   
     8     17     1.5842e+05    199.52    -0.57837     1      199.52     -0.16609     5.2998e-07     -0.00053       9   
     9     19     1.2595e+05    199.43    -0.93185     1      199.43     -0.26771     9.6905e-07    -0.000514       9   
    10     20          99978    199.52     -1.0675     1      199.53     -0.30655     4.8914e-07     -0.00048       9   
    11     21          79453    199.44      -1.707     1      199.44     -0.49038      1.132e-06    -0.000485       9   
    12     23          63078    199.49     -2.2827     1      199.51     -0.65557     4.9528e-07    -0.000492       9   
    13     24          50103    199.51     -3.1223     1      199.53     -0.89659     4.9509e-07    -0.000495       9   
    14     25          39811    199.48     -3.9843     1      199.52      -1.1442     5.1864e-07    -0.000489       9   
    15     27          31609    199.51     -5.0752     1      199.57      -1.4572     5.1111e-07    -0.000495       9   

plot(data.Zreal,-data.Zimag)
xlabel('Z_{real}(\Omega.cm^2)', 'FontSize', 12)
ylabel('-Z_{imag}(\Omega.cm^2)','FontSize', 12)

[Leandro]

Hello Cris,

The error message is:

Brace indexing is not supported for variables of this type.

Error in nyquist_gamry (line 8)

data{a} = read_gamry_data(strcat(dir_files,'/', fname{a}));

I've tried tracking 'ZCURVE' because other files start in line number 51, for example, this file S1.txt attached. My .mat files goes here too.

Would you have any other suggestion?

Thanks in advance!

[Cris LaPierre]

The issue is that fname is a structure, not a cell array.

Another issue is that the number format is not consistant between your files. Specifically, the decimal separator is a period in the first file you shared, but a comma in the second one. Once that is consistant, the error below goes away. Since a period is the default one, the code below shows how to use readtable to load a file with a comma as the separator.

It's a bit more, but I load the file first as text, find the ZCURVE TABLE row, then use that as an input to readtable to set the number of headerlines.

fname = dir('*.txt')

fname = 2x1 struct array with fields:
    name
    folder
    date
    bytes
    isdir
    datenum

You can access the EIS folder as you currently do, but I would update the input to the read function to use fullfile based on the results of dir.

area = (pi/4)*1.5^2;
for a = 1:length(fname)
    str = readlines(fullfile(fname(a).folder, fname(a).name));
    idx = find(str=="ZCURVE	TABLE");
    data{a} = readtable(fullfile(fname(a).folder, fname(a).name),'numHeaderLines',idx,"DecimalSeparator",",");
    
    data{a}(:,["Zreal","Zimag"]) = area.*data{a}(:,["Zreal","Zimag"]);
    plot(data{a}.Zreal,-data{a}.Zimag)
    hold on
end

Error using .* (line 36)
Applying the function 'times' to the variable 'Zreal' generated an error.

Caused by:
Undefined function 'times' for input arguments of type 'cell'.

hold off
xlabel('Z_{real}(\Omega.cm^2)', 'FontSize', 12)
ylabel('-Z_{imag}(\Omega.cm^2)','FontSize', 12)

[Leandro]

Now it is working! Thanks for your time.

Do you mind if I ask how would you update this specifically? I couldnt get what you said here: "update the input to the read function to use fullfile based on the results of dir"

It would be helpful if I can separate it in folders per batch of samples.

Kindly

[Cris LaPierre]

I mean do this

fullfile(fname(a).folder, fname(a).name)

instead of this

strcat(dir_files,'/', fname{a})