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

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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
  1 Comment
Cris LaPierre
Cris LaPierre on 16 Apr 2024
Edited: Cris LaPierre on 16 Apr 2024
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).

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Accepted Answer

Cris LaPierre
Cris LaPierre on 16 Apr 2024
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)
  4 Comments
Leandro
Leandro on 17 Apr 2024
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
Cris LaPierre on 17 Apr 2024
I mean do this
fullfile(fname(a).folder, fname(a).name)
instead of this
strcat(dir_files,'/', fname{a})

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