How to write the MATLAB code for AFM data?

I am a research scholar and have a paper that analyse the AFM data. I have the AFM data in ASCII xyz format. I have to calculate the parameters given in the journal paper. I have attached herewith the paper and the data file.

Please help.

I shall be grateful to you.

Answer 1

[Star Strider]

I will defer to you to do the analysis, however getting the data as matrices is not obvious. I can help with that.

Your data are gridded so use reshape to create matrices from them:

A = dlmread('Figure 3(a).txt', '\t', 4, 0);
rs = mean(diff(find(A(:,1) == 0)));
X = reshape(A, rs, rs, []);

figure
meshc(X(:,:,1), X(:,:,2), X(:,:,3))
xlabel('X (Å)')
ylabel('Y (Å)')
zlabel('Z (nm)')

I leave the rest to you.

EDIT — (24 Jan 2024 at 14:21)

Using the ability to run this here that was not available when this originally posted (and adding a few tweaks) —

T1 = readtable('Figure 3(a).txt', 'VariableNamingRule','preserve', 'Delimiter',{' ','\t'}, 'MultipleDelimsAsOne',true, 'HeaderLines',2, 'EmptyLineRule','skip')

T1 = 65536×3 table
     X[Å]     Y[Å]    Z[nm] 
    ______    ____    ______

         0     0      65.582
    413.38     0      73.069
    826.76     0      85.213
    1240.1     0      94.007
    1653.5     0      100.76
    2066.9     0      97.298
    2480.3     0      76.108
    2893.7     0      83.187
      3307     0      84.546
    3720.4     0      66.053
    4133.8     0      63.409
    4547.2     0      58.314
    4960.6     0      52.484
    5373.9     0      45.347
    5787.3     0      31.428
    6200.7     0      55.909

VN = T1.Properties.VariableNames;
A = table2array(T1);
rs = mean(diff(find(A(:,1) == 0)));
X = reshape(A, rs, rs, []);
SizeX = size(X)

SizeX = 1×3

256 256 3

figure(3)
hmc = meshc(X(:,:,1), X(:,:,2), X(:,:,3));
hmc(1).EdgeColor = 'interp';
hmc(1).FaceColor = 'interp';
colormap(turbo)
xlabel(VN{1})
ylabel(VN{2})
zlabel(VN{3})
title('Figure 3(a)')

The code uses reshape to transform ‘A’ (65536 x 3) to ‘X’ (256 x 256 x 3) and then plots it as a surf plot.

.

[Somsubhra Saha]

sorry, I cant understand. Can you please tell me in detail as I am new in this field.

[Somsubhra Saha]

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