How to plot XRD data as 3D plot?
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I have a series of XRD diffractograms from a single sample, at different depths. I want to plot the spectra as a 3D line plot, as seen as below:
(From https://link.springer.com/article/10.1016%2FS1672-6529%2806%2960003-6)
I use the following code to view my XRD data in Matlab:
data = importdata('example_data.dat') ; % load the data from text file
semilogy(data(:,1),data(:,2)) ; % plot the data
How do I go from here?
TIA
Accepted Answer
Star Strider
on 7 Sep 2021
Edited: Star Strider
on 7 Sep 2021
When I click on the link, I get a ‘DOI Not Found’ error. (EDIT — The new link is to an article behind a paywall, so I do not have access to it.)
That problem aside, if the data are in a matrix, it is likely possible just use surf to plot the matrix. The axis tick labels might need to be added manually in separate statements, however this is not difficult.
If you want to upload / attach the .XRD file, it would be necessary to put it into a .zip file first. Any information you have on its contents and format would be helpful, since I dioubt many here are familiar with that format (I am not, since .dat files can contain anything).
The complete matrix, with the values imported and plotted —
Uz = unzip('Plot3D[1].zip')
x = readmatrix(Uz{1}, 'Range','A:A')
ymtx = NaN(numel(x),numel(Uz));
for k = 1:numel(Uz)
ymtx(:,k) = readmatrix(Uz{k}, 'Range','B:B');
end
ymtx
figure
surf(ymtx, 'EdgeColor','none')
grid on
xticklabels = string(x);
yt = yticks;
NrYticks = 9; % Choose Any Integer Divisor of '54'
set(gca, 'YTick',linspace(min(yt), max(yt), NrYticks), 'YTickLabel',linspace(0, -54, NrYticks))
xlabel('x')
ylabel('y')
zlabel('z')
view(60,30)
% shading('interp')
Experiment to get different results.
.
10 Comments
Sam
on 7 Sep 2021
Star Strider
on 7 Sep 2021
As always, my pleasure!
I’m certain you’d have worked it out. It likely would have taken only a bit longer than it did me.
.
Sam
on 7 Sep 2021
Star Strider
on 7 Sep 2021
No worries. My apologies for the delay — I was out running errands.
I have edited my Answer to include the y-axis tick values.
Sam
on 8 Sep 2021
Star Strider
on 8 Sep 2021
As always, my pleasure!
.
Star Strider
on 11 Jan 2022
Edited: Star Strider
on 11 Jan 2022
I sort of forgot where we were here (it’s been 4 months) so it took a few minutes to figure this out.
Depending on what the desired result is, there are two ways to do this:
- To simply restrict the plot, use the ylim function (straightforward),
- To select matrix rows that limit the values used in the surf call (as I did here), find the closest matrix row corresponding to the desired result, and plot only those rows.
The code here trims the matrix to the desired values, so that same approach can be used if only those values (limited row range of ‘ymtx’) are needed in other calculations. The ‘ChooseYVal’ value controls where the plot begins.
Uz = unzip('https://www.mathworks.com/matlabcentral/answers/uploaded_files/731649/Plot3D%5B1%5D.zip')
x = readmatrix(Uz{1}, 'Range','A:A')
ymtx = NaN(numel(x),numel(Uz));
for k = 1:numel(Uz)
ymtx(:,k) = readmatrix(Uz{k}, 'Range','B:B');
end
ymtx
figure
surf(ymtx, 'EdgeColor','none')
grid on
xticklabels = string(x);
yt = yticks;
NrYticks = 9; % Choose Any Integer Divisor of '54'
ytixrows = linspace(0, -54, size(ymtx,1)); % Row Coordinates As 'Y-Tick' Values
ChooseYVal = -7.5; % Next Plot Begins Here
rowidx = ceil(interp1(ytixrows, (1:size(ymtx,1)), ChooseYVal)) % Row Index Corresponding To 'ChooseYVal'
set(gca, 'YTick',linspace(min(yt), max(yt), NrYticks), 'YTickLabel',linspace(0, -54, NrYticks))
xlabel('x')
ylabel('y')
zlabel('z')
title('Original With All Values Plotted')
view(60,30)
% shading('interp')
figure
surf(ymtx(rowidx:end,:), 'EdgeColor','none') % Uses Values Calculated In Previous Plot Code
grid on
xticklabels = string(x);
yt = yticks;
NrYticks = 9; % Choose Any Integer Divisor of '54'
% ytixrows = linspace(0, -54, size(ymtx,1)) % Row Coordinates As 'Y-Tick' Values
% ChooseYVal = -7.5;
% rowidx = ceil(interp1(ytixrows, (1:size(ymtx,1)), ChooseYVal)) % Row Index Corresponding To 'ChooseYVal'
set(gca, 'YTick',linspace(min(yt), max(yt), NrYticks), 'YTickLabel',linspace(ChooseYVal, -54, NrYticks))
xlabel('x')
ylabel('y')
zlabel('z')
title('Restricted To Values ≤-7.5 Plotted')
view(60,30)
.
Sam
on 11 Jan 2022
Star Strider
on 11 Jan 2022
As always, my pleasure!
If you have further questions and have problems figuring out how the code works, don’t struggle longer than necessary. Just ask, and I’ll do my best to provide an appropriate solution (or explain the reason a solution isn’t possible).
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