How to plot XRD data as 3D plot?

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

Answer 1

[Star Strider]

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')

Uz = 1×103 cell array
    {'Plot3D/569965_0-0.dat'}    {'Plot3D/569965_0-1.dat'}    {'Plot3D/569965_0-10.dat'}    {'Plot3D/569965_0-100.dat'}    {'Plot3D/569965_0-101.dat'}    {'Plot3D/569965_0-102.dat'}    {'Plot3D/569965_0-11.dat'}    {'Plot3D/569965_0-12.dat'}    {'Plot3D/569965_0-13.dat'}    {'Plot3D/569965_0-14.dat'}    {'Plot3D/569965_0-15.dat'}    {'Plot3D/569965_0-16.dat'}    {'Plot3D/569965_0-17.dat'}    {'Plot3D/569965_0-18.dat'}    {'Plot3D/569965_0-19.dat'}    {'Plot3D/569965_0-2.dat'}    {'Plot3D/569965_0-20.dat'}    {'Plot3D/569965_0-21.dat'}    {'Plot3D/569965_0-22.dat'}    {'Plot3D/569965_0-23.dat'}    {'Plot3D/569965_0-24.dat'}    {'Plot3D/569965_0-25.dat'}    {'Plot3D/569965_0-26.dat'}    {'Plot3D/569965_0-27.dat'}    {'Plot3D/569965_0-28.dat'}    {'Plot3D/569965_0-29.dat'}    {'Plot3D/569965_0-3.dat'}    {'Plot3D/569965_0-30.dat'}    {'Plot3D/569965_0-31.dat'}    {'Plot3D/569965_0-32.dat'}    {'Plot3D/569965_0-33.dat'}    {'Plot3D/569965_0-34.dat'}    {'Plot3D/569965_0-35.dat'}    {'Plot3D/569965_0-36.dat'}    {'Plot3D/569965_0-37.dat'}    {'Plot3D/569965_0-38.dat'}    {'Plot3D/569965_0-39.dat'}    {'Plot3D/569965_0-4.dat'}    {'Plot3D/569965_0-40.dat'}    {'Plot3D/569965_0-41.dat'}    {'Plot3D/569965_0-42.dat'}    {'Plot3D/569965_0-43.dat'}    {'Plot3D/569965_0-44.dat'}    {'Plot3D/569965_0-45.dat'}    {'Plot3D/569965_0-46.dat'}    {'Plot3D/569965_0-47.dat'}    {'Plot3D/569965_0-48.dat'}    {'Plot3D/569965_0-49.dat'}    {'Plot3D/569965_0-5.dat'}    {'Plot3D/569965_0-50.dat'}    {'Plot3D/569965_0-51.dat'}    {'Plot3D/569965_0-52.dat'}    {'Plot3D/569965_0-53.dat'}    {'Plot3D/569965_0-54.dat'}    {'Plot3D/569965_0-55.dat'}    {'Plot3D/569965_0-56.dat'}    {'Plot3D/569965_0-57.dat'}    {'Plot3D/569965_0-58.dat'}    {'Plot3D/569965_0-59.dat'}    {'Plot3D/569965_0-6.dat'}    {'Plot3D/569965_0-60.dat'}    {'Plot3D/569965_0-61.dat'}    {'Plot3D/569965_0-62.dat'}    {'Plot3D/569965_0-63.dat'}    {'Plot3D/569965_0-64.dat'}    {'Plot3D/569965_0-65.dat'}    {'Plot3D/569965_0-66.dat'}    {'Plot3D/569965_0-67.dat'}    {'Plot3D/569965_0-68.dat'}    {'Plot3D/569965_0-69.dat'}    {'Plot3D/569965_0-7.dat'}    {'Plot3D/569965_0-70.dat'}    {'Plot3D/569965_0-71.dat'}    {'Plot3D/569965_0-72.dat'}    {'Plot3D/569965_0-73.dat'}    {'Plot3D/569965_0-74.dat'}    {'Plot3D/569965_0-75.dat'}    {'Plot3D/569965_0-76.dat'}    {'Plot3D/569965_0-77.dat'}    {'Plot3D/569965_0-78.dat'}    {'Plot3D/569965_0-79.dat'}    {'Plot3D/569965_0-8.dat'}    {'Plot3D/569965_0-80.dat'}    {'Plot3D/569965_0-81.dat'}    {'Plot3D/569965_0-82.dat'}    {'Plot3D/569965_0-83.dat'}    {'Plot3D/569965_0-84.dat'}    {'Plot3D/569965_0-85.dat'}    {'Plot3D/569965_0-86.dat'}    {'Plot3D/569965_0-87.dat'}    {'Plot3D/569965_0-88.dat'}    {'Plot3D/569965_0-89.dat'}    {'Plot3D/569965_0-9.dat'}    {'Plot3D/569965_0-90.dat'}    {'Plot3D/569965_0-91.dat'}    {'Plot3D/569965_0-92.dat'}    {'Plot3D/569965_0-93.dat'}    {'Plot3D/569965_0-94.dat'}    {'Plot3D/569965_0-95.dat'}    {'Plot3D/569965_0-96.dat'}    {'Plot3D/569965_0-97.dat'}    {'Plot3D/569965_0-98.dat'}    {'Plot3D/569965_0-99.dat'}

x = readmatrix(Uz{1}, 'Range','A:A')

x = 1432×1

2.4604 2.4967 2.5330 2.5693 2.6056 2.6419 2.6782 2.7145 2.7508 2.7871

ymtx = NaN(numel(x),numel(Uz));
for k = 1:numel(Uz)
    ymtx(:,k) = readmatrix(Uz{k}, 'Range','B:B');
end
ymtx

ymtx = 1432×103

1.0e+03 * 1.2665 1.2390 1.2957 1.3295 1.2866 1.2756 1.3268 1.2701 1.2829 1.2226 1.2783 1.2601 1.2372 1.3058 1.2701 1.2336 1.2683 1.3149 1.2665 1.2528 1.2866 1.2747 1.2875 1.2546 1.2372 1.2482 1.3030 1.2144 1.2601 1.2327 1.4501 1.4590 1.5009 1.4444 1.4293 1.4477 1.4837 1.4664 1.4704 1.4638 1.4245 1.4523 1.4647 1.4399 1.4495 1.4558 1.4585 1.4437 1.4214 1.4375 1.4426 1.4605 1.3969 1.4208 1.4349 1.4192 1.4393 1.3960 1.4216 1.4406 1.5363 1.5556 1.5773 1.5481 1.5332 1.5465 1.5618 1.5608 1.5676 1.5171 1.5129 1.5126 1.5346 1.5261 1.5019 1.5353 1.5379 1.5365 1.5386 1.5538 1.5134 1.5041 1.4984 1.5068 1.5035 1.5194 1.5506 1.5214 1.5161 1.5338 1.5478 1.5654 1.5978 1.5399 1.5437 1.5322 1.5942 1.6009 1.5492 1.5622 1.5534 1.5291 1.5382 1.5195 1.5467 1.5613 1.5274 1.5388 1.5266 1.5480 1.5368 1.5309 1.5295 1.5255 1.5020 1.5091 1.5594 1.5322 1.5028 1.5248 1.4311 1.4366 1.4876 1.4550 1.4216 1.4367 1.4829 1.4560 1.4595 1.4462 1.4493 1.4380 1.4247 1.4277 1.4316 1.4370 1.4438 1.4556 1.4439 1.4534 1.4486 1.4815 1.4257 1.4244 1.4333 1.4281 1.4484 1.4249 1.4361 1.4369 1.2854 1.2920 1.3296 1.2637 1.2814 1.2909 1.3275 1.3605 1.3120 1.2900 1.2933 1.2971 1.2904 1.2928 1.2848 1.2823 1.3208 1.2892 1.2776 1.2796 1.2881 1.2830 1.2718 1.2602 1.2691 1.2963 1.2687 1.2730 1.2636 1.2779 1.0883 1.0985 1.1391 1.1115 1.1109 1.0882 1.1312 1.1230 1.1519 1.1412 1.1091 1.1299 1.1354 1.1099 1.1019 1.0860 1.1173 1.1026 1.1176 1.1082 1.1124 1.1322 1.0924 1.1117 1.1133 1.1100 1.0867 1.1197 1.1160 1.1154 0.9009 0.8975 0.9614 0.9353 0.9231 0.9332 0.9357 0.9385 0.9338 0.9446 0.9514 0.9479 0.9511 0.9505 0.9511 0.8918 0.9264 0.9319 0.9417 0.9383 0.9411 0.9382 0.9312 0.9162 0.9311 0.9320 0.8924 0.9365 0.9382 0.9440 0.7658 0.7547 0.8386 0.8016 0.7964 0.8062 0.8311 0.8224 0.8386 0.8390 0.8350 0.8314 0.8377 0.8427 0.8188 0.7682 0.8285 0.8411 0.8219 0.8207 0.8176 0.8246 0.8032 0.8206 0.8204 0.8089 0.7647 0.8138 0.8006 0.7879 0.6761 0.6596 0.7479 0.7089 0.7084 0.7049 0.7126 0.7284 0.7231 0.7455 0.7445 0.7436 0.7518 0.7280 0.7464 0.6505 0.7565 0.7515 0.7362 0.7359 0.7348 0.7378 0.7407 0.7288 0.7355 0.7176 0.6595 0.7250 0.7209 0.7094

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.

.

[Sam]

This has worked brilliantly, thank you so much, I don't think I would have been able to work this out alone!

[Star Strider]

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]

Sorry, one last question, how do I edit the x and y values as they don't seem to co-ordinate with the data, e.g. the y axis should go from 0 to ~54

[Star Strider]

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]

No need to apologise, you have been so quick to help!

Thank you so much!

[Star Strider]

As always, my pleasure!

.

[Star Strider]

[Star Strider]

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:

1. To simply restrict the plot, use the ylim function (straightforward),
2. 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')

Uz = 1×103 cell array
    {'Plot3D/569965_0-0.dat'}    {'Plot3D/569965_0-1.dat'}    {'Plot3D/569965_0-10.dat'}    {'Plot3D/569965_0-100.dat'}    {'Plot3D/569965_0-101.dat'}    {'Plot3D/569965_0-102.dat'}    {'Plot3D/569965_0-11.dat'}    {'Plot3D/569965_0-12.dat'}    {'Plot3D/569965_0-13.dat'}    {'Plot3D/569965_0-14.dat'}    {'Plot3D/569965_0-15.dat'}    {'Plot3D/569965_0-16.dat'}    {'Plot3D/569965_0-17.dat'}    {'Plot3D/569965_0-18.dat'}    {'Plot3D/569965_0-19.dat'}    {'Plot3D/569965_0-2.dat'}    {'Plot3D/569965_0-20.dat'}    {'Plot3D/569965_0-21.dat'}    {'Plot3D/569965_0-22.dat'}    {'Plot3D/569965_0-23.dat'}    {'Plot3D/569965_0-24.dat'}    {'Plot3D/569965_0-25.dat'}    {'Plot3D/569965_0-26.dat'}    {'Plot3D/569965_0-27.dat'}    {'Plot3D/569965_0-28.dat'}    {'Plot3D/569965_0-29.dat'}    {'Plot3D/569965_0-3.dat'}    {'Plot3D/569965_0-30.dat'}    {'Plot3D/569965_0-31.dat'}    {'Plot3D/569965_0-32.dat'}    {'Plot3D/569965_0-33.dat'}    {'Plot3D/569965_0-34.dat'}    {'Plot3D/569965_0-35.dat'}    {'Plot3D/569965_0-36.dat'}    {'Plot3D/569965_0-37.dat'}    {'Plot3D/569965_0-38.dat'}    {'Plot3D/569965_0-39.dat'}    {'Plot3D/569965_0-4.dat'}    {'Plot3D/569965_0-40.dat'}    {'Plot3D/569965_0-41.dat'}    {'Plot3D/569965_0-42.dat'}    {'Plot3D/569965_0-43.dat'}    {'Plot3D/569965_0-44.dat'}    {'Plot3D/569965_0-45.dat'}    {'Plot3D/569965_0-46.dat'}    {'Plot3D/569965_0-47.dat'}    {'Plot3D/569965_0-48.dat'}    {'Plot3D/569965_0-49.dat'}    {'Plot3D/569965_0-5.dat'}    {'Plot3D/569965_0-50.dat'}    {'Plot3D/569965_0-51.dat'}    {'Plot3D/569965_0-52.dat'}    {'Plot3D/569965_0-53.dat'}    {'Plot3D/569965_0-54.dat'}    {'Plot3D/569965_0-55.dat'}    {'Plot3D/569965_0-56.dat'}    {'Plot3D/569965_0-57.dat'}    {'Plot3D/569965_0-58.dat'}    {'Plot3D/569965_0-59.dat'}    {'Plot3D/569965_0-6.dat'}    {'Plot3D/569965_0-60.dat'}    {'Plot3D/569965_0-61.dat'}    {'Plot3D/569965_0-62.dat'}    {'Plot3D/569965_0-63.dat'}    {'Plot3D/569965_0-64.dat'}    {'Plot3D/569965_0-65.dat'}    {'Plot3D/569965_0-66.dat'}    {'Plot3D/569965_0-67.dat'}    {'Plot3D/569965_0-68.dat'}    {'Plot3D/569965_0-69.dat'}    {'Plot3D/569965_0-7.dat'}    {'Plot3D/569965_0-70.dat'}    {'Plot3D/569965_0-71.dat'}    {'Plot3D/569965_0-72.dat'}    {'Plot3D/569965_0-73.dat'}    {'Plot3D/569965_0-74.dat'}    {'Plot3D/569965_0-75.dat'}    {'Plot3D/569965_0-76.dat'}    {'Plot3D/569965_0-77.dat'}    {'Plot3D/569965_0-78.dat'}    {'Plot3D/569965_0-79.dat'}    {'Plot3D/569965_0-8.dat'}    {'Plot3D/569965_0-80.dat'}    {'Plot3D/569965_0-81.dat'}    {'Plot3D/569965_0-82.dat'}    {'Plot3D/569965_0-83.dat'}    {'Plot3D/569965_0-84.dat'}    {'Plot3D/569965_0-85.dat'}    {'Plot3D/569965_0-86.dat'}    {'Plot3D/569965_0-87.dat'}    {'Plot3D/569965_0-88.dat'}    {'Plot3D/569965_0-89.dat'}    {'Plot3D/569965_0-9.dat'}    {'Plot3D/569965_0-90.dat'}    {'Plot3D/569965_0-91.dat'}    {'Plot3D/569965_0-92.dat'}    {'Plot3D/569965_0-93.dat'}    {'Plot3D/569965_0-94.dat'}    {'Plot3D/569965_0-95.dat'}    {'Plot3D/569965_0-96.dat'}    {'Plot3D/569965_0-97.dat'}    {'Plot3D/569965_0-98.dat'}    {'Plot3D/569965_0-99.dat'}

x = readmatrix(Uz{1}, 'Range','A:A')

x = 1432×1

2.4604 2.4967 2.5330 2.5693 2.6056 2.6419 2.6782 2.7145 2.7508 2.7871

ymtx = NaN(numel(x),numel(Uz));
for k = 1:numel(Uz)
    ymtx(:,k) = readmatrix(Uz{k}, 'Range','B:B');
end
ymtx

ymtx = 1432×103

1.0e+03 * 1.2665 1.2390 1.2957 1.3295 1.2866 1.2756 1.3268 1.2701 1.2829 1.2226 1.2783 1.2601 1.2372 1.3058 1.2701 1.2336 1.2683 1.3149 1.2665 1.2528 1.2866 1.2747 1.2875 1.2546 1.2372 1.2482 1.3030 1.2144 1.2601 1.2327 1.4501 1.4590 1.5009 1.4444 1.4293 1.4477 1.4837 1.4664 1.4704 1.4638 1.4245 1.4523 1.4647 1.4399 1.4495 1.4558 1.4585 1.4437 1.4214 1.4375 1.4426 1.4605 1.3969 1.4208 1.4349 1.4192 1.4393 1.3960 1.4216 1.4406 1.5363 1.5556 1.5773 1.5481 1.5332 1.5465 1.5618 1.5608 1.5676 1.5171 1.5129 1.5126 1.5346 1.5261 1.5019 1.5353 1.5379 1.5365 1.5386 1.5538 1.5134 1.5041 1.4984 1.5068 1.5035 1.5194 1.5506 1.5214 1.5161 1.5338 1.5478 1.5654 1.5978 1.5399 1.5437 1.5322 1.5942 1.6009 1.5492 1.5622 1.5534 1.5291 1.5382 1.5195 1.5467 1.5613 1.5274 1.5388 1.5266 1.5480 1.5368 1.5309 1.5295 1.5255 1.5020 1.5091 1.5594 1.5322 1.5028 1.5248 1.4311 1.4366 1.4876 1.4550 1.4216 1.4367 1.4829 1.4560 1.4595 1.4462 1.4493 1.4380 1.4247 1.4277 1.4316 1.4370 1.4438 1.4556 1.4439 1.4534 1.4486 1.4815 1.4257 1.4244 1.4333 1.4281 1.4484 1.4249 1.4361 1.4369 1.2854 1.2920 1.3296 1.2637 1.2814 1.2909 1.3275 1.3605 1.3120 1.2900 1.2933 1.2971 1.2904 1.2928 1.2848 1.2823 1.3208 1.2892 1.2776 1.2796 1.2881 1.2830 1.2718 1.2602 1.2691 1.2963 1.2687 1.2730 1.2636 1.2779 1.0883 1.0985 1.1391 1.1115 1.1109 1.0882 1.1312 1.1230 1.1519 1.1412 1.1091 1.1299 1.1354 1.1099 1.1019 1.0860 1.1173 1.1026 1.1176 1.1082 1.1124 1.1322 1.0924 1.1117 1.1133 1.1100 1.0867 1.1197 1.1160 1.1154 0.9009 0.8975 0.9614 0.9353 0.9231 0.9332 0.9357 0.9385 0.9338 0.9446 0.9514 0.9479 0.9511 0.9505 0.9511 0.8918 0.9264 0.9319 0.9417 0.9383 0.9411 0.9382 0.9312 0.9162 0.9311 0.9320 0.8924 0.9365 0.9382 0.9440 0.7658 0.7547 0.8386 0.8016 0.7964 0.8062 0.8311 0.8224 0.8386 0.8390 0.8350 0.8314 0.8377 0.8427 0.8188 0.7682 0.8285 0.8411 0.8219 0.8207 0.8176 0.8246 0.8032 0.8206 0.8204 0.8089 0.7647 0.8138 0.8006 0.7879 0.6761 0.6596 0.7479 0.7089 0.7084 0.7049 0.7126 0.7284 0.7231 0.7455 0.7445 0.7436 0.7518 0.7280 0.7464 0.6505 0.7565 0.7515 0.7362 0.7359 0.7348 0.7378 0.7407 0.7288 0.7355 0.7176 0.6595 0.7250 0.7209 0.7094

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'

rowidx = 200

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]

Oh wow, thank you so much for such a quick response. As I'm not too familar with the language used at the start, I was struggling on this for quite a while.

[Star Strider]

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).

Answer 2

[KSSV]

Read about surf. This is your function.

Answer 3

[Sam]

Thank you for pointing this out, I have edited this!

My data is in three columns, the third column is redundant (errors), but the first and second column are my x and y, respectively.

The z values are in the file title, i.e. 569965_0-2.dat = 569965 (scan name); 0 (line number); 2 (spot/depth number, there are 102 spots for depth, this will be the z I assume)

I have attached one line here in my zip.