how to plot 2D contour lines from the data file

I tried to plot the 2D contour from my data file (which has three columns ,such as X,Y and intensity value) , I had plotted from scatter command it is filling ,but we need line contours,how to build it,thanks inadvance.

[Adam Danz]

Kona Veera Ganesh's answer moved here as a comment.

please check this file .I am unable to plot it .

[Adam Danz]

@Kona Veera Ganesh see "Working with non-gridded data" in my answer.

Answer 1

[Benjamin Großmann]

contour(x, y, z) gives you the contour plot, z is the intensity value

Contour plot of matrix - MATLAB contour

EDIT:

To create matrices of proper size, look at the scatteredInterpolant object. I do not recommend using approaches with unique since you have noisy data.:

% Define the object
F = scatteredInterpolant(x,y,v);
% !! Please have a close look at interpolation method and extrapolation
% method


% Create a proper mesh
xm = [min(x):max(diff(x)):max(x)];
ym = [min(y):max(diff(y)):max(y)];
[Xm,Ym] = meshgrid(xm, ym);

% Interpolate Z values
Z = F(Xm,Ym);

% create contour plot
contour(Xm,Ym,Z)

[Adam Danz]

Yes but while x and y are vectors, z must be a matrix and the OP only has a vector of data for z

[Benjamin Großmann]

Sorry, missed that point. Thanks for the advice.

[Adam Danz]

FWIW I think the contour family of functions should accept the syntax you described as long as x and y are defined according to a grid but for now, we're stuck with the requirement to reshape the data.

Answer 2

[Adam Danz]

Contour plots require z to be a matrix. contour(Z)

You can define the x and y values, too, and they can be vectors or matrices contour(X,Y,Z)

The important thing is that each element of z is defined in x and y.

Working with gridded data

If you're working with three vectors x,y,intensity, I assume you've got duplicates in x and y that define a grid similar to the example below in which case you just need to reshape the intensity data.

% Create nx3 matrix of [x,y,intensity] values
xyz(:,1) = repelem(1:10,1,10)';
xyz(:,2) = repmat(1:10,1,10)';
xyz(:,3) = reshape(magic(10),100,1)

xyz = 100×3

1 1 92 1 2 98 1 3 4 1 4 85 1 5 86 1 6 17 1 7 23 1 8 79 1 9 10 1 10 11

% Reshape the intensity vector into a matrix
[xUnq,~,xIdx] = unique(xyz(:,1)); 
[yUnq,~,yIdx] = unique(xyz(:,2)); 
zMat = nan(numel(yUnq),numel(xUnq)); 
zIdx = sub2ind(size(zMat),yIdx,xIdx);
zMat(zIdx) = xyz(:,3);
% Plot contour
contour(xUnq,yUnq,zMat)

Working with non-gridded data

After providing your data, it turns out that your x and y values do not form a grid. This means you must design a grid and average all of the intensity values within the grid.

This demo creates a 50x50 grid but you can design the grid differently by specifying the x and y grid edges or by changing the number of bins (see contour documentation).

Load data

filename = unzip('210.zip');
data = readmatrix('210.txt');
data(1:20,:) % show the first 20 rows

ans = 20×3

-433.0130 -198.0000 -0.0002 -433.0130 -199.0000 -0.0001 -432.1470 -197.5000 0.0002 -432.1470 -198.5000 -0.0000 -432.1470 -199.5000 -0.0001 -431.2810 -198.0000 -0.0001 -431.2810 -199.0000 -0.0002 -430.4150 -197.5000 0.0002 -430.4150 -198.5000 -0.0001 -430.4150 -199.5000 -0.0001

Create the 2D grid

nbins = 50; % Number of bins for x and y
[xBinNum, xEdges] = discretize(data(:,1),nbins); 
[yBinNum, yEdges] = discretize(data(:,2),nbins); 
[unqXYbins, ~, zBinNum] = unique([xBinNum(:), yBinNum(:)],'rows');

Average the z values within each bin of the 2D grid

xyz is a matrix containing the x and y bin numbers and the averaged z values within each bin. Missing data will be ignored. Missing data are undefined intensities for some combinations of x and y bins.

zBinMean = splitapply(@(x)mean(x,'omitnan'),data(:,3), zBinNum);
xyz = [unqXYbins, zBinMean];
xyz(1:20,:);

Reshape the z values into a matrix

Rows and columns of the matrix are defined by the bin edges.

zMat = nan(nbins,nbins); 
zIdx = sub2ind(size(zMat),xyz(:,2),xyz(:,1));
zMat(zIdx) = xyz(:,3);

Plot the contour map and compare it to the raw data shown as a 3D scatter plot

The x and y values will be the bin centers xBinCnt, yBinCnt

xBinCnt = xEdges(2:end) - diff(xEdges);
yBinCnt = yEdges(2:end) - diff(yEdges);
figure()
tiledlayout(1,3,'TileSpacing','compact','Padding','none')
nexttile
contour(xBinCnt, yBinCnt, zMat)
grid on
title('binned averages')
axis square

nexttile
scatter3(data(:,1), data(:,2), data(:,3), 30, data(:,3), 'filled')
grid on
view(-56, 5)
title('raw data')

Plot the contour again but zoom into relevant section

nexttile
contour(xBinCnt, yBinCnt, zMat)
xlim([-40 22])
ylim([-10 2])
title('zoomed in')
grid on
axis square

As you can see, your data are mostly flat along the XY plane at z=0 except for a column of data at about (0,0). That explains the relatively flat contour plot except for the activity around (0,0).

[Paulo Valente]

Thank you! That is a very helpful answer with a very elegant algorithm.

[Adam Danz]

Thanks for the feedback, Paulo Valente.