How to remove discontinuous edges of 3D surf plot?

I have a matrix of 30*10 dimension and want to create a surf plot of it such that X and Y are indices of the matrix and matrix elements are plotted on the Z axis. With linear scale for Z axis, the plot looks fine; however, I want the Z axis in logarithmic scale and once I set it via:

set(gca,'ZScale','log')

The surface looks strange and discontinuous at one side (the image is attached); Here is the piece of code to plot the matrix which is attached in a text file:

 [X,Y] = meshgrid(1:10,1:30);
 figure
 surf(X,Y,Z)
 colormap parula
 shading interp
 set(gca,'ZScale','log')
 set(gca,'YDir','reverse')

I wonder why does it happen and how it can be fixed? Any help is highly appreciated.

[jonas]

The reason is happens is because some elements of Z are equal to zero, and are thus undefined in logscale. Is there reason you need to plot it as a log? It looks good on a linear axis.

[Mozhdeh Gholibeigi]

Thanks Jonas for your reply; The reason is that my supervisor wants it in log scale :D I checked the "0" elements of the matrix one-by-one and noticed that some of them seem to have higher values on the Z axis, giving rise to such discontinuity. But for other "0" valued elements it doesn't happen. Can you clarify such behaviour please?

[jonas]

See for example Z(1)=0. At [x=1;y=1] in your log-scale plot there is no value. Why? Because log(0)=-inf

Add this line to your code and see what happens.

Z(Z<10^-12)=10^-12;

It will substitute all zeros for 10^-12 and your plot will look nice, but the data is manipulated.

Edit: Forgot to mention that some values may appear as 0 because they are extremely small. If you write Z==0, then you will see which values are truly equal to zero.

Answer 1

[jonas]

Looks messy because log(0) is undefined. You can manipulate the data a bit and adjust the ZLim to make it look OK. Note that I also split the data set in 3 pieces.

[X,Y] = meshgrid(1:10,1:30);
figure;hold on
Z(Z<10^-5)=10^-5;
h1=surf(X(1:10,:),Y(1:10,:),Z(1:10,1:10))
h2=surf(X(11:20,:),Y(11:20,:),Z(11:20,1:10))
h3=surf(X(21:30,:),Y(21:30,:),Z(21:30,1:10))
colormap parula
set(gca,'ZScale','log')
set(gca,'YDir','reverse')
cb=colorbar
set(gca,'zlim',[10^-5 10^-1])
grid on;box on;
cb.Ruler.Scale = 'log';
cb.Ruler.MinorTick = 'on';

Remove the last two lines if you are running a release older than 2018a

[Mozhdeh Gholibeigi]

Hi Jonas and many thanks for your response; I tried your first suggestion and the result is attached. Actually, i tried it earlier and because all the small values are equally set to a constant number, the resulting graph has a sharp increase after that point. I wonder whether it is also possible to define gradually increasing values, so a range of values instead of only "Z(Z<10^-12)=10^-12", so that the resulting graph has a more smooth growth?

I tried your second suggestion and the result is not illustrative in terms of values on the Z axis; So, I think the first suggestion is a better one for my case. Thank you once again.

[jonas]

When I run my own code I get the attached results, which is a bit different.

"I wonder whether it is also possible to define gradually increasing values..."

Anything is possible, but I would be careful with manipulating the data to make it appear more smooth than it actually is. Setting a definite threshold is OK because you can easily describe what you have done in text or and/or change the last label to (<10^-12).

The most illustrative option might be to use a 2D-perspective, or contourf (see attachment 2). Its often easier to perceive color changes than values from a 3D-perspective.

In the end it's up to you to decide how to best present your data. I can only work with the visual aspects :)

[Mozhdeh Gholibeigi]

Thanks Jonas for your help and guide. I absolutely agree with you and will consider it in my work.