colored isosurface could not be maintained

Hello Matlab community,

I am visualizing a turbulent flow field with sphereical particles and encountered a strange problem.

I use "isosurface" to visualize the vortex structures, and color them with the local flow velocity. The plot looked fine, but when I add some particles into the plot with "surf", the colored isosurface of vortex structure became single colored.

Here is my script for the plot (the data files are pretty large so I don't upload them)

clear all;

Re = 11279.5;

visc = 0.004;

ny = 512;

vscale = Re*0.004/ny;

lscale = 20;

scale = vscale/lscale;

rad = 10;

A1 = load('qvalue3D0000500.dat');

A3 = load('ux0000500.dat');

x = [0.5:2:512-0.5];

y = [0.5:2:512-0.5];

z= [0.5:2:512-0.5];

[X,Y,Z] = meshgrid(y,x,z);

Qvalue = A1(:)/vscale/vscale*lscale*lscale;

streamvel = A3(:)/vscale;

Qvalue = reshape(Qvalue,256,256,256);

streamvel = reshape(streamvel,256,256,256);

Qvalue = smooth3(Qvalue,'gaussian',[3,3,3]);

streamvel = smooth3(streamvel,'gaussian',[3,3,3]);

maximumQ = max(max(max(Qvalue)));

minimumQ = min(min(min(Qvalue)));

maxstreamvel = max(max(max(streamvel)));

minstreamvel = min(min(min(streamvel)));

streamvel = (streamvel - minstreamvel)/(maxstreamvel - minstreamvel);

A2 = load('partS10000500.dat');

partx = A2(:,2); party = A2(:,3); partz = A2(:,4);

figure(1)

aaa = 0.2;

isosurface(X,Y,Z,Qvalue,aaa,streamvel);

hold on;

for id = 1:length(partx)

partx9 = partx(id); party9 = party(id); partz9 = partz(id);

[X1,Y1,Z1] = sphere(30);

r = rad;

X2 = X1 * r;

Y2 = Y1 * r;

Z2 = Z1 * r;

s1 = surf(X2+partx9,Y2+party9,Z2+partz9);

hold on;

set(s1,'FaceColor',[1 1 1], ...

'FaceAlpha',0.8,'FaceLighting','gouraud','EdgeColor','none');

end

%camlight

axis([0 512 0 512 0 512]);

brighten(0.0);

daspect([1 1 1]);

set(gca,'box','on')

ax = gca;

ax.BoxStyle = 'full';

xticks([]);

yticks([]);

zticks([]);

Before I insert particle, the plot looks like

But once I insert particles, it looks like

As you can see, the colored vortex structures turns uniformly purple.

I wonder if someone can explain the reason and offer me suggests to maintain color isosurface with particles.

Thanks a lot for your help,

Cheng

Answer 1

[Adam Danz]

Why do the isosurface colors change when adding another surface object?

By default, the range of colors in the axes' colormap is defined by the range of color values specied by objects within the axes.

To demonstrate this, create an isosurface with a range of isovalues and add a colorbar. Notice that the colorbar limits are from 0 to 1.

[x,y,z] = meshgrid([-3:0.25:3]); 
V = x.*exp(-x.^2 -y.^2 -z.^2);
isovalues = rand(size(x));
isosurface(x,y,z,V,isovalues);     
colorbar()
axis equal

When you add a surface object which also relys on the colormap, the axes adjusts the color scaling to cover the range of colors in all objects in the axes.

figure()
% copied from previous block
isosurface(x,y,z,V,isovalues);     
colorbar()
axis equal

% Add surface obj
hold on
[xx,yy,zz] = sphere(20); 
s1 = surf(xx+2, yy+2, zz+2);
set(s1,'FaceColor',[1 1 1], 'FaceAlpha',0.8,'EdgeColor','none');

Notice that the colorbar limits changed from 0:1 to 0:3 to accomodate the wider range of colors in the sphere. The values that define colors in the isosurface object haven't changed, they are still 0:1, but as you can see in the colorbar, 0:1 is within the blue hues which is why the isosurface appears as blue-ish.

How to prevent the isosurface colors from changing

Now that we understand that the shift in colors is due to a change in the colormap limits, the question is, how do we add additional surface objects without affecting the original colormap limits?

One way is to store the original colormap limits prior to adding the surface and then returning the original colormap limits after the additional surface object is added.

% Create isosurface

h = isosurface(__);

% Store the colormap limits

originalColorLimits = clim(gca); % replace gca with the axes handle

% Add surface or whatever you'd like

surf(__)

% Return the original colormap limits

clim(gca, originalColorLimits) % replace gca with the axes handle

Here's that logic applied to my demo above

figure()
% copied from previous block
isosurface(x,y,z,V,isovalues);     
colorbar()
axis equal
originalColorLimits = clim(gca);

% Add surface obj
hold on
[xx,yy,zz] = sphere(20); 
s1 = surf(xx+2, yy+2, zz+2);
set(s1,'FaceColor',[1 1 1], 'FaceAlpha',0.8,'EdgeColor','none');
clim(gca, originalColorLimits) 

[程 彭]

Hello Adam,

Many thanks for the answer! Now I understand the reason why the color of isosurface changed.

Is "clim" a new function in MATLAB? My R2020a version doesn't seem to recognize this function. Is there a way I can do the same with R2020a?

Thanks,

Cheng

[程 彭]

Hello Adam,

I see clim is the renamed function of caxis. Now my script works! Thanks for your help.

Cheng

[Adam Danz]

You got it, @程 彭!

caxis doc 20a.