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Is there any way to speed this up?

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Gavin
Gavin on 23 May 2024 at 18:44
Commented: Gavin on 24 May 2024 at 19:53
I have a large (100x100x100) dataset of very small probabilites for electron locations in the hydrogen atom. I am attempting to create a 3-D heatmap of sorts, which I have done, using isosurface and layering many of them ontop of eachother using this code.
figure()
Psi = importdata("psi.mat");
n = 4;
l = 2;
m = 0;
isovalues1 = 1*10^(-(n+2)):1*10^(-(n+2)):1*10^(-n);
for i=1:length(isovalues1)
isosurface(Psi.^2,isovalues1(i))
alpha(isovalues1(i)*10^(n-2));
end
axis equal
axis vis3d
ax=gca; ax.SortMethod='childorder';
colorbar
title(['N = ',num2str(n),', L = ',num2str(l),', M = ',num2str(m)])
This works. But as you can imagine, making 100 isosurfaces at a time can be quite slow. I was wondering if there was any way to speed up what I have or perhaps another way to make a 3-D heatmap.

Accepted Answer

Cris LaPierre
Cris LaPierre on 23 May 2024 at 21:40
Edited: Cris LaPierre on 24 May 2024 at 2:41
My question is if it has to be done with isosurfaces. Here's an approach that uses scatter3. You can adjust the marker size to change how the data is displayed. It does look different, but it seems all the important info is still there.
load("psi.mat",'Psi');
n = 4;
l = 2;
m = 0;
% create (x,y,z) coordinates
[X,Y,Z] = meshgrid(1:size(Psi,2),1:size(Psi,1),1:size(Psi,3));
isovalues1 = 1*10^(-(n+2)):1*10^(-(n+2)):1*10^(-n);
% discretize the data by isovalues
[bin,edges] = discretize(Psi.^2,isovalues1);
% Plot data
idx = bin(:)>0;
scatter3(X(idx),Y(idx),Z(idx),1,isovalues1(bin(idx)),'filled')
alpha(isovalues1(bin(idx)).*10^(n-2))
axis equal
axis vis3d
colorbar('TickLabels',isovalues1)
title(['N = ',num2str(n),', L = ',num2str(l),', M = ',num2str(m)])
  1 Comment
Gavin
Gavin on 24 May 2024 at 19:53
wow yes thank you! thats perfect. Im still a little new to matlab so this didnt even cross my mind as a possibility.
thanks again

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