Neighbour voxels of a list of voxels

I am trying to find all the neighbours voxels of a list of voxels. I already used a function findNeigbours that I downloaded (https://www.mathworks.com/matlabcentral/fileexchange/68549-findneighbours) but it only works for a single voxel and I need to apply the function to a vector.

In my code, I used for loop but it's takiing too long time since the vector list is large. Any solution?

These are the lines I used in my code:

for i = 1:size(vector,1)
    surrounding{i} = findNeighbours(vector(i), [[pxl_x, pxl_y, pxl_z], 26)
end

[KSSV]

You can use inbuilt functions to achieve this fast. Show us how your voxels are.

[Razakamandimby Tiana]

The vector is in the excel file and the size of array in 3dimension is 60 x 60 x 67

Answer 1

[Matt J]

If you have lists of xCoordinates, yCoordinates, and zCoordinates of the voxels, you may simply do,

[dx,dy,dz]=ndgrid([-1,0,1]);
dx=dx(:).'; dy=dy(:).'; dz=dz(:).';

X=xCoordinates(:)+dx; Y=yCoordinates(:)+dy; Z=zCoordinates(:)+dz; %neighbor coordinates

and if the voxel grid has dimensions MxNxP, you might then discard out-of-bounds voxel coordinates by doing,

X(X<1 | X>M)=nan;
Y(Y<1 | Y>N)=nan;
Z(Z<1 | Z>P)=nan;

[Razakamandimby Tiana]

Thanks but I have the voxels indexes not their coordinates. But I will try to get the coordinates from the inndexes and see if I get results faster

[Matt J]

Just use ind2sub().

Answer 2

[Razakamandimby Tiana]

I could solve this issue. The following code gives all the neighbour voxels (connectivity 26 in 3D) of each voxels in the vector list.

vector % The attached excel file
matrix = [121 121 117];
conn = 26;
neighbor = arrayfun(@(vector) findNeighbours(vector,matrix,conn), vector,'UniformOutput', false)

[Matt J]

But you are using arrayfun. I don't think you could be getting faster speed from arrayfun than with a loop.

[Razakamandimby Tiana]

you are right, finding the coordinates was faster. Thank you