Preallocation with object structures

Hello,

I have a question about preallocation with object-oriented programming.

I have this object:

This is the result of a few loops. I could have one only loop, but I prefere to do it step by step to better control that I'm not wasting my time with dumb errors. I think it's not important, but I'll show an example.

This is an object containing the tooth 11 (FDI nomenclature) of six different samples (STL-files) of teeth.

First I rotate and translate a tooth to fit a reference tooth (in this case tooth in second row). For this I get tform (transformation matrix) and movingReg (new set of points/vertices).

Then I do a nearest point analysis and get k and dist an calculate Fk which is the distance vector with which I calculate the MeanVertices for the reference tooth (that's why there is only one matrix, in the second row).

Matlab tells me to preallocate the whole time, which I don't know how to do with this object. How can I preallocate (for example) FDINumber11.Vertices (see the code bellow this paragraph) before reading the data and not knowing how many points the file has? I think solution would apply to the other characteristics.

for i=1:m % m is the amount of teeth, which is defined at the beginning
        FDINumber11_STL  = stlread(FDINumber11(i).STLPath);
        FDINumber11(i).Vertices= FDINumber11_STL.Points;
        FDINumber11(i).Faces = FDINumber11_STL.ConnectivityList;
end

The whole process takes a little while, not too much but I hope to one day try it with many more teeth, so optimization would be a good thing to do. The worst case is that I learn a good programming practice, so even in case I cannot preallocate here, I would be glad to get a good explanation of it.

As always thank you very much.

Diego

PS: I have an example of a preallocation here, used in this code and it seems to work.

summe1 = 0.0;

for i=1:m   
    summe1 = summe1 + (FDINumber11(i).Fk - FDINumber11(r).Vertices)/(m-1); 
  end

Answer 1

[J. Alex Lee]

I don't think you are understanding "preallocation" correctly based on your last example...matlab is [probably] asking you to "reserve space fo the m different stl files you want to process". In this case, m=6 if I understand your description. There is a simple fix:

for i = m:-1:1
    FDINumber11_STL  = stlread(FDINumber11(i).STLPath);
    FDINumber11(i).Vertices= FDINumber11_STL.Points;
    FDINumber11(i).Faces = FDINumber11_STL.ConnectivityList;
end

What this does is instead of go i = 1,2,3,4,5,6 it will go i = 6,5,4,3,2,1. This matters because

clear % clear all variables
x(6) = 1

is a way to implicitly tell matlab to preallocate 6 elements to the 1-D array x before assigning the 6th element. It works for structure arrays too.

It's also likely that you want to enapsulate all the analysis you do on an individual stl file into a single function, rather than do things in a loop with indices.

function results = stlAnalysis(stlpath)
% do stuff
end

[Diego Hens]

Thanks for the answer. I got a bit confused on when to use:

clear % clear all variables
x(6) = 1

is it before or after the for loop? Would that x be m in my case?

Either way, I like the idea of the function, I did not think of that. That I know how to do :D

Edit: The code runs twice as fast now :)

[J. Alex Lee]

clear % clear all variables
x(6) = 1

It was just to illustrate how to preallocate, so put it before a loop:

x(6) = 1
x(5) = 1
% ...
x(1) = 1

is the same as

for i = 6:-1:1
    x(i) = 1
end

The more common way you see is

x = nan(6) % or zeros() or ones() to preallocate
for i = 1:6
    x(i) = 1
end

[Diego Hens]

Ok, thank you. I think I've understood it.

I cannot use it in this case, because I don't know how big my matrices are, so I cannot say which number goes inside the parenthesis of nan. Right?

[J. Alex Lee]

My point is, based on your first bit of code I think matlab wants you to tell it how many stl files you have (m=6), not how big your stl parsing results are. Simply reversing your loop order should resolve your mlint warning (literally replace your first bit of code with my first bit of code). I don't think it will affect performance much. If you are having different preallocation warnings, please show the code that's generating them

[Diego Hens]

Yes, that I have understood. When I replaced my code with a function I did not get the warning. I was just asking about the general use of preallocation. So, when I want to do a preallocation, I need to know the size of the matrix, right? In this case there is no preallocation, just the order of the loop.

[J. Alex Lee]

https://www.mathworks.com/help/matlab/matlab_prog/preallocating-arrays.html

Yes ordering the loop backward IS a way of preallocation.