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I am trying to speed these loops up but I couldn't. please help me.

this code to calculate the shortest distance between lines and the distance between the mid point of the line and the the point of minimum distance vector between them then compare it with 0, if it is less than zero it will beark the second loop and change the orientation of the new line and check it with ALL previous lines. I tried 2000 lines with 100 trails the PC takes more than 48 hrs.

n=2000;

maxtrial=100;

Rx=rand(n,1)*0.2;

Ry=rand(n,1)*0.2;

Rz=rand(n,1)*0.2;

MT=0;

k=1;

while k<=n

% Create the angels for fiber oreintation

%For Phi

Phi_min=-0.1745329; %Angle Phi minimum value

Phi_max=0.1745329; %Angle Phi maximum value

Phi=Phi_min+rand(1,1)*(Phi_max-Phi_min);

%For theta

Z = (-1) + (1-(-1)) * rand(1,1); % value of Z to use in angle theta which will be within +- 10 degree

theta = acos (Z);

d1= sin(theta)*sin(Phi);

d2= sin(theta)*cos(Phi);

d3=cos(theta);

%first point coordinats

x2= Rx(k)+(Lf*0.5*d1);

y2= Ry(k)+(Lf*0.5*d2);

z2= Rz(k)+(Lf*0.5*d3);

%second point coordinats

x3= Rx(k)-(Lf*0.5*d1);

y3= Ry(k)-(Lf*0.5*d2);

z3= Rz(k)-(Lf*0.5*d3);

P=[x3-x2 y3-y2 z3-z2]; %orientation vector

P_all(k,:)=P;

if k>=2 && k<=n

t=k-1;

for t=1:k-1

normal_vector=((cross(P_all(k-t,:),P_all(k,:))/(norm(cross(P_all(k-t,:),P_all(k,:)))))); % unit vector normal to both lines

min_distance= norm(dot((R_all(k-t,:)-R_all(k,:)),normal_vector))-Df; % the minimum distance between two lines

L_ij=(-(dot((R_all(k-t,:)-R_all(k,:)),P_all(k-t,:)))+(dot((R_all(k-t,:)-R_all(k,:)),P_all(k,:)))*dot(P_all(k-t,:),P_all(k,:)))/(1-(dot(P_all(k-t,:),P_all(k,:)))^2); % distance between the center of line and the point that minimum distance occure at

if min_distance<0 && L_ij<=Lf/2

k=k-1;

MT=MT+1;

break

else

MT=0;

end

end

end

if MT==maxtrial

x2=0;

x3=0;

y2=0;

y3=0;

z2=0;

z3=0;

break

end

G1(k,:)= [z2 x2 y2]; %first points coordinates matrix

G2(k,:)= [z3 x3 y3]; %second points coordinates matrix

k=k+1;

end

Jan
on 23 Nov 2019

You see warnings in the editor already, which explain the disadvantages of iteratively growing arrays. Use a proper pre-allocation in any way.

A simple code will not run faster, but it is easier to read: Compare

Z = (-1) + (1-(-1)) * rand(1,1)

with

Z = 2 * rand - 1;

I cannot run your code, because Lf, Df and R_all are undefined. It looks strange, that MT is not reset and comparing MT==maxtrial can match 1 time only.

Please post a running code.

Jan
on 23 Nov 2019

Edited: Jan
on 23 Nov 2019

This line is expensive:

normal_vector = ((cross(P_all(k-t,:),P_all(k,:)) / ...

(norm(cross(P_all(k-t,:),P_all(k,:))))));

Matlab's cross() is not efficient and norm() can be accelerated also. Calling cross() twice for the same data is a waste of time in addition. P_all(k, :) is available as P also. Faster and nicer:

v = cross(P_all(k-t, :), P);

normal_vector = v / norm(v);

Or use a faster M-function:

normal_vector = NormCross(P_all(k-t, :), P);

function c = NormCross(a, b)

c = [a(2) * b(3) - a(3) * b(2), ...

a(3) * b(1) - a(1) * b(3), ...

a(1) * b(2) - a(2) * b(1)];

c = c / sqrt(c(1) * c(1) + c(2) * c(2) + c(3) * c(3));

end

Equivalent improvements can be applied to the DOT commands also.

By the way: The 2 leading and trailing parentheses in "normal_vector = ((" decrease the readability of the code only.

A short run time test:

P = rand(100, 3);

t = 100;

tic

for r = 1:1e5

for k = 1:100

v = cross(P(k, : ), P(t, :)) / norm(cross(P(k, :), P(t, :)));

end

end

toc

tic

for r = 1:1e5

Pt = P(t, :);

for k = 1:100

v = NormCross(P(k, : ), Pt);

end

end

toc

% Elapsed time is 11.122618 seconds.

% Elapsed time is 2.686646 seconds.

4 times faster just by avoiding calling cross twice and norm.

Instead of comparing min_distance=norm(...), you can compare the squared distance to save the computational time for the square root:

v = rand(1, 3);

min_distance = norm(v) - Df;

if min_distance < 0

...

end

Df2 = Df ^ 2;

...

v = rand(1, 3);

min_dist2 = v * v' - Df2; % Faster than: sum(v .* v)

if min_dist2 < 0

...

end

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