I want to write a function that approximates integrals with the trapezoidal rule.
I first defined a function in one file:
function[y] = integrand(x)
y = x*exp(-x^2); %This will be integrand I want to approximate
end
Then I wrote my function that approximates definite integrals with lower bound a and upper bound b (also in another file):
function [result] = trapez(integrand,a,b,k)
sum = 0;
h = (b-a)/k; %split up the interval in equidistant spaces
for j = 1:k
x_j = a + j*h; %this are the points in the interval
sum = sum + ((x_j - x_(j-1))/2) * (integrand(x_(j-1)) + integrand(x_j));
end
result = sum
end
But when I want to call this function from the command window, using result = trapez(integrand,0,1,10) for example, I always get an error 'not enough input arguments'. I don't know what I'm doing wrong?
There are numerous issues with your code:
x_(j-1) is not defined, and is not really a valid Matlab syntax (assuming you want that to be a variable).
By calling trapez(integrand,0,1,10) you're actually calling integrand function with no input arguments. If you want to pass a handle, use #integrand instead. But in this case there's no need to pass it at all.
You should avoid variable names that coincide with Matlab functions, such as sum. This can easily lead to issues which are difficult to debug, if you also try to use sum as a function.
Here's a working version (note also a better code style):
function res = trapez(a, b, k)
res = 0;
h = (b-a)/k; % split up the interval in equidistant spaces
for j = 1:k
x_j1 = a + (j-1)*h;
x_j = a + j*h; % this are the points in the interval
res = res+ ((x_j - x_j1)/2) * (integrand(x_j1) + integrand(x_j));
end
end
function y = integrand(x)
y = x*exp(-x^2); % This will be integrand I want to approximate
end
And the way to call it is: result = trapez(0, 1, 10);
Your integrandfunction requires an input argument x, which you are not supplying in your command line function call
Related
I am trying to use 'mle' with a custom negative log-likelihood function, but I get the following error:
Requested 1200000x1200000 (10728.8GB) array exceeds maximum array size preference (15.6GB). This might cause MATLAB to become unresponsive.
The data I am using is a 1x1200000 binary array (which I had to convert to double), and the function has 10 arguments: one for the data, 3 known paramenters, and 6 to be optimized. I tried setting 'OptimFun' to both 'fminsearch' and 'fmincon'. Also, optimizing the parameters using 'fminsearch' and 'fminunc' instead of 'mle' works fine.
The problem happens in the 'checkFunErrs' functions, inside the 'mlecustom.m' file (call at line 173, actuall error at line 705).
With 'fminunc' I could calculate the optimal parameters, but it does not give me confidence intervals. Is there a way to circumvent this? Or am I doing something wrong?
Thanks for the help.
T_1 = 50000;
T_2 = 100000;
npast = 10000;
start = [0 0 0 0 0 0];
func = #(x, data, cens, freq)loglike(data, [x(1) x(2) x(3) x(4) x(5) x(6)],...
T_1, T_2, npast);
params = mle(data, 'nloglf', func, 'Start', start, 'OptimFun', 'fmincon');
% Computes the negative log likehood
function out = loglike(data, params, T_1, T_2, npast)
size = length(data);
if npast == 0
past = 0;
else
past = zeros(1, size);
past(npast+1:end) = movmean(data(npast:end-1),[npast-1, 0]); % Average number of events in the previous n years
end
lambda = params(1) + ...
(params(2)*cos(2*pi*(1:size)/T_1)) + ...
(params(3)*sin(2*pi*(1:size)/T_1)) + ...
(params(4)*cos(2*pi*(1:size)/T_2)) + ...
(params(5)*sin(2*pi*(1:size)/T_2)) + ...
params(6)*past;
out = sum(log(1+exp(lambda))-data.*lambda);
end
Your issue is line 228 (as of MATLAB R2017b) of the in-built mle function, which happens just before the custom function is called:
data = data(:);
The input variable data is converted to a column array without warning. This is typically done to ensure that all further calculations are robust to the orientation of the input vector.
However, this is causing you issues, because your custom function assumes data is a row vector, specifically this line:
out = sum(log(1+exp(lambda))-data.*lambda);
Due to implicit expansion, when the row vector lambda and the column vector data interact, you get a huge square matrix per your error message.
Adding these two lines to make it explicit that both are column vectors resolves the issue, avoids implicit expansion, and applies the calculation element-wise as you intended.
lambda = lambda(:);
data = data(:);
So your function becomes
function out = loglike(data, params, T_1, T_2, npast)
N = length(data);
if npast == 0
past = 0;
else
past = zeros(1,N);
past(npast+1:end) = movmean(data(npast:end-1),[npast-1, 0]); % Average number of events in the previous n years
end
lambda = params(1) + ...
(params(2)*cos(2*pi*(1:N)/T_1)) + ...
(params(3)*sin(2*pi*(1:N)/T_1)) + ...
(params(4)*cos(2*pi*(1:N)/T_2)) + ...
(params(5)*sin(2*pi*(1:N)/T_2)) + ...
params(6)*past;
lambda = lambda(:);
data = data(:);
out = sum(log(1+exp(lambda))-data.*lambda);
end
An alternative would be to re-write your function so that it uses column vectors, but you create new row vectors with the (1:N) steps and the concatenation within the movmean. The suggested approach is arguably "lazier", but also robust to row or column inputs.
Note also I've changed your variable name from size to N, since size is an in-built function which you should avoid shadowing.
function [y] = sumsqu(xx)
d = length(xx);
sum = 0;
for ii = 1:d
xi = xx(ii);
sum = sum + ii*xi^2;
end
y = sum;
end
Above is the code for d variables. Whenever I call the function I get the sum as expected. Now I want to find the numerical gradient of the function. But since the function is returning a scalar value, gradient returns 0 obviously. What can I do so that gradient first evaluates in its variable form then return an array corresponding to [x1 x2 x3....xd]?
As you can see in the picture, I want it in that order. And I also want d as a variable so that code can be generic. Hope you understood my problem.
Your function does exactly this:
y = sum(xx.^2 .* (1:numel(xx)));
The derivatives then are:
y = 2*xx .* (1:numel(xx));
(according to the hand-written equations).
You should avoid using sum as a variable name, you can see above that it is an important function, if you assign a value to sum, you hide the function and can no longer use it.
For your specific function, you can calculate the gradient analytically like:
g = 2*(1:length(xx)).*xx;
You can also replace the call for length(xx) by d if it is given.
When I type help gmres in MATLAB I get the following example:
n = 21; A = gallery('wilk',n); b = sum(A,2);
tol = 1e-12; maxit = 15;
x1 = gmres(#(x)afun(x,n),b,10,tol,maxit,#(x)mfun(x,n));
where the two functions are:
function y = afun(x,n)
y = [0; x(1:n-1)] + [((n-1)/2:-1:0)'; (1:(n-1)/2)'].*x+[x(2:n); 0];
end
and
function y = mfun(r,n)
y = r ./ [((n-1)/2:-1:1)'; 1; (1:(n-1)/2)'];
end
I tested it and it works great. My question is in both those functions what is the value for x since we never give it one?
Also shouldn't the call to gmres be written like this: (y in the #handle)
x1 = gmres(#(y)afun(x,n),b,10,tol,maxit,#(y)mfun(x,n));
Function handles are one way to parametrize functions in MATLAB. From the documentation page, we find the following example:
b = 2;
c = 3.5;
cubicpoly = #(x) x^3 + b*x + c;
x = fzero(cubicpoly,0)
which results in:
x =
-1.0945
So what's happening here? fzero is a so-called function function, that takes function handles as inputs, and performs operations on them -- in this case, finds the root of the given function. Practically, this means that fzero decides which values for the input argument x to cubicpoly to try in order to find the root. This means the user just provides a function - no need to give the inputs - and fzero will query the function with different values for x to eventually find the root.
The function you ask about, gmres, operates in a similar manner. What this means is that you merely need to provide a function that takes an appropriate number of input arguments, and gmres will take care of calling it with appropriate inputs to produce its output.
Finally, let's consider your suggestion of calling gmres as follows:
x1 = gmres(#(y)afun(x,n),b,10,tol,maxit,#(y)mfun(x,n));
This might work, or then again it might not -- it depends whether you have a variable called x in the workspace of the function eventually calling either afun or mfun. Notice that now the function handles take one input, y, but its value is nowhere used in the expression of the function defined. This means it will not have any effect on the output.
Consider the following example to illustrate what happens:
f = #(y)2*x+1; % define a function handle
f(1) % error! Undefined function or variable 'x'!
% the following this works, and g will now use x from the workspace
x = 42;
g = #(y)2*x+1; % define a function handle that knows about x
g(1)
g(2)
g(3) % ...but the result will be independent of y as it's not used.
I have a Mechanical system with following equation:
xdot = Ax+ Bu
I want to solve this equation in a loop because in every step I need to update u but solvers like ode45 or lsim solving the differential equation for a time interval.
for i = 1:10001
if x(i,:)>= Sin1 & x(i,:)<=Sout2
U(i,:) = Ueq - (K*(S/Alpha))
else
U(i,:) = Ueq - (K*S)
end
% [y(i,:),t,x(i+1,:)]=lsim(sys,U(i,:),(time=i/1000),x(i,:));
or %[t,x] = ode45(#(t,x)furuta(t,x,A,B,U),(time=i/1000),x)
end
Do I have another ways to solve this equation in a loop for a single time(Not single time step).
There are a number of methods for updating and storing data across function calls.
For the ODE suite, I've come to like what is called "closures" for doing that.
A closure is basically a nested function accessing or modifying a variable from its parent function.
The code below makes use of this feature by wrapping the right-hand side function passed to ode45 and the 'OutputFcn' in a parent function called odeClosure().
You'll notice that I am using logical-indexing instead of an if-statement.
Vectors in if-statements will only be true if all elements are true and vice-versa for false.
Therefore, I create a logical array and use it to make the denominator either 1 or Alpha depending on the signal value for each row of x/U.
The 'OutputFcn' storeU() is called after a successful time step by ode45.
The function grows the U storage array and updates it appropriately.
The array U will have the same number of columns as the number of solution points requested by tspan (12 in this made-up example).
If a successful full step leaps over any requested points, the function is called with intermediate all requested times and their associated solution values (so x may be rectangular and not just a vector); this is why I used bsxfun in storeU and not in rhs.
Example function:
function [sol,U] = odeClosure()
% Initilize
% N = 10 ;
A = [ 0,0,1.0000,0; 0,0,0,1.0000;0,1.3975,-3.7330,-0.0010;0,21.0605,-6.4748,-0.0149];
B = [0;0;0.6199;1.0752 ] ;
x0 = [11;11;0;0];
K = 100;
S = [-0.2930;4.5262;-0.5085;1.2232];
Alpha = 0.2 ;
Ueq = [0;-25.0509;6.3149;-4.5085];
U = Ueq;
Sin1 = [-0.0172;-4.0974;-0.0517;-0.2993];
Sout2 = [0.0172 ; 4.0974; 0.0517; 0.2993];
% Solve
options = odeset('OutputFcn', #(t,x,flag) storeU(t,x,flag));
sol = ode45(#(t,x) rhs(t,x),[0,0.01:0.01:0.10,5],x0,options);
function xdot = rhs(~,x)
between = (x >= Sin1) & (x <= Sout2);
uwork = Ueq - K*S./(1 + (Alpha-1).*between);
xdot = A*x + B.*uwork;
end
function status = storeU(t,x,flag)
if isempty(flag)
% grow array
nAdd = length(t) ;
iCol = size(U,2) + (1:nAdd);
U(:,iCol) = 0 ;
% update U
between = bsxfun(#ge,x,Sin1) & bsxfun(#le,x,Sout2);
U(:,iCol) = Ueq(:,ones(1,nAdd)) - K*S./(1 + (Alpha-1).*between);
end
status = 0;
end
end
My main script contains following code:
%# Grid and model parameters
nModel=50;
nModel_want=1;
nI_grid1=5;
Nth=1;
nRow.Scale1=5;
nCol.Scale1=5;
nRow.Scale2=5^2;
nCol.Scale2=5^2;
theta = 90; % degrees
a_minor = 2; % range along minor direction
a_major = 5; % range along major direction
sill = var(reshape(Deff_matrix_NthModel,nCell.Scale1,1)); % variance of the coarse data matrix of size nRow.Scale1 X nCol.Scale1
%# Covariance computation
% Scale 1
for ihRow = 1:nRow.Scale1
for ihCol = 1:nCol.Scale1
[cov.Scale1(ihRow,ihCol),heff.Scale1(ihRow,ihCol)] = general_CovModel(theta, ihCol, ihRow, a_minor, a_major, sill, 'Exp');
end
end
% Scale 2
for ihRow = 1:nRow.Scale2
for ihCol = 1:nCol.Scale2
[cov.Scale2(ihRow,ihCol),heff.Scale2(ihRow,ihCol)] = general_CovModel(theta, ihCol/(nCol.Scale2/nCol.Scale1), ihRow/(nRow.Scale2/nRow.Scale1), a_minor, a_major, sill/(nRow.Scale2*nCol.Scale2), 'Exp');
end
end
%# Scale-up of fine scale values by averaging
[covAvg.Scale2,var_covAvg.Scale2,varNorm_covAvg.Scale2] = general_AverageProperty(nRow.Scale2/nRow.Scale1,nCol.Scale2/nCol.Scale1,1,nRow.Scale1,nCol.Scale1,1,cov.Scale2,1);
I am using two functions, general_CovModel() and general_AverageProperty(), in my main script which are given as following:
function [cov,h_eff] = general_CovModel(theta, hx, hy, a_minor, a_major, sill, mod_type)
% mod_type should be in strings
angle_rad = theta*(pi/180); % theta in degrees, angle_rad in radians
R_theta = [sin(angle_rad) cos(angle_rad); -cos(angle_rad) sin(angle_rad)];
h = [hx; hy];
lambda = a_minor/a_major;
D_lambda = [lambda 0; 0 1];
h_2prime = D_lambda*R_theta*h;
h_eff = sqrt((h_2prime(1)^2)+(h_2prime(2)^2));
if strcmp(mod_type,'Sph')==1 || strcmp(mod_type,'sph') ==1
if h_eff<=a
cov = sill - sill.*(1.5*(h_eff/a_minor)-0.5*((h_eff/a_minor)^3));
else
cov = sill;
end
elseif strcmp(mod_type,'Exp')==1 || strcmp(mod_type,'exp') ==1
cov = sill-(sill.*(1-exp(-(3*h_eff)/a_minor)));
elseif strcmp(mod_type,'Gauss')==1 || strcmp(mod_type,'gauss') ==1
cov = sill-(sill.*(1-exp(-((3*h_eff)^2/(a_minor^2)))));
end
and
function [PropertyAvg,variance_PropertyAvg,NormVariance_PropertyAvg]=...
general_AverageProperty(blocksize_row,blocksize_col,blocksize_t,...
nUpscaledRow,nUpscaledCol,nUpscaledT,PropertyArray,omega)
% This function computes average of a property and variance of that averaged
% property using power averaging
PropertyAvg=zeros(nUpscaledRow,nUpscaledCol,nUpscaledT);
%# Average of property
for k=1:nUpscaledT,
for j=1:nUpscaledCol,
for i=1:nUpscaledRow,
sum=0;
for a=1:blocksize_row,
for b=1:blocksize_col,
for c=1:blocksize_t,
sum=sum+(PropertyArray((i-1)*blocksize_row+a,(j-1)*blocksize_col+b,(k-1)*blocksize_t+c).^omega); % add all the property values in 'blocksize_x','blocksize_y','blocksize_t' to one variable
end
end
end
PropertyAvg(i,j,k)=(sum/(blocksize_row*blocksize_col*blocksize_t)).^(1/omega); % take average of the summed property
end
end
end
%# Variance of averageed property
variance_PropertyAvg=var(reshape(PropertyAvg,...
nUpscaledRow*nUpscaledCol*nUpscaledT,1),1,1);
%# Normalized variance of averageed property
NormVariance_PropertyAvg=variance_PropertyAvg./(var(reshape(...
PropertyArray,numel(PropertyArray),1),1,1));
Question: Using Matlab, I would like to optimize covAvg.Scale2 such that it matches closely with cov.Scale1 by perturbing/varying any (or all) of the following variables
1) a_minor
2) a_major
3) theta
I am aware I can use fminsearch, however, how I am not able to perturb the variables I want to while using this fminsearch.
I won't pretend to understand everything that you are doing. But it sounds like a typical minimization problem. What you want to do is to come up with a single function that takes a_minor, a_major and theta as arguments, and returns the square of the difference between covAvg.Scale2 and cov.Scale1. Something like this:
function diff = minimize_me(a_minor, a_major, theta)
... your script goes here
diff = (covAvg.Scale2 - cov.Scale1)^2;
end
Then you need matlab to minimize this function. There's more than one option here. Since you only have three variables to minimize over, fminsearch is a good place to start. You would call it something like this:
opts = optimset('display', 'iter');
x = fminsearch( #(x) minimize_me(x(1), x(2), x(3)), [a_minor_start a_major_start theta_start], opts)
The first argument to fminsearch is the function you want to optimize. It must take a single argument: a vector of the variables that will be perturbed in order to find the minimum value. Here I use an anonymous function to extract the values from this vector and pass them into minimize_me. The second argument to fminsearch is a vector containing the values to start searching at. The third argument are options that affect the search; it's a good idea to set display to iter when you first start optimizing, so that you can get an idea of well the optimizer is converging.
If your parameters have restricted domains (e.g. they must all be positive) take a look at fminsearchbnd on the file exchange.
If I have misunderstood your problem, and this doesn't help at all, try posting code that we can run to reproduce the problem ourselves.