I have a problem in performing a non linear fit with Gnu Octave. Basically I need to perform a global fit with some shared parameters, while keeping others fixed.
The following code works perfectly in Matlab, but Octave returns an error
error: operator *: nonconformant arguments (op1 is 34x1, op2 is 4x1)
Attached my code and the data to play with:
clear
close all
clc
pkg load optim
D = dlmread('hd', ';'); % raw data
bkg = D(1,2:end); % 4 sensors bkg
x = D(2:end,1); % input signal
Y = D(2:end,2:end); % 4 sensors reposnse
W = 1./Y; % weights
b0 = [7 .04 .01 .1 .5 2 1]; % educated guess for start the fit
%% model function
F = #(b) ((bkg + (b(1) - bkg).*(1-exp(-(b(2:5).*x).^b(6))).^b(7)) - Y) .* W;
opts = optimset("Display", "iter");
lb = [5 .001 .001 .001 .001 .01 1];
ub = [];
[b, resnorm, residual, exitflag, output, lambda, Jacob\] = ...
lsqnonlin(F,b0,lb,ub,opts)
To give more info, giving array b0, b0(1), b0(6) and b0(7) are shared among the 4 dataset, while b0(2:5) are peculiar of each dataset.
Thank you for your help and suggestions! ;)
Raw data:
0,0.3105,0.31342,0.31183,0.31117
0.013229,0.329,0.3295,0.332,0.372
0.013229,0.328,0.33,0.33,0.373
0.021324,0.33,0.3305,0.33633,0.399
0.021324,0.325,0.3265,0.333,0.397
0.037763,0.33,0.3255,0.34467,0.461
0.037763,0.327,0.3285,0.347,0.456
0.069405,0.338,0.3265,0.36533,0.587
0.069405,0.3395,0.329,0.36667,0.589
0.12991,0.357,0.3385,0.41333,0.831
0.12991,0.358,0.3385,0.41433,0.837
0.25368,0.393,0.347,0.501,1.302
0.25368,0.3915,0.3515,0.498,1.278
0.51227,0.458,0.3735,0.668,2.098
0.51227,0.47,0.3815,0.68467,2.124
1.0137,0.61,0.4175,1.008,3.357
1.0137,0.599,0.422,1,3.318
2.0162,0.89,0.5335,1.645,5.006
2.0162,0.872,0.5325,1.619,4.938
4.0192,1.411,0.716,2.674,6.595
4.0192,1.418,0.7205,2.691,6.766
8.0315,2.34,1.118,4.195,7.176
8.0315,2.33,1.126,4.161,6.74
16.04,3.759,1.751,5.9,7.174
16.04,3.762,1.748,5.911,7.151
32.102,5.418,2.942,7.164,7.149
32.102,5.406,2.941,7.164,7.175
64.142,7.016,4.478,7.174,7.176
64.142,7.018,4.402,7.175,7.175
128.32,7.176,6.078,7.175,7.176
128.32,7.175,6.107,7.175,7.173
255.72,7.165,7.162,7.165,7.165
255.72,7.165,7.164,7.166,7.166
511.71,7.165,7.165,7.165,7.165
511.71,7.165,7.165,7.166,7.164
Giving the function definition above, if you call it by F(b0) in the command windows, you will get a 34x4 matrix which is correct, since variable Y has the same size.
In that way I can (in theory) compute the standard formula for lsqnonlin (fit - measured)^2
I was trying to solve a system of non-linear equations and check the stability of its equilibrium points. Initially, I declared two equations
adot = -a + 2*a^3 + b
bdot = -a -b
By equating both the equations with 0, I get the equilibrium points. Now, I am trying to get the Jacobian of the [adot;bdot] matrix using the jacobian([adot;bdot],[a,b]) method of symbolic package in Octave, which should just return a matrix whose items are the partial derivatives of "adot" and "bdot" w.r.t. "a" and "b", but it gives the following error
error: subscript indices must be integers or boolean
Can anyone tell me where I'm going wrong with this?
Edit: I'm adding the complete code down below:
pkg load symbolic
syms x y
xdot = -x + 2*x^3 + y;
ydot = -x - y;
[xeq,yeq] = solve(xdot==0,ydot==0);
xeq = double(xeq);
yeq = double(yeq);
jacobian_matrix = jacobian([xdot;ydot]);
At this point I'm getting the above mentioned error. The values in the [xeq,yeq] matrix are the equilibrium points of the system, which are to be used later on.
I'm new to octave and if this as been asked and answered then I'm sorry but I have no idea what the phrase is for what I'm looking for.
I trying to remove the DC component from a large matrix, but in chunks as I need to do calculations on each chuck.
What I got so far
r = dlmread('test.csv',';',0,0);
x = r(:,2);
y = r(:,3); % we work on the 3rd column
d = 1
while d <= (length(y) - 256)
e = y(d:d+256);
avg = sum(e) / length(e);
k(d:d+256) = e - avg; % this is the part I need help with, how to get the chunk with the right value into the matrix
d += 256;
endwhile
% to check the result I like to see it
plot(x, k, '.');
if I change the line into:
k(d:d+256) = e - 1024;
it works perfectly.
I know there is something like an element-wise operation, but if I use e .- avg I get this:
warning: the '.-' operator was deprecated in version 7
and it still doesn't do what I expect.
I must be missing something, any suggestions?
GNU Octave, version 7.2.0 on Linux(Manjaro).
Never mind the code works as expected.
The result (K) got corrupted because the chosen chunk size was too small for my signal. Changing 256 to 4096 got me a better result.
+ and - are always element-wise. Beware that d:d+256 are 257 elements, not 256. So if then you increment d by 256, you have one overlaying point.
I am trying to solve the following ODE using Octave, and in particular the function ode45.
dx/dt = x(1-x/2), 0<= t <= 10
with the initial condition x(0) = 0.5
But the graphs I get are not what I expect.
I think that the graph with red crosses represents x' vs x and not x vs t.
The code is the following:
clear all
close all
% Differential Equation: x' = x(1-x/2)
function dx = f(x,t)
dx = x*(1-x./2);
endfunction
% Exacte Solution: 2*e^t/(3+e^t)
function xexac =solexac(t)
xexac = (2*exp(t))./(3+exp(t));
endfunction
x0=0.5; %%Initial condition
T=10; %% maximum time T
t=[0:0.1:T]; %% we choose the times t(k) where is calculated 'y'
sol=ode45(#f,[0,T],x0); %% numerical solution of (E)
tt=sol.x;y=sol.y; %% extraction of the results
clf;hold on ; %% plot the exact and numerical solutionss
plot(tt,y,'xr')
plot(t,solexac(t),'-b')
xlabel('t')
ylabel('x(t)')
title('Chemostat Model')
legend("Numerical Solution","Exacte Solution ")
It would we great that any of you could help me with this code.
ode45 expects the ODE function to have arguments in the order (time, state), so exactly the other way around. What you effectively did was integrate t-t^2/2, and the resulting function 0.5+t^2/2-t^3/6 is what you got in the plot.