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
Please help me. I'm trying to learn Python and I'm very beginner. I tried reading and watching videos but I don't understand this logic:
def myFunction(y):
x = y + y #Local
print(x)
return x
x = 5 #Global
myFunction(x)
print(x)
I get the values 10 and 5.
Really, I can't understand why 10. This is breaking my mind. If x equals 5, than the result of the line 2 shouldn't be 2.5? I have 5 = y + y.
My mind is on a loop. Please help, you're my only hope.
You are passing x as the argument of your function myFunction().
Thus if x=5 you get:
myFunction(5):
x = 5 + 5
return(x) #10
this is why you are getting 10. If you change x=5 to x=10 you will see that the result of the function will be 20 and so on...
You are not replacing the x in the function itself. However, the x you stated will indeed remain a global variable and thus will be printed on the second line.
32-bit Octave has a limit on the maximum number of elements in an array. I have recompiled from source (following the script at https://github.com/calaba/octave-3.8.2-enable-64-ubuntu-14.04 ), and now have 64-bit indexing.
Nevertheless, when I attempt to perform elementwise multiplication using a broadcast function, I get error: out of memory or dimension too large for Octave's index type
Is this a bug, or an undocumented feature? If it's a bug, does anyone have a reasonably efficient workaround?
Minimal code to reproduce the problem:
function indexerror();
% both of these are formed without error
% a = zeros (2^32, 1, 'int8');
% b = zeros (1024*1024*1024*3, 1, 'int8');
% sizemax % returns 9223372036854775806
nnz = 1000 % number of non-zero elements
rowmax = 250000
colmax = 100000
irow = zeros(1,nnz);
icol = zeros(1,nnz);
for ind =1:nnz
irow(ind) = round(rowmax/nnz*ind);
icol(ind) = round(colmax/nnz*ind);
end
sparseMat = sparse(irow,icol,1,rowmax,colmax);
% column vector to be broadcast
broad = 1:rowmax;
broad = broad(:);
% this gives "dimension too large" error
toobig = bsxfun(#times,sparseMat,broad);
% so does this
toobig2 = sparse(repmat(broad,1,size(sparseMat,2)));
mult = sparse( sparseMat .* toobig2 ); % never made it this far
end
EDIT:
Well, I have an inefficient workaround. It's slower than using bsxfun by a factor of 3 or so (depending on the details), but it's better than having to sort through the error in the libraries. Hope someone finds this useful some day.
% loop over rows, instead of using bsxfun
mult_loop = sparse([],[],[],rowmax,colmax);
for ind =1:length(broad);
mult_loop(ind,:) = broad(ind) * sparseMat(ind,:);
end
The unfortunate answer is that yes, this is a bug. Apparently #bsxfun and repmat are returning full matrices rather than sparse. Bug has been filed here:
http://savannah.gnu.org/bugs/index.php?47175
I can't make matrices with variables in it for some reason. I get following message.
>>> A= [a b ;(-1-a) (1-b); (1+a) b]
error: horizontal dimensions mismatch (2x3 vs 1x1)
Why is it? Please show me correct way if I'm wrong.
In Matlab you first need to assign a variable before you can use it,
a = 1;
b = a+1;
This will thus give an error,
clear;
b = a+1; % ERROR! Undefined function or variable 'a
Matlab does never accept unassigned variables. This is because, on the lowest level, you do not have a. You will have machine code which is assgined the value of a. This is handled by the JIT compiler in Matlab, so you do not need to worry about this though.
If you want to use something as the variable which you have in maths you can specifically express this to matlab. The object is called a sym and the syntax that define the sym x to a variable xis,
syms x;
That said, you can define a vector or a matrix as,
syms a b x y; % Assign the syms
A = [x y]; % Vector
B = A= [a b ;(-1-a) (1-b); (1+a) b]; % Matrix.
The size of a matrix can be found with size(M) or for dim n size(M,n). You can calcuate the matrix product M3=M1*M2 if and only if M1 have the size m * n and M2 have the size n * p. The size of M3 will then be m * p. This will also mean that the operation A^N = A * A * ... is only allowed when m=n so to say, the matrix is square. This can be verified in matlab by the comparison,
syms a b
A = [a,1;56,b]
if size(A,1) == size(A,2)
disp(['A is a square matrix of size ', num2str(size(A,1)]);
else
disp('A is not square');
end
These are the basic rules for assigning variables in Matlab as well as for matrix multiplication. Further, a google search on the error error: 'x' undefined does only give me octave hits. Are you using octave? In that case I cannot guarantee that you can use sym objects or that the syntaxes are correct.
Let i = [1 2] and j = [3 5]. Now in octave:
arrayfun(#(x,y) x+y,i,j)
we get [4 7]. But I want to apply the function on the combinations of i vs. j to get [i(1)+j(1) i(1)+j(2) i(2)+j(1) i(2)+j(2)]=[4 6 5 7].
How do I accomplish this? I know I can go with for-loopsl but I want vectorized-code because it's faster.
In Octave, for finding summations between two vectors, you can use a truly vectorized approach with broadcasting like so -
out = reshape(ii(:).' + jj(:),[],1)
Here's a runtime test on ideone for the input vectors of size 1 x 100 each -
-------------------- With FOR-LOOP
Elapsed time is 0.148444 seconds.
-------------------- With BROADCASTING
Elapsed time is 0.00038299 seconds.
If you want to keep it generic to accommodate operations other than just summations, you can use anonymous functions like so -
func1 = #(I,J) I+J;
out = reshape(func1(ii,jj.'),1,[])
In MATLAB, you could accomplish the same with two bsxfun alternatives as listed next.
I. bsxfun with Anonymous Function -
func1 = #(I,J) I+J;
out = reshape(bsxfun(func1,ii(:).',jj(:)),1,[]);
II. bsxfun with Built-in #plus -
out = reshape(bsxfun(#plus,ii(:).',jj(:)),1,[]);
With the input vectors of size 1 x 10000 each, the runtimes at my end were -
-------------------- With FOR-LOOP
Elapsed time is 1.193941 seconds.
-------------------- With BSXFUN ANONYMOUS
Elapsed time is 0.252825 seconds.
-------------------- With BSXFUN BUILTIN
Elapsed time is 0.215066 seconds.
First, your first example is not the best because the most efficient way to accomplish what you're doing with arrayfun would be to vectorize:
a = [1 2];
b = [3 5];
out = a+b
Second, in Matlab at least, arrayfun is not necessarily faster than a simple for loop. arrayfun is mainly a convenience (especially for it's more advanced options). Try this simple timing example yourself:
a = 1:1e5;
b = a+1;
y = arrayfun(#(x,y)x+y,a,b); % Warm up
tic
y = arrayfun(#(x,y)x+y,a,b);
toc
y = zeros(1,numel(a));
for k = 1:numel(a)
y(k) = a(k)+b(k); % Warm up
end
tic
y = zeros(1,numel(a));
for k = 1:numel(a)
y(k) = a(k)+b(k);
end
toc
In Matlab R2015a, the for loop method is over 70 times faster run from the Command window and over 260 times faster when run from an M-file function. Octave may be different, but you should experiment.
Finally, you can accomplish what you want using meshgrid:
a = [1 2];
b = [3 5];
[x,y] = meshgrid(a,b);
out = x(:).'+y(:).'
which returns [4 6 5 7] as in your question. You can also use ndgrid to get output in a different order.