Scipy
Scipy is a big Python library often compared with Matlab. Its homepage is at http://www.scipy.org
It is sponsored by the company Enthought but the software itself is open-source. The major field of application is numerical computing, in mathematics, science and engineering.
Scipy depends on NumPy (related to Numeric) which provides fast array manipulation. Yet it is not a pure Python library. Rather than rewriting from scratch in pure Python the reliable algorithms already implemented in Fortran in EISPACK, LAPACk, ATLAS, FFTW libraries, Scipy instead offers Python interfaces to these compiled "native machine" routines. The result is that Scipy is fast!. Scipy installs and runs in most architectures and what's more, it is free. More and more scientific computing people are using Scipy each day. Most users have encountered problems in the installation of Scipy and it will be compounded if you don't have enough memory and hard disk space to install and your chosen OS distribution does not have a good package manager.
People wonder why Scipy is not well known such or as widely adopted as R. I guess we can blame it more on freedom of choice. There is no standard gui for Scipy for example, and there is no SINGLE plotting package for Scipy. You can use MATPLOTLIB, chaco, and others with scipy.
Scipy Optimize optimization library
Well in this article, we shall focus on the optimization library called "optimize". Various algorithms are available from Nelder Mead to BGSS to Newton conjugate gradient and others.
Lets try the example in the tutorial which uses the Nelder Mead algorithm and requires function evaluations only.
The Rosenbrock function and fmin (Nelder-Mead)
The definition of the Rosenbrock function is given by
$$!\sum_{i=1}^{n-1] 100(X_i-X_{i-1}^2)^2 + (1 - x_{i-1})^2$$
Here is the implementation code from the tutorial:
from scipy.optimize import fmin
def rosen(x): # The Rosenbrock function
return sum(100.0*(x[1:]-x[:-1]**2.0)**2.0 + (1-x[:-1])**2.0)
def rosen_der(x):
xm = x[1:-1]
xm_m1 = x[:-2]
xm_p1 = x[2:]
der = zeros(x.shape,x.typecode())
der[1:-1] = 200*(xm-xm_m1**2) - 400*(xm_p1 - xm**2)*xm - 2*(1-xm)
der[0] = -400*x[0]*(x[1]-x[0]**2) - 2*(1-x[0])
der[-1] = 200*(x[-1]-x[-2]**2)
return der
x0 = [1.3, 0.7, 0.8, 1.9, 1.2]
xopt = fmin(rosen, x0)
print xopt
Function rosen() evaluates the famous Rosenbrock "Banana" function. The dimension of the function is implied by the size of the input x numpy array. Notice that the function is written in vector form which may not be familiar to most Python programmers outside of scientific computing.
Function rosen_der() returns the derivative or gradient vector which we shall use in the future. Again vector processing is used resulting in more compact code and we hope more understandable as one is more exposed to this kind of programming. When the above code is run it prints in my computer the following output:
python rosenbrock.py
Optimization terminated successfully.
Current function value: 0.000066
Iterations: 141
Function evaluations: 243
[ 0.99910115 0.99820923 0.99646346 0.99297555 0.98600385]
Contrast this with the output from the tutorial:
x0 = [1.3, 0.7, 0.8, 1.9, 1.2]
>>> xopt = fmin(rosen, x0)
Optimization terminated successfully.
Current function value: 0.000000
Iterations: 516
Function evaluations: 825
>>> print xopt
[ 1. 1. 1. 1.
1.]
why the difference. We think that a lot of things have changed like the default values for input arguments since the tutorial. If you look at the help file for fmin under IPython,
Documentation for fmin
fmin(func, x0, args=(), xtol=0.0001, ftol=0.0001, maxiter=None, maxfun=None, full_output=0, disp=1, retall=0, callback=None)
Minimize a function using the downhill simplex algorithm.
:Parameters:
func : callable func(x,*args)
The objective function to be minimized.
x0 : ndarray
Initial guess.
args : tuple
Extra arguments passed to func, i.e. ``f(x,*args)``.
callback : callable
Called after each iteration, as callback(xk), where xk is the
current parameter vector.
:Returns: (xopt, {fopt, iter, funcalls, warnflag})
xopt : ndarray
Parameter that minimizes function.
fopt : float
Value of function at minimum: ``fopt = func(xopt)``.
iter : int
Number of iterations performed.
funcalls : int
Number of function calls made.
warnflag : int
1 : Maximum number of function evaluations made.
2 : Maximum number of iterations reached.
allvecs : list
Solution at each iteration.
*Other Parameters*:
xtol : float
Relative error in xopt acceptable for convergence.
ftol : number
Relative error in func(xopt) acceptable for convergence.
maxiter : int
Maximum number of iterations to perform.
:
Calling the fmin function with both xtol and ftol set to 1.0e-5 resulted in much closer matching output:
python rosenbrock.py
Optimization terminated successfully.
Current function value: 0.000000
Iterations: 267
Function evaluations: 444
[ 1.00000002 0.99999975 0.99999956 0.9999988 0.9999975 ]
