Mailman 3 May 2009 - SciPy-User

basic usage of fmin_tnc and fmin_l_bfgs_b
by physeco 31 May '09

31 May '09

I'm new to multidimensional optimization with scipy. Sorry for asking the simple question, but I can't figure out the syntax for fmin_tnc and fmin_l_bfgs_b. Here's a simple example of the error I'm getting: Executing: >def f(x): return (x[0]*x[1]-1)**2+1 >g=0.1,0.1 >b=[(-10,10),(-10,10)] >so.fmin_tnc(f,g,bounds=b) Leads to the error: --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- /usr/lib/python2.5/site-packages/scipy/optimize/tnc.py in fmin_tnc(func, x0, fprime, args, approx_grad, bounds, epsilon, scale, offset, messages, maxCGit, maxfun, eta, stepmx, accuracy, fmin, ftol, xtol, pgtol, rescale) 244 rc, nf, x = moduleTNC.minimize(func_and_grad, x0, low, up, scale, offset, 245 messages, maxCGit, maxfun, eta, stepmx, accuracy, --> 246 fmin, ftol, xtol, pgtol, rescale) 247 return array(x), nf, rc 248 /usr/lib/python2.5/site-packages/scipy/optimize/tnc.py in func_and_grad(x) 203 def func_and_grad(x): 204 x = asarray(x) --> 205 f, g = func(x, *args) 206 return f, list(g) 207 else: <type 'exceptions.TypeError'>: 'numpy.float64' object is not iterable --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- I get a similar error from so.fmin_l_bfgs_b(f,g,bounds=b). If you can point out my mistake, it would be greatly appreciate. Thank you! -- View this message in context: http://www.nabble.com/basic-usage-of-fmin_tnc-and-fmin_l_bfgs_b-tp23798939p… Sent from the Scipy-User mailing list archive at Nabble.com.

3 4

how to find projection of a point to subspace?
by Dmitrey 31 May '09

31 May '09

hi all, Suppose I have point x = [x0, ..., xn-1] and linear subspace defined by Ax=b, A is m x n matrix, b is vector of length m. What is the best way to find projection of the point x to the subspace? (Suitable for ill-conditioned cases) Does anyone have some code (preferably Python or MATLAB)? Search in google yields 1st place for the article http://cat.inist.fr/?aModele=afficheN&cpsidt=18593975 but the one is unavailable for free. Thank you in advance, D.

2 2

Stineman interpolation
by Krishna Bhagavatula 30 May '09

30 May '09

Hi, Stineman interpolation is supposed to be a well behaved method of interpolation. Can someone explain why it's behaving wildly in a simple case: x = (0, 10, 70, 100) y = (0, 535, 595, 1000) xx = arange(0,100,1) yy = stineman_interp(xx,x,y,yp=None) plot(x,y,'x') plot(xx,yy) Are there any exceptions when it does not behave well?

3 3

f2py problem
by Dmitrey 30 May '09

30 May '09

Hi all, I try to construct a Python wrapper around the fortran routine toms587, you can download it here: ftp://ftp.linux.kiev.ua/pub/projects/openopt/files/soft/toms587.f So I invoke f2py -c -m toms587 toms587.f Then I try to run the code: from toms587 import lsei from numpy import * W = array([8.94558004, 7.3286058, 3.0, 2.05011463, 0.43314039, 70.31767878, -12.29662251, -13.91359675, 75.74379415]) me,ma,mg,n,prgopt,xf,rnorme,rnorml,mode,ws,ip = 0, 3, 0, 2, ravel(1.), ravel(0.), -15.0, -15.0, -15, ravel(-15.), array((-15, -15, -15)) lsei(W,me,ma,mg,n,prgopt,xf,rnorme,rnorml,mode,ws,ip) StdErr: *** glibc detected *** /usr/bin/python: free(): invalid next size (fast): 0x0000000000cfb390 *** Any ideas? I use KUBUNTU 9.04, AMD 3800+ X2. Thank you in advance, D.

1 0

Re: [SciPy-user] creating an array with changing resolution
by Oz Nahum 30 May '09

30 May '09

>You can also write: >In [30]:r_[1:10:3, 10:20:2] >Out[30]:array([ 1, 4, 7, 10, 12, 14, 16, 18]) Thanks Eike, That does the trick, Oz.

1 0

creating an array with changing resolution
by Oz Nahum 30 May '09

30 May '09

Hi everyone I have an X,Y domain I would like to explore in different detail levels. In octave, I can define a vector like: v = [1:1:40,40:0.1:50,50:1:100] is this the only way to do it in numpy ? v = numpy.r_[arange(0.0,40.0, 1),arange(40.0,50.0, 0.1),arange(50.0,100.0, 1)] Not that it's bad, but i just thought maybe there's another way to do it. Thanks in advance for any suggestion Oz. -- ---- Imagine there's no countries It isn't hard to do Nothing to kill or die for And no religion too Imagine all the people Living life in peace -- ---- Imagine there's no countries It isn't hard to do Nothing to kill or die for And no religion too Imagine all the people Living life in peace

2 1

Strange discontinuity in noncentral chisquare
by Neal Becker 29 May '09

29 May '09

def pmiss2 (x, esnodB, N): esno = 10**(0.1 * esnodB) * N var = 1/esno _lambda = 1/(0.5*var) return ncx2.cdf (x, 2, _lambda) x = np.arange (0, 50, 0.1) p1 = [pmiss2 (e, 3.5, 24) for e in x] What's with this strange discontinuity? print p1: ... 3.475382846574262e-21, 4.2226227741362447e-21, 5.1248671653198949e-21, 6.2130949241675783e-21, 7.5242411687161146e-21, 9.1022970542215721e-21, 5.8787514615651664e-09, 6.2565279721932619e-09, 6.656924144742753e-09, 7.0811937641411923e-09, 7.5306544171300622e-09, 8.0066904400027596e-09, 8.5107559880675483e-09, 9.044378231221098e-09, 9.6091606801490766e-09, ...

3 6

Install failure on AIX 5.3 due to missing linker flag prefix for compiler
by Loris Bennett 29 May '09

29 May '09

Hi, I am trying to install SciPy 0.7.0 on AIX 5.3. I have managed to install NumPy 1.3.0 (although there was a minor problem there: http://bugs.python.org/issue941346 Now I am getting the following error when I try to install SciPy: g++ g++ -pthread -bI:/opt/sw/python/Python-2.6.2/lib/python2.6/config/python.exp build/temp.aix-5.3-2.6/scipy/interpolate/src/_interpolate.o -Lbuild/temp.aix-5.3-2.6 -o build/lib.aix-5.3-2.6/scipy/interpolate/_interpolate.so g++: '-b' must come at the start of the command line g++: '-b' must come at the start of the command line error: Command "g++ g++ -pthread -bI:/opt/sw/python/Python-2.6.2/lib/python2.6/config/python.exp build/temp.aix-5.3-2.6/scipy/interpolate/src/_interpolate.o -Lbuild/temp.aix-5.3-2.6 -o build/lib.aix-5.3-2.6/scipy/interpolate/_interpolate.so" failed with exit status 1 This is essentially the same problem, in that parameters which need to be passed to the linker need to be prefixed with "-Wl,", which does not happen. The problem has been reported here: http://www.mail-archive.com/numpy-discussion@scipy.org/msg02578.html but the solution there no longer applies to the current sources. Any help will be much appreciated. Loris -- Dr. Loris Bennett Computer Centre Freie Universität Berlin Berlin, Germany

2 2

linear regression
by jason-sage＠creativetrax.com 29 May '09

29 May '09

Is there a recommended way now of calculating the slope of a linear regression? Using the scipy.stats.linregress function gives a deprecation warning, apparently because that function uses the scipy.mean function: sage: import numpy sage: import scipy.stats sage: scipy.stats.linregress(numpy.asarray([4,3,2,1,2,3,4]), numpy.asarray([1,2,3,4,3,2,1])) /home/jason/download/sage-sage-4.0.alpha0.5/local/lib/python2.5/site-packages/scipy/stats/stats.py:420: DeprecationWarning: scipy.stats.mean is deprecated; please update your code to use numpy.mean. Please note that: - numpy.mean axis argument defaults to None, not 0 - numpy.mean has a ddof argument to replace bias in a more general manner. scipy.stats.mean(a, bias=True) can be replaced by numpy.mean(x, axis=0, ddof=1). axis=0, ddof=1).""", DeprecationWarning) (-1.0, 5.0, -1.0, 1.9206748078018268e-50, 0.0) This is scipy 0.7.0. Thanks, Jason -- Jason Grout

7 31

pcolor plot with points from a data file?
by Joseph Smidt 28 May '09

28 May '09

Hi, I need a plot that looks just like this: http://matplotlib.sourceforge.net/examples/pylab_examples/pcolor_demo.html. However, I need it to be done for a 100x100 matrix I am providing from a data file called clout.dat that looks like: 1.22 1.22 1.24 ... 6.78 ... 3.43 3.46 3.52 ... 1.11 Is there a way to make that same type of plot for using a data file like this? Thanks. Joseph Smidt -- ------------------------------------------------------------------------ Joseph Smidt <josephsmidt(a)gmail.com> Physics and Astronomy 4129 Frederick Reines Hall Irvine, CA 92697-4575 Office: 949-824-3269

2 1