Mailman 3 March 2008 - SciPy-User

indexes in very large matrices
by Kurt J 17 Mar '08

17 Mar '08

Hi List, I have a rather large matrix (15k x 15k) and I was hoping there was a nice efficient way to search thru it. Currently I am just using for loops to go thru the rows and columns... for i, iKey in enumerate(self.matrixKey): > for j, jKey in enumerate(self.matrixKey): > if self.matrix[i][j] <= threshold and not self.matrix[i][j] > == 0.0: > print "threshold at " + str(iKey) + " and " +str(jKey) > Can I do something more clever? Quicker? BTW Numpy and Scipy rock!!! Cheers, Kurt J

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by edschofield＠gmail.com 17 Mar '08

17 Mar '08

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hello
by edschofield＠gmail.com 17 Mar '08

17 Mar '08

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array slice problems ...
by Stef Mientki 16 Mar '08

16 Mar '08

hello, from any input ( list, 1-dim array, 2-dim array), I need to take a slice and pass it as a 2-dimensional array. But I'm having trouble with taking slices from such an array. If I have a 2-dimensional array [[1 2 3 4]] then a_array [:][1:3] returns an empty 2-dimensional array. while I think the expression means: - take all elements along the first axis - then take from each of the found elements, the subelements 1 up to 3 which certainly shouldn't be empty ??? I also tried with a real 2-dimensional array, with the same results :-( What am I doing wrong ? Maybe someone can enlighten me about array slices. (a copy of the program is below) thanks, Stef Mientki from numpy import * ## VERSION 1.0.3.dev3722 # whatever I get, I must construct a 2-dimensional array # where the first axis is the signal # and the second axis are the datasamples of that signal a_list = [ 1,2,3,4 ] a_array = array ( a_list ) a_array = a_array.reshape ( len ( a_array ), 1 ) r = a_array print '2-dim array',r.shape, r.ndim, r ## 1-dim array (1, 4) 2 [[1 2 3 4]] r = a_array [:] print '2-dim array [:]',r.shape, r.ndim, r ## 1-dim array [:] (1, 4) 2 [[1 2 3 4]] # DOESN'T WORK r = a_array [:][1:3] print '2-dim array [:][1:3]',r.shape, r.ndim, r ## 1-dim array [:][1:3] (0, 4) 2 [] # WORKS b = a_array [0] b = b [1:3] b = b.reshape ( 1, len ( b ) ) r = b print '1-dim array special',r.shape, r.ndim, r ## 1-dim array special (1, 2) 2 [[2 3]]

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Pb with scipy.interpolate.spalde and numpy.float64
by LB 16 Mar '08

16 Mar '08

Hi, scipy.interpolate.spalde accepts float as first argument but does not work with numpy.float64 : With python's float : In [166]: c, type(c) Out[166]: (0.52752752752752752, <type 'float'>) In [167]: x, y = interpolate.spalde(c, tck) => no pb. With numpy.float64 : In [168]: b, type(b) Out[168]: (0.52752752752752752, <type 'numpy.float64'>) In [169]: x, y = interpolate.spalde(b, tck) --------------------------------------------------------------------------- <type 'exceptions.TypeError'> Traceback (most recent call last) /home/loic/Python/test_profil/<ipython console> in <module>() /home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/ interpolate/fitpack.py in spalde(x, tck) 575 parametric = False 576 if parametric: --> 577 return _ntlist(map(lambda c,x=x,t=t,k=k:spalde(x, [t,c,k]),c)) 578 else: 579 try: x=x.tolist() /home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/ interpolate/fitpack.py in <lambda>(c, x, t, k) 575 parametric = False 576 if parametric: --> 577 return _ntlist(map(lambda c,x=x,t=t,k=k:spalde(x, [t,c,k]),c)) 578 else: 579 try: x=x.tolist() /home/loic/tmp/bluelagoon/lib/python2.5/site-packages/scipy/ interpolate/fitpack.py in spalde(x, tck) 581 try: x=list(x) 582 except: x=[x] --> 583 if len(x)>1: 584 return map(lambda x,tck=tck:spalde(x,tck),x) 585 d,ier=_fitpack._spalde(t,c,k,x[0]) <type 'exceptions.TypeError'>: object of type 'float' has no len() It seems to come from the method 'tolist' of numpy.float64, which does not return a list : In [174]: c.tolist() --------------------------------------------------------------------------- <type 'exceptions.AttributeError'> Traceback (most recent call last) /home/loic/Python/test_profil/<ipython console> in <module>() <type 'exceptions.AttributeError'>: 'float' object has no attribute 'tolist' In [175]: b.tolist() Out[175]: 0.52752752752752752 So my question is : why do numpy.float64 have a tolist method, and why does it not return a list ? for information, In [179]: numpy.__version__, scipy.__version__ Out[179]: ('1.0.5.dev4854', '0.7.0.dev4004') -- LB

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Zeros
by Natali Melgarejo Diaz 15 Mar '08

15 Mar '08

Good afternoon to everyone!! I want to make a column vector using numpy, like in Matlab when you do zeros(N,1). I've been doing it with zeros(N) and i already get an array. It maybe be the same but the results get are different with the formulas involved. Thanks ;)) ********Natali********

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[optimization] OpenOpt 0.17
by dmitrey 15 Mar '08

15 Mar '08

Greetings, We're pleased to announce: OpenOpt 0.17 (release), free (license: BSD) optimization framework for Python language programmers, is available for download. Changes since previous release 0.15 (December 15): * new classes: GLP (global problem), MMP (mini-max problem) * several new solvers written: goldenSection, nsmm * some more solvers connected: scipy_slsqp, bvls, galileo * possibility to change default solver parameters * user-defined callback functions * changes in auto derivatives check * "noise" parameter for noisy functions * some changes to NLP/NSP solver ralg * some changes in graphical output, initial estimations xlim, ylim * scaling * some bugfixes Newsline: http://openopt.blogspot.com/ Homepage: http://scipy.org/scipy/scikits/wiki/OpenOpt

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Matplotlib improper rendering of latex
by David Arnold 14 Mar '08

14 Mar '08

All, I have: #! /usr/local/bin/python from pylab import * x=arange(0,2,0.01) y=2*sin(2*pi*(x-pi/4)) plot(x,y) xlabel('x-axis') ylabel('y-axis') title(r'$y=2\sin (2\pi(x-\pi/4))$') show() Running gives me this error: code $ python simple.py --verbose-helpful matplotlib data path /Library/Frameworks/Python.framework/Versions/ 2.5/lib/python2.5/site-packages/matplotlib/mpl-data $HOME=/Users/darnold CONFIGDIR=/Users/darnold/.matplotlib loaded rc file /Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/site-packages/matplotlib/mpl-data/matplotlibrc matplotlib version 0.90.1 verbose.level helpful interactive is False units is True platform is darwin numerix numpy 1.0.4 font search path ['/Library/Frameworks/Python.framework/Versions/2.5/ lib/python2.5/site-packages/matplotlib/mpl-data/fonts/ttf', '/Library/ Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/ matplotlib/mpl-data/fonts/afm'] loaded ttfcache file /Users/darnold/.matplotlib/ttffont.cache backend TkAgg version 8.4 Could not match Bitstream Vera Serif, New Century Schoolbook, Century Schoolbook L, Utopia, ITC Bookman, Bookman, Nimbus Roman No9 L, Times New Roman, Times, Palatino, Charter, serif, normal, normal. Returning /Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/site-packages/matplotlib/mpl-data/fonts/ttf/Vera.ttf Could not match Bitstream Vera Serif, New Century Schoolbook, Century Schoolbook L, Utopia, ITC Bookman, Bookman, Nimbus Roman No9 L, Times New Roman, Times, Palatino, Charter, serif, normal, normal. Returning /Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/site-packages/matplotlib/mpl-data/fonts/ttf/Vera.ttf Exception in Tkinter callback Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/lib-tk/Tkinter.py", line 1403, in __call__ return self.func(*args) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/site-packages/matplotlib/backends/backend_tkagg.py", line 151, in resize self.show() File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/site-packages/matplotlib/backends/backend_tkagg.py", line 154, in draw FigureCanvasAgg.draw(self) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/site-packages/matplotlib/backends/backend_agg.py", line 392, in draw self.figure.draw(renderer) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/site-packages/matplotlib/figure.py", line 601, in draw for a in self.axes: a.draw(renderer) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/site-packages/matplotlib/axes.py", line 1286, in draw a.draw(renderer) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/site-packages/matplotlib/text.py", line 410, in draw bbox, info = self._get_layout(renderer) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/site-packages/matplotlib/text.py", line 255, in _get_layout line, self._fontproperties, ismath=self.is_math_text()) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/site-packages/matplotlib/backends/backend_agg.py", line 246, in get_text_width_height s, self.dpi.get(), prop.get_size_in_points()) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/site-packages/matplotlib/mathtext.py", line 1587, in __call__ handler.expr.set_size_info(fontsize, dpi) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/site-packages/matplotlib/mathtext.py", line 1203, in set_size_info self.elements[0].set_size_info(self._scale*fontsize, dpi) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/site-packages/matplotlib/mathtext.py", line 1114, in set_size_info Element.set_size_info(self, fontsize, dpi) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/site-packages/matplotlib/mathtext.py", line 1027, in set_size_info element.set_size_info(self.fontsize, dpi) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/site-packages/matplotlib/mathtext.py", line 1114, in set_size_info Element.set_size_info(self, fontsize, dpi) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/site-packages/matplotlib/mathtext.py", line 1027, in set_size_info element.set_size_info(self.fontsize, dpi) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/site-packages/matplotlib/mathtext.py", line 1114, in set_size_info Element.set_size_info(self, fontsize, dpi) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/site-packages/matplotlib/mathtext.py", line 1027, in set_size_info element.set_size_info(self.fontsize, dpi) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/site-packages/matplotlib/mathtext.py", line 1116, in set_size_info self.font, self.sym, self.fontsize, dpi) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/site-packages/matplotlib/mathtext.py", line 597, in get_metrics self._get_info(font, sym, fontsize, dpi) File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ python2.5/site-packages/matplotlib/mathtext.py", line 616, in _get_info raise ValueError('unrecognized symbol "%s"' % sym) ValueError: unrecognized symbol "\sin"

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How to forbid a standard output of OpenOpt solvers
by 302302 13 Mar '08

13 Mar '08

Hi, I've used linear solver (cvxopt_glpk) from OpenOpt. Can I somehow forbid a printing description of solving problem to the standard output? I supposed there should be some parameter in the running command, but I can't find any useful documentation with this topic. example of standard output of th solver: starting solver cvxopt_glpk (license: GPL v.2) with problem unnamed lpx_simplex: original LP has 135 rows, 51 columns, 755 non-zeros lpx_simplex: presolved LP has 80 rows, 51 columns, 700 non-zeros lpx_adv_basis: size of triangular part = 80 0: objval = 0.000000000e+00 infeas = 1.000000000e+00 (0) 56: objval = 6.888030023e+01 infeas = 0.000000000e+00 (0) * 56: objval = 6.888030023e+01 infeas = 0.000000000e+00 (0) * 86: objval = 4.104563153e+01 infeas = 0.000000000e+00 (0) OPTIMAL SOLUTION FOUND solver cvxopt_glpk has finished solving the problem unnamed istop: 1000 (optimal) Solver: Time Elapsed = 0.01 CPU Time Elapsed = 0.01 objFunValue: 41.0456315344 (feasible, max constraint = 8.88178e-16) python's executing commands p = LP(f, A=A, b=b, lb=lb, ub=ub) r = p.solve('cvxopt_glpk') Thanks Cz

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Python Spreadsheet with Python as Core Macro Language
by luis cota 13 Mar '08

13 Mar '08

Has anyone seen a Python spreadsheet with Python as the core macro language? I'm aware of IronPython and this is about as close as I have seen to what I am looking for except that it runs on the wrong OS and can't use the standard python libraries. :) I've run into a few other options that look promising, just not.quite.theresuch as GNU Numeric, OpenOffice, and Picalo. All I'm looking for is a basic grid that i can use to dynamically test functions and to print results for evaluation. Perhaps what is needed is a new project using a wxPython grid? - Luis

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