Mailman 3 October 2004 - SciPy-User

Has some met such a problem?
by libsvm 13 Oct '04

13 Oct '04

Hi everyone, I try to learn the ga (genetic algorithm) module of scipy, but when I run the example file in the $scipy_root/ga/ directory, it raise the following errors. Can someone help me? Any suggestion is welcome. Best wishes, Qingliang Errors like this: Warning: The key "migrants" in not a valid setting. The valid settings are ['pop_size', 'p_replace', 'p_cross', 'p_mutate', 'p_deviation', 'gens', 'rand_seed', 'rand_alg', 'dbase', 'update_rate'] Warning: The key "num_pops" in not a valid setting. The valid settings are ['pop_size', 'p_replace', 'p_cross', 'p_mutate', 'p_deviation', 'gens', 'rand_seed', 'rand_alg', 'dbase', 'update_rate'] initializing... seed = 1808493040 beigninning genome generation finished generation: 0.23 evals: 250 evaluation time: 0.03 gen: 0 max: 1.6958428271114823 dev: 0.59946054180519071 eval time: 0.33999999999999997 Traceback (most recent call last): File "/usr/lib/python2.2/site-packages/scipy/ga/examples.py", line 64, in ? ex1() File "/usr/lib/python2.2/site-packages/scipy/ga/examples.py", line 60, in ex1 galg.evolve() File "/usr/lib/python2.2/scipy/ga/algorithm.py", line 133, in evolve self.step() File "/usr/lib/python2.2/scipy/ga/algorithm.py", line 107, in step self.stats['mutations'] = self.stats['mutations'] + self.pop[sz:].mutate() File "/usr/lib/python2.2/scipy/ga/population.py", line 185, in mutate for ind in self: mutations = mutations + ind.mutate() File "/usr/lib/python2.2/scipy/ga/genome.py", line 94, in mutate if self.mutator.evaluate(self): File "/usr/lib/python2.2/scipy/ga/genome.py", line 158, in evaluate for gene in genome: mutated = gene.mutate() or mutated File "/usr/lib/python2.2/scipy/ga/gene.py", line 104, in mutate self._value = self.mutator.evaluate(self) File "/usr/lib/python2.2/scipy/ga/gene.py", line 196, in evaluate f = rv.norm(old,w)[0] AttributeError: rv_frozen instance has no attribute '__getitem__'

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ANN: SciPy 0.3.2 Released
by Pearu Peterson 13 Oct '04

13 Oct '04

Hi, Scipy 0.3.2 has been released and binaries are available from the scipy.org site: http://www.scipy.org Scipy 0.3.2 is a bug fix release of Scipy 0.3 including the following new features: - wxPython 2.5 support - reading/writing dense/sparse matrices in Matrix Market format - iterative solvers, new functions sqrtm, hessenberg - Constrained Optimization BY Linear Approximation - discrete Boltzmann, Planck, Levy distributions - Scipy tests pass now also on 64-bit systems and Mac OSX etc. The complete release notes can be found here: http://www.scipy.org/download/scipy_release_notes_0.3.2.html Best regards, Pearu BTW Scipy is: ------------- Scipy is an open source library of scientific tools for Python. Scipy supplements the popular Numeric module, gathering a variety of high level science and engineering modules together as a single package. Scipy includes modules for graphics and plotting, optimization, integration, special functions, signal and image processing, genetic algorithms, ODE solvers, and others.

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Help needed: Problem in translating a file read routine from Matlab to Python-Scipy
by Guasina Luca 12 Oct '04

12 Oct '04

I am trying to translate a Matlab program to Python - Scipy. The task consist of reading a big data file from a FORTRAN code; the file is written UNFORMATTED and contain a series of arrays. Anyone can help me ? I am new user of Python and Scipy... I am working in Windows XP with IDLE 1.02 and Python 2.3.3 See the attached files: luca.zip contain 5 files: a test data file named luca.grm (202k) a MATLAB program workin OK named luca.m his output output_matlab.txt My program in Python (NOT working) named luca.py his output named output_python.txt . (D:\U\work\bin is my working directory) In the test I try to read just the first part of the file: The first lines contain a first array of size 4 = (nx,ny,nz,ndiel); nx, ny, nz, ndiel are the dimensions of arrays that follow. Then I have in the file nx float that I want to read in the array x (... And then others arrays follows ...) In the example nx=1000, ny=10, nz=5, ndiel=12 . The MATLAB program read correctly the first lines and nx=1000 data in the x array My luca.py read nx=1000 but the statement x = numpyio.fread(fid,nx,'f') only read 151 data... I don't understand why! ?! You can see that in the luca.m I need to skip 2 data for every reading, cooresponding to som FORTRAN record mark using: nu = fread(fid,2,'float32'); (Matlab) I do the same in luca.py using: nu = numpyio.fread(fid,2,'f') Any suggestion ? Thanks ! Luca

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Rank-Revealing QR factorization of dense matrices in scipy
by Nils Wagner 12 Oct '04

12 Oct '04

Hi all, Has someone written a function for Rank-Revealing QR factorization of dense matrices in scipy ? Is there a function to determine the numerical rank of a matrix in scipy ? Any pointer would be appreciated. Nils

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upgrading to scipy 0.3.2
by Manoj Kumar Singh 12 Oct '04

12 Oct '04

I have installed scipy 0.3 and want to upgrade to scipy 0.3.2. I used 'python setup.py install' command to install scipy 0.3 and its prerequisites. Should i use the same command 'python setup.py install' to scipy_core 0.3.2 and scipy 0.3.2 to upgrade or something else is also needed? I am working with fedora core 2 and python 2.3.4. Thanks in advance Manoj

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Unexpected behavior (bug?): scipy x Numeric.argmin
by krivilli＠unberwoot.net 11 Oct '04

11 Oct '04

HI, -I got myself confused by a strange (for me at least) 'problem' since I dont know much about Numpy and how, sometimes, some operations that seems to be the same, arent (like matrix[i,j] instead of matrix[i][j]). -So let me show what my problem is: #################### import Numeric def MakeLC(matrix,vz): tmp=matrix>=vz # boolean matrix tmp=Numeric.argmin(tmp,0) print tmp if __name__=="__main__": Matrix = [ Numeric.zeros(20), Numeric.array([-0.0123,-0.0156,-0.0199,-0.0254,-0.0267,-0.0285,-0.313,-0.376,-0.0475,-0.0534,-0.0578,-0.0634,-0.0679,-0.0735,-0.0879,-0.0981,-0.112,-0.115,-0.116,-0.118]), Numeric.array([0.0023, 0.0056,0.0099,0.0054,0.0067,0.0085,0.013,0.076,0.0075,0.0034,0.0078,0.0034,0.0079,0.0035,0.0079,0.0081,0.012,0.015,0.016,0.018]), Numeric.array([0.0103,0.0106,0.0109,0.0204,0.0207,0.0205,0.303,0.306,0.0405,0.0504,0.0508,0.0604,0.0609,0.0705,0.0809,0.0901,0.102,0.105,0.106,0.108]), Numeric.array([0.1120,0.1006,0.1009,0.1004,0.1007,0.1200,0.100,0.206,0.2405,0.2504,0.2508,0.2604,0.2609,0.2705,0.2809,0.3081,0.302,0.335,0.306,0.318]), Numeric.array([0.0983,0.0876,0.0854,0.0834,0.0813,0.0798,0.776,0.071,0.0678,0.0630,0.0634,0.0610,0.0588,0.0564,0.0580,0.0522,0.050,0.048,0.040,0.036])] Matrix = Numeric.array(Matrix) LC=MakeLC(Matrix,-0.0564) #################### -Output for this is: [0 0 0 0 0 0 1 1 0 0 1 1 1 1 1 1 1 1 1 1] -But when I have "import scipy" on the head of file like in: #################### import scipy import Numeric . . . (rest is identical) -The output is now: [0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0] -The same occurs even if I dont use 'import Numeric' and use 'scipy.argmin', 'scipy.zeros' and 'scipy.array' instead. -The 'problem' seems to go away when we replace in Numeric.py, the following line (line:295, Numpy version 23.5) 295c295 < a = -array(a, copy=0) --- > a = -1*array(a, copy=0) -Any hint is welcome! regards, -- roberto janny (krivilli)

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question marks in xplt.eps generated files
by Nils Wagner 08 Oct '04

08 Oct '04

Hi all, I found some mysterious question marks in xplt.eps generated files. (see attachment) Nils

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Re: Numeric 23.6 ?
by Travis Oliphant 07 Oct '04

07 Oct '04

Nils Wagner wrote: > Travis, > > please can you provide a new release including the latest bugfixes ? > > Thanks in advance. > > Nils > Just go and get a new Numeric-23.5 --- I must have messed up which tarball got put on Sourceforge. -Travis

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Sparse format support in io.loadmat
by Nils Wagner 07 Oct '04

07 Oct '04

Hi all, AFAIK there is no support for reading sparse matrices via io.loadmat. Traceback (most recent call last): File "io.py", line 2, in ? print io.loadmat('test.mat', appendmat=0) File "/usr/lib/python2.3/site-packages/scipy/io/mio.py", line 744, in loadmat raise ValueError, "Cannot handle sparse matrices, yet." ValueError: Cannot handle sparse matrices, yet. Since io has many new features e.g. Matrix Market (and hopefully NASTRAN's op4 in the near future) it would be nice to have support for sparse matrices in io.loadmat. Any comments ? Nils

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from scipy.cplt import *
by Nils Wagner 07 Oct '04

07 Oct '04

Travis, Unfortunately, I cannot confirm your statement. >>> from scipy.xplt import * Traceback (most recent call last): File "<stdin>", line 1, in ? File "/usr/lib/python2.3/site-packages/scipy_base/ppimport.py", line 303, in __getattr__ module = self._ppimport_importer() File "/usr/lib/python2.3/site-packages/scipy_base/ppimport.py", line 262, in _ppimport_importer raise PPImportError,\ scipy_base.ppimport.PPImportError: Traceback (most recent call last): File "/usr/lib/python2.3/site-packages/scipy_base/ppimport.py", line 273, in _ppimport_importer module = __import__(name,None,None,['*']) File "/usr/lib/python2.3/site-packages/scipy/xplt/__init__.py", line 12, in ? from Mplot import * File "/usr/lib/python2.3/site-packages/scipy/xplt/Mplot.py", line 1015, in ? import colorbar File "/usr/lib/python2.3/site-packages/scipy/xplt/colorbar.py", line 9, in ? from slice3 import * File "/usr/lib/python2.3/site-packages/scipy/xplt/slice3.py", line 1581, in ? _poly_permutations4 = _construct3 (0) File "/usr/lib/python2.3/site-packages/scipy/xplt/slice3.py", line 1575, in _construct3 mask = find_mask (below, _node_edges3 [itype]) TypeError: Array can not be safely cast to required type >>> scipy.__version__ '0.3.1_287.4326' Any pointer ? Nils

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