Mailman 3 September 2003 - SciPy-User

Kronecker product kron(a,b)
by Nils Wagner Sept. 24, 2003

Sept. 24, 2003

Dear experts, There is another useful function which might be interesting for scipy, the so-called Kronecker product of two matrices. def kron(a,b): if not a.iscontiguous(): a = reshape(a, a.shape) if not b.iscontiguous(): b = reshape(b, b.shape) o = outerproduct(a,b) o.shape = a.shape + b.shape return concatenate(concatenate(o, axis=1), axis=1) It would be great, if this becomes a standard function in scipy. Any comments ? Nils

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Matrix sign function
by Nils Wagner Sept. 24, 2003

Sept. 24, 2003

Dear experts, It would be nice to have the matrix sign function in scipy. Nils Reference: Spectral decomposition of a matrix using the generalized sign matrix, Applied Mathematics and Computation, Vol.8 (1981) pp. 237-250

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SciPy 0.2 release
by Travis Oliphant Sept. 24, 2003

Sept. 24, 2003

We are going to release SciPy 0.2 next week (Thursday 1:00pm Central Time). Please report any remaining outstanding issues that must be resolved before we tag the CVS tree with the release number. SciPy will still undergo improvements so SciPy 0.3 does not have to be far behind. Thanks for all of your reports so far. -Travis Oliphant

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issue for 0.2: python2.3 float deprecation warnings ???
by Gary Pajer Sept. 24, 2003

Sept. 24, 2003

I'm sure you're on to this issue, but I can't find much mention of it: E.g.:, with python2.3 *only* >>from scipy import plt >>plt.plot((1., 2., 3.)) /usr/local/lib/python2.3/site-packages/wxPython/gdi.py:283: DeprecationWarning: integer argument expected, got float self.this = gdic.new_wxColour(*_args,**_kwargs) /usr/local/lib/python2.3/site-packages/wxPython/gdi.py:570: DeprecationWarning: integer argument expected, got float val = gdic.wxDC_DrawRotatedText(self, *_args, **_kwargs) /usr/local/lib/python2.3/site-packages/wxPython/gdi.py:702: DeprecationWarning: integer argument expected, got float val = gdic.wxDC_SetClippingRegion(self, *_args, **_kwargs) these warnings have something to do with a change made in python in going to v. 2.3. I can't tell if the problem is with scipy or wxPython. I checked the wxPython bug tracker and mailing list archive, and it's mentioned there with the advice to clean up one's source code. -Gary

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New bmat constructor in SciPy
by Travis E. Oliphant Sept. 23, 2003

Sept. 23, 2003

One of SciPy's goals is to ease transition to Python for Matlab users. In that light r_[] and c_[] were added some time ago (but perhaps not well documented) As I mentioned before F = r_[c_[A,B],c_[C,D]] would construct F = [A B] [C D] now, a new function has been added that does the same thing, but also creates a matrix object. bmat (short for build matrix) bmat([[A,B],[C,D]]) = bmat('A,B; C,D') = bmat(r_[c_[A,B],c_[C,D]]) This returns a Matrix object (* is matrix multiplication for this guy) constructed from the blocks A, B, C and D. Of course these blocks must have the right shapes or an error will be generated. Incidentally, r_['A,B;C,D'] does the same thing. I hope this helps. -Travis O.

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scipy general_function segfault
by Arnd Baecker Sept. 23, 2003

Sept. 23, 2003

Hi, it seems that scipy.special.general_function (which allows to "vectorize" any scalar function) is broken (at least in two of my installations ;-) leading to a segmentation fault. A simple example for the problem is: ################################################# from scipy import * def addsubtract(a,b): if a > b: return a - b else: return a + b gfunc=special.general_function(addsubtract) gfunc([0,3,6,9],[1,3,5,7]) ################################################# For me it does work with Python 2.2.2, scipy.__version__: '0.2.0_alpha_183.4048' However, Python 2.2.3, scipy.__version__, '0.2.0_alpha_200.4160' Python 2.3, scipy.__version__, '0.2.0_alpha_210.4098' fail with a segmentation fault. Can someone confirm this problem (for which python/scipy version?) Even better would be a fix for this ... ;-) Many thanks, Arnd

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Couple of Matrix() questions
by Jeffrey B. Layton Sept. 23, 2003

Sept. 23, 2003

Good morning! I've got a couple of quick questions regarding the matrix() class (mat() class?). Anyway, I want to erase a column or a row of a two-dimensional matrix. I create the matrix using, >>> A=mat('[0,3,2];[5,1,2];[9,-6,7]') and I want to blank the second column using something like the following (complete with error message), >>> A[:,1]=[] Traceback (most recent call last): File "<stdin>", line 1, in ? File "/usr/lib/python2.2/site-packages/Numeric/Matrix.py", line 184, in __setitem__ self.array[index] = value How do I blank (or set to zero) the appropriate slice of the matrix? My second question is how to concatenate matrices create with mat(). I tried the following (complete with error messages), >>> A=mat('[0,1];[2,3]') >>> B=mat('[4,5];[6,7]') >>> C=mat('[8,9];[10,11]') >>> D=mat('[12,13];[14,15]') >>> E=mat('[A,B];[C,D]') Traceback (most recent call last): File "<stdin>", line 1, in ? File "/usr/lib/python2.2/site-packages/Numeric/Matrix.py", line 69, in __init__ data = _convert_from_string(data) File "/usr/lib/python2.2/site-packages/Numeric/Matrix.py", line 36, in _convert_from_string newrow.extend(map(_eval,temp)) File "/usr/lib/python2.2/site-packages/Numeric/Matrix.py", line 24, in _eval return eval(astr.translate(_table,_todelete)) File "<string>", line 0 ^ SyntaxError: unexpected EOF while parsing >>> E=[A,B; C,D] File "<stdin>", line 1 E=[A,B; C,D] I know this is a holdover from Matlab, but I would like to get is the following, E=[0, 1, 4 ,5; 2, 3, 6, 7; 8, 9, 12, 13; 10, 11, 14, 15] How do I do this in scipy? TIA! Jeff

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NameError: global name 'ogrid' is not defined
by Nils Wagner Sept. 23, 2003

Sept. 23, 2003

Dear experts, Pleae can you fix this problem in the cvs tree. Traceback (most recent call last): File "pseudospectra.py", line 91, in ? P1 =2*(linalg.logm((gamma-rho)*identity(7)-A)-linalg.logm((gamma+rho)*identity(7)-A)) File "/usr/local/lib/python2.1/site-packages/scipy/linalg/matfuncs.py", line 215, in logm X,Y = ogrid[1:N+1,1:N+1] NameError: global name 'ogrid' is not defined Thanks in advance Nils

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Reference to Scipy
by Nils Wagner Sept. 23, 2003

Sept. 23, 2003

How can I reference scipy in a journal paper ? Nils

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Re: [SciPy-user] [weave] newbie : compilation issue
by Eric Jones Sept. 21, 2003

Sept. 21, 2003

Hey JBR, The docs are out of date compared to the CVS. I don't have all your source to check against, but I would expect the following is fairly close to what you want. Weave sould do all the work translating Python variables to C/C++ for you, at least in the case of "standard" argument types which you are using, so the PyObject* stuff you have in your code isn't necessary. If the code below doesn't work, attach the C files your using and I see what I can do to help out. eric from weave import ext_tools def build_date(): """contruit le module d'extension """ module = ext_tools.ext_module('date_ext') #fonction de positionnement dans un fichier """ positionne_flot a 4 arguments, un p_pointeur de fichier en lecture, un p_pointeur de fichier en écriture (log), un caractère et une date (double) """ fichier_date_c = open('date.c','r') code_date_c = fichier_date_c.read() # arguments fichier_src = fichier_date_c fichier_log = open('log.log','w') pdt = 'a' date = 1.23 ext_code = "return_val = positionne_flot(&p_file,pdt[0],date,&p_log);" fonction = ext_tools.ext_function('c_positionne_flot',ext_code,['fichier_src','pdt','date','fichier_log']) fonction.customize.add_support_code(code_date_c) module.add_function(fonction) module.compile() try: import date_ext except ImportError: build_date() import date_ext Jean-Baptiste Richet - AREAS <jb.richet.areas(a)normandnet.fr> wrote .. > Hi, > > I'm trying to have weave take my C functions into Python. I try to build > a module with ext_tools, but I don't know much about writing Python > extensions (actually, nothing). I just try to guess how to do from the > tutorial and its examples. But of course it doesn't work. > First, let me give you the error message: > ============================= > jb@areas:~/routines/commun$ python ext_date.py > /home/jb/routines/commun/date_ext.cpp: In function `struct PyObject * > c_positionne_flot(PyObject *, PyObject *, PyObject *)': > /home/jb/routines/commun/date_ext.cpp:925: `raw_locals' undeclared > (first use this function) > /home/jb/routines/commun/date_ext.cpp:925: (Each undeclared identifier > is reported only once > /home/jb/routines/commun/date_ext.cpp:925: for each function it appears > in.) > /home/jb/routines/commun/date_ext.cpp:925: `raw_globals' undeclared > (first use this function) > /home/jb/routines/commun/date_ext.cpp:925: implicit declaration of > function `int get_variable(...)' > Traceback (most recent call last): > File "ext_date.py", line 50, in ? > build_date() > File "ext_date.py", line 45, in build_date > module.compile() > File "/usr/local/lib/python2.3/site-packages/weave/ext_tools.py", line > 349, in compile > verbose = verbose, **kw) > File "/usr/local/lib/python2.3/site-packages/weave/build_tools.py", > line 194, > in build_extension > setup(name = module_name, ext_modules = [ext],verbose=verb) > File "/usr/local/lib/python2.3/distutils/core.py", line 166, in setup > raise SystemExit, "error: " + str(msg) > weave.build_tools.CompileError: error: command 'gcc' failed with exit > status 1 > jb@areas:~/routines/commun$ > ==================================== > > Maybe I lack some #include or something like that ? > The line : > PyObject* py_file = get_variable("fichier_src",raw_locals,raw_globals); > from which the error is raised, was found in the weave tutorial about file > conversions. I can hardly understand what it does. > Here is the code at the bottom of the message. > [I hesitate to give the date.c code, or the date_ext.cpp code, it's a bit > long, and there's no compile error from it. If you need it to help me, > please tell me.] > > thanks for your help, > JBR > > ================ ext_date.py ========================= > # -*- coding: UTF-8 -*- > > #test d'utilisation de weave pour créer une bibliothèque > > from weave import ext_tools > > fichier_date_c = open('date.c','r') > code_date_c = fichier_date_c.read() > > fichier_src = fichier_date_c > fichier_log = open('log.log','w') > pdt = 'a' > date = 1.23 > def build_date(): > """contruit le module d'extension > """ > module = ext_tools.ext_module('date_ext') > > #fonction de positionnement dans un fichier > """ > positionne_flot a 4 arguments, un p_pointeur de fichier en lecture, > un p_pointeur de fichier en écriture (log), un caractère et une > date (double) > """ > ext_code = """ > PyObject* py_file = get_variable("fichier_src",raw_locals,raw_globals); > FILE* file = py_to_file(py_file,"fichier_src"); > PyObject* py_log = get_variable("fichier_log",raw_locals,raw_globals); > FILE* log = py_to_file(py_log,"fichier_log"); > > FILE** p_file = &file; > FILE** p_log = &log; > > char c_pdt = std::string(pdt).c_str()[0]; > > int resultat; > > resultat = positionne_flot(p_file,c_pdt,date,p_log); > > return_val = Py::new_reference_to(Py::Int(resultat)); > """ > fonction = ext_tools.ext_function('c_positionne_flot',ext_code,['fichier_src','pdt','date','fichier_log']) > fonction.customize.add_support_code(code_date_c) > module.add_function(fonction) > module.compile() > > try: > import date_ext > except ImportError: > build_date() > import date_ext > ============================================= > > -- > Jean-Baptiste Richet > AREAS > _________________________________ > Association régionale pour l'étude > et l'amélioration des sols > 2, avenue Foch > 76460 Saint Valéry en Caux > tél : +33 2 35 97 25 12 > fax : +33 2 35 97 25 73 > _________________________________ > > > _______________________________________________ > SciPy-user mailing list > SciPy-user(a)scipy.net > http://www.scipy.net/mailman/listinfo/scipy-user

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