Mailman 3 September 2008 - SciPy-User

Help required regding Eigenvectors
by Sudheer Phani March 14, 2022

March 14, 2022

Hello All, I have been encountering some strange problems with the calculation of eigen vectors using python. The problem is with the sign of the eigen vectors calculated. On Very few occasions the eigen vectors calculated using python have an opposite sign than the actual eigenvectors, though the magnitude is correct. Can any one of you plz help me in this regard and suggest me some solution if you have encoutered similar problems . Any help in this regd is appreciated Thanks in Advace regds Sudheer

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scipy/numpy on CentOS 5/ Dependency problem
by Matthias Blaicher Dec. 8, 2010

Dec. 8, 2010

Hello, I want to install SciPy and numpy on a CentOS 5 system. It contains a fresh install with up-to-date packages. I use the "official" Suse Build repos by DavidCournapeau. It fails with a conflict between refblas3 and blas. [root@localhost yum.repos.d]# yum install python-numpy python-scipy Loading "fastestmirror" plugin Loading mirror speeds from cached hostfile * home_ashigabou: download.opensuse.org * extras: mirrors.tummy.com * updates: dds.gina.alaska.edu * base: mirror.hmc.edu * addons: mirrors.tummy.com extras 100% |=========================| 1.1 kB 00:00 updates 100% |=========================| 951 B 00:00 base 100% |=========================| 1.1 kB 00:00 addons 100% |=========================| 951 B 00:00 Setting up Install Process Parsing package install arguments Resolving Dependencies --> Running transaction check ---> Package python-scipy.i386 0:0.6.0-2.1 set to be updated --> Processing Dependency: libblas.so.3 for package: python-scipy --> Processing Dependency: libblas.so.3 for package: python-scipy --> Processing Dependency: liblapack.so.3 for package: python-scipy --> Processing Dependency: libgfortran.so.1 for package: python-scipy --> Processing Dependency: liblapack.so.3 for package: python-scipy ---> Package python-numpy.i386 0:1.2.0-1.1 set to be updated --> Processing Dependency: gcc-gfortran for package: python-numpy --> Processing Dependency: refblas3 for package: python-numpy --> Processing Dependency: lapack3 < 3.1 for package: python-numpy --> Running transaction check ---> Package gcc-gfortran.i386 0:4.1.2-42.el5 set to be updated --> Processing Dependency: gcc = 4.1.2-42.el5 for package: gcc-gfortran ---> Package blas.i386 0:3.0-37.el5 set to be updated ---> Package lapack3.i386 0:3.0-19.1 set to be updated ---> Package lapack.i386 0:3.0-37.el5 set to be updated ---> Package refblas3.i386 0:3.0-11.1 set to be updated ---> Package libgfortran.i386 0:4.1.2-42.el5 set to be updated --> Running transaction check ---> Package gcc.i386 0:4.1.2-42.el5 set to be updated --> Processing Dependency: libgomp.so.1 for package: gcc --> Processing Dependency: glibc-devel >= 2.2.90-12 for package: gcc --> Processing Dependency: libgomp = 4.1.2-42.el5 for package: gcc --> Running transaction check ---> Package glibc-devel.i386 0:2.5-24 set to be updated --> Processing Dependency: glibc-headers for package: glibc-devel --> Processing Dependency: glibc-headers = 2.5-24 for package: glibc-devel ---> Package libgomp.i386 0:4.1.2-42.el5 set to be updated --> Running transaction check ---> Package glibc-headers.i386 0:2.5-24 set to be updated --> Processing Dependency: kernel-headers for package: glibc-headers --> Processing Dependency: kernel-headers >= 2.2.1 for package: glibc-headers --> Running transaction check ---> Package kernel-headers.i386 0:2.6.18-92.1.13.el5 set to be updated --> Processing Conflict: refblas3 conflicts blas --> Finished Dependency Resolution Error: refblas3 conflicts with blas Is there anything I'm doing wrong here, as I don't want to compile all dependencies by myself.. Sincerly, Matthias Blaicher

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3D plotting
by Robert Cimrman Sept. 10, 2009

Sept. 10, 2009

Hi, I need to do some simple 3D plots, so I tried the two Cookbook recipes (xplt, mplot3d) and failed: * xplt: does not work when using a custom installation directory such as python setup.py install --root=/home/share/software apparently the gistdata directory path is wrong: gist.error: failed to create drawing -- Gist work.gs style sheet missing * mplot3d: does not work with my version of matplotlib (0.80). I have made the changes mentioned in the Cookbook to no avail. (Axes.__init__() args apparently changed, as well as some other matplotlib object attributes) Any ideas? mplot3d looks great, I would really like to use it! thanks, r.

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assign to diagonal values?
by Carlos Scheidegger July 7, 2009

July 7, 2009

Say I have a matrix m whose diagonal values I want to replace with the contents of vector new_diagonal. Right now, I'm using m -= diag(m) m += diag(new_diagonal) but that seems pretty wasteful (especially if diag() creates new arrays, which I suspect it does). Is there a standard (or any efficient) way to assign the diagonal values directly without an explicit for loop? Googling for "site:www.scipy.org assign diagonal" only returned results for sparse matrices, which is not the case here - these are plain numpy arrays. Thanks in advance, -carlos

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Is numpy's argsort lying about its numpy.int32 types?
by Rob Clewley May 15, 2009

May 15, 2009

Hi, I'm having a problem comparing some types when using numpy's argsort. I'm using numpy 1.0.2. I can reproduce it simply: Python 2.4.4 (#71, Oct 18 2006, 08:34:43) [MSC v.1310 32 bit (Intel)] << snip >> In [1]: from numpy import argsort, sort, int32, array In [2]: x=array([1,3,2]) In [3]: aa=argsort(x) In [4]: as=sort(x) In [5]: type(aa[0]) Out[5]: <type 'numpy.int32'> In [6]: type(as[0]) Out[6]: <type 'numpy.int32'> In [7]: int32 Out[7]: <type 'numpy.int32'> In [8]: type(as[0])==int32 Out[8]: True In [9]: type(aa[0])==int32 Out[9]: False Any of the three indices in aa give me the same problem. Can someone explain if I should be doing this a different way, and if this is a bug?! Thanks, Rob

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signal.lti(A,B,C,D) with D=0
by William Purcell Feb. 18, 2009

Feb. 18, 2009

I am trying to set up state space representation of a system using signal.lti. The system has no feedforward so D = 0. I've tried the three options listed in the code below to represent D. The only way I can get it to work is option 2 if C has 1 row. If C has more than 1 row it won't work. Any thoughts? -Bill Code --------------------------------------------------------------- from numpy import ones,matrix from scipy import signal r = ones(3) A = matrix([r,r,r]) B = matrix([r]).T C = matrix([r,r]) #three options of D to make it 0 #1) D=0 #2) D = matrix([0,0]).T #3) D = None D = 0 #D = None #D = matrix([0,0]).T Gss = signal.lti(A,B,C,D) ----------------------------------------------------------- Tracebacks ----------------------------------------------------------- Option 1 /usr/lib/python2.5/site-packages/scipy/signal/ltisys.py in abcd_normalize(A, B, C, D) 101 raise ValueError, "A and C must have the same number of columns." 102 if MD != MC: --> 103 raise ValueError, "C and D must have the same number of rows." 104 if ND != NB: 105 raise ValueError, "B and D must have the same number of columns." <type 'exceptions.ValueError'>: C and D must have the same number of rows. WARNING: Failure executing file: <testlti.py> Option 2 (with C as two rows...if C is a single row I do not get this traceback) /usr/lib/python2.5/site-packages/scipy/signal/ltisys.py in ss2tf(A, B, C, D, input) 147 148 num_states = A.shape[0] --> 149 type_test = A[:,0] + B[:,0] + C[0,:] + D 150 num = numpy.zeros((nout, num_states+1), type_test.dtype) 151 for k in range(nout): <type 'exceptions.ValueError'>: shape mismatch: objects cannot be broadcast to a single shape WARNING: Failure executing file: <testlti.py> Option 3 same as 1

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weave problems, weave_imp.o no such file or directory
by Søren Nielsen Dec. 2, 2008

Dec. 2, 2008

Hi, I've done a fresh install of MinGw 5.14, Python 2.4.4, Scipy 0.6.0, Numpy 1.1.0 and numarray 1.5.2 When I try to use weave i get this: C:\>test_weave.py <weave: compiling> running build_ext running build_src building extension "sc_552cccf5dbf4f6eadd273cdcbd5860523" sources customize Mingw32CCompiler customize Mingw32CCompiler using build_ext customize Mingw32CCompiler customize Mingw32CCompiler using build_ext building 'sc_552cccf5dbf4f6eadd273cdcbd5860523' extension compiling C++ sources C compiler: g++ -mno-cygwin -O2 -Wall compile options: '-IC:\Python24\lib\site-packages\scipy\weave -IC:\Python24\lib\ site-packages\scipy\weave\scxx -IC:\Python24\lib\site-packages\numpy\core\includ e -IC:\Python24\include -IC:\Python24\PC -c' g++ -mno-cygwin -O2 -Wall -IC:\Python24\lib\site-packages\scipy\weave -IC:\Pytho n24\lib\site-packages\scipy\weave\scxx -IC:\Python24\lib\site-packages\numpy\cor e\include -IC:\Python24\include -IC:\Python24\PC -c C:\Python24\lib\site-package s\scipy\weave\scxx\weave_imp.cpp -o c:\docume~1\lisear~1\lokale~1\temp\Lise Arle th\python24_intermediate\compiler_08edc7e348e1c33f63a33ab500aef08e\Release\pytho n24\lib\site-packages\scipy\weave\scxx\weave_imp.o Found executable C:\MinGw\bin\g++.exe g++.exe: Arleth\python24_intermediate\compiler_08edc7e348e1c33f63a33ab500aef08e\ Release\python24\lib\site-packages\scipy\weave\scxx\weave_imp.o: No such file or directory Traceback (most recent call last): File "C:\test_weave.py", line 341, in ? main() File "C:\test_weave.py", line 224, in main weave.inline('printf("%d\\n",a);',['a'], verbose=2, type_converters=converte rs.blitz) #, compiler = 'msvc', verbpse=2, type_converters=converters.blitz, au to_downcast=0) #'msvc' or 'gcc' or 'mingw32' File "C:\Python24\Lib\site-packages\scipy\weave\inline_tools.py", line 338, in inline auto_downcast = auto_downcast, File "C:\Python24\Lib\site-packages\scipy\weave\inline_tools.py", line 447, in compile_function verbose=verbose, **kw) File "C:\Python24\Lib\site-packages\scipy\weave\ext_tools.py", line 365, in co mpile verbose = verbose, **kw) File "C:\Python24\Lib\site-packages\scipy\weave\build_tools.py", line 269, in build_extension setup(name = module_name, ext_modules = [ext],verbose=verb) File "C:\Python24\Lib\site-packages\numpy\distutils\core.py", line 184, in set up return old_setup(**new_attr) File "C:\Python24\lib\distutils\core.py", line 166, in setup raise SystemExit, "error: " + str(msg) distutils.errors.CompileError: error: Command "g++ -mno-cygwin -O2 -Wall -IC:\Py thon24\lib\site-packages\scipy\weave -IC:\Python24\lib\site-packages\scipy\weave \scxx -IC:\Python24\lib\site-packages\numpy\core\include -IC:\Python24\include - IC:\Python24\PC -c C:\Python24\lib\site-packages\scipy\weave\scxx\weave_imp.cpp -o c:\docume~1\lisear~1\lokale~1\temp\Lise Arleth\python24_intermediate\compiler _08edc7e348e1c33f63a33ab500aef08e\Release\python24\lib\site-packages\scipy\weave \scxx\weave_imp.o" failed with exit status 1 the test_weave file was something i found on the scipy dev wiki... I also tried some of my older files that also uses weave and they all give the same error... Can anyone help me with this?

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scipy workflow
by João Quinta da Fonseca Oct. 13, 2008

Oct. 13, 2008

I have given up Matlab and I it feels great to use scipy for my scientific computing needs. However, I find that I use scipy just like I used matlab, with ipython as my terminal. Although this works OK, some things are a little frustrating: updated modules need to be reimported after modification, running scripts requires the run command etc., but this is to be expected because scipy is not matlbab. Now I don't want the matlab way necessarily and I am happy to learn a new way to do things. I guess what I would like to do is do things the python way, which I think means writing my code as classes with the _main_ bit at the end etc., but I am not sure whether that is the best way and if so, what is the best way to learn it. Does any one feel like sharing what their workflow with scipy is? Any tips for me? Thanks, Joao

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Inconsistent standard deviation and variance implementation in scipy vs. scipy.stats
by Johann Rohwer Oct. 7, 2008

Oct. 7, 2008

Hi It seems that the default implementation of std and var differs between numpy/scipy and scipy.stats, in that numpy/scipy is using the "biased" formulation (i.e. dividing by N) whereas scipy.stats is using the "unbiased" formulation (dividing by N-1) by default. Is this intentional (it could be potentially confusing...)? I realise that the "biased" version can be accessed in sp.stats with a kwarg, but what is the reason for two different implementations of the function(s)? In [30]: a Out[30]: array([ 1., 2., 3., 2., 3., 1.]) In [31]: np.std(a) Out[31]: 0.81649658092772603 In [32]: sp.std(a) Out[32]: 0.81649658092772603 In [33]: sp.stats.std(a) Out[33]: 0.89442719099991586 In [34]: sp.stats.std(a, bias=True) Out[34]: 0.81649658092772603 Same for np.var vs scipy.stats.var Johann

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Gaussian quadrature error
by Dan Murphy Oct. 7, 2008

Oct. 7, 2008

I am trying out the integrate.quadrature function on the function f(x)=e**x to the left of the y-axis. If the lower bound in not too negative, I get a reasonable answer, but if the lower bound is too negative, I get 0.0 as the value of the integral. Here is the code: from scipy import * def f(x): return e**x integrate.quadrature(f,-10.0,0.0) # answer is (0.999954600065, 3.14148596026e-010) but integrate.quadrature(f,-1000.0,0.0) # yields (8.35116510531e-090, 8.35116510531e-090) Note that 'val' and 'err' are equal. Is this a bug in quadrature? Thanks. Dan

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