Mailman 3 January 2009 - 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

5 5

pupynere/scipy.io.netcdf
by Ryan May March 6, 2013

March 6, 2013

Hi, Anyone know if pupynere (a version of which is in scipy.io.netcdf) supports writing files with 64-bit offsets? This allows writing files larger than 2GB. Ryan -- Ryan May Graduate Research Assistant School of Meteorology University of Oklahoma

7 6

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

3 2

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.

6 6

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

11 17

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

5 6

cdf and integration for multivariate normal distribution in stats.kde
by josef.pktd＠gmail.com April 6, 2009

April 6, 2009

I found the fortran code for rectangular integration of the multivariate normal distribution in stats kde, which can be used to calculate the cdf. I didn't see this function exposed anywhere in scipy. Did I miss it? I wrote a quick wrapper, with two functions mvstdnormcdf(lower,upper,corrcoef, **kwds) direct convenience wrapper with just some reparameterization for convenience, for standard normal mvnormcdf(lower, upper, mu, cov, **kwds) allows non-standard multivariate normal distribution, normalizes distribution and calls mvstdnormcdf Both calculate the integral only for a single are, no vectorization yet. Also, this is not yet a clean version. I wanted to ask first if I missed it, and it's already used somewhere in scipy. Josef

5 9

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

4 8

Computational Economics with SciPy
by Peter Skomoroch Feb. 7, 2009

Feb. 7, 2009

Just stumbled across a new book by John Stachurski using scipy which will ship later this month Economic Dynamics: Theory and Computation John Stachurski MIT Press, 2009 http://www.amazon.com/Economic-Dynamics-Computation-John-Stachurski/dp/0262… http://johnstachurski.net/book/book.html There are some nice tutorials using scipy here as well: http://johnstachurski.net/lectures/index.html *Economic Dynamics: Theory and Computation* is a graduate level introduction > to deterministic and stochastic dynamics, dynamic programming and > computational methods with economic applications. > Topics > > - Programming techniques > - Basic analysis (real analysis, metric spaces, fixed points) > - Deterministic dynamic systems > - Finite state Markov chains > - Finite state dynamic programming > - Continuous state stochastic dynamics > - Continuous state dynamic programming > > -Pete -- Peter N. Skomoroch peter.skomoroch(a)gmail.com http://www.datawrangling.com http://del.icio.us/pskomoroch

3 3

SciPy and GUI
by Lorenzo Isella Feb. 3, 2009

Feb. 3, 2009

Dear All, I hope this is not too off-topic. Given you Python code, relying on SciPy for number-crunching, which tools would you use to create a GUI in order to allow someone else to use it, without his knowing much (or anything) about scipy and programming?I know Python is great for this, but I do not know of anything specific. Cheers Lorenzo -- I went to the race track once and bet on a horse that was so good that it took seven others to beat him!

19 32