Mailman 3 May 2009 - SciPy-User

Help required regding Eigenvectors
by Sudheer Phani 14 Mar '22

14 Mar '22

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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pupynere/scipy.io.netcdf
by Ryan May 06 Mar '13

06 Mar '13

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

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scipy/numpy on CentOS 5/ Dependency problem
by Matthias Blaicher 08 Dec '10

08 Dec '10

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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64 bit on Mac?
by Keflavich 26 Sep '10

26 Sep '10

Hi folks, I'd really like to work with some of the large images I have; I work on a galactic plane survey that has lots of images with ~10^8 floating point pixels. I'm also using a mac. Unfortunately I can't get a 64-bit version of python compiled and google has been unhelpful in resolving the problem. Is there a workaround to get 64 bit numpy working without 64 bit python installed? I doubt that, but if anyone has tips I'd appreciate them. On a related note, I also use a linux machine with 64 bit python installed, but it crashes with large arrays giving a segfault where my mac spits out the "ValueError: dimensions too large." error. Any ideas there? Thanks, Adam

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problems with splrep,splev
by Christian K. 08 Jun '10

08 Jun '10

Hi, I am having problems with the spline functions from scipy.interpolate. Reading the doc strings I expected the following to work: from scipy.interpolate import splev,splrep import numpy as N x = N.linspace(-4,10,5) y = x**2 t,c,l = splrep(x,y,xb=0,xe=4) Traceback (most recent call last): File "C:\pythonxy\python\lib\site-packages\scipy\interpolate\fitpack.py", line 406, in splrep n,c,fp,ier = dfitpack.curfit(task, x, y, w, t, wrk, iwrk, xb, xe, k, s) error: (xb<=x[0]) failed for 1st keyword xb Second, I want to fit several curves using the same knots, thus I tried the following: y2 = x**2-3*x+4 t2,c2,l2 = splrep(x,y2,t=t) Traceback (most recent call last): File "C:\pythonxy\python\lib\site-packages\scipy\interpolate\fitpack.py", line 418, in splrep raise _iermess[ier][1],_iermess[ier][0] ValueError: Error on input data Are those bugs or am I misunderstanding something? Eventually I would like to morph one spline into another, therefor I want to stick with the knots. If anyone has experiences with splines and morphing I would be very interested to hear about it. Regards, Christian

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3D plotting
by Robert Cimrman 10 Sep '09

10 Sep '09

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 07 Jul '09

07 Jul '09

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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Compile Error: error: expected `)' before 'PRIdPTR'
by loris.bennett＠fu-berlin.de 11 Jun '09

11 Jun '09

Hi, I am still trying to install SciPy 0.7.0 on AIX 5.3. I have managed to install NumPy 1.3.0. When I try to install SciPym I get scipy/sparse/sparsetools/csr_wrap.cxx: In function 'int require_size(PyArrayObject*, npy_intp*, int)': scipy/sparse/sparsetools/csr_wrap.cxx:2910: error: expected `)' before 'PRIdPTR' >From the reading the list I see that this problem has occurred before and has apparently been fixed. Any ideas why this is still happening? Cheers Loris

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Segmentation fault with 0.7
by Matthieu Brucher 08 Jun '09

08 Jun '09

Hi, I've also tested scipy 0.7 with the MKL (no choice, I don't have atlas or refblas installed, and I found a way of using the latest by preloading libmkl_core.so), and I got a segmentation fault on a LAPACK function: test_y_bad_size (test_fblas.TestZswap) ... ok test_y_stride (test_fblas.TestZswap) ... ok test_clapack_dsyev (test_esv.TestEsv) ... SKIP: Skipping test: test_clapack_dsyev Clapack empty, skip clapack test test_clapack_dsyevr (test_esv.TestEsv) ... SKIP: Skipping test: test_clapack_dsyevr Clapack empty, skip clapack test test_clapack_dsyevr_ranges (test_esv.TestEsv) ... SKIP: Skipping test: test_clapack_dsyevr_ranges Clapack empty, skip clapack test test_clapack_ssyev (test_esv.TestEsv) ... SKIP: Skipping test: test_clapack_ssyev Clapack empty, skip clapack test test_clapack_ssyevr (test_esv.TestEsv) ... SKIP: Skipping test: test_clapack_ssyevr Clapack empty, skip clapack test test_clapack_ssyevr_ranges (test_esv.TestEsv) ... SKIP: Skipping test: test_clapack_ssyevr_ranges Clapack empty, skip clapack test test_dsyev (test_esv.TestEsv) ... ok test_dsyevr (test_esv.TestEsv) ... Segmentation fault Is it a new function or something like that? I don't remember encoutering this error in previous packages (although I didn't always launched the full tests). Matthieu -- Information System Engineer, Ph.D. Website: http://matthieu-brucher.developpez.com/ Blogs: http://matt.eifelle.com and http://blog.developpez.com/?blog=92 LinkedIn: http://www.linkedin.com/in/matthieubrucher

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How to use pcolor and scatter plot in one image?
by wierob 01 Jun '09

01 Jun '09

Hi, how can I use pcolor and a scatter plot in one image? I have a scatter plot where a lot of data points are so close to each other that they are drawn as (almost) one point in the scatter plot. So I'm trying to visualize which area of the scatter plot contains the most data points. Using pcolor I can draw a gird where each cell visualizes the relative number of data points by a different color. If I try to draw the scatter plot and the grid in the same image, only the scatter plot will be drawn. Regardless of the invocation order of plot and pcolor. ... plot(...) pcolor(...) show() ... pcolor(...) plot(...) show() Both return only the scatter plot. I'm new to Scipy. What am I doing wrong? Thanks in advance. kind regards robert

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