NumPy-Discussion March 2013

numpy-discussion@python.org

85 participants
75 discussions

Re: [Numpy-discussion] example reading binary Fortran file

by Neil Martinsen-Burrell

David Froger <david.froger.info <at> gmail.com> writes: > Hy,My question is about reading Fortran binary file (oh no this question > again...) I've posted this before, but I finally got it cleaned up for the Cookbook. For this purpose I use a subclass of file that has methods for reading unformatted Fortran data. See http://www.scipy.org/Cookbook/FortranIO/FortranFile. I'd gladly see this in numpy or scipy somewhere, but I'm not sure where it belongs. > program makeArray > implicit none > integer,parameter:: nx=10,ny=20 > real(4),dimension(nx,ny):: ux,uy,p > integer :: i,j > open(11,file='uxuyp.bin',form='unformatted') > do i = 1,nx > do j = 1,ny > ux(i,j) = real(i*j) > uy(i,j) = real(i)/real(j) > p (i,j) = real(i) + real(j) > enddo > enddo > write(11) ux,uy > write(11) p > close(11) > end program makeArray When I run the above program compiled with gfortran on my Intel Mac, I can read it back with:: >>> import numpy as np >>> from fortranfile import FortranFile >>> f=FortranFile('uxuyp.bin', endian='<') >>> uxuy = f.readReals(prec='f') # 'f' for default reals >>> len(uxuy) 400 >>> ux = np.array(uxuy[:200]).reshape((20,10)).T >>> uy = np.array(uxuy[200:]).reshape((20,10)).T >>> p = f.readReals('f').reshape((20,10)).T >>> ux array([[ 1., 2., 3., 4., 5., 6., 7., 8., 9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20.], [ 2., 4., 6., 8., 10., 12., 14., 16., 18., 20., 22., 24., 26., 28., 30., 32., 34., 36., 38., 40.], [ 3., 6., 9., 12., 15., 18., 21., 24., 27., 30., 33., 36., 39., 42., 45., 48., 51., 54., 57., 60.], [ 4., 8., 12., 16., 20., 24., 28., 32., 36., 40., 44., 48., 52., 56., 60., 64., 68., 72., 76., 80.], [ 5., 10., 15., 20., 25., 30., 35., 40., 45., 50., 55., 60., 65., 70., 75., 80., 85., 90., 95., 100.], [ 6., 12., 18., 24., 30., 36., 42., 48., 54., 60., 66., 72., 78., 84., 90., 96., 102., 108., 114., 120.], [ 7.,Proxy-Connection: keep-alive Cache-Control: max-age=0 14., 21., 28., 35., 42., 49., 56., 63., 70., 77., 84., 91., 98., 105., 112., 119., 126., 133., 140.], [ 8., 16., 24., 32., 40., 48., 56., 64., 72., 80., 88., 96., 104., 112., 120., 128., 136., 144., 152., 160.], [ 9., 18., 27., 36., 45., 54., 63., 72., 81., 90., 99., 108., 117., 126., 135., 144., 153., 162., 171., 180.], [ 10., 20., 30., 40., 50., 60., 70., 80., 90., 100., 110., 120., 130., 140., 150., 160., 170., 180., 190., 200.]]) >>> uy array([[ 1. , 0.5 , 0.33333334, 0.25 , 0.2 , 0.16666667, 0.14285715, 0.125 , 0.11111111, 0.1 , 0.09090909, 0.08333334, 0.07692308, 0.07142857, 0.06666667, 0.0625 , 0.05882353, 0.05555556, 0.05263158, 0.05 ], [ 2. , 1. , 0.66666669, 0.5 , 0.40000001, 0.33333334, 0.2857143 , 0.25 , 0.22222222, 0.2 , 0.18181819, 0.16666667, 0.15384616, 0.14285715, 0.13333334, 0.125 , 0.11764706, 0.11111111, 0.10526316, 0.1 ], [ 3. , 1.5 , 1. , 0.75 , 0.60000002, 0.5 , 0.42857143, 0.375 , 0.33333334, 0.30000001, 0.27272728, 0.25 , 0.23076923, 0.21428572, 0.2 , 0.1875 , 0.17647059, 0.16666667, 0.15789473, 0.15000001], [ 4. , 2. , 1.33333337, 1. , 0.80000001, 0.66666669, 0.5714286 , 0.5 , 0.44444445, 0.40000001, 0.36363637, 0.33333334, 0.30769232, 0.2857143 , 0.26666668, 0.25 , 0.23529412, 0.22222222, 0.21052632, 0.2 ], [ 5. , 2.5 , 1.66666663, 1.25 , 1. , 0.83333331, 0.71428573, 0.625 , 0.55555558, 0.5 , 0.45454547, 0.41666666, 0.38461539, 0.35714287, 0.33333334, 0.3125 , 0.29411766, 0.27777779, 0.2631579 , 0.25 ], [ 6. , 3. , 2. , 1.5 , 1.20000005, 1. , 0.85714287, 0.75 , 0.66666669, 0.60000002, 0.54545456, 0.5 , 0.46153846, 0.42857143, 0.40000001, 0.375 , 0.35294119, 0.33333334, 0.31578946, 0.30000001], [ 7. , 3.5 , 2.33333325, 1.75 , 1.39999998, 1.16666663, 1. , 0.875 , 0.77777779, 0.69999999, 0.63636363, 0.58333331, 0.53846157, 0.5 , 0.46666667, 0.4375 , 0.41176471, 0.3888889 , 0.36842105, 0.34999999], [ 8. , 4. , 2.66666675, 2. , 1.60000002, 1.33333337, 1.14285719, 1. , 0.8888889 , 0.80000001, 0.72727275, 0.66666669, 0.61538464, 0.5714286 , 0.53333336, 0.5 , 0.47058824, 0.44444445, 0.42105263, 0.40000001], [ 9. , 4.5 , 3. , 2.25 , 1.79999995, 1.5 , 1.28571427, 1.125 , 1. , 0.89999998, 0.81818181, 0.75 , 0.69230771, 0.64285713, 0.60000002, 0.5625 , 0.52941179, 0.5 , 0.47368422, 0.44999999], [ 10. , 5. , 3.33333325, 2.5 , 2. , 1.66666663, 1.42857146, 1.25 , 1.11111116, 1. , 0.90909094, 0.83333331, 0.76923078, 0.71428573, 0.66666669, 0.625 , 0.58823532, 0.55555558, 0.52631581, 0.5 ]]) >>> p array([[ 2., 3., 4., 5., 6., 7., 8., 9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21.], [ 3., 4., 5., 6., 7., 8., 9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22.], [ 4., 5., 6., 7., 8., 9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23.], [ 5., 6., 7., 8., 9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23., 24.], [ 6., 7., 8., 9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23., 24., 25.], [ 7., 8., 9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23., 24., 25., 26.], [ 8., 9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23., 24., 25., 26., 27.], [ 9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23., 24., 25., 26., 27., 28.], [ 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23., 24., 25., 26., 27., 28., 29.], [ 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23., 24., 25., 26., 27., 28., 29., 30.]]) Note that you have to provide the shape information for ux and uy because fortran writes them together as a stream of 400 numbers. -Neil

4 months, 2 weeks

C-API: multidimensional array indexing?

by Johann Bauer

Dear experts, is there a C-API function for numpy which implements Python's multidimensional indexing? Say, I have a 2d-array PyArrayObject * M; and an index int i; how do I extract the i-th row or column M[i,:] respectively M[:,i]? I am looking for a function which gives again a PyArrayObject * and which is a view to M (no copied data; the result should be another PyArrayObject whose data and strides points to the correct memory portion of M). I searched the API documentation, Google and mailing lists for quite a long time but didn't find anything. Can you help me? Thanks, Johann

5 years, 8 months

SVD errors

by mtrumpis＠berkeley.edu

Hello list.. I've run into two SVD errors over the last few days. Both errors are identical in numpy/scipy. I've submitted a ticket for the 1st problem (numpy ticket #990). Summary is: some builds of the lapack_lite module linking against system LAPACK (not the bundled dlapack_lite.o, etc) give a "LinAlgError: SVD did not converge" exception on my matrix. This error does occur using Mac's Accelerate framework LAPACK, and a coworker's Ubuntu LAPACK version. It does not seem to happen using ATLAS LAPACK (nor using Octave/Matlab on said Ubuntu) Just today I've come across a negative singular value cropping up in an SVD of a different matrix. This error does occur on my ATLAS LAPACK based numpy, as well as on the Ubuntu setup. And once again, it does not happen in Octave/Matlab. I'm using numpy 1.3.0.dev6336 -- don't know what the Ubuntu box is running. Here are some npy files for the two different cases: https://cirl.berkeley.edu/twiki/pub/User/MikeTrumpis/noconverge_operator.npy https://cirl.berkeley.edu/twiki/pub/User/MikeTrumpis/negsval_operator.npy Mike

8 years, 6 months

pyhdf packaging

by Andreas Hilboll

Hi, I would like to package pyhdf for Ubuntu and make the package publicly available. Since the license is not totally clear to me (I cannot find any information in the sources, and the cheeseshop says "public", which doesn't mean anything to me), I tried to contact the maintainer, Andre Gosselin, however the email bounces, so I guess he's gone. Can anyone point me to how to proceed from here? Cheers, Andreas.

8 years, 6 months

Any plans for windows 64-bit installer for 1.7?

by Matthew Brett

Hi, I see there is no Windows 64 bit installer for the 1.7 rc1. Is there any prospect of a 64 bit installer for the full release? Can I help? I have a Windows 7 64 bit machine that I use as a build slave; I am happy to give access. Cheers, Matthew

8 years, 7 months

Scheduling the 1.7.1 and 1.8 releases

by Charles R Harris

Hi All, There are now some 14 non-merge commits in the 1.7.x branch including the critical diagonal leak fix. I think there is maybe one more critical backport and perhaps several low priority fixes, documentation and such, but I think we should start up the release process with a goal of getting 1.7.1 out by the middle of April. The development branch has been accumulating stuff since last summer, I suggest we look to get it out in May, branching at the end of this month. Thoughts? Chuck

8 years, 7 months

OpenOpt Suite release 0.45

by Dmitrey

Hi all, > I'm glad to inform you about new OpenOpt Suite release 0.45 (2013-March-15): * Essential improvements for FuncDesigner interval analysis (thus affect interalg) * Temporary walkaround for a serious bug in FuncDesigner automatic differentiation kernel due to a bug in some versions of Python or NumPy, may affect optimization problems, including (MI)LP, (MI)NLP, TSP etc * Some other minor bugfixes and improvements > > --------------------------- > Regards, D. > http://openopt.org/Dmitrey

8 years, 7 months

Growing the contributor base of Numpy

by Jonathan Rocher

Dear all, One recurring question is how to *grow the contributor base* to NumPy and provide help and relief to core developers and maintainers. One way to do this would be to *leverage the upcoming SciPy conference* in 2 ways: 1. Provide an intermediate or advanced level tutorial on NumPy focusing on teaching the C-API and the architecture of the package to help people navigate the source code, and find answers to precise deep questions. I think that many users would be interested in being better able to understand the underlayers to become powerful users (and contributors if they want to). 2. Organize a Numpy sprint to leverage all this freshly graduated students apply what they learned to tackle some of the work under the guidance of core developers. This would be a great occasion to share and grow knowledge that is fundamental to our community. And the fact that the underlayers are in C is fine IMHO: SciPy is about scientific programming in Python and that is done with a lot of C. *Thoughts? Anyone interested in leading a tutorial (can be a team of people)? Anyone willing to coordinate the sprint? Who would be willing to be present and help during the sprint? * Note that there is less than 1 week left until the tutorial submission deadline. I am happy to help brainstorm on this to make it happen. Thanks, Jonathan and Andy, for the SciPy2013 organizers -- Jonathan Rocher, PhD Scientific software developer SciPy2013 conference co-chair Enthought, Inc. jrocher(a)enthought.com 1-512-536-1057 http://www.enthought.com

8 years, 7 months

ANN: NumPy 1.7.1rc1 release

by Ondřej Čertík

Hi, I'm pleased to announce the availability of the first release candidate of NumPy 1.7.1rc1. Sources and binary installers can be found at https://sourceforge.net/projects/numpy/files/NumPy/1.7.1rc1/ Please test it and report any bugs. It fixes a few bugs, listed below. I would like to thank everybody who contributed patches to this release: Nathaniel J. Smith, Sebastian Berg, Charles Harris, Bradley M. Froehle, Ralf Gommers, Christoph Gohlke, Mark Wiebe and Maximilian Albert. Cheers, Ondrej ========================= NumPy 1.7.1 Release Notes ========================= This is a bugfix only release in the 1.7.x series. Issues fixed ------------ gh-2973 Fix `1` is printed during numpy.test() gh-2983 BUG: gh-2969: Backport memory leak fix 80b3a34. gh-3007 Backport gh-3006 gh-2984 Backport fix complex polynomial fit gh-2982 BUG: Make nansum work with booleans. gh-2985 Backport large sort fixes gh-3039 Backport object take gh-3105 Backport nditer fix op axes initialization gh-3108 BUG: npy-pkg-config ini files were missing after Bento build. gh-3124 BUG: PyArray_LexSort allocates too much temporary memory. gh-3131 BUG: Exported f2py_size symbol prevents linking multiple f2py modules. gh-3117 Backport gh-2992 gh-3135 DOC: Add mention of PyArray_SetBaseObject stealing a reference gh-3134 DOC: Fix typo in fft docs (the indexing variable is 'm', not 'n'). gh-3136 Backport #3128 Checksums ========= 28c3f3e71b5eaa6bfab6e8340dbd35e7 release/installers/numpy-1.7.1rc1.tar.gz 436f416dee10d157314bd9da7ab95c9c release/installers/numpy-1.7.1rc1-win32-superpack-python2.7.exe a543c8cf69f66ff2b4c9565646105863 release/installers/numpy-1.7.1rc1-win32-superpack-python2.6.exe 6dfcbbd449b7fe4e841c5fd1bfa7af7c release/installers/numpy-1.7.1rc1-win32-superpack-python2.5.exe 22912792a1b6155ae2bdbc30bee8fadc release/installers/numpy-1.7.1rc1-win32-superpack-python3.2.exe 95bc5a5fcce9fcbc2717a774dccae31b release/installers/numpy-1.7.1rc1-win32-superpack-python3.3.exe 33cf283765a148846b49b89fb96d67d5 release/installers/numpy-1.7.1rc1-win32-superpack-python3.1.exe 9761de4b35493fed38c5d177da9c3b37 release/installers/numpy-1.7.1rc1.zip

8 years, 8 months

Bug in np.records?

by Pierre Barbier de Reuille

Hey, I am trying to use titles for the record arrays. In the documentation, it is specified that any column can set to "None". However, trying this fails on numpy 1.6.2 because in np.core.records, on line 195, the "strip" method is called on the title object. This is really annoying. Could we fix this by replacing line 195 with: self._titles = [n.strip() if n is not None else None for n in titles[:self._nfields]] ? Thank you, -- Barbier de Reuille Pierre

8 years, 8 months

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NumPy-Discussion March 2013