Mailman 3 May 2015 - NumPy-Discussion

Invalid value encoutered : how to prevent numpy.where to do this?
by Eric Emsellem 18 Feb '23

18 Feb '23

Dear all, I have a code using lots of "numpy.where" to make some constrained calculations as in: data = arange(10) result = np.where(data == 0, 0., 1./data) # or data1 = arange(10) data2 = arange(10)+1.0 result = np.where(data1 > data2, np.sqrt(data1-data2), np.sqrt(data2-data2)) which then produces warnings like: /usr/bin/ipython:1: RuntimeWarning: invalid value encountered in sqrt or for the first example: /usr/bin/ipython:1: RuntimeWarning: divide by zero encountered in divide How do I avoid these messages to appear? I know that I could in principle use numpy.seterr. However, I do NOT want to remove these warnings for other potential divide/multiply/sqrt etc errors. Only when I am using a "where", to in fact avoid such warnings! Note that the warnings only happen once, but since I am going to release that code, I would like to avoid the user to get such messages which are irrelevant here (because I am testing, with the where, when NOT to divide by zero or take a sqrt of a negative number). thanks! Eric

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Re: [Numpy-discussion] example reading binary Fortran file
by Neil Martinsen-Burrell 22 Jul '21

22 Jul '21

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

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C-API: multidimensional array indexing?
by Johann Bauer 31 Mar '16

31 Mar '16

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

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Generalize hstack/vstack --> stack; Block matrices like in matlab
by Stefan Otte 09 Jan '16

09 Jan '16

Hey, quite often I work with block matrices. Matlab offers the convenient notation [ a b; c d ] to stack matrices. The numpy equivalent is kinda clumsy: vstack([hstack([a,b]), hstack([c,d])]) I wrote the little function `stack` that does exactly that: stack([[a, b], [c, d]]) In my case `stack` replaced `hstack` and `vstack` almost completely. If you're interested in including it in numpy I created a pull request [1]. I'm looking forward to getting some feedback! Best, Stefan [1] https://github.com/numpy/numpy/pull/5057

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F2PY and multi-dimension arrays - unexpected array size error
by Backing Olof 01 Jul '15

01 Jul '15

Hi I am helping out with a Python and Fortran project. Let me give you some background: * Fortran source: C Bergstrom FCC C User subroutine VUMAT subroutine VUMAT( C Read only - * nblock, ndir, nshr, nstatev, nprops, * stepTime, dt, * props, * density, strainInc, * tempOld, * stressOld, stateOld, enerInternOld, enerInelasOld, C Write only - * stressNew, stateNew, enerInternNew, enerInelasNew ) C include 'vaba_param.inc' C dimension props(nprops), 1 density(nblock), strainInc(nblock,ndir+nshr), 2 tempOld(nblock), 5 stressOld(nblock,ndir+nshr), stateOld(nblock,nstatev), 6 enerInternOld(nblock), enerInelasOld(nblock), 2 stressNew(nblock,ndir+nshr), stateNew(nblock,nstatev), 3 enerInternNew(nblock), enerInelasNew(nblock) * Corresponding .pyf integer :: nblock integer :: ndir integer :: nshr integer :: nstatev integer :: nprops real :: steptime real :: dt real dimension(nprops) :: props real dimension(nblock) :: density real dimension(nblock,ndir+nshr) :: straininc real dimension(nblock) :: tempold real dimension(nblock,ndir+nshr) :: stressold real dimension(nblock,nstatev) :: stateold real dimension(nblock) :: enerinternold real dimension(nblock) :: enerinelasold real dimension(nblock,ndir+nshr),intent(out) :: stressnew real dimension(nblock,nstatev),intent(out) :: statenew real dimension(nblock),intent(out) :: enerinternnew real dimension(nblock),intent(out) :: enerinelasnew * Python source with call of Fortran routine: nblock = 1 ndir = 3 nshr = 3 nstatev = 3 nprops = 11 stepTime = 1 dt = 1 props = np.array([10, 0.5, 1e10, 5, 1e12, 3e-6, 8e-6, 27, 2], float) density = np.array([[7.8e3]], float) strainInc = np.array([[1,-0.5,-0.5,0,0,0]], float) tempOld = np.array([[1]], float) stressOld = np.array([[1,1,1,1,1,1]], float) stateOld = np.array([[1,1,1]], float) enerInternOld = np.array([1], float) enerInelasOld = np.array([1], float) stressNew = np.array([[]], float) stateNew = np.array([[]], float) enerInternNew = np.array([[]], float) enerInelasNew = np.array([[]], float) stressNew, stateNew, enerInternNew, enerInelasNew = vumat(nblock, ndir, nshr, nstatev, nprops, stepTime, dt, props, density, strainInc, tempOld, stressOld, stateOld, enerInternOld, enerInelasOld) When trying to run with Python 2.7 I get: olof@ubuntu:~$ ./demo.py unexpected array size: new_size=4, got array with arr_size=1 Traceback (most recent call last): File "./demo.py", line 33, in <module> main() File "./demo.py", line 30, in main stressNew, stateNew, enerInternNew, enerInelasNew = vumat(nblock, ndir, nshr, nstatev, nprops, stepTime, dt, props, density, strainInc, tempOld, stressOld, stateOld, enerInternOld, enerInelasOld) VUMAT_Bergstrom_FCC.error: failed in converting 9th argument `stressold' of VUMAT_Bergstrom_FCC.vumat to C/Fortran array Other stuff: * python 2.7.6 * numpy/f2py 1.8.2 * gcc/gfortran 4.8.2 * ubuntu 14.04 LTS 32-bit I have tried to google, read the f2py manual, fortran tutorials etc, but to no avail. I must also admit that my knowledge in python is so-so and fortran even less(!). What is the missing statement/syntax that I can’t get correct? Your humble programmer, Olof

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PR added: frozen dimensions in gufunc signatures
by Jaime Fernández del Río 23 Jun '15

23 Jun '15

Hi, I have just sent a PR (https://github.com/numpy/numpy/pull/5015), adding the possibility of having frozen dimensions in gufunc signatures. As a proof of concept, I have added a `cross1d` gufunc to `numpy.core.umath_tests`: In [1]: import numpy as np In [2]: from numpy.core.umath_tests import cross1d In [3]: cross1d.signature Out[3]: '(3),(3)->(3)' In [4]: a = np.random.rand(1000, 3) In [5]: b = np.random.rand(1000, 3) In [6]: np.allclose(np.cross(a, b), cross1d(a, b)) Out[6]: True In [7]: %timeit np.cross(a, b) 10000 loops, best of 3: 76.1 us per loop In [8]: %timeit cross1d(a, b) 100000 loops, best of 3: 13.1 us per loop In [9]: c = np.random.rand(1000, 2) In [10]: d = np.random.rand(1000, 2) In [11]: cross1d(c, d) --------------------------------------------------------------------------- ValueError Traceback (most recent call last) <ipython-input-11-72c66212e40c> in <module>() ----> 1 cross1d(c, d) ValueError: cross1d: Operand 0 has a mismatch in its core dimension 0, with gufunc signature (3),(3)->(3) (size 2 is different from 3) The speed up over `np.cross` is nice, and while `np.cross` is not the best of examples, as it needs to handle more sizes, in many cases this will allow producing gufuncs that work without a Python wrapper redoing checks that are best left to the iterator, such as dimension sizes. It still needs tests, but before embarking on fully developing those, I wanted to make sure that there is an interest on this. I would also like to further enhance gufuncs providing computed dimensions, e.g. making it possible to e.g. define `pairwise_cross` with signature '(n, 3)->($m, 3)', where the $ indicates that m is a computed dimension, that would have to be calculated by a function passed to the gufunc constructor and stored in the gufunc object, based on the other core dimensions. In this case it would make $m be n*(n-1), so that all pairwise cross products between 3D vectors could be computed. The syntax with '$' is kind of crappy, so any suggestions on how to better express this in the signature are more than welcome, as well as any feedback on the merits (or lack of them) of implementing this. Jaime -- (\__/) ( O.o) ( > <) Este es Conejo. Copia a Conejo en tu firma y ayúdale en sus planes de dominación mundial.

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Backwards-incompatible improvements to numpy.random.RandomState
by Antony Lee 09 Jun '15

09 Jun '15

Hi, As mentioned in #1450: Patch with Ziggurat method for Normal distribution #5158: ENH: More efficient algorithm for unweighted random choice without replacement #5299: using `random.choice` to sample integers in a large range #5851: Bug in np.random.dirichlet for small alpha parameters some methods on np.random.RandomState are implemented either non-optimally (#1450, #5158, #5299) or have outright bugs (#5851), but cannot be easily changed due to backwards compatibility concerns. While some have suggested new methods deprecating the old ones (see e.g. #5872), some consensus has formed around the following ideas (see #5299 for original discussion, followed by private discussions with @njsmith): - Backwards compatibility should only be provided to those who were explicitly instantiating a seeded RandomState object or reseeding a RandomState object to a given value, and drawing variates from it: using the global methods (or a None-seeded RandomState) was already non-reproducible anyways as e.g. other libraries could be drawing variates from the global RandomState (of which the free functions in np.random are actually methods). Thus, the global RandomState object should use the latest implementation of the methods. - "RandomState(seed)" and "r = RandomState(...); r.seed(seed)" should offer backwards-compatibility guarantees (see e.g. https://docs.python.org/3.4/library/random.html#notes-on-reproducibility). As such, we propose the following improvements to the API: - RandomState gains a (keyword-only) parameter, "version", also accessible as a read-only attribute. This indicates the version of the methods on the object. The current version of RandomState is retroactively assigned version 0. The latest available version is available as np.random.LATEST_VERSION. Backwards-incompatible improvements to RandomState methods can be introduced but increase the LAGTEST_VERSION. - The global RandomState is instantiated as RandomState(version=LATEST_VERSION). - RandomState() and rs.seed() sets the version to LATEST_VERSION. - RandomState(seed[!=None]) and rs.seed(seed[!=None]) sets the version to 0. A proof-of-concept implementation, still missing tests, is tracked as #5911. It includes the patch proposed in #5158 as an example of how to include an improved version of random.choice. Comments, and help for writing tests (in particular to make sure backwards compatibility is maintained) are welcome. Antony Lee

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matmul needs some clarification.
by Charles R Harris 04 Jun '15

04 Jun '15

Hi All, The problem arises when multiplying a stack of matrices times a vector. PEP465 defines this as appending a '1' to the dimensions of the vector and doing the defined stacked matrix multiply, then removing the last dimension from the result. Note that in the middle step we have a stack of matrices and after removing the last dimension we will still have a stack of matrices. What we want is a stack of vectors, but we can't have those with our conventions. This makes the result somewhat unexpected. How should we resolve this? Chuck

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Verify your sourceforge windows installer downloads
by Julian Taylor 01 Jun '15

01 Jun '15

hi, It has been reported that sourceforge has taken over the gimp unofficial windows downloader page and temporarily bundled the installer with unauthorized adware: https://plus.google.com/+gimp/posts/cxhB1PScFpe As NumPy is also distributing windows installers via sourceforge I recommend that when you download the files you verify the downloads via the checksums in the README.txt before using them. The README.txt is clearsigned with my gpg key so it should be safe from tampering. Unfortunately as I don't use windows I cannot give any advice on how to do the verifcation on these platforms. Maybe someone familar with available tools can chime in. I have checked the numpy downloads and they still match what I uploaded, but as sourceforge does redirect based on OS and geolocation this may not mean much. Cheers, Julian Taylor

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ANN: SfePy 2015.2
by Robert Cimrman 29 May '15

29 May '15

I am pleased to announce release 2015.2 of SfePy. Description ----------- SfePy (simple finite elements in Python) is a software for solving systems of coupled partial differential equations by the finite element method or by the isogeometric analysis (preliminary support). It is distributed under the new BSD license. Home page: http://sfepy.org Mailing list: http://groups.google.com/group/sfepy-devel Git (source) repository, issue tracker, wiki: http://github.com/sfepy Highlights of this release -------------------------- - major code simplification (removed element groups) - time stepping solvers updated for interactive use - improved finding of reference element coordinates of physical points - reorganized examples - reorganized installation on POSIX systems (sfepy-run script) For full release notes see http://docs.sfepy.org/doc/release_notes.html#id1 (rather long and technical). Best regards, Robert Cimrman and Contributors (*) (*) Contributors to this release (alphabetical order): Lubos Kejzlar, Vladimir Lukes, Anton Gladky, Matyas Novak

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NumPy-Discussion May 2015