Mailman 3 June 2012 - NumPy-Discussion

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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SVD errors
by mtrumpis＠berkeley.edu 04 Jun '13

04 Jun '13

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

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example reading binary Fortran file
by David Froger 13 Feb '13

13 Feb '13

Hy, My question is about reading Fortran binary file (oh no this question again...) Until now, I was using the unpack module like that : def lread(f,fourBeginning,fourEnd,*tuple): from struct import unpack """Reading a Fortran binary file in litte-endian""" if fourBeginning: f.seek(4,1) for array in tuple: for elt in xrange(array.size): transpose(array).flat[elt] = unpack(array.dtype.char,f.read(array.itemsize))[0] if fourEnd: f.seek(4,1) After googling, I read that fopen and npfille was deprecated, and we should use numpy.fromfile and ndarray.tofile, but despite of the documentaion, the cookbook, the mailling list and google, I don't succed in making a simple example. Considering the simple Fortran code below what is the Python script to read the four arrrays? What about if my pc is little endian and the file big endian? I think it will be a good idea to put the Fortran writting-arrays code and the Python reading-array script in the cookbook and maybe a page to help people comming from Fortran to start with Python ? Best, David Froger 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

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Issue tracking
by Charles R Harris 23 Oct '12

23 Oct '12

Hi All, The issue tracking discussion seems to have died. Since github issues looks to be a viable alternative at this point, I propose to turn it on for the numpy repository and start directing people in that direction. Thoughts? Chuck

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Fwd: [numpy] ENH: Initial implementation of a 'neighbor' calculation (#303)
by Nathaniel Smith 15 Oct '12

15 Oct '12

[Manual PR notification] ---------- Forwarded message ---------- From: timcera Date: Sat, Jun 9, 2012 at 10:13 PM Subject: [numpy] ENH: Initial implementation of a 'neighbor' calculation (#303) To: njsmith <njs(a)pobox.com> Each element is assigned the result of a function based on it's neighbors. Neighbors are selected based on a weight array. It uses the new pad routines to pad arrays if neighboring values are required that would be off the edge of the input array. Will be great to have the masked array settled because right now you can only sort of exclude from the neighborhood using a zero in the weight array. Zero or np.IGNORE don't affect np.sum, but functions like np.mean and np.std would give different answers. Because of this my early implementations of neighbor included an optional mask array along with the weight array, but I decided would be best to wait for the new masked arrays. This in some ways could be considered a generalization of a convolution, and comparison with existing numpy/scipy convolution results are included in the tests. The advantage to neighbor is that any function that accepts a 1-d array, and returns a single result, can be used instead of convolution only using summation. The convolution functions require the weight array to be flipped to get the same answer as neighbor. You can merge this Pull Request by running: git pull https://github.com/timcera/numpy neighbor Or you can view, comment on it, or merge it online at: https://github.com/numpy/numpy/pull/303 -- Commit Summary -- * ENH: Initial implementation of a 'neighbor' calculation where the each -- File Changes -- M numpy/lib/__init__.py (2) A numpy/lib/neighbor.py (305) A numpy/lib/tests/test_neighbor.py (278) -- Patch Links -- https://github.com/numpy/numpy/pull/303.patch https://github.com/numpy/numpy/pull/303.diff --- Reply to this email directly or view it on GitHub: https://github.com/numpy/numpy/pull/303

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dtype '|S0' not understood
by David Warde-Farley 07 Oct '12

07 Oct '12

Howdy, It seems it's possible using e.g. In [25]: dtype([('foo', str)])Out[25]: dtype([('foo', '|S0')]) to get yourself a zero-length string. However dtype('|S0') results in a TypeError: data type not understood. I understand the stupidity of creating a 0-length string field but it's conceivable that it's accidental. For example, it could lead to a situation where you've created that field, are missing all the data you had meant to put in it, serialize with np.save, and upon np.load aren't able to get _any_ of your data back because the dtype descriptor is considered bogus (can you guess why I thought of this scenario?). It seems that either dtype(str) should do something more sensible than zero-length string, or it should be possible to create it with dtype('| S0'). Which should it be? David

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Long-standing issue with using numpy in embedded CPython
by Yang Zhang 25 Sep '12

25 Sep '12

It turns out that there's a long-standing problem in numpy that prevents it from being used in embedded CPython environments: http://stackoverflow.com/questions/7592565/when-embedding-cpython-in-java-w… http://mail.scipy.org/pipermail/numpy-discussion/2009-July/044046.html Is there any fix or workaround for this? Thanks. -- Yang Zhang http://yz.mit.edu/

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Debian/Ubuntu patch help (was: ANN: NumPy 1.6.2 release candidate 1)
by Ralf Gommers 07 Sep '12

07 Sep '12

On Sat, May 12, 2012 at 9:17 PM, Ralf Gommers <ralf.gommers(a)googlemail.com>wrote: > > > On Sat, May 12, 2012 at 6:22 PM, Sandro Tosi <matrixhasu(a)gmail.com> wrote: > >> Hello, >> >> On Sat, May 5, 2012 at 8:15 PM, Ralf Gommers >> <ralf.gommers(a)googlemail.com> wrote: >> > Hi, >> > >> > I'm pleased to announce the availability of the first release candidate >> of >> > NumPy 1.6.2. This is a maintenance release. Due to the delay of the >> NumPy >> > 1.7.0, this release contains far more fixes than a regular NumPy bugfix >> > release. It also includes a number of documentation and build >> improvements. >> > >> > Sources and binary installers can be found at >> > https://sourceforge.net/projects/numpy/files/NumPy/1.6.2rc1/ >> > >> > Please test this release and report any issues on the numpy-discussion >> > mailing list. >> ... >> > BLD: add support for the new X11 directory structure on Ubuntu & co. >> >> We've just discovered that this fix is not enough. Actually the new >> directories are due to the "multi-arch" feature of Debian systems, >> that allows to install libraries from other (foreign) architectures >> than the one the machine is (the classic example, i386 libraries on a >> amd64 host). >> >> the fix included to look up in additional directories is currently >> only for X11, while for example Debian has fftw3 that's >> multi-arch-ified and thus will fail to be detected. >> >> Could this fix be extended to include all other things that are >> checked? for reference the bug in Debian is [1]; there was also a >> patch[2] in previous versions, that was using gcc to get the >> multi-arch paths - you might use as a reference, or to implement >> something debian-systems-specific. >> >> [1] http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=640940 >> [2] >> http://anonscm.debian.org/viewvc/python-modules/packages/numpy/trunk/debian… >> >> It would be awesome is such support would end up in 1.6.2 . >> > > Hardcoding some more paths to check in distutils/system_info.py should be > OK, also for 1.6.2 (will require a new RC). > > The --print-multiarch thing looks very questionable. As far as I can tell, > it's a Debian specific gcc patch, only available in gcc 4.6 and up. Ubuntu > before 11.10 release also doesn't have it. Therefore I don't think use of > --print-multiarch is appropriate for numpy for now, and certainly not a > change I'd like to make to distutils right before a release. > > If anyone with access to a Debian/Ubuntu system could come up with a patch > which adds the right paths to system_info.py, that would be great. > Hi, if there's anyone wants to have a look at the above issue this week, that would be great. If there's a patch by this weekend I can create a second RC, so we can still have the final release before the end of this month (needed for Debian freeze). Otherwise a second RC won't be needed. Ralf

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"Symbol table not found" compiling numpy from git repository on Windows
by John Salvatier 18 Jul '12

18 Jul '12

Hello, I'm trying to compile numpy on Windows 7 using the command: "python setup.py config --compiler=mingw32 build" but I get an error about a symbol table not found. Anyone know how to work around this or what to look into? building library "npymath" sources Building msvcr library: "C:\Python26\libs\libmsvcr90.a" (from C:\Windows\winsxs\amd64_microsoft.vc90.crt_1fc8b3b9a1e18e3b_9.0.21022.8_none_750b37ff97f4f68b\msvcr90.dll) objdump.exe: C:\Windows\winsxs\amd64_microsoft.vc90.crt_1fc8b3b9a1e18e3b_9.0.21022.8_none_750b37ff97f4f68b\msvcr90.dll: File format not recognized Traceback (most recent call last): File "setup.py", line 214, in <module> setup_package() File "setup.py", line 207, in setup_package configuration=configuration ) File "C:\Users\jsalvatier\workspace\numpy\numpy\distutils\core.py", line 186, in setup return old_setup(**new_attr) File "C:\Python26\lib\distutils\core.py", line 152, in setup dist.run_commands() File "C:\Python26\lib\distutils\dist.py", line 975, in run_commands self.run_command(cmd) File "C:\Python26\lib\distutils\dist.py", line 995, in run_command cmd_obj.run() File "C:\Users\jsalvatier\workspace\numpy\numpy\distutils\command\build.py", line 37, in run old_build.run(self) File "C:\Python26\lib\distutils\command\build.py", line 134, in run self.run_command(cmd_name) File "C:\Python26\lib\distutils\cmd.py", line 333, in run_command self.distribution.run_command(command) File "C:\Python26\lib\distutils\dist.py", line 995, in run_command cmd_obj.run() File "C:\Users\jsalvatier\workspace\numpy\numpy\distutils\command\build_src.py", line 152, in run self.build_sources() File "C:\Users\jsalvatier\workspace\numpy\numpy\distutils\command\build_src.py", line 163, in build_sources self.build_library_sources(*libname_info) File "C:\Users\jsalvatier\workspace\numpy\numpy\distutils\command\build_src.py", line 298, in build_library_sources sources = self.generate_sources(sources, (lib_name, build_info)) File "C:\Users\jsalvatier\workspace\numpy\numpy\distutils\command\build_src.py", line 385, in generate_sources source = func(extension, build_dir) File "numpy\core\setup.py", line 646, in get_mathlib_info st = config_cmd.try_link('int main(void) { return 0;}') File "C:\Python26\lib\distutils\command\config.py", line 257, in try_link self._check_compiler() File "C:\Users\jsalvatier\workspace\numpy\numpy\distutils\command\config.py", line 45, in _check_compiler old_config._check_compiler(self) File "C:\Python26\lib\distutils\command\config.py", line 107, in _check_compiler dry_run=self.dry_run, force=1) File "C:\Users\jsalvatier\workspace\numpy\numpy\distutils\ccompiler.py", line 560, in new_compiler compiler = klass(None, dry_run, force) File "C:\Users\jsalvatier\workspace\numpy\numpy\distutils\mingw32ccompiler.py", line 94, in __init__ msvcr_success = build_msvcr_library() File "C:\Users\jsalvatier\workspace\numpy\numpy\distutils\mingw32ccompiler.py", line 362, in build_msvcr_library generate_def(dll_file, def_file) File "C:\Users\jsalvatier\workspace\numpy\numpy\distutils\mingw32ccompiler.py", line 282, in generate_def raise ValueError("Symbol table not found") ValueError: Symbol table not found Thank you, John

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NumPy-Discussion June 2012