Mailman 3 May 2008 - NumPy-Discussion

segmentation fault
by Keith Goodman 28 May '08

28 May '08

Does anyone else get this seg fault? >> def fn(): x = np.random.rand(5,2) x.cumsum(None, out=x) return x ....: >> fn() *** glibc detected *** /usr/bin/python: double free or corruption (out): 0x08212dc8 *** I'm running 1.0.4 from Debian Lenny with python 2.5.2 compiled with gcc 4.2.3-3, if that matters.

10 25

proposal on ufunc shift operators.
by Charles R Harris 28 May '08

28 May '08

Hi All, Currently we have: In [2]: ones(1,dtype=int8) << ones(1,dtype=uint8) Out[2]: array([2], dtype=int16) In [4]: ones(1,dtype=int64) << ones(1,dtype=uint64) Out[4]: array([2], dtype=object) Note the increased size in the first case and the return of a Python long integer object in the second. I propose that these operators should preserve the type of the first argument, although this is not easy to do with the current ufunc setup. It is impossible to use a type of sufficient size for all shift values and preserving the type of the first argument is what I think most folks would expect. Chuck

2 1

proposal on ufunc bit ops
by Charles R Harris 28 May '08

28 May '08

Hi All, I would like to propose that the bit_ops preserve the length of the relevant types. Currently we have: In [1]: ones(1,dtype=int8) & ones(1,dtype=uint8) Out[1]: array([1], dtype=int16) In [3]: ones(1,dtype=int64) & ones(1,dtype=uint64) Out[3]: array([1], dtype=object) Note the increased size in the first case and the return of a Python long integer object in the second. As all the high order bits will be zeroed in any case when the smaller elements are sign extended, I propose that in these mixed cases an unsigned type be returned of the same size as the largest input size. I think this conforms with the rule of least surprise. Chuck

1 0

logical masking, wrong length mask
by John Hunter 28 May '08

28 May '08

I just spent a while tracking down a bug in my code, and found out the problem was numpy was letting me get away with using a logical mask of smaller size than the array it was masking. In [19]: x = np.random.rand(10) In [20]: x Out[20]: array([ 0.72253623, 0.8412243 , 0.12835194, 0.01595052, 0.62208366, 0.57229259, 0.46099861, 0.44114786, 0.23687212, 0.89507604]) In [21]: y = np.random.rand(11) In [22]: mask = x>.5 In [23]: x[mask] Out[23]: array([ 0.72253623, 0.8412243 , 0.62208366, 0.57229259, 0.89507604]) In [24]: y[mask] Out[24]: array([ 0.13440315, 0.83610533, 0.75390136, 0.79046615, 0.34776165]) In [25]: mask Out[25]: array([ True, True, False, False, True, True, False, False, False, True], dtype=bool) I initially thought line 24 below should raise an error, or coerce True to 1 and False to 0 and give me either y[0] or y[1] accordingly, but neither appear to be happening. Instead, I appear to be getting y[:len(mask)][mask] . In [27]: y[:10][mask] Out[27]: array([ 0.13440315, 0.83610533, 0.75390136, 0.79046615, 0.34776165]) In [28]: y[mask] Out[28]: array([ 0.13440315, 0.83610533, 0.75390136, 0.79046615, 0.34776165]) In [29]: len(y) Out[29]: 11 In [30]: len(mask) Out[30]: 10 In [31]: y[:len(mask)][mask] Out[31]: array([ 0.13440315, 0.83610533, 0.75390136, 0.79046615, 0.34776165]) In [32]: np.__version__ Out[32]: '1.2.0.dev5243' Bug or feature?

2 1

Binary ufuncs: minimum
by Charles R Harris 28 May '08

28 May '08

Note that min('b','Q') will fit in b. Do we want to produce a double in this case? minimum not symmetric in1 ? , b , B , h , H , i , I , l , L , q , Q , f , d , g , F , D , G , -------------------------------------------------------------------------------------- in2 ? | ? , b , B , h , H , i , I , i , I , q , Q , f , d , g , F , D , G , in2 b | b , b , h , h , i , i , q , i , q , q , d , f , d , g , F , D , G , in2 B | B , h , B , h , H , i , I , i , I , q , Q , f , d , g , F , D , G , in2 h | h , h , h , h , i , i , q , i , q , q , d , f , d , g , F , D , G , in2 H | H , i , H , i , H , i , I , i , I , q , Q , f , d , g , F , D , G , in2 i | i , i , i , i , i , i , q , i , q , q , d , d , d , g , D , D , G , in2 I | I , q , I , q , I , q , I , q , I , q , Q , d , d , g , D , D , G , in2 l | l , l , l , l , l , l , q , l , q , q , d , d , d , g , D , D , G , in2 L | L , q , L , q , L , q , L , q , L , q , Q , d , d , g , D , D , G , in2 q | q , q , q , q , q , q , q , q , q , q , d , d , d , g , D , D , G , in2 Q | Q , d , Q , d , Q , d , Q , d , Q , d , Q , d , d , g , D , D , G , in2 f | f , f , f , f , f , d , d , d , d , d , d , f , d , g , F , D , G , in2 d | d , d , d , d , d , d , d , d , d , d , d , d , d , g , D , D , G , in2 g | g , g , g , g , g , g , g , g , g , g , g , g , g , g , G , G , G , in2 F | F , F , F , F , F , D , D , D , D , D , D , F , D , G , F , D , G , in2 D | D , D , D , D , D , D , D , D , D , D , D , D , D , G , D , D , G , in2 G | G , G , G , G , G , G , G , G , G , G , G , G , G , G , G , G , G , Chuck

9 30

Current ufunc signatures for review
by Charles R Harris 27 May '08

27 May '08

Hi All, Here is the current behavior of the ufuncs and some comments. They don't yet cover mixed types for binary functions, but when they do we will see things like: In [7]: power(True,10) Out[7]: array([ 0.5822807 , 0.66568381, 0.11748811, 0.97047323, 0.60095205, 0.81218886, 0.0167618 , 0.80544138, 0.59540082, 0.82414302]) Which looks suspect ;) 1) Help strings on ufuncs don't work. This seems to be a problem with the help function, as printing the relevant __doc__ works fine. The docstrings are currently defined in code_generators/generate_umath.py and add_newdoc doesn't seem to work for them. 2) Complex divmod(), // and % are deprecated, should we make them raise errors? 3) The current behavior of remainder for complex is bizarre. Nor does it raise a deprecation warning. 4) IMHO, absolute('?') should return 'b' 5) Negative applied to '?' is equivalent to not. This gives me mixed feelings; the same functionality is covered by invert and logical_not. 6) The fmod ufunc applied to complex returns AttributeError. Shouldn't it be a TypeError? 7) Should degrees and radians work on complex? Hey, they work on booleans and it's just scaling. conjugate in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: b , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , absolute in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , f , d , g , negative in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , sign in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: b , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , invert in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: ? , b , h , i , l , q , B , H , I , L , Q , err, err, err, err, err, err, degrees in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: f , f , f , d , d , d , f , f , d , d , d , f , d , g , err, err, err, radians in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: f , f , f , d , d , d , f , f , d , d , d , f , d , g , err, err, err, arccos in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: f , f , f , d , d , d , f , f , d , d , d , f , d , g , F , D , G , arccosh in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: f , f , f , d , d , d , f , f , d , d , d , f , d , g , F , D , G , arcsin in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: f , f , f , d , d , d , f , f , d , d , d , f , d , g , F , D , G , arcsinh in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: f , f , f , d , d , d , f , f , d , d , d , f , d , g , F , D , G , arctan in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: f , f , f , d , d , d , f , f , d , d , d , f , d , g , F , D , G , arctanh in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: f , f , f , d , d , d , f , f , d , d , d , f , d , g , F , D , G , cos in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: f , f , f , d , d , d , f , f , d , d , d , f , d , g , F , D , G , sin in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: f , f , f , d , d , d , f , f , d , d , d , f , d , g , F , D , G , tan in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: f , f , f , d , d , d , f , f , d , d , d , f , d , g , F , D , G , cosh in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: f , f , f , d , d , d , f , f , d , d , d , f , d , g , F , D , G , sinh in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: f , f , f , d , d , d , f , f , d , d , d , f , d , g , F , D , G , tanh in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: f , f , f , d , d , d , f , f , d , d , d , f , d , g , F , D , G , exp in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: f , f , f , d , d , d , f , f , d , d , d , f , d , g , F , D , G , expm1 in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: f , f , f , d , d , d , f , f , d , d , d , f , d , g , F , D , G , log in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: f , f , f , d , d , d , f , f , d , d , d , f , d , g , F , D , G , log10 in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: f , f , f , d , d , d , f , f , d , d , d , f , d , g , F , D , G , log1p in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: f , f , f , d , d , d , f , f , d , d , d , f , d , g , F , D , G , sqrt in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: f , f , f , d , d , d , f , f , d , d , d , f , d , g , F , D , G , ceil in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: f , f , f , d , d , d , f , f , d , d , d , f , d , g , err, err, err, floor in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: f , f , f , d , d , d , f , f , d , d , d , f , d , g , err, err, err, fabs in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: f , f , f , d , d , d , f , f , d , d , d , f , d , g , err, err, err, rint in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: f , f , f , d , d , d , f , f , d , d , d , f , d , g , F , D , G , isnan in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , isinf in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , isfinite in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , signbit in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , err, err, err, left_shift in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: b , b , h , i , l , q , B , H , I , L , Q , err, err, err, err, err, err, right_shift in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: b , b , h , i , l , q , B , H , I , L , Q , err, err, err, err, err, err, add in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , subtract in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , multiply in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , divide in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: b , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , floor_divide in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: b , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , true_divide in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: f , f , f , d , d , d , f , f , d , d , d , f , d , g , F , D , G , fmod in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: b , b , h , i , l , q , B , H , I , L , Q , f , d , g , err, err, err, power in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: b , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , greater in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , greater_equal in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , less in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , less_equal in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , equal in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , not_equal in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , logical_and in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , logical_not in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , logical_or in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , logical_xor in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , ? , maximum in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , minimum in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , bitwise_and in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: ? , b , h , i , l , q , B , H , I , L , Q , err, err, err, err, err, err, bitwise_or in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: ? , b , h , i , l , q , B , H , I , L , Q , err, err, err, err, err, err, bitwise_xor in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: ? , b , h , i , l , q , B , H , I , L , Q , err, err, err, err, err, err, arctan2 in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: f , f , f , d , d , d , f , f , d , d , d , f , d , g , err, err, err, remainder in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: b , b , h , i , l , q , B , H , I , L , Q , f , d , g , O , O , err, hypot in: ? , b , h , i , l , q , B , H , I , L , Q , f , d , g , F , D , G , out: f , f , f , d , d , d , f , f , d , d , d , f , d , g , err, err, err, Chuck

5 12

Possible errors in type promotion in binary ufuncs
by Charles R Harris 27 May '08

27 May '08

Attached as a zip file. The mailing list is still stuck in the microzone, 40kb limit. Chuck

2 2

Dot in C extension
by jordan＠math.ucsb.edu 27 May '08

27 May '08

Hi all, I'm trying to write a Gauss-Seidel function in C++. The function works however it is too slow because I'm not using any acceleration for the vector multiplication. I'm not really sure how to access the dot function in my extension, nor what all the arguments are for. Is this the right function to use (found in ndarrayobject.h): typedef void (PyArray_DotFunc)(void *, npy_intp, void *, npy_intp, void *, npy_intp, void *); I guess the voids are array objects, the two to be dotted and the output. What's the fourth? Thanks all! Cheers

3 3

Controlling the way a module is imported
by David Cournapeau 27 May '08

27 May '08

Hi, This is not numpy specific, but I need it for numpy/scipy. More specifically, I would like to be able to have one module interface which load imp1, imp2, imp3, etc... depending on some options. I see two obvious solutions: monkey patching, and file configuration, but I try to avoid the former, and there is no mechanism for the later in scipy. I read that import hooks could be used for this purpose, but I don't quite understand the pep: http://www.python.org/dev/peps/pep-0302/ Has anyone played with it ? cheers, David

6 8

problem re-installing my own package
by lorenzo bolla 27 May '08

27 May '08

I'm having problems re-installing a package of mine, that uses numpy and scipy. can it be due to some recent changes in numpy (scons?) here is the error message I have: ======================= $ python setup.py install running install running build running scons Traceback (most recent call last): File "setup.py", line 71, in <module> setup_package() File "setup.py", line 64, in setup_package configuration = configuration) File "c:\Python25\Lib\site-packages\numpy\distutils\core.py", line 184, in setup return old_setup(**new_attr) File "c:\Python25\lib\distutils\core.py", line 151, in setup dist.run_commands() File "c:\Python25\lib\distutils\dist.py", line 974, in run_commands self.run_command(cmd) File "c:\Python25\lib\distutils\dist.py", line 994, in run_command cmd_obj.run() File "c:\Python25\Lib\site-packages\numpy\distutils\command\install.py", line 16, in run r = old_install.run(self) File "c:\Python25\lib\distutils\command\install.py", line 506, in run self.run_command('build') File "c:\Python25\lib\distutils\cmd.py", line 333, in run_command self.distribution.run_command(command) File "c:\Python25\lib\distutils\dist.py", line 994, in run_command cmd_obj.run() File "c:\Python25\Lib\site-packages\numpy\distutils\command\build.py", line 38, in run self.run_command('scons') File "c:\Python25\lib\distutils\cmd.py", line 333, in run_command self.distribution.run_command(command) File "c:\Python25\lib\distutils\dist.py", line 993, in run_command cmd_obj.ensure_finalized() File "c:\Python25\lib\distutils\cmd.py", line 117, in ensure_finalized self.finalize_options() File "c:\Python25\Lib\site-packages\numpy\distutils\command\scons.py", line 234, in finalize_options force=self.force) File "c:\Python25\Lib\site-packages\numpy\distutils\ccompiler.py", line 366, in new_compiler compiler = klass(None, dry_run, force) File "c:\Python25\Lib\site-packages\numpy\distutils\mingw32ccompiler.py", line 46, in __init__ verbose,dry_run, force) File "c:\Python25\lib\distutils\cygwinccompiler.py", line 84, in __init__ get_versions() File "c:\Python25\lib\distutils\cygwinccompiler.py", line 424, in get_versions ld_version = StrictVersion(result.group(1)) File "c:\Python25\lib\distutils\version.py", line 40, in __init__ self.parse(vstring) File "c:\Python25\lib\distutils\version.py", line 107, in parse raise ValueError, "invalid version number '%s'" % vstring ValueError: invalid version number '2.18.50.20080523' ======================= thank you in advance. L.

1 0