Mailman 3 December 2006 - NumPy-Discussion

shuffle bug
by Tom Holroyd 08 Dec '06

08 Dec '06

This is certainly a bug. It has been mentioned before, but there was no comment. shuffle() doesn't handle arrays. >>> from numpy import * >>> from numpy.random import * >>> a = arange(12) >>> a.shape = (6,2) >>> a array([[ 0, 1], [ 2, 3], [ 4, 5], [ 6, 7], [ 8, 9], [10, 11]]) >>> shuffle(a) >>> a array([[ 0, 1], [ 2, 3], [ 2, 3], [ 0, 1], [ 4, 5], [10, 11]]) This is with numpy 1.0. The [0, 1] element was duplicated. That's not right. Tom Holroyd, Ph.D. We experience the world not as it is, but as we expect it to be.

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installation error in cygwin
by Wei 08 Dec '06

08 Dec '06

Hi, I just got my new intel core duo laptop. So I downloaded the new cygwin (including everything) but couldn't get the numarray or numpy modules installed correctly. I always got the following error. Can some one help? Many thanks! Wei python setup.py install Using EXTRA_COMPILE_ARGS = [] Using builtin 'lite' BLAS and LAPACK running config Wrote config.h running install running build running build_py copying Lib/numinclude.py -> build/lib.cygwin-1.5.22-i686-2.4/numarray running build_ext building 'numarray.libnumarray' extension gcc -shared -Wl,--enable-auto-image-base build/temp.cygwin-1.5.22-i686-2.4/Src/libnumarraymodule.o -L/usr/lib/python2.4/config -lpython2.4 -o build/lib.cygwin-1.5.22-i686-2.4/numarray/libnumarray.dll -lm -L/lib -lm -lc -lgcc -L/lib/mingw -lmingwex /lib/mingw/libmingwex.a(feclearexcept.o):feclearexcept.c:(.text+0x21): undefined reference to `___cpu_features' /lib/mingw/libmingwex.a(fetestexcept.o):fetestexcept.c:(.text+0x7): undefined reference to `___cpu_features' collect2: ld returned 1 exit status error: command 'gcc' failed with exit status 1

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pickling arrays: numpy 1.0 can't unpickle numpy 1.0.1
by Emanuele Olivetti 08 Dec '06

08 Dec '06

I'm running numpy 1.0 and 1.0.1 on several hosts and today I've found that pickling arrays in 1.0.1 generates problems to 1.0. An example: --- numpy 1.0.1 --- import numpy import pickle a = numpy.array([1,2,3]) f=open('test1.pickle','w') pickle.dump(a,f) f.close() --- If I unpickle test1.pickle in numpy 1.0 I got: --- numpy 1.0 >>> import numpy >>> import pickle >>> f=open('test1.pickle') >>> a=pickle.load(f) Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/hardmnt/virgo0/sra/olivetti/myapps/lib/python2.5/pickle.py", line 1370, in load return Unpickler(file).load() File "/hardmnt/virgo0/sra/olivetti/myapps/lib/python2.5/pickle.py", line 858, in load dispatch[key](self) File "/hardmnt/virgo0/sra/olivetti/myapps/lib/python2.5/pickle.py", line 1217, in load_build setstate(state) TypeError: argument 1 must be sequence of length 5, not 8 ----------------- How can I let access pickled arrays made in numpy 1.0.1 to numpy 1.0 ? Help! Thanks in advance, Emanuele

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Strange numpy behaviour with pickle
by Jerome Fuselier 08 Dec '06

08 Dec '06

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Numpy and Python 2.2 on RHEL3
by David Bogen 07 Dec '06

07 Dec '06

All: Is it possible to build Numpy using Python 2.2? I haven't been able to find anything that explicitly lists the versions of Python with which Numpy functions so I've been working under the assumption that the two bits will mesh together somehow. When I try to build Numpy 1.0.1 on RedHat Enterprise Linux 3 using Python 2.2.3, I get the following error: $ /usr/bin/python2.2 setup.py build Running from numpy source directory. Traceback (most recent call last): File "setup.py", line 89, in ? setup_package() File "setup.py", line 59, in setup_package from numpy.distutils.core import setup File "numpy/distutils/__init__.py", line 5, in ? import ccompiler File "numpy/distutils/ccompiler.py", line 11, in ? import log File "numpy/distutils/log.py", line 4, in ? from distutils.log import * ImportError: No module named log Through extensive trial and error I've been able to hack the distutils files enough to make that error go away, but then I start getting an error describing an invalid syntax with the directive "yield os.path" which seems to be a deeper, more complex error to fix. Am I attempting the impossible here or am I just doing something fundamentally and obviously wrong? David -- David Bogen :: (608) 263-0168 Unix SysAdmin :: IceCube Project david.bogen(a)icecube.wisc.edu

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numarray-1.5.2 and Py_NONE refcount crash
by Daniel Drake 07 Dec '06

07 Dec '06

Hi, I know that numarray is outdated now, but it's too big a job to change to numpy right now. On the offchance that someone can help: After upgrading from numarray-1.3.1 to numarray-1.5.2, we get occasional crashes where python tries to free Py_NONE I'm aware of the NA_FromDimsStridesDescrAndData fix at http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=399440 however this doesn't solve the problem here and that particular function doesn't seem to be in our codepath anyway. Any ideas? Thanks -- Daniel Drake Brontes Technologies, A 3M Company

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Re: [Numpy-discussion] equivalent to isempty command in matlab (newbie question), (Robert Kern)
by Giorgio Luciano 07 Dec '06

07 Dec '06

> Today's Topics: > > 1. Re: equivalent to isempty command in matlab (newbie question) > (Robert Kern) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 06 Dec 2006 11:20:19 -0600 > From: Robert Kern <robert.kern(a)gmail.com> > Subject: Re: [Numpy-discussion] equivalent to isempty command in > matlab (newbie question) > To: Discussion of Numerical Python <numpy-discussion(a)scipy.org> > Message-ID: <4576FBD3.3090601(a)gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Filip Wasilewski wrote: > > >> Just like for other Python objects: >> >> if ifs3: >> print "not empty" >> > > No, that doesn't work. numpy arrays do not have a truth value. They raise an > error when you try to use them in such a context. > > Does it exist a workaround for that to make numpy understand when an array is empty ? Giorgio

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Indices returned by where()
by Christian Marquardt 07 Dec '06

07 Dec '06

Dear list, apologies if the answer to my question is obvious... Is the following intentional? $>python Python 2.4 (#1, Mar 22 2005, 21:42:42) [GCC 3.3.5 20050117 (prerelease) (SUSE Linux)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import numpy as np >>> print np.__version__ 1.0 >>> x = np.array([1., 2., 3., 4., 5.]) >>> idx = np.where(x > 6.) >>> print len(idx) 1 The reason is of course that where() returns a tuple of index arrays instead of simply an index array: >>> print idx (array([], dtype=int32),) Does that mean that one always has to explicitely request the first element of the returned tuple in order to check how many matches were found, even for 1d arrays? What's the reason for designing it that way? Many thanks, Christian

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Overlapping copy with object_ arrays
by James Flowers 06 Dec '06

06 Dec '06

Hello, Having a problem with overlapping copies. Memory being freed twice ??? See below: ActivePython 2.4.3 Build 11 (ActiveState Software Inc.) based on Python 2.4.3 (#1, Apr 3 2006, 18:07:14) [GCC 4.0.1 (Apple Computer, Inc. build 5247)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import numpy >>> print numpy.__version__ 1.0.1 >>> x = numpy.zeros(10, numpy.object_) >>> x[:] = [], # set the array to empy lists >>> x[0] is x[1] # everyone is of course identical True >>> x[3:-1] = x[4:] # overlappping copy >>> x # all is right in the universe array([[], [], [], [], [], [], [], [], [], []], dtype=object) >>> for i in range(10): x[i] = [] # set the array with a loop ... >>> x[0] is x[1] # everyone is of course different False >>> x[3:-1] = x[4:] # overlapping copy >>> x # oops, situation not OK, heap apparently corrupted by overlapping copy Bus error Jim ____________________________________________________________________________________ Cheap talk? Check out Yahoo! Messenger's low PC-to-Phone call rates. http://voice.yahoo.com

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Resizing without allocating additional memory
by David Huard 06 Dec '06

06 Dec '06

Hi, I have fortran subroutines wrapped with f2py that take arrays as arguments, and I often need to use resize(a, N) to pass an array of copies of an element. The resize call , however, is becoming the speed bottleneck, so my question is: Is it possible to create an (1xN) array from a scalar without allocating additional memory for the array, ie just return a new "view" of the array where all elements point to the same scalar. Thanks, David

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