Mailman 3 December 2008 - NumPy-Discussion

PyArray_EMPTY and Cython
by Gabriel Gellner 04 Dec '08

04 Dec '08

After some discussion on the Cython lists I thought I would try my hand at writing some Cython accelerators for empty and zeros. This will involve using PyArray_EMPTY, I have a simple prototype I would like to get working, but currently it segfaults. Any tips on what I might be missing? import numpy as np cimport numpy as np cdef extern from "numpy/arrayobject.h": PyArray_EMPTY(int ndims, np.npy_intp* dims, int type, bint fortran) cdef np.ndarray empty(np.npy_intp length): cdef np.ndarray[np.double_t, ndim=1] ret cdef int type = np.NPY_DOUBLE cdef int ndims = 1 cdef np.npy_intp* dims dims = &length print dims[0] print type ret = PyArray_EMPTY(ndims, dims, type, False) return ret def test(): cdef np.ndarray[np.double_t, ndim=1] y = empty(10) return y The code seems to print out the correct dims and type info but segfaults when the PyArray_EMPTY call is made. Thanks, Gabriel

2 1

Apply a function to an array elementwise
by Elfnor 04 Dec '08

04 Dec '08

Hi I want to apply a function (myfunc which takes and returns a scalar) to each element in a multi-dimensioned array (data): I can do this: newdata = numpy.array([myfunc(d) for d in data.flat]).reshape(data.shape) But I'm wondering if there's a faster more numpy way. I've looked at the vectorize function but can't work it out. thanks Eleanor -- View this message in context: http://www.nabble.com/Apply-a-function-to-an-array-elementwise-tp20823768p2… Sent from the Numpy-discussion mailing list archive at Nabble.com.

3 2

in(np.nan) on python 2.6
by Pierre GM 04 Dec '08

04 Dec '08

All, Sorry to bump my own post, and I was kinda threadjacking anyway: Some functions of numy.ma (eg, ma.max, ma.min...) accept explicit outputs that may not be MaskedArrays. When such an explicit output is not a MaskedArray, a value that should have been masked is transformed into np.nan. That worked great in 2.5, with np.nan automatically transformed to 0 when the explicit output had a int dtype. With Python 2.6, a ValueError is raised instead, as np.nan can no longer be casted to int. What should be the recommended behavior in this case ? Raise a ValueError or some other exception, to follow the new Python2.6 convention, or silently replace np.nan by some value acceptable by int dtype (0, or something else) ? Thanks for any suggestion, P.

4 5

Re: [Numpy-discussion] Py3k and numpy
by Tommy Grav 04 Dec '08

04 Dec '08

On Dec 4, 2008, at 2:03 PM, Robert Kern wrote: > It does. What problems are people seeing? Is it just the Windows build > that causes people to say "numpy doesn't work with Python 2.6"? There is currently no official Mac OSX binary for numpy for python 2.6, but you can build it from source. Is there any time table for generating a 2.6 Mac OS X binary? Cheers Tommy

2 1

Broadcasting question
by Olivier Grisel 04 Dec '08

04 Dec '08

Hi list, Suppose I have array a with dimensions (d1, d3) and array b with dimensions (d2, d3). I want to compute array c with dimensions (d1, d2) holding the squared euclidian norms of vectors in a and b with size d3. My first take was to use a python level loop: >>> from numpy import * >>> c = array([sum((a_i - b) ** 2, axis=1) for a_i in a]) But this is too slow and allocate a useless temporary list of python references. To avoid the python level loop I then tried to use broadcasting as follows: >>> c = sum((a[:,newaxis,:] - b) ** 2, axis=2) But this build a useless and huge (d1, d2, d3) temporary array that does not fit in memory for large values of d1, d2 and d3... Do you have any better idea? I would like to simulate a runtime behavior similar to: >>> c = dot(a, b.T) but for for squared euclidian norms instead of dotproducts. I can always write a the code in C and wrap it with ctypes but I wondered whether this is possible only with numpy. -- Olivier

3 4

Compiler options for mingw?
by Zachary Pincus 04 Dec '08

04 Dec '08

Hi all, I'm curious about how to control compiler options for mingw builds of numpy on windows... Specifically, I want to build binaries without SSE support, so that they can run on older hardware. Setting a CFLAGS variable on the command-line doesn't appear to do anything, but perhaps appearances are deceiving. Thanks for any suggestions -- I've googled fruitlessly for a while. Zach

3 5

genloadtxt: second serving (tests)
by Pierre GM 04 Dec '08

04 Dec '08

And now for the tests:

1 0

Re: [Numpy-discussion] np.loadtxt : yet a new implementation...
by Pierre GM 03 Dec '08

03 Dec '08

Well, looks like the attachment is too big, so here's the implementation. The tests will come in another message.

7 21

trouble subclassing ndarray
by Sébastien Barthélemy 03 Dec '08

03 Dec '08

Hello, I'm trying to write a small library of differential geometry, and I have some trouble subclassing ndarray. I'd like an HomogeneousMatrix class that subclasse ndarray and overloads some methods, such as inv(). Here is my first try, the inv() function and the inv_v1() method work as expected, but the inv_v2() and inv_v3() methods do not change the object at all. Can somebody explain me what is happening here ? import numpy as np def inv(H): """ inverse of an homogeneous matrix """ R = H[0:3,0:3] p = H[0:3,3:4] return np.vstack( (np.hstack((R.T,-np.dot(R.T,p))), [0,0,0,1])) class HomogeneousMatrix(np.ndarray): def __new__(subtype, data=np.eye(4)): subarr = np.array(data) if htr.ishomogeneousmatrix(subarr): return subarr.view(subtype) else: raise ValueError def inv_v1(self): self[0:4,0:4] = htr.inv(self) def inv_v2(self): data = htr.inv(self) self = HomogeneousMatrix(data) def inv_v3(self): self = htr.inv(self) Thank you ! -- Sébastien

3 4

[F2PY] Fortran call fails in IDLE / PyScripter
by Christophe Chappet 03 Dec '08

03 Dec '08

>What version of gfortran are you using (i.e. exactly which binary did >you download)? GNU Fortran (GCC) 4.4.0 20080603 (experimental) [trunk revision 136333] >Is this a write to standard output "write (*,*) szText" ? yes, it is. I forgot to say that it also works with pydev in Eclipse but I'm looking for a simple interactive python shell that can execute some programs. IPython does the job but is less friendly than IDLE in term of program editing. Anyway, I think I will use it for now. Thanks for your reply. Regards, Christophe On Tue, Dec 2, 2008 at 08:26, Christophe Chappet <Christophe.Chappet(a)onera.fr <http://projects.scipy.org/mailman/listinfo/numpy-discussion>> wrote: >/ Hi all, />/ I compile the followinq code using "f2py -c --fcompiler=gnu95 />/ --compiler=mingw32" -m hello />/ subroutine AfficheMessage(szText) />/ character szText*100 />/ write (*,*) szText />/ return />/ end />/ />/ Using python console : />>>>/import hello />>>>/hello.affichemessage(" />/ Hello") />/ works fine ! />/ />/ I do the same in the program window of IDLE and : />/ - no message is displayed. />/ - the shell restart (or IDLE crah if launched with -n) />/ />/ Same problem with PyScripter IDE. (crash)./

1 0