On Tue, Nov 16, 2010 at 10:31 AM, Darren Dale dsdale24@gmail.com wrote:
On Tue, Nov 16, 2010 at 9:55 AM, Pauli Virtanen pav@iki.fi wrote:
Tue, 16 Nov 2010 09:41:04 -0500, Darren Dale wrote: [clip]
That loop takes 0.33 seconds to execute, which is a good start. I need some help converting this example to return an actual numpy array. Could anyone please offer a suggestion?
Easiest way is probably to use ndarray buffers and resize them when needed. For example:
https://github.com/pv/scipy-work/blob/enh/interpnd-smooth/scipy/spatial/qhul...
Thank you Pauli. That makes it *incredibly* simple:
import time cimport numpy as np import numpy as np
cdef extern from 'stdlib.h': double atof(char*)
def test(): py_string = '100' cdef char* c_string = py_string cdef int i, j cdef double val i = 0 j = 2048*1200 cdef np.ndarray[np.float64_t, ndim=1] ret
ret_arr = np.empty((2048*1200,), dtype=np.float64) ret = ret_arr
d = time.time() while i<j: c_string = py_string ret[i] = atof(c_string) i += 1 ret_arr.shape = (1200, 2048) print ret_arr, ret_arr.shape, time.time()-d
The loop now takes only 0.11 seconds to execute. Thanks again.
One follow-up issue: I can't cythonize this code for python-3. I've installed numpy with the most recent changes to the 1.5.x maintenance branch, then re-installed cython-0.13, but when I run "python3 setup.py build_ext --inplace" with this setup script:
from distutils.core import setup from distutils.extension import Extension from Cython.Distutils import build_ext
import numpy
setup( cmdclass = {'build_ext': build_ext}, ext_modules = [ Extension( "test_open", ["test_open.pyx"], include_dirs=[numpy.get_include()] ) ] )
I get the following error. Any suggestions what I need to fix, or should I report it to the cython list?
$ python3 setup.py build_ext --inplace running build_ext cythoning test_open.pyx to test_open.c
Error converting Pyrex file to C: ------------------------------------------------------------ ... # For use in situations where ndarray can't replace PyArrayObject*, # like PyArrayObject**. pass
ctypedef class numpy.ndarray [object PyArrayObject]: cdef __cythonbufferdefaults__ = {"mode": "strided"} ^ ------------------------------------------------------------
/Users/darren/.local/lib/python3.1/site-packages/Cython/Includes/numpy.pxd:173:49: "mode" is not a buffer option
Error converting Pyrex file to C: ------------------------------------------------------------ ... cdef char* c_string = py_string cdef int i, j cdef double val i = 0 j = 2048*1200 cdef np.ndarray[np.float64_t, ndim=1] ret ^ ------------------------------------------------------------
/Users/darren/temp/test/test_open.pyx:16:8: 'ndarray' is not a type identifier building 'test_open' extension /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/darren/.local/lib/python3.1/site-packages/numpy/core/include -I/opt/local/Library/Frameworks/Python.framework/Versions/3.1/include/python3.1 -c test_open.c -o build/temp.macosx-10.6-x86_64-3.1/test_open.o test_open.c:1:2: error: #error Do not use this file, it is the result of a failed Cython compilation. error: command '/usr/bin/gcc-4.2' failed with exit status 1