On Tue, Nov 16, 2010 at 10:31 AM, Darren Dale <[email protected]> wrote:
> On Tue, Nov 16, 2010 at 9:55 AM, Pauli Virtanen <[email protected]> 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/qhull.pyx#L980
>
> 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
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