Thanks, Dag! I appreciate your help -- that indeed fixed everything. The only surprising thing here is that the original developers of the code I'm using report no difficulties with that code as-is, using similar versions of cython. Perhaps they have some old cruft laying around from previous installs...
Anyhow, your help is appreciated, as are your efforts on integrating numpy support in cython -- I'm excited to start using this tool more! Zach On Mar 1, 2009, at 4:13 PM, Dag Sverre Seljebotn wrote: > All of these are expected, I don't see any issues here (except > perhaps lack of documentation; feel free to submit improvements). > > 1) You should set the INCLUDE environment variable prior to running > runtests.py. > > 2) cimport and import are different things; you need both. > > 3) The "dimensions" field is in Cython renamed "shape" to be closer > to the Python interface. This is done in Cython/Includes/numpy.pxd > > Dag Sverre Seljebotn > -----Original Message----- > From: Zachary Pincus <[email protected]> > Date: Sunday, Mar 1, 2009 9:35 pm > Subject: [Cython] cython / numpy / mac(?) issue > To: [email protected]: [email protected] > > Hello all, >> >> I've run into a problem using some cython+numpy code that some folks >> recently made available. After some back and forth with the original >> authors, we've determined that the problem appears to be with cython >> on my box. I've attached the offending code and will post a test-case >> below, but first some configuration details: >> >> I'm using OS X 10.5.6 and a python 2.5.2 that's installed as a >> "framework" (the standard OS X way of installing Python) -- the only >> major difference is that the python directories live in /Library/ >> Frameworks/[etc.] instead of /usr/local. >> >> First, I should note that on my system, using both the latest stable >> Cython release as well as the tip of cython-devel from hg, cython's >> numpy tests fail utterly, due to some sort of error with include >> paths: hg clone http://hg.cython.org/cython-devel/ >> cd cython-devel >> make local >> make test >> [...output...] >> compiling (c) and running numpy_test ... numpy_test.c: >> 129:31:numpy_test.c:129:31: error: error: numpy/arrayobject.h: No >> such file or directorynumpy/arrayobject.h: No such file or directory >> >> The error using cython 0.10.3 is pretty much the same, except with >> the >> spacing errors fixed: >> compiling (c) and running numpy_test ... numpy_test.c:112:31: error: >> numpy/arrayobject.h: No such file or directory >> >> Also, I should point out that the default OS X filesystem is case- >> insensitive, so using a directory named 'BUILD' for building the >> tests >> is not a great idea, as it is the same as the python 'build' >> directory, so the latter gets nuked by the 'rm -rf BUILD' in 'make >> test'. >> >> Anyhow, if I install cython despite these issues, I can build numpy- >> using projects fine... for some reason, the right include directories >> get pulled in. However, thereafter I have further issues. >> >> I've attached the troublesome code; it's pretty simple but I don't >> really know enough cython yet to pull it into a minimal test case. (I >> suspect from the nature of the errors that this should be easy.) >> >> Anyhow, here's the test case and error: >> cd stefanv-bilateral >> python setup.py build_ext -i >> python >> >> Python 2.5.2 (r252:60911, Feb 22 2008, 07:57:53) >> [GCC 4.0.1 (Apple Computer, Inc. build 5363)] on darwin >> Type "help", "copyright", "credits" or "license" for more >> information. >>>>> import numpy >>>>> print numpy.version.version >> 1.3.0.dev6359 >>>>> import Cython.Compiler.Version >>>>> print Cython.Compiler.Version.version >> 0.11.beta >>>>> import bilateral >>>>> bilateral.bilateral(numpy.zeros((4,4)), 4, 4) >> Traceback (most recent call last): >> File "<stdin>", line 1, in <module> >> File "bilateral/bilateral.py", line 38, in bilateral >> filter_fcn = _BB.Bilat_fcn(xy_sig, z_sig, filter_size) >> File "bilateral_base.pyx", line 40, in >> bilateral.bilateral_base.Bilat_fcn.__init__ (bilateral/ >> bilateral_base.c:752) >> NameError: np >> >> Now, bilateral_base.pyx has the line 'cimport numpy as np' at the >> top, >> but somehow a NameError gets thrown the first time that 'np' is used, >> at the end of this snippet: >> def __init__(self, spat_sig, inten_sig, filter_size=None): >> if filter_size is not None and filter_size >= 2: >> self.xy_size = int(filter_size) >> else: >> self.xy_size = int(round(spat_sig*4)) >> # Make filter size odd >> self.xy_size += 1-self.xy_size%2 >> x = np.arange(self.xy_size, dtype=float) >> >> >> Just for fun, I tried adding 'import numpy as np' to >> bilateral_base.pyx after the cimport line (this is what >> numpy_text.pyx >> does in the cython tests). Here then is the error that I get: >> >>>>> bilateral.bilateral(numpy.zeros((4,4)), 4, 4) >> Traceback (most recent call last): >> File "<stdin>", line 1, in <module> >> File "bilateral/bilateral.py", line 40, in bilateral >> return generic_filter(mat, filter_fcn.cfilter, size=size, >> mode=mode) >> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/ >> python2.5/site-packages/scipy/ndimage/filters.py", line 992, in >> generic_filter >> cval, origins, extra_arguments, extra_keywords) >> File "bilateral_base.pyx", line 73, in >> bilateral.bilateral_base.Bilat_fcn.cfilter (bilateral/ >> bilateral_base.c: >> 1443) >> AttributeError: 'numpy.ndarray' object has no attribute 'dimensions' >> >> This corresponds to the last line in this snippet: >> def cfilter(self, np.ndarray data): >> 'An optimized implementation' >> cdef np.ndarray kernel = self.xy_ker >> cdef double sigma = self.inten_sig >> cdef double weight_i, weight, result, centre, dat_i >> cdef double *pdata=<double *>data.data, *pker=<double >> *>kernel.data >> cdef int i, dim = data.dimensions[0] >> >> Now, numpy arrays don't expose a dimensions attribute in python, but >> the array struct has such a member, which I suppose should be exposed >> to cython via 'cimport numpy'. >> >> So, clearly something is going wrong with cython's numpy support on >> my >> system -- the tests fail, as well as actual use of numpy, but the >> failures are different. The authors of this code can't reproduce this >> with the same versions of cython and numpy on their linux systems, so >> I suspect that this might be a mac issue, perhaps relating to some >> assumptions about where the numpy headers live? >> >> On a framework install, Python.h lives in: >> /Library/Frameworks/Python.framework/Versions/2.5/include >> but numpy/arrayobject.h is in: >> /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site- >> packages/numpy/core/include >> >> >> Can anyone offer any suggestions here? >> >> Thanks, >> >> >> Zach Pincus >> Postdoctoral Fellow, lab of Frank Slack >> Molecular, Cellular and Developmental Biology >> Yale University >> >> >> >> >> > > _______________________________________________ > Cython-dev mailing list > [email protected] > http://codespeak.net/mailman/listinfo/cython-dev _______________________________________________ Cython-dev mailing list [email protected] http://codespeak.net/mailman/listinfo/cython-dev
