C attributes cannot be added in implementation part of extension type defined in a pxd

[Zahra Sheikh]

Hello,

I am trying to use a class namely "Matrix" which is written in a cython script "matrix.pyx", in another cython script "Sampling_debugger.pyx".  Here you can find part of my codes

matrix.pyx

import ctypes

cimport numpy as np

cimport cython                                               

from libc.math cimport log, exp, pow                                              

from libc.stdint cimport *

from cython.parallel import parallel, prange

cdef class Matrix:

     

     cdef vector[double] matrix   

     cdef int _rows

     cdef int _columns

     def __cinit__(self, int rows=0, int columns=0, bint Identity=False):

         self._rows=rows

         self._columns=columns

         self.matrix.resize(rows*columns)

         if Identity:

            self._IdentityMatrix()

         

     property rows:

        def __get__(self):

            return self._rows

        def __set__(self, int x):

            self._rows = x    

     property columns:

        def __get__(self):

            return self._columns

        def __set__(self, int y):

            self._columns = y    

     cpdef double getVal(self, int r, int c):

           return self.matrix[r*self._columns+c]

 

     cpdef void setVal(self, int r, int c, double v): 

           self.matrix[r*self._columns+c] = v

matrix.pxd

from libcpp.vector cimport vector

cdef class Matrix:

     cdef public:

          int _rows

          int _columns

          bint Identity

     cpdef double getVal(self, int r, int c)

     cpdef void setVal(self, int r, int c, double v)

Sampling_debugger.pyx

import numpy as np

cimport numpy as np

cimport cython

from cython_gsl cimport *

 

from matrix cimport *

from matrix import *

cdef extern from "stdlib.h":         

    long rand()                    

    void srand(int seed)                    

cdef extern from "time.h":

    ctypedef long time_t

    time_t time(time_t*)

cdef gsl_rng *r = gsl_rng_alloc(gsl_rng_mt19937)

srand(time(NULL))

     

cdef Matrix initialWeight(double alpha, int K ):

     cdef:

          Matrix mu = Matrix(K,1)

          int i

          int seed = rand()

     #generate random seed

     gsl_rng_set(r, seed)

     cdef double prev_mu

     for i from 0 <= i < K:

         if i >= 1:

            prev_mu *= gsl_ran_beta(r, alpha, 1)            

         else:

            prev_mu = gsl_ran_beta(r, alpha, 1)

                

         mu.setVal( i, 0, prev_mu)

     return mu

 

cpdef void run( int k, double alpha):

      cdef:

          int i

          Matrix mu = initialWeight(alpha, k )           

    

      for i from 0 <= i < k:

          print mu.getVal(i,0)

      return 

and eventually, my "setup.py" script is:

from distutils.core import setup

from distutils.extension import Extension

from Cython.Distutils import build_ext

from Cython.Build import cythonize

from numpy import get_include

import numpy

import cython_gsl

modules = [

    Extension("matrix", sources=["matrix.pyx"],language="c++",libraries=cython_gsl.get_libraries(),include_dirs=[numpy.get_include(), cython_gsl.get_include()]),

    Extension("Sampling_debugger", sources=["Sampling_debugger.pyx"],language="c++",libraries=cython_gsl.get_libraries(),include_dirs=[numpy.get_include(), cython_gsl.get_include()])

]

setup(

    cmdclass={'build_ext': build_ext},

    ext_modules=cythonize(modules)

)

when I compile my scripts, I get these error messages  

cdef class Matrix:

     

     cdef vector[double] matrix   

                        ^

------------------------------------------------------------

matrix.pyx:55:25: C attributes cannot be added in implementation part of extension type defined in a pxd

Error compiling Cython file:

------------------------------------------------------------

...

     

cdef class Matrix:

     

     cdef vector[double] matrix   

     cdef int _rows

             ^

------------------------------------------------------------

matrix.pyx:56:14: C attributes cannot be added in implementation part of extension type defined in a pxd

Error compiling Cython file:

------------------------------------------------------------

...

         

cdef class Matrix:

     

     cdef vector[double] matrix   

     cdef int _rows

             ^

------------------------------------------------------------

matrix.pyx:56:14: '_rows' redeclared 

If I individually compile "matrix.pyx" without the header file "matrix.pxd", it gets compiled without any error. I will appreciate if one of the experts here explains what I am doing wrong?!!

Thanks in advance.

[Nils Bruin]

I suspect the problem is that C attributes cannot be added in implementation part of extension type defined in a pxd. The attributes "matrix" and "_rows" affect the memory layout of Matrix object. When you "cimport matrix", cython needs the memory layout of the object in order to address entries appropriately. cdef methods do not affect the memory layout of the individual objects, so it's fine to declare those in a "pyx" but not in the accompanying pxd.

[Zahra Sheikh]

So to be clear about what you suggest: I should not redeclare  "vector[double] matrix" or "int _rows" in my pxd script. Did I understand it correctly? If I remove these lines I still get this error:

 C attributes cannot be added in implementation part of extension type defined in a pxd

but no longer the following error:

'_rows' redeclared

Thanks

[Chris Barker - NOAA Federal]

On Dec 14, 2017, at 2:58 AM, Zahra Sheikh <sheikh...@gmail.com> wrote:

So to be clear about what you suggest: I should not redeclare  "vector[double] matrix" or "int _rows" in my pxd script. Did I understand it correctly?

I think you may need to do it the other way around:

Declare it in the pxd, use it in the pyx.

Pxd is for declarations, after all.

(Untested)

-CHB

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[Robert Bradshaw]

Exactly. The declaration information must be in the pxd so cimporting
modules can access it (for the aforementioned reasons of memory layout
as well as access).