[Cython] c-array of numpy ndarrays?

[Brian Blais]

On May 8, 2009, at 10:27 , Dag Sverre Seljebotn wrote:

> Brian Blais wrote:
>> Hello,
>>
>> In my question for optimization of my routines, I am trying to pre- 
>> fill
>> a static c-array from a list of numpy ndarrays.  Previously, I did
>> something like:
>>
>> cdef double *w[30]
>> cdef int r[30],c[30]
>>
>> and then I'd run through my list, and get the shape info and the data
>> pointer, and fill in these arrays.  This works, but then I have to do
>> all my 2D -> 1D indexing, like:
>>
>> w[k][i+c[k]*j]
>>
>> which is ugly, and prone to typos.  I'd like to do:
>
> So the underlying problem here is that each array has a (widely
> different) size?

the underlying problem is that the difference between the following  
two pieces is about a factor of 20:

# using a list of objects, getting an array (called weights) from  
each one
# and doing some calculations
         cdef np.ndarray[DTYPE_t,ndim=2] weights

         for c in self.connections_to:
             num_incell=c.incell.N
             num_outcell=c.outcell.N
             weights=c.weights

             for __i in range(num_outcell):
                 for __j in range(num_incell):
                     a+=weights[__i,__j]


and

# using an array of structures, prefilled from a list of objects,
# getting an pointer to the data (called weights) from each one
# and doing some calculations
     cdef double *weights

     for cg from 0<=cg<number_of_connections_to:
         num_incell=s.c_num_incell[cg]
         num_outcell=s.c_num_outcell[cg]
         weights=s.c_weights[cg]

         for ni from 0<=ni<num_incell:
             for no from 0<=no<num_outcell:
                a+=weights[no+ni*num_outcell]


#===========


I think this is because of the python calls in the former, and the  
number of times I call this little snippet.  I am going to try to see  
if it is the running through the list, or the obtaining the  
attributes, which is the problem.


			bb


>
> You can always wrap the solution above into e.g. a cdef class, so that
> you can write
>
> yourspecialarrayobject.get(k, i, j)

that's a nice idea...  thanks.



			bb

--
Brian Blais
bblais at gmail.com
http://web.bryant.edu/~bblais

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