[Rcpp-devel] Wrapping uBlas vectors into Rcpp Vectors.

[Romain Francois]

Le 01/06/11 14:28, Cedric Ginestet a écrit :
> Dear Romain,
>
> Thank you very much for your help. I tried what you suggested by
> including the following templated function in templatedFunction.h, as
> follows:
> template <typename T>
> Rcpp::Vector< Rcpp::traits::r_sexptype_traits<T>::rtype >
> ublas2rcpp( const vector<T>& x ){
> return Rcpp::Vector< r_sexptype_traits<T>::rtype >(
> x.begin(), x.end()
> ) ;
> }
> In addition, I have tested the function using in subgraph.cpp:
> Rcpp::Vector<int> xY = ublas2rcpp(Y);
>
> And I got the following error messages:
> templatedFunction.h: In function
> ‘Rcpp::Vector<Rcpp::traits::r_sexptype_traits<T>::rtype>
> ublas2rcpp(const boost::numeric::ublas::vector<T>&)’:
> templatedFunction.h:50:26: error: ‘r_sexptype_traits’ was not declared
> in this scope
> templatedFunction.h:50:45: error: template argument 1 is invalid
> subgraph.cpp: In function ‘SEXPREC* cxx_Mask2Graph(SEXPREC*, SEXPREC*,
> SEXPREC*, SEXPREC*)’:
> subgraph.cpp:32:19: error: type/value mismatch at argument 1 in template
> parameter list for ‘template<int RTYPE> class Rcpp::Vector’
> subgraph.cpp:32:19: error: expected a constant of type ‘int’, got ‘int’
> subgraph.cpp:32:24: error: invalid type in declaration before ‘=’ token
> subgraph.cpp:32:38: error: invalid conversion from ‘SEXPREC*’ to ‘int’
> subgraph.cpp:34:8: error: invalid conversion from ‘int’ to ‘SEXPREC*’
> ...

Sure. This was a typo/thinko: go with something like this :

template <typename T>
Rcpp::Vector< Rcpp::traits::r_sexptype_traits<T>::rtype >
ublas2rcpp( const vector<T>& x ){
     return Rcpp::Vector< Rcpp::traits::r_sexptype_traits<T>::rtype >(
         x.begin(), x.end()
     )  ;
}

and Rcpp::Vector<int> makes no sense, you probably want IntegerVector, 
or (the same class):

Rcpp::Vector< r_sexptype_traits<int>::rtype >

Rcpp::Vector is templated by the SEXP type.

> Also, as an aside, I was wondering what I should use instead of
> push_back for Rcpp Vectors. Do I necessarily have to specify the size of
> the vector before I assign its elements to specific values?

That is much better yes. ublas probably gives a way to access the size 
of the vector.

> Thanks a lot,
> Cedric
>
>
> On 01/06/11 11:44, Romain Francois wrote:
>> Hi,
>>
>> I've not used uBlas, but what you are trying to do is quite similar to
>> what we do in RcppArmadillo.
>>
>> You can probably manage to guess the output type from the input type,
>> so you only have to parameterise your template on the input type.
>> something like (untested) :
>>
>> template <typename T>
>> Rcpp::Vector< Rcpp::traits::r_sexptype_traits<T>::rtype >
>> ublas2rcpp( const vector<T>& x ){
>> return Rcpp::Vector< r_sexptype_traits<T>::rtype >(
>> x.begin(), x.end()
>> ) ;
>> }
>>
>> This way you don't have to specify template parameter when you call
>> ublas2rcpp because the compiler is smart enough.
>>
>> Nicer than this would be to implement wrap and as for ublas vectors,
>> the way to go is documented in the Rcpp-extended vignettes, with
>> examples implementations in RcppArmadillo and RcppGSL.
>>
>> As a side note, you don't want to use push_back on Rcpp types, because
>> it creates a new vector each time, so this is HUGE memory waste.
>>
>> Now, this could get much smarter as ublas has vector expressions,
>> similar to armadillo, so I suppose someone could write something like
>> RcppUBlas with nice goodies. This is not me, at least not now ;-)
>>
>> Romain
>>
>>
>> Le 01/06/11 12:24, Cedric Ginestet a écrit :
>>> Dear Rcpp experts,
>>>
>>> I have started to use the uBlas library, and I am trying to ensure that
>>> I can pass from uBlas vectors to Rcpp vectors relatively easily. So far,
>>> I have tried the following templated function:
>>>
>>> ///////////////////////////////////////////////////////////////////////
>>> using namespace Rcpp;
>>> using namespace boost::numeric::ublas;
>>>
>>> template <class T1, class T2>
>>> T1 ublas2rcpp(T2& uVec){
>>> T1 rcppVec;
>>> for(int i=0; i<uVec.size(); ++i) rcppVec.push_back(uVec(i));
>>> return rcppVec;
>>> }//ublas2rcpp.
>>>
>>> ////////
>>> SEXP foo(vector<int> &y){
>>> ...
>>> IntegerVector rcppY=ublas2rcpp<IntegerVector,vector<int> >(y);
>>> ....
>>> return rcppY;
>>> }
>>> ///////////////////////////////////////////////////////////////////////
>>>
>>> I have got two questions:
>>> a. This templated function doesn't work. It compiles fine, but hangs
>>> when I try to run it in R. What do you think is faulty in the codes
>>> above?
>>> b. Is there a better way to wrap uBlas vectors into Rcpp ones? Is that
>>> something that you are planning to implement (or have already
>>> implemented) within the Rcpp suite?
>>>
>>> Thank you very much for your help,
>>>
>>> --
>>> Cedric Ginestet, PhD
>>> Centre for Neuroimaging Sciences (L3.04)
>>> NIHR Biomedical Research Centre
>>> Department of Neuroimaging
>>> Institute of Psychiatry, Box P089
>>> King's College London
>>> De Crespigny Park
>>> London
>>> SE5 8AF
>>> http://arxiv.org/find/q-bio/1/au:+Ginestet_C/0/1/0/all/0/1
>>
>


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Romain Francois
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