[Rcpp-devel] Wrapping uBlas Matrices into Rcpp Matrices

[Cedric Ginestet]

Hi again,

I have tried to do the same for Matrices. Here my naive attempt:
////////////////////////////////////////////////////////////////
template <typename T>
Rcpp::Matrix< Rcpp::traits::r_sexptype_traits<T>::rtype >
ublas2rcpp( const matrix<T>& x ){
     return Rcpp::Matrix< Rcpp::traits::r_sexptype_traits<T>::rtype >(
         x.begin(), x.end()
     );
}
//////////////////////////////////////////////////////////////
Obviously that doesn't work, and I get the following error message:
templatedFunction.h:63:5: error: ‘const class 
boost::numeric::ublas::matrix<int>’ has no member named ‘begin’
templatedFunction.h:63:5: error: ‘const class 
boost::numeric::ublas::matrix<int>’ has no member named ‘end’

I suppose that I either need to 'vectorized' the matrices or to run 
through both set of row and column indices. What is the best way to do so?

Best wishes,
Cedric


On 01/06/11 14:14, Romain Francois wrote:
> 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
>>>
>>
>
>