[Rcpp-devel] Wrapping uBlas Matrices into Rcpp Matrices

Romain Francois romain at r-enthusiasts.com
Mon Jun 6 13:55:26 CEST 2011 

Le 02/06/11 14:43, Cedric Ginestet a écrit :
> 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

Again untested, but you might like this constructor from Rcpp::Matrix:

	template <typename Iterator>
	Matrix( const int& nrows_, const int& ncols, Iterator start ) :
	    VECTOR( start, start + (nrows_*ncols) ),
	    nrows(nrows_)
	{
		VECTOR::attr( "dim" ) = Dimension( nrows, ncols ) ;
	}
	

So you'd use it something like this:


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.size1(), x.size2(), x.begin1()
     );
}

This is untested by guessing what would do the functions found in the 
documentation of uBlas: 
http://www.boost.org/doc/libs/1_42_0/libs/numeric/ublas/doc/matrix.htm

Romain

> 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
>>>>
>>>
>>
>>
>


-- 
Romain Francois
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