Custom Templated as and wrap Functions within Rcpp.

James Joseph Balamuta — written Jun 25, 2016 — source

Introduction

Consider a need to be able to interface with a data type that is not presently supported by Rcpp. The data type might come from a new library, or from within one of our own applications. In either cases, Rcpp is faced with an issue of consciousness as the new data type is not similar to known types so the autocoversion or seamless R to C++ integration cannot be applied correctly. The issue is two-fold as we need to consider both directions:

Converting from R to C++ using Rcpp::as<T>(obj)
Converting from C++ to R using Rcpp::wrap(obj)

Luckily, there is a wonderful Rcpp vignette called Extending Rcpp that addresses custom objects. However, the details listed are more abstracted than one would like. So, I am going to try to take you through the steps with a bit of commentary. Please note that the approach used is via Templates and partial specialization and will result in some nice automagic at the end.

The overview of the discussion will focus on:

Stage 1 - Forward Declarations
Stage 2 - Including the Rcpp Header
Stage 3 - Implementation of Forward Declarations
Stage 4 - Testing Functionality
Stage 5 - All together

Explanation of Stages

Stage 1 - Forward Declarations

In the first stage, we must declare our intent to the features we wish to use prior to engaging Rcpp.h. To do so, we will load a different header file and add some definitions to the Rcpp::traits namespace.

Principally, when we start writing the file, the first header that we must load is RcppCommon.h and not the usual Rcpp.h!! If we do not place the forward declaration prior to the Rcpp.h call, we will be unable to appropriately register our extension.

Then, we must add in the different plugin markup for sourceCpp() to set the appropriate flags during the compilation of the code. After the plugins, we will include the actual headers that we want to use. In this document, we will focus on Boost headers for the concrete example. Lastly, we must add two special Rcpp function declaration, Rcpp::as<T>(obj) and Rcpp::wrap(obj), within the Rcpp::traits namespace. To enable multiple types, we must create an Exporter class instead of a more direct call to template <> ClassName as( SEXP ).

// -------------- Stage 1: Forward Declarations with `RcppCommon.h`

#include <RcppCommon.h>

// Flags for C++ compiler: include Boost headers, use the C++11 standard

// [[Rcpp::depends(BH)]]
// [[Rcpp::plugins("cpp11")]]

// Third party library includes that provide the template class of ublas
#include <boost/numeric/ublas/matrix_sparse.hpp>
#include <boost/numeric/ublas/matrix.hpp>

// Provide Forward Declarations
namespace Rcpp {

    namespace traits{
  
        // Setup non-intrusive extension via template specialization for
        // 'ublas' class boost::numeric::ublas
    
        // Support for wrap
        template <typename T> SEXP wrap(const boost::numeric::ublas::vector<T> & obj);
    
        // Support for as<T>
        template <typename T> class Exporter< boost::numeric::ublas::vector<T> >;
  
    }
}

Stage 2 - Include the `Rcpp.h` header

It might seem frivolous to have a stage just to declare import order, but if Rcpp.h is included before the forward declaration then Rcpp::traits is not updated and we enter the abyss. Template programming can be delicate, respecting this include order is one of many small details one must get right.

Thus:

// -------------- Stage 2: Including Rcpp.h

// ------ Place <Rcpp.h> AFTER the Forward Declaration!!!!

#include <Rcpp.h>

// ------ Place Implementations of Forward Declarations AFTER <Rcpp.h>!

Stage 3 - Implementing the Declarations

Now, we must actually implement the forward declarations. In particular, the only implementation that will be slightly problematic is the as<> since the wrap() is straight forward.

`wrap()`

To implement wrap() we must appeal to a built-in type conversion index within Rcpp which is called Rcpp::traits::r_sexptype_traits<T>::rtype. From this, we are able to obtain an int containing the RTYPE and then construct an Rcpp::Vector. For the construction of a matrix, the same ideas hold true.

`as()`

For as<>(), we need to consider the template that will be passed in. Furthermore, we setup a typedef directly underneath the Exporter class definition to easily define an OUT object to be used within the get() method. Outside of that, we use the same trick to move back and forth from a C++ T template type to an R type (implemented as one of several SEXP types).

In order to accomplish the as<>, or the direct port from R to C++, I had to do something dirty: I copied the vector contents. The code that governs this output is given within the get() of the Exporter class. You may wish to spend some time looking into changing the assignment using pointers perhaps. I am not very well versed with ublas so I did not see an easy approach to resolve the pointer pass.

// -------------- Stage 3: Implementation the Declarations

// Define template specializations for as<> and wrap
namespace Rcpp {

    namespace traits{
  
        // Defined wrap case
        template <typename T> SEXP wrap(const boost::numeric::ublas::vector<T> & obj){
            const int RTYPE = Rcpp::traits::r_sexptype_traits<T>::rtype ;
      
            return Rcpp::Vector< RTYPE >(obj.begin(), obj.end());
        };
    
    
        // Defined as< > case
        template<typename T> class Exporter< boost::numeric::ublas::vector<T> > {
            typedef typename boost::numeric::ublas::vector<T> OUT ;
      
            // Convert the type to a valid rtype. 
            const static int RTYPE = Rcpp::traits::r_sexptype_traits< T >::rtype ;
            Rcpp::Vector<RTYPE> vec;
      
            public:
            Exporter(SEXP x) : vec(x) {
                if (TYPEOF(x) != RTYPE)
                    throw std::invalid_argument("Wrong R type for mapped 1D array");
            }
            OUT get() {
        
                // Need to figure out a way to perhaps do a pointer pass?
                OUT x(vec.size());
        
                std::copy(vec.begin(), vec.end(), x.begin()); // have to copy data
        
                return x;
            }
        };
    }
}

Stage 4 - Testing

Okay, let’s see if what we worked on paid off (spoiler It did! spoiler). To check, we should look at two different areas:

Trace diagnostics within the function and;
An automagic test.

Both of which are given below. Note that I’ve opted to shorten the ublas setup to just be:

// -------------- Stage 4: Testing

// Here we define a shortcut to the Boost ublas class to enable multiple ublas
// types via a template.
// ublas::vector<T> => ublas::vector<double>, ... , ublas::vector<int>
namespace ublas = ::boost::numeric::ublas;

Trace Diagnostics

// [[Rcpp::export]]
void containment_test(Rcpp::NumericVector x1) {
  
    Rcpp::Rcout << "Converting from Rcpp::NumericVector to ublas::vector<double>" << std::endl;

    // initialize the vector to all zero
    ublas::vector<double> x = Rcpp::as< ublas::vector<double> >(x1); 
  
    Rcpp::Rcout << "Running output test with ublas::vector<double>" << std::endl;
  
    for (unsigned i = 0; i < x.size (); ++ i)
        Rcpp::Rcout  << x(i) << std::endl;
  
    Rcpp::Rcout << "Converting from ublas::vector<double> to Rcpp::NumericVector" << std::endl;
  
    Rcpp::NumericVector test = Rcpp::wrap(x);
  
    Rcpp::Rcout << "Running output test with Rcpp::NumericVector" << std::endl;
  
    for (unsigned i = 0; i < test.size (); ++ i)
        Rcpp::Rcout  << test(i) << std::endl;
  
}

Test Call:

containment_test(c(1,2,3,4))

Results:

Converting from Rcpp::NumericVector to ublas::vector<double>
Running output test with ublas::vector<double>
1
2
3
4
Converting from ublas::vector<double> to Rcpp::NumericVector
Running output test with Rcpp::NumericVector
1
2
3
4

This test performed as expected. Onto the next test!

Automagic test

// [[Rcpp::export]]
ublas::vector<double> automagic_ublas_rcpp(ublas::vector<double> x1) {
    return x1;
}

Test Call:

automagic_ublas_rcpp(c(1,2,3.2,1.2))

Results:

automagic_ublas_rcpp(c(1,2,3.2,1.2))

[1] 1.0 2.0 3.2 1.2

Success!

Stage 5 - All together

Here is the combination of the above code chunks given by stage. If you copy and paste this into your .cpp file, then everything should work. If not, let me know.

// -------------- Stage 1: Forward Declarations with `RcppCommon.h`

#include <RcppCommon.h>

// Flags for C++ compiler: include Boost headers, use the C++11 standard

// [[Rcpp::depends(BH)]]
// [[Rcpp::plugins("cpp11")]]

// Third party library includes that provide the template class of ublas
#include <boost/numeric/ublas/matrix_sparse.hpp>
#include <boost/numeric/ublas/matrix.hpp>

// Provide Forward Declarations
namespace Rcpp {

    namespace traits{
  
        // Setup non-intrusive extension via template specialization for
        // 'ublas' class boost::numeric::ublas
    
        // Support for wrap
        template <typename T> SEXP wrap(const boost::numeric::ublas::vector<T> & obj);
    
        // Support for as<T>
        template <typename T> class Exporter< boost::numeric::ublas::vector<T> >;
  
    }
}

// -------------- Stage 2: Including Rcpp.h

// ------ Place <Rcpp.h> AFTER the Forward Declaration!!!!

#include <Rcpp.h>

// ------ Place Implementations of Forward Declarations AFTER <Rcpp.h>!

// -------------- Stage 3: Implementation the Declarations

// Define template specializations for as<> and wrap
namespace Rcpp {

    namespace traits{
  
        // Defined wrap case
        template <typename T> SEXP wrap(const boost::numeric::ublas::vector<T> & obj){
            const int RTYPE = Rcpp::traits::r_sexptype_traits<T>::rtype ;
      
            return Rcpp::Vector< RTYPE >(obj.begin(), obj.end());
        };
    
    
        // Defined as< > case
        template<typename T> class Exporter< boost::numeric::ublas::vector<T> > {
            typedef typename boost::numeric::ublas::vector<T> OUT ;
      
            // Convert the type to a valid rtype. 
            const static int RTYPE = Rcpp::traits::r_sexptype_traits< T >::rtype ;
            Rcpp::Vector<RTYPE> vec;
      
            public:
            Exporter(SEXP x) : vec(x) {
                if (TYPEOF(x) != RTYPE)
                    throw std::invalid_argument("Wrong R type for mapped 1D array");
            }
            OUT get() {
        
                // Need to figure out a way to perhaps do a pointer pass?
                OUT x(vec.size());
        
                std::copy(vec.begin(), vec.end(), x.begin()); // have to copy data
        
                return x;
            }
        };
    }
}

// -------------- Stage 4: Testing

// Here we define a shortcut to the Boost ublas class to enable multiple ublas
// types via a template.
// ublas::vector<T> => ublas::vector<double>, ... , ublas::vector<int>
namespace ublas = ::boost::numeric::ublas;


// [[Rcpp::export]]
void containment_test(Rcpp::NumericVector x1) {
  
    Rcpp::Rcout << "Converting from Rcpp::NumericVector to ublas::vector<double>" << std::endl;

    // initialize the vector to all zero
    ublas::vector<double> x = Rcpp::as< ublas::vector<double> >(x1); 
  
    Rcpp::Rcout << "Running output test with ublas::vector<double>" << std::endl;
  
    for (unsigned i = 0; i < x.size (); ++ i)
        Rcpp::Rcout  << x(i) << std::endl;
  
    Rcpp::Rcout << "Converting from ublas::vector<double> to Rcpp::NumericVector" << std::endl;
  
    Rcpp::NumericVector test = Rcpp::wrap(x);
  
    Rcpp::Rcout << "Running output test with Rcpp::NumericVector" << std::endl;
  
    for (unsigned i = 0; i < test.size (); ++ i)
        Rcpp::Rcout  << test(i) << std::endl;
  
}


// [[Rcpp::export]]
ublas::vector<double> automagic_ublas_rcpp(ublas::vector<double> x1) {
    return x1;
}

Closing Remarks

Whew… That was a lot. Hopefully, the above provided enough information as you may want to extend this post’s content past 1D vectors to perhaps a ublas::matrix and so on. In addition, then you now have the autoconvert magic of Rcpp for ublas::vector<double>! Moreover, all one needs to do is specify the either the parameters or return type of the function to be ublas::vector<double> – and Voilà, automagic conversion!

tags: basics boost

Extending R with C++ and Fortran — Dirk Eddelbuettel and JBrandon Duck-Mayr
Benchmarking Rcpp code with RcppClock — Zach DeBruine
Simulation Smoother using RcppArmadillo — Tomasz Woźniak