pybind with array as class attribute

Question

I want to wrap the following C++ code into python using pybind

class Galaxy {

public:
    double x[3];
    double v[3];

};

class GalaxyCatalogue {

public:
    long n_tracers;
    Galaxy *object;

    GalaxyCatalogue(long n_tracers);

    ~GalaxyCatalogue();

};

GalaxyCatalogue::GalaxyCatalogue(long n_tracers) : n_tracers(n_tracers) {

    std::cout << "from galaxies " << n_tracers << std::endl;
    object = new Galaxy[n_tracers];
    std::cout << "has been allocated " << std::endl;

}

GalaxyCatalogue::~GalaxyCatalogue() {

    delete[] object;

}

The first problem I have is that Galaxy doesn't have a constructor, so I'm not sure what to do with that. Even if I declare an empty constructor I don't know how to treat the array in a way that I don't get an error when compiling. This is what I've tried:

#include <pybind11/pybind11.h>
#include <iostream>
namespace py = pybind11;

class Galaxy {
   public:
  Galaxy();
 double x[3];
};

PYBIND11_MODULE(example, m){
  py::class_<Galaxy>(m, "Galaxy")
 .def(py::init<>())
 .def_readwrite("x", &Galaxy::x);
 }

This is how I compile it:

c++ -O3 -Wall -shared -std=c++11 -fPIC `python3 -m pybind11 --includes` gal.cpp -o example`python3-config --extension-suffix`

and this is the error I get:

In file included from gal.cpp:1:
/home/florpi/.conda/envs/virtualito/include/python3.5m/pybind11/pybind11.h: In instantiation of ‘pybind11::class_<type_, options>& pybind11::class_<type_, options>::def_readwrite(const char*, D C::*, const Extra& ...) [with C = Galaxy; D = double [3]; Extra = {}; type_ = Galaxy; options = {}]’:
gal.cpp:19:33:   required from here
/home/florpi/.conda/envs/virtualito/include/python3.5m/pybind11/pybind11.h:1163:65: error: invalid array assignment
                      fset([pm](type &c, const D &value) { c.*pm = value; }, is_method(*this));
                                                           ~~~~~~^~~~~~~
In file included from gal.cpp:1:

/home/florpi/.conda/envs/virtualito/include/python3.5m/pybind11/pybind11.h:64:5: error: ‘pybind11::cpp_function::cpp_function(Func&&, const Extra& ...) [with Func = pybind11::class_<type_, options>::def_readwrite(const char*, D C::*, const Extra& ...) [with C = Galaxy; D = double [3]; Extra = {}; type_ = Galaxy; options = {}]::<lambda(pybind11::class_<Galaxy>::type&, const double (&)[3])>; Extra = {pybind11::is_method}; <template-parameter-1-3> = void]’, declared using local type ‘pybind11::class_<type_, options>::def_readwrite(const char*, D C::*, const Extra& ...) [with C = Galaxy; D = double [3]; Extra = {}; type_ = Galaxy; options = {}]::<lambda(pybind11::class_<Galaxy>::type&, const double (&)[3])>’, is used but never defined [-fpermissive]
     cpp_function(Func &&f, const Extra&... extra) {
     ^~~~~~~~~~~~

Thank you in advance.

Peter · Accepted Answer · 2018-09-04 18:33:34Z

2

In C++, you can't assign directly to an array, which is what pybind11 is trying to do inside its wrapping magic. In general, C++ arrays are not great abstractions for numerical arrays. As you've noticed, you can't even say galaxy.x = other_galaxy.x.

Your best bet is to use a higher-level library for matrices and vectors, which will a) give you a much better experience writing your C++ b) perform better c) map more cleanly to Python

Eigen is a good choice. pybind11 automatically knows how to map Eigen matrices and vectors to numpy arrays. Your Galaxy would become:

class Galaxy {
  public:
    Eigen::Vector3d x;
    Eigen::Vector3d v;
};

If you absolutely can't do this, you'll have to supply manual getter/setter functions to the property, where you do your own conversion to and from python types: https://pybind11.readthedocs.io/en/master/classes.html?highlight=def_property#instance-and-static-fields

answered Sep 4, 2018 at 18:33

Peter

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1 Comment

Tom de Geus Over a year ago

Should you use exclusively 'lists' and you don't want to use another third-partly library you can also use std::vector, which is also wrapped by pybind11.

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