问题
My question is similar to the one asked here - Passing C++ vector to Numpy through Cython without copying and taking care of memory management automatically I am also getting a segmentation fault but before I can fix it I have some compilation errors to take of with the move method in Cython.
This is the simplest example I have (just an extension of the Rectangle example provided in the net
What I want to do My C++ code returns a deque of Points. It can return a vector of points as well. Any container will do
In the cython code I want to store the returned deque of points(one for each iteration of the for loop) in a collection(such as vector or deque). This collection will be an instance variable.
Later on I want to iterate through the collection and convert that deque of deque of points into a python list of lists. Here is where I believe I am getting the segmentation fault.
Point.h
#ifndef POINT_H
#define POINT_H
class Point
{
private:
double coordinate1,coordinate2;
public:
virtual double getCoordinate1() const;
virtual double getCoordinate2() const ;
virtual void setCoordinate1(double coordinate1);
virtual void setCoordinate2(double coordinate2);
};
Rectangle.h
#include <deque>
#include "Point.h"
using std:deque;
deque<Point> getAllPoints(Point query);
Rectangle.cpp
include "Rectangle.h"
deque<Point> Rectangle::getAllPoints(Point query)
{
deque<Point> deq;
for (int i = 0;i < 10000; ++i)
{
deq.push_back(query);
}
return deq;
Note Unlike the linked question I am not returning an address but returning a reference
rect.pxd
cdef extern from "<utility>" namespace "std" nogil:
T move[T](T) #
cdef extern from "Point.h":
cdef cppclass Point:
Point() nogil except +
double getCoordinate1()
double getCoordinate2()
void setCoordinate1(double coordinate1) nogil
void setCoordinate2(double coordinate2) nogil
cdef cppclass SphericalPoint(Point):
SphericalPoint() nogil except +
double getCoordinate1()
double getCoordinate2()
void setCoordinate1(double lat) nogil
void setCoordinate2(double lon) nogil
cdef extern from "Rectangle.h" namespace "shapes":
cdef cppclass Rectangle:
Rectangle(int, int, int, int) except + nogil
deque[Point] getArea(Point p) nogil
And finally
rect.pyx
cdef class PyRectangle:
cdef Rectangle *rect
cdef deque[Point] colOfPoints
def __cinit__(self, int x0, int y0, int x1, int y1):
self.rect = new Rectangle(x0, y0, x1, y1)
self.colOfPoints = deque[Point]()
def performCalc(self,maxDistance,chunk):
cdef deque[Point] area
cdef double[:,:] gPoints
gPoints = memoryview(chunk)
for i in range(0,len(gPoints)):
with nogil:
area = self.getArea(gPoints[i])
self.colOfPoints = move(area)
cdef deque[Point] getArea(self,double[:] p) nogil:
cdef deque[Point] area
area = self.rect.getArea(point)
return area
I believe I am setting the C++ 17 in setup.pyx
setup.py
os.environ['CFLAGS'] = '-O3 -Wall -std=c++17'
ext_modules = [Extension("rect",
["rect.pyx","Rectangle.cpp"],
include_dirs=['/usr/local/include'],
extra_link_args=["-std=c++17"],
language='c++',
)]
extensions = cythonize(ext_modules, language_level = "3")
I am getting these compilation errors
rect.cpp: In function ‘PyObject* __pyx_pf_4rect_11PyRectangle_6performCalc(__pyx_obj_4rect_PyRectangle*, PyObject*, PyObject*)’:
rect.cpp:3781:81: error: no matching function for call to ‘move<std::deque<Point, std::allocator<Point> > >(std::deque<Point>&)’
__pyx_v_self->colOfPoints = std::move<std::deque<Point> >(__pyx_v_area);
^
In file included from /usr/include/c++/7 /bits/nested_exception.h:40:0,
from /usr/include/c++/7/exception:143,
from /usr/include/c++/7/ios:39,
from rect.cpp:632:
/usr/include/c++/7/bits/move.h:98:5: note: candidate: template<class _Tp> constexpr typename std::remove_reference< <template-parameter-1-1> >::type&& std::move(_Tp&&)
move(_Tp&& __t) noexcept
^~~~
/usr/include/c++/7/bits/move.h:98:5: note: template argument deduction/substitution failed:
rect.cpp:3781:81: note: cannot convert ‘__pyx_v_area’ (type ‘std::deque<Point>’) to type ‘std::deque<Point>&&’
__pyx_v_self->colOfPoints = std::move<std::deque<Point> >(__pyx_v_area);
^
In file included from /usr/include/c++/7/bits/char_traits.h:39:0,
from /usr/include/c++/7/ios:40,
from rect.cpp:632:
/usr/include/c++/7/bits/stl_algobase.h:479:5: note: candidate: template<class _II, class _OI> _OI std::move(_II, _II, _OI)
move(_II __first, _II __last, _OI __result)
^~~~
/usr/include/c++/7/bits/stl_algobase.h:479:5: note: template argument deduction/substitution failed:
rect.cpp:3781:81: note: candidate expects 3 arguments, 1 provided
__pyx_v_self->colOfPoints = std::move<std::deque<Point> >(__pyx_v_area);
^
In file included from /usr/include/c++/7/deque:66:0,
from rect.cpp:636:
/usr/include/c++/7/bits/deque.tcc:1048:5: note: candidate: template<class _Tp> std::_Deque_iterator<_Tp, _Tp&, _Tp*> std::move(std::_Deque_iterator<_Tp, const _Tp&, const _Tp*>, std::_Deque_iterator<_Tp, const _Tp&, const _Tp*>, std::_Deque_iterator<_Tp, _Tp&, _Tp*>)
move(_Deque_iterator<_Tp, const _Tp&, const _Tp*> __first,
^~~~
/usr/include/c++/7/bits/deque.tcc:1048:5: note: template argument deduction/substitution failed:
rect.cpp:3781:81: note: candidate expects 3 arguments, 1 provided
__pyx_v_self->colOfPoints = std::move<std::deque<Point> >(__pyx_v_area);
^
In file included from /usr/include/c++/7/deque:64:0,
from rect.cpp:636:
/usr/include/c++/7/bits/stl_deque.h:424:5: note: candidate: template<class _Tp> std::_Deque_iterator<_Tp, _Tp&, _Tp*> std::move(std::_Deque_iterator<_Tp, _Tp&, _Tp*>, std::_Deque_iterator<_Tp, _Tp&, _Tp*>, std::_Deque_iterator<_Tp, _Tp&, _Tp*>)
move(_Deque_iterator<_Tp, _Tp&, _Tp*> __first,
^~~~
/usr/include/c++/7/bits/stl_deque.h:424:5: note: template argument deduction/substitution failed:
rect.cpp:3781:81: note: candidate expects 3 arguments, 1 provided
__pyx_v_self->colOfPoints = std::move<std::deque<Point> >(__pyx_v_area);
回答1:
Below is the slightly simplifier version that I used to reproduce your issue. I'm just including it as an illustration of how to cut your example down further - note that I don't need to use C++ files - I can just include the code directly in the pyx file by putting it in the docstring.
#distutils: language = c++
from libcpp.deque cimport deque
cdef extern from *:
"""
#include <deque>
using std::deque;
class Point{};
deque<Point> getAllPoints() {
deque<Point> deq;
for (int i=0; i<10000; ++i) {
deq.push_back(Point{});
}
return deq;
}
"""
cdef cppclass Point:
pass
deque[Point] getAllPoints()
cdef extern from "<utility>" namespace "std" nogil:
T move[T](T)
cdef class PyRectange:
cdef deque[Point] colOfPoints
def something(self):
cdef deque[Point] area = self.getArea()
self.colOfPoints = move(area)
cdef deque[Point] getArea(self):
return getAllPoints()
The basic problem is that when Cython generates C++ code for templates it writes std::move<deque<Point>>(area) rather that std::move(area) and letting C++ deduce the template type. For reasons I don't fully understand this seems to generate the wrong code a lot of the time.
I have two and a half solutions:
Don't tell Cython that
moveis a template function. Instead just tell it about the overloads you want:cdef extern from "<utility>" namespace "std" nogil: deque[Point] move(deque[Point])This is easiest I think and probably my approach.
If you avoid creating the temporary
areathen the C++ code does work with the template:self.colOfPoints = move(self.getArea())I suspect in this case you might not even need the
move- C++ will probably automatically use the move assignment operator anyway.This answer claimed to come up with a small wrapper helps Cython call the correct
move(it also slightly missed the actually problem on the question it was answering...). I haven't tested it myself, but it might be worth a go if you want a templated move.
来源：https://stackoverflow.com/questions/57344884/compilation-error-when-using-the-move-method-in-cython