Homec4science
Diffusion akantu (bugfixes/Unexpected-behaviour-in-energy-computation-structural-model) Browse

rAKA/python/py_aka_array.hh
a23d4b76944ebugfixes/Unexpected…

Last Change
Raw File

py_aka_array.hh
View Options

/**
* @file py_aka_array.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Oct 31 2018
* @date last modification: Fri Nov 13 2020
*
* @brief pybind11 interface to akantu Arrays
*
*
* @section LICENSE
*
* Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <aka_array.hh>
/* -------------------------------------------------------------------------- */
#include <pybind11/numpy.h>
#include <pybind11/pybind11.h>
/* -------------------------------------------------------------------------- */
namespace py = pybind11;
namespace _aka = akantu;
namespace akantu {
namespace detail {
template <class T> struct is_array_type : public std::false_type {};
template <class T> struct is_array_type<Vector<T>> : public std::true_type {};
template <class T> struct is_array_type<Matrix<T>> : public std::true_type {};
template <class T> struct is_array_type<Array<T>> : public std::true_type {};
/* ------------------------------------------------------------------------ */
template <typename T> class ArrayProxy : public Array<T> {
protected:
// deallocate the memory
void deallocate() final {}
// allocate the memory
void allocate(UInt /*size*/, UInt /*nb_component*/) final {}
// allocate and initialize the memory
void allocate(UInt /*size*/, UInt /*nb_component*/,
const T & /*value*/) final {}
public:
ArrayProxy(T * data, UInt size, UInt nb_component) {
this->values = data;
this->size_ = size;
this->nb_component = nb_component;
}
ArrayProxy(const Array<T> & src) {
this->values = src.storage();
this->size_ = src.size();
this->nb_component = src.getNbComponent();
}
~ArrayProxy() override { this->values = nullptr; }
void resize(UInt size, const T & /*val*/) final {
if (size != this->size()) {
AKANTU_EXCEPTION("cannot resize a temporary array");
}
//std::fill(this->begin(), this->end(), val);
}
void resize(UInt new_size) final {
if (new_size != this->size()) {
AKANTU_EXCEPTION("cannot resize a temporary array");
}
}
void reserve(UInt /*size*/, UInt /*new_size*/) final {
AKANTU_EXCEPTION("cannot resize a temporary array");
}
};
/* ------------------------------------------------------------------------ */
template <typename T> struct ProxyType {};
template <typename T> struct ProxyType<Vector<T>> { using type = Vector<T>; };
template <typename T> struct ProxyType<Matrix<T>> { using type = Matrix<T>; };
template <typename T> struct ProxyType<Array<T>> {
using type = ArrayProxy<T>;
};
template <typename array> using ProxyType_t = typename ProxyType<array>::type;
} // namespace detail
} // namespace akantu
namespace pybind11 {
namespace detail {
template <typename T> struct AkaArrayType {
using type =
array_t<typename T::value_type, array::c_style | array::forcecast>;
};
template <typename T> struct AkaArrayType<_aka::Vector<T>> {
using type = array_t<T, array::f_style | array::forcecast>;
};
template <typename T> struct AkaArrayType<_aka::Matrix<T>> {
using type = array_t<T, array::f_style | array::forcecast>;
};
template <typename U> using array_type_t = typename AkaArrayType<U>::type;
/* ------------------------------------------------------------------------ */
template <typename T>
decltype(auto) create_proxy(array_type_t<_aka::Vector<T>> & ref,
const _aka::Vector<T> * /*unused*/) {
return std::make_unique<_aka::detail::ProxyType_t<_aka::Vector<T>>>(
ref.mutable_data(), ref.shape(0));
}
template <typename T>
decltype(auto) create_proxy(array_type_t<_aka::Matrix<T>> & ref,
const _aka::Matrix<T> * /*unused*/) {
return std::make_unique<_aka::detail::ProxyType_t<_aka::Matrix<T>>>(
ref.mutable_data(), ref.shape(0), ref.shape(1));
}
template <typename T>
decltype(auto) create_proxy(array_type_t<_aka::Array<T>> & ref,
const _aka::Array<T> * /*unused*/) {
return std::make_unique<_aka::detail::ProxyType_t<_aka::Array<T>>>(
ref.mutable_data(), ref.shape(0), ref.shape(1));
}
/* ------------------------------------------------------------------------ */
template <typename T>
py::handle aka_array_cast(const _aka::Array<T> & src,
py::handle base = handle(), bool writeable = true) {
array a;
a = array_type_t<_aka::Array<T>>({src.size(), src.getNbComponent()},
src.storage(), base);
if (not writeable) {
array_proxy(a.ptr())->flags &= ~detail::npy_api::NPY_ARRAY_WRITEABLE_;
}
return a.release();
}
template <typename T>
py::handle aka_array_cast(const _aka::Vector<T> & src,
py::handle base = handle(), bool writeable = true) {
array a;
a = array_type_t<_aka::Vector<T>>({src.size()}, src.storage(), base);
if (not writeable) {
array_proxy(a.ptr())->flags &= ~detail::npy_api::NPY_ARRAY_WRITEABLE_;
}
return a.release();
}
template <typename T>
py::handle aka_array_cast(const _aka::Matrix<T> & src,
py::handle base = handle(), bool writeable = true) {
array a;
a = array_type_t<_aka::Matrix<T>>({src.size(0), src.size(1)}, src.storage(),
base);
if (not writeable) {
array_proxy(a.ptr())->flags &= ~detail::npy_api::NPY_ARRAY_WRITEABLE_;
}
return a.release();
}
/* ------------------------------------------------------------------------ */
template <typename AkaArrayType>
class type_caster<
AkaArrayType,
std::enable_if_t<_aka::detail::is_array_type<AkaArrayType>::value>> {
protected:
using T = typename AkaArrayType::value_type;
using type = AkaArrayType;
using proxy_type = _aka::detail::ProxyType_t<AkaArrayType>;
using array_type = array_type_t<AkaArrayType>;
std::unique_ptr<proxy_type> array_proxy;
array_type_t<AkaArrayType> copy_or_ref;
public:
#if PYBIND11_VERSION_MAJOR >= 2 && PYBIND11_VERSION_MINOR >= 3
static constexpr auto name = _("AkaArray");
operator type &&() && { return std::move(*array_proxy); }
template <typename T_>
using cast_op_type = pybind11::detail::movable_cast_op_type<T_>;
#else
static PYBIND11_DESCR name() { return type_descr(_("AkaArray")); };
template <typename _T>
using cast_op_type = pybind11::detail::cast_op_type<_T>;
#endif
operator type *() { return array_proxy.get(); }
operator type &() { return *array_proxy; }
/**
* Conversion part 1 (Python->C++)
*/
bool load(handle src, bool convert) {
bool need_copy = not isinstance<array_type>(src);
auto && fits = [&](auto && aref) {
auto && dims = aref.ndim();
if (dims < 1 || dims > 2) {
return false;
}
return true;
};
if (not need_copy) {
// We don't need a converting copy, but we also need to check whether
// the strides are compatible with the Ref's stride requirements
auto aref = py::cast<array_type>(src);
if (not fits(aref)) {
return false;
}
copy_or_ref = std::move(aref);
} else {
if (not convert) {
return false;
}
auto copy = array_type::ensure(src);
if (not copy) {
return false;
}
if (not fits(copy)) {
return false;
}
copy_or_ref = std::move(array_type::ensure(src));
loader_life_support::add_patient(copy_or_ref);
}
AkaArrayType * dispatch = nullptr; // cannot detect T from the expression
array_proxy = create_proxy(copy_or_ref, dispatch);
return true;
}
/**
* Conversion part 2 (C++ -> Python)
*/
static handle cast(const type & src, return_value_policy policy,
handle parent) {
switch (policy) {
case return_value_policy::copy:
return aka_array_cast<T>(src);
case return_value_policy::reference_internal:
return aka_array_cast<T>(src, parent);
case return_value_policy::reference:
case return_value_policy::automatic:
case return_value_policy::automatic_reference:
return aka_array_cast<T>(src, none());
default:
pybind11_fail("Invalid return_value_policy for ArrayProxy type");
}
}
};
} // namespace detail
} // namespace pybind11
c4science · Help