Ublas vector wrapping support is broken #11
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bug
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Also add support for
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kwabenantim
changed the title
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The existing E.g, to solve the example described in this issue,
and the line
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Merged
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The solution provided in the previous comment only appears to fix some of the failures. Further investigation shows that the |
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Using the test script The program throws a I have investigated the call stack to this point with gdb, and for both zero and non-zero values, the types involved are identical. The only difference is that in the non-zero ones, the base GDB trace for non-zero value given below: |
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Possible Workaround |
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Simplified example with typecaster A simplified example seems to work fine with the current typecaster: #include <pybind11/numpy.h>
#include <pybind11/pybind11.h>
#include <pybind11/stl.h>
#include <boost/numeric/ublas/vector.hpp>
#include <memory>
#include <string>
#include <vector>
using boost::numeric::ublas::c_vector;
// Typecaster for c_vector<double, 2>
namespace pybind11
{
namespace detail
{
template <>
struct type_caster<c_vector<double, 2>>
{
public:
typedef c_vector<double, 2> c_vector_double_2_t;
PYBIND11_TYPE_CASTER(c_vector_double_2_t, const_name("c_vector_double_2_t"));
bool load(handle src, bool convert)
{
if (!convert && !array_t<double>::check_(src)) { return false; }
auto buf = array_t<double, array::c_style | array::forcecast>::ensure(src);
if (!buf) { return false; }
if (buf.ndim() != 1 or buf.shape()[0] != 2) { return false; }
value.resize(2);
for (int i = 0; i < 2; i++)
{
value[i] = buf.data()[i];
}
return true;
}
static handle cast(const c_vector<double, 2> &src, return_value_policy policy, handle parent)
{
std::vector<size_t> shape(1, 2);
std::vector<size_t> strides(1, sizeof(double));
double *data = src.size() ? const_cast<double *>(&src[0]) : static_cast<double *>(NULL);
array a(std::move(shape), std::move(strides), data);
return a.release();
}
};
}
}
// Simplified CellPopulation
template <unsigned SPACE_DIM>
class CellPopulation
{
public:
unsigned getDim() { return SPACE_DIM; }
};
template class CellPopulation<2>;
// Simplified BoundaryCondition
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
class BoundaryCondition
{
public:
BoundaryCondition(CellPopulation<SPACE_DIM> *population, c_vector<double, 2> point, c_vector<double, 2> normal)
{
_total = point[0] + point[1] + normal[0] + normal[1] + population->getDim();
}
double getTotal() { return _total; }
private:
double _total;
};
template class BoundaryCondition<2, 2>;
// Pybind11 Bindings
namespace py = pybind11;
PYBIND11_MODULE(example, m)
{
py::class_<CellPopulation<2>>(m, "CellPopulation2")
.def(py::init<>())
.def("getDim", &CellPopulation<2>::getDim);
py::class_<BoundaryCondition<2, 2>>(m, "BoundaryCondition2_2")
.def(py::init<CellPopulation<2> *, c_vector<double, 2>, c_vector<double, 2>>())
.def("getTotal", &BoundaryCondition<2, 2>::getTotal);
}
Python: import numpy as np
from example import CellPopulation2, BoundaryCondition2_2
pop = CellPopulation2()
print(pop.getDim())
point = np.array([0.0,0.0])
normal = np.array([0.1,0.0])
bc = BoundaryCondition2_2(pop, point, normal)
print(bc.getTotal()) |
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Passing Tests
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TestVertexBasedCellSimulationsPythonTutorial Error Trace OffLatticeSimulation::Solve(...);
OffLatticeSimulation::ApplyBoundaries(...);
PlaneBoundaryCondition::ImposeBoundaryCondition(...);
if (dynamic_cast<AbstractOffLatticeCellPopulation<ELEMENT_DIM, SPACE_DIM>*>(this->mpCellPopulation) == nullptr){...} |
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TestPetscToolsPython Error |
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Closing this issue as the remaining failing tests are unrelated to |
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It appears that the errors in constructors which contained |
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Describe the bug
See PyChaste/issues/4
To Reproduce
Install PyChaste from conda:
In Python:
Error
The text was updated successfully, but these errors were encountered: