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// Copyright 2020 Global Phasing Ltd.
#include "gemmi/recgrid.hpp"
#include "gemmi/fourier.hpp" // for get_size_for_hkl, get_f_phi_on_grid
#include "tostr.hpp"
#include "common.h"
#include <pybind11/numpy.h>
#include <pybind11/stl.h>
namespace py = pybind11;
using namespace gemmi;
namespace gemmi {
std::ostream& operator<< (std::ostream& os, const ValueSigma<float>& vs) {
os << vs.value << " +/- " << vs.sigma;
return os;
}
}
template<typename T, typename F>
py::array_t<float> make_new_column(const AsuData<T>& asu_data, F f) {
if (!asu_data.unit_cell().is_crystal())
throw std::runtime_error("AsuData: unknown unit cell parameters");
py::array_t<float> arr(asu_data.size());
py::buffer_info buf = arr.request();
float* ptr = (float*) buf.ptr;
for (size_t i = 0; i < asu_data.size(); ++i)
ptr[i] = static_cast<float>(f(asu_data.unit_cell(), asu_data.get_hkl(i)));
return arr;
}
template<typename T> void add_to_asu_data(T&) {}
template<> void add_to_asu_data(py::class_<AsuData<std::complex<float>>>& cl) {
using AsuData = AsuData<std::complex<float>>;
cl.def("get_size_for_hkl", &get_size_for_hkl<AsuData>,
py::arg("min_size")=std::array<int,3>{{0,0,0}}, py::arg("sample_rate")=0.);
cl.def("data_fits_into", &data_fits_into<AsuData>, py::arg("size"));
cl.def("get_f_phi_on_grid", get_f_phi_on_grid<float, AsuData>,
py::arg("size"), py::arg("half_l")=false, py::arg("order")=AxisOrder::XYZ);
cl.def("transform_f_phi_to_map", &transform_f_phi_to_map2<float, AsuData>,
py::arg("min_size")=std::array<int,3>{{0,0,0}},
py::arg("sample_rate")=0.,
py::arg("exact_size")=std::array<int,3>{{0,0,0}},
py::arg("order")=AxisOrder::XYZ);
cl.def("calculate_correlation", [](const AsuData& self, const AsuData& other) {
return calculate_hkl_complex_correlation(self.v, other.v);
});
}
template<> void add_to_asu_data(py::class_<AsuData<float>>& cl) {
using AsuData = AsuData<float>;
cl.def("calculate_correlation", [](const AsuData& self, const AsuData& other) {
return calculate_hkl_value_correlation(self.v, other.v);
});
}
template<typename T>
void add_asudata(py::module& m, const std::string& prefix) {
py::class_<HklValue<T>>(m, (prefix + "HklValue").c_str())
.def_readonly("hkl", &HklValue<T>::hkl)
.def_readwrite("value", &HklValue<T>::value)
.def("__repr__", [prefix](const HklValue<T>& self) {
return tostr("<gemmi.", prefix, "HklValue (",
self.hkl[0], ',', self.hkl[1], ',', self.hkl[2], ") ",
self.value, '>');
});
using AsuData = AsuData<T>;
py::class_<AsuData> asu_data(m, (prefix + "AsuData").c_str());
asu_data
.def(py::init([](const UnitCell& unit_cell, const SpaceGroup* sg,
py::array_t<int> hkl, py::array_t<T> values) {
auto h = hkl.unchecked<2>();
if (h.shape(1) != 3)
throw std::domain_error("error: the size of the second dimension != 3");
auto v = values.template unchecked<1>();
if (h.shape(0) != v.shape(0))
throw std::domain_error("error: arrays have different lengths");
AsuData* ret = new AsuData;
ret->spacegroup_ = sg;
ret->unit_cell_ = unit_cell;
ret->unit_cell_.set_cell_images_from_spacegroup(ret->spacegroup_);
ret->v.reserve(h.shape(0));
for (py::ssize_t i = 0; i < h.shape(0); ++i)
ret->v.push_back({{{h(i, 0), h(i, 1), h(i, 2)}}, v(i)});
return ret;
}), py::arg("cell"), py::arg("sg").none(false),
py::arg("miller_array"), py::arg("value_array"))
.def("__iter__", [](AsuData& self) { return py::make_iterator(self.v); },
py::keep_alive<0, 1>())
.def("__len__", [](const AsuData& self) { return self.v.size(); })
.def("__getitem__", [](AsuData& self, int index) -> HklValue<T>& {
return self.v.at(normalize_index(index, self.v));
}, py::arg("index"), py::return_value_policy::reference_internal)
.def_readwrite("spacegroup", &AsuData::spacegroup_)
.def_readwrite("unit_cell", &AsuData::unit_cell_)
.def_property_readonly("miller_array", [](const AsuData& self) {
const HklValue<T>* data = self.v.data();
py::array::ShapeContainer shape({(py::ssize_t)self.v.size(), 3});
py::array::StridesContainer strides({(const char*)(data+1) - (const char*)data,
sizeof(int)});
return py::array_t<int>(shape, strides, &data->hkl[0], py::cast(self));
}, py::return_value_policy::reference_internal)
.def_property_readonly("value_array", [](const AsuData& self) {
const HklValue<T>* data = self.v.data();
py::ssize_t stride = (const char*)(data+1) - (const char*)data;
return py::array_t<T>({(py::ssize_t)self.v.size()}, {stride},
&data->value, py::cast(self));
}, py::return_value_policy::reference_internal)
.def("make_1_d2_array", [](const AsuData& asu_data) {
return make_new_column(asu_data, [](const UnitCell& cell, Miller hkl) {
return cell.calculate_1_d2(hkl);
});
})
.def("make_d_array", [](const AsuData& asu_data) {
return make_new_column(asu_data, [](const UnitCell& cell, Miller hkl) {
return cell.calculate_d(hkl);
});
})
.def("count_equal_values", [](const AsuData& self, const AsuData& other) {
return count_equal_values(self.v, other.v);
})
.def("ensure_sorted", &AsuData::ensure_sorted)
.def("ensure_asu", &AsuData::ensure_asu, py::arg("tnt_asu")=false)
.def("copy", [](const AsuData& self) {
return new AsuData(self);
})
.def("__repr__", [prefix](const AsuData& self) {
return tostr("<gemmi.", prefix, "AsuData with ", self.v.size(), " values>");
});
add_to_asu_data(asu_data);
}
template<typename TA, typename TG=TA>
void add_asudata_and_recgrid(py::module& m,
const std::string& prefix_asu,
const std::string& rgrid_name) {
using RecGr = ReciprocalGrid<TG>;
py::class_<RecGr, GridBase<TG>> recgrid(m, rgrid_name.c_str());
add_asudata<TA>(m, prefix_asu);
recgrid
.def_readonly("half_l", &RecGr::half_l)
.def(py::init<>())
.def(py::init([](int nx, int ny, int nz) {
RecGr* grid = new RecGr();
grid->set_size_without_checking(nx, ny, nz);
grid->axis_order = AxisOrder::XYZ;
return grid;
}), py::arg("nx"), py::arg("ny"), py::arg("nz"))
.def(py::init([](py::array_t<TG> arr, const UnitCell *cell, const SpaceGroup* sg) {
auto r = arr.template unchecked<3>();
RecGr* grid = new RecGr();
grid->set_size_without_checking((int)r.shape(0), (int)r.shape(1), (int)r.shape(2));
grid->axis_order = AxisOrder::XYZ;
for (int k = 0; k < r.shape(2); ++k)
for (int j = 0; j < r.shape(1); ++j)
for (int i = 0; i < r.shape(0); ++i)
grid->data[grid->index_q(i, j, k)] = r(i, j, k);
if (cell)
grid->unit_cell = *cell;
if (sg)
grid->spacegroup = sg;
return grid;
}), py::arg().noconvert(), py::arg("cell")=nullptr, py::arg("spacegroup")=nullptr)
.def("get_value", &RecGr::get_value)
.def("get_value_or_zero", &RecGr::get_value_or_zero)
.def("set_value", &RecGr::set_value)
.def("to_hkl", &RecGr::to_hkl)
.def("calculate_1_d2", &RecGr::calculate_1_d2)
.def("calculate_d", &RecGr::calculate_d)
.def("get_value_by_hkl", [](RecGr &self, py::array_t<int> hkl, double unblur, bool mott_bethe) {
auto h = hkl.unchecked<2>();
if (h.shape(1) != 3)
throw std::domain_error("error: the size of the second dimension != 3");
py::array_t<TA> vals(h.shape(0));
TA* ptr = (TA*) vals.request().ptr;
for (py::ssize_t i = 0; i < h.shape(0); ++i) {
ptr[i] = self.get_value_by_hkl({{h(i, 0), h(i, 1), h(i, 2)}}, unblur, mott_bethe);
}
return vals;
}, py::arg("hkl"), py::arg("unblur")=0, py::arg("mott_bethe")=false)
.def("prepare_asu_data", &RecGr::template prepare_asu_data<TA>,
py::arg("dmin")=0., py::arg("unblur")=0.,
py::arg("with_000")=false, py::arg("with_sys_abs")=false,
py::arg("mott_bethe")=false)
.def("__repr__", [=](const RecGr& self) {
return tostr("<gemmi.", rgrid_name, '(', self.nu, ", ", self.nv, ", ", self.nw, ")>");
});
}
void add_recgrid(py::module& m) {
using VS = ValueSigma<float>;
try {
PYBIND11_NUMPY_DTYPE(VS, value, sigma);
} catch (py::error_already_set &) {
// numpy can't be imported, that's ok
}
py::class_<VS>(m, "ValueSigma")
.def_readwrite("value", &VS::value)
.def_readwrite("sigma", &VS::sigma)
.def("__repr__", [](const VS& self) {
return tostr("<gemmi.ValueSigma(", self.value, ", ", self.sigma, ")>");
});
py::class_<ComplexCorrelation>(m, "ComplexCorrelation")
.def_readonly("n", &ComplexCorrelation::n)
.def("coefficient", &ComplexCorrelation::coefficient)
.def("mean_ratio", &ComplexCorrelation::mean_ratio)
;
add_asudata_and_recgrid<int, int8_t>(m, "Int", "ReciprocalInt8Grid");
add_asudata_and_recgrid<float>(m, "Float", "ReciprocalFloatGrid");
add_asudata_and_recgrid<std::complex<float>>(m, "Complex", "ReciprocalComplexGrid");
add_asudata<VS>(m, "ValueSigma");
}
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