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// Copyright 2019 Global Phasing Ltd.
#include "gemmi/unitcell.hpp"
#include "gemmi/refln.hpp"
#include "gemmi/fourier.hpp" // for get_size_for_hkl, get_f_phi_on_grid, ...
#include "tostr.hpp"
#include "gemmi/fprime.hpp" // for cromer_liberman
#include "gemmi/reciproc.hpp" // for count_reflections, make_miller_vector
#include "gemmi/cif2mtz.hpp" // for CifToMtz
#include "gemmi/mtz2cif.hpp" // for MtzToCif
#include "gemmi/intensit.hpp" // for Intensities
#include "gemmi/binner.hpp" // for Binner
#include "gemmi/ecalc.hpp" // for calculate_amplitude_normalizers
#include "common.h"
#include "arrvec.h" // py_array_from_vector
#include <pybind11/stl.h>
#include <pybind11/stl_bind.h>
#include <pybind11/numpy.h>
namespace py = pybind11;
using namespace gemmi;
PYBIND11_MAKE_OPAQUE(std::vector<ReflnBlock>)
namespace gemmi {
// operator<< is used by stl_bind for vector's __repr__
inline std::ostream& operator<< (std::ostream& os, const ReflnBlock& rb) {
os << "<gemmi.ReflnBlock " << rb.block.name << " with ";
if (rb.default_loop)
os << rb.default_loop->width() << " x " << rb.default_loop->length();
else
os << " no ";
os << " loop>";
return os;
}
}
void add_hkl(py::module& m) {
py::class_<ReflnBlock> pyReflnBlock(m, "ReflnBlock");
py::bind_vector<std::vector<ReflnBlock>>(m, "ReflnBlocks");
pyReflnBlock
.def_readonly("block", &ReflnBlock::block)
.def_readonly("entry_id", &ReflnBlock::entry_id)
.def_readonly("cell", &ReflnBlock::cell)
.def_readonly("spacegroup", &ReflnBlock::spacegroup)
.def_readonly("wavelength", &ReflnBlock::wavelength)
.def_readonly("default_loop", &ReflnBlock::default_loop)
.def("column_labels", &ReflnBlock::column_labels)
.def("make_int_array",
[](ReflnBlock& self, const std::string& tag, int null) {
return py_array_from_vector(self.make_vector(tag, null));
}, py::arg("tag"), py::arg("null"))
.def("make_float_array",
[](ReflnBlock& self, const std::string& tag, double null) {
return py_array_from_vector(self.make_vector(tag, null));
}, py::arg("tag"), py::arg("null")=NAN)
.def("make_miller_array", [](ReflnBlock& self) {
return py::array_t<int>(py::cast(self.make_miller_vector()));
})
.def("make_1_d2_array", [](ReflnBlock& self) {
return py_array_from_vector(self.make_1_d2_vector());
})
.def("make_d_array", [](ReflnBlock& self) {
return py_array_from_vector(self.make_d_vector());
})
.def("get_size_for_hkl",
[](const ReflnBlock& self,
std::array<int,3> min_size, double sample_rate) {
return get_size_for_hkl(ReflnDataProxy(self), min_size, sample_rate);
}, py::arg("min_size")=std::array<int,3>{{0,0,0}},
py::arg("sample_rate")=0.)
.def("data_fits_into", [](const ReflnBlock& self, std::array<int,3> size) {
return data_fits_into(ReflnDataProxy(self), size);
}, py::arg("size"))
.def("get_f_phi_on_grid", [](const ReflnBlock& self,
const std::string& f_col,
const std::string& phi_col,
std::array<int, 3> size,
bool half_l, AxisOrder order) {
size_t f_idx = self.get_column_index(f_col);
size_t phi_idx = self.get_column_index(phi_col);
FPhiProxy<ReflnDataProxy> fphi(ReflnDataProxy{self}, f_idx, phi_idx);
return get_f_phi_on_grid<float>(fphi, size, half_l, order);
}, py::arg("f"), py::arg("phi"), py::arg("size"),
py::arg("half_l")=false, py::arg("order")=AxisOrder::XYZ)
.def("get_value_on_grid", [](const ReflnBlock& self,
const std::string& column,
std::array<int, 3> size,
bool half_l, AxisOrder order) {
size_t col_idx = self.get_column_index(column);
return get_value_on_grid<float>(ReflnDataProxy(self), col_idx,
size, half_l, order);
}, py::arg("column"), py::arg("size"), py::arg("half_l")=false,
py::arg("order")=AxisOrder::XYZ)
.def("transform_f_phi_to_map", [](const ReflnBlock& self,
const std::string& f_col,
const std::string& phi_col,
std::array<int, 3> min_size,
std::array<int, 3> exact_size,
double sample_rate,
AxisOrder order) {
size_t f_idx = self.get_column_index(f_col);
size_t phi_idx = self.get_column_index(phi_col);
FPhiProxy<ReflnDataProxy> fphi(ReflnDataProxy{self}, f_idx, phi_idx);
return transform_f_phi_to_map2<float>(fphi, min_size, sample_rate,
exact_size, order);
}, py::arg("f"), py::arg("phi"),
py::arg("min_size")=std::array<int,3>{{0,0,0}},
py::arg("exact_size")=std::array<int,3>{{0,0,0}},
py::arg("sample_rate")=0.,
py::arg("order")=AxisOrder::XYZ)
.def("get_float", &make_asu_data<float, ReflnBlock>,
py::arg("col"), py::arg("as_is")=false)
.def("get_int", &make_asu_data<int, ReflnBlock>,
py::arg("col"), py::arg("as_is")=false)
.def("get_f_phi", [](const ReflnBlock& self, const std::string& f_col,
const std::string& phi_col,
bool as_is) {
return make_asu_data<std::complex<float>, 2>(self, {f_col, phi_col}, as_is);
}, py::arg("f"), py::arg("phi"), py::arg("as_is")=false)
.def("get_value_sigma", [](const ReflnBlock& self, const std::string& f_col,
const std::string& sigma_col,
bool as_is) {
return make_asu_data<ValueSigma<float>, 2>(self, {f_col, sigma_col}, as_is);
}, py::arg("f"), py::arg("sigma"), py::arg("as_is")=false)
.def("is_unmerged", &ReflnBlock::is_unmerged)
.def("use_unmerged", &ReflnBlock::use_unmerged)
.def("__bool__", [](const ReflnBlock& self) { return self.ok(); })
.def("__repr__", [](const ReflnBlock& self) { return tostr(self); })
;
m.def("as_refln_blocks",
[](cif::Document& d) { return as_refln_blocks(std::move(d.blocks)); });
m.def("hkl_cif_as_refln_block", &hkl_cif_as_refln_block, py::arg("block"));
m.def("transform_f_phi_grid_to_map", [](FPhiGrid<float> grid) {
return transform_f_phi_grid_to_map<float>(std::move(grid));
}, py::arg("grid"));
m.def("transform_map_to_f_phi", &transform_map_to_f_phi<float>,
py::arg("map"), py::arg("half_l")=false, py::arg("use_scale")=true);
m.def("cromer_liberman", [](int z, double energy) {
std::pair<double, double> r;
r.first = cromer_liberman(z, energy, &r.second);
return r;
}, py::arg("z"), py::arg("energy"));
m.def("count_reflections", &count_reflections,
py::arg("cell"), py::arg("spacegroup"), py::arg("dmin"),
py::arg("dmax")=0., py::arg("unique")=true);
m.def("make_miller_array", [](const UnitCell& cell, const SpaceGroup* sg,
double dmin, double dmax, bool unique) {
return py::array_t<int>(py::cast(
gemmi::make_miller_vector(cell, sg, dmin, dmax, unique)));
}, py::arg("cell"), py::arg("spacegroup"), py::arg("dmin"),
py::arg("dmax")=0., py::arg("unique")=true);
py::class_<CifToMtz>(m, "CifToMtz")
.def(py::init<>())
.def_readwrite("title", &CifToMtz::title)
.def_readwrite("history", &CifToMtz::history)
.def_readwrite("spec_lines", &CifToMtz::spec_lines)
.def("convert_block_to_mtz", [](const CifToMtz& self, const ReflnBlock& rb) {
std::ostringstream out;
return new Mtz(self.convert_block_to_mtz(rb, out));
})
;
py::class_<MtzToCif>(m, "MtzToCif")
.def(py::init<>())
.def_readwrite("spec_lines", &MtzToCif::spec_lines)
.def_readwrite("with_comments", &MtzToCif::with_comments)
.def_readwrite("with_history", &MtzToCif::with_history)
.def_readwrite("skip_empty", &MtzToCif::skip_empty)
.def_readwrite("skip_negative_sigi", &MtzToCif::skip_negative_sigi)
.def_readwrite("wavelength", &MtzToCif::wavelength)
.def_readwrite("free_flag_value", &MtzToCif::free_flag_value)
.def("write_cif_to_string", [](MtzToCif& self, const Mtz& mtz, const Mtz* mtz2) {
std::ostringstream out;
self.write_cif(mtz, mtz2, nullptr, out);
return out.str();
}, py::arg("mtz"), py::arg("mtz2")=nullptr)
;
py::enum_<DataType>(m, "DataType")
.value("Unknown", DataType::Unknown)
.value("Unmerged", DataType::Unmerged)
.value("Mean", DataType::Mean)
.value("Anomalous", DataType::Anomalous)
;
m.def("check_data_type_under_symmetry", [](const ReflnBlock& data) {
return check_data_type_under_symmetry(ReflnDataProxy(data));
});
m.def("check_data_type_under_symmetry", [](const Mtz& data) {
return check_data_type_under_symmetry(MtzDataProxy{data});
});
py::class_<Intensities>(m, "Intensities")
.def(py::init<>())
.def_readwrite("spacegroup", &Intensities::spacegroup)
.def_readwrite("unit_cell", &Intensities::unit_cell)
.def_readwrite("type", &Intensities::type)
.def("resolution_range", &Intensities::resolution_range)
.def("remove_systematic_absences", &Intensities::remove_systematic_absences)
.def("merge_in_place", &Intensities::merge_in_place, py::arg("itype"))
.def("read_mtz", &Intensities::read_mtz, py::arg("mtz"), py::arg("type"))
.def("prepare_merged_mtz", &Intensities::prepare_merged_mtz,
py::arg("with_nobs"))
.def_property_readonly("miller_array", [](const Intensities& self) {
const Intensities::Refl* data = self.data.data();
py::array::ShapeContainer shape({(py::ssize_t)self.data.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 Intensities& self) {
const Intensities::Refl* data = self.data.data();
py::ssize_t stride = (const char*)(data+1) - (const char*)data;
return py::array_t<double>({(py::ssize_t)self.data.size()}, {stride},
&data->value, py::cast(self));
}, py::return_value_policy::reference_internal)
.def_property_readonly("sigma_array", [](const Intensities& self) {
const Intensities::Refl* data = self.data.data();
py::ssize_t stride = (const char*)(data+1) - (const char*)data;
return py::array_t<double>({(py::ssize_t)self.data.size()}, {stride},
&data->sigma, py::cast(self));
}, py::return_value_policy::reference_internal)
.def_property_readonly("nobs_array", [](const Intensities& self) {
const Intensities::Refl* data = self.data.data();
py::ssize_t stride = (const char*)(data+1) - (const char*)data;
return py::array_t<short>({(py::ssize_t)self.data.size()}, {stride},
&data->nobs, py::cast(self));
}, py::return_value_policy::reference_internal)
.def_property_readonly("isign_array", [](const Intensities& self) {
const Intensities::Refl* data = self.data.data();
py::ssize_t stride = (const char*)(data+1) - (const char*)data;
return py::array_t<short>({(py::ssize_t)self.data.size()}, {stride},
&data->isign, py::cast(self));
}, py::return_value_policy::reference_internal)
.def("set_data", [](Intensities& self, const UnitCell& unit_cell,
const SpaceGroup* sg, py::array_t<int> hkl,
py::array_t<double> values, py::array_t<double> sigmas) {
auto h = hkl.unchecked<2>();
if (h.shape(1) != 3)
throw std::domain_error("the hkl array must have size N x 3");
auto v = values.template unchecked<1>();
auto s = sigmas.template unchecked<1>();
if (h.shape(0) != v.shape(0) || h.shape(0) != s.shape(0))
throw std::domain_error("arrays have different lengths");
self.unit_cell = unit_cell;
self.spacegroup = sg;
self.data.reserve(h.shape(0));
for (py::ssize_t i = 0; i < h.shape(0); ++i)
if (!std::isnan(v(i)) && s(i) > 0)
self.data.push_back({{{h(i, 0), h(i, 1), h(i, 2)}}, 1, 0, v(i), s(i)});
self.switch_to_asu_indices();
self.type = DataType::Unmerged;
}, py::arg("cell"), py::arg("sg").none(false),
py::arg("miller_array"), py::arg("value_array"), py::arg("sigma_array"))
;
py::class_<Binner> binner(m, "Binner");
py::enum_<Binner::Method>(binner, "Method")
.value("EqualCount", Binner::Method::EqualCount)
.value("Dstar", Binner::Method::Dstar)
.value("Dstar2", Binner::Method::Dstar2)
.value("Dstar3", Binner::Method::Dstar3)
;
binner
.def(py::init<>())
.def("setup", [](Binner& self, int nbins, Binner::Method method,
const Mtz& mtz, const UnitCell* cell) {
self.setup(nbins, method, MtzDataProxy{mtz}, cell);
}, py::arg("nbins"), py::arg("method"), py::arg("mtz"), py::arg("cell")=nullptr)
.def("setup", [](Binner& self, int nbins, Binner::Method method,
const ReflnBlock& r, const UnitCell* cell) {
self.setup(nbins, method, ReflnDataProxy(r), cell);
}, py::arg("nbins"), py::arg("method"), py::arg("r"), py::arg("cell")=nullptr)
.def("setup", [](Binner& self, int nbins, Binner::Method method,
py::array_t<int> hkl, const UnitCell* cell) {
auto h = hkl.unchecked<2>();
if (h.shape(1) != 3)
throw std::domain_error("the hkl array must have size N x 3");
std::vector<double> inv_d2(h.shape(0));
if (cell)
for (size_t i = 0; i < inv_d2.size(); ++i)
inv_d2[i] = cell->calculate_1_d2_double(h(i, 0), h(i, 1), h(i, 2));
self.setup_from_1_d2(nbins, method, std::move(inv_d2), cell);
}, py::arg("nbins"), py::arg("method"), py::arg("hkl"), py::arg("cell"))
.def("setup_from_1_d2", [](Binner& self, int nbins, Binner::Method method,
py::array_t<double> inv_d2, const UnitCell* cell) {
double* ptr = (double*) inv_d2.request().ptr;
auto len = inv_d2.shape(0);
self.setup_from_1_d2(nbins, method, std::vector<double>(ptr, ptr+len), cell);
}, py::arg("nbins"), py::arg("method"), py::arg("inv_d2"), py::arg("cell"))
.def("get_bin", &Binner::get_bin)
.def("get_bins", [](Binner& self, const Mtz& mtz) {
return py_array_from_vector(self.get_bins(MtzDataProxy{mtz}));
})
.def("get_bins", [](Binner& self, const ReflnBlock& r) {
return py_array_from_vector(self.get_bins(ReflnDataProxy(r)));
})
.def("get_bins", [](Binner& self, py::array_t<int> hkl) {
self.ensure_limits_are_set();
auto h = hkl.unchecked<2>();
if (h.shape(1) != 3)
throw std::domain_error("the hkl array must have size N x 3");
auto len = h.shape(0);
int hint = 0;
py::array_t<int> arr(len);
int* ptr = (int*) arr.request().ptr;
for (int i = 0; i < len; ++i)
ptr[i] = self.get_bin_hinted({{h(i, 0), h(i, 1), h(i, 2)}}, hint);
return arr;
})
.def("get_bins_from_1_d2", [](Binner& self, py::array_t<double> inv_d2) {
self.ensure_limits_are_set();
auto v = inv_d2.unchecked<1>();
auto len = v.shape(0);
int hint = 0;
py::array_t<int> arr(len);
int* ptr = (int*) arr.request().ptr;
for (int i = 0; i < len; ++i)
ptr[i] = self.get_bin_from_1_d2_hinted(v(i), hint);
return arr;
})
.def("dmin_of_bin", &Binner::dmin_of_bin)
.def("dmax_of_bin", &Binner::dmax_of_bin)
.def_property_readonly("size", &Binner::size)
.def_readonly("limits", &Binner::limits)
.def_readwrite("cell", &Binner::cell)
.def_readonly("min_1_d2", &Binner::min_1_d2)
.def_readonly("max_1_d2", &Binner::max_1_d2)
;
m.def("combine_correlations", &combine_correlations);
m.def("calculate_amplitude_normalizers",
[](const Mtz& mtz, const std::string& f_col, const Binner& binner) {
const Mtz::Column& f = mtz.get_column_with_label(f_col);
return py_array_from_vector(
calculate_amplitude_normalizers(MtzDataProxy{mtz}, f.idx, binner));
});
py::class_<HklMatch>(m, "HklMatch")
.def(py::init([](py::array_t<int, py::array::c_style> hkl,
py::array_t<int, py::array::c_style> ref) {
auto hkl_ = hkl.unchecked<2>();
if (hkl_.shape(1) != 3)
throw std::domain_error("the hkl array must have size N x 3");
auto ref_ = ref.unchecked<2>();
if (ref_.shape(1) != 3)
throw std::domain_error("the ref array must have size N x 3");
return new HklMatch((Miller*)hkl.request().ptr, hkl.shape(0),
(Miller*)ref.request().ptr, ref.shape(0));
}), py::arg("hkl"), py::arg("ref"))
.def("aligned", [](HklMatch& self, py::array_t<double> vec) {
auto v = vec.unchecked<1>();
if (v.shape(0) != (py::ssize_t) self.hkl_size)
fail("HklMatch.aligned(): wrong data, size differs");
py::array_t<double> result(self.pos.size());
double* ptr = (double*) result.request().ptr;
for (size_t i = 0; i != self.pos.size(); ++i)
ptr[i] = self.pos[i] >= 0 ? v(self.pos[i]) : NAN;
return result;
})
.def_readonly("pos", &HklMatch::pos)
;
}
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