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// Copyright 2018 Global Phasing Ltd.
#include <complex>
// for symmetrize_min and symmetrize_max
bool operator<(const std::complex<float>& a, const std::complex<float>& b) {
return std::norm(a) < std::norm(b);
}
bool operator>(const std::complex<float>& a, const std::complex<float>& b) {
return std::norm(a) > std::norm(b);
}
#include "gemmi/grid.hpp"
#include "gemmi/floodfill.hpp" // for flood_fill_above
#include "gemmi/solmask.hpp" // for SolventMasker, mask_points_in_constant_radius
#include "gemmi/blob.hpp" // for Blob, find_blobs_by_flood_fill
#include "gemmi/asumask.hpp" // for MaskedGrid
#include "tostr.hpp"
#include "common.h"
#include <pybind11/complex.h>
#include <pybind11/stl.h>
#include <pybind11/numpy.h>
namespace py = pybind11;
using namespace gemmi;
template<typename T>
py::class_<GridBase<T>, GridMeta> add_grid_base(py::module& m, const char* name) {
using GrBase = GridBase<T>;
using GrPoint = typename GridBase<T>::Point;
py::class_<GrBase, GridMeta> grid_base(m, name, py::buffer_protocol());
py::class_<GrPoint>(grid_base, "Point")
.def_readonly("u", &GrPoint::u)
.def_readonly("v", &GrPoint::v)
.def_readonly("w", &GrPoint::w)
.def_property("value",
[](const GrPoint& self) { return *self.value; },
[](GrPoint& self, T x) { *self.value = x; })
.def("__repr__", [=](const GrPoint& self) {
return tostr("<gemmi.", name, ".Point (", self.u, ", ", self.v, ", ",
self.w, ") -> ", +*self.value, '>');
});
grid_base
.def_buffer([](GrBase& g) {
return py::buffer_info(g.data.data(),
{g.nu, g.nv, g.nw}, // dimensions
{sizeof(T), // strides
sizeof(T) * g.nu,
sizeof(T) * g.nu * g.nv});
})
.def_property_readonly("array", [](const GrBase& g) {
return py::array_t<T>({g.nu, g.nv, g.nw},
{sizeof(T), sizeof(T) * g.nu, sizeof(T) * g.nu * g.nv},
g.data.data(), py::cast(g));
}, py::return_value_policy::reference_internal)
.def("point_to_index", &GrBase::point_to_index)
.def("index_to_point", &GrBase::index_to_point)
.def("fill", &GrBase::fill, py::arg("value"))
.def("sum", &GrBase::sum)
.def("__iter__", [](GrBase& self) { return py::make_iterator(self); },
py::keep_alive<0, 1>())
;
return grid_base;
}
template<typename T>
py::class_<Grid<T>, GridBase<T>> add_grid_common(py::module& m, const std::string& name) {
using Gr = Grid<T>;
using GrPoint = typename GridBase<T>::Point;
using Masked = MaskedGrid<T>;
py::class_<Gr, GridBase<T>> grid(m, name.c_str());
py::class_<Masked> masked_grid (m, ("Masked" + name).c_str());
grid
.def(py::init<>())
.def(py::init([](int nx, int ny, int nz) {
Gr* grid = new Gr();
grid->set_size(nx, ny, nz);
return grid;
}), py::arg("nx"), py::arg("ny"), py::arg("nz"))
.def(py::init([](py::array_t<T> arr, const UnitCell *cell, const SpaceGroup* sg) {
auto r = arr.template unchecked<3>();
Gr* grid = new Gr();
grid->set_size((int)r.shape(0), (int)r.shape(1), (int)r.shape(2));
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->set_unit_cell(*cell);
if (sg)
grid->spacegroup = sg;
return grid;
}), py::arg().noconvert(), py::arg("cell")=nullptr, py::arg("spacegroup")=nullptr)
.def_property_readonly("spacing", [](const Gr& self) {
return py::make_tuple(self.spacing[0], self.spacing[1], self.spacing[2]);
})
.def("set_size", &Gr::set_size)
.def("get_value", &Gr::get_value)
.def("set_value", &Gr::set_value)
.def("get_point", &Gr::get_point)
.def("get_nearest_point", (GrPoint (Gr::*)(const Position&)) &Gr::get_nearest_point)
.def("point_to_fractional", &Gr::point_to_fractional)
.def("point_to_position", &Gr::point_to_position)
.def("change_values", &Gr::change_values, py::arg("old_value"), py::arg("new_value"))
.def("copy_metadata_from", &Gr::copy_metadata_from)
.def("setup_from", &Gr::template setup_from<Structure>,
py::arg("st"), py::arg("spacing"))
.def("set_unit_cell", (void (Gr::*)(const UnitCell&)) &Gr::set_unit_cell)
.def("set_points_around", &Gr::set_points_around,
py::arg("position"), py::arg("radius"), py::arg("value"), py::arg("use_pbc")=true)
.def("symmetrize_min", &Gr::symmetrize_min)
.def("symmetrize_max", &Gr::symmetrize_max)
.def("symmetrize_abs_max", &Gr::symmetrize_abs_max)
.def("symmetrize_sum", &Gr::symmetrize_sum)
.def("resample_to", &Gr::resample_to, py::arg("dest"), py::arg("order"))
.def("masked_asu", &masked_asu<T>, py::keep_alive<0, 1>())
.def("mask_points_in_constant_radius", &mask_points_in_constant_radius<T>,
py::arg("model"), py::arg("radius"), py::arg("value"))
.def("get_subarray",
[](const Gr& self, std::array<int,3> start, std::array<int,3> shape) {
py::array_t<T> arr({shape[0], shape[1], shape[2]},
{sizeof(T), sizeof(T)*shape[0], sizeof(T)*shape[0]*shape[1]});
self.get_subarray((T*) arr.request().ptr, start, shape);
return arr;
}, py::arg("start"), py::arg("shape"))
.def("set_subarray",
[](Gr& self, py::array_t<T, py::array::f_style | py::array::forcecast> arr,
std::array<int,3> start) {
self.set_subarray((T*) arr.request().ptr, start,
{(int)arr.shape(0), (int)arr.shape(1), (int)arr.shape(2)});
}, py::arg("arr"), py::arg("start"))
.def("clone", [](const Gr& self) { return new Gr(self); })
.def("__repr__", [=](const Gr& self) {
return tostr("<gemmi.", name, '(', self.nu, ", ", self.nv, ", ", self.nw, ")>");
});
masked_grid
.def_readonly("grid", &Masked::grid, py::return_value_policy::reference)
.def_property_readonly("mask_array", [](const Masked& self) {
const Gr& gr = *self.grid;
py::array::ShapeContainer shape({gr.nu, gr.nv, gr.nw});
py::array::StridesContainer strides({gr.nv * gr.nw, gr.nw, 1});
return py::array_t<std::int8_t>(shape, strides, self.mask.data(), py::cast(self));
}, py::return_value_policy::reference_internal)
.def("__iter__", [](Masked& self) { return py::make_iterator(self); },
py::keep_alive<0, 1>())
;
return grid;
}
template<typename T>
void add_grid_interpolation(py::class_<Grid<T>, GridBase<T>>& grid) {
using Gr = Grid<T>;
grid
.def("interpolate_value",
(T (Gr::*)(const Fractional&) const) &Gr::interpolate_value)
.def("interpolate_value",
(T (Gr::*)(const Position&) const) &Gr::interpolate_value)
// TODO: find a better name for this func, perhaps interpolate_array?
.def("interpolate_values",
[](const Gr& self, py::array_t<T> arr, const Transform& tr, int order) {
auto r = arr.template mutable_unchecked<3>();
for (int i = 0; i < r.shape(0); ++i)
for (int j = 0; j < r.shape(1); ++j)
for (int k = 0; k < r.shape(2); ++k) {
Position pos(tr.apply(Vec3(i, j, k)));
Fractional fpos = self.unit_cell.fractionalize(pos);
r(i, j, k) = self.interpolate(fpos, order);
}
}, py::arg().noconvert(), py::arg(), py::arg("order")=2)
.def("tricubic_interpolation",
(double (Gr::*)(const Fractional&) const) &Gr::tricubic_interpolation)
.def("tricubic_interpolation",
(double (Gr::*)(const Position&) const) &Gr::tricubic_interpolation)
.def("tricubic_interpolation_der",
(std::array<double,4> (Gr::*)(const Fractional&) const)
&Gr::tricubic_interpolation_der)
;
}
void add_grid(py::module& m) {
py::enum_<AxisOrder>(m, "AxisOrder")
.value("Unknown", AxisOrder::Unknown)
.value("XYZ", AxisOrder::XYZ)
.value("ZYX", AxisOrder::ZYX);
py::class_<GridMeta>(m, "GridMeta")
.def_readwrite("spacegroup", &GridMeta::spacegroup)
.def_readwrite("unit_cell", &GridMeta::unit_cell)
.def_readonly("nu", &GridMeta::nu, "size in the first (fastest-changing) dim")
.def_readonly("nv", &GridMeta::nv, "size in the second dimension")
.def_readonly("nw", &GridMeta::nw, "size in the third (slowest-changing) dim")
.def_readonly("axis_order", &GridMeta::axis_order)
.def_property_readonly("point_count", &GridMeta::point_count)
.def("get_position", &GridMeta::get_position)
.def("get_fractional", &GridMeta::get_fractional)
.def_property_readonly("shape", [](const GridMeta& self) {
return py::make_tuple(self.nu, self.nv, self.nw);
});
add_grid_base<int8_t>(m, "Int8GridBase")
.def("get_nonzero_extent", &get_nonzero_extent<int8_t>);
add_grid_common<int8_t>(m, "Int8Grid");
add_grid_base<float>(m, "FloatGridBase")
.def("calculate_correlation", &calculate_correlation<float>)
.def("get_nonzero_extent", &get_nonzero_extent<float>)
;
auto grid_float = add_grid_common<float>(m, "FloatGrid");
add_grid_interpolation<float>(grid_float);
grid_float.def("normalize", &Grid<float>::normalize);
grid_float.def("add_soft_edge_to_mask", &add_soft_edge_to_mask<float>);
add_grid_base<std::complex<float>>(m, "ComplexGridBase");
// from solmask.hpp
py::enum_<AtomicRadiiSet>(m, "AtomicRadiiSet")
.value("VanDerWaals", AtomicRadiiSet::VanDerWaals)
.value("Cctbx", AtomicRadiiSet::Cctbx)
.value("Refmac", AtomicRadiiSet::Refmac)
.value("Constant", AtomicRadiiSet::Constant);
py::class_<SolventMasker>(m, "SolventMasker")
.def(py::init<AtomicRadiiSet, double>(),
py::arg("choice"), py::arg("constant_r")=0.)
.def_readwrite("atomic_radii_set", &SolventMasker::atomic_radii_set)
.def_readwrite("rprobe", &SolventMasker::rprobe)
.def_readwrite("rshrink", &SolventMasker::rshrink)
.def_readwrite("island_min_volume", &SolventMasker::island_min_volume)
.def_readwrite("constant_r", &SolventMasker::constant_r)
.def("set_radii", &SolventMasker::set_radii,
py::arg("choice"), py::arg("constant_r")=0.)
.def("put_mask_on_int8_grid", &SolventMasker::put_mask_on_grid<int8_t>)
.def("put_mask_on_float_grid", &SolventMasker::put_mask_on_grid<float>)
.def("set_to_zero", &SolventMasker::set_to_zero)
;
m.def("interpolate_grid", &interpolate_grid<float>,
py::arg("dest"), py::arg("src"), py::arg("tr"), py::arg("order")=2);
m.def("interpolate_grid_of_aligned_model2", &interpolate_grid_of_aligned_model2<float>,
py::arg("dest"), py::arg("src"), py::arg("tr"),
py::arg("dest_model"), py::arg("radius"), py::arg("order")=2);
// from blob.hpp
py::class_<Blob>(m, "Blob")
.def_readonly("volume", &Blob::volume)
.def_readonly("score", &Blob::score)
.def_readonly("peak_value", &Blob::peak_value)
.def_readonly("centroid", &Blob::centroid)
.def_readonly("peak_pos", &Blob::peak_pos)
;
m.def("find_blobs_by_flood_fill",
[](const Grid<float>& grid, double cutoff, double min_volume,
double min_score, double min_peak, bool negate) {
BlobCriteria crit;
crit.cutoff = cutoff;
crit.min_volume = min_volume;
crit.min_score = min_score;
crit.min_peak = min_peak;
return find_blobs_by_flood_fill(grid, crit, negate);
}, py::arg("grid"), py::arg("cutoff"), py::arg("min_volume")=10.,
py::arg("min_score")=15., py::arg("min_peak")=0., py::arg("negate")=false);
// from floodfill.hpp
m.def("flood_fill_above", &flood_fill_above,
py::arg("grid"), py::arg("seeds"), py::arg("threshold"), py::arg("negate")=false);
// from asumask.hpp
py::class_<AsuBrick>(m, "AsuBrick")
.def_readonly("size", &AsuBrick::size)
.def_readonly("incl", &AsuBrick::incl)
.def("get_extent", &AsuBrick::get_extent)
.def("str", &AsuBrick::str)
;
m.def("find_asu_brick", &find_asu_brick);
}
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