IMPEM2D_BEGIN_INTERNAL_NAMESPACE
ProjectionSphere::ProjectionSphere(unsigned int n, double r) :
grid_(0.1, // voxel size
IMP::algebra::BoundingBox3D(IMP::algebra::Vector3D(-1.01, -1.01, -1.01),
IMP::algebra::Vector3D(1.01, 1.01, 1.01))) {
IMP::algebra::SphericalVector3Ds spherical_coords;
quasi_evenly_spherical_distribution(n, spherical_coords, r);
// convert sphere coordinate to rotation and axis
for (unsigned int i = 0; i < spherical_coords.size(); i++) {
IMP::algebra::SphericalVector3D v = spherical_coords[i];
double cy = cos(v[1] / 2.0);
double cz = cos(v[2] / 2.0);
double sy = sin(v[1] / 2.0);
double sz = sin(v[2] / 2.0);
// this is a rotation about z axis by an angle v[2]
// followed by rotation about y axis by an angle v[1]
IMP::algebra::Rotation3D r(cy * cz, sy * sz, sy * cz, cy * sz);
rotations_.push_back(r);
axes_.push_back(v.get_cartesian_coordinates());
}
// fill grid
for (unsigned int i = 0; i < axes_.size(); i++) {
Grid::Index grid_index = grid_.get_nearest_index(axes_[i]);
grid_[grid_index].push_back(i);
}
}
void compute_projections(const Particles& all_particles,
const Particles& lig_particles,
unsigned int projection_number,
double pixel_size, double resolution,
boost::ptr_vector<Projection>& projections,
int image_size) {
// get coordinates, radius and mass
IMP::algebra::Vector3Ds all_points(all_particles.size());
std::vector<double> all_radii(all_particles.size());
for (unsigned int i = 0; i < all_particles.size(); i++) {
all_points[i] = core::XYZ(all_particles[i]).get_coordinates();
all_radii[i] = core::XYZR(all_particles[i]).get_radius();
}
IMP::algebra::Vector3Ds lig_points(lig_particles.size());
std::vector<double> lig_radii(lig_particles.size());
std::vector<double> lig_mass(lig_particles.size());
for (unsigned int i = 0; i < lig_particles.size(); i++) {
lig_points[i] = core::XYZ(lig_particles[i]).get_coordinates();
lig_radii[i] = core::XYZR(lig_particles[i]).get_radius();
lig_mass[i] = atom::Mass(lig_particles[i]).get_mass();
}
int axis_size = image_size;
// use image_size if given
if (!(image_size > 0)) {
double max_dist = compute_max_distance(all_points);
static IMP::em::KernelParameters kp(resolution);
double radius = 3.0;
const IMP::em::RadiusDependentKernelParameters& params =
kp.get_params(radius);
double wrap_length = 2 * params.get_kdist() + 1.0;
axis_size =
(int)((max_dist + 2 * wrap_length + 2 * pixel_size) / pixel_size + 2);
if (axis_size <= image_size) axis_size = image_size;
}
// storage for rotated points
IMP::algebra::Vector3Ds rotated_points(all_points.size());
IMP::algebra::Vector3Ds rotated_ligand_points(lig_points.size());
// points on a sphere
IMP::algebra::SphericalVector3Ds spherical_coords;
quasi_evenly_spherical_distribution(projection_number, spherical_coords, 1.0);
for (unsigned int i = 0; i < spherical_coords.size(); i++) {
// convert sphere coordinate to rotation
IMP::algebra::SphericalVector3D v = spherical_coords[i];
double cy = cos(v[1] / 2.0);
double cz = cos(v[2] / 2.0);
double sy = sin(v[1] / 2.0);
double sz = sin(v[2] / 2.0);
// this is a rotation about z axis by an angle v[2]
// followed by rotation about y axis by an angle v[1]
IMP::algebra::Rotation3D r(cy * cz, sy * sz, sy * cz, cy * sz);
// rotate points
for (unsigned int p_index = 0; p_index < all_points.size(); p_index++)
rotated_points[p_index] = r * all_points[p_index];
for (unsigned int p_index = 0; p_index < lig_points.size(); p_index++)
rotated_ligand_points[p_index] = r * lig_points[p_index];
// project
std::auto_ptr<Projection> p(
new Projection(rotated_points, rotated_ligand_points, lig_radii,
lig_mass, pixel_size, resolution, axis_size));
p->set_rotation(r);
p->set_axis(IMP::algebra::Vector3D(v.get_cartesian_coordinates()));
p->set_id(i);
// rasmol
// std::cout << "#projection " << i+1 <<"\nreset\nrotate Z "
//<< IMP_RAD_2_DEG(v[2]);
// std::cout << "\nrotate Y -" << IMP_RAD_2_DEG(v[1]) << std::endl;
// chimera
// std::cout << "#projection " << i+1
//<<"\nreset;turn x 180; turn z -" << IMP_RAD_2_DEG(v[2]);
// std::cout << ";turn y -" << IMP_RAD_2_DEG(v[1])
//<< ";wait;sleep 3;"<< std::endl;
// string file_name = "projection_" +
// string(boost::lexical_cast<string>(i+1)) + ".pgm";
// p.write_PGM(file_name);
projections.push_back(p.release());
}
}
void compute_projections(const Particles& particles,
unsigned int projection_number, double pixel_size,
double resolution,
boost::ptr_vector<Projection>& projections,
int image_size) {
// get coordinates, radius and mass
IMP::algebra::Vector3Ds points(particles.size());
std::vector<double> mass(particles.size());
for (unsigned int i = 0; i < particles.size(); i++) {
points[i] = core::XYZ(particles[i]).get_coordinates();
mass[i] = atom::Mass(particles[i]).get_mass();
}
// estimate max image size
double max_dist = compute_max_distance(points);
static IMP::em::KernelParameters kp(resolution);
double wrap_length = 2 * kp.get_rkdist() + 1.0;
int axis_size =
(int)((max_dist + 2 * wrap_length + 2 * pixel_size) / pixel_size + 2);
if (axis_size <= image_size) axis_size = image_size;
// storage for rotated points
IMP::algebra::Vector3Ds rotated_points(points.size());
// points on sphere
IMP::algebra::SphericalVector3Ds spherical_coords;
quasi_evenly_spherical_distribution(projection_number, spherical_coords, 1.0);
for (unsigned int i = 0; i < spherical_coords.size(); i++) {
// convert sphere coordinate to rotation
IMP::algebra::SphericalVector3D v = spherical_coords[i];
double cy = cos(v[1] / 2.0);
double cz = cos(v[2] / 2.0);
double sy = sin(v[1] / 2.0);
double sz = sin(v[2] / 2.0);
// this is a rotation about z axis by an angle v[2]
// followed by rotation about y axis by an angle v[1]
IMP::algebra::Rotation3D r(cy * cz, sy * sz, sy * cz, cy * sz);
// rotate points
for (unsigned int point_index = 0; point_index < points.size();
point_index++) {
rotated_points[point_index] = r * points[point_index];
}
// project
IMP_UNIQUE_PTR<Projection> p(new Projection(rotated_points, mass,
pixel_size, resolution,
axis_size));
p->set_rotation(r);
p->set_axis(IMP::algebra::Vector3D(v.get_cartesian_coordinates()));
p->set_id(i);
// rasmol
// std::cout << "#projection " << i+1
//<<"\nreset\nrotate Z " << RAD_2_DEG(v[2]);
// std::cout << "\nrotate Y -" << IMP_RAD_2_DEG(v[1]) << std::endl;
// chimera
// std::cout << "#projection " << i+1
//<<"\nreset;turn x 180; turn z -" << IMP_RAD_2_DEG(v[2]);
// std::cout << ";turn y -" << IMP_RAD_2_DEG(v[1])
// << ";wait;sleep 3;"<< std::endl;
// string file_name = "projection_" +
// string(boost::lexical_cast<string>(i+1)) + ".pgm";
// p.write_PGM(file_name);
projections.push_back(p.release());
}
}