double Fine2DRegistrationRestraint::unprotected_evaluate(
DerivativeAccumulator *accum) const {
IMP_UNUSED(accum);
calls_++;
IMP_USAGE_CHECK(accum == nullptr,
"Fine2DRegistrationRestraint: This restraint does not "
"provide derivatives ");
// projection_ needs to be mutable, son this const function can change it.
// project_particles changes the matrix of projection_
ProjectingOptions options(params_.pixel_size, params_.resolution);
double score = 0;
try {
do_project_particles(ps_, projection_->get_data(), PP_.get_rotation(),
PP_.get_translation(), options, masks_);
score = score_function_->get_score(subject_, projection_);
}
catch (cv::Exception &e) {
IMP_LOG(WARNING,
"Fine2DRegistration. Error computing the score: "
"Returning 1 (maximum score). Most probably because projecting "
"out of the image size."
<< e.what() << std::endl);
score = 1.0;
}
IMP_LOG_VERBOSE("Fine2DRegistration. Score: " << score << std::endl);
return score;
}
void get_projection(em2d::Image *img, const ParticlesTemp &ps,
const RegistrationResult ®,
const ProjectingOptions &options, MasksManagerPtr masks,
String name) {
IMP_LOG_VERBOSE("Generating projection in a em2d::Image" << std::endl);
if (masks == MasksManagerPtr()) {
masks = MasksManagerPtr(
new MasksManager(options.resolution, options.pixel_size));
masks->create_masks(ps);
IMP_LOG_VERBOSE("Masks generated from get_projection()" << std::endl);
}
algebra::Vector3D translation = options.pixel_size * reg.get_shift_3d();
algebra::Rotation3D R = reg.get_rotation();
do_project_particles(ps, img->get_data(), R, translation, options, masks);
if (options.normalize) em2d::do_normalize(img, true);
reg.set_in_image(img->get_header());
img->get_header().set_object_pixel_size(options.pixel_size);
if (options.save_images) {
if (name.empty()) {
IMP_THROW("get_projection: File name string is empty ", IOException);
}
if (options.srw == Pointer<ImageReaderWriter>()) {
IMP_THROW(
"The options class does not have an "
"ImageReaderWriter assigned. Create an ImageReaderWriter "
"and assigned to the srw member of ProjectingOptions.",
IOException);
}
img->write(name, options.srw);
}
}
void CollisionCrossSection::set_model_particles(
const ParticlesTemp &ps) {
IMP_LOG_TERSE("CollisionCrossSection: Model particles set"
<< std::endl);
for (unsigned int i = 0; i < ps.size(); ++i) {
IMP_USAGE_CHECK(
(core::XYZR::get_is_setup(ps[i]) && atom::Mass::get_is_setup(ps[i])),
"Particle " << i << " does not have the required attributes"
<< std::endl);
}
masks_manager_->create_masks(ps);
// Compute projections
collision_cross_section_ = 0.0;
for (unsigned int i = 0; i < n_projections_; ++i) {
ProjectingOptions options(pixel_size_, resolution_);
do_project_particles(ps, average_projection_, regs_[i].get_rotation(),
pixel_size_ * regs_[i].get_shift_3d(), options,
masks_manager_);
collision_cross_section_ += get_projected_area(average_projection_);
}
collision_cross_section_ /= static_cast<double>(n_projections_);
particles_set_ = true;
}