IMPEM2D_BEGIN_NAMESPACE
ResultAlign2D get_complete_alignment(const cv::Mat &input, cv::Mat &m_to_align,
bool apply) {
IMP_LOG_TERSE("starting complete 2D alignment " << std::endl);
cv::Mat autoc1, autoc2, aux1, aux2, aux3;
algebra::Transformation2D transformation1, transformation2;
ResultAlign2D RA;
get_autocorrelation2d(input, autoc1);
get_autocorrelation2d(m_to_align, autoc2);
RA = get_rotational_alignment(autoc1, autoc2, false);
double angle1 = RA.first.get_rotation().get_angle();
get_transformed(m_to_align, aux1, RA.first); // rotate
RA = get_translational_alignment(input, aux1);
algebra::Vector2D shift1 = RA.first.get_translation();
transformation1.set_rotation(angle1);
transformation1.set_translation(shift1);
get_transformed(m_to_align, aux2, transformation1);
double ccc1 = get_cross_correlation_coefficient(input, aux2);
// Check for both angles that can be the solution
double angle2;
if (angle1 < PI) {
angle2 = angle1 + PI;
} else {
angle2 = angle1 - PI;
}
// rotate
algebra::Rotation2D R2(angle2);
algebra::Transformation2D tr(R2);
get_transformed(m_to_align, aux3, tr);
RA = get_translational_alignment(input, aux3);
algebra::Vector2D shift2 = RA.first.get_translation();
transformation2.set_rotation(angle2);
transformation2.set_translation(shift2);
get_transformed(m_to_align, aux3, transformation2);
double ccc2 = get_cross_correlation_coefficient(input, aux3);
if (ccc2 > ccc1) {
if (apply) {
aux3.copyTo(m_to_align);
}
IMP_LOG_VERBOSE(" Transformation= " << transformation2
<< " cross_correlation = " << ccc2
<< std::endl);
return em2d::ResultAlign2D(transformation2, ccc2);
} else {
if (apply) {
aux2.copyTo(m_to_align);
}
IMP_LOG_VERBOSE(" Transformation= " << transformation1
<< " cross_correlation = " << ccc1
<< std::endl);
return em2d::ResultAlign2D(transformation1, ccc1);
}
}
void ProjectionFinder::do_preprocess_subject(unsigned int i) {
IMP_LOG_TERSE("ProjectionFinder: Preprocessing subject " << i << std::endl);
if (params_.coarse_registration_method == ALIGN2D_PREPROCESSING) {
cv::Mat autoc, polar_autoc;
get_fft_using_optimal_size(subjects_[i]->get_data(), SUBJECTS_[i]);
get_autocorrelation2d(subjects_[i]->get_data(), autoc);
do_resample_polar(autoc, polar_autoc, polar_params_);
get_fft_using_optimal_size(polar_autoc, SUBJECTS_POLAR_AUTOC_[i]);
}
if (params_.coarse_registration_method == ALIGN2D_WITH_CENTERS) {
do_preprocess_for_fast_coarse_registration(
subjects_[i]->get_data(), subjects_cog_[i], SUBJECTS_POLAR_AUTOC_[i]);
}
}
