ResultAlign2D get_complete_alignment_no_preprocessing(
const cv::Mat &input, const cv::Mat &INPUT, const cv::Mat &POLAR1,
cv::Mat &m_to_align, const cv::Mat &POLAR2, bool apply) {
IMP_LOG_TERSE("starting complete 2D alignment with no preprocessing"
<< std::endl);
cv::Mat aux1, aux2, aux3, aux4; // auxiliary matrices
cv::Mat AUX1, AUX2, AUX3; // ffts
algebra::Transformation2D transformation1, transformation2;
double angle1 = 0, angle2 = 0;
ResultAlign2D RA = get_rotational_alignment_no_preprocessing(POLAR1, POLAR2);
angle1 = RA.first.get_rotation().get_angle();
get_transformed(m_to_align, aux1, RA.first); // rotate
get_fft_using_optimal_size(aux1, AUX1);
RA = get_translational_alignment_no_preprocessing(INPUT, AUX1);
algebra::Vector2D shift1 = RA.first.get_translation();
transformation1.set_rotation(angle1);
transformation1.set_translation(shift1);
get_transformed(m_to_align, aux2, transformation1); // rotate
double ccc1 = get_cross_correlation_coefficient(input, aux2);
// Check the opposed angle
if (angle1 < PI) {
angle2 = angle1 + PI;
} else {
angle2 = angle1 - PI;
}
algebra::Rotation2D R2(angle2);
algebra::Transformation2D tr(R2);
get_transformed(m_to_align, aux3, tr); // rotate
get_fft_using_optimal_size(aux3, AUX3);
RA = get_translational_alignment_no_preprocessing(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(" Align2D complete Transformation= "
<< transformation2 << " cross_correlation = " << ccc2
<< std::endl);
return ResultAlign2D(transformation2, ccc2);
} else {
if (apply) {
aux3.copyTo(m_to_align);
}
IMP_LOG_VERBOSE(" Align2D complete Transformation= "
<< transformation1 << " cross_correlation = " << ccc1
<< std::endl);
return 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]);
}
}
void ProjectionFinder::do_preprocess_projection(unsigned int j) {
IMP_LOG_TERSE("ProjectionFinder: Preprocessing projection " << j
<< std::endl);
// FFT PREPROCESSING
if(params_.coarse_registration_method == ALIGN2D_PREPROCESSING) {
cv::Mat autoc,polar_autoc;
em2d::get_autocorrelation2d(projections_[j]->get_data(),autoc);
em2d::do_resample_polar(autoc,polar_autoc,polar_params_);
get_fft_using_optimal_size(polar_autoc,PROJECTIONS_POLAR_AUTOC_[j]);
}
// CENTERS OF GRAVITY AND ROTATIONAL FFT PREPROCESSING
if(params_.coarse_registration_method == ALIGN2D_WITH_CENTERS) {
do_preprocess_for_fast_coarse_registration(projections_[j]->get_data(),
projections_cog_[j],
SUBJECTS_POLAR_AUTOC_[j]);
}
}
