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);
}
}
ResultAlign2D get_rotational_alignment(const cv::Mat &input,
cv::Mat &m_to_align,bool apply) {
IMP_LOG_TERSE(
"starting 2D rotational alignment" << std::endl);
IMP_USAGE_CHECK((input.rows==m_to_align.rows) &&
(input.cols==m_to_align.cols),
"em2d::align_rotational: Matrices have different size.");
cv::Mat polar1,polar2,corr;
// Build maps for resampling
PolarResamplingParameters polar_params(input.rows,input.cols);
polar_params.set_estimated_number_of_angles(std::min(input.rows,input.cols));
polar_params.create_maps_for_resampling();
do_resample_polar(input,polar1,polar_params); // subject image
do_resample_polar(m_to_align,polar2,polar_params); // projection image
ResultAlign2D RA= get_translational_alignment(polar1,polar2);
algebra::Vector2D shift=RA.first.get_translation();
// column shift[0] is the optimal angle to bring m_to_align to input
double angle =shift[0]*polar_params.get_angle_step();
RA.first.set_rotation(angle);
RA.first.set_translation(algebra::Vector2D(0.0,0.0));
// Apply the rotation if requested
if(apply) {
cv::Mat result;
get_transformed(m_to_align,result,RA.first);
result.copyTo(m_to_align);
}
IMP_LOG_VERBOSE("Rotational alingment: Transformation= "
<< RA.first << " cross_correlation = " << RA.second << std::endl);
return RA;
}
