double WeightedExcludedVolumeRestraint::unprotected_evaluate(
DerivativeAccumulator *accum) const
{
bool calc_deriv = accum? true: false;
IMP_LOG_VERBOSE("before resample\n");
// //generate the transformed maps
// std::vector<DensityMap*> transformed_maps;
// for(int rb_i=0;rb_i<rbs_.size();rb_i++){
// DensityMap *dm=create_density_map(
// atom::get_bounding_box(atom::Hierarchy(rbs_[rb_i])),spacing);
// get_transformed_into(
// rbs_surface_maps_[rb_i],
// rbs_[rb_i].get_transformation()*rbs_orig_trans_[rb_i],
// dm,
// false);
// transformed_maps.push_back(dm);
// }
double score=0.;
// MRCReaderWriter mrw;
// for(int i=0;i<transformed_maps.size();i++){
// std::stringstream ss;
// ss<<"transformed_map_"<<i<<".mrc";
// std::stringstream s1;
// s1<<"transformed_pdb_"<<i<<".pdb";
// atom::write_pdb(atom::Hierarchy(rbs_[i]),s1.str().c_str());
// write_map(transformed_maps[i],ss.str().c_str(),mrw);
// for(int j=i+1;j<transformed_maps.size();j++){
// if (get_interiors_intersect(transformed_maps[i],
// transformed_maps[j])){
// score += CoarseCC::cross_correlation_coefficient(
// *transformed_maps[i],
// *transformed_maps[j],1.,false,true);
// }
// }
// }
em::SurfaceShellDensityMaps resampled_surfaces;
for(unsigned int i=0; i<rbs_.size(); i++) {
kernel::ParticlesTemp rb_ps=rb_refiner_->get_refined(rbs_[i]);
resampled_surfaces.push_back(new em::SurfaceShellDensityMap(rb_ps,1.));
}
for(unsigned int i=0; i<rbs_.size(); i++) {
for(unsigned int j=i+1; j<rbs_.size(); j++) {
if (get_interiors_intersect(resampled_surfaces[i],
resampled_surfaces[j])) {
score += em::CoarseCC::cross_correlation_coefficient(
resampled_surfaces[i],
resampled_surfaces[j],1.,true,FloatPair(0.,0.));
}
}
}
if (calc_deriv) {
IMP_WARN("WeightedExcludedVolumeRestraint currently"
<<" does not support derivatives\n");
}
/*for(int i=resampled_surfaces.size()-1;i<0;i--){
delete(resampled_surfaces[i]);
}*/
return score;
}
IntPairs QuadraticClosePairsFinder::get_close_pairs(
const algebra::BoundingBox3Ds &bbs) const {
set_was_used(true);
IMP_OBJECT_LOG;
IMP_LOG_TERSE("Adding close pairs from "
<< bbs.size() << " boxes with threshold " << get_distance()
<< std::endl);
IntPairs ret;
const double d2 = get_distance() / 2.0;
for (unsigned int i = 0; i < bbs.size(); ++i) {
algebra::BoundingBox3D bi = bbs[i] + d2;
for (unsigned int j = 0; j < i; ++j) {
algebra::BoundingBox3D bj = bbs[j] + d2;
if (get_interiors_intersect(bi, bj)) {
ret.push_back(IntPair(i, j));
}
}
}
return ret;
}
IntPairs NearestNeighborsClosePairsFinder::get_close_pairs(
const algebra::BoundingBox3Ds &bas,
const algebra::BoundingBox3Ds &bbs) const {
set_was_used(true);
IMP_OBJECT_LOG;
IMP_LOG_TERSE("Quadratic add_close_pairs called with "
<< bas.size() << " and " << bbs.size() << std::endl);
IntPairs ret;
const double d2 = get_distance() / 2.0;
for (unsigned int i = 0; i < bas.size(); ++i) {
algebra::BoundingBox3D bi = bas[i] + d2;
for (unsigned int j = 0; j < bbs.size(); ++j) {
algebra::BoundingBox3D bj = bbs[j] + d2;
if (get_interiors_intersect(bi, bj)) {
ret.push_back(IntPair(i, j));
}
}
}
return ret;
}
double CoarseCC::cross_correlation_coefficient(const DensityMap *grid1,
const DensityMap *grid2,
float grid2_voxel_data_threshold,
bool allow_padding,
FloatPair norm_factors) {
IMP_LOG_VERBOSE("Going to calculate correlation score with values: "
<< "grid2_voxel_data_threshold:" << grid2_voxel_data_threshold
<< " allow_padding:" << allow_padding << " norm factors:"
<< norm_factors.first << "," << norm_factors.second << "\n");
// run validation checks
const DensityHeader *grid2_header = grid2->get_header();
const DensityHeader *grid1_header = grid1->get_header();
IMP_INTERNAL_CHECK(
grid2_header->dmax > grid2_voxel_data_threshold,
"voxel_data_threshold: " << grid2_voxel_data_threshold
<< " is not within the map range: "
<< grid2_header->dmin << "-"
<< grid2_header->dmax << std::endl);
IMP_INTERNAL_CHECK(grid1_header->is_top_calculated(),
"Top should be calculated for grid1\n");
IMP_INTERNAL_CHECK(grid2_header->is_top_calculated(),
"Top should be calculated for grid2\n");
IMP_INTERNAL_CHECK(grid1->same_voxel_size(grid2),
"Both grids should have the same spacing\n");
if (!allow_padding) {
// additional validity checks
IMP_USAGE_CHECK(
grid1->same_dimensions(grid2),
"This function cannot handle density maps of different size. "
<< "First map dimensions : " << grid1_header->get_nx() << " x "
<< grid1_header->get_ny() << " x " << grid1_header->get_nz() << "; "
<< "Second map dimensions: " << grid2_header->get_nx() << " x "
<< grid2_header->get_ny() << " x " << grid2_header->get_nz());
IMP_USAGE_CHECK(
grid1->same_voxel_size(grid2),
"This function cannot handle density maps of different pixelsize. "
<< "First grid pixelsize : " << grid1_header->get_spacing() << "; "
<< "Second grid pixelsize: " << grid2_header->get_spacing());
return cross_correlation_coefficient_internal(
grid1, grid2, grid2_voxel_data_threshold, norm_factors);
} else {
IMP_LOG_VERBOSE("calculated correlation between padded maps\n");
// create a padded version of the grids
// copy maps to contain the same extent
if (!get_interiors_intersect(get_bounding_box(grid1),
get_bounding_box(grid2))) {
return 0.;
}
algebra::BoundingBox3D merged_bb =
get_bounding_box(grid1) + get_bounding_box(grid2);
PointerMember<DensityMap> padded_grid1 =
create_density_map(merged_bb, grid1_header->get_spacing());
padded_grid1->add(grid1);
padded_grid1->get_header_writable()->set_resolution(
grid1->get_header()->get_resolution());
PointerMember<DensityMap> padded_grid2 =
create_density_map(merged_bb, grid2_header->get_spacing());
padded_grid2->add(grid2);
padded_grid2->get_header_writable()->set_resolution(
grid2->get_header()->get_resolution());
padded_grid1->calcRMS();
padded_grid2->calcRMS();
IMP_LOG_VERBOSE("calculate correlation internal " << std::endl);
double score = cross_correlation_coefficient_internal(
padded_grid1, padded_grid2, grid2_voxel_data_threshold, norm_factors);
// release the padded versions of the grids
return score;
}
}
