Skip to content
Snippets Groups Projects
Commit 7db60348 authored by valerio's avatar valerio
Browse files

Split EntityToDensity into two functions, fixed bug 

git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2286 5a81b35b-ba03-0410-adc8-b2c5c5119f08
parent 735cbb19
Branches
Tags
No related merge requests found
Hide whitespace changes
Inline Side-by-side
modules/mol/alg/pymod/export_entity_to_density.cc
+ 10
− 36
View file @ 7db60348
......@@ -21,6 +21,9 @@
* Author Juergen Haas
*/
#include <boost/python.hpp>
#include <ost/config.hh>
#if OST_IMG_ENABLED
#include <ost/mol/alg/entity_to_density.hh>
......@@ -28,48 +31,19 @@ using namespace boost::python;
using namespace ost;
using namespace ost::mol::alg;
#if OST_IMG_ENABLED
#include <ost/mol/alg/entity_to_density.hh>
//"thin wrappers" for default parameters
int etd1(const mol::EntityView& entity_view,
img::MapHandle& map,
const DensityType& density_type,
Real falloff_start,
Real falloff_end,
bool clear_map_flag)
{
EntityToDensity(entity_view, map, density_type, falloff_start,
falloff_end, clear_map_flag);
return 0;
}
int etd2(const mol::EntityView& entity_view,
img::MapHandle& map,
const DensityType& density_type,
Real falloff_start,
Real falloff_end)
{
EntityToDensity(entity_view, map, density_type, falloff_start,
falloff_end);
return 0;
}
BOOST_PYTHON_FUNCTION_OVERLOADS(etd_rosetta, EntityToDensityRosetta, 4, 6)
BOOST_PYTHON_FUNCTION_OVERLOADS(etd_scattering, EntityToDensityScattering, 4, 6)
void export_entity_to_density()
{
def("EntityToDensity",EntityToDensity);
def("EntityToDensity",etd1);
def("EntityToDensity",etd2);
def("EntityToDensityRosetta",EntityToDensityRosetta,etd_rosetta());
def("EntityToDensityScattering",EntityToDensityScattering,etd_scattering());
enum_<DensityType>("DensityType")
.value("SCATTERING_FACTORS", SCATTERING_FACTORS)
.value("ROSETTA_HIGH_RESOLUTION", ROSETTA_HIGH_RESOLUTION)
.value("ROSETTA_LOW_RESOLUTION", ROSETTA_LOW_RESOLUTION)
.value("HIGH_RESOLUTION", HIGH_RESOLUTION)
.value("LOW_RESOLUTION", LOW_RESOLUTION)
.export_values()
;
}
}
#endif
modules/mol/alg/src/entity_to_density.cc
+ 82
− 58
View file @ 7db60348
......@@ -42,8 +42,10 @@ void FillAtomScatteringPropsTable(AtomScatteringPropsTable& table)
boost::filesystem::path loc(fullpath);
boost::filesystem::ifstream infile(loc);
if (!infile) {
LOGN_ERROR("Couldn't find " << fullpath);
return;
String msg;
std::stringstream msgstr(msg);
msgstr << "Couldn't find " << fullpath << std::endl;
throw ost::Error(msg);
}
String line;
std::getline(infile, line);
......@@ -67,7 +69,6 @@ void FillAtomScatteringPropsTable(AtomScatteringPropsTable& table)
>> atom_props.b4;
table.push_back(atom_props);
}
std::cout << table.size() << std::endl;
};
......@@ -91,14 +92,17 @@ class EntityToDensityHelperBase
public:
EntityToDensityHelperBase (const ost::mol::EntityView entity_view,
const ost::mol::alg::DensityType& density_type,
Real falloff_start,
Real falloff_end,
Real source_wavelength):
density_type_(density_type), entity_view_(entity_view),
Real source_wavelength,
geom::Vec3 map_start,
geom::Vec3 map_end
):
entity_view_(entity_view),
falloff_start_frequency_(1.0/falloff_start),
falloff_end_frequency_(1.0/falloff_end),
source_wavelength_(source_wavelength)
source_wavelength_(source_wavelength),
map_start_(map_start),map_end_(map_end)
{
if (scattering_props_table_loaded_ == false)
{
......@@ -109,8 +113,7 @@ public:
void VisitState(img::ComplexHalfFrequencyImageState& is) const
{
geom::Vec3 map_start=is.IndexToCoord(is.GetExtent().GetStart());
geom::Vec3 map_end=is.IndexToCoord(is.GetExtent().GetEnd());
geom::Vec3 frequency_sampling =
is.GetSampling().GetFrequencySampling();
......@@ -133,15 +136,15 @@ public:
while (found != true && table_iter!=scatt_props_table_.end())
{
if ( (*table_iter).element == (*iterator).GetAtomProps().element)
{
{
geom::Vec3 coord = (*iterator).GetPos();
if (coord[0] >= map_start[0] &&
coord[0] <= map_end[0] &&
coord[1] >= map_start[1] &&
coord[1] <= map_end[1] &&
coord[2] >= map_start[2] &&
coord[2] <= map_end[2])
if (coord[0] >= map_start_[0] &&
coord[0] <= map_end_[0] &&
coord[1] >= map_start_[1] &&
coord[1] <= map_end_[1] &&
coord[2] >= map_start_[2] &&
coord[2] <= map_end_[2])
{
// This part of the code assumes that the three axes
......@@ -149,7 +152,7 @@ public:
// Eventually, when maps and images will be merged,
// it will substituted by the map's xyz2uvw method
geom::Vec3 adjusted_coord = coord-map_start;
geom::Vec3 adjusted_coord = coord-map_start_;
for (img::ExtentIterator mp_it(reduced_extent);
!mp_it.AtEnd();++mp_it)
......@@ -217,6 +220,9 @@ private:
static AtomScatteringPropsTable scatt_props_table_;
static bool scattering_props_table_loaded_;
Real source_wavelength_;
geom::Vec3 map_start_;
geom::Vec3 map_end_;
};
AtomScatteringPropsTable EntityToDensityHelperBase::scatt_props_table_ =
......@@ -253,7 +259,7 @@ public:
mol::EntityView effective_entity_view=entity_view_;
Real k,C;
if (density_type_ == ROSETTA_HIGH_RESOLUTION)
if (density_type_ == HIGH_RESOLUTION)
{
k = (M_PI*M_PI)/(resolution_*resolution_);
C = sqrt((M_PI*M_PI*M_PI)/(k*k*k));
......@@ -292,9 +298,8 @@ public:
coord[2] >= map_start[2] &&
coord[2] <= map_end[2])
{
geom::Vec3 adjusted_coord = geom::Vec3(coord[0]-map_start[0],
coord[1]-map_start[1],
coord[2]-map_start[2]);
geom::Vec3 adjusted_coord = coord-map_start;
geom::Vec3 pixel_coord=is.CoordToIndex(coord);
img::Point rounded_pixel_coord(round(pixel_coord[0]),
round(pixel_coord[1]),
......@@ -366,53 +371,72 @@ typedef img::ImageStateConstModIPAlgorithm<EntityToDensityRosettaHelperBase>
} // namespace
void EntityToDensity (const mol::EntityView& entity_view,
img::MapHandle& map,
const DensityType& density_type,
Real falloff_start,
Real falloff_end,
bool clear_map_flag,
Real source_wavelength)
void EntityToDensityScattering(const mol::EntityView& entity_view,
img::MapHandle& map,
Real falloff_start,
Real falloff_end,
bool clear_map_flag,
Real source_wavelength)
{
if(falloff_start<=0.0) throw std::runtime_error("Invalid falloff start");
if(falloff_end<=0.0 || falloff_end>falloff_start)
throw std::runtime_error("Invalid falloff end");
if (density_type == SCATTERING_FACTORS)
{
if (clear_map_flag==true) {
img::MapHandle mm=img::CreateImage(img::Extent(map.GetSize(),
img::Point(0,0)),
img::COMPLEX,img::HALF_FREQUENCY);
// swap newly created map into place
mm.SetAbsoluteOrigin(map.GetAbsoluteOrigin());
map.Swap(mm);
} else {
map.ApplyIP(img::alg::DFT());
}
detail::EntityToDensityHelper e_to_d_helper(entity_view,density_type,
falloff_start,
falloff_end,
source_wavelength);
map.ApplyIP(e_to_d_helper);
geom ::Vec3 rs_sampl = map.GetSpatialSampling();
geom ::Vec3 abs_orig = map.GetAbsoluteOrigin();
geom::Vec3 map_start = geom::Vec3(abs_orig[0]+map.GetExtent().GetStart()[0]*rs_sampl[0],
abs_orig[1]+map.GetExtent().GetStart()[1]*rs_sampl[1],
abs_orig[2]+map.GetExtent().GetStart()[2]*rs_sampl[2]);
geom::Vec3 map_end = geom::Vec3(abs_orig[0]+map.GetExtent().GetEnd()[0]*rs_sampl[0],
abs_orig[1]+map.GetExtent().GetEnd()[1]*rs_sampl[1],
abs_orig[2]+map.GetExtent().GetEnd()[2]*rs_sampl[2]);
detail::EntityToDensityHelper e_to_d_helper(entity_view,
falloff_start,
falloff_end,
source_wavelength, map_start,map_end);
if (clear_map_flag==true) {
img::MapHandle mm=img::CreateImage(img::Extent(map.GetSize(),
img::Point(0,0)),
img::COMPLEX,img::HALF_FREQUENCY);
// swap newly created map into place
mm.SetSpatialSampling(map.GetSpatialSampling());
mm.SetAbsoluteOrigin(map.GetAbsoluteOrigin());
map.Swap(mm);
} else {
map.ApplyIP(img::alg::DFT());
} else {
if (clear_map_flag==true) {
img::MapHandle mm=img::CreateImage(img::Extent(img::Point(0,0),
map.GetSize()));
// swap newly created map into place
mm.SetAbsoluteOrigin(map.GetAbsoluteOrigin());
map.Swap(mm);
}
Real resolution = (falloff_start+falloff_end)/2.0;
detail::EntityToDensityRosettaHelper e_to_d_r_helper
}
map.ApplyIP(e_to_d_helper);
map.ApplyIP(img::alg::DFT());
}
void EntityToDensityRosetta(const mol::EntityView& entity_view,
img::MapHandle& map,
const DensityType& density_type,
Real resolution,
bool clear_map_flag,
Real source_wavelength)
{
if(resolution <=0.0) throw std::runtime_error("Invalid resolution");
if (clear_map_flag==true) {
img::MapHandle mm=img::CreateImage(img::Extent(img::Point(0,0),
map.GetSize()));
// swap newly created map into place
mm.SetSpatialSampling(map.GetSpatialSampling());
mm.SetAbsoluteOrigin(map.GetAbsoluteOrigin());
map.Swap(mm);
}
detail::EntityToDensityRosettaHelper e_to_d_r_helper
(entity_view,density_type,
resolution);
map.ApplyIP(e_to_d_r_helper);
}
map.ApplyIP(e_to_d_r_helper);
}
}}} // ns
modules/mol/alg/src/entity_to_density.hh
+ 32
− 17
View file @ 7db60348
......@@ -12,20 +12,43 @@ namespace ost { namespace mol { namespace alg {
/// \brief type of density being created by the EntityToDensity function
enum DensityType
{
SCATTERING_FACTORS,
ROSETTA_HIGH_RESOLUTION,
ROSETTA_LOW_RESOLUTION
HIGH_RESOLUTION,
LOW_RESOLUTION
};
/// \brief create a density representation of an entity in a density map (using electron scattering factors)
///
/// This functions creates a density representation of the entity provided by
/// the user in a density map, in Fourier space using the correct scattering
/// factors for the elements involved.
///
/// The user can also choose if the density map should be cleared of its
/// previous content before creating the density representation.
///
/// The density is generated in Fourier space. In order to
/// avoid artifacts in the final density representation, the function avoids
/// sharp frequency cutoffs by applying a Gaussian falloff. The user must
/// provide the resolutions at which the cutoff should begin and end, as opposed
/// to a single resolution cutoff value.
///
/// This function will only create a density represenation of the entities
/// (or portion of entities ) that fall within the borders of the map.
/// The user must take care that this condition is verified for all
/// entities for which he wants a representation.
///
void DLLEXPORT_OST_MOL_ALG EntityToDensityScattering(const mol::EntityView& entity_view,
img::MapHandle& map,
Real falloff_start,
Real falloff_end,
bool clear_map_flag = false,
Real source_wavelength = 1.5418);
/// \brief create a density representation of an entity in a density map
///
/// This function creates a density representation of the entity provided by
/// the user in a density map, also provided by the user. The user can choose
/// the type of density of the output map:
///
/// SCATTERING_FACTORS density, generated in Fourier space using the
/// correct scattering factors for the elements
/// involved.
/// ROSETTA_HIGH_RESOLUTION gaussian spheres in real space to represent
/// density, one per atom, see Dimaio et al.,
/// Refinement of Protein Structures into Low-Resolution
......@@ -38,27 +61,19 @@ enum DensityType
/// The user can also choose if the density map should be cleared of its
/// previous content before creating the density representation.
///
/// The first two types of density are generated in Fourier space. In order to
/// avoid artifacts in the final density representation, the function avoids
/// sharp frequency cutoffs by applying a Gaussian falloff. The user must
/// provide the resolutions at which the cutoff should begin and end, as opposed
/// to a single resolution cutoff value. For the other two density types, which
/// are generated in real space, the average of the two falloff values is used
/// as resolution parameter.
/// The user must also provide a resolution parameter.
///
/// This function will only create a density represenation of the entities
/// (or portion of entities ) that fall within the borders of the map.
/// The user must take care that this condition is verified for all
/// entities for which he wants a representation.
///
void DLLEXPORT_OST_MOL_ALG EntityToDensity(const mol::EntityView& entity_view,
void DLLEXPORT_OST_MOL_ALG EntityToDensityRosetta(const mol::EntityView& entity_view,
img::MapHandle& map,
const DensityType& density_type,
Real falloff_start,
Real falloff_end,
Real resolution,
bool clear_map_flag = false,
Real source_wavelength = 1.5418);
}}} // ns
#endif // OST_ENTITY_TO_DENSITY
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment