DensityMap.h File Reference

Class for handling density maps. More...

#include <IMP/base/Pointer.h>
#include <IMP/em/em_config.h>
#include "DensityHeader.h"
#include "MapReaderWriter.h"
#include <IMP/base/Object.h>
#include <IMP/algebra/Vector3D.h>
#include <IMP/algebra/BoundingBoxD.h>
#include <IMP/algebra/Transformation3D.h>
#include <boost/scoped_array.hpp>
#include <iostream>
#include <iomanip>
#include <IMP/algebra/standard_grids.h>
#include <IMP/kernel/base_types.h>

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Classes
class	IMP::em::DensityMap
	Class for handling density maps. More...

Namespaces
	IMP
	Synonym for IMP::kernel.
	IMP::em
	Basic utilities for handling cryo-electron microscopy 3D density maps.

Typedefs
typedef IMP::base::Vector < IMP::base::Pointer < DensityMap > >	IMP::em::DensityMaps
typedef IMP::base::Vector < IMP::base::WeakPointer < DensityMap > >	IMP::em::DensityMapsTemp

Functions
void	IMP::em::add_to_map (DensityMap *dm, const kernel::Particles &pis)
Float	IMP::em::approximate_molecular_mass (DensityMap *m, Float threshold)
DensityMap *	IMP::em::binarize (DensityMap *orig_map, float threshold, bool reverse=false)
double	IMP::em::convolute (const DensityMap *m1, const DensityMap *m2)
DensityMap *	IMP::em::create_density_map (const DensityMap *other)
	create a copy of another map More...
DensityMap *	IMP::em::create_density_map (const algebra::BoundingBox3D &bb, double spacing)
	Create an empty density map from a bounding box. More...
DensityMap *	IMP::em::create_density_map (int nx, int ny, int nz, double spacing)
	Create an empty density map. More...
template<class S , class V , class E >
DensityMap *	IMP::em::create_density_map (const IMP::algebra::GridD< 3, S, V, E > &arg)
DensityMap *	IMP::em::create_density_map (const algebra::GridD< 3, algebra::DenseGridStorageD< 3, float >, float > &grid)
DensityMap *	IMP::em::get_binarized_interior (DensityMap *dmap)
	Return a binaries density map with 1 for voxels that are internal. More...
algebra::BoundingBoxD< 3 >	IMP::em::get_bounding_box (const DensityMap *m, Float threshold)
algebra::BoundingBoxD< 3 >	IMP::em::get_bounding_box (const DensityMap *m)
double	IMP::em::get_density (const DensityMap *m, const algebra::Vector3D &v)
algebra::GridD < 3, algebra::DenseGridStorageD < 3, float >, float >	IMP::em::get_grid (DensityMap *in_map)
bool	IMP::em::get_interiors_intersect (const DensityMap *d1, const DensityMap *d2)
DensityMap *	IMP::em::get_max_map (DensityMaps maps)
DensityMap *	IMP::em::get_resampled (DensityMap *input, double scaling)
	Get a resampled version of the map. More...
DensityMap *	IMP::em::get_segment (DensityMap *map_to_segment, int nx_start, int nx_end, int ny_start, int ny_end, int nz_start, int nz_end)
	Get a segment of the map according to xyz indexes. More...
DensityMap *	IMP::em::get_segment (DensityMap *map_to_segment, algebra::Vector3Ds vecs, float dist)
	Get a segment of the map covered by the input points. More...
DensityMap *	IMP::em::get_segment_by_masking (DensityMap *map_to_segment, DensityMap *mask, float mas_threshold)
	Get a segment of the map covered by another map. More...
double	IMP::em::get_sum (const DensityMap *m1)
	Return the sum of all voxels. More...
DensityMap *	IMP::em::get_threshold_map (const DensityMap *orig_map, float threshold)
DensityMap *	IMP::em::get_transformed (const DensityMap *input, const algebra::Transformation3D &tr, double threshold)
	Return a new density map containing a rotated version of the old one. More...
DensityMap *	IMP::em::get_transformed (DensityMap *input, const algebra::Transformation3D &tr)
	Return a new density map containing a rotated version of the old one. More...
void	IMP::em::get_transformed_into (const DensityMap *source, const algebra::Transformation3D &tr, DensityMap *into, bool calc_rms=true)
	Rotate a density map into another map. More...
void	IMP::em::get_transformed_into2 (const DensityMap *source, const algebra::Transformation3D &tr, DensityMap *into)
DensityMap *	IMP::em::interpolate_map (DensityMap *in_map, double new_spacing)
DensityMap *	IMP::em::multiply (const DensityMap *m1, const DensityMap *m2)
DensityMap *	IMP::em::read_map (std::string filename, MapReaderWriter *reader)
	Read a density map from a file and return it. More...
DensityMap *	IMP::em::read_map (std::string filename)
	Read a density map from a file and return it. More...
void	IMP::em::write_map (DensityMap *m, std::string filename, MapReaderWriter *writer)
	Write a density map to a file. More...
void	IMP::em::write_map (DensityMap *m, std::string filename)
	Write a density map to a file. More...

Detailed Description

Class for handling density maps.

Copyright 2007-2014 IMP Inventors. All rights reserved.

Definition in file DensityMap.h.