DensityMap.h File Reference

Class for handling density maps. More...

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

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

Namespaces
	IMP
	Base functionality and abstract base classes for representation, scoring and sampling.
	IMP::em
	Basic utilities for handling cryo-electron microscopy 3D density maps.

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

Functions
Float	IMP::em::approximate_molecular_mass (DensityMap *m, Float threshold)
	Estimate the molecular mass from a map. More...
DensityMap *	IMP::em::binarize (DensityMap *orig_map, float threshold, bool reverse=false)
	Return a map with 0 for all voxels below the threshold and 1 for those above. More...
double	IMP::em::convolute (const DensityMap *m1, const DensityMap *m2)
	Return a convolution between density maps m1 and m2. More...
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)
	Create a density map from an arbitrary IMP::algebra::GridD. More...
algebra::BoundingBoxD< 3 >	IMP::em::get_bounding_box (const DensityMap *m, Float threshold)
	Get the bounding box for a map. More...
algebra::BoundingBoxD< 3 >	IMP::em::get_bounding_box (const DensityMap *m)
algebra::GridD < 3, algebra::DenseGridStorageD < 3, float >, float >	IMP::em::get_grid (DensityMap *in_map)
	Return a dense grid containing the voxels of the passed density map. More...
bool	IMP::em::get_interiors_intersect (const DensityMap *d1, const DensityMap *d2)
DensityMap *	IMP::em::get_max_map (DensityMaps maps)
	Return a map where each voxel is the maximum value from the input maps. 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)
	Return a map with 0 for all voxels below the threshold. 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)
	Return a new map with an updated spacing. More...
DensityMap *	IMP::em::multiply (const DensityMap *m1, const DensityMap *m2)
	Return a density map for which voxel i contains the result of m1[i]*m2[i]. More...

Detailed Description

Class for handling density maps.

Copyright 2007-2022 IMP Inventors. All rights reserved.

Definition in file DensityMap.h.