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IMP Reference Guide  develop.182d9373c4,2021/04/12
The Integrative Modeling Platform
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 <iostream>
#include <iomanip>
#include <IMP/algebra/standard_grids.h>
#include <IMP/base_types.h>
+ Include dependency graph for DensityMap.h:
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Go to the source code of this file.


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


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


typedef IMP::Vector
< IMP::Pointer< DensityMap > > 
typedef IMP::Vector
< IMP::WeakPointer< DensityMap > > 


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)
< 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 2007-2021 IMP Inventors. All rights reserved.

Definition in file DensityMap.h.