IMP Reference Guide
2.20.2
The Integrative Modeling Platform
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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>
Go to the source code of this file.
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... | |
Class for handling density maps.
Copyright 2007-2022 IMP Inventors. All rights reserved.
Definition in file DensityMap.h.