model_map.cpp File Reference

Function to generate a map from a model. More...

#include "rwmodel.h"
#include "rwmodel_param.h"
#include "model_links.h"
#include "model_transform.h"
#include "model_extract_build.h"
#include "model_mol.h"
#include "model_util.h"
#include "rwimg.h"
#include "img_combine.h"
#include "scatter.h"
#include "utilities.h"

Functions
Bmodel *	model_from_images (Bimage *plist)
	Creates one or more models from 3D images. More...
Bmodel *	model_from_graph_segments (Bimage *p, GSgraph &gs)
	Creates one or more models from graph segments. More...
Bimage *	img_from_model (Bmodel *model, Vector3< double > ori, Vector3< long > size, Vector3< double > sam, double sigma)
	Calculates a map from model component coordinates. More...
int	model_catenate_maps (Bmodel *model, Bstring &filename)
	Concatenates all model maps into one multi-image file. More...
int	model_shell_fit (Bmodel *model, double hires, double lores, int neg)
	Fits a shell model as a rigid body to a map. More...
int	model_shell_radial_profile (Bmodel *model)
	Calculates a radial profile from a shell model. More...
Bimage *	model_shell_power_spectrum (Bmodel *model, Vector3< long > size, Vector3< double > origin, int ft_size, int ann_min, int ann_max, double hires, double lores)
	Calculates a radial profile from a shell model. More...
int	comp_set_fom_sym (Bcomponent *comp, Bimage *p, long minorder, long maxorder)
int	model_component_symmetry (Bmodel *model, long nangles, long ann_min, long ann_max, long ann_width, long zmin, long zmax, long zinc, long minorder, long maxorder)
	Determines the cyclic symmetry of components. More...
int	scatter_one (Bcomponent *comp, Bimage *p, vector< double > &scurve, CTFparam cp, double ds, double scut, int flag)
Bimage *	scatter_one_img (Bcomponent *comp, Bimage *p, vector< double > &scurve, CTFparam cp, double ds, double scut, int flag)
Bimage *	scatter_to_img (const vector< Bcomponent * > &carr, long ib, long ie, Bimage *p, map< string, vector< double > > &scat, CTFparam &cp, double ds, double scut, int flag)
Bimage *	scatter_slice_to_img (const vector< Bcomponent * > &carr, Bimage *p, map< string, vector< double > > &scat, CTFparam &cp, double ds, double scut, int flag)
int	img_add (Bimage *ps, vector< Complex< float > > &v)
int	img_add_fast_old (Bimage *ps, Bimage *p)
int	img_add_fast (Bimage *ps, Bimage *p)
int	img_electron_scattering (Bmodel *model, Bimage *p, CTFparam &cp, double dose, double stdev, map< string, vector< double > > &scat, double ds, double scut, int flag)
int	img_electron_scattering_chunks (Bmodel *model, Bimage *p, CTFparam &cp, double dose, double stdev, map< string, vector< double > > &scat, double ds, double scut, int flag)
int	img_electron_scattering_slices (Bmodel *model, Bimage *p, CTFparam &cp, map< string, vector< double > > &scat, double ds, double scut, int flag)
int	img_electron_scattering (Bmodel *model, Bimage *p, CTFparam &cp, double dose, double stdev, Bstring &atompropfile, int flag)

Variables
int	verbose

Detailed Description

Function to generate a map from a model.

Author

Bernard Heymann

Date

Created: 20081112

Modified: 20220419

Function Documentation

comp_set_fom_sym()

int comp_set_fom_sym	(	Bcomponent *	comp,
		Bimage *	p,
		long	minorder,
		long	maxorder
	)

img_add()

int img_add	(	Bimage *	ps,
		vector< Complex< float > > &	v
	)

img_add_fast()

int img_add_fast	(	Bimage *	ps,
		Bimage *	p
	)

img_add_fast_old()

int img_add_fast_old	(	Bimage *	ps,
		Bimage *	p
	)

img_electron_scattering() [1/2]

int img_electron_scattering	(	Bmodel *	model,
		Bimage *	p,
		CTFparam &	cp,
		double	dose,
		double	stdev,
		Bstring &	atompropfile,
		int	flag
	)

img_electron_scattering() [2/2]

int img_electron_scattering	(	Bmodel *	model,
		Bimage *	p,
		CTFparam &	cp,
		double	dose,
		double	stdev,
		map< string, vector< double > > &	scat,
		double	ds,
		double	scut,
		int	flag
	)

img_electron_scattering_chunks()

int img_electron_scattering_chunks	(	Bmodel *	model,
		Bimage *	p,
		CTFparam &	cp,
		double	dose,
		double	stdev,
		map< string, vector< double > > &	scat,
		double	ds,
		double	scut,
		int	flag
	)

img_electron_scattering_slices()

int img_electron_scattering_slices	(	Bmodel *	model,
		Bimage *	p,
		CTFparam &	cp,
		map< string, vector< double > > &	scat,
		double	ds,
		double	scut,
		int	flag
	)

img_from_model()

Bimage * img_from_model	(	Bmodel *	model,
		Vector3< double >	ori,
		Vector3< long >	size,
		Vector3< double >	sam,
		double	sigma
	)

Calculates a map from model component coordinates.

Parameters

*model	model.
ori	origin within new map.
size	size of new map.
sam	voxel size of new map.
sigma	gaussian sphere width.

Returns

Bimage* new map.

model_catenate_maps()

int model_catenate_maps	(	Bmodel *	model,
		Bstring &	filename
	)

Concatenates all model maps into one multi-image file.

Parameters

*model	model.
&filename	new map file name.

Returns

int 0.

The model map file name must be set and point to a valid file.

model_component_symmetry()

int model_component_symmetry	(	Bmodel *	model,
		long	nangles,
		long	ann_min,
		long	ann_max,
		long	ann_width,
		long	zmin,
		long	zmax,
		long	zinc,
		long	minorder,
		long	maxorder
	)

Determines the cyclic symmetry of components.

Parameters

*model	model parameters.
nangles	number of angles.
ann_min	minimum annulus.
ann_max	maximum annulus.
ann_width	annular width.
zmin	minimum z limit.
zmax	maximum z limit.
zinc	z increment.
minorder	minimum cyclic order to search for.
maxorder	maximum cyclic order to search for.

Returns

int 0.

model_from_graph_segments()

Bmodel * model_from_graph_segments	(	Bimage *	p,
		GSgraph &	gs
	)

Creates one or more models from graph segments.

Parameters

*p	image.
&gs	graph segments.

Returns

Bmodel* new model.

The regions are assumed to be number consecutively.

model_from_images()

Bmodel * model_from_images

(

Bimage *

plist

)

Creates one or more models from 3D images.

Parameters

*plist

list of images.

Returns

Bmodel* new model.

The model ID's are derived from the image filenames.

model_shell_fit()

int model_shell_fit	(	Bmodel *	model,
		double	hires,
		double	lores,
		int	neg
	)

Fits a shell model as a rigid body to a map.

Parameters

*model	model.
hires	high resolution limit.
lores	low resolution limit.
neg	flag to set contrast negative.

Returns

int 0.

The model map file name must be set and point to a valid file.

model_shell_power_spectrum()

Bimage * model_shell_power_spectrum	(	Bmodel *	model,
		Vector3< long >	size,
		Vector3< double >	origin,
		int	ft_size,
		int	ann_min,
		int	ann_max,
		double	hires,
		double	lores
	)

Calculates a radial profile from a shell model.

Parameters

*model	model.
size	size of component density to extract.
origin	origin for extracted densities.
ft_size	Fourier transform size.
ann_min	minimum annulus for rotational alignment.
ann_max	maximum annulus for rotational alignment.
hires	high resolution limit for cross-correlation.
lores	low resolution limit for cross-correlation.

Returns

Bimage* 0.

The model map file name must be set and point to a valid file.

model_shell_radial_profile()

int model_shell_radial_profile

(

Bmodel *

model

)

Calculates a radial profile from a shell model.

Parameters

*model

model.

Returns

int 0.

The model map file name must be set and point to a valid file.

scatter_one()

int scatter_one	(	Bcomponent *	comp,
		Bimage *	p,
		vector< double > &	scurve,
		CTFparam	cp,
		double	ds,
		double	scut,
		int	flag
	)

scatter_one_img()

Bimage * scatter_one_img	(	Bcomponent *	comp,
		Bimage *	p,
		vector< double > &	scurve,
		CTFparam	cp,
		double	ds,
		double	scut,
		int	flag
	)

scatter_slice_to_img()

Bimage * scatter_slice_to_img	(	const vector< Bcomponent * > &	carr,
		Bimage *	p,
		map< string, vector< double > > &	scat,
		CTFparam &	cp,
		double	ds,
		double	scut,
		int	flag
	)

scatter_to_img()

Bimage * scatter_to_img	(	const vector< Bcomponent * > &	carr,
		long	ib,
		long	ie,
		Bimage *	p,
		map< string, vector< double > > &	scat,
		CTFparam &	cp,
		double	ds,
		double	scut,
		int	flag
	)

Variable Documentation

verbose

int verbose

extern