model_mask.cpp File Reference

Generating a mask from an atomic model. More...

#include "rwmodel.h"
#include "model_mask.h"
#include "model_shell.h"
#include "model_util.h"
#include "matrix_linear.h"
#include "Vector3.h"
#include "linked_list.h"
#include "utilities.h"

Functions
Bimage *	model_create_mask (Bmodel *model, Vector3< long > size, Vector3< double > ori, Vector3< double > sam, double edge)
	Calculates a mask of the components and links of a model structure. More...
Bimage *	model_create_hull_mask (Bmodel *model, Vector3< long > size, Vector3< double > ori, Vector3< double > sam, int curv_flag, int fast)
	Calculates a mask based on the periphery of a model structure. More...
Bimage *	model_create_shell_mask (Bmodel *model, Vector3< long > size, Vector3< double > ori, Vector3< double > sam, double shell_width, int curv_flag, int fast)
	Calculates a shell mask covering a model structure. More...
Bimage *	model_create_level_mask (Bmodel *model, Vector3< long > size, Vector3< double > ori, Vector3< double > sam)
	Calculates a mask with one level per model. More...
Bimage *	img_extract_segments_using_model (Bimage *p, Bmodel *model, int multi_level)
	Extracts segmentss from a multi-level mask around points defined by a model. More...
int	img_add_model_to_mask (Bimage *p, Bmodel *model)
	Adds to the mask the component locations. More...
Bmodel *	model_from_multilevel_mask (Bimage *p)
	Generates components at the center of mass of each mask level. More...
Bimage *	model_create_projected_mask (Bmodel *model, Vector3< long > size, Vector3< double > ori, Vector3< double > sam, double dang, Bsymmetry &sym)
	Calculates a set of 2D masks for the projections of a model structure. More...

Variables
int	verbose

Detailed Description

Generating a mask from an atomic model.

Author

Bernard Heymann

Date

Created: 20060301

Modified: 20200329

Function Documentation

img_add_model_to_mask()

int img_add_model_to_mask	(	Bimage *	p,
		Bmodel *	model
	)

Adds to the mask the component locations.

Parameters

*p	mask.
*model	model.

Returns

int 0, <0 on error.

At each component location, the voxel is added to the mask.

img_extract_segments_using_model()

Bimage * img_extract_segments_using_model	(	Bimage *	p,
		Bmodel *	model,
		int	multi_level
	)

Extracts segmentss from a multi-level mask around points defined by a model.

Parameters

*p	multi-level mask.
*model	model marking regions in mask.
multi_level	flag to retain multiple levels.

Returns

Bimage* new mask from marked segments.

Each segment should only be marked by a maximum of one component.

model_create_hull_mask()

Bimage * model_create_hull_mask	(	Bmodel *	model,
		Vector3< long >	size,
		Vector3< double >	ori,
		Vector3< double >	sam,
		int	curv_flag,
		int	fast
	)

Calculates a mask based on the periphery of a model structure.

Parameters

*model	model structure.
size	size of the new mask.
ori	origin of the new mask.
sam	pixel size of the new mask.
curv_flag	flag to indicate curved surface.
fast	flag to use fast algorithm.

Returns

Bimage* new mask.

Each point in the new image is tested for inclusion in the mask,
by calculating whether it falls inside the closest 3 vertices.
Only the first model in the linked list is used.

model_create_level_mask()

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

Calculates a mask with one level per model.

Parameters

*model	model structure.
size	size of the new mask.
ori	origin of the new mask.
sam	pixel size of the new mask.

Returns

Bimage* new mask.

A level is defined as those voxels closest to the vertices of one model.

model_create_mask()

Bimage * model_create_mask	(	Bmodel *	model,
		Vector3< long >	size,
		Vector3< double >	ori,
		Vector3< double >	sam,
		double	edge
	)

Calculates a mask of the components and links of a model structure.

Parameters

*model	model structure.
size	size of the new mask.
ori	origin of the new mask.
sam	pixel size of the new mask.
edge	edge width in angstrom.

Returns

Bimage* new mask.

Each component is used to generate a sphere and each link a bar.
Only the first model in the linked list is used.

model_create_projected_mask()

Bimage * model_create_projected_mask	(	Bmodel *	model,
		Vector3< long >	size,
		Vector3< double >	ori,
		Vector3< double >	sam,
		double	dang,
		Bsymmetry &	sym
	)

Calculates a set of 2D masks for the projections of a model structure.

Parameters

*model	model structure.
size	size of the new mask.
ori	origin of the new mask.
sam	pixel size of the new mask.
dang	angular step size.
sym	point group symmetry.

Returns

Bimage* new mask.

Each component is used to set  the corresponding projected pixel in each 2D image.
The projection directions are calculated within the asymmetric unit.

model_create_shell_mask()

Bimage * model_create_shell_mask	(	Bmodel *	model,
		Vector3< long >	size,
		Vector3< double >	ori,
		Vector3< double >	sam,
		double	shell_width,
		int	curv_flag,
		int	fast
	)

Calculates a shell mask covering a model structure.

Parameters

*model	model structure.
size	size of the new mask.
ori	origin of the new mask.
sam	pixel size of the new mask.
shell_width	width of shell mask.
curv_flag	flag to indicate curved surface.
fast	flag to use fast algorithm.

Returns

Bimage* new mask.

Each point in the new image is tested for inclusion in the mask,
by calculating whether it falls inside the closest 3 vertices.
Only the first model in the linked list is used.

model_from_multilevel_mask()

Bmodel * model_from_multilevel_mask

(

Bimage *

p

)

Generates components at the center of mass of each mask level.

Parameters

*p	multi-level mask.

Returns

Bmodel* new model.

The mask is expected to be of integer data type.

Variable Documentation

verbose

int verbose

extern