mg_multislice.cpp File Reference

Generates and manipulates projects for multislice calculations. More...

#include "mg_processing.h"
#include "mg_ctf.h"
#include "molecule_to_map.h"
#include "mol_transform.h"
#include "mol_edit.h"
#include "Complex.h"
#include "Vector3.h"
#include "linked_list.h"
#include "random_numbers.h"
#include "utilities.h"

Functions
Bimage *	img_calc_wave_propagator (Vector3< long > size, Vector3< double > sam, double thickness, double volt)
	Calculates the wave propagation function between slices. More...
Bimage *	img_calc_multi_slice (Bimage *pgrate, double thickness, double volt)
	Simulates the electron imaging process using a multi-slice approach. More...
Bimage *	img_calc_multi_slice_correct (Bimage *pgrate, double thickness, double volt)
Bimage *	img_calc_potential (Bmolgroup *molgroup, Vector3< long > size, Vector3< double > origin, Vector3< double > sam, double thickness, double resolution, double Bfactor, Bstring &paramfile, int type)
	Calculates the atomic potential. More...
int	img_calc_phase_grating (Bimage *p, double volt)
	Calculates the phase grating approximation from the atomic potential. More...
int	img_apply_complex_CTF (Bimage *p, CTFparam &cp)
	Applies a complex CTF function to a Fourier transform. More...
Bproject *	project_generate (int nfield, int nmg, int npart, Vector3< double > pixel_size, double img_origin, CTFparam &cp, double def_min, double def_max, double dose, double tsigma, Bstring &fieldbase, Bstring &mgbase, Bstring &partbase, int fieldnumber, int mgnumber, int partnumber)
	Generates a project for multislice simulations. More...
Bproject *	project_generate_asu (Bstring &symmetry_string, Vector3< double > pixel_size, double img_origin, double theta_step, double phi_step, CTFparam &cp, double defocus, double dose, Bstring &mgbase, Bstring &partbase)
	Generates a project for multislice calculations of an asymmetric unit. More...
int	project_generate_potential (Bmolgroup *molgroup, Bmolgroup *water, Bproject *project, Bstring &fieldname, Bstring &mgname, int partselect, Vector3< long > size, double thickness, double resolution, double Bfactor, int pottype, Bstring &paramfile)
	Generates potential images using a multislice calculation. More...
int	project_generate_image (Bproject *project, double thickness, double resolution)
	Generates final images from a multislice calculation. More...
int	project_apply_distortions (Bproject *project, int poisson, double gauss, double kmtf)
	Applies imaging distortions to the final images from a multislice calculation. More...

Variables
int	verbose

Detailed Description

Generates and manipulates projects for multislice calculations.

Author

Bernard Heymann

Date

Created: 20030805

Modified: 20221024

Function Documentation

img_apply_complex_CTF()

int img_apply_complex_CTF	(	Bimage *	p,
		CTFparam &	cp
	)

Applies a complex CTF function to a Fourier transform.

Parameters

*p	complex Fourier transform (modified).
&cp	CTF parameters.

Returns

int 0.

The CTF is applied as a multiplication with a complex number.
Both input and output are complex transforms.

img_calc_multi_slice()

Bimage * img_calc_multi_slice	(	Bimage *	pgrate,
		double	thickness,
		double	volt
	)

Simulates the electron imaging process using a multi-slice approach.

Parameters

*pgrate	phase grating multi-image.
thickness	slice thickness (in angstrom).
volt	acceleration voltage (volt).

Returns

Bimage* simulated projection image transform.

The passage of the electron beam is simulated as the interaction of
a planar wave with successive planar phase gratings spaced at regular 
intervals, with the wave propagated between the 2D gratings. The
phase gratings are derived from slabs of the atomic potential 
calculated from the atomic structure using scattering profiles.
Note: The final product is a 2D transform of the exit wave.
Reference: Cowley, J. M. (1995) Diffraction Physics. 3rd Rev. Ed. 
    Elsevier Science, Amsterdam.

img_calc_multi_slice_correct()

Bimage * img_calc_multi_slice_correct	(	Bimage *	pgrate,
		double	thickness,
		double	volt
	)

img_calc_phase_grating()

int img_calc_phase_grating	(	Bimage *	p,
		double	volt
	)

Calculates the phase grating approximation from the atomic potential.

Parameters

*p	atomic potential image (modified).
volt	acceleration voltage (volt).

Returns

int 0.

All calculations are complex.

img_calc_potential()

Bimage * img_calc_potential	(	Bmolgroup *	molgroup,
		Vector3< long >	size,
		Vector3< double >	origin,
		Vector3< double >	sam,
		double	thickness,
		double	resolution,
		double	Bfactor,
		Bstring &	paramfile,
		int	type
	)

Calculates the atomic potential.

Parameters

*molgroup	set of molecules.
size	size of projection image (z = 1).
origin	origin in x and y.
sam	voxel size.
thickness	slice thickness (in angstrom).
resolution	resolution limit (angstrom).
Bfactor	overall temperature factor.
&paramfile	parameter file for atomic scattering coefficients.
type	type of potential calculation: 0=reciprocal space, 1=real space, 2=gaussian

Returns

Bimage* complex potential image.

img_calc_wave_propagator()

Bimage * img_calc_wave_propagator	(	Vector3< long >	size,
		Vector3< double >	sam,
		double	thickness,
		double	volt
	)

Calculates the wave propagation function between slices.

Parameters

size	size of projection image (z = 1).
sam	pixel size in x and y, slice thickness in z.
thickness	slice thickness (in angstrom).
volt	acceleration voltage (volt).

Returns

Bimage* wave propagation function image.

project_apply_distortions()

int project_apply_distortions	(	Bproject *	project,
		int	poisson,
		double	gauss,
		double	kmtf
	)

Applies imaging distortions to the final images from a multislice calculation.

Parameters

*project	project structure with parameters.
poisson	flag to add Poisson noise.
gauss	width of gaussian noise to add (0=no noise).
kmtf	mass transfer decay constant (0=no decay).

Returns

int 0.

project_generate()

Bproject * project_generate	(	int	nfield,
		int	nmg,
		int	npart,
		Vector3< double >	pixel_size,
		double	img_origin,
		CTFparam &	cp,
		double	def_min,
		double	def_max,
		double	dose,
		double	tsigma,
		Bstring &	fieldbase,
		Bstring &	mgbase,
		Bstring &	partbase,
		int	fieldnumber,
		int	mgnumber,
		int	partnumber
	)

Generates a project for multislice simulations.

Parameters

nfield	number of fields-of-view.
nmg	number of micrographs per field-of-view.
npart	number of particles per micrograph.
pixel_size	micrograph pixel size.
img_origin	image origin within the simulation box.
cp	CTF parameters).
def_min	defocus minimum (angstrom).
def_max	defocus maximum (angstrom).
dose	electron dose (e/angstrom^2).
tsigma	translation standard deviation (pixels).
&fieldbase	field base name.
&mgbase	micrograph base name.
&partbase	particle image base name.
fieldnumber	field-of-view number.
mgnumber	micrograph number.
partnumber	particle number.

Returns

Bproject* project structure.

project_generate_asu()

Bproject * project_generate_asu	(	Bstring &	symmetry_string,
		Vector3< double >	pixel_size,
		double	img_origin,
		double	theta_step,
		double	phi_step,
		CTFparam &	cp,
		double	defocus,
		double	dose,
		Bstring &	mgbase,
		Bstring &	partbase
	)

Generates a project for multislice calculations of an asymmetric unit.

Parameters

&symmetry_string	symmetry designation.
pixel_size	micrograph pixel size.
img_origin	image origin within the simulation box.
theta_step	step size in theta (radians).
phi_step	step size in phi (radians).
cp	CTF parameters).
defocus	defocus minimum (angstrom).
dose	electron dose (e/angstrom^2).
&mgbase	micrograph base name.
&partbase	particle image base name.

Returns

Bproject* project structure.

project_generate_image()

int project_generate_image	(	Bproject *	project,
		double	thickness,
		double	resolution
	)

Generates final images from a multislice calculation.

Parameters

*project	project structure with parameters.
thickness	thickness of slices for the multislice calculation (angstrom).
resolution	resolution for the multislice calculation (angstrom).

Returns

int 0.

project_generate_potential()

int project_generate_potential	(	Bmolgroup *	molgroup,
		Bmolgroup *	water,
		Bproject *	project,
		Bstring &	fieldname,
		Bstring &	mgname,
		int	partselect,
		Vector3< long >	size,
		double	thickness,
		double	resolution,
		double	Bfactor,
		int	pottype,
		Bstring &	paramfile
	)

Generates potential images using a multislice calculation.

Parameters

*molgroup	molecule group structure.
*water	block of water as solvent.
*project	project structure with parameters.
&fieldname	selected field name (if "" do all).
&mgname	selected micrograph (if "" do all).
partselect	selected particle ( if <1 do all).
size	size of simulation block (angstrom).
thickness	thickness of slices for the multislice calculation (angstrom).
resolution	resolution for the multislice calculation (angstrom).
Bfactor	B-factor to apply to the multislice calculation (angstrom^2).
pottype	type of potential to calculate (???).
&paramfile	parameter file for scattering curves (???).

Returns

int 0.

Variable Documentation

verbose

int verbose

extern