Functions for reconstruction. More...

#include "rwimg.h"
#include "rwmg.h"
#include "mg_processing.h"
#include "mg_select.h"
#include "mg_img_proc.h"
#include "mg_particle_select.h"
#include "mg_reconstruct.h"
#include "mg_ctf.h"
#include "Complex.h"
#include "symmetry.h"
#include "utilities.h"
#include <sys/stat.h>
#include <fcntl.h>

Functions
int	part_ft_size (int xsize, double scale, int pad_factor)
	Sets the Fourier transform size for 2D particle images for reconstruction. More...

Bimage *	particle_reconstruct (Bparticle *partlist, Bsymmetry sym, int sym_mode, double hi_res, Vector3< double > scale, Vector3< double > sam, Vector3< long > size, int ft_size, fft_plan plan, int interp_type, int ctf_action, double wiener, int flags, int first)
	Reciprocal space reconstruction from 2D particle images. More...

Bimage *	img_reconstruction_sum_weigh (Bimage **pacc, int imap, int nmaps, int maps_per_class, double hi_res)
	Combines and weighs a map from several partial maps and weight sets. More...

double	part_single_reconstruction (Bparticle part, Vector3< long > size, Bimage pmask, Bsymmetry &sym, double hi_res, Vector3< double > scale, int ft_size, fft_plan img_plan, fft_plan map_plan, double part_weight, int interp_type, CTFparam *mg_ctf, int ctf_action, double wiener, int flags)

long	project_single_particle_reconstruction (Bproject *project, Bstring &maskfile, Bsymmetry &sym, int num_select, double hi_res, Vector3< double > scale, Vector3< long > size, int pad_factor, int interp_type, int ctf_action, double wiener, int flags)
	Reciprocal space reconstruction from the images in a multi-image file. More...

Vector3< long >	project_set_reconstruction_size (Bproject *project, Vector3< double > &sam, double scale, int twoD_flag)
	Sets the reconstruction size for reconstruction from 2D particle images. More...

int	project_configure_for_reconstruction (Bproject *project, Bstring classes, long &nmaps, int &nthreads)
	Sets up the particle selection for reconstruction. More...

int	project_update_class_averages (Bproject project, Bimage prec, Bstring file_name)

Bimage *	project_reconstruct_2D (Bproject *project, Bstring file_name, int transform_output)
	Creates a 2D reconstruction from the images in a multi-image file. More...

Bparticle *	img_reconstruct_2D (long i, Bproject project, Bimage prec, double hires, fft_plan planf, fft_plan planb)

long	img_reconstruct_2D_fspace (long i, Bproject project, Bimage prec, double hires, fft_plan planf, fft_plan planb)

Bimage *	project_reconstruct_2D_fast (Bproject *project, Bstring file_name)

Bimage *	project_reconstruct_3D (Bproject *project, long selnum, int calcfom, Vector3< long > size)
	Transforms 3D maps and calculates an average. More...

Bimage *	project_reconstruct_3D (Bproject *project, long selnum, Vector3< long > size, double resolution)
	Transforms 3D maps and calculates an average. More...

Bimage *	project_back_projection (Bproject *project, long num_select, Vector3< long > map_size, Vector3< double > sam, double scale, double resolution, fft_plan planf, fft_plan planb)
	Back projects a set of 2D images into a 3D volume. More...

Bimage *	img_backprojection_accumulate (Bimage **pacc, int imap, int nmaps, int nthreads)
	Accumulates multiple backprojections. More...

Variables
int	verbose

Detailed Description

Functions for reconstruction.

Author: Bernard Heymann

Date: Created: 20010403; Modified: 20220221

Function Documentation

◆ img_backprojection_accumulate()

Bimage * img_backprojection_accumulate	(	Bimage **	pacc,
		int	imap,
		int	nmaps,
		int	nthreads
	)

Accumulates multiple backprojections.

Parameters

**pacc	array of partial maps with linked weight maps.
imap	which output map to weigh.
nmaps	number of output maps (1,2,3).
nthreads	number of threads per map (= number of partial maps).

Returns: int 0.

◆ img_reconstruct_2D()

Bparticle * img_reconstruct_2D	(	long	i,
		Bproject *	project,
		Bimage *	prec,
		double	hires,
		fft_plan	planf,
		fft_plan	planb
	)

◆ img_reconstruct_2D_fspace()

long img_reconstruct_2D_fspace	(	long	i,
		Bproject *	project,
		Bimage *	prec,
		double	hires,
		fft_plan	planf,
		fft_plan	planb
	)

◆ img_reconstruction_sum_weigh()

Bimage * img_reconstruction_sum_weigh	(	Bimage **	pacc,
		int	imap,
		int	nmaps,
		int	maps_per_class,
		double	hi_res
	)

Combines and weighs a map from several partial maps and weight sets.

Parameters

**pacc	array of partial maps with linked weight maps.
imap	which output map to weigh.
nmaps	number of output maps (1,2,3).
maps_per_class	number of threads per map (= number of partial maps).
hi_res	high resolution limit.

Returns

Bimage* weighed reconstruction with FOM block.

The input is a set of partially integrated complex maps with associated 
weigths as follows:
    voxel power sums            FOM block of map.
    voxel weight sums           linked image.
    voxel weight squared sums   linked image FOM block.
The partial sums are completed into corresponding blocks in three possible
ways based on the value of imap and nmap:
    nmap    imap    result
    1       0       one map from all input maps
    2       0,1     one map from half of the input maps
    3       0       one map from all input maps
    3       1,2     one map from half of the input maps
The total number of maps in the array is nclasses*nmaps.

◆ part_ft_size()

int part_ft_size	(	int	xsize,
		double	scale,
		int	pad_factor
	)

Sets the Fourier transform size for 2D particle images for reconstruction.

Parameters

xsize	size of x dimension.
scale	scale of reconstruction.
pad_factor	factor that determines image padding.

Returns

int transform size.

The reconstruction size must be set.

◆ part_single_reconstruction()

double part_single_reconstruction	(	Bparticle *	part,
		Vector3< long >	size,
		Bimage *	pmask,
		Bsymmetry &	sym,
		double	hi_res,
		Vector3< double >	scale,
		int	ft_size,
		fft_plan	img_plan,
		fft_plan	map_plan,
		double	part_weight,
		int	interp_type,
		CTFparam *	mg_ctf,
		int	ctf_action,
		double	wiener,
		int	flags
	)

◆ particle_reconstruct()

Bimage * particle_reconstruct	(	Bparticle *	partlist,
		Bsymmetry	sym,
		int	sym_mode,
		double	hi_res,
		Vector3< double >	scale,
		Vector3< double >	sam,
		Vector3< long >	size,
		int	ft_size,
		fft_plan	plan,
		int	interp_type,
		int	ctf_action,
		double	wiener,
		int	flags,
		int	first
	)

Reciprocal space reconstruction from 2D particle images.

Parameters

*partlist	a list of 2D particle image parameters.
*sym	point group symmetry.
sym_mode	0=apply symmetry, 1=C1, 2=random symmetry view
hi_res	high resolution limit.
scale	scale of reconstruction.
sam	sampling/voxel size of reconstruction.
size	size of reconstruction.
ft_size	Fourier transform size.
plan	Fourier transform plan.
interp_type	interpolation type.
ctf_action	flag to apply CTF to projections.
wiener	Wiener factor.
flags	1=rescale particles, 2=2D reconstruction, 4=bootstrap, 8=Ewald.
first	flag to indicate the first thread.

Returns

Bimage* 3D reconstructed map.

The orientation parameters, view vector, angle of rotation and origin,
must all be set. Each image is padded to at least two times its size 
and its Fourier transform packed into 3D reciprocal space.
The figure-of-merit calculated for each reciprocal space voxel is:
           sum(w*re)^2 + sum(w*im)^2
    FOM = ---------------------------
          sum(w)*sum(w*(re^2 + im^2))
where
    re  real part
    im  imaginary part
    w   weight (inverse distance of image pixel to closest grid point)
For voxels with only one data pixel contributing to it, FOM = 0.
A bootstrap reconstruction uses the particle selection to weigh each
selected particle.

◆ project_back_projection()

Bimage * project_back_projection	(	Bproject *	project,
		long	num_select,
		Vector3< long >	map_size,
		Vector3< double >	sam,
		double	scale,
		double	resolution,
		fft_plan	planf,
		fft_plan	planb
	)

Back projects a set of 2D images into a 3D volume.

Parameters

*project	image processing parameter structure.
num_select	selection number from the selection column.
map_size	3-valued vector for the new map size.
sam	3-value vector for the voxel size in angstrom.
scale	reconstruction scale.
resolution	resolution for low-pass filtering.
planf	2D forward Fourier transform plan.
planb	2D backward Fourier transform plan.

Returns

Bimage* the new 3D reconstruction map.

All the information needed to do a 3D reconstruction is passed in through
an image processing structure. The new 3D volume is initialized.
Each sub-image in each particle file is read individually and 
back-projected within the new volume. The orientation parameters from
the image processing structure is transferred to the sub-image
structure in the 2D image before calling the function packing one
image into the volume. The default origin is the center of the image.

◆ project_configure_for_reconstruction()

int project_configure_for_reconstruction	(	Bproject *	project,
		Bstring	classes,
		long &	nmaps,
		int &	nthreads
	)

Sets up the particle selection for reconstruction.

Parameters

*project	project parameter structure.
classes	string specifying classes to use.
nmaps	number of maps per class (1,2,3).
nthreads	number of threads per class (must be even if nmaps > 1).

Returns

int number of classes.

The classes are specified in a string of comma-separated numbers,
also allowing hyphened ranges (e.g., "2,5-7,9").
The selection numbers for the particles in the project are set to
calculate partial maps so that there are nthread maps per class.
Each such partial map will be calculated in its own thread and
integrated with others from the same class afterwards.

◆ project_reconstruct_2D()

Bimage * project_reconstruct_2D	(	Bproject *	project,
		Bstring	file_name,
		int	transform_output
	)

Creates a 2D reconstruction from the images in a multi-image file.

Parameters

*project	image processing parameter structure.
file_name	2D reconstruction file name.
transform_output	flag to output transformed images.

Returns

Bimage* 2D reconstruction image.

The angle of rotation and the x,y origins must already have been found 
and placed in the appropriate arrays within the Bproject structure.
Each selected image is transformed, and then added to the reconstruction
image corresponding to the original projection image chosen.
If the transform_output flag is set, then the transformed images are written
into a new image with a "_proj.spi" ending.

◆ project_reconstruct_2D_fast()

Bimage * project_reconstruct_2D_fast	(	Bproject *	project,
		Bstring	file_name
	)

◆ project_reconstruct_3D() [1/2]

Bimage * project_reconstruct_3D	(	Bproject *	project,
		long	selnum,
		int	calcfom,
		Vector3< long >	size
	)

Transforms 3D maps and calculates an average.

Parameters

*project	parameter structure with all parameters.
selnum	selection number of reconstructions or particles.
calcfom	flag to calculate FOM block (1=var, 2=std).
size	size of particles to extract (only when extraction needed).

Returns

Bimage* average map with FOM block defined.

The orientations of the maps in the project must already be specified.
Each map is transformed and added to an average map.
A FOM block is optionally calculated with either the variance or
standard deviation.

◆ project_reconstruct_3D() [2/2]

Bimage * project_reconstruct_3D	(	Bproject *	project,
		long	selnum,
		Vector3< long >	size,
		double	resolution
	)

Transforms 3D maps and calculates an average.

Parameters

*project	parameter structure with all parameters.
selnum	selection number of reconstructions or particles.
size	size of particles to extract (only when extraction needed).
resolution	maximum reconstruction resolution (in angstrom, default Nyquest).

Returns

Bimage* average map with FOM block defined.

The orientations of the maps in the project must already be specified.
Each map is transformed and added to an average map.
A FOM block is optionally calculated with either the variance or
standard deviation.

◆ project_set_reconstruction_size()

Vector3< long > project_set_reconstruction_size	(	Bproject *	project,
		Vector3< double > &	sam,
		double	scale,
		int	twoD_flag
	)

Sets the reconstruction size for reconstruction from 2D particle images.

Parameters

*project	project parameter structure.
&sam	sampling/voxel size of new map.
scale	scale of reconstruction.
twoD_flag	doing a 2D reconstruction rather than 3D.

Returns

Vector3<long> reconstruction size.

The reconstruction size is set from the first particle image size found.

◆ project_single_particle_reconstruction()

long project_single_particle_reconstruction	(	Bproject *	project,
		Bstring &	maskfile,
		Bsymmetry &	sym,
		int	num_select,
		double	hi_res,
		Vector3< double >	scale,
		Vector3< long >	size,
		int	pad_factor,
		int	interp_type,
		int	ctf_action,
		double	wiener,
		int	flags
	)

Reciprocal space reconstruction from the images in a multi-image file.

Parameters

*project	image processing parameter structure.
&maskfile	mask to determine density statistics.
*sym	point group symmetry.
num_select	selection number from the selection column.
hi_res	high resolution limit.
scale	scale of reconstruction.
size	size of reconstruction.
pad_factor	image padding factor.
interp_type	interpolation type (provisional).
ctf_action	flag to apply CTF to projections.
wiener	Wiener factor.
flags	option flags.

Returns

long particles processed.

The orientation parameters, view vector, angle of rotation and origin,
must all be set. Each image is padded to at least two times its size 
and its Fourier transform packed into 3D reciprocal space.
The figure-of-merit calculated for each reciprocal space voxel is:
           sum(w*re)^2 + sum(w*im)^2
    FOM = ---------------------------
          sum(w)*sum(w*(re^2 + im^2))
where
    re  real part
    im  imaginary part
    w   weight (inverse distance of image pixel to closest grid point)
For voxels with only one data pixel contributing to it, FOM = 0.
An image is used in the reconstruction if its selection flag has been set.
If the selection number is less than zero, all particles with selection flags
greater than zero are used. If the selection number is zero or above, all
particles with the selection flag set to the same number are used.
A bootstrap reconstruction uses the particle selection to weigh each
selected particle.

◆ project_update_class_averages()

int project_update_class_averages	(	Bproject *	project,
		Bimage *	prec,
		Bstring	file_name
	)

Variable Documentation

◆ verbose

int verbose

extern

Functions

Variables

Detailed Description

Function Documentation

◆ img_backprojection_accumulate()

◆ img_reconstruct_2D()

◆ img_reconstruct_2D_fspace()

◆ img_reconstruction_sum_weigh()

◆ part_ft_size()

◆ part_single_reconstruction()

◆ particle_reconstruct()

◆ project_back_projection()

◆ project_configure_for_reconstruction()

◆ project_reconstruct_2D()

◆ project_reconstruct_2D_fast()

◆ project_reconstruct_3D() [1/2]

◆ project_reconstruct_3D() [2/2]

◆ project_set_reconstruction_size()

◆ project_single_particle_reconstruction()

◆ project_update_class_averages()

Variable Documentation

◆ verbose