Functions to do a tomographic reconstruction. More...

#include "mg_processing.h"
#include "rwimg.h"

Functions
Bimage *	project_tomo_reconstruct (Bproject *project, double hi_res, double scale, Vector3< long > size, int interp_type, int pad_factor, double edge_width, double marker_radius, int fill_type, double fill, int action, double wiener)
	Reciprocal space reconstruction from the images in a multi-image file. More...

Bimage *	project_fourier_reconstruction_slab (Bproject *project, double hi_res, double scale, Vector3< long > size, int slab_start, int slab_end, double marker_radius, int fill_type, double fill, int action, double wiener)
	Reciprocal space reconstruction from the images in a multi-image file. More...

long	project_tomo_reconstruct_particles (Bproject *project, double resolution, int interp_type, int pad_factor, int ctf_action, double wiener, Bsymmetry &sym, Bstring &partbase, Bstring &partpath, Bstring &partext)
	Reconstructs particles from a tilt series. More...

long	img_pack_2D_in_recip_space_slab (Bimage p, Bimage prec, long zsize, long slab_start, float weight, float weight2, double hi_res, Matrix3 mat, double scale)
	Packs a 2D Fourier transform into a 3D reciprocal space volume. More...

int	img_backtransform_slices (Bimage *p)
	Backtransforms 2D slices in a 3D volume. More...

int	img_phase_shift_slab_to_origin (Bimage *p, int zsize, int slab_start)
	Phase shifts a set of reflections to the image origin. More...

int	mg_fft_write (Bproject *project, Vector3< int > size, double scale, int pad_factor, DataType datatype, double marker_radius, int fill_type, double fill)
	Fourier transform micrographs and write to disk. More...

Bimage *	img_extract_ytile (Bstring *file_list, int ystart, int ysize)
	Extracts a tile from the image with limits in y. More...

Bimage *	img_backtransform_z_on_disk (Bstring *file_list, Bstring &recfile, DataType datatype, double avg, double std, double cutmin, double cutmax)
	The lines along the z-dimensions of a disk-based block is Fourier back-transformed. More...

int	img_backtransform_z_lines (Bimage *p)
	The lines along the z-dimensions of a disk-based block is Fourier back-transformed. More...

Bimage *	project_missing_mask (Bproject *project, Vector3< long > size, Vector3< double > origin, double hi_res, double scale)
	Creates a reciprocal space mask from the tilt series orientations. More...

Detailed Description

Functions to do a tomographic reconstruction.

Author: Bernard Heymann

Date: Created: 20020416; Modified: 20180629

Function Documentation

◆ img_backtransform_slices()

int img_backtransform_slices ( Bimage * p )

Backtransforms 2D slices in a 3D volume.

Parameters

*p	3D complex volume.

Returns

int 0.

Each slice is extracted, backtransformed and copied back into the
original volume.
Note: The phases are now not hermitian any more.

◆ img_backtransform_z_lines()

int img_backtransform_z_lines ( Bimage * p )

The lines along the z-dimensions of a disk-based block is Fourier back-transformed.

Parameters

*p	image header information (statistics updated).

Returns

int 0.

Each 2D xz plane is read from the raw complex data block.
Each z-line in the plane is back-transformed.
The transformed 2D plane is written back into the raw data block.

◆ img_backtransform_z_on_disk()

Bimage * img_backtransform_z_on_disk	(	Bstring *	file_list,
		Bstring &	recfile,
		DataType	datatype,
		double	avg,
		double	std,
		double	cutmin,
		double	cutmax
	)

The lines along the z-dimensions of a disk-based block is Fourier back-transformed.

Parameters

*file_list	list of image file names.
&recfile	new reconstruction file name.
datatype	data type for new reconstruction file.
avg	target average.
std	target standard deviation.
cutmin	minimum for truncation.
cutmax	maximum for truncation.

Returns

int 0.

Each 2D xz plane is read from the raw complex data block.
Each z-line in the plane is back-transformed.
The transformed 2D plane is written back into the raw data block.

◆ img_extract_ytile()

Bimage * img_extract_ytile	(	Bstring *	file_list,
		int	ystart,
		int	ysize
	)

Extracts a tile from the image with limits in y.

Parameters

*file_list	list of image file names.
ystart	first y index.
ysize	size in y.

Returns

Bimage* tile, NULL on failure.

From a series of z-slab images, tiles are extracted from a defined start in y,
and with a defined size in y.
A file indicating the origins of the tiles, "y.tiles", is written to
be used with bpatch to assemble the tiles.

◆ img_pack_2D_in_recip_space_slab()

long img_pack_2D_in_recip_space_slab	(	Bimage *	p,
		Bimage *	prec,
		long	zsize,
		long	slab_start,
		float *	weight,
		float *	weight2,
		double	hi_res,
		Matrix3	mat,
		double	scale
	)

Packs a 2D Fourier transform into a 3D reciprocal space volume.

Parameters

*p	2D Fourier transform
*prec	3D reciprocal space slab volume.
zsize	intentional z dimension of reconstruction.
slab_start	start of current slab.
*weight	weigth array.
*weight2	weight squared array.
hi_res	high resolution limit.
mat	affine matrix.
scale	scale of reconstruction and particle magnification.

Returns

long 0.

The rotation matrix is used to determine the plane in reciprocal space
to which the 2D transform data is added. The map is assumed to be cubic
and the 2D transform square. The real space 2D image must be supplied.
This is then padded to more than twice its original size, fourier
transformed, and packed into the 3D reciprocal space block.

◆ img_phase_shift_slab_to_origin()

int img_phase_shift_slab_to_origin	(	Bimage *	p,
		int	zsize,
		int	slab_start
	)

Phase shifts a set of reflections to the image origin.

Parameters

*p	complex image.
zsize	slab thickness.
slab_start	slab start.

Returns

int 0.

A real space translation with wrapping is equivalent to phase shifting
in reciprocal space. The phases are shifted based on the embedded
sub-image origins.

◆ mg_fft_write()

int mg_fft_write	(	Bproject *	project,
		Vector3< int >	size,
		double	scale,
		int	pad_factor,
		DataType	datatype,
		double	marker_radius,
		int	fill_type,
		double	fill
	)

Fourier transform micrographs and write to disk.

Parameters

*project	image processing parameter structure.
size	intended reconstruction size.
scale	reconstruction scale.
pad_factor	factor that determines image padding.
datatype	datatype (default complex float).
marker_radius	flag to mask out markers.
fill_type	FILL_AVERAGE, FILL_BACKGROUND, FILL_USER
fill	value to paint markers.

Returns

Bimage* reconstruction, NULL on failure.

Each micrograph is padded to a square size that has power of 2
dimensions. The micrograph is transformed and the phases shifted
to the origin.
A pad factor of zero indicates use of original size.

◆ project_fourier_reconstruction_slab()

Bimage * project_fourier_reconstruction_slab	(	Bproject *	project,
		double	hi_res,
		double	scale,
		Vector3< long >	size,
		int	slab_start,
		int	slab_end,
		double	marker_radius,
		int	fill_type,
		double	fill,
		int	action,
		double	wiener
	)

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

Parameters

*project	image processing parameter structure.
hi_res	high resolution limit.
scale	scale of reconstruction.
size	size of reconstruction.
slab_start	start of reconstruction slab.
slab_end	end of reconstruction slab.
marker_radius	flag and radius to mask out markers.
fill_type	FILL_AVERAGE, FILL_BACKGROUND, FILL_USER
fill	value to paint markers.
action	flag to apply CTF to projections.
wiener	Wiener factor.

Returns

Bimage* reconstruction, NULL on failure.

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.

◆ project_missing_mask()

Bimage * project_missing_mask	(	Bproject *	project,
		Vector3< long >	size,
		Vector3< double >	origin,
		double	hi_res,
		double	scale
	)

Creates a reciprocal space mask from the tilt series orientations.

Parameters

*project	project parameter structure.
size	size of mask.
origin	origin of mask.
hi_res	high resolution limit.
scale	scale of mask.

Returns

Bimage* mask, NULL on failure.

The orientation parameters of the micrographs must all be set. 
A 2D mask is overlayed onto the 3D image for each micrograph.

◆ project_tomo_reconstruct()

Bimage * project_tomo_reconstruct	(	Bproject *	project,
		double	hi_res,
		double	scale,
		Vector3< long >	size,
		int	interp_type,
		int	pad_factor,
		double	edge_width,
		double	marker_radius,
		int	fill_type,
		double	fill,
		int	action,
		double	wiener
	)

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

Parameters

*project	image processing parameter structure.
hi_res	high resolution limit.
scale	scale of reconstruction.
size	size of reconstruction.
interp_type	interpolation type.
pad_factor	factor that determines image padding.
edge_width	edge smoothing width for masks.
marker_radius	flag and radius to mask out markers.
fill_type	FILL_AVERAGE, FILL_BACKGROUND, FILL_USER
fill	value to paint markers.
action	flag to apply CTF to projections.
wiener	Wiener factor.

Returns

Bimage* reconstruction, NULL on failure.

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.

◆ project_tomo_reconstruct_particles()

long project_tomo_reconstruct_particles	(	Bproject *	project,
		double	resolution,
		int	interp_type,
		int	pad_factor,
		int	ctf_action,
		double	wiener,
		Bsymmetry &	sym,
		Bstring &	partbase,
		Bstring &	partpath,
		Bstring &	partext
	)

Reconstructs particles from a tilt series.

Parameters

*project	micrograph project.
resolution	high resolution limit for reconstruction.
interp_type	interpolation type.
pad_factor	factor that determines image padding.
ctf_action	flag to apply CTF to projections.
wiener	Wiener factor.
*sym	point group symmetry.
&partbase	particle base name for new particle reconstructions.
&partpath	directory for new particle reconstructions.
&partext	extension of new reconstructions.

Returns

long number of particles.

Requires the particles to be defined in all micrographs.
The partbase, partpath and partext arguments can be left empty to
use defaults.