Functions for micrograph processing. More...

#include "mg_processing.h"
#include "mg_select.h"
#include "mg_tags.h"
#include "qsort_functions.h"
#include "linked_list.h"
#include "math_util.h"
#include "random_numbers.h"
#include "utilities.h"
#include <fstream>

Functions
Bproject *	project_create (int nmg, int nrec)
	Creates a micrograph processing project parameter structure. More...

int	project_equal_mg_part_files (Bproject *project)
	Sets micrograph and particle files to be the same. More...

Bfield *	field_add (Bfield **field, Bstring &field_id)
	Adds a field-of-view parameter structure to a linked list. More...

Bmicrograph *	micrograph_add (Bmicrograph **mg, Bstring &mg_id)
	Adds a micrograph parameter structure to a linked list. More...

Bframe *	frame_add (Bframe **frame, int pid)
	Adds a movie frame parameter structure to a linked list. More...

Bparticle *	particle_add (Bparticle **part, int pid)
	Adds a particle parameter structure to a linked list. More...

int	mg_part_links (Bmicrograph *mg)
	Sets the links from particles to micrographs. More...

int	rec_part_links (Breconstruction *rec)
	Sets the links from particles to reconstructions. More...

Bparticle *	part_find_first (Bproject *project)
	Finds the first particle in a project. More...

Bfilament *	filament_add (Bfilament **fil, int pid)
	Adds a filament parameter structure to a linked list. More...

Bfilnode *	filament_node_add (Bfilnode **fnode, int pid)
	Adds a filament node parameter structure to a linked list. More...

double	filament_length (Bfilament *fil)
	Calculates the length of a filament. More...

Breconstruction *	reconstruction_add (Breconstruction **rec, Bstring &rec_id)
	Adds a reconstruction parameter structure to a linked list. More...

int	project_kill (Bproject *project)
	Frees a whole project. More...

int	field_kill (Bfield *field)
	Frees a whole field-of-view structure. More...

int	micrograph_kill (Bmicrograph *mg)
	Frees a whole micrograph parameter structure. More...

int	particle_kill (Bparticle *part)
	Frees a list of particles. More...

int	filament_kill (Bfilament *fil)
	Frees a list of filaments. More...

int	reconstruction_kill (Breconstruction *rec)
	Frees a whole reconstruction parameter structure. More...

Bparticle *	particle_copy (Bparticle *partlist, Bparticle part)
	Adds one particle onto a list of particle parameters. More...

Bparticle *	particle_copy (Bparticle *partlist)
	Copies a list of particle parameters to a new list. More...

Bbadarea *	particle_bad_copy (Bbadarea *badlist)

Bfilament *	filament_copy (Bfilament *fillist)

Bstrucfac *	structurefactor_copy (Bstrucfac *sflist)

Blayerline *	layerline_copy (Blayerline *layerlist)

Bmicrograph *	micrograph_copy (Bmicrograph *mg)
	Copies a micrograph. More...

int	project_update (Bproject project, Bproject proj_new, int fom_index)
	Updates an existing project with new information. More...

int	micrograph_update (Bmicrograph mg, Bmicrograph nu_mg, int fom_index, int flags)
	Updates an existing micrograph with new information. More...

int	reconstruction_update (Breconstruction rec, Breconstruction nu_rec, int fom_index, int flags)
	Updates an existing reconstruction with new information. More...

int	particle_update (Bparticle part, Bparticle nu_part)
	Updates one existing particle with new information. More...

int	particle_update (Bparticle *pnt_part, Bparticle nu_part, int fom_index)
	Updates an existing particle list with new information. More...

int	project_merge_part_parameters (Bproject project, Bproject partproject)
	Puts particle parameters from one project into another. More...

long	project_set_part_links (Bproject *project)
	Sets the links from particles back to the micrographs and reconstructions. More...

long	micrograph_set_part_links (Bmicrograph *mg)
	Sets the links from particles back to the micrograph. More...

long	reconstruction_set_part_links (Breconstruction *rec)
	Sets the links from particles back to the reconstruction. More...

long	project_divide (Bproject *project, long n)
	Divides a project into a number of micrograph subsets. More...

Bmicrograph **	project_micrograph_array (Bproject *project, long &nmg)
	Sets up an array of selected micrograph pointers. More...

Bparticle **	project_mg_particle_array (Bproject *project, int part_select, long &npart)
	Sets up an array of selected particle pointers. More...

Bparticle **	project_rec_particle_array (Bproject *project, int part_select, long &npart)
	Sets up an array of selected particle pointers. More...

Bparticle **	particle_array (Bparticle *partlist, int part_select, long &npart)
	Sets up an array of selected particle pointers. More...

int	project_revert_filenames (Bproject project, Bproject project_old, int flag)
	Reverts file names to what it was in an old project. More...

int	project_set_field_id (Bproject *project, int nseries, Bstring &field_id)
	Sets the field id's according to a regular series. More...

long	project_show_hierarchy (Bproject *project)
	Shows the project hierarchy. More...

long	project_show_class_averages (Bproject *project)
	Shows the class averages in a project. More...

long	project_dump (Bproject *project, Bstring &filename)
	Dumps particle info in the project hierarchy. More...

Bstring	path_update (Bstring &filename, Bstring &path)

int	project_set_micrograph_path (Bproject *project, Bstring &path)
	Sets the path to micrograph files for all the micrographs. More...

int	project_set_frame_path (Bproject *project, Bstring &path)
	Sets the path to micrograph frames files for all the micrographs. More...

int	project_set_powerspectrum_path (Bproject *project, Bstring &path)
	Sets the path to powerspectrum files for all the micrographs. More...

int	project_set_particle_path (Bproject *project, Bstring &path)
	Sets the path to particle files for all the micrographs. More...

int	project_set_filament_path (Bproject *project, Bstring &path)
	Sets the path to filament files for all the micrographs. More...

int	project_set_magnification (Bproject *project, double mag)
	Sets the magnification for all the micrographs. More...

int	project_set_scan_sampling (Bproject *project, double sampling)
	Sets the scan sampling for all the micrographs. More...

int	project_set_mg_pixel_size (Bproject *project, Vector3< double > pixel_size)
	Sets the pixel size for all the micrographs. More...

int	project_set_frame_pixel_size (Bproject *project, Vector3< double > pixel_size)
	Sets the pixel size for all the micrograph frames. More...

int	project_set_rec_voxel_size (Bproject *project, Vector3< double > pixel_size)
	Sets the pixel size for all the reconstructions. More...

int	project_set_part_pixel_size (Bproject *project, Vector3< double > pixel_size)
	Sets the pixel size for all the particles. More...

int	project_set_tilt (Bproject *project, double tilt_axis, double tilt_angle)
	Sets the tilt parameters for all the micrographs. More...

int	project_set_exposure (Bproject *project, double exposure)
	Sets the aquisition time of all the micrographs. More...

int	project_set_dose (Bproject *project, double dose)
	Sets the electron dose of all the micrographs. More...

int	project_set_dose (Bproject *project, JSvalue &dose_frac)
	Sets the dose fractionation scheme of all the micrographs. More...

int	project_set_micrograph_origins (Bproject *project, Vector3< double > origin)
	Sets micrograph origins to the given origin. More...

int	project_add_origins_to_coords (Bproject *project)
	Adds the particle origins to the micrograph coordinates. More...

int	project_flip_origins (Bproject *project, int flip)
	Flip origin coordinates. More...

long	project_renumber_particles (Bproject *project)
	Renumbers particles. More...

int	project_set_particle_box_size (Bproject *project, Vector3< long > box_size)
	Sets particle box size to the given value. More...

int	project_set_particle_box_size (Bproject *project, long box_size)
	Sets particle box size to the given value. More...

int	project_set_particle_origins (Bproject *project, Vector3< double > origin)
	Sets particle origins to given values. More...

int	project_set_particle_asu_views (Bproject *project, Bstring &symmetry_asu)
	Sets particle views within the asymmetric unit. More...

int	project_set_particle_asu_views (Bproject *project, Bsymmetry &sym)

int	project_rotate_particle_views (Bproject *project, View view)
	Rotates particle views with respect to a reference view. More...

int	project_apply_map_magnifications (Bproject project, int mag_num, float mag)
	Change particle pixel sizes for particles based on map magnifications. More...

long	project_reset (Bproject *project, Bstring &reset)
	Reset a particle parameter from its micrograph. More...

View *	views_from_project (Bproject *project, int selection)
	Retrieves the particle views from a project. More...

Bstring	get_fom_tag (FOMType fom_type)
	Returns the tag associated with a particular FOM. More...

Variables
int	verbose

Detailed Description

Functions for micrograph processing.

Author: Bernard Heymann

Date: Created: 20010206; Modified: 20210722

Function Documentation

◆ field_add()

Bfield * field_add	(	Bfield **	field,
		Bstring &	field_id
	)

Adds a field-of-view parameter structure to a linked list.

Parameters

**field	pointer to any field-of-view in the list.
field_id	field identifier.

Returns

Bfield* new field-of-view.

The function allocates memory for a new field-of-view structure.
If the content of the pointer is null, the new structure is
the first in the list. Otherwise, the end of the list is found
and the new structure added to it.

◆ field_kill()

int field_kill ( Bfield * field )

Frees a whole field-of-view structure.

Frees all the structures down the hierarchy.

Parameters

*field field-of-view parameter structure.

Returns: int 0.

◆ filament_add()

Bfilament * filament_add	(	Bfilament **	fil,
		int	pid
	)

Adds a filament parameter structure to a linked list.

Parameters

**fil	pointer to any filament in the list.
pid	filament number in file (starts at 1).

Returns

Bfilament* new filament.

The function allocates memory for a new filament structure.
If the content of the pointer is null, the new structure is
the first in the list. Otherwise, the end of the list is found
and the new structure added to it.

◆ filament_copy()

Bfilament * filament_copy ( Bfilament * fillist )

◆ filament_kill()

int filament_kill ( Bfilament * fil )

Frees a list of filaments.

Frees all the structures down the hierarchy.

Parameters

*fil	filament parameter structure.

Returns: int 0.

◆ filament_length()

double filament_length ( Bfilament * fil )

Calculates the length of a filament.

Parameters

*fil	pointer to a filament.

Returns

double length in coordinate units.

The length is defined as the sum of the link lengths connecting the nodes.

◆ filament_node_add()

Bfilnode * filament_node_add	(	Bfilnode **	fnode,
		int	pid
	)

Adds a filament node parameter structure to a linked list.

Parameters

**fnode	pointer to any filament node in the list.
pid	filament node number in file (starts at 1).

Returns

Bfilnode* new filament node.

The function allocates memory for a new filament node structure.
If the content of the pointer is null, the new structure is
the first in the list. Otherwise, the end of the list is found
and the new structure added to it.

◆ frame_add()

Bframe * frame_add	(	Bframe **	frame,
		int	pid
	)

Adds a movie frame parameter structure to a linked list.

Parameters

**frame	pointer to any frame in the list.
pid	particle number in file (starts at 1).

Returns

Bframe* new frame.

The function allocates memory for a new frame structure.
If the content of the pointer is null, the new structure is
the first in the list. Otherwise, the end of the list is found
and the new structure added to it.

◆ get_fom_tag()

Bstring get_fom_tag ( FOMType fom_type )

Returns the tag associated with a particular FOM.

Parameters

fom_type type of FOM.

Returns: Bstring FOM tag.

◆ layerline_copy()

Blayerline * layerline_copy ( Blayerline * layerlist )

◆ mg_part_links()

int mg_part_links ( Bmicrograph * mg )

Sets the links from particles to micrographs.

Parameters

*mg	pointer to micrograph.

Returns: int 0.

◆ micrograph_add()

Bmicrograph * micrograph_add	(	Bmicrograph **	mg,
		Bstring &	mg_id
	)

Adds a micrograph parameter structure to a linked list.

Parameters

**mg	pointer to any micrograph in the list.
mg_id	micrograph identifier.

Returns

Bmicrograph* new micrograph.

The function allocates memory for a new micrograph structure.
If the content of the pointer is null, the new structure is
the first in the list. Otherwise, the end of the list is found
and the new structure added to it.

◆ micrograph_copy()

Bmicrograph * micrograph_copy ( Bmicrograph * mg )

Copies a micrograph.

Parameters

*mg	micrograph structure to be copied.

Returns: Bmicrograph* new micrograph.

◆ micrograph_kill()

int micrograph_kill ( Bmicrograph * mg )

Frees a whole micrograph parameter structure.

Frees all the structures down the hierarchy.

Parameters

*mg	micrograph parameter structure.

Returns: int 0.

◆ micrograph_set_part_links()

long micrograph_set_part_links ( Bmicrograph * mg )

Sets the links from particles back to the micrograph.

Parameters

*mg	micrograph parameter structure.

Returns: long number of particles.

◆ micrograph_update()

int micrograph_update	(	Bmicrograph *	mg,
		Bmicrograph *	nu_mg,
		int	fom_index,
		int	flags
	)

Updates an existing micrograph with new information.

Parameters

*mg	micrograph structure to be updated.
*nu_mg	micrograph structure with new information.
fom_index	index of FOM to select on.
flags	flags indicating which parts to update.

Returns

int 0.

The new information is encoded as a micrograph structure.
All fields are updated if the new fields contain non-default data.
Defaults are defined here as zero-length strings or zeroes.
The particles in the original micrograph are matched by ID with 
those in the new micrograph and updated, with any new particles 
added from the new micrograph.
The bad area and marker coordinates are replaced if they exist 
in the new structure.
The new micrograph structure is not modified, except for deletion 
of bad areas and markers.

Flags:
    1   particles
    2   bad areas
    4   filaments
    8   structure factors
    16  layer lines
    32  markers

◆ part_find_first()

Bparticle * part_find_first ( Bproject * project )

Finds the first particle in a project.

Parameters

*project pointer to project.

Returns

Bparticle* first particle with a filename.

The function searches for the first particle with a filename.

◆ particle_add()

Bparticle * particle_add	(	Bparticle **	part,
		int	pid
	)

Adds a particle parameter structure to a linked list.

Parameters

**part	pointer to any particle in the list.
pid	particle number in file (starts at 1).

Returns

Bparticle* new particle.

The function allocates memory for a new particle structure.
If the content of the pointer is null, the new structure is
the first in the list. Otherwise, the end of the list is found
and the new structure added to it.

◆ particle_array()

Bparticle ** particle_array	(	Bparticle *	partlist,
		int	part_select,
		long &	npart
	)

Sets up an array of selected particle pointers.

Parameters

*partlist	particle linked list.
part_select	particle selection (-1 if none).
&npart	array length (modified).

Returns

Bparticle** particle pointer array.

FOM's of non-selected particles are zeroed.

◆ particle_bad_copy()

Bbadarea * particle_bad_copy ( Bbadarea * badlist )

◆ particle_copy() [1/2]

Bparticle * particle_copy	(	Bparticle **	partlist,
		Bparticle *	part
	)

Adds one particle onto a list of particle parameters.

Parameters

**partlist	destination particle list.
*part	particle.

Returns: Bparticle* new particle.

◆ particle_copy() [2/2]

Bparticle * particle_copy ( Bparticle * partlist )

Copies a list of particle parameters to a new list.

Parameters

*partlist source particle list.

Returns: Bparticle* new list.

◆ particle_kill()

int particle_kill ( Bparticle * part )

Frees a list of particles.

Frees all the structures down the hierarchy.

Parameters

*part particle parameter structure.

Returns: int 0.

◆ particle_update() [1/2]

int particle_update	(	Bparticle **	pnt_part,
		Bparticle *	nu_part,
		int	fom_index
	)

Updates an existing particle list with new information.

Parameters

**pnt_part	particle structure list to be updated.
*nu_part	particle structure list with new information.
fom_index	index of FOM to select on.

Returns

int 0.

The new information is encoded as a particle structure.
All fields are updated if the new fields contain non-default data.
Defaults are defined here as zeroes.
The new particle structure is not modified.

◆ particle_update() [2/2]

int particle_update	(	Bparticle *	part,
		Bparticle *	nu_part
	)

Updates one existing particle with new information.

Parameters

*part	particle structure to be updated.
*nu_part	particle structure with new information.

Returns

int 0.

The new information is encoded as a particle structure.
All fields are updated if the new fields contain non-default data.
Defaults are defined here as zeroes.
The new particle structure is not modified.

◆ path_update()

Bstring path_update	(	Bstring &	filename,
		Bstring &	path
	)

◆ project_add_origins_to_coords()

int project_add_origins_to_coords ( Bproject * project )

Adds the particle origins to the micrograph coordinates.

Parameters

*project project parameter structure.

Returns

int 0.

The coordinates of particles from a micrograph and particle origins
in an image processing parameter structure are added. The old
micrograph coordinates are overwritten with the results.
Requirement: The box radius for picked particles must be specified.

◆ project_apply_map_magnifications()

int project_apply_map_magnifications	(	Bproject *	project,
		int	mag_num,
		float *	mag
	)

Change particle pixel sizes for particles based on map magnifications.

Parameters

*project	project parameter structure.
mag_num	number of maps;
*mag	array of map magnifications.

Returns: int 0.

◆ project_create()

Bproject * project_create	(	int	nmg,
		int	nrec
	)

Creates a micrograph processing project parameter structure.

Parameters

nmg	number of micrograph structures.
nrec	number of reconstruction structures.

Returns

Bproject* project parameter structure.

The function allocates memory for the project structure, a field-of-view structure,
and the requested number of micrographs and reconstructions.

◆ project_divide()

long project_divide	(	Bproject *	project,
		long	n
	)

Divides a project into a number of micrograph subsets.

Parameters

*project	project parameter structure.
n	number of subsets.

Returns

long number of new projects created.

Only selected micrographs are considered in the subdivision.

◆ project_dump()

long project_dump	(	Bproject *	project,
		Bstring &	filename
	)

Dumps particle info in the project hierarchy.

Parameters

*project	project parameter structure.
&filename	output file name.

Returns: long number of particles dumped.

◆ project_equal_mg_part_files()

int project_equal_mg_part_files ( Bproject * project )

Sets micrograph and particle files to be the same.

Parameters

*project project parameter structure.

Returns

int 0.

If the micrograph file name exists, that is used, otherwise the
particle file name is used.

◆ project_flip_origins()

int project_flip_origins	(	Bproject *	project,
		int	flip
	)

Flip origin coordinates.

Parameters

*project	project parameter structure.
flip	axes to flip.

Returns

int 0.

The particle origins are reversed.
The specification of axes to flip is embedded in the flip number:
    first bit  - x
    second bit - y
    third bit  - z

◆ project_kill()

int project_kill ( Bproject * project )

Frees a whole project.

Frees all the structures down the hierarchy.

Parameters

*project project parameter structure.

Returns: int 0.

◆ project_merge_part_parameters()

int project_merge_part_parameters	(	Bproject *	project,
		Bproject *	partproject
	)

Puts particle parameters from one project into another.

Parameters

*project	project parameter structure with all parameters.
*partproject	project parameter structure with particle parameters.

Returns: int 0.

◆ project_mg_particle_array()

Bparticle ** project_mg_particle_array	(	Bproject *	project,
		int	part_select,
		long &	npart
	)

Sets up an array of selected particle pointers.

Parameters

*project	project parameter structure.
part_select	particle selection (-1 if none).
&npart	array length (modified).

Returns

Bparticle** particle pointer array.

FOM's of non-selected particles are zeroed.

◆ project_micrograph_array()

Bmicrograph ** project_micrograph_array	(	Bproject *	project,
		long &	nmg
	)

Sets up an array of selected micrograph pointers.

Parameters

*project	project parameter structure.
&nmg	array length (modified).

Returns

Bmicrograph** micrograph pointer array.

FOM's of non-selected micrographs are zeroed.

◆ project_rec_particle_array()

Bparticle ** project_rec_particle_array	(	Bproject *	project,
		int	part_select,
		long &	npart
	)

Sets up an array of selected particle pointers.

Parameters

*project	project parameter structure.
part_select	particle selection (-1 if none).
&npart	array length (modified).

Returns

Bparticle** particle pointer array.

FOM's of non-selected particles are zeroed.

◆ project_renumber_particles()

long project_renumber_particles ( Bproject * project )

Renumbers particles.

Parameters

*project project parameter structure.

Returns

long total number of particles.

For each micrograph the particles are renumbered starting from 1.

◆ project_reset()

long project_reset	(	Bproject *	project,
		Bstring &	reset
	)

Reset a particle parameter from its micrograph.

Parameters

*project	project parameter structure.
&reset	a string specifying the parameter.

Returns: long number of particles changed.

◆ project_revert_filenames()

int project_revert_filenames	(	Bproject *	project,
		Bproject *	project_old,
		int	flag
	)

Reverts file names to what it was in an old project.

Parameters

*project	project parameter structure.
*project_old	project parameter structure with old file names.
flag	1=mg, 2=ps, 4=rec, 8=part, 16=frames.

Returns: int 0.

◆ project_rotate_particle_views()

int project_rotate_particle_views	(	Bproject *	project,
		View	view
	)

Rotates particle views with respect to a reference view.

Author: Eduardo Sanz-Garcia

Parameters

*project	project parameter structure.
view	reference view.

Returns: int 0.

◆ project_set_dose() [1/2]

int project_set_dose	(	Bproject *	project,
		double	dose
	)

Sets the electron dose of all the micrographs.

Parameters

*project	project parameter structure.
dose	electron dose (e/A2).

Returns: int 0.

◆ project_set_dose() [2/2]

int project_set_dose	(	Bproject *	project,
		JSvalue &	dose_frac
	)

Sets the dose fractionation scheme of all the micrographs.

Parameters

*project	project parameter structure.
dose_frac	electron dose fractionation scheme.

Returns: int 0.

◆ project_set_exposure()

int project_set_exposure	(	Bproject *	project,
		double	exposure
	)

Sets the aquisition time of all the micrographs.

Parameters

*project	project parameter structure.
exposure	aquisition time (seconds).

Returns: int 0.

◆ project_set_field_id()

int project_set_field_id	(	Bproject *	project,
		int	nseries,
		Bstring &	field_id
	)

Sets the field id's according to a regular series.

The micrograph data blocks must be arranged in a regular order with
every nseries micrographs from the same field-of-view.
The field id's are taken from the first micrograph id in a series.

Parameters

*project	project parameter structure.
nseries	number of micrographs per field-of-view.
&field_id	a user-specified field ID.

Returns: int 0.

◆ project_set_filament_path()

int project_set_filament_path	(	Bproject *	project,
		Bstring &	path
	)

Sets the path to filament files for all the micrographs.

Parameters

*project	project parameter structure.
&path	path to filament files.

Returns

int 0.

If the requested path is "." or "./", the path is completely removed.

◆ project_set_frame_path()

int project_set_frame_path	(	Bproject *	project,
		Bstring &	path
	)

Sets the path to micrograph frames files for all the micrographs.

Parameters

*project	project parameter structure.
&path	path to micrograph frames files.

Returns

int 0.

If the requested path is "." or "./", the path is completely removed.

◆ project_set_frame_pixel_size()

int project_set_frame_pixel_size	(	Bproject *	project,
		Vector3< double >	pixel_size
	)

Sets the pixel size for all the micrograph frames.

Parameters

*project	project parameter structure.
pixel_size	pixel size.

Returns: int 0.

◆ project_set_magnification()

int project_set_magnification	(	Bproject *	project,
		double	mag
	)

Sets the magnification for all the micrographs.

Parameters

*project	project parameter structure.
mag	magnification.

Returns: int 0.

◆ project_set_mg_pixel_size()

int project_set_mg_pixel_size	(	Bproject *	project,
		Vector3< double >	pixel_size
	)

Sets the pixel size for all the micrographs.

Parameters

*project	project parameter structure.
pixel_size	pixel size.

Returns: int 0.

◆ project_set_micrograph_origins()

int project_set_micrograph_origins	(	Bproject *	project,
		Vector3< double >	origin
	)

Sets micrograph origins to the given origin.

Parameters

*project	project parameter structure.
origin	particle origin.

Returns

int 0.

For each micrograph the micrograph origin is set to the given origin.

◆ project_set_micrograph_path()

int project_set_micrograph_path	(	Bproject *	project,
		Bstring &	path
	)

Sets the path to micrograph files for all the micrographs.

Parameters

*project	project parameter structure.
&path	path to micrograph files.

Returns

int 0.

If the requested path is "." or "./", the path is completely removed.

◆ project_set_part_links()

long project_set_part_links ( Bproject * project )

Sets the links from particles back to the micrographs and reconstructions.

Parameters

*project project parameter structure.

Returns: long number of particles.

◆ project_set_part_pixel_size()

int project_set_part_pixel_size	(	Bproject *	project,
		Vector3< double >	pixel_size
	)

Sets the pixel size for all the particles.

Parameters

*project	project parameter structure.
pixel_size	pixel size.

Returns: int 0.

◆ project_set_particle_asu_views() [1/2]

int project_set_particle_asu_views	(	Bproject *	project,
		Bstring &	symmetry_asu
	)

Sets particle views within the asymmetric unit.

Parameters

*project	project parameter structure.
&symmetry_asu	point group string.

Returns

int 0.

For each micrograph or reconstruction the particle view is set to within the asymmetric unit.

◆ project_set_particle_asu_views() [2/2]

int project_set_particle_asu_views	(	Bproject *	project,
		Bsymmetry &	sym
	)

◆ project_set_particle_box_size() [1/2]

int project_set_particle_box_size	(	Bproject *	project,
		long	box_size
	)

Sets particle box size to the given value.

Parameters

*project	project parameter structure.
box_size	particle box size.

Returns

int 0.

For each micrograph or reconstruction the particle box size is set 
to the given radius and the particle origins are adjusted as well.

◆ project_set_particle_box_size() [2/2]

int project_set_particle_box_size	(	Bproject *	project,
		Vector3< long >	box_size
	)

Sets particle box size to the given value.

Parameters

*project	project parameter structure.
box_size	particle box size.

Returns

int 0.

For each micrograph or reconstruction the particle box size is set 
to the given radius and the particle origins are adjusted as well.

◆ project_set_particle_origins()

int project_set_particle_origins	(	Bproject *	project,
		Vector3< double >	origin
	)

Sets particle origins to given values.

Parameters

*project	project parameter structure.
origin	particle origin.

Returns

int 0.

For each micrograph or reconstruction the particle origin is set to the given origin.

◆ project_set_particle_path()

int project_set_particle_path	(	Bproject *	project,
		Bstring &	path
	)

Sets the path to particle files for all the micrographs.

Parameters

*project	project parameter structure.
&path	path to particle files.

Returns

int 0.

If the requested path is "." or "./", the path is completely removed.

◆ project_set_powerspectrum_path()

int project_set_powerspectrum_path	(	Bproject *	project,
		Bstring &	path
	)

Sets the path to powerspectrum files for all the micrographs.

Parameters

*project	project parameter structure.
&path	path to powerspectrum files.

Returns

int 0.

If the requested path is "." or "./", the path is completely removed.

◆ project_set_rec_voxel_size()

int project_set_rec_voxel_size	(	Bproject *	project,
		Vector3< double >	pixel_size
	)

Sets the pixel size for all the reconstructions.

Parameters

*project	project parameter structure.
pixel_size	pixel size.

Returns: int 0.

◆ project_set_scan_sampling()

int project_set_scan_sampling	(	Bproject *	project,
		double	sampling
	)

Sets the scan sampling for all the micrographs.

Parameters

*project	project parameter structure.
sampling	sampling.

Returns

int 0.

Sampling is isotropic.

◆ project_set_tilt()

int project_set_tilt	(	Bproject *	project,
		double	tilt_axis,
		double	tilt_angle
	)

Sets the tilt parameters for all the micrographs.

Parameters

*project	project parameter structure.
tilt_axis	micrograph tilt axis angle.
tilt_angle	micrograph tilt angle.

Returns: int 0.

◆ project_show_class_averages()

long project_show_class_averages ( Bproject * project )

Shows the class averages in a project.

Parameters

*project project parameter structure.

Returns: long number of class averages.

◆ project_show_hierarchy()

long project_show_hierarchy ( Bproject * project )

Shows the project hierarchy.

Parameters

*project project parameter structure.

Returns: long number of particles selected.

◆ project_update()

int project_update	(	Bproject *	project,
		Bproject *	proj_new,
		int	fom_index
	)

Updates an existing project with new information.

Parameters

*project	project parameter structure to be updated.
*proj_new	project parameter structure with new information.
fom_index	index of FOM to select on.

Returns: int 0.

The new information is encoded as a project hierarchy.
The original project hierarchy is searched for the micrograph ID
tags that correspond to the original project hierarchy and those
micrograph parameters are updated. Because the micrograph ID tags
should be unique in themselves, the field ID tags are ignored and
the two project hierarchies may have different field designations.
If a micrograph ID from the new project hierarchy is not found in
the original project hierarchy, it is added.
The new project hierarchy is not modified.

◆ rec_part_links()

int rec_part_links ( Breconstruction * rec )

Sets the links from particles to reconstructions.

Parameters

*rec	pointer to reconstruction.

Returns: int 0.

◆ reconstruction_add()

Breconstruction * reconstruction_add	(	Breconstruction **	rec,
		Bstring &	rec_id
	)

Adds a reconstruction parameter structure to a linked list.

Parameters

**rec	pointer to any reconstruction in the list.
&rec_id	reconstruction identifier.

Returns

Breconstruction* new reconstruction.

The function allocates memory for a new micrograph structure.
If the content of the pointer is null, the new structure is
the first in the list. Otherwise, the end of the list is found
and the new structure added to it.

◆ reconstruction_kill()

int reconstruction_kill ( Breconstruction * rec )

Frees a whole reconstruction parameter structure.

Frees all the structures down the hierarchy.

Parameters

*rec	reconstruction parameter structure.

Returns: int 0.

◆ reconstruction_set_part_links()

long reconstruction_set_part_links ( Breconstruction * rec )

Sets the links from particles back to the reconstruction.

Parameters

*rec	reconstruction parameter structure.

Returns: long number of particles.

◆ reconstruction_update()

int reconstruction_update	(	Breconstruction *	rec,
		Breconstruction *	nu_rec,
		int	fom_index,
		int	flags
	)

Updates an existing reconstruction with new information.

Parameters

*rec	reconstruction structure to be updated.
*nu_rec	reconstruction structure with new information.
fom_index	index of FOM to select on.
flags	flags indicating which parts to update.

Returns

int 0.

The new information is encoded as a reconstruction structure.
The update is only done if the FOM of the new reconstruction is better.
All fields are updated if the new fields contain non-default data.
Defaults are defined here as zero-length strings or zeroes.
The particles in the original reconstruction are matched by ID with 
those in the new reconstruction and updated, with any new particles 
added from the new reconstruction.
The bad area and marker coordinates are replaced if they exist 
in the new structure.
The new reconstruction structure is not modified, except for deletion 
of bad areas and markers.

◆ structurefactor_copy()

Bstrucfac * structurefactor_copy ( Bstrucfac * sflist )

◆ views_from_project()

View * views_from_project	(	Bproject *	project,
		int	selection
	)

Retrieves the particle views from a project.

Parameters

*project	project parameter structure.
selection	selection number (-1 selects positives, 0 selects all).

Returns: View* linked list of views.

Variable Documentation

◆ verbose

int verbose

extern

Functions

Variables

Detailed Description

Function Documentation

◆ field_add()

◆ field_kill()

◆ filament_add()

◆ filament_copy()

◆ filament_kill()

◆ filament_length()

◆ filament_node_add()

◆ frame_add()

◆ get_fom_tag()

◆ layerline_copy()

◆ mg_part_links()

◆ micrograph_add()

◆ micrograph_copy()

◆ micrograph_kill()

◆ micrograph_set_part_links()

◆ micrograph_update()

◆ part_find_first()

◆ particle_add()

◆ particle_array()

◆ particle_bad_copy()

◆ particle_copy() [1/2]

◆ particle_copy() [2/2]

◆ particle_kill()

◆ particle_update() [1/2]

◆ particle_update() [2/2]

◆ path_update()

◆ project_add_origins_to_coords()

◆ project_apply_map_magnifications()

◆ project_create()

◆ project_divide()

◆ project_dump()

◆ project_equal_mg_part_files()

◆ project_flip_origins()

◆ project_kill()

◆ project_merge_part_parameters()

◆ project_mg_particle_array()

◆ project_micrograph_array()

◆ project_rec_particle_array()

◆ project_renumber_particles()

◆ project_reset()

◆ project_revert_filenames()

◆ project_rotate_particle_views()

◆ project_set_dose() [1/2]

◆ project_set_dose() [2/2]

◆ project_set_exposure()

◆ project_set_field_id()

◆ project_set_filament_path()

◆ project_set_frame_path()

◆ project_set_frame_pixel_size()

◆ project_set_magnification()

◆ project_set_mg_pixel_size()

◆ project_set_micrograph_origins()

◆ project_set_micrograph_path()

◆ project_set_part_links()

◆ project_set_part_pixel_size()

◆ project_set_particle_asu_views() [1/2]

◆ project_set_particle_asu_views() [2/2]

◆ project_set_particle_box_size() [1/2]

◆ project_set_particle_box_size() [2/2]

◆ project_set_particle_origins()

◆ project_set_particle_path()

◆ project_set_powerspectrum_path()

◆ project_set_rec_voxel_size()

◆ project_set_scan_sampling()

◆ project_set_tilt()

◆ project_show_class_averages()

◆ project_show_hierarchy()

◆ project_update()

◆ rec_part_links()

◆ reconstruction_add()

◆ reconstruction_kill()

◆ reconstruction_set_part_links()

◆ reconstruction_update()

◆ structurefactor_copy()

◆ views_from_project()

Variable Documentation