Header file for micrograph processing. More...

#include "ctf.h"
#include "symmetry.h"
#include "marker.h"
#include "View.h"
#include "Euler.h"
#include "Bstring.h"

Functions
Bfield *	field_find_id (Bfield *field, Bstring &field_id)
	Finds a field-of-view based on its identifier. More...

Bmicrograph *	field_find_micrograph (Bfield *field, int mg_select, int mg_index, double mg_ang)
	Returns a pointer to a specific micrograph in a field-of-view structure based on a unique characteristic of that micrograph. More...

Bmicrograph *	field_find_micrograph_n (Bfield *field, int n)
	Returns a pointer to the nth micrograph in a field-of-view structure. More...

Bmicrograph *	field_find_micrograph_by_focus (Bfield *field, int focus_opt, int index)
	Returns a pointer to the micrograph in a field-of-view structure based on the focus level and iteration index. More...

Bmicrograph *	field_find_micrograph_by_rotang (Bfield *field, double rotang)
	Returns a pointer to the micrograph in a field-of-view structure with the specified in-plane rotational angle. More...

Bmicrograph *	field_find_micrograph_by_tiltang (Bfield *field, double tiltang)
	Returns a pointer to the micrograph in a field-of-view structure with the specified tilt angle. More...

Bmicrograph *	field_find_zero_tilt_mg (Bfield *field)
	Finds the micrograph closest to a zero degree tilt in a series. More...

Bmicrograph *	field_find_low_tilt_mg_with_markers (Bfield *field)
	Finds the micrograph closest to a zero degree tilt in a series with markers. More...

long	project_count_fields (Bproject *project)
	Counts all the fields in the project structure. More...

long	project_count_micrographs (Bproject *project)
	Counts all the micrographs in the project structure. More...

long	project_count_mg_selected (Bproject *project)
	Counts all the selected micrographs in the project structure. More...

long	project_count_reconstructions (Bproject *project)
	Counts all the reconstructions in the project structure. More...

long	project_count_rec_selected (Bproject *project)
	Counts all the selected reconstructions in the project structure. More...

long	project_count_mg_particles (Bproject *project)
	Counts all the particles in the project structure. More...

long	project_count_mg_part_selected (Bproject *project)
	Counts the number of particles in a project. More...

long	project_count_mg_part_selected (Bproject *project, int num_select)
	Counts the number of particles in a project. More...

long	project_count_mg_groups (Bproject *project)
	Counts the number of groups of particles in the project structure. More...

long	project_count_mg_groups_selected (Bproject *project)
	Counts the number of groups of particles in the project structure. More...

long	project_count_rec_particles (Bproject *project)
	Counts all the particles in the project structure. More...

long	project_count_rec_part_selected (Bproject *project)
	Counts all the particles in the project structure. More...

long	project_count_rec_groups (Bproject *project)
	Counts all the particles in the project structure. More...

long	project_count_mg_filaments (Bproject *project)
	Counts the number of filaments in a project. More...

long	project_count_mg_filament_nodes (Bproject *project)
	Counts the number of filament nodes in a project. More...

long	project_count_rec_filaments (Bproject *project)
	Counts the number of filaments in a project. More...

long	project_count_rec_filament_nodes (Bproject *project)
	Counts the number of filaments in a project. More...

long	field_count (Bfield *field)
	Counts the number of fields-of-view in a linked list. More...

long	field_count_micrographs (Bfield *field)
	Counts all the micrographs in the field-of-view structure. More...

long	field_count_mg_selected (Bfield *field)
	Counts all the micrographs in the field-of-view structure. More...

long	field_count_particles (Bfield *field)
	Counts all the particles in the field-of-view structure. More...

long	micrograph_count (Bmicrograph *mg)
	Counts the number of micrographs in a linked list. More...

long	micrograph_count_particles (Bmicrograph *mg)
	Counts all the particles in the micrograph structure. More...

long	particle_count (Bparticle *part)
	Counts the number of particles in a linked list. More...

long	particle_count_selected (Bparticle *part)
	Counts the number of particles in a linked list. More...

long	filament_count (Bfilament *fil)
	Counts the number of filaments in a linked list of filaments. More...

long	filament_node_count (Bfilament *fil)
	Counts the number of filament nodes in a linked list of filaments. More...

long	project_maximum_selection (Bproject *project)
	Finds the maximum selection number for a project. More...

long	project_show_selection_numbers (Bproject *project)
	Shows the selection numbers for the particles in a project. More...

long	project_show_selected (Bproject *project)
	Shows the selected particles in a project. More...

long	project_show_selected_parameters (Bproject *project, int show)
	Shows the selected particle parameters in a project. More...

long	project_show_mg_parameter (Bproject *project, Bstring &tag)
	Shows the micrograph parameter indicated by the tag in a project. More...

long	project_show_part_parameter (Bproject *project, Bstring &tag)
	Shows the particle parameter indicated by the tag in a project. More...

long	project_show_fom_histogram (Bproject *project, long bins, double min, double max)
	Shows a histogram of the FOM values. More...

long	project_show_mag_histogram (Bproject *project, long bins, double increment)
	Shows the histogram for magnification values for selected particles. More...

int	project_select_field (Bproject *project, Bstring &field_id)
	Selects a field from the project and deletes the rest. More...

int	project_select_micrograph (Bproject *project, Bstring &mg_id)
	Selects a micrograph from the project and deletes the rest. More...

long	project_select_with_particles (Bproject *project, long part_sel)
	Selects micrographs with particles. More...

vector< pair< Bmicrograph *, double > >	project_mg_sort (Bproject *project, Bstring tag)
	Sorts the micrographs by a selected parameter. More...

Detailed Description

Header file for micrograph processing.

Author: Bernard Heymann

Date: Created: 20000426; Modified: 20210515

Function Documentation

◆ field_count()

long field_count ( Bfield * field )

Counts the number of fields-of-view in a linked list.

The function counts fields-of-view in the list from the given pointer,
and does not count fields-of-view prior to this one.

Parameters

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

Returns: long number of fields-of-view.

◆ field_count_mg_selected()

long field_count_mg_selected ( Bfield * field )

Counts all the micrographs in the field-of-view structure.

Parameters

*field field-of-view parameter structure.

Returns: long number of micrographs of field.

◆ field_count_micrographs()

long field_count_micrographs ( Bfield * field )

Counts all the micrographs in the field-of-view structure.

Parameters

*field field-of-view parameter structure.

Returns: long number of micrographs of field.

◆ field_count_particles()

long field_count_particles ( Bfield * field )

Counts all the particles in the field-of-view structure.

Parameters

*field field-of-view parameter structure.

Returns: long number of particles in field.

◆ field_find_id()

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

Finds a field-of-view based on its identifier.

Parameters

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

Returns

Bfield* field-of-view or NULL if not found.

The function searches a linked list for the field-of-view
identifier and returns a pointer to that structure or NULL if
it cannot find it.

◆ field_find_low_tilt_mg_with_markers()

Bmicrograph * field_find_low_tilt_mg_with_markers ( Bfield * field )

Finds the micrograph closest to a zero degree tilt in a series with markers.

Parameters

*field field-of-view.

Returns

Bmicrograph* micrograph closest to zero degrees tilt with markers.

The first micrograph with the smallest deviation from zero degree
tilt with defined markers is returned.

◆ field_find_micrograph()

Bmicrograph * field_find_micrograph	(	Bfield *	field,
		int	mg_select,
		int	mg_index,
		double	mg_ang
	)

Returns a pointer to a specific micrograph in a field-of-view structure based on a unique characteristic of that micrograph.

Author: David Belnap

Parameters

*field	field-of-view.
mg_select	selection criterion.
mg_index	Reference by its index in field (for mg_ref_select=0\|1\|2).
mg_ang	Reference by micrograph rotation or tilt angle (for mg_ref_select=3\|4).

Returns

Bmicrograph* Pointer to the selected micrograph

Calls functions that find a micrograph by index number within the
field, by focus level, in-plane rotational angle, tilt angle, or
tilt angle plus focus level or index number:

criterion                        mg_select   mg_index  mg_ang
--------------------------------------------------------------
nth closest-to-focus                 0           n        -
nth farthest-from-focus              1           n        -
index number in series (1...n)       2         index      -
in-plane rotation angle              3           -      angle
tilt angle                           4           -      angle

◆ field_find_micrograph_by_focus()

Bmicrograph * field_find_micrograph_by_focus	(	Bfield *	field,
		int	focus_opt,
		int	iselect
	)

Returns a pointer to the micrograph in a field-of-view structure based on the focus level and iteration index.

Author: David Belnap and Bernard Heymann

Parameters

*field	a field-of-view structure
focus_opt	0=closest-to-focus, 1=farthest-from-focus
iselect	0,1,...,n; select (index+1)th-closest or (index+1)th-farthest focus

Returns: Bmicrograph* mg Micrograph at specified focus level Loops through micrographs in the field-of-view. Orders focus values in an array from smallest to largest. Selects the (index+1)th closest-to-focus or farthest-from-focus value. (focus_opt determines whether the closest or farthest value is selected.) Loops through micrographs again to find the micrograph with the selected value. Tests if there are zero or multiple micrographs with the same focus value and exits program if so. Otherwise, the pointer to the micrograph with the specified focus level is returned. An example, if index=1 and focus_opt=0, a pointer to the 2nd closest-to-focus micrograph will be returned. To get the closest-to-focus or farthest-from-focus value, the index must be zero.

◆ field_find_micrograph_by_rotang()

Bmicrograph * field_find_micrograph_by_rotang	(	Bfield *	field,
		double	rotang
	)

Returns a pointer to the micrograph in a field-of-view structure with the specified in-plane rotational angle.

Author: David Belnap and Bernard Heymann

Parameters

*field	a field-of-view
rotang	in-plane rotational angle of micrograph (in radians)

Returns

Bmicrograph* mg Pointer to micrograph with rotang

Loop through all micrographs in the field-of-view to find
micrograph with the specified angle.  Test if there are zero or
multiple micrographs with the same rotational angle, halt program 
if true.  If not true, then return pointer to the micrograph with 
the specified angle.

◆ field_find_micrograph_by_tiltang()

Bmicrograph * field_find_micrograph_by_tiltang	(	Bfield *	field,
		double	tiltang
	)

Returns a pointer to the micrograph in a field-of-view structure with the specified tilt angle.

Author: David Belnap

Parameters

*field	a field-of-view
tiltang	tilt angle of micrograph (in radians)

Returns

Bmicrograph* micrograph with rotang

Loop through all micrographs in the field-of-view to find
micrograph with the specified tilt angle.  Test if there are zero
or multiple micrographs with the same angle, halt program if true.
If not true, then return pointer to the micrograph with the 
specified angle.

◆ field_find_micrograph_n()

Bmicrograph * field_find_micrograph_n	(	Bfield *	field,
		int	n
	)

Returns a pointer to the nth micrograph in a field-of-view structure.

Author: David Belnap and Bernard Heymann

Parameters

*field	a field-of-view
n	nth micrograph index (first index number = 1)

Returns

Bmicrograph* Pointer to the nth micrograph

Loop through micrographs in the field-of-view until the nth 
micrograph is reached.  Return pointer to that micrograph.
Tests whether n is within the appropriate range.

◆ field_find_zero_tilt_mg()

Bmicrograph * field_find_zero_tilt_mg ( Bfield * field )

Finds the micrograph closest to a zero degree tilt in a series.

Parameters

*field field-of-view.

Returns

Bmicrograph* micrograph closest to zero degrees tilt.

The first micrograph with the smallest deviation from zero degree
tilt is returned.

◆ filament_count()

long filament_count ( Bfilament * fil )

Counts the number of filaments in a linked list of filaments.

The function counts filaments in the list from the given pointer,
and does not count filaments prior to this one.

Parameters

*fil	pointer to any filament in the list.

Returns: long number of filaments.

◆ filament_node_count()

long filament_node_count ( Bfilament * fil )

Counts the number of filament nodes in a linked list of filaments.

The function counts filament nodes in the list from the given pointer,
and does not count filaments prior to this one.

Parameters

*fil	pointer to any filament in the list.

Returns: long number of filament nodes.

◆ micrograph_count()

long micrograph_count ( Bmicrograph * mg )

Counts the number of micrographs in a linked list.

The function counts micrographs in the list from the given pointer,
and does not count micrographs prior to this one.

Parameters

*mg	pointer to any micrograph in the list.

Returns: long number of micrographs.

◆ micrograph_count_particles()

long micrograph_count_particles ( Bmicrograph * mg )

Counts all the particles in the micrograph structure.

Parameters

*mg	micrograph parameter structure.

Returns: long number of particles in micrograph.

◆ particle_count()

long particle_count ( Bparticle * part )

Counts the number of particles in a linked list.

The function counts particles in the list from the given pointer,
and does not count particles prior to this one.

Parameters

*part pointer to any particle in the list.

Returns: long number of particles.

◆ particle_count_selected()

long particle_count_selected ( Bparticle * part )

Counts the number of particles in a linked list.

The function counts particles in the list from the given pointer,
and does not count particles prior to this one.

Parameters

*part pointer to any particle in the list.

Returns: long number of particles selected.

◆ project_count_fields()

long project_count_fields ( Bproject * project )

Counts all the fields in the project structure.

Parameters

*project project parameter structure.

Returns: long number of fields in project.

◆ project_count_mg_filament_nodes()

long project_count_mg_filament_nodes ( Bproject * project )

Counts the number of filament nodes in a project.

Parameters

*project project.

Returns

long number of filament nodes.

The function counts all the filament nodes in a project.

◆ project_count_mg_filaments()

long project_count_mg_filaments ( Bproject * project )

Counts the number of filaments in a project.

Parameters

*project project.

Returns

long number of filaments.

The function counts all the filaments in a project.

◆ project_count_mg_groups()

long project_count_mg_groups ( Bproject * project )

Counts the number of groups of particles in the project structure.

Parameters

*project project parameter structure.

Returns: long number of groups in project.

◆ project_count_mg_groups_selected()

long project_count_mg_groups_selected ( Bproject * project )

Counts the number of groups of particles in the project structure.

Parameters

*project project parameter structure.

Returns: long number of groups selected in project.

◆ project_count_mg_part_selected() [1/2]

long project_count_mg_part_selected ( Bproject * project )

Counts the number of particles in a project.

Parameters

*project project.

Returns

long number of particles selected.

The function counts all the selected particles in a project.

◆ project_count_mg_part_selected() [2/2]

long project_count_mg_part_selected	(	Bproject *	project,
		int	num_select
	)

Counts the number of particles in a project.

Parameters

*project	project.
num_select	selection number.

Returns

long number of particles selected.

The function counts all the selected particles in a project.

◆ project_count_mg_particles()

long project_count_mg_particles ( Bproject * project )

Counts all the particles in the project structure.

Parameters

*project project parameter structure.

Returns: long number of particles in project.

◆ project_count_mg_selected()

long project_count_mg_selected ( Bproject * project )

Counts all the selected micrographs in the project structure.

Parameters

*project project parameter structure.

Returns: long number of micrographs selected in project.

◆ project_count_micrographs()

long project_count_micrographs ( Bproject * project )

Counts all the micrographs in the project structure.

Parameters

*project project parameter structure.

Returns: long number of micrographs in project.

◆ project_count_rec_filament_nodes()

long project_count_rec_filament_nodes ( Bproject * project )

Counts the number of filaments in a project.

The function counts all the filaments in a project.

Parameters

*project project.

Returns: long number of filaments.

◆ project_count_rec_filaments()

long project_count_rec_filaments ( Bproject * project )

Counts the number of filaments in a project.

Parameters

*project project.

Returns

long number of filaments.

The function counts all the filaments in a project.

◆ project_count_rec_groups()

long project_count_rec_groups ( Bproject * project )

Counts all the particles in the project structure.

Parameters

*project project parameter structure.

Returns: long number of particles in project.

◆ project_count_rec_part_selected()

long project_count_rec_part_selected ( Bproject * project )

Counts all the particles in the project structure.

Parameters

*project project parameter structure.

Returns: long number of particles in project.

◆ project_count_rec_particles()

long project_count_rec_particles ( Bproject * project )

Counts all the particles in the project structure.

Parameters

*project project parameter structure.

Returns: long number of particles in project.

◆ project_count_rec_selected()

long project_count_rec_selected ( Bproject * project )

Counts all the selected reconstructions in the project structure.

Parameters

*project project parameter structure.

Returns: long number of reconstructions selected in project.

◆ project_count_reconstructions()

long project_count_reconstructions ( Bproject * project )

Counts all the reconstructions in the project structure.

Parameters

*project project parameter structure.

Returns: long number of reconstructions in project.

◆ project_maximum_selection()

long project_maximum_selection ( Bproject * project )

Finds the maximum selection number for a project.

Parameters

*project project parameter structure.

Returns: long maximum selection number.

◆ project_mg_sort()

vector< pair< Bmicrograph *, double > > project_mg_sort	(	Bproject *	project,
		Bstring	tag
	)

Sorts the micrographs by a selected parameter.

Parameters

*project	project parameter structure.
tag	parameter tag.

Returns: vector<pair<Bmicrograph*,double>> array of micrograph links and values.

◆ project_select_field()

int project_select_field	(	Bproject *	project,
		Bstring &	field_id
	)

Selects a field from the project and deletes the rest.

Parameters

*project	project parameter structure.
&field_id	field to select.

Returns: int 0.

◆ project_select_micrograph()

int project_select_micrograph	(	Bproject *	project,
		Bstring &	mg_id
	)

Selects a micrograph from the project and deletes the rest.

Parameters

*project	project parameter structure.
&mg_id	micrograph to select.

Returns: int 0.

◆ project_select_with_particles()

long project_select_with_particles	(	Bproject *	project,
		long	part_sel
	)

Selects micrographs with particles.

Parameters

*project	project parameter structure.
part_sel	flag to select only with this selection number

Returns: long number of particles.

◆ project_show_fom_histogram()

long project_show_fom_histogram	(	Bproject *	project,
		long	bins,
		double	min,
		double	max
	)

Shows a histogram of the FOM values.

Parameters

*project	project parameter structure.
bins	number of bins, if 0, set to 100.
min	FOM for the first bin.
max	FOM for the last bin.

Returns: long number of particles selected.

◆ project_show_mag_histogram()

long project_show_mag_histogram	(	Bproject *	project,
		long	bins,
		double	increment
	)

Shows the histogram for magnification values for selected particles.

Parameters

*project	project parameter structure.
bins	number of bins.
increment	increment between bins.

Returns: long number of particles selected.

◆ project_show_mg_parameter()

long project_show_mg_parameter	(	Bproject *	project,
		Bstring &	tag
	)

Shows the micrograph parameter indicated by the tag in a project.

Parameters

*project	project parameter structure.
&tag	parameter tag.

Returns: long number of micrographs selected.

◆ project_show_part_parameter()

long project_show_part_parameter	(	Bproject *	project,
		Bstring &	tag
	)

Shows the particle parameter indicated by the tag in a project.

Parameters

*project	project parameter structure.
&tag	parameter tag.

Returns: long number of particles selected.

◆ project_show_selected()

long project_show_selected ( Bproject * project )

Shows the selected particles in a project.

Parameters

*project project parameter structure.

Returns: long number of particles selected.

◆ project_show_selected_parameters()

long project_show_selected_parameters	(	Bproject *	project,
		int	show
	)

Shows the selected particle parameters in a project.

Parameters

*project	project parameter structure.
show	selection number to show.

Returns: long number of particles selected.

◆ project_show_selection_numbers()

long project_show_selection_numbers ( Bproject * project )

Shows the selection numbers for the particles in a project.

Parameters

*project project parameter structure.

Returns: long number of particles selected.

Functions

Detailed Description

Function Documentation

◆ field_count()

◆ field_count_mg_selected()

◆ field_count_micrographs()

◆ field_count_particles()

◆ field_find_id()

◆ field_find_low_tilt_mg_with_markers()

◆ field_find_micrograph()

◆ field_find_micrograph_by_focus()

◆ field_find_micrograph_by_rotang()

◆ field_find_micrograph_by_tiltang()

◆ field_find_micrograph_n()

◆ field_find_zero_tilt_mg()

◆ filament_count()

◆ filament_node_count()

◆ micrograph_count()

◆ micrograph_count_particles()

◆ particle_count()

◆ particle_count_selected()

◆ project_count_fields()

◆ project_count_mg_filament_nodes()

◆ project_count_mg_filaments()

◆ project_count_mg_groups()

◆ project_count_mg_groups_selected()

◆ project_count_mg_part_selected() [1/2]

◆ project_count_mg_part_selected() [2/2]

◆ project_count_mg_particles()

◆ project_count_mg_selected()

◆ project_count_micrographs()

◆ project_count_rec_filament_nodes()

◆ project_count_rec_filaments()

◆ project_count_rec_groups()

◆ project_count_rec_part_selected()

◆ project_count_rec_particles()

◆ project_count_rec_selected()

◆ project_count_reconstructions()

◆ project_maximum_selection()

◆ project_mg_sort()

◆ project_select_field()

◆ project_select_micrograph()

◆ project_select_with_particles()

◆ project_show_fom_histogram()

◆ project_show_mag_histogram()

◆ project_show_mg_parameter()

◆ project_show_part_parameter()

◆ project_show_selected()

◆ project_show_selected_parameters()

◆ project_show_selection_numbers()