Functions to manage tomographic series of images. More...

#include "mg_processing.h"
#include "mg_tomography.h"
#include "mg_select.h"
#include "mg_img_proc.h"
#include "rwimg.h"
#include "matrix_linear.h"
#include "simplex.h"
#include "linked_list.h"
#include "utilities.h"
#include "timer.h"

Functions
int	mg_marker_init (Bmicrograph mg, Bmarker model)
	Initializes markers from the reference. More...

int	mg_marker_update (Bmicrograph mg, Bmarker model, Vector3< double > oriref, int update_location)
	Calculates the predicted positions of markers from the reference. More...

Vector3< double >	mg_3D_location_from_marker (Vector3< double > loc, Vector3< double > ori3D, Matrix3 mat, Vector3< double > ori)

int	mg_update_model (Bmicrograph mg, Bmarker model, Vector3< double > oriref)
	Fills in missing markers in the 3D model from micrograph markers. More...

Vector3< double >	mg_location_from_3D_model (Vector3< double > loc3D, Matrix3 mat, Vector3< double > ori)
	Calculates the 2D location of a marker from a 3D model. More...

Vector3< double >	mg_location_from_3D_model (Vector3< double > loc3D, Matrix3 mat, Vector3< double > ori, Vector3< double > scale)

Vector3< double >	mg_location_from_3D_model (Vector3< double > loc3D, Vector3< double > ori3D, Matrix3 mat, Vector3< double > ori)

Vector3< double >	mg_location_from_3D_model (Vector3< double > loc3D, Vector3< double > ori3D, Matrix3 mat, Vector3< double > ori, Vector3< double > scale)

Bimage *	img_gold_particle (Vector3< long > size, double radius)
	Generates an image representing a gold particle. More...

Bmarker *	img_find_gold_particles (Bimage *p, int img_select, double radius, long edge, double cutoff)
	Finds gold particles in micrograph images. More...

int	project_mass_normalize (Bproject *project, double avg, double std, int norm_type, DataType datatype, int setinputZslices, int setoutputZslices, double cutmin, double cutmax, double replace_threshold)
	Normalizes a set of images in a project to a desired average and standard deviation. More...

double	lambda_R (Bsimplex &simp)

vector< double >	simplex_fit_tilt_intensities (vector< double > &a, vector< double > &I)

Bplot *	project_intensity_plot (Bproject *project)
	Transfers the micrograph intensities for a field into a plot. More...

double	project_fit_intensities (Bproject project, Bplot plot, int flag)
	Determines the thickness to mean free path ratio from a tilt series. More...

double	project_thickness_to_lambda_ratio (Bproject *project)
	Determines the thickness to mean free path ratio from a tilt series. More...

double	project_lambda (Bproject *project, double thickness)
	Determines the mean free path from a tilt series and thickness. More...

double	project_thickness (Bproject *project, double lambda)
	Determines the thickness from a tilt series and mean free path. More...

int	project_sort_markers_by_id (Bproject *project)
	Sorts markers for each micrograph by ID number. More...

double	project_tomo_residuals (Bproject *project, int show)
	Calculates the residuals for an alignment solution. More...

double	mg_tomo_residuals (Bmicrograph mg, Bmarker model, Vector3< double > oriref)
	Calculates the residuals for an alignment solution of one micrograph. More...

double	project_tomo_errors (Bproject *project)
	Analyzes marker errors. More...

int	project_calculate_model (Bproject *project)
	Calculates the z-coordinates of the marker model. More...

int	project_generate_markers (Bproject *project)
	Generates missing micrograph and model markers. More...

long	img_erase_markers (Bimage p, Bmarker mark, double marker_radius)
	Erases or paints markers in an image. More...

Bimage *	mg_erase_markers (Bmicrograph *mg, double marker_radius)
	Erases or paints markers in micrographs. More...

int	project_erase_markers (Bproject *project, double marker_radius)
	Erases or paints markers in micrographs. More...

int	mg_reset_model (Bmicrograph mg, Bmarker model)
	Resets the model x and y coordinates from the zero-tilt micrograph. More...

long	project_find_markers (Bproject *project, long edge, int add)
	Finds all markers in a project. More...

long	mg_find_markers (Bmicrograph *mg, long edge, int add)
	Finds markers in a micrograph. More...

Bimage *	mg_composite_particle (Bmicrograph *mg, Vector3< long > size)
	Generates an average particle image from a micrograph. More...

long	project_count_markers (Bproject *project)
	Counts the markers in a project hierarchy. More...

long	project_show_markers (Bproject *project)
	Shows the markers in a project hierarchy. More...

long	project_show_errors (Bproject *project, double error_cutoff)
	Shows the errors in marker coordinates in a project hierarchy. More...

long	project_deselect_markers (Bproject *project, Bstring &deselect_list)
	Deletes selected markers in a project hierarchy. More...

long	project_delete_markers (Bproject *project, Bstring &delete_list)
	Deletes selected markers in a project hierarchy. More...

long	project_renumber_markers (Bproject *project)
	Renumbers the markers in a project hierarchy. More...

long	project_mg_select (Bproject *project, Bstring &mg_select)
	Selects micrographs in a project hierarchy. More...

long	project_mg_exclude (Bproject *project, Bstring &mg_exclude)
	Deselects micrographs in a project hierarchy. More...

int	project_set_tilt_axis (Bproject *project, double tilt_axis)
	Sets the tilt axis angle in a project parameter structure. More...

int	project_invert_tilt_axis (Bproject *project)
	Inverts the tilt axis in a project parameter structure. More...

int	project_set_tilt_angles (Bproject *project, double tilt_start, double tilt_step)
	Sets the tilt and tilt axis angles in a project parameter structure. More...

int	project_mg_tilt_to_matrix (Bproject *project)
	Sets the matrix from the tilt and axis angles for each micrograph. More...

int	project_calculate_angles (Bproject *project)
	Calculates tilt and tilt axis angles from matrices in a project parameter structure. More...

int	project_invert_matrices (Bproject *project)
	Inverts the micrograph matrices in a project parameter structure. More...

int	project_mg_marker_select (Bproject *project, double fom)
	Selects markers. More...

int	project_set_marker_radius (Bproject *project, double mark_radius)
	Sets the marker radius in a project parameter structure. More...

int	project_check_markers (Bproject *project, int flags)
	Checks if the markers in a project parameter structure fall within micrographs. More...

int	project_fix_markers (Bproject *project)
	Checks if the markers in a project parameter structure fall within micrographs. More...

int	img_clear_extraneous_areas (Bimage *p, double tilt_axis, double tilt_angle, long thickness, double width)
	Clears extraneous areas from a micrograph. More...

int	micrograph_clear_extraneous_areas (Bmicrograph mg, Bimage p, long thickness, double width)
	Clears extraneous areas from a micrograph. More...

int	project_clear_extraneous_areas (Bproject *project, long thickness, double width)
	Clears areas from a tilt series not used in a reconstruction. More...

double	project_marker_rotation_axis (Bproject *project)
	Determines the most likely rotation axis location for a tilt series. More...

int	project_merge_rec_markers (Bproject *project)
	Merges the markers for two reconstructions. More...

Variables
int	verbose

Detailed Description

Functions to manage tomographic series of images.

Author: Bernard Heymann

Date: Created: 20020416; Modified: 20200306

Function Documentation

◆ img_clear_extraneous_areas()

int img_clear_extraneous_areas	(	Bimage *	p,
		double	tilt_axis,
		double	tilt_angle,
		long	thickness,
		double	width
	)

Clears extraneous areas from a micrograph.

Parameters

*p	micrograph image.
tilt_axis	tilt axis angle (radians).
tilt_angle	tilt angle (radians).
thickness	intended thickness of reconstruction.
width	edge smoothing width.

Returns: int 0.

◆ img_erase_markers()

long img_erase_markers	(	Bimage *	p,
		Bmarker *	mark,
		double	marker_radius
	)

Erases or paints markers in an image.

Parameters

*p	image parameter structure.
*mark	linked list of markers.
marker_radius	radius to mask out markers.

Returns

long number of markers erased.

Markers can be either erased to a background value or painted in with
a set value.

◆ img_find_gold_particles()

Bmarker * img_find_gold_particles	(	Bimage *	p,
		int	img_select,
		double	radius,
		long	edge,
		double	cutoff
	)

Finds gold particles in micrograph images.

Parameters

*p	image.
img_select	selected subimage, -1 if all.
radius	gold particle radius in voxel units.
edge	edge width to eliminate particles.
cutoff	FOM cutoff, if 0 then half of maximum FOM.

Returns

Bmarker* list of markers.

An image of the size of an input sub-image is generated with a gold
particle (black or negative density) at its center.
Each sub-image is cross-correlated with the gold particle image
and the position within the image reported.
The FOM cutoff is used to select cross-correlation peaks, except it
is reset for the following:
    cutoff == 0 ==> cutoff = FOMavg + FOMstd
    cutoff <  0 ==> cutoff = FOMmax/2

◆ img_gold_particle()

Bimage * img_gold_particle	(	Vector3< long >	size,
		double	radius
	)

Generates an image representing a gold particle.

Parameters

size	size of image to generate.
radius	gold particle radius in voxel units.

Returns

Bimage* gold particle image.

An image of the size of an input sub-image is generated with a gold
particle (black or negative density) at its center.

◆ lambda_R()

double lambda_R ( Bsimplex & simp )

◆ mg_3D_location_from_marker()

Vector3< double > mg_3D_location_from_marker	(	Vector3< double >	loc,
		Vector3< double >	ori3D,
		Matrix3	mat,
		Vector3< double >	ori
	)

◆ mg_composite_particle()

Bimage * mg_composite_particle	(	Bmicrograph *	mg,
		Vector3< long >	size
	)

Generates an average particle image from a micrograph.

Parameters

*mg	micrograph to extract marker images from.
size	size of image.

Returns: Bimage* composite marker projection image.

◆ mg_erase_markers()

Bimage * mg_erase_markers	(	Bmicrograph *	mg,
		double	marker_radius
	)

Erases or paints markers in micrographs.

Parameters

*mg	micrograph parameter structure.
marker_radius	radius to mask out markers.

Returns

Bimage* new micrograph image with erased markers.

Markers can be either erased to a background value or painted in with
a set value.

◆ mg_find_markers()

long mg_find_markers	(	Bmicrograph *	mg,
		long	edge,
		int	add
	)

Finds markers in a micrograph.

Parameters

*mg	project parameter structure.
edge	edge to exclude.
add	flag to add rather than replace the markers.

Returns

long number of markers.

The markers are located by cross-correlation with a synthetic reference
whose size is defined by the marker radius. Markers close to the edge
are eliminated using the given edge size. The main intent is to find 
the seed for a 3D marker model in a zero degree tilt micrograph.

◆ mg_location_from_3D_model() [1/4]

Vector3< double > mg_location_from_3D_model	(	Vector3< double >	loc3D,
		Matrix3	mat,
		Vector3< double >	ori
	)

Calculates the 2D location of a marker from a 3D model.

Parameters

loc3D	3D marker location.
mat	micrograph view matrix.
ori	micrograph origin.

Returns: Vector3<double> transformed 2D marker location.

◆ mg_location_from_3D_model() [2/4]

Vector3< double > mg_location_from_3D_model	(	Vector3< double >	loc3D,
		Matrix3	mat,
		Vector3< double >	ori,
		Vector3< double >	scale
	)

◆ mg_location_from_3D_model() [3/4]

Vector3< double > mg_location_from_3D_model	(	Vector3< double >	loc3D,
		Vector3< double >	ori3D,
		Matrix3	mat,
		Vector3< double >	ori
	)

◆ mg_location_from_3D_model() [4/4]

Vector3< double > mg_location_from_3D_model	(	Vector3< double >	loc3D,
		Vector3< double >	ori3D,
		Matrix3	mat,
		Vector3< double >	ori,
		Vector3< double >	scale
	)

◆ mg_marker_init()

int mg_marker_init	(	Bmicrograph *	mg,
		Bmarker *	model
	)

Initializes markers from the reference.

Parameters

*mg	micrograph to initialize.
*model	marker model.

Returns: int 0.

◆ mg_marker_update()

int mg_marker_update	(	Bmicrograph *	mg,
		Bmarker *	model,
		Vector3< double >	oriref,
		int	update_location
	)

Calculates the predicted positions of markers from the reference.

Parameters

*mg	micrograph to update.
*model	marker model.
oriref	reference origin.
update_location	flag to update location based on marker model.

Returns

int 0.

If the marker does not exist in the micrograph, a new one is generated.

◆ mg_reset_model()

int mg_reset_model	(	Bmicrograph *	mg,
		Bmarker *	model
	)

Resets the model x and y coordinates from the zero-tilt micrograph.

Parameters

*mg	reference micrograph parameter structure.
*model	model marker list.

Returns

int markers selected in model.

Missing model markers are added in and excessive model markers deleted.

◆ mg_tomo_residuals()

double mg_tomo_residuals	(	Bmicrograph *	mg,
		Bmarker *	model,
		Vector3< double >	oriref
	)

Calculates the residuals for an alignment solution of one micrograph.

Parameters

*mg	micrograph.
*model	model marker list.
oriref	reference origin.

Returns

double average residual.

Requires the matrices in the micrograph structures to be defined.

◆ mg_update_model()

int mg_update_model	(	Bmicrograph *	mg,
		Bmarker *	model,
		Vector3< double >	oriref
	)

Fills in missing markers in the 3D model from micrograph markers.

Parameters

*mg	micrograph to update.
*model	marker model.
oriref	reference origin.

Returns

int 0.

If the marker does not exist in the model, a new one is generated.

◆ micrograph_clear_extraneous_areas()

int micrograph_clear_extraneous_areas	(	Bmicrograph *	mg,
		Bimage *	p,
		long	thickness,
		double	width
	)

Clears extraneous areas from a micrograph.

Parameters

*mg	micrograph parameter structure.
*p	micrograph image.
thickness	intended thickness of reconstruction.
width	edge smoothing width.

Returns: int 0.

◆ project_calculate_angles()

int project_calculate_angles ( Bproject * project )

Calculates tilt and tilt axis angles from matrices in a project parameter structure.

Parameters

*project project parameter structure.

Returns

int 0.

From each matrix, a quaternion is calculated, giving the tilt axis
and rotation angle.
The level angle is calculated as the arcsin of the z-coordinate of the axis.

◆ project_calculate_model()

int project_calculate_model ( Bproject * project )

Calculates the z-coordinates of the marker model.

Parameters

*project project parameter structure.

Returns

int 0.

If the project does not have markers, it returns without any change.
If the reconstruction model is not defined, it is created.

◆ project_check_markers()

int project_check_markers	(	Bproject *	project,
		int	flags
	)

Checks if the markers in a project parameter structure fall within micrographs.

Parameters

*project	project parameter structure.
flags	flags to modify actions.

Returns

int 0.

Markers outside the boundaries are dealt with based on the flags variable:
1   show markers outside the image boundaries.
2   set marker selections to zero.
4   set marker fom's to zero.
8   set marker errors to zero.

◆ project_clear_extraneous_areas()

int project_clear_extraneous_areas	(	Bproject *	project,
		long	thickness,
		double	width
	)

Clears areas from a tilt series not used in a reconstruction.

Parameters

*project	project parameter structure.
thickness	intended thickness of reconstruction.
width	edge smoothing width.

Returns: int 0.

◆ project_count_markers()

long project_count_markers ( Bproject * project )

Counts the markers in a project hierarchy.

Parameters

*project project parameter structure.

Returns: long number of markers.

◆ project_delete_markers()

long project_delete_markers	(	Bproject *	project,
		Bstring &	delete_list
	)

Deletes selected markers in a project hierarchy.

Parameters

*project	project parameter structure.
&delete_list	list of markers to deselect.

Returns

long number of markers.

All the occurrences of selected markers in the tilt series are deleted.

◆ project_deselect_markers()

long project_deselect_markers	(	Bproject *	project,
		Bstring &	deselect_list
	)

Deletes selected markers in a project hierarchy.

Parameters

*project	project parameter structure.
&deselect_list	list of markers to deselect.

Returns

long number of markers.

All the occurrences of selected markers in the tilt series are deleted.

◆ project_erase_markers()

int project_erase_markers	(	Bproject *	project,
		double	marker_radius
	)

Erases or paints markers in micrographs.

Parameters

*project	project parameter structure.
marker_radius	radius to mask out markers.

Returns

int 0, <0 on error.

Markers can be either erased to a background value or painted in with
a set value.

◆ project_find_markers()

long project_find_markers	(	Bproject *	project,
		long	edge,
		int	add
	)

Finds all markers in a project.

Parameters

*project	project parameter structure.
edge	edge to exclude.
add	flag to add rather than replace the markers.

Returns

long number of markers.

Markers are located in each micrograph by cross-correlation.

◆ project_fit_intensities()

double project_fit_intensities	(	Bproject *	project,
		Bplot *	plot,
		int	flag
	)

Determines the thickness to mean free path ratio from a tilt series.

Parameters

*project	project structure.
*plot	plot structure with intensity-tilt data.
flag	flag to apply tilt angle adjustment.

Returns

double ratio.

The micrographs should be unmodified gain-corrected images obtained from the detector.

◆ project_fix_markers()

int project_fix_markers ( Bproject * project )

Checks if the markers in a project parameter structure fall within micrographs.

Parameters

*project project parameter structure.

Returns: int 0.

◆ project_generate_markers()

int project_generate_markers ( Bproject * project )

Generates missing micrograph and model markers.

Parameters

*project project parameter structure.

Returns

int 0, <0 on error.

First the 3D model is updated to represent all markers from all micrographs.
Then the missing markers in the micrographs are generated from the
updated model.

◆ project_intensity_plot()

Bplot * project_intensity_plot ( Bproject * project )

Transfers the micrograph intensities for a field into a plot.

Parameters

*project project structure.

Returns

Bplot* plot structure.

The micrographs should be unmodified gain-corrected images obtained from the detector.

◆ project_invert_matrices()

int project_invert_matrices ( Bproject * project )

Inverts the micrograph matrices in a project parameter structure.

Parameters

*project project parameter structure.

Returns

int 0.

The tilt axis angle for all the micrographs are set to the same value.

◆ project_invert_tilt_axis()

int project_invert_tilt_axis ( Bproject * project )

Inverts the tilt axis in a project parameter structure.

Parameters

*project project parameter structure.

Returns

int 0.

The tilt axis angle for all the micrographs are set to the same value.

◆ project_lambda()

double project_lambda	(	Bproject *	project,
		double	thickness
	)

Determines the mean free path from a tilt series and thickness.

Parameters

*project	project structure.
thickness	tomogram thickness (in angstrom).

Returns

double ratio.

The micrographs should be unmodified gain-corrected images obtained from the detector.

◆ project_marker_rotation_axis()

double project_marker_rotation_axis ( Bproject * project )

Determines the most likely rotation axis location for a tilt series.

Parameters

*project project parameter structure.

Returns

double average z offset from marker z average.

All micrographs must have associated markers.

◆ project_mass_normalize()

int project_mass_normalize	(	Bproject *	project,
		double	avg,
		double	std,
		int	norm_type,
		DataType	datatype,
		int	setinputZslices,
		int	setoutputZslices,
		double	cutmin,
		double	cutmax,
		double	replace_threshold
	)

Normalizes a set of images in a project to a desired average and standard deviation.

Parameters

*project	project structure.
avg	desired average.
std	desired standard deviation (if 0, use defaults).
norm_type	type of determining the effective average and standard deviation: 0=simple, 1=Gaussian, 2=Poisson.
datatype	data type for normalized images.
setinputZslices	convert z-slices in the input to 2D images.
setoutputZslices	convert output image back to z-slices.
cutmin	truncate to minimum.
cutmax	truncate to maximum.
replace_threshold	replace maxima above this threshold.

Returns

int 0, <0 on error.

The effective average and standard deviation for each image is obtained
in one of three ways:
    0.      The simple avergae and standard devaition for the image.
    1.      Gaussian fit of the histogram.
    2.      Poisson fit of the histogram.
A histogram of an image is calculated with a given number of bins.
The histogram is fit to a Gaussian or Poisson function with exclusion of a
small number of bins in the histogram (defined as outliers).
The effective average and standard deviation are used to 
rescale the data for each image.

◆ project_merge_rec_markers()

int project_merge_rec_markers ( Bproject * project )

Merges the markers for two reconstructions.

Parameters

*project project parameter structure.

Returns

int number of markers merged.

The reconstructions must have corresponding markers.
The marker locations are set to the average of the two.
The second reconstruction is removed.

◆ project_mg_exclude()

long project_mg_exclude	(	Bproject *	project,
		Bstring &	mg_exclude
	)

Deselects micrographs in a project hierarchy.

Parameters

*project	project parameter structure.
&mg_exclude	list of micrograph numbers.

Returns: long number of micrographs excluded.

◆ project_mg_marker_select()

int project_mg_marker_select	(	Bproject *	project,
		double	fom
	)

Selects markers.

Parameters

*project	project parameter structure.
fom	fom cutoff.

Returns

int 0.

Selects all micrograph markers above the given fom cutoff.

◆ project_mg_select()

long project_mg_select	(	Bproject *	project,
		Bstring &	mg_select
	)

Selects micrographs in a project hierarchy.

Parameters

*project	project parameter structure.
&mg_select	list of micrograph numbers.

Returns

long number of micrographs selected.

A micrograph is only selected when it has its selection already set
and it is in the list of numbers.

◆ project_mg_tilt_to_matrix()

int project_mg_tilt_to_matrix ( Bproject * project )

Sets the matrix from the tilt and axis angles for each micrograph.

Parameters

*project project parameter structure.

Returns

int 0.

This is in preparation for reconstruction.

◆ project_renumber_markers()

long project_renumber_markers ( Bproject * project )

Renumbers the markers in a project hierarchy.

Parameters

*project project parameter structure.

Returns

long number of markers.

The markers are assumed to correspond across micrographs and reconstructions.
The existing marker ids are mapped to an array, and new marker ids generated.

◆ project_set_marker_radius()

int project_set_marker_radius	(	Bproject *	project,
		double	mark_radius
	)

Sets the marker radius in a project parameter structure.

Parameters

*project	project parameter structure.
mark_radius	gold fiducial marker radius (voxels).

Returns: int 0.

◆ project_set_tilt_angles()

int project_set_tilt_angles	(	Bproject *	project,
		double	tilt_start,
		double	tilt_step
	)

Sets the tilt and tilt axis angles in a project parameter structure.

Parameters

*project	project parameter structure.
tilt_start	starting tilt angle (usually negative).
tilt_step	tilt increment angle.

Returns

int 0.

The single tilt series is defined by a starting tilt angle and a
tilt increment angle, as well as the tilt axis angle.

◆ project_set_tilt_axis()

int project_set_tilt_axis	(	Bproject *	project,
		double	tilt_axis
	)

Sets the tilt axis angle in a project parameter structure.

Parameters

*project	project parameter structure.
tilt_axis	tilt axis angle (wrt x-axis).

Returns

int 0.

The tilt axis angle for all the micrographs are set to the same value.

◆ project_show_errors()

long project_show_errors	(	Bproject *	project,
		double	error_cutoff
	)

Shows the errors in marker coordinates in a project hierarchy.

Parameters

*project	project parameter structure.
error_cutoff	threshold to show errors (distance in pixels).

Returns: long number of errors above threshold.

◆ project_show_markers()

long project_show_markers ( Bproject * project )

Shows the markers in a project hierarchy.

Parameters

*project project parameter structure.

Returns: long number of markers.

◆ project_sort_markers_by_id()

int project_sort_markers_by_id ( Bproject * project )

Sorts markers for each micrograph by ID number.

Parameters

*project micrograph project.

Returns

int 0.

Requires the matrices in the micrograph structures to be defined.

◆ project_thickness()

double project_thickness	(	Bproject *	project,
		double	lambda
	)

Determines the thickness from a tilt series and mean free path.

Parameters

*project	project structure.
lambda	proportionality parameter (in angstrom).

Returns

double ratio.

The micrographs should be unmodified gain-corrected images obtained from the detector.

◆ project_thickness_to_lambda_ratio()

double project_thickness_to_lambda_ratio ( Bproject * project )

Determines the thickness to mean free path ratio from a tilt series.

Parameters

*project project structure.

Returns

double ratio.

The micrographs should be unmodified gain-corrected images obtained from the detector.

◆ project_tomo_errors()

double project_tomo_errors ( Bproject * project )

Analyzes marker errors.

Parameters

*project micrograph project.

Returns

double 0.

Requires the marker errors to be calculated.

◆ project_tomo_residuals()

double project_tomo_residuals	(	Bproject *	project,
		int	show
	)

Calculates the residuals for an alignment solution.

Parameters

*project	micrograph project.
show	flag to indicate showing lists.

Returns

double average residual.

Requires the matrices in the micrograph structures to be defined.

◆ simplex_fit_tilt_intensities()

vector< double > simplex_fit_tilt_intensities	(	vector< double > &	a,
		vector< double > &	I
	)

Variable Documentation

◆ verbose

int verbose

extern

Functions

Variables

Detailed Description

Function Documentation

◆ img_clear_extraneous_areas()

◆ img_erase_markers()

◆ img_find_gold_particles()

◆ img_gold_particle()

◆ lambda_R()

◆ mg_3D_location_from_marker()

◆ mg_composite_particle()

◆ mg_erase_markers()

◆ mg_find_markers()

◆ mg_location_from_3D_model() [1/4]

◆ mg_location_from_3D_model() [2/4]

◆ mg_location_from_3D_model() [3/4]

◆ mg_location_from_3D_model() [4/4]

◆ mg_marker_init()

◆ mg_marker_update()

◆ mg_reset_model()

◆ mg_tomo_residuals()

◆ mg_update_model()

◆ micrograph_clear_extraneous_areas()

◆ project_calculate_angles()

◆ project_calculate_model()

◆ project_check_markers()

◆ project_clear_extraneous_areas()

◆ project_count_markers()

◆ project_delete_markers()

◆ project_deselect_markers()

◆ project_erase_markers()

◆ project_find_markers()

◆ project_fit_intensities()

◆ project_fix_markers()

◆ project_generate_markers()

◆ project_intensity_plot()

◆ project_invert_matrices()

◆ project_invert_tilt_axis()

◆ project_lambda()

◆ project_marker_rotation_axis()

◆ project_mass_normalize()

◆ project_merge_rec_markers()

◆ project_mg_exclude()

◆ project_mg_marker_select()

◆ project_mg_select()

◆ project_mg_tilt_to_matrix()

◆ project_renumber_markers()

◆ project_set_marker_radius()

◆ project_set_tilt_angles()

◆ project_set_tilt_axis()

◆ project_show_errors()

◆ project_show_markers()

◆ project_sort_markers_by_id()

◆ project_thickness()

◆ project_thickness_to_lambda_ratio()

◆ project_tomo_errors()

◆ project_tomo_residuals()

◆ simplex_fit_tilt_intensities()

Variable Documentation

◆ verbose