Functions for dealing with markers and linkers. More...

#include "rwmodel.h"
#include "marker.h"
#include "matrix_linear.h"
#include "Matrix3.h"
#include "Matrix.h"
#include "ps_marker.h"
#include "qsort_functions.h"
#include "linked_list.h"
#include "utilities.h"
#include "timer.h"
#include <fstream>

Functions
int	markers_findOneToOne (Bmarker refset, Bmarker applyset)

double *	markers_RoughMatch (Bmarker setA, Bmarker setB, double dist_cutoff)

int	markers_sort_rel_distance (Bmarker set, Bmarker ref)

long	marker_stats (Bmarker *markers)
	Calculating marker statistics. More...

Vector3< double >	marker_minimum (Bmarker *markers)
	Calculating the minimum marker location. More...

Vector3< double >	marker_maximum (Bmarker *markers)
	Calculating the maximum marker location. More...

Vector3< double >	marker_range (Bmarker *markers)
	Calculating the marker location range. More...

Bmarker *	markers_copy (Bmarker *mark, int sel_flag)
	Copies a set of markers. More...

Bmarker *	markers_copy (Bmarker *mark)
	Copies a set of markers. More...

Bmarker *	markers_copy_selected (Bmarker *mark)
	Copies a set of markers based on selection. More...

long	markers_add (Bmarker *mark, Bmarker mark2, double mindist, int sel)
	Adds a set of markers to another. More...

long	markers_delete_non_selected (Bmarker **mark)
	Deletes markers not selected. More...

int	marker_shift (Bmarker *markers, Vector3< double > shift)
	Shifting markers. More...

int	marker_scale (Bmarker *markers, Vector3< double > scale)
	Scaling markers. More...

int	marker_transform (Bmarker *markers, Transform t)
	Transforming markers. More...

double	marker_compare (Bmarker mark1, Bmarker mark2)
	Compare marker sets and calculates the root-mean-square deviation. More...

Matrix3	marker_find_matrix (Bmarker markers1, Bmarker markers2, Vector3< double > origin1, Vector3< double > origin2)
	Determines the rotation matrix between two sets of markers. More...

Transform	marker_find_transform (Bmarker markers1, Bmarker markers2, Vector3< double > origin)
	Determines the rotation matrix between two sets of markers. More...

Transform	markers_find_rottrans (Bmarker set1, Bmarker set2, double tolerance)
	Finds the rotation and shift between two sets of vectors. More...

Transform *	markers_map_and_find_transform (Bmarker **set, int nseries, int refset, Vector3< long > size)
	This function finds the transform parameters between sets of coordinates. These sets are expected to have a large intersection, but do not have to be 1 to 1. More...

long	markers_limit (int target_num, int sign, Bmarker **set)
	This method constricts a marker set to target_num points. More...

Bmodel *	model_from_markers (Bmarker *markers, Vector3< double > origin, Vector3< double > sam)
	Convert markers to a model. More...

Vector3< double >	marker_plane (Bmarker *markers, Vector3< double > origin)
	Fits a plane to a set of markers. More...

Bmarker *	markers_sort_by_id (Bmarker **mark)
	Sorts a set of markers by ID number. More...

long	markers_renumber (Bmarker *mark)
	Renumbers a set of markers. More...

long	markers_center (Bmarker *mark, Vector3< double > center)
	Centers a set of markers. More...

Bmarker *	marker_set_at_radius (double rad, double ainc)
	Generates a marker set at a given radius with z=0. More...

int	marker_sets_to_bild (Bstring &filename, Bmarker mark1, Bmarker mark2)
	Generates a bild file with the two marker sets. More...

Variables
int	verbose

Detailed Description

Functions for dealing with markers and linkers.

Author: Bernard Heymann

Date: Created: 20020619; Modified: 20210112

Function Documentation

◆ marker_compare()

double marker_compare	(	Bmarker *	mark1,
		Bmarker *	mark2
	)

Compare marker sets and calculates the root-mean-square deviation.

Parameters

*mark1	linked list of markers.
*mark2	linked list of markers.

Returns: double RMSD.

◆ marker_find_matrix()

Matrix3 marker_find_matrix	(	Bmarker *	markers1,
		Bmarker *	markers2,
		Vector3< double >	origin1,
		Vector3< double >	origin2
	)

Determines the rotation matrix between two sets of markers.

Parameters

*markers1	linked list of markers.
*markers2	linked list of markers.
origin1	origin of first set.
origin2	origin of second set.

Returns

Matrix3 rotation matrix.

The function calculates the rotation matrix required to superimposed 
the first set onto the second set.
Requirement: The two marker sets must share a significant number of markers.

◆ marker_find_transform()

Transform marker_find_transform	(	Bmarker *	markers1,
		Bmarker *	markers2,
		Vector3< double >	origin
	)

Determines the rotation matrix between two sets of markers.

Parameters

*markers1	linked list of markers.
*markers2	linked list of markers.
origin	origin of rotation.

Returns

Transform transform structure.

The function calculates the rotation matrix required to superimposed 
the first set onto the second set.
Requirement: The two marker sets must share a significant number of markers.

◆ marker_maximum()

Vector3< double > marker_maximum ( Bmarker * markers )

Calculating the maximum marker location.

Parameters

*markers list of markers.

Returns: Vector3<double> location maximum.

◆ marker_minimum()

Vector3< double > marker_minimum ( Bmarker * markers )

Calculating the minimum marker location.

Parameters

*markers list of markers.

Returns: Vector3<double> location minimum.

◆ marker_plane()

Vector3< double > marker_plane	(	Bmarker *	markers,
		Vector3< double >	origin
	)

Fits a plane to a set of markers.

Parameters

*markers	linked list of markers.
origin	marker origin.

Returns

Vector3<double> normal to the plane.

The plane is given by:
    a*x + b*y + c*z = d
The fit is assessed by calculating the distance of each marker to
the plane:
    R = sqrt(sum(|a*x + b*y + c*z - d|^2)/n)

◆ marker_range()

Vector3< double > marker_range ( Bmarker * markers )

Calculating the marker location range.

Parameters

*markers list of markers.

Returns: Vector3<double> location range.

◆ marker_scale()

int marker_scale	(	Bmarker *	markers,
		Vector3< double >	scale
	)

Scaling markers.

Parameters

*markers	linked list of markers.
scale	scale vector.

Returns: int error code (<0 means failure).

◆ marker_set_at_radius()

Bmarker * marker_set_at_radius	(	double	rad,
		double	ainc
	)

Generates a marker set at a given radius with z=0.

Parameters

rad	radius.
ainc	angular increment.

Returns

int 0, <0 on error.

Markers are generated at the given radius and angular increments.

◆ marker_sets_to_bild()

int marker_sets_to_bild	(	Bstring &	filename,
		Bmarker *	mark1,
		Bmarker *	mark2
	)

Generates a bild file with the two marker sets.

Parameters

&filename	bild format file name.
*mark1	marker list 1.
*mark2	marker list 2.

Returns

int 0, <0 on error.

A sphere is drawn for every marker.
The first set is red and the second set is blue.

◆ marker_shift()

int marker_shift	(	Bmarker *	markers,
		Vector3< double >	shift
	)

Shifting markers.

Parameters

*markers	linked list of markers.
shift	shift vector.

Returns: int error code (<0 means failure).

◆ marker_stats()

long marker_stats ( Bmarker * markers )

Calculating marker statistics.

Parameters

*markers list of markers.

Returns: long number of markers (<0 means failure).

◆ marker_transform()

int marker_transform	(	Bmarker *	markers,
		Transform	t
	)

Transforming markers.

Parameters

*markers	linked list of markers.
t	transform structure.

Returns: int number of markers.

◆ markers_add()

long markers_add	(	Bmarker **	mark,
		Bmarker *	mark2,
		double	mindist,
		int	sel
	)

Adds a set of markers to another.

Parameters

**mark	marker list.
*mark2	marker list to add.
mindist	minimum distance between markers.
sel	selection flag to set for second list.

Returns

Bmarker* new marker list.

The second list of markers are checked to eliminate those close to
markers in the first set. The remaining markers are then added and 
their selection flags set if the variable sel is greater than zero.

◆ markers_center()

long markers_center	(	Bmarker *	mark,
		Vector3< double >	center
	)

Centers a set of markers.

Parameters

**mark	pointer to marker list.
center	center to shift to.

Returns

long number of markers.

The marker center is calculated and the all markers shifted by the
difference with the target center.

◆ markers_copy() [1/2]

Bmarker * markers_copy ( Bmarker * mark )

Copies a set of markers.

Parameters

*mark marker list.

Returns: Bmarker* new marker list.

◆ markers_copy() [2/2]

Bmarker * markers_copy	(	Bmarker *	mark,
		int	sel_flag
	)

Copies a set of markers.

Parameters

*mark	marker list.
sel_flag	flag for selection.

Returns: Bmarker* new marker list.

◆ markers_copy_selected()

Bmarker * markers_copy_selected ( Bmarker * mark )

Copies a set of markers based on selection.

Parameters

*mark marker list.

Returns: Bmarker* new marker list.

◆ markers_delete_non_selected()

long markers_delete_non_selected ( Bmarker ** mark )

Deletes markers not selected.

Parameters

**mark pointer to marker list.

Returns: long number of remaining markers.

◆ markers_find_rottrans()

Transform markers_find_rottrans	(	Bmarker *	set1,
		Bmarker *	set2,
		double	tolerance
	)

Finds the rotation and shift between two sets of vectors.

Parameters

*set1	first coordinate set.
*set2	second coordinate set.
tolerance	acceptable deviation for fit.

Returns

Transform structure with shift, scale, rotation angle, and R factor.

A large number of angles is tested and the shift calculated at each angle.
The best angle is selected based on the sum of the standard deviations of
the x, y and z shifts.
Outliers are iteratively removed until the shift standard deviations drop
below a tolerance value.
The angle returned is the rotation applied to the first set to obtain
an estimate of the second set.
Requirement: The two sets must have the same number of points.

◆ markers_findOneToOne()

int markers_findOneToOne	(	Bmarker *	refset,
		Bmarker *	applyset
	)

◆ markers_limit()

long markers_limit	(	int	target_num,
		int	sign,
		Bmarker **	set
	)

This method constricts a marker set to target_num points.

Author: Samuel Payne

Parameters

target_num	number of points desired in set.
sign	sign to direct sorting.
**set	pointer to set containing all the points.

Returns

long number of points selected.

This finds the target_num darkest points in the set.  The extreme 
grey scale value associated with each point is held in value field
of the Point structure.  This is copied into an array and sorted. The 
cutoff value is the target_num index in the array.  A new array of 
points is created containing points below the cutoff and then returned.

◆ markers_map_and_find_transform()

Transform * markers_map_and_find_transform	(	Bmarker **	set,
		int	nseries,
		int	refset,
		Vector3< long >	size
	)

This function finds the transform parameters between sets of coordinates. These sets are expected to have a large intersection, but do not have to be 1 to 1.

Author: Samuel Payne

Parameters

**set	set of coordinates from images to be aligned.
nseries	number of images in the set.
refset	reference set number.
size	size of images/frames of sets.

Returns

Transform* list with shift, scale, rotation angle, and R factor.

Gets a one to one mapping of the two coordinate sets using
markers_find_rottrans to compare pairs of sets. 
A postscript file is made to graphically show the deviations of each 
point from its calculated position. 
Assumptions: This assumes each set has been sorted according to
distance from the center of the set.

◆ markers_renumber()

long markers_renumber ( Bmarker * mark )

Renumbers a set of markers.

Parameters

**mark pointer to marker list.

Returns: long number of markers.

◆ markers_RoughMatch()

double * markers_RoughMatch	(	Bmarker *	setA,
		Bmarker *	setB,
		double	dist_cutoff
	)

◆ markers_sort_by_id()

Bmarker * markers_sort_by_id ( Bmarker ** mark )

Sorts a set of markers by ID number.

Parameters

**mark pointer to marker list.

Returns: Bmarker* new pointer to marker list.

◆ markers_sort_rel_distance()

int markers_sort_rel_distance	(	Bmarker *	set,
		Bmarker *	ref
	)

◆ model_from_markers()

Bmodel * model_from_markers	(	Bmarker *	markers,
		Vector3< double >	origin,
		Vector3< double >	sam
	)

Convert markers to a model.

Parameters

*markers	linked list of markers.
origin	marker origin.
sam	scaling marker coordinates.

Returns: Bmodel* new model.

Variable Documentation

◆ verbose

int verbose

extern

Functions

Variables

Detailed Description

Function Documentation

◆ marker_compare()

◆ marker_find_matrix()

◆ marker_find_transform()

◆ marker_maximum()

◆ marker_minimum()

◆ marker_plane()

◆ marker_range()

◆ marker_scale()

◆ marker_set_at_radius()

◆ marker_sets_to_bild()

◆ marker_shift()

◆ marker_stats()

◆ marker_transform()

◆ markers_add()

◆ markers_center()

◆ markers_copy() [1/2]

◆ markers_copy() [2/2]

◆ markers_copy_selected()

◆ markers_delete_non_selected()

◆ markers_find_rottrans()

◆ markers_findOneToOne()

◆ markers_limit()

◆ markers_map_and_find_transform()

◆ markers_renumber()

◆ markers_RoughMatch()

◆ markers_sort_by_id()

◆ markers_sort_rel_distance()

◆ model_from_markers()

Variable Documentation

◆ verbose