| Bsoft 2.0.5 Bernard's software package

mg_subtomo.h
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1
12 #include "rwimg.h"
13 #include "View.h"
14 #include "symmetry.h"
15 #include "mg_processing.h"
16
17 // Sphere structure
18 #ifndef _Sphere_
19 #define _Sphere_
20 struct Sphere {
21 double A,B,C; // Sphere coordinates
22 double R; // Sphere radius
23 } ;
24 #endif
25
26 // Function prototypes
27
28 long reconstruction_search_subtomo(Breconstruction* rec,
29 Bimage* p, Bimage* ptemp, Bimage* pmask, Bimage* pmask2,
30 double alpha_step, double theta_step, double phi_step,
31 double alpha_limit, double thetaphi_limit,
32 double hires, double lores, double shiftlimit, double mindist,
33 double threshold, int maxhits, Vector3<long> bin, Bsymmetry* sym,
34 int refinepeaks, Bstring ccmax_file);
35
36 long reconstruction_refine_subtomo(Breconstruction* rec,
37 Bimage* p, Bimage* ptemp, Bimage* pmask, Bimage* pmask2,
38 double alpha_step, double theta_step, double phi_step,
39 double alpha_limit, double thetaphi_limit,
40 double hires, double lores, double shiftlimit,
41 double shiftlimitz, double shiftlimitxy, double mindist,
42 Vector3<long> bin, Bsymmetry* sym, int iters, int refinepeaks, Bstring ccmax_file);
43
44 Bparticle* img_find_refine_peaks(Bimage* pcc, View view, double shift_limit,
45 double shift_along, double shift_orthogonal, double mindist,
46 double threshold, int maxhits, int refinepeaks);
47
48 double img_find_peak_subtomo(Bimage* p, View view, double shift,
49 double shift_along, double shift_orthogonal);
50
51
52
53
54 Vector3<double> closest_point_line(Vector3<double> point, Vector3<double> endpoint1, Vector3<double> endpoint2);
55 double closest_point_line_distance2(Vector3<double> point, Vector3<double> endpoint1, Vector3<double> endpoint2);
56 //double closest_point_plane_distance2(Vector3<double> point, Vector3<double> point2, View view);
57 double closest_point_disc_distance2(Vector3<double> point, Vector3<double> point2, View view, double radius);
58
59 //Vector3<double> closest_point_plane(Vector3<double> point, Vector3<double> point2, View vieW);
60
61 Sphere locations_fit_sphere(Bparticle* part, int N, double Nstop);
62
symmetry.h
Header file for general symmetry functions.
Breconstruction
Definition: mg_processing.h:280
locations_fit_sphere
Sphere locations_fit_sphere(Bparticle *part, int N, double Nstop)
Least squares fit a sphere to 3D data (particle locations)
Definition: mg_subtomo.cpp:906
Sphere::C
double C
Definition: mg_subtomo.h:21
closest_point_disc_distance2
double closest_point_disc_distance2(Vector3< double > point, Vector3< double > point2, View view, double radius)
Calculates the squared distance to the closest point on a disc from a given point.
Definition: mg_subtomo.cpp:834
Bimage
General image parameter class.
Definition: Bimage.h:163
closest_point_line_distance2
double closest_point_line_distance2(Vector3< double > point, Vector3< double > endpoint1, Vector3< double > endpoint2)
Calculates the squared distance to the closest point on a line segment from a given point.
Definition: mg_subtomo.cpp:793
img_find_refine_peaks
Bparticle * img_find_refine_peaks(Bimage *pcc, View view, double shift_limit, double shift_along, double shift_orthogonal, double mindist, double threshold, int maxhits, int refinepeaks)
Finds peaks in an image to the nearest voxel iteratively.
Definition: mg_subtomo.cpp:600
Sphere::A
double A
Definition: mg_subtomo.h:21
reconstruction_refine_subtomo
long reconstruction_refine_subtomo(Breconstruction *rec, Bimage *p, Bimage *ptemp, Bimage *pmask, Bimage *pmask2, double alpha_step, double theta_step, double phi_step, double alpha_limit, double thetaphi_limit, double hires, double lores, double shiftlimit, double shiftlimitz, double shiftlimitxy, double mindist, Vector3< long > bin, Bsymmetry *sym, int iters, int refinepeaks, Bstring ccmax_file)
Refines the view vectors for particles already in the project.
Definition: mg_subtomo.cpp:333
img_find_peak_subtomo
double img_find_peak_subtomo(Bimage *p, View view, double shift, double shift_along, double shift_orthogonal)
Finds the peak in an image to the nearest voxel.
Definition: mg_subtomo.cpp:667
Bsymmetry
Definition: symmetry.h:38
Bparticle
Definition: mg_processing.h:89
Bstring
Definition: Bstring.h:29
reconstruction_search_subtomo
long reconstruction_search_subtomo(Breconstruction *rec, Bimage *p, Bimage *ptemp, Bimage *pmask, Bimage *pmask2, double alpha_step, double theta_step, double phi_step, double alpha_limit, double thetaphi_limit, double hires, double lores, double shiftlimit, double mindist, double threshold, int maxhits, Vector3< long > bin, Bsymmetry *sym, int refinepeaks, Bstring ccmax_file)
Definition: mg_subtomo.cpp:140
closest_point_line
Vector3< double > closest_point_line(Vector3< double > point, Vector3< double > endpoint1, Vector3< double > endpoint2)
Calculates the closest point on a line segment from a given point.
Definition: mg_subtomo.cpp:754
Vector3< long >
View
Definition: View.h:26
mg_processing.h
Header file for micrograph processing.
rwimg.h
Header file for 2D and 3D image I/O.
Sphere::R
double R
Definition: mg_subtomo.h:22
View.h
View object.
Sphere
Definition: mg_subtomo.h:20
Sphere::B
double B
Definition: mg_subtomo.h:21