| Bsoft 2.0.5 Bernard's software package

mg_extract.h
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1
9 #include "mg_processing.h"
10 #include "rwimg.h"
11
12 // Function prototypes
13 int particle_setup_filenames(Bparticle* part, Bstring filename, Bstring partpath);
14 int filament_setup_filenames(Bfilament* fil, Bstring filename, Bstring filpath);
15 Vector3<double>* vector3_spline_from_nodes(Bfilnode* fnode, long& nspline);
16 long project_extract_particles(Bproject* project, double scale,
17 int back_flag, int norm_flag, int fill_type, double fill, int mask_width,
18 int split, Bstring& partbase, Bstring& partpath, Bstring& partext);
19 long micrograph_extract_particles(Bmicrograph* mg, Bimage* p, double scale,
20 int back_flag, int norm_flag, double fill, int mask_width);
21 long reconstruction_extract_particles(Breconstruction* rec, Bimage* p, double scale,
22 int back_flag, int norm_flag, double fill, int mask_width);
23 Bimage* particle_extract(Bparticle* particles, Bbadarea* bad_areas, Bimage* p,
24 Vector3<long> size, double scale, double bad_radius,
25 int back_flag, int norm_flag, double fill, int mask_width);
26 Bimage* micrograph_extract_gold(Bmicrograph* mg, Bimage* p, double radius);
27 Bimage* reconstruction_extract_gold(Breconstruction* rec, Bimage* p, double radius);
28 Bimage* marker_extract_gold(Bmarker* marker_list, Bimage* p, int img_num, double radius);
29 long project_extract_filaments(Bproject* project, int filament_width, int axis,
30 Bstring& base, Bstring& path, Bstring& ext, int split);
31 long micrograph_extract_filaments(Bmicrograph* mg, Bimage* p, double width, int axis);
32 long reconstruction_extract_filaments(Breconstruction* rec, Bimage* p, double width, int axis);
33 Bimage* filament_extract(Bfilament* filaments, Bimage* p, double width, int axis);
34 int project_filaments_to_particles(Bproject* project, Vector3<long> box_size,
35 double boxing_interval, double rise, double angle);
36 int micrograph_filaments_to_particles(Bmicrograph* mg, Vector3<long> box_size,
37 double boxing_interval, double rise, double angle);
38 int reconstruction_filaments_to_particles(Breconstruction* rec, Vector3<long> box_size,
39 double boxing_interval, double rise, double angle);
40 Bparticle* filaments_to_particles(Bfilament* filaments, double pixel_size, Vector3<long> box_size,
41 double boxing_interval, double rise, double angle);
42 int project_mask_filament_particles(Bproject* project, int mask_width);
43 int project_rotate_mask_filament_particles(Bproject* project,
44 int rotation_axis, int back_flag, int mask_width);
45
particle_setup_filenames
int particle_setup_filenames(Bparticle *part, Bstring filename, Bstring partpath)
Sets up individual particle file names for extraction.
Definition: mg_extract.cpp:35
reconstruction_extract_gold
Bimage * reconstruction_extract_gold(Breconstruction *rec, Bimage *p, double radius)
Extracts gold particle images from a reconstruction.
Definition: mg_extract.cpp:591
project_filaments_to_particles
int project_filaments_to_particles(Bproject *project, Vector3< long > box_size, double boxing_interval, double rise, double angle)
Converts filaments to sets of particles.
Definition: mg_extract.cpp:914
Bbadarea
Definition: mg_processing.h:142
particle_extract
Bimage * particle_extract(Bparticle *particles, Bbadarea *bad_areas, Bimage *p, Vector3< long > size, double scale, double bad_radius, int back_flag, int norm_flag, double fill, int mask_width)
Extracts particle images from an image.
Definition: mg_extract.cpp:403
Bfilnode
Definition: mg_processing.h:115
Breconstruction
Definition: mg_processing.h:280
project_rotate_mask_filament_particles
int project_rotate_mask_filament_particles(Bproject *project, int rotation_axis, int back_flag, int mask_width)
Rotates and masks particles extracted from filaments.
Definition: mg_extract.cpp:1115
micrograph_extract_gold
Bimage * micrograph_extract_gold(Bmicrograph *mg, Bimage *p, double radius)
Extracts gold particle images from a micrograph.
Definition: mg_extract.cpp:573
Bmarker
Definition: marker.h:21
project
Bproject * project
Definition: bshow.cpp:31
marker_list
Tcl_Obj * marker_list(Bproject *project)
Definition: tcltk_bmarker.cpp:535
Bimage
General image parameter class.
Definition: Bimage.h:163
filaments_to_particles
Bparticle * filaments_to_particles(Bfilament *filaments, double pixel_size, Vector3< long > box_size, double boxing_interval, double rise, double angle)
Converts filaments to sets of particles.
Definition: mg_extract.cpp:1021
base
string base(string &filename)
Definition: string_util.cpp:28
Bmicrograph
Definition: mg_processing.h:200
project_mask_filament_particles
int project_mask_filament_particles(Bproject *project, int mask_width)
Masks particles extracted from filaments.
Definition: mg_extract.cpp:1083
reconstruction_extract_particles
long reconstruction_extract_particles(Breconstruction *rec, Bimage *p, double scale, int back_flag, int norm_flag, double fill, int mask_width)
Extracts particle images from a reconstruction.
Definition: mg_extract.cpp:363
micrograph_filaments_to_particles
int micrograph_filaments_to_particles(Bmicrograph *mg, Vector3< long > box_size, double boxing_interval, double rise, double angle)
Converts filaments to sets of particles.
Definition: mg_extract.cpp:948
project_extract_particles
long project_extract_particles(Bproject *project, double scale, int back_flag, int norm_flag, int fill_type, double fill, int mask_width, int split, Bstring &partbase, Bstring &partpath, Bstring &partext)
Extracts particle images from micrographs defined in a project.
Definition: mg_extract.cpp:160
project_extract_filaments
long project_extract_filaments(Bproject *project, int filament_width, int axis, Bstring &base, Bstring &path, Bstring &ext, int split)
Extracts filament images from micrographs defined in a project.
Definition: mg_extract.cpp:674
Bparticle
Definition: mg_processing.h:89
Bstring
Definition: Bstring.h:29
reconstruction_extract_filaments
long reconstruction_extract_filaments(Breconstruction *rec, Bimage *p, double width, int axis)
Extracts filament images from a micrograph.
Definition: mg_extract.cpp:809
Vector3< double >
reconstruction_filaments_to_particles
int reconstruction_filaments_to_particles(Breconstruction *rec, Vector3< long > box_size, double boxing_interval, double rise, double angle)
Converts filaments to sets of particles.
Definition: mg_extract.cpp:984
micrograph_extract_particles
long micrograph_extract_particles(Bmicrograph *mg, Bimage *p, double scale, int back_flag, int norm_flag, double fill, int mask_width)
Extracts particle images from a micrograph.
Definition: mg_extract.cpp:332
mg_processing.h
Header file for micrograph processing.
vector3_spline_from_nodes
Vector3< double > * vector3_spline_from_nodes(Bfilnode *fnode, long &nspline)
Calculates a spline curve from a set of filament nodes.
Definition: mg_extract.cpp:127
filament_setup_filenames
int filament_setup_filenames(Bfilament *fil, Bstring filename, Bstring filpath)
Sets up individual filament file names for extraction.
Definition: mg_extract.cpp:85
rwimg.h
Header file for 2D and 3D image I/O.
filament_extract
Bimage * filament_extract(Bfilament *filaments, Bimage *p, double width, int axis)
Extracts filament images from a micrograph.
Definition: mg_extract.cpp:842
split
vector< string > split(const string &s)
Splits a string on whitespace.
Definition: string_util.cpp:92
Bproject
Definition: mg_processing.h:333
micrograph_extract_filaments
long micrograph_extract_filaments(Bmicrograph *mg, Bimage *p, double width, int axis)
Extracts filament images from a micrograph.
Definition: mg_extract.cpp:783
Bfilament
Definition: mg_processing.h:128
marker_extract_gold
Bimage * marker_extract_gold(Bmarker *marker_list, Bimage *p, int img_num, double radius)
Extracts gold particle images from an image.
Definition: mg_extract.cpp:610