| Bsoft 2.0.5 Bernard's software package

mg_tomography.h
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1
9 #include "mg_processing.h"
10 #include "rwimg.h"
11 #include "Matrix3.h"
12
13 // Function prototypes
14 int mg_marker_init(Bmicrograph* mg, Bmarker* model);
15 int mg_marker_update(Bmicrograph* mg, Bmarker* model, Vector3<double> oriref, int update_location);
16 Vector3<double> mg_location_from_3D_model(Vector3<double> loc, Matrix3 mat,
17 Vector3<double> ori);
18 Vector3<double> mg_location_from_3D_model(Vector3<double> loc, Matrix3 mat,
19 Vector3<double> ori, Vector3<double> scale);
20 Vector3<double> mg_location_from_3D_model(Vector3<double> loc3D, Vector3<double> ori3D,
21 Matrix3 mat, Vector3<double> ori);
22 Vector3<double> mg_location_from_3D_model(Vector3<double> loc3D, Vector3<double> ori3D,
23 Matrix3 mat, Vector3<double> ori, Vector3<double> scale);
24 Bimage* img_gold_particle(Vector3<long> size, double radius);
25 Bmarker* img_find_gold_particles(Bimage* p, int img_select, double radius, long edge, double cutoff);
26 int project_mass_normalize(Bproject* project, double avg, double std, int norm_type,
27 DataType datatype, int setinputZslices, int setoutputZslices,
28 double cutmin, double cutmax, double replace_threshold, string& label);
29 double project_thickness_to_lambda_ratio(Bproject* project);
30 double project_lambda(Bproject* project, double thickness);
31 double project_thickness(Bproject* project, double lambda);
32 int project_sort_markers_by_id(Bproject* project);
33 double project_tomo_residuals(Bproject* project, int show);
34 double mg_tomo_residuals(Bmicrograph* mg, Bmarker* model, Vector3<double> oriref);
35 double project_tomo_errors(Bproject* project);
36 int project_calculate_model(Bproject* project);
37 int project_generate_markers(Bproject* project);
38 Bimage* mg_erase_markers(Bmicrograph* mg, double marker_radius);
39 int project_erase_markers(Bproject* project, double marker_radius);
40 int mg_reset_model(Bmicrograph* mg, Bmarker* model);
41 long project_find_markers(Bproject* project, long edge, int add);
42 long mg_find_markers(Bmicrograph* mg, long edge, int add);
43 Bimage* mg_composite_particle(Bmicrograph* mg, Vector3<long> size);
44 long project_count_markers(Bproject* project);
45 long project_show_markers(Bproject* project);
46 long project_show_errors(Bproject* project, double error_cutoff);
47 long project_deselect_markers(Bproject* project, Bstring& deselect_list);
48 long project_delete_markers(Bproject* project, Bstring& delete_list);
49 long project_renumber_markers(Bproject* project);
50 long project_mg_select(Bproject* project, Bstring& mg_select);
51 long project_mg_exclude(Bproject* project, Bstring& mg_exclude);
52 int project_set_tilt_axis(Bproject* project, double tilt_axis);
53 int project_invert_tilt_axis(Bproject* project);
54 int project_set_tilt_angles(Bproject* project, double tilt_start, double tilt_step);
55 int project_calculate_angles(Bproject* project);
56 int project_invert_matrices(Bproject* project);
57 int project_mg_marker_select(Bproject* project, double fom);
58 int project_set_marker_radius(Bproject* project, double mark_radius);
59 int project_check_markers(Bproject* project, int flags);
60 int project_fix_markers(Bproject* project);
61 int project_mg_tilt_to_matrix(Bproject* project);
62 int micrograph_clear_extraneous_areas(Bmicrograph* mg, Bimage* p, long thickness, double width);
63 int project_clear_extraneous_areas(Bproject* project, long thickness, double width);
64 double project_marker_rotation_axis(Bproject* project);
65 int project_merge_rec_markers(Bproject* project);
66
67
DataType
DataType
Base data type specifier.
Definition: utilities.h:146
project_delete_markers
long project_delete_markers(Bproject *project, Bstring &delete_list)
Deletes selected markers in a project hierarchy.
Definition: mg_tomography.cpp:1445
mg_marker_init
int mg_marker_init(Bmicrograph *mg, Bmarker *model)
Initializes markers from the reference.
Definition: mg_tomography.cpp:29
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.
Definition: mg_tomography.cpp:59
project_show_markers
long project_show_markers(Bproject *project)
Shows the markers in a project hierarchy.
Definition: mg_tomography.cpp:1321
project_invert_tilt_axis
int project_invert_tilt_axis(Bproject *project)
Inverts the tilt axis in a project parameter structure.
Definition: mg_tomography.cpp:1694
project_mg_select
long project_mg_select(Bproject *project, Bstring &mg_select)
Selects micrographs in a project hierarchy.
Definition: mg_tomography.cpp:1585
Bmarker
Definition: marker.h:21
Matrix3
Definition: Matrix3.h:17
project
Bproject * project
Definition: bshow.cpp:31
project_marker_rotation_axis
double project_marker_rotation_axis(Bproject *project)
Determines the most likely rotation axis location for a tilt series.
Definition: mg_tomography.cpp:2124
project_tomo_errors
double project_tomo_errors(Bproject *project)
Analyzes marker errors.
Definition: mg_tomography.cpp:843
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.
Definition: mg_tomography.cpp:227
project_erase_markers
int project_erase_markers(Bproject *project, double marker_radius)
Erases or paints markers in micrographs.
Definition: mg_tomography.cpp:1080
img_gold_particle
Bimage * img_gold_particle(Vector3< long > size, double radius)
Generates an image representing a gold particle.
Definition: mg_tomography.cpp:187
Matrix3.h
3x3 Matrix manipulation functions
project_set_marker_radius
int project_set_marker_radius(Bproject *project, double mark_radius)
Sets the marker radius in a project parameter structure.
Definition: mg_tomography.cpp:1862
Bimage
General image parameter class.
Definition: Bimage.h:163
project_check_markers
int project_check_markers(Bproject *project, int flags)
Checks if the markers in a project parameter structure fall within micrographs.
Definition: mg_tomography.cpp:1891
project_fix_markers
int project_fix_markers(Bproject *project)
Checks if the markers in a project parameter structure fall within micrographs.
Definition: mg_tomography.cpp:1926
project_generate_markers
int project_generate_markers(Bproject *project)
Generates missing micrograph and model markers.
Definition: mg_tomography.cpp:1007
project_count_markers
long project_count_markers(Bproject *project)
Counts the markers in a project hierarchy.
Definition: mg_tomography.cpp:1293
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.
Definition: mg_tomography.cpp:1960
Bmicrograph
Definition: mg_processing.h:200
project_tomo_residuals
double project_tomo_residuals(Bproject *project, int show)
Calculates the residuals for an alignment solution.
Definition: mg_tomography.cpp:671
mg_reset_model
int mg_reset_model(Bmicrograph *mg, Bmarker *model)
Resets the model x and y coordinates from the zero-tilt micrograph.
Definition: mg_tomography.cpp:1135
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.
Definition: mg_tomography.cpp:1719
mg_find_markers
long mg_find_markers(Bmicrograph *mg, long edge, int add)
Finds markers in a micrograph.
Definition: mg_tomography.cpp:1205
project_sort_markers_by_id
int project_sort_markers_by_id(Bproject *project)
Sorts markers for each micrograph by ID number.
Definition: mg_tomography.cpp:647
project_find_markers
long project_find_markers(Bproject *project, long edge, int add)
Finds all markers in a project.
Definition: mg_tomography.cpp:1180
model
Bmodel * model
Definition: bshow.cpp:32
mg_erase_markers
Bimage * mg_erase_markers(Bmicrograph *mg, double marker_radius)
Erases or paints markers in micrographs.
Definition: mg_tomography.cpp:1038
project_lambda
double project_lambda(Bproject *project, double thickness)
Determines the mean free path from a tilt series and thickness.
Definition: mg_tomography.cpp:598
mg_tomo_residuals
double mg_tomo_residuals(Bmicrograph *mg, Bmarker *model, Vector3< double > oriref)
Calculates the residuals for an alignment solution of one micrograph.
Definition: mg_tomography.cpp:809
project_renumber_markers
long project_renumber_markers(Bproject *project)
Renumbers the markers in a project hierarchy.
Definition: mg_tomography.cpp:1516
Bstring
Definition: Bstring.h:29
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.
Definition: mg_tomography.cpp:2043
project_deselect_markers
long project_deselect_markers(Bproject *project, Bstring &deselect_list)
Deletes selected markers in a project hierarchy.
Definition: mg_tomography.cpp:1389
Vector3< double >
project_set_tilt_axis
int project_set_tilt_axis(Bproject *project, double tilt_axis)
Sets the tilt axis angle in a project parameter structure.
Definition: mg_tomography.cpp:1672
show
int show(0)
project_mg_marker_select
int project_mg_marker_select(Bproject *project, double fom)
Selects markers.
Definition: mg_tomography.cpp:1841
micrograph_clear_extraneous_areas
int micrograph_clear_extraneous_areas(Bmicrograph *mg, Bimage *p, long thickness, double width)
Clears extraneous areas from a micrograph.
Definition: mg_tomography.cpp:2015
project_calculate_angles
int project_calculate_angles(Bproject *project)
Calculates tilt and tilt axis angles from matrices in a project parameter structure.
Definition: mg_tomography.cpp:1749
mg_processing.h
Header file for micrograph processing.
project_thickness
double project_thickness(Bproject *project, double lambda)
Determines the thickness from a tilt series and mean free path.
Definition: mg_tomography.cpp:623
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.
Definition: mg_tomography.cpp:504
rwimg.h
Header file for 2D and 3D image I/O.
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, string &label)
Normalizes a set of images in a project to a desired average and standard deviation.
Definition: mg_tomography.cpp:379
project_show_errors
long project_show_errors(Bproject *project, double error_cutoff)
Shows the errors in marker coordinates in a project hierarchy.
Definition: mg_tomography.cpp:1351
project_calculate_model
int project_calculate_model(Bproject *project)
Calculates the z-coordinates of the marker model.
Definition: mg_tomography.cpp:886
project_mg_exclude
long project_mg_exclude(Bproject *project, Bstring &mg_exclude)
Deselects micrographs in a project hierarchy.
Definition: mg_tomography.cpp:1623
project_merge_rec_markers
int project_merge_rec_markers(Bproject *project)
Merges the markers for two reconstructions.
Definition: mg_tomography.cpp:2163
project_invert_matrices
int project_invert_matrices(Bproject *project)
Inverts the micrograph matrices in a project parameter structure.
Definition: mg_tomography.cpp:1819
mg_location_from_3D_model
Vector3< double > mg_location_from_3D_model(Vector3< double > loc, Matrix3 mat, Vector3< double > ori)
Calculates the 2D location of a marker from a 3D model.
Definition: mg_tomography.cpp:139
Bproject
Definition: mg_processing.h:333
mg_composite_particle
Bimage * mg_composite_particle(Bmicrograph *mg, Vector3< long > size)
Generates an average particle image from a micrograph.
Definition: mg_tomography.cpp:1240