| Bsoft 2.0.5 Bernard's software package

mg_align.h
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1
9 #include "mg_processing.h"
10 #include "Bimage.h"
11 #include "Vector3.h"
12
13 // Function prototypes
14 int mg_align_coordinates(Bproject* project, int refset);
15 int mg_align_micrographs(Bproject* project, int refset,
16 Vector3<long> tile_size, double res_lo, double res_hi,
17 double max_shift, int filter_flag, int refine_flag);
18 int mg_align_feature_extraction(Bproject* project, int max_features,
19 double res_low, double res_high, double thresh, int extract_method);
20 int mg_apply_transform(Bmicrograph* mg_ref, Bmicrograph* mg_apply);
21 int mg_merge_focal_series(Bproject* project, int use_old_origins);
22 double project_write_average_frames(Bproject* project, Bimage* pgr,
23 Bstring& path, DataType datatype, Bstring& subset, Bstring& label);
24 double project_write_aligned_averages(Bproject* project, Bimage* pgr,
25 Bstring& imgfile, DataType datatype, Bstring& subset, Bstring& label);
26 double project_write_aligned_images(Bproject* project, Bimage* pgr,
27 Bstring& imgfile, DataType datatype, Bstring& label);
28 double project_align_frames(Bproject* project, int ref_img, Bimage* pgr,
29 Bimage* pmask, Vector3<double> origin, double hi_res, double lo_res,
30 double shift_limit, double edge_width, double gauss_width,
31 Vector3<long> bin, JSvalue& dose_frac, Bstring& subset, int flag);
32 double project_align_series(Bproject* project, int ref_img, Bimage* pgr,
33 Bimage* pmask, Vector3<double> origin, double hi_res, double lo_res,
34 double shift_limit, double edge_width, double gauss_width,
35 Vector3<long> bin, Bstring& subset, int flag);
36 long project_tomo_align(Bproject* project, long thickness, long iter, double dchange,
37 long dimg, double resolution, double shift_limit, double edge_width, double gauss_width);
38 double project_ssnr(Bproject* project);
39
Bimage.h
Header file for image class.
DataType
DataType
Base data type specifier.
Definition: utilities.h:146
project_align_series
double project_align_series(Bproject *project, int ref_img, Bimage *pgr, Bimage *pmask, Vector3< double > origin, double hi_res, double lo_res, double shift_limit, double edge_width, double gauss_width, Vector3< long > bin, Bstring &subset, int flag)
Aligns a series of micrographs by cross-correlation.
Definition: mg_align.cpp:1532
project
Bproject * project
Definition: bshow.cpp:31
Bimage
General image parameter class.
Definition: Bimage.h:163
project_write_aligned_images
double project_write_aligned_images(Bproject *project, Bimage *pgr, Bstring &imgfile, DataType datatype, Bstring &label)
Calculates aligned micrograph images and write them to a file.
Definition: mg_align.cpp:950
mg_align_coordinates
int mg_align_coordinates(Bproject *project, int refset)
Aligns the particle coordinates of a series of micrographs.
Definition: mg_align.cpp:38
mg_merge_focal_series
int mg_merge_focal_series(Bproject *project, int use_old_origins)
Merges corresponding particle images in each focal series.
Definition: mg_align.cpp:762
project_ssnr
double project_ssnr(Bproject *project)
Definition: mg_align.cpp:1939
Bmicrograph
Definition: mg_processing.h:200
JSvalue
Definition: json.h:53
mg_align_micrographs
int mg_align_micrographs(Bproject *project, int refset, Vector3< long > tile_size, double res_lo, double res_hi, double max_shift, int filter_flag, int refine_flag)
Aligns a focal series of micrographs.
Definition: mg_align.cpp:315
Bstring
Definition: Bstring.h:29
project_write_average_frames
double project_write_average_frames(Bproject *project, Bimage *pgr, Bstring &path, DataType datatype, Bstring &subset, Bstring &label)
Calculates average micrograph frame images and write them to a file.
Definition: mg_align.cpp:1067
Vector3< long >
Vector3.h
Class for 3-value vectors.
mg_processing.h
Header file for micrograph processing.
mg_align_feature_extraction
int mg_align_feature_extraction(Bproject *project, int max_features, double res_low, double res_high, double thresh, int extract_method)
Aligns images by feature extraction.
Definition: mg_align.cpp:541
project_align_frames
double project_align_frames(Bproject *project, int ref_img, Bimage *pgr, Bimage *pmask, Vector3< double > origin, double hi_res, double lo_res, double shift_limit, double edge_width, double gauss_width, Vector3< long > bin, JSvalue &dose_frac, Bstring &subset, int flag)
Aligns a series of micrographs by cross-correlation.
Definition: mg_align.cpp:1307
project_tomo_align
long project_tomo_align(Bproject *project, long thickness, long iter, double dchange, long dimg, double resolution, double shift_limit, double edge_width, double gauss_width)
Definition: mg_align.cpp:1783
Bproject
Definition: mg_processing.h:333
mg_apply_transform
int mg_apply_transform(Bmicrograph *mg_ref, Bmicrograph *mg_apply)
Applies a transformation to particle coordinates in a reference micrograph and writes them into an ap...
Definition: mg_align.cpp:630
project_write_aligned_averages
double project_write_aligned_averages(Bproject *project, Bimage *pgr, Bstring &imgfile, DataType datatype, Bstring &subset, Bstring &label)
Calculates aligned micrograph images and write them to a file.
Definition: mg_align.cpp:1122