A tool to merge data from micrograph reconstruction and model files. More...

#include "mg_processing.h"
#include "rwmg.h"
#include "rwimg.h"
#include "rwmodel.h"
#include "model_transform.h"
#include "marker.h"
#include "linked_list.h"
#include "utilities.h"
#include "options.h"
#include "timer.h"

Functions
Bmodel *	project_model_generate (Bproject project, Bmodel temp, int flags)
	Generates a model from each particle defined in a reconstruction. More...

int	project_model_consolidate (Bproject project, Bmodel model)
	Exchanges information between reconstruction and model structures. More...

int	main (int argc, char **argv)

Variables
int	verbose

const char *	use []

Detailed Description

A tool to merge data from micrograph reconstruction and model files.

Author: Bernard Heymann

Date: Created: 20090828; Modified: 20110725

Function Documentation

◆ main()

int main	(	int	argc,
		char **	argv
	)

◆ project_model_consolidate()

int project_model_consolidate	(	Bproject *	project,
		Bmodel *	model
	)

Exchanges information between reconstruction and model structures.

Parameters

*project	project parameter structure.
*model	model parameter structures.

Returns

int 0.

This function assumes there is a 1-1 relationship between models and
particles derived from reconstructions and that they are in corresponding
sequence.
The type id and hand from each model is converted into an integer and
the particle group set to it.
Each model id is reset to a combined reconstruction and particle id.

◆ project_model_generate()

Bmodel * project_model_generate	(	Bproject *	project,
		Bmodel *	temp,
		int	flags
	)

Generates a model from each particle defined in a reconstruction.

Parameters

*project	project parameter structure.
*temp	template model.
flags	conversion options: 1=images.

Returns

Bmodel* new model referencing the particle map files.

The model id is a combined reconstruction and particle id.
The model type id is taken from the particle group id.
The selection and FOM is taken from the particle properties.
The model map file name is taken from the particle file name if it
is defined, otherwise it is taken from the reconstruction structure
and the image number is taken from the particle id.
Flags:
    1   transform each particle images to standard orientation.
    2   write a model file for each particle.

Variable Documentation

◆ use

const char* use[]

Initial value:

= {
" ",
"Usage: brecmod [options] in.star",
"--------------------------------",
"Merges data from micrograph and model files.",
" ",
"Actions:",
"-consolidate mod.star    Consolidate project and model parameters.",
"-images                  Convert particle images (use with -outmodel).",
"-submodels               Generate particle models (use with -outmodel).",
" ",
"Parameters:",
"-verbose 7               Verbosity of output.",
"-sampling 1.5,1.5,1.5    Sampling of images (A/pixel; a single value can be given).",
" ",
"Input:",
"-template model.star     Template to associate with each particle.",
" ",
"Output:",
"-output newmg.star       New micrograph parameter file.",
"-outmodel partmod.star   New model file from particles.",
"-outmark markmod.star    New model file from markers.",
" ",
NULL
}

◆ verbose

int verbose

extern

Functions

Variables