#include <micrograph_automatic_picking2.h>

Inheritance diagram for ProgMicrographAutomaticPicking2:

Collaboration diagram for ProgMicrographAutomaticPicking2:

Public Member Functions
void	readParams ()
	Read parameters. More...

void	show ()
	Show parameters. More...

void	defineParams ()
	Define Parameters. More...

void	run ()

Public Member Functions inherited from XmippProgram
const char *	getParam (const char *param, int arg=0)

const char *	getParam (const char param, const char subparam, int arg=0)

int	getIntParam (const char *param, int arg=0)

int	getIntParam (const char param, const char subparam, int arg=0)

double	getDoubleParam (const char *param, int arg=0)

double	getDoubleParam (const char param, const char subparam, int arg=0)

float	getFloatParam (const char *param, int arg=0)

float	getFloatParam (const char param, const char subparam, int arg=0)

void	getListParam (const char *param, StringVector &list)

int	getCountParam (const char *param)

bool	checkParam (const char *param)

bool	existsParam (const char *param)

void	addParamsLine (const String &line)

void	addParamsLine (const char *line)

ParamDef *	getParamDef (const char *param) const

virtual void	quit (int exit_code=0) const

virtual int	tryRun ()

void	initProgress (size_t total, size_t stepBin=60)

void	setProgress (size_t value=0)

void	endProgress ()

void	processDefaultComment (const char param, const char left)

void	setDefaultComment (const char param, const char comment)

virtual void	initComments ()

void	setProgramName (const char *name)

void	addUsageLine (const char *line, bool verbatim=false)

void	clearUsage ()

void	addExampleLine (const char *example, bool verbatim=true)

void	addSeeAlsoLine (const char *seeAlso)

void	addKeywords (const char *keywords)

const char *	name () const

virtual void	usage (int verb=0) const

virtual void	usage (const String &param, int verb=2)

int	version () const

virtual void	show () const

virtual void	read (int argc, const char **argv, bool reportErrors=true)

virtual void	read (int argc, char **argv, bool reportErrors=true)

void	read (const String &argumentsLine)

	XmippProgram ()

	XmippProgram (int argc, const char **argv)

virtual	~XmippProgram ()

Public Attributes
FileName	fn_micrograph
	Micrograph filename. More...

FileName	fn_model
	Model rootname. More...

FileName	fn_train
	Training coordinates. More...

String	mode
	Mode. More...

FileName	fn_root

std::unique_ptr< AutoParticlePicking2 >	autoPicking

Public Attributes inherited from XmippProgram
bool	doRun

bool	runWithoutArgs

int	verbose
	Verbosity level. More...

int	debug

Additional Inherited Members
Protected Member Functions inherited from XmippProgram
void	defineCommons ()

Protected Attributes inherited from XmippProgram
int	errorCode

ProgramDef *	progDef
	Program definition and arguments parser. More...

std::map< String, CommentList >	defaultComments

int	argc
	Original command line arguments. More...

const char **	argv

Detailed Description

Definition at line 355 of file micrograph_automatic_picking2.h.

Member Function Documentation

◆ defineParams()

void ProgMicrographAutomaticPicking2::defineParams ( )

virtual

Define Parameters.

Reimplemented from XmippProgram.

Definition at line 1806 of file micrograph_automatic_picking2.cpp.

 {
     addUsageLine("Automatic particle picking for micrographs");
     addUsageLine("+The algorithm is designed to learn the particles from the user, as well as from its own errors.");
     addUsageLine("+The algorithm is fully described in [[http://www.ncbi.nlm.nih.gov/pubmed/19555764][this paper]].");
     AutoParticlePicking2::defineParams(this);
 }

◆ readParams()

void ProgMicrographAutomaticPicking2::readParams ( )

virtual

Read parameters.

Reimplemented from XmippProgram.

Definition at line 1752 of file micrograph_automatic_picking2.cpp.

 {
     fn_micrograph = getParam("-i");
     fn_model = getParam("--model");
     mode = getParam("--mode");
     if (mode == "buildinv")
     {
         fn_train = getParam("--mode", 1);
     }
     fn_root = getParam("--outputRoot");
     autoPicking = std::make_unique<AutoParticlePicking2>();
     autoPicking->readParams(this);
 }

◆ run()

void ProgMicrographAutomaticPicking2::run ( )

virtual

Run

Reimplemented from XmippProgram.

Definition at line 1815 of file micrograph_automatic_picking2.cpp.

 {
     int proc_prec;
     MetaDataVec MD;
     FileName fnAutoParticles = formatString("particles_auto@%s.pos", fn_root.c_str());
     MD.read(fn_model.beforeLastOf("/")+"/config.xmd");
     MD.getValue( MDL_PICKING_AUTOPICKPERCENT,proc_prec,MD.firstRowId());
 
     autoPicking = std::make_unique<AutoParticlePicking2>(autoPicking->particle_size,autoPicking->filter_num,autoPicking->corr_num,autoPicking->NPCA,fn_model, std::vector<MDRowSql>());
     autoPicking->automaticWithouThread(fn_micrograph,proc_prec,fnAutoParticles);
 }