#include <coordinates_noisy_zones_filter.h>

Inheritance diagram for ProgCoordinatesNoisyZonesFilter:

Collaboration diagram for ProgCoordinatesNoisyZonesFilter:

Public Member Functions
virtual void	defineParams ()

virtual void	readParams ()

virtual void	show ()

virtual 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	fnInCoord

FileName	fnInMic

FileName	fnOut

int	patchSize

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

Generic class to filtrate the coordinates in noisy zones

Definition at line 38 of file coordinates_noisy_zones_filter.h.

Member Function Documentation

◆ defineParams()

void ProgCoordinatesNoisyZonesFilter::defineParams ( )

virtual

Function in which the param of each Program are defined.

Reimplemented from XmippProgram.

Definition at line 28 of file coordinates_noisy_zones_filter.cpp.

 {
     // Parameters
     addParamsLine(" --pos <coordinates> : Input coordinates");
     addParamsLine(" --mic <micrograph> : Reference volume");
     addParamsLine(" [--patchSize <n=50>] : Patch size for the variance filter");
     addParamsLine(" [-o <coordinates>] : Output coordinates (if not passed, "
                                                    "the input is overwritten)");
 }

◆ readParams()

void ProgCoordinatesNoisyZonesFilter::readParams ( )

virtual

Function in which each program will read parameters that it need. If some error occurs the usage will be printed out.

Reimplemented from XmippProgram.

Definition at line 38 of file coordinates_noisy_zones_filter.cpp.

 {
     fnInCoord = getParam("--pos");
     fnInMic = getParam("--mic");
     if (checkParam("-o"))
         fnOut = getParam("-o");
     else
         fnOut = fnInCoord;
     patchSize = getIntParam("--patchSize");
 }

◆ run()

void ProgCoordinatesNoisyZonesFilter::run ( )

virtual

This function will be start running the program. it also should be implemented by derived classes.

Reimplemented from XmippProgram.

Definition at line 61 of file coordinates_noisy_zones_filter.cpp.

 {
     show();
 
     Micrograph mic;
     mic.open_micrograph(fnInMic);
     mic.read_coordinates(0, (String)"particles@"+fnInCoord);
     mic.add_label("");
 
     Image<double> im;
     im.read(fnInMic);
 
     // std::cout << " - Starting normalization " << std::endl;
     MultidimArray<double> &matrixMic = im();
     matrixMic.selfNormalizeInterval();
 
     if (verbose>1)
     {
         Image<double> aux(matrixMic);
         aux.write(fnInCoord.withoutExtension()+"_normalized.mrc");
     }
 
     // giniCoeff(Image, patchSize) returns the giniCoeff of the Image and
     //   applies a variance filter to the Image with a patchSize 
     double giniV = giniCoeff(matrixMic, patchSize);
 
     if (verbose>1)
     {
         Image<double> aux(matrixMic);
         aux.write(fnInCoord.withoutExtension()+"_varianceFilter.mrc");
         std::cout << " Gini Coeff: " << giniV << std::endl
                   << "(" << fnInMic << ")" << std::endl;
     }
     
     // adding the variance value of the zone to every coordinate
     std::vector<Particle_coords> &allCoords=mic.coords;
     std::vector<double> varValue;
     for (size_t i=0; i<allCoords.size(); ++i)
     {
         Particle_coords &coord=allCoords[i];
         varValue.push_back(DIRECT_A2D_ELEM(matrixMic,coord.Y,coord.X));
     }
 
     // creating a MetaData with the coordinates and the Scores VAR and GINI
     MetaDataVec MD;
     int imax = allCoords.size();
     size_t id;
     for (int i = 0; i < imax; i++)
         if (allCoords[i].valid && allCoords[i].cost > 0
             && allCoords[i].label == 0)
         {
             id = MD.addObject();
             MD.setValue(MDL_XCOOR, allCoords[i].X, id);
             MD.setValue(MDL_YCOOR, allCoords[i].Y, id);
             MD.setValue(MDL_SCORE_BY_VAR, varValue[i], id);
             MD.setValue(MDL_SCORE_BY_GINI, giniV, id);            
         }
     MD.write((String)"particles@"+fnOut);
 }

◆ show()

void ProgCoordinatesNoisyZonesFilter::show ( )

virtual

Definition at line 49 of file coordinates_noisy_zones_filter.cpp.

 {
     if (verbose)
         std::cout
         << "Input Coordinates:     " << fnInCoord  << std::endl
         << "Input Micrograph:      " << fnInMic  << std::endl
         << "Output coordinates:    " << fnOut << std::endl
         << "Patch size:            " << patchSize << std::endl
         ;
 }