#include <image_eliminate_empty_particles.h>

Inheritance diagram for ProgEliminateEmptyParticles:

Collaboration diagram for ProgEliminateEmptyParticles:

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

void	show ()
	Show. More...

void	defineParams ()
	Define input parameters. More...

void	run ()
	Execute. More...

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	fnIn
	Name of the input metadata. More...

FileName	fnOut
	Name of the output metadata. More...

FileName	fnElim
	Name of the eliminated particle metadata. More...

float	threshold
	Threshold for variance of variance. More...

bool	addFeatures
	Add features. More...

bool	useDenoising
	Turning on denoising. More...

int	denoise
	Param for denoising. More...

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 34 of file image_eliminate_empty_particles.h.

Member Function Documentation

◆ defineParams()

void ProgEliminateEmptyParticles::defineParams ( )

virtual

Define input parameters.

Reimplemented from XmippProgram.

Definition at line 61 of file image_eliminate_empty_particles.cpp.

 {
     addUsageLine("Eliminates empty particles (false positives from picking)");
     addParamsLine("  -i <selfile>                       : Selfile containing set of input particles");
     addParamsLine("  [-o <selfile=\"output.xmd\">]      : Output selfile");
     addParamsLine("  [-e <selfile=\"eliminated.xmd\">]  : Eliminated particles selfile");
     addParamsLine("  [-t <float=-1>]                    : Threshold used by algorithm. Set to -1 for no elimination.");
     addParamsLine("  [--addFeatures]                    : Add the emptiness features to the input particles");
     addParamsLine("  [--useDenoising]                   : Option for turning on denoising method while computing emptiness feature");
     addParamsLine("  [-d <int=50>]                      : Parameter for denoising, higher value means stronger denoising and slower computation");
 }

◆ readParams()

void ProgEliminateEmptyParticles::readParams ( )

virtual

Read input parameters.

Reimplemented from XmippProgram.

Definition at line 33 of file image_eliminate_empty_particles.cpp.

 {
     fnIn = getParam("-i");
     fnOut = getParam("-o");
     fnElim = getParam("-e");
     threshold = getDoubleParam("-t");
     addFeatures = checkParam("--addFeatures");
     useDenoising = checkParam("--useDenoising");
     denoise = getIntParam("-d");
 }

◆ run()

void ProgEliminateEmptyParticles::run ( )

virtual

Execute.

Reimplemented from XmippProgram.

Definition at line 73 of file image_eliminate_empty_particles.cpp.

 {
     MetaDataVec SF;
     SF.read(fnIn);
     FileName fnImg;
     Image<double> I;
     CorrelationAux aux;
     MDRowVec row;
     MetaDataVec MDclass, MDclassEl, MDclassT, MDclassElT;
     ProgExtractFeatures ef;
     int countItems = 0;
     std::vector<double> fv;
 
     init_progress_bar(SF.size());
     std::size_t extraPath = fnOut.find_last_of("/");
     // these files are for streaming and will be later removed in Scipion
     FileName fnDone = fnOut.substr(0, extraPath+1) + "outTemp.xmd";
     FileName fnElDone = fnOut.substr(0, extraPath+1) + "elimTemp.xmd";
 
     std::ifstream ifile1(fnOut.c_str());
     if (ifile1) MDclass.read(fnOut);
     std::ifstream ifile2(fnElim.c_str());
     if (ifile2) MDclassEl.read(fnElim);
 
     for (size_t objId : SF.ids())
     {
         countItems++;
         SF.getValue(MDL_IMAGE, fnImg, objId);
         SF.getRow(row, countItems);
 
         I.read(fnImg);
         I().setXmippOrigin();
         centerImageTranslationally(I(), aux);
 
         if (useDenoising)
             realGaussianFilter(I(), denoise);
             bandpassFilter(I(), 0, 0.1, 0.02);
 
         ef.extractVariance(I(), fv);
 
         double ratio = fv.back();
         row.setValue(MDL_SCORE_BY_EMPTINESS, ratio);
         if (addFeatures)
             row.setValue(MDL_SCORE_BY_VARIANCE, fv);
         if (threshold<0 || ratio > threshold)
         {
             MDclass.addRow(row);
             MDclassT.addRow(row);
         }
         else
         {
             MDclassEl.addRow(row);
             MDclassElT.addRow(row);
         }
 
         fv.clear();
         if (countItems%100==0)
             progress_bar(countItems);
     }
     progress_bar(SF.size());
 
     if (MDclass.size()>0)
         MDclass.write(formatString("@%s", fnOut.c_str()), MD_APPEND);
     if (MDclassEl.size()>0)
         MDclassEl.write(formatString("@%s", fnElim.c_str()), MD_APPEND);
     if (MDclassT.size()>0)
         MDclassT.write(formatString("@%s", fnDone.c_str()), MD_APPEND);
     if (MDclassElT.size()>0)
         MDclassElT.write(formatString("@%s", fnElDone.c_str()), MD_APPEND);
 }

◆ show()

void ProgEliminateEmptyParticles::show ( )

Show.

Definition at line 45 of file image_eliminate_empty_particles.cpp.

 {
     if (verbose==0)
         return;
     std::cerr
     << "Input selfile:           " << fnIn         << std::endl
     << "Output selfile:          " << fnOut        << std::endl
     << "Eliminated selfile:      " << fnElim       << std::endl
     << "Threshold:               " << threshold    << std::endl
     << "Add features:            " << addFeatures  << std::endl
     << "Turn on denoising:       " << useDenoising << std::endl
     << "Denosing parameter:      " << denoise      << std::endl
     ;
 }