ProgEvaluateCoordinates Class Reference

#include <evaluate_coordinates.h>

Inheritance diagram for ProgEvaluateCoordinates:

Collaboration diagram for ProgEvaluateCoordinates:

Public Member Functions
void	readParams ()
	Read argument. More...
void	show ()
	Show. More...
void	defineParams ()
	Define parameters. More...
void	run ()
	Main routine. 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
MetaDataVec	GT
MetaDataVec	Eval
FileName	fnGt
FileName	fnEval
FileName	rootName
int	numMic
int	errMargin
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 evaluate_coordinates.h.

Member Function Documentation

defineParams()

void ProgEvaluateCoordinates::defineParams ( )

virtual

Define parameters.

Reimplemented from XmippProgram.

Definition at line 53 of file evaluate_coordinates.cpp.

{
    addUsageLine("Evaluates the set of coordinates against the ground truth");
    addParamsLine("  -g <selfile>      : Selfile containing ground truth coordinates");
    addParamsLine("  -e <selfile>      : Selfile containing coordinates to evaluate");
    addParamsLine("  -n <int>          : Number of micrographs");
    addParamsLine("  [-t <int=10>]     : Tolerance of center misplacement");
    addParamsLine("  --root <rootName> : Root name of the micrographs");
}

readParams()

void ProgEvaluateCoordinates::readParams ( )

virtual

Read argument.

Reimplemented from XmippProgram.

Definition at line 29 of file evaluate_coordinates.cpp.

{
    fnGt = getParam("-g");
    fnEval = getParam("-e");
    numMic = getIntParam("-n");
    errMargin = getIntParam("-t");
    rootName = getParam("--root");
}

run()

void ProgEvaluateCoordinates::run ( )

virtual

Main routine.

Reimplemented from XmippProgram.

Definition at line 63 of file evaluate_coordinates.cpp.

{
    int evalXCoor, evalYCoor, gtXCoor, gtYCoor;
    int truePosivites = 0, totalEval = 0, totalGT = 0;

    for (int m = 1; m <= numMic; m++)
    {
        // Here you need to change the identifiers based on datasets
        // TODO: loading names and counts of mics automatically?
        FileName micGT = formatString("%s_%04d@%s", rootName.c_str(), m, fnGt.c_str());
        FileName micEval = formatString("%s_%04d@%s", rootName.c_str(), m, fnEval.c_str());

        GT.read(micGT);
        Eval.read(micEval);

        int iterE = 1;
        for (size_t objIdEval : Eval.ids())
        {
            MDRowVec row;
            Eval.getRow(row, iterE);
            row.getValue(MDL_XCOOR, evalXCoor);
            row.getValue(MDL_YCOOR, evalYCoor);

            int iterG = 1;
            for (size_t objIdGT : GT.ids())
            {
                GT.getRow(row, iterG);
                row.getValue(MDL_XCOOR, gtXCoor);
                row.getValue(MDL_YCOOR, gtYCoor);

                if ((evalXCoor > (gtXCoor-errMargin-1)) &&
                    (evalXCoor < (gtXCoor+errMargin+1)) &&
                    (evalYCoor > (gtYCoor-errMargin-1)) &&
                    (evalYCoor < (gtYCoor+errMargin+1)))
                    truePosivites++;

                iterG++;
            }
            iterE++;
        }
        totalEval += Eval.size();
        totalGT += GT.size();
    }

    std::cout << std::endl;
    std::cout << "True positives (correctly picked particles): ";
    std::cout << truePosivites << std::endl;
    std::cout << "False positives (incorrectly picked particles): ";
    std::cout << totalEval - truePosivites << std::endl;
    std::cout << "False negatives (missed particles): ";
    std::cout << totalGT - truePosivites << std::endl << std::endl;

    std::cout << "How many relevant particles are picked:" << std::endl;
    std::cout << "True positive rate: ";
    double truePositiveRate = (0 == totalGT) ? 0 : (double) truePosivites / totalGT;
    std::cout << truePositiveRate << std::endl << std::endl;

    std::cout << "Ratio of wrongly picked particles and all picked particles:";
    std::cout << std::endl;
    std::cout << "False positive rate: ";
    std::cout << (double) (totalEval - truePosivites) / totalEval;
    std::cout << std::endl << std::endl;
}

show()

void ProgEvaluateCoordinates::show

(

)

Show.

Definition at line 39 of file evaluate_coordinates.cpp.

{
    if (verbose==0)
        return;
    std::cerr
    << "Ground truth coordinates:          " << fnGt         << std::endl
    << "Coordinates to evaluate:           " << fnEval       << std::endl
    << "Number of micrographs:             " << numMic       << std::endl
    << "Tolerance of center misplacement:  " << errMargin    << std::endl
    << "Root name:                         " << rootName     << std::endl
    ;
}

Member Data Documentation

errMargin

int ProgEvaluateCoordinates::errMargin

Error margin (toleration of misplacement of object center)

Definition at line 56 of file evaluate_coordinates.h.

Eval

MetaDataVec ProgEvaluateCoordinates::Eval

Definition at line 41 of file evaluate_coordinates.h.

fnEval

FileName ProgEvaluateCoordinates::fnEval

Filename of evaluated file with coordinates

Definition at line 47 of file evaluate_coordinates.h.

fnGt

FileName ProgEvaluateCoordinates::fnGt

Filename of ground truth coordinates

Definition at line 44 of file evaluate_coordinates.h.

GT

MetaDataVec ProgEvaluateCoordinates::GT

Definition at line 38 of file evaluate_coordinates.h.

numMic

int ProgEvaluateCoordinates::numMic

Number of micrographs

Definition at line 53 of file evaluate_coordinates.h.

rootName

FileName ProgEvaluateCoordinates::rootName

Rootname

Definition at line 50 of file evaluate_coordinates.h.

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The documentation for this class was generated from the following files:

• xmipp/legacy/libraries/reconstruction/evaluate_coordinates.h
• xmipp/legacy/libraries/reconstruction/evaluate_coordinates.cpp