ProgEvaluateClass Class Reference

#include <classify_evaluate_classes.h>

Inheritance diagram for ProgEvaluateClass:

Collaboration diagram for ProgEvaluateClass:

Public Member Functions
void	readParams ()
	Read input parameters. More...
void	defineParams ()
	Define input parameters. More...
void	show ()
	Show. 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	fnClass
	Name of the classification metadata. More...
FileName	fnOut
	Name of the output metadata. 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 58 of file classify_evaluate_classes.h.

Member Function Documentation

defineParams()

void ProgEvaluateClass::defineParams ( )

virtual

Define input parameters.

Reimplemented from XmippProgram.

Definition at line 81 of file classify_evaluate_classes.cpp.

{
    addUsageLine("Evaluate the quality of a set of classes");
    addUsageLine("+The program associates to each class a number of quality measures:");
    addUsageLine("+");
    addUsageLine("+FRC_05 is the digital frequency (<0.5) at which the Fourier Ring Correlation drops below 0.5 ");
    addUsageLine("+(to convert from a digital frequency to one measured in Angstrom invert the digital frequency and multiply by the sampling rate).");
    addUsageLine("+");
    addUsageLine("+DPR_05 is the Differential Phase Residual at the frequency of FRC_05");
    addParamsLine(" -i <infile>             : Metadata with the classification (normally the output of CL2D or ML2D)");
    addParamsLine(" [-o <outfile=\"\">]     : Output file");
    addExampleLine("xmipp_classify_evaluate_classes -i 2D/CL2D/run_001/results_level_00_classes.xmd");
}

readParams()

void ProgEvaluateClass::readParams ( )

virtual

Read input parameters.

Reimplemented from XmippProgram.

Definition at line 75 of file classify_evaluate_classes.cpp.

{
    fnClass=getParam("-i");
    fnOut=getParam("-o");
}

run()

void ProgEvaluateClass::run ( )

virtual

Execute.

Reimplemented from XmippProgram.

Definition at line 104 of file classify_evaluate_classes.cpp.

{
    MetaDataVec MD((String)"classes@"+fnClass), MDclass;
    ClassEvaluation eval;
    if (verbose>0)
        init_progress_bar(MD.size());
    int idx=0;
    for (size_t objId : MD.ids())
    {
        int classNo;
        MD.getValue(MDL_REF,classNo,objId);
        MDclass.read(formatString("class%06d_images@%s",classNo,fnClass.c_str()));
        evaluateClass(MDclass,eval);
        MD.setValue(MDL_CLASSIFICATION_FRC_05,eval.FRC_05,objId);
        MD.setValue(MDL_CLASSIFICATION_DPR_05,eval.DPR_05,objId);
        idx++;
        if (verbose>0)
            progress_bar(idx);
    }
    if (verbose>0)
        progress_bar(MD.size());
    if (fnOut=="")
        fnOut=fnClass;
    MD.write((String)"classes@"+fnOut,MD_APPEND);
}

show()

void ProgEvaluateClass::show

(

)

Show.

Definition at line 95 of file classify_evaluate_classes.cpp.

{
    if (!verbose)
        return;
    std::cout
    << "Input:  " << fnClass << std::endl
    << "Output: " << fnOut << std::endl;
}

Member Data Documentation

fnClass

FileName ProgEvaluateClass::fnClass

Name of the classification metadata.

Definition at line 62 of file classify_evaluate_classes.h.

fnOut

FileName ProgEvaluateClass::fnOut

Name of the output metadata.

Definition at line 64 of file classify_evaluate_classes.h.

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

• xmipp/libraries/reconstruction/classify_evaluate_classes.h
• xmipp/libraries/reconstruction/classify_evaluate_classes.cpp