ProgExtractSubset Class Reference

#include <prog_extract_subset_main.h>

Inheritance diagram for ProgExtractSubset:

Collaboration diagram for ProgExtractSubset:

Public Member Functions
virtual void	readParams () override
virtual void	defineParams () override
virtual void	show () const override
virtual void	run () override
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	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 ()

Additional Inherited Members
Public Attributes inherited from XmippProgram
bool	doRun
bool	runWithoutArgs
int	verbose
	Verbosity level. More...
int	debug
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 33 of file prog_extract_subset_main.h.

Member Function Documentation

defineParams()

void ProgExtractSubset::defineParams ( )

overridevirtual

Function in which the param of each Program are defined.

Reimplemented from XmippProgram.

Definition at line 29 of file prog_extract_subset_main.cpp.

                                     {
    addUsageLine("Extract a subset of particles into a new file. "
        "By default, only 'Enabled' particles will be kept.");

    addParamsLine(" -i <md_file>                : Input metadata");
    addParamsLine(" -o <md_file>                : Output metadata");
    addParamsLine(" [--odir <outputDir=\".\">]  : Output directory");
    addParamsLine(" [--keepDisabled]            : Ignore 'Enable' flag, i.e. include also disabled particles");
    addParamsLine(" [--first <n=10>]            : Extract first up to n particles");
    addParamsLine(" [--last <n=10>]             : Extract last up to n particles");
    addParamsLine(" [--range <s=0> <e=10>]      : Extract particles within this zero-based range");
}

readParams()

void ProgExtractSubset::readParams ( )

overridevirtual

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 42 of file prog_extract_subset_main.cpp.

                                   {
    m_settings.skipDisabled = ! checkParam("--keepDisabled");
    MetaData &md = m_settings.md;
    md.read(getParam("-i"));
    if (m_settings.skipDisabled) {
        md.removeDisabled();
    }
    size_t n = md.size();

    if (checkParam(OPT_FIRST)) {
        m_settings.first = 0;
        m_settings.count = std::min(n, (size_t)getIntParam(OPT_FIRST));
    } else if (checkParam(OPT_LAST)) {
        m_settings.count = std::min(n, (size_t)getIntParam(OPT_LAST));
        m_settings.first = (0 == m_settings.count) ? 0 : n - m_settings.count;
    } else if (checkParam(OPT_RANGE)) {
        size_t reqS = getIntParam(OPT_RANGE, 0);
        size_t reqE = getIntParam(OPT_RANGE, 1);
        size_t last = std::min((0 == n ? 0 : n - 1), reqE);
        m_settings.first = std::min((0 == n ? 0 : n - 1), reqS);
        m_settings.count = last - m_settings.first + 1;
    } else {
        m_settings.first = 0;
        m_settings.count = n;
    }

    prepareOutput();
}

run()

void ProgExtractSubset::run ( )

overridevirtual

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

Reimplemented from XmippProgram.

Definition at line 99 of file prog_extract_subset_main.cpp.

                            {
    show();
    ExtractSubset::createSubset(m_settings);
}

show()

void ProgExtractSubset::show ( ) const

overridevirtual

Show parameters

Reimplemented from XmippProgram.

Definition at line 93 of file prog_extract_subset_main.cpp.

                                   {
    if (verbose < 1) return;

    std::cout << m_settings;
}

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

• xmipp/legacy/applications/programs/extract_subset/prog_extract_subset_main.h
• xmipp/legacy/applications/programs/extract_subset/prog_extract_subset_main.cpp