ProgAngularBreakSymmetry Class Reference

#include <angular_break_symmetry.h>

Inheritance diagram for ProgAngularBreakSymmetry:

Collaboration diagram for ProgAngularBreakSymmetry:

Public Member Functions
void	readParams ()
	Read argument from command line. More...
void	show ()
	Show. More...
void	defineParams ()
	Define parameters. More...
void	produce_side_info ()
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	fn_ang
FileName	fn_sym
FileName	fn_out
MetaDataVec	DF
SymList	SL
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

Angular Distance parameters.

Definition at line 37 of file angular_break_symmetry.h.

Member Function Documentation

defineParams()

void ProgAngularBreakSymmetry::defineParams ( )

virtual

Define parameters.

Reimplemented from XmippProgram.

Definition at line 50 of file angular_break_symmetry.cpp.

{
    addUsageLine("randomize angle input file ");
    addParamsLine("   -i <Metadata>        : Angular document file");
    addParamsLine("   -o <Metadata>        : Output file");
    addParamsLine("   --sym <symmetry>     : Symmetry file");
}

produce_side_info()

void ProgAngularBreakSymmetry::produce_side_info

(

)

Produce side info. Read all document files and symmetry list if any. An exception is thrown if both files are not of the same length.

Definition at line 59 of file angular_break_symmetry.cpp.

{
    SL.readSymmetryFile(fn_sym);
    DF.read(fn_ang);
}

readParams()

void ProgAngularBreakSymmetry::readParams ( )

virtual

Read argument from command line.

Reimplemented from XmippProgram.

Definition at line 32 of file angular_break_symmetry.cpp.

{
    fn_ang = getParam("-i");
    fn_out  = getParam("-o");
    fn_sym  = getParam("--sym");
}

run()

void ProgAngularBreakSymmetry::run ( )

virtual

Run

Reimplemented from XmippProgram.

Definition at line 67 of file angular_break_symmetry.cpp.

{
    produce_side_info();

    for (size_t objId : DF.ids())
    {
        // Read input data
        double rot,  tilt,  psi;

        DF.getValue(MDL_ANGLE_ROT,  rot, objId);
        DF.getValue(MDL_ANGLE_TILT, tilt, objId);
        DF.getValue(MDL_ANGLE_PSI,  psi, objId);


        // Apply random rotation within symmetry matrices
        SL.breakSymmetry(rot, tilt, psi,
                         rot, tilt, psi);

        // Bring both angles to a normalized set
        //rot2  = realWRAP(rot2, -180, 180);
        //tilt2 = realWRAP(tilt2, -180, 180);
        //psi2  = realWRAP(psi2, -180, 180);

        DF.setValue(MDL_ANGLE_ROT, rot, objId);
        DF.setValue(MDL_ANGLE_TILT,tilt, objId);
        DF.setValue(MDL_ANGLE_PSI, psi, objId);
    }

    DF.write(fn_out);
}

show()

void ProgAngularBreakSymmetry::show

(

)

Show.

Definition at line 40 of file angular_break_symmetry.cpp.

{
    std::cout
    << "Angular metadata File (IN): " << fn_ang       << std::endl
    << "Angular metadata (OUT)    : " << fn_out    << std::endl
    << "Symmetry file    : " << fn_sym        << std::endl
    ;
}

Member Data Documentation

DF

MetaDataVec ProgAngularBreakSymmetry::DF

Definition at line 48 of file angular_break_symmetry.h.

fn_ang

FileName ProgAngularBreakSymmetry::fn_ang

Filename angle metadata

Definition at line 41 of file angular_break_symmetry.h.

fn_out

FileName ProgAngularBreakSymmetry::fn_out

Filename of output file with merging

Definition at line 45 of file angular_break_symmetry.h.

fn_sym

FileName ProgAngularBreakSymmetry::fn_sym

Filename symmetry file

Definition at line 43 of file angular_break_symmetry.h.

SL

SymList ProgAngularBreakSymmetry::SL

Definition at line 50 of file angular_break_symmetry.h.

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

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