ProgAngularEstimateTiltAxis Class Reference

#include <angular_estimate_tilt_axis.h>

Inheritance diagram for ProgAngularEstimateTiltAxis:

Collaboration diagram for ProgAngularEstimateTiltAxis:

Public Member Functions
void	defineParams ()
	Define parameters in the command line. More...
void	readParams ()
	Read parameters from the command line. More...
void	run ()
	Run over the whole input metadata. 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	fnUntilted
FileName	fnTilted
FileName	fnOut
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

Centilt parameters.

Definition at line 37 of file angular_estimate_tilt_axis.h.

Member Function Documentation

defineParams()

void ProgAngularEstimateTiltAxis::defineParams ( )

virtual

Define parameters in the command line.

Reimplemented from XmippProgram.

Definition at line 33 of file angular_estimate_tilt_axis.cpp.

{
    //Usage
    addUsageLine("Estimate the tilt axis from a set of corresponding particles");

    // Params
    addParamsLine("  --untilted <posfile>       : Input coordinates in the untilted micrograph");
    addParamsLine("  --tilted <posfile>         : Input coordinates in the tilted micrograph");
    addParamsLine("  -o <metadata>              : Output metadata file with tilt axis angles");
}

readParams()

void ProgAngularEstimateTiltAxis::readParams ( )

virtual

Read parameters from the command line.

Reimplemented from XmippProgram.

Definition at line 45 of file angular_estimate_tilt_axis.cpp.

{
    fnUntilted = getParam("--untilted");
    fnTilted = getParam("--tilted");
    fnOut = getParam("-o");
}

run()

void ProgAngularEstimateTiltAxis::run ( )

virtual

Run over the whole input metadata.

Reimplemented from XmippProgram.

Definition at line 53 of file angular_estimate_tilt_axis.cpp.

{
    MetaDataVec mdU, mdT;
    mdU.read(fnUntilted);
    mdT.read(fnTilted);
    TiltPairAligner aligner;
    MetaDataVec mdOut;
    size_t id;
    double alphaU, alphaT, gamma;

    if (mdU.size()==0)
    {
        id=mdOut.addObject();
        mdOut.setValue(MDL_ANGLE_Y,id);
        mdOut.setValue(MDL_ANGLE_Y2,id);
        mdOut.setValue(MDL_ANGLE_TILT,id);
        mdOut.write(fnOut);
        return;
    }

    auto idItU = mdU.ids().begin();
    auto idItT = mdT.ids().begin();
    const auto totalSize = mdU.ids().end();
    for (; idItU != totalSize; ++idItU, ++idItT)
    {
        int xu, yu, xt, yt;
        mdU.getValue(MDL_XCOOR,xu,*idItU);
        mdU.getValue(MDL_YCOOR,yu,*idItU);
        mdT.getValue(MDL_XCOOR,xt,*idItT);
        mdT.getValue(MDL_YCOOR,yt,*idItT);

        aligner.addCoordinatePair(xu,yu,xt,yt);
    }
    aligner.calculatePassingMatrix();
    aligner.computeGamma();

    gamma=aligner.gamma;
    aligner.computeAngles(alphaU, alphaT, gamma);

    if (fnOut.exists())
        mdOut.read(fnOut);

    MDRowVec row;
    row.setValue(MDL_ANGLE_Y, alphaU);
    row.setValue(MDL_ANGLE_Y2, alphaT);
    row.setValue(MDL_ANGLE_TILT, gamma);
    mdOut.addRow(row);

    mdOut.write(fnOut);


}

Member Data Documentation

fnOut

FileName ProgAngularEstimateTiltAxis::fnOut

Filename output document file

Definition at line 45 of file angular_estimate_tilt_axis.h.

fnTilted

FileName ProgAngularEstimateTiltAxis::fnTilted

Filename input tilted coords

Definition at line 43 of file angular_estimate_tilt_axis.h.

fnUntilted

FileName ProgAngularEstimateTiltAxis::fnUntilted

Filename input untilted coords

Definition at line 41 of file angular_estimate_tilt_axis.h.

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

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