ProgAngularRotate Class Reference

Inheritance diagram for ProgAngularRotate:

Collaboration diagram for ProgAngularRotate:

Protected Member Functions
void	defineParams ()
void	readParams ()
void	run ()
Protected Member Functions inherited from XmippProgram
void	defineCommons ()

Protected Attributes
FileName	fnIn
FileName	fnOut
MetaDataVec	mdIn
MetaDataVec	mdOut
Matrix2D< double >	R
Matrix2D< double >	T
Matrix2D< double >	B
bool	writeMatrix
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

Additional Inherited Members
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 inherited from XmippProgram
bool	doRun
bool	runWithoutArgs
int	verbose
	Verbosity level. More...
int	debug

Detailed Description

Definition at line 33 of file angular_rotate.cpp.

Member Function Documentation

defineParams()

void ProgAngularRotate::defineParams ( )

inlineprotectedvirtual

Function in which the param of each Program are defined.

Reimplemented from XmippProgram.

Definition at line 41 of file angular_rotate.cpp.

    {
        addUsageLine("Calculate the Euler angles after applying a rotation to a geometry set from a metadata.");
        addKeywords("angular, geometry, rotate");
        addSeeAlsoLine("transform_geometry");

        addParamsLine("  -i <metadata>   : Input metadata file");
        addParamsLine(" [-o <metadata>]  : Output metadata file, if not provided result will overwrite input file");
        addParamsLine("    --ang <angle>                  : Rotate in plane");
        addParamsLine(" or --euler <rot> <tilt> <psi>     : Rotate with these Euler angles");
        addParamsLine(" or --alignZ <x> <y> <z>           : Align (x,y,z) with Z axis");
        addParamsLine(" or --axis <ang> <x=0> <y=0> <z=1> : Rotate <ang> degrees around (x,y,z)");
        addParamsLine("[--write_matrix]                    : Print transformation matrix to screen");

        addExampleLine("Modify the geometry of a selfile applying a rotation of 0.1 degrees around (x,y,z)=(1,1,1) direction:", false);
        addExampleLine("xmipp_angular_rotate -i selfile.sel -o newselfile.sel --axis 0.1 1 1 1");

    }

readParams()

void ProgAngularRotate::readParams ( )

inlineprotectedvirtual

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 60 of file angular_rotate.cpp.

    {
        fnIn = getParam("-i");
        fnOut = (checkParam("-o"))? getParam("-o") : fnIn;

        mdIn.read(fnIn);
        int dim;

        if (mdIn.containsLabel(MDL_ANGLE_PSI) || mdIn.containsLabel(MDL_ANGLE_TILT))
            dim = 3;
        else
            dim = 2;

        R.initIdentity(dim + 1);
        B.initIdentity(dim + 1);
        Matrix1D<double> xyz(3);

        if (checkParam("--ang"))
            Euler_angles2matrix(0., 0.,getDoubleParam("--ang"), R, true);
        else if (checkParam("--axis"))
        {
            double ang = getDoubleParam("--axis", 0);
            XX(xyz) = getDoubleParam("--axis", 1); //axis x
            YY(xyz) = getDoubleParam("--axis", 2); //y
            ZZ(xyz) = getDoubleParam("--axis", 3);//z
            rotation3DMatrix(ang, xyz, R, true);
        }
        else if (checkParam("--euler"))
        {
            XX(xyz) = getDoubleParam("--euler", 0); //rot
            YY(xyz) = getDoubleParam("--euler", 1); //tilt
            ZZ(xyz) = getDoubleParam("--euler", 2);//psi
            Euler_angles2matrix(XX(xyz), YY(xyz), ZZ(xyz), R, true);
        }
        else if (checkParam("--alignZ"))
        {
            XX(xyz) = getDoubleParam("--alignZ", 0); //rot
            YY(xyz) = getDoubleParam("--alignZ", 1); //tilt
            ZZ(xyz) = getDoubleParam("--alignZ", 2);//psi
            alignWithZ(xyz, R);
        }

        writeMatrix = checkParam("--write_matrix");
    }

run()

void ProgAngularRotate::run ( )

inlineprotectedvirtual

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

Reimplemented from XmippProgram.

Definition at line 105 of file angular_rotate.cpp.

    {
        bool containsScale=mdIn.containsLabel(MDL_SCALE);
        for (auto& input : mdIn)
        {
            geo2TransformationMatrix(input, B);

            T = R * B;

            transformationMatrix2Geo(T, input);
            if (!containsScale)
                input.setValue(MDL_SCALE,1.0);
            mdOut.addRow(dynamic_cast<MDRowVec&>(input));

            if (writeMatrix)
                std::cout << T << std::endl;
        }

        mdOut.write(fnOut);
    }

Member Data Documentation

B

Matrix2D<double> ProgAngularRotate::B

protected

Definition at line 38 of file angular_rotate.cpp.

fnIn

FileName ProgAngularRotate::fnIn

protected

Definition at line 36 of file angular_rotate.cpp.

fnOut

FileName ProgAngularRotate::fnOut

protected

Definition at line 36 of file angular_rotate.cpp.

mdIn

MetaDataVec ProgAngularRotate::mdIn

protected

Definition at line 37 of file angular_rotate.cpp.

mdOut

MetaDataVec ProgAngularRotate::mdOut

protected

Definition at line 37 of file angular_rotate.cpp.

R

Matrix2D<double> ProgAngularRotate::R

protected

Definition at line 38 of file angular_rotate.cpp.

T

Matrix2D<double> ProgAngularRotate::T

protected

Definition at line 38 of file angular_rotate.cpp.

writeMatrix

bool ProgAngularRotate::writeMatrix

protected

Definition at line 39 of file angular_rotate.cpp.

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

• xmipp/libraries/reconstruction/angular_rotate.cpp