Phantom_transform_parameters Class Reference

Inheritance diagram for Phantom_transform_parameters:

Collaboration diagram for Phantom_transform_parameters:

Public Member Functions
void	defineParams ()
void	readParams ()
void	show ()
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_in
FileName	fn_out
bool	Euler_mode
bool	PDBmode
bool	centerPDB
double	rot
double	tilt
double	psi
bool	Align_mode
bool	Axis_mode
Matrix1D< double >	axis
double	ang
Matrix1D< double >	shift
Matrix1D< double >	scale
Matrix2D< double >	A3D
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 32 of file phantom_transform.cpp.

Member Function Documentation

defineParams()

void Phantom_transform_parameters::defineParams ( )

inlinevirtual

Function in which the param of each Program are defined.

Reimplemented from XmippProgram.

Definition at line 47 of file phantom_transform.cpp.

    {
        addUsageLine("Apply a geometrical transformation to a phantom description or PDB.");
        addSeeAlsoLine("phantom_create, volume_from_pdb");
        addParamsLine(" -i <file>       : Phantom description file (.descr) or PDB (.pdb)");
        addParamsLine("[-o <file=\"\">] : Phantom description file (.descr) or PDB (.pdb)");
        addParamsLine("                 : For PDB files, you must explicitly give an output file, different from input");
        addParamsLine(" --operation <op>: Operation to perform");
        addParamsLine("      where <op>");
        addParamsLine("            shift <x> <y> <z> : Shift vector");
        addParamsLine("            scale <x> <y> <z> : Scale vector");
        addParamsLine("            rotate_euler <rot> <tilt> <psi> :Rotate with these Euler angles ");
        addParamsLine("            rotate_align_with_z <x> <y> <z> : Align (x,y,z) with Z");
        addParamsLine("            rotate_axis <x> <y> <z> <ang>: Rotate <ang> degrees around (x,y,z)");
        addParamsLine(" [--center_pdb]  : Subtract the center of mass from coordinates.");
        addParamsLine("                 :+Only valid for PDB files");
        addExampleLine("xmipp_phantom_transform -i model.pdb -o shifted.pdb --operation shift 1 2 3");
    }

readParams()

void Phantom_transform_parameters::readParams ( )

inlinevirtual

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 66 of file phantom_transform.cpp.

    {
        fn_in = getParam("-i");
        fn_out = getParam("-o");
        if (fn_out=="")
            fn_out=fn_in;
        PDBmode=fn_in.contains(".pdb");
        String operation;
        shift.initZeros(3);
        scale.resize(3);
        scale.initConstant(1);
        A3D.initIdentity(4);
        Euler_mode = Align_mode = Axis_mode = false;
        centerPDB = checkParam("--center_pdb");
        operation=getParam("--operation");
        if (operation=="shift")
        {
            double x=getDoubleParam("--operation",1);
            double y=getDoubleParam("--operation",2);
            double z=getDoubleParam("--operation",3);
            shift=vectorR3(x,y,z);
        }
        else if (operation=="scale")
        {
            double x=getDoubleParam("--operation",1);
            double y=getDoubleParam("--operation",2);
            double z=getDoubleParam("--operation",3);
            scale=vectorR3(x,y,z);
        }
        else if (operation=="rotate_euler")
        {
            Euler_mode = true;
            rot  = getDoubleParam("--operation",1);
            tilt = getDoubleParam("--operation",2);
            psi  = getDoubleParam("--operation",3);
            Euler_angles2matrix(rot, tilt, psi, A3D, true);
        }
        else if (operation=="rotate_align_with_z")
        {
            Align_mode = true;
            double x=getDoubleParam("--operation",1);
            double y=getDoubleParam("--operation",2);
            double z=getDoubleParam("--operation",3);
            axis=vectorR3(x,y,z);
            alignWithZ(axis, A3D);
        }
        else if (operation=="rotate_axis")
        {
            Axis_mode = true;
            double x=getDoubleParam("--operation",1);
            double y=getDoubleParam("--operation",2);
            double z=getDoubleParam("--operation",3);
            ang=getDoubleParam("--operation",4);
            axis=vectorR3(x,y,z);
            rotation3DMatrix(ang, axis, A3D);
        }

        // Apply shift
        A3D(0, 3) = XX(shift);
        A3D(1, 3) = YY(shift);
        A3D(2, 3) = ZZ(shift);

        // Apply scale
        A3D(0, 0) *= XX(scale);
        A3D(0, 1) *= YY(scale);
        A3D(0, 2) *= ZZ(scale);
        A3D(1, 0) *= XX(scale);
        A3D(1, 1) *= YY(scale);
        A3D(1, 2) *= ZZ(scale);
        A3D(2, 0) *= XX(scale);
        A3D(2, 1) *= YY(scale);
        A3D(2, 2) *= ZZ(scale);
    }

run()

void Phantom_transform_parameters::run ( )

inlinevirtual

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

Reimplemented from XmippProgram.

Definition at line 161 of file phantom_transform.cpp.

    {
        show();
        if (PDBmode)
            applyGeometryToPDBFile(fn_in, fn_out, A3D, centerPDB);
        else
        {
            Phantom P;
            P.read(fn_in, false); // Read phantom without applying scale
            P.selfApplyGeometry(A3D, xmipp_transformation::IS_NOT_INV);
            P.write(fn_out);
        }
    }

show()

void Phantom_transform_parameters::show ( )

inline

Definition at line 140 of file phantom_transform.cpp.

    {
        if (verbose==0)
            return;
        std::cout << "Input file : " << fn_in  << std::endl
        << "Output file: " << fn_out << std::endl;
        if (PDBmode)
            std::cout << "Input file is PDB\n";
        if (centerPDB)
            std::cout << "Centering PDB\n";
        if (Euler_mode)
            std::cout << "Euler angles (rot, tilt, psi): " << rot << " " << tilt
            << " " << psi << std::endl;
        else if (Align_mode)
            std::cout << "Aligning " << axis.transpose() << " with Z\n";
        else if (Axis_mode)
            std::cout << "Rotating " << ang << " degrees around "
            << axis.transpose() << std::endl;
        std::cout << "Transformation matrix\n" << A3D << std::endl;
    }

Member Data Documentation

A3D

Matrix2D<double> Phantom_transform_parameters::A3D

Definition at line 45 of file phantom_transform.cpp.

Align_mode

bool Phantom_transform_parameters::Align_mode

Definition at line 38 of file phantom_transform.cpp.

ang

double Phantom_transform_parameters::ang

Definition at line 41 of file phantom_transform.cpp.

axis

Matrix1D<double> Phantom_transform_parameters::axis

Definition at line 40 of file phantom_transform.cpp.

Axis_mode

bool Phantom_transform_parameters::Axis_mode

Definition at line 39 of file phantom_transform.cpp.

centerPDB

bool Phantom_transform_parameters::centerPDB

Definition at line 36 of file phantom_transform.cpp.

Euler_mode

bool Phantom_transform_parameters::Euler_mode

Definition at line 36 of file phantom_transform.cpp.

fn_in

FileName Phantom_transform_parameters::fn_in

Definition at line 35 of file phantom_transform.cpp.

fn_out

FileName Phantom_transform_parameters::fn_out

Definition at line 35 of file phantom_transform.cpp.

PDBmode

bool Phantom_transform_parameters::PDBmode

Definition at line 36 of file phantom_transform.cpp.

psi

double Phantom_transform_parameters::psi

Definition at line 37 of file phantom_transform.cpp.

rot

double Phantom_transform_parameters::rot

Definition at line 37 of file phantom_transform.cpp.

scale

Matrix1D<double> Phantom_transform_parameters::scale

Definition at line 43 of file phantom_transform.cpp.

shift

Matrix1D<double> Phantom_transform_parameters::shift

Definition at line 42 of file phantom_transform.cpp.

tilt

double Phantom_transform_parameters::tilt

Definition at line 37 of file phantom_transform.cpp.

---

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

• xmipp/libraries/reconstruction/phantom_transform.cpp