ProgTomoMapBack Class Reference

#include <tomo_map_back.h>

Inheritance diagram for ProgTomoMapBack:

Collaboration diagram for ProgTomoMapBack:

Public Member Functions
void	readParams ()
	Read arguments. More...
void	show () const
	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	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_tomo
	Input. More...
FileName	fn_geom
FileName	fn_ref
FileName	fn_out
String	modeStr
Image< double >	tomo
Image< double >	reference
MetaDataVec	mdGeom
int	mode
double	K
double	threshold
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

Map back parameters.

Definition at line 36 of file tomo_map_back.h.

Member Function Documentation

defineParams()

void ProgTomoMapBack::defineParams ( )

virtual

Define parameters.

Reimplemented from XmippProgram.

Definition at line 61 of file tomo_map_back.cpp.

{
    addUsageLine("This program takes a tomogram, a reference subtomogram and a metadata with geometrical parameters");
    addUsageLine("(x,y,z) and places the reference subtomogram on the tomogram at the designated locations (map back).");
    addUsageLine("The program has several 'painting' options:");
    addUsageLine("   1. Copying the reference onto the tomogram");
    addUsageLine("   2. Setting the region occupied by the reference in the tomogram to the average value of that region");
    addUsageLine("   3. Add the reference multiplied by a constant to the location specified");
    addUsageLine("   4. Copy a binarized version of the reference onto the tomogram");
    addParamsLine("   -i <tomogram>           : Original tomogram");
    addParamsLine("  [-o <tomogram=\"\">]     : Output tomogram mapped back");
    addParamsLine("   --geom <geometry>       : Subtomograms coordinates and rotation angles (it must be a metadata)");
    addParamsLine("   --ref <reference>       : Subtomogram reference");
    addParamsLine("  [--method <mode=copy>]   : Painting mode");
    addParamsLine("     where <mode>");
    addParamsLine("        copy");
    addParamsLine("        avg <threshold=0.5>");
    addParamsLine("        highlight <K=1>");
    addParamsLine("        copy_binary <threshold=0.5>");
}

produce_side_info()

void ProgTomoMapBack::produce_side_info

(

)

Produce side info.

Definition at line 83 of file tomo_map_back.cpp.

{
    tomo.read(fn_tomo);
    mdGeom.read(fn_geom);
    reference.read(fn_ref);
    reference().setXmippOrigin();
    const MultidimArray<double> &mReference=reference();

    if (modeStr=="copy")
        mode=1;
    else if (modeStr=="avg")
        mode=2;
    else if (modeStr=="highlight")
        mode=3;
    else if (modeStr=="copy_binary")
        mode=4;

    if (mode==4 || mode==2)
    {
        FOR_ALL_ELEMENTS_IN_ARRAY3D(mReference)
            A3D_ELEM(mReference,k,i,j)=(A3D_ELEM(mReference,k,i,j)>threshold) ? 1:0;
    }
}

readParams()

void ProgTomoMapBack::readParams ( )

virtual

Read arguments.

Reimplemented from XmippProgram.

Definition at line 30 of file tomo_map_back.cpp.

{

    fn_tomo = getParam("-i");
    fn_geom = getParam("--geom");
    fn_ref = getParam("--ref");
    fn_out = getParam("-o");
    if (fn_out=="")
        fn_out=fn_tomo;
    modeStr = getParam("--method");
    if (modeStr=="highlight")
        K=getDoubleParam("--method",1);
    if (modeStr=="avg" || modeStr=="copy_binary")
        threshold=getDoubleParam("--method",1);
}

run()

void ProgTomoMapBack::run ( )

virtual

Run

Reimplemented from XmippProgram.

Definition at line 118 of file tomo_map_back.cpp.

{
    show();
    produce_side_info();
    int x,y,z;
    const MultidimArray<double> &mReference=reference();
    MultidimArray<double> &mTomo=tomo();
    MultidimArray<double> referenceRotated;
    Matrix2D<double> A;
    A.initIdentity(4);

    for (const auto& row : mdGeom)
    {
        row.getValue(MDL_XCOOR,x);
        row.getValue(MDL_YCOOR,y);
        row.getValue(MDL_ZCOOR,z);
        geo2TransformationMatrix(row,A);
        applyGeometry(xmipp_transformation::LINEAR, referenceRotated, mReference, A, xmipp_transformation::IS_NOT_INV, xmipp_transformation::DONT_WRAP);

        double avg=0, avgN=0;
        if (mode==2)
        {
            FOR_ALL_ELEMENTS_IN_ARRAY3D(referenceRotated)
            {
                GET_TOMO_COORD
                avg+=DIRECT_A3D_ELEM(mTomo,zp,yp,xp);
                avgN+=1;
            }
            if (avgN>0)
                avg/=avgN;
        }

        FOR_ALL_ELEMENTS_IN_ARRAY3D(referenceRotated)
        {
            GET_TOMO_COORD
            double val=A3D_ELEM(referenceRotated,k,i,j);
            switch (mode)
            {
            case 1:
            case 4:
                DIRECT_A3D_ELEM(mTomo,zp,yp,xp)=val;
                break;
            case 2:
                if (val>0)
                    DIRECT_A3D_ELEM(mTomo,zp,yp,xp)=avg;
                break;
            case 3:
                DIRECT_A3D_ELEM(mTomo,zp,yp,xp)+=K*val;
                break;
            }
        }
    }

    tomo.write(fn_out);
}

show()

void ProgTomoMapBack::show ( ) const

virtual

Show.

Reimplemented from XmippProgram.

Definition at line 47 of file tomo_map_back.cpp.

{
    if (verbose>0)
    {
        std::cout
        << "Input tomogram    : " << fn_tomo    << std::endl
        << "Input geometry    : " << fn_geom    << std::endl
        << "Input reference   : " << fn_ref     << std::endl
        << "Painting mode     : " << modeStr    << std::endl
        ;
    }
}

Member Data Documentation

fn_geom

FileName ProgTomoMapBack::fn_geom

Definition at line 40 of file tomo_map_back.h.

fn_out

FileName ProgTomoMapBack::fn_out

Definition at line 40 of file tomo_map_back.h.

fn_ref

FileName ProgTomoMapBack::fn_ref

Definition at line 40 of file tomo_map_back.h.

fn_tomo

FileName ProgTomoMapBack::fn_tomo

Input.

Definition at line 40 of file tomo_map_back.h.

K

double ProgTomoMapBack::K

Definition at line 48 of file tomo_map_back.h.

mdGeom

MetaDataVec ProgTomoMapBack::mdGeom

Definition at line 46 of file tomo_map_back.h.

mode

int ProgTomoMapBack::mode

Definition at line 47 of file tomo_map_back.h.

modeStr

String ProgTomoMapBack::modeStr

Definition at line 41 of file tomo_map_back.h.

reference

Image<double> ProgTomoMapBack::reference

Definition at line 45 of file tomo_map_back.h.

threshold

double ProgTomoMapBack::threshold

Definition at line 49 of file tomo_map_back.h.

tomo

Image<double> ProgTomoMapBack::tomo

Definition at line 45 of file tomo_map_back.h.

---

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

• xmipp/libraries/tomo/tomo_map_back.h
• xmipp/libraries/tomo/tomo_map_back.cpp