#include <angular_neighbourhood.h>

Inheritance diagram for ProgAngularNeighbourhood:

Collaboration diagram for ProgAngularNeighbourhood:

Public Member Functions
void	readParams ()
	Read argument from command line. More...

void	show ()
	Show. More...

void	defineParams ()
	Usage. More...

double	check_symmetries (double rot1, double tilt1, double &rot2, double &tilt2)

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_ref

FileName	fn_sel

double	maxdist

FileName	fn_sym

FileName	fn_out

bool	check_mirrors

MetaDataVec	DF1

MetaDataVec	DF2

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

Projection Neighbourhood parameters.

Definition at line 38 of file angular_neighbourhood.h.

Member Function Documentation

◆ check_symmetries()

double ProgAngularNeighbourhood::check_symmetries	(	double	rot1,
		double	tilt1,
		double &	rot2,
		double &	tilt2
	)

Check symmetries. Given two sets of angles, this function modifies set 2 so that the difference with set 1 are minimized searching in the symmetry list and the second set. Return the angle distance.

◆ defineParams()

void ProgAngularNeighbourhood::defineParams ( )

virtual

Usage.

Reimplemented from XmippProgram.

Definition at line 60 of file angular_neighbourhood.cpp.

 {
     addUsageLine("Computes the images in Metadata1 that are within the neighbourhood of");
     addUsageLine("images in Metadata2. ");
     addParamsLine("   --i1 <metadata>         : Metadata1 with images and their angles");
     addParamsLine("   --i2 <metadata>         : Metadata2 with images and their angles");
     addParamsLine("   -o <metadata>           : Output metadata ");
     addParamsLine("                           :+For each image in Metadata2, there is a block ");
     addParamsLine("                           :+in the output metadata corresponding to all ");
     addParamsLine("                           :+images in Metadata1 within its neighbourhood.");
     addParamsLine("  [--dist  <d=10>        ] : Maximum neighbourhood distance ");
     addParamsLine("  [--sym <symmetry=\"\"> ] : Symmetry description if any");
     addParamsLine("                             :+The definition of the symmetry is described at [[transform_symmetrize_v3][transform_symmetrize]]");
     addParamsLine("  [--check_mirrors]        : Check mirrors");
     addSeeAlsoLine("angular_distance");
 }

◆ readParams()

void ProgAngularNeighbourhood::readParams ( )

virtual

Read argument from command line.

Reimplemented from XmippProgram.

Definition at line 33 of file angular_neighbourhood.cpp.

 {
     fn_sel = getParam("--i1");
     fn_ref = getParam("--i2");
     fn_out = getParam("-o");
     maxdist = getDoubleParam("--dist");
     fn_sym = getParam("--sym");
     if (fn_sym != "")
         SL.readSymmetryFile(fn_sym);
     check_mirrors=checkParam("--check_mirrors");
     DF2.read(fn_ref);
     DF1.read(fn_sel);
 }

◆ run()

void ProgAngularNeighbourhood::run ( )

virtual

Compute distance. Compute the distance between the two document files loaded. The average distance is returned.

Reimplemented from XmippProgram.

Definition at line 78 of file angular_neighbourhood.cpp.

 {
     show();
     fn_out.deleteFile();
     MetaDataVec SF_out;
     FileName fn2, fn1, fnAux;
 
     std::cerr << "Calculating ...\n";
     for (size_t objId : DF2.ids())
     {
         // Read reference projection direction
         double rot2, tilt2;
         DF2.getValue(MDL_IMAGE,fn2,objId);
         DF2.getValue(MDL_ANGLE_ROT,rot2,objId);
         DF2.getValue(MDL_ANGLE_TILT,tilt2,objId);
         for (size_t objId2 : DF1.ids())
         {
             // Read assigned angles from document file
             double rot1, tilt1, psi1;
             DF1.getValue(MDL_ANGLE_ROT,rot1,objId2);
             DF1.getValue(MDL_ANGLE_TILT,tilt1,objId2);
             DF1.getValue(MDL_ANGLE_PSI,psi1,objId2);
             double dist = SL.computeDistance(rot2, tilt2, 0., rot1, tilt1, psi1,
                                              true, check_mirrors, false, false);
             if (dist <= maxdist)
             {
                 MDRowVec row;
                 DF1.getRow(row, objId2);
                 
                 // Use the symmetry closest to the projection angle
                 // which is provided by computeDistance
                 row.setValue(MDL_ANGLE_ROT, rot1);
                 row.setValue(MDL_ANGLE_TILT, tilt1);
                 row.setValue(MDL_ANGLE_PSI, psi1);
 
                 SF_out.addRow(row);
             }
         }
 
         // finished reading all particles for this neighbourhood
         fnAux=fn2.replaceCharacter('/','_');
         fnAux=fnAux.replaceCharacter('@','_');
         fnAux=fnAux.replaceCharacter('.','_');
         SF_out.write((String)"neighbourhoodOf_"+fnAux.c_str()+"@"+fn_out,MD_APPEND);
         SF_out.clear();
     }
 }

◆ show()

void ProgAngularNeighbourhood::show ( )

Show.

Definition at line 48 of file angular_neighbourhood.cpp.

 {
     std::cerr
     << "Selfile                      : " << fn_sel  << std::endl
     << "Neighbourhoods docfile       : " << fn_ref  << std::endl
     << "Output root                  : " << fn_out  << std::endl
     << "Max. neighbour distance      : " << maxdist << std::endl
     << "Symmetry file                : " << fn_sym  << std::endl
     ;
 }

Member Data Documentation

◆ check_mirrors

bool ProgAngularNeighbourhood::check_mirrors

Check mirrors

Definition at line 52 of file angular_neighbourhood.h.

◆ DF1

MetaDataVec ProgAngularNeighbourhood::DF1

Definition at line 55 of file angular_neighbourhood.h.

◆ DF2

MetaDataVec ProgAngularNeighbourhood::DF2

Definition at line 57 of file angular_neighbourhood.h.

◆ fn_out

FileName ProgAngularNeighbourhood::fn_out

Filename of output file

Definition at line 50 of file angular_neighbourhood.h.

◆ fn_ref

FileName ProgAngularNeighbourhood::fn_ref

Filename reference projection directions document file

Definition at line 42 of file angular_neighbourhood.h.

◆ fn_sel

FileName ProgAngularNeighbourhood::fn_sel

Filename selection file containing the images

Definition at line 44 of file angular_neighbourhood.h.

◆ fn_sym

FileName ProgAngularNeighbourhood::fn_sym

Filename symmetry file

Definition at line 48 of file angular_neighbourhood.h.

◆ maxdist

double ProgAngularNeighbourhood::maxdist

Double maximum neighbour distance

Definition at line 46 of file angular_neighbourhood.h.

◆ SL

SymList ProgAngularNeighbourhood::SL

Definition at line 59 of file angular_neighbourhood.h.

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

xmipp/libraries/reconstruction/angular_neighbourhood.h
xmipp/libraries/reconstruction/angular_neighbourhood.cpp

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ check_symmetries()

◆ defineParams()

◆ readParams()

◆ run()

◆ show()

Member Data Documentation

◆ check_mirrors

◆ DF1

◆ DF2

◆ fn_out

◆ fn_ref

◆ fn_sel

◆ fn_sym

◆ maxdist

◆ SL