#include <mpi_reconstruct_significant.h>

Inheritance diagram for MpiProgReconstructSignificant:

Collaboration diagram for MpiProgReconstructSignificant:

Public Member Functions
	MpiProgReconstructSignificant ()=default

	MpiProgReconstructSignificant (const MpiProgReconstructSignificant &)=delete

	MpiProgReconstructSignificant (const MpiProgReconstructSignificant &&)=delete

	~MpiProgReconstructSignificant ()

MpiProgReconstructSignificant &	operator= (const MpiProgReconstructSignificant &)=delete

MpiProgReconstructSignificant &	operator= (const MpiProgReconstructSignificant &&)=delete

void	read (int argc, char **argv)

void	synchronize ()
	Synchronize with other processors. More...

void	gatherAlignment ()
	Gather alignment. More...

Public Member Functions inherited from ProgReconstructSignificant
	ProgReconstructSignificant ()
	Empty constructor. More...

virtual void	readParams ()
	Read arguments from command line. More...

void	defineParams ()
	Read arguments from command line. More...

void	show ()

void	run ()

void	produceSideinfo ()
	Produce side info: fill arrays with relevant transformation matrices. More...

void	reconstructCurrent ()
	Reconstruct current volume. More...

void	generateProjections ()
	Generate projections from the current volume. More...

void	numberOfProjections ()

void	alignImagesToGallery ()
	Align images to gallery projections. 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
MpiNode *	node =nullptr

Public Attributes inherited from ProgReconstructSignificant
FileName	fnIn

FileName	fnDir

FileName	fnSym

FileName	fnInit

FileName	fnFirstGallery

double	alpha0

double	alphaF

double	deltaAlpha2

int	Niter

bool	keepIntermediateVolumes

double	angularSampling

double	maxShift

double	tilt0

double	tiltF

bool	useImed

bool	strict

double	angDistance

int	Nvolumes

bool	applyFisher

bool	doReconstruct

bool	useForValidation

size_t	numOrientationsPerParticle

bool	dontCheckMirrors

size_t	rank

size_t	Nprocessors

MetaDataDb	mdIn

size_t	Xdim

std::vector< MetaDataDb >	mdReconstructionPartial

std::vector< MetaDataDb >	mdReconstructionProjectionMatching

MultidimArray< double >	cc

MultidimArray< double >	weight

std::vector< std::vector< GalleryImage > >	mdGallery

std::vector< Image< double > >	gallery

std::vector< AlignmentTransforms *>	galleryTransforms

int	iter

double	currentAlpha

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

Significant reconstruction parameters.

Definition at line 37 of file mpi_reconstruct_significant.h.

Constructor & Destructor Documentation

◆ MpiProgReconstructSignificant() [1/3]

MpiProgReconstructSignificant::MpiProgReconstructSignificant ( )

default

◆ MpiProgReconstructSignificant() [2/3]

MpiProgReconstructSignificant::MpiProgReconstructSignificant ( const MpiProgReconstructSignificant & )

delete

◆ MpiProgReconstructSignificant() [3/3]

MpiProgReconstructSignificant::MpiProgReconstructSignificant ( const MpiProgReconstructSignificant && )

delete

◆ ~MpiProgReconstructSignificant()

MpiProgReconstructSignificant::~MpiProgReconstructSignificant ( )

Definition at line 28 of file mpi_reconstruct_significant.cpp.

 {
     delete node;
 }

Member Function Documentation

◆ gatherAlignment()

void MpiProgReconstructSignificant::gatherAlignment ( )

virtual

Gather alignment.

Reimplemented from ProgReconstructSignificant.

Definition at line 47 of file mpi_reconstruct_significant.cpp.

 {
     // Share weights and cc volumes
     MultidimArray<double> aux;
     if (rank==0)
         aux.resizeNoCopy(cc);
     xmipp_MPI_Reduce(MULTIDIM_ARRAY(weight), MULTIDIM_ARRAY(aux), MULTIDIM_SIZE(weight), MPI_DOUBLE, MPI_MAX, 0, MPI_COMM_WORLD);
     if (rank==0)
         weight=aux;
     xmipp_MPI_Reduce(MULTIDIM_ARRAY(cc), MULTIDIM_ARRAY(aux), MULTIDIM_SIZE(cc), MPI_DOUBLE, MPI_MAX, 0, MPI_COMM_WORLD);
     if (rank==0)
         cc=aux;
 
     // Write all metadatas
     if (rank!=0)
         for (size_t n=0; n<mdReconstructionPartial.size(); ++n)
         {
             FileName fnPartial=formatString("%s/partial_node%03d_%03d.xmd",fnDir.c_str(),(int)rank,(int)n);
             FileName fnProjectionMatching=formatString("%s/projmatch_node%03d_%03d.xmd",fnDir.c_str(),(int)rank,(int)n);
 
             if (mdReconstructionPartial[n].size()>0)
                 mdReconstructionPartial[n].write(fnPartial);
             if (mdReconstructionProjectionMatching[n].size()>0)
                 mdReconstructionProjectionMatching[n].write(fnProjectionMatching);
         }
     synchronize();
 
     // Now the master takes all of them
     if (rank==0)
     {
         MetaDataDb MDAux;
         for (size_t otherRank=1; otherRank<Nprocessors; ++otherRank)
         {
             for (size_t n=0; n<mdReconstructionPartial.size(); ++n)
             {
                 FileName fnPartial=formatString("%s/partial_node%03d_%03d.xmd",fnDir.c_str(),(int)otherRank,(int)n);
                 FileName fnProjectionMatching=formatString("%s/projmatch_node%03d_%03d.xmd",fnDir.c_str(),(int)otherRank,(int)n);
 
                 if (fnPartial.exists())
                 {
                     MDAux.read(fnPartial);
                     mdReconstructionPartial[n].unionAll(MDAux);
                     deleteFile(fnPartial);
                 }
                 if (fnProjectionMatching.exists())
                 {
                     MDAux.read(fnProjectionMatching);
                     mdReconstructionProjectionMatching[n].unionAll(MDAux);
                     deleteFile(fnProjectionMatching);
                 }
             }
         }
     }
 
     // std::cout << "synchronize" << std::endl;
     synchronize();
 
 }

◆ operator=() [1/2]

MpiProgReconstructSignificant& MpiProgReconstructSignificant::operator= ( const MpiProgReconstructSignificant & )

delete

◆ operator=() [2/2]

MpiProgReconstructSignificant& MpiProgReconstructSignificant::operator= ( const MpiProgReconstructSignificant && )

delete

◆ read()

void MpiProgReconstructSignificant::read	(	int	argc,
		char **	argv
	)

Definition at line 33 of file mpi_reconstruct_significant.cpp.

 {
     node = new MpiNode(argc, argv);
     rank = node->rank;
     Nprocessors = node->size;
 
     ProgReconstructSignificant::read(argc, (const char **)argv);
 }