ProgMPIRecWbp Class Reference

#include <mpi_reconstruct_wbp.h>

Inheritance diagram for ProgMPIRecWbp:

Collaboration diagram for ProgMPIRecWbp:

Public Member Functions
	ProgMPIRecWbp (int argc, char **argv)
	ProgMPIRecWbp (const std::shared_ptr< MpiNode > &node)
void	defineParams ()
void	readParams ()
void	read (int argc, char **argv)
void	produceSideInfo ()
	Fill arrays with relevant transformation matrices. More...
void	showProgress ()
bool	getImageToProcess (size_t &objId) override
	Get 1 image to process. More...
void	finishProcessing ()
Public Member Functions inherited from ProgRecWbp
void	readParams ()
	Read arguments from command line. More...
void	show ()
	Show. More...
void	defineParams ()
	Define parameters. More...
void	run ()
void	setIO (const FileName &fn_in, const FileName &fn_out)
void	getAnglesForImage (size_t id, double &rot, double &tilt, double &psi, double &xoff, double &yoff, bool &flip, double &weight)
	Get angles (either from reading the header or from a docfile) More...
void	getAllMatrices (MetaData &SF)
	Fill array with transformation matrices needed for arbitrary geometry filter. More...
void	getSampledMatrices (MetaData &SF)
void	simpleBackprojection (Projection &img, MultidimArray< double > &vol, int diameter)
void	filterOneImage (Projection &proj, Tabsinc &TSINC)
void	apply2DFilterArbitraryGeometry ()
Public Member Functions inherited from ProgReconsBase
virtual	~ProgReconsBase ()
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
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 Member Functions inherited from MpiMetadataProgram
	MpiMetadataProgram ()
	MpiMetadataProgram (const MpiMetadataProgram &)=delete
	MpiMetadataProgram (const MpiMetadataProgram &&)=delete
	~MpiMetadataProgram ()
MpiMetadataProgram &	operator= (const MpiMetadataProgram &)=delete
MpiMetadataProgram &	operator= (const MpiMetadataProgram &&)=delete
void	read (int argc, char **argv)
void	defineParams ()
void	readParams ()
void	createTaskDistributor (MetaData &mdIn, size_t blockSize=0)
virtual void	preProcess ()
bool	getTaskToProcess (size_t &objId, size_t &objIndex)
Public Member Functions inherited from XmippMpiProgram
void	read (int argc, char **argv)
virtual int	tryRun ()

Additional Inherited Members
Public Attributes inherited from ProgRecWbp
FileName	fn_out
FileName	fn_sym
FileName	fn_sel
MetaDataVec	SF
double	threshold
int	count_thr
int	diameter
size_t	dim
int	no_mats
WBPInfo *	mat_g
WBPInfo *	mat_f
double	sampling
bool	do_all_matrices
bool	do_weights
SymList	SL
size_t	time_bar_step
	Time bar variables. More...
size_t	time_bar_size
size_t	time_bar_done
std::unique_ptr< MetaDataVec::id_iterator >	iter
	Iterator over input metadata. More...
Image< double >	reconstructedVolume
	Reconstructed volume. More...
Public Attributes inherited from XmippProgram
bool	doRun
bool	runWithoutArgs
int	verbose
	Verbosity level. More...
int	debug
Protected Member Functions inherited from XmippProgram
void	defineCommons ()
Protected Member Functions inherited from XmippMpiProgram
void	setNode (const std::shared_ptr< MpiNode > &node)
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
Protected Attributes inherited from MpiMetadataProgram
int	blockSize
std::vector< size_t >	imgsId
MpiTaskDistributor *	distributor =nullptr
size_t	first
size_t	last
Protected Attributes inherited from XmippMpiProgram
std::shared_ptr< MpiNode >	node
size_t	nProcs
size_t	numberOfJobs
MPI_Status	status

Detailed Description

Definition at line 36 of file mpi_reconstruct_wbp.h.

Constructor & Destructor Documentation

ProgMPIRecWbp() [1/2]

ProgMPIRecWbp::ProgMPIRecWbp	(	int	argc,
		char **	argv
	)

Definition at line 28 of file mpi_reconstruct_wbp.cpp.

{
    this->read(argc, argv);
}

ProgMPIRecWbp() [2/2]

ProgMPIRecWbp::ProgMPIRecWbp

(

const std::shared_ptr< MpiNode > &

node

)

Definition at line 32 of file mpi_reconstruct_wbp.cpp.

{
    this->setNode(node);
}

Member Function Documentation

defineParams()

void ProgMPIRecWbp::defineParams ( )

virtual

Function in which the param of each Program are defined.

Reimplemented from XmippProgram.

Definition at line 36 of file mpi_reconstruct_wbp.cpp.

{
    ProgRecWbp::defineParams();
    MpiMetadataProgram::defineParams();
}

finishProcessing()

void ProgMPIRecWbp::finishProcessing ( )

virtual

finishProcessing

Reimplemented from MpiMetadataProgram.

Definition at line 69 of file mpi_reconstruct_wbp.cpp.

{
    MultidimArray<double> aux;
    aux.resizeNoCopy(reconstructedVolume());
    MPI_Allreduce(MULTIDIM_ARRAY(reconstructedVolume()), MULTIDIM_ARRAY(aux),
                  MULTIDIM_SIZE(aux), MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
    int iaux;
    MPI_Allreduce(&count_thr, &iaux, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);

    if (node->isMaster())
    {
        reconstructedVolume()=aux;
        count_thr=iaux;
        ProgRecWbp::finishProcessing();
    }
}

getImageToProcess()

bool ProgMPIRecWbp::getImageToProcess ( size_t &  objId )

overridevirtual

Get 1 image to process.

Reimplemented from ProgRecWbp.

Definition at line 64 of file mpi_reconstruct_wbp.cpp.

{
    size_t tmp;
    return getTaskToProcess(objId, tmp);
}

produceSideInfo()

void ProgMPIRecWbp::produceSideInfo ( )

virtual

Fill arrays with relevant transformation matrices.

Reimplemented from ProgRecWbp.

Definition at line 51 of file mpi_reconstruct_wbp.cpp.

{
    ProgRecWbp::produceSideInfo();
    createTaskDistributor(SF);
}

read()

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

Definition at line 46 of file mpi_reconstruct_wbp.cpp.

{
    MpiMetadataProgram::read(argc,argv);
    ProgRecWbp::read(argc, (const char **)argv);
}

readParams()

void ProgMPIRecWbp::readParams ( )

virtual

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 41 of file mpi_reconstruct_wbp.cpp.

{
    MpiMetadataProgram::readParams();
    ProgRecWbp::readParams();
}

showProgress()

void ProgMPIRecWbp::showProgress ( )

virtual

Show progress

Reimplemented from ProgRecWbp.

Definition at line 56 of file mpi_reconstruct_wbp.cpp.

{
    if ( verbose > 0 )
    {
        time_bar_done=first+1;
        progress_bar(time_bar_done);
    }
}

---

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

• xmipp/libraries/parallel/mpi_reconstruct_wbp.h
• xmipp/libraries/parallel/mpi_reconstruct_wbp.cpp