#include <mpi_ml_align2d.h>

Inheritance diagram for MpiProgML2D:

Collaboration diagram for MpiProgML2D:

Public Member Functions
	MpiProgML2D ()

	MpiProgML2D (MpiNode *node)

void	setNumberOfLocalImages ()

void	produceSideInfo2 ()

void	writeOutputFiles (const ModelML2D &model, OutputType outputType=OUT_FINAL)
	Write model parameters. More...

void	expectation ()
	After normal ML2D expectation, data must be collected from nodes. More...

void	endIteration ()
	Redefine endIteration for some synchronization. More...

void	printModel (const String &msg, const ModelML2D &model)

virtual void	usage (int verb=0) const

Public Member Functions inherited from ProgML2D
void	readParams ()
	Read arguments from command line. More...

void	defineParams ()
	Params definition. More...

	ProgML2D ()

virtual void	show ()
	Show info at starting program. More...

virtual void	produceSideInfo ()
	Try to merge produceSideInfo1 and 2. More...

void	calculatePdfInplane ()
	Calculate probability density distribution for in-plane transformations. More...

void	rotateReference ()
	Fill vector of matrices with all rotations of reference. More...

void	reverseRotateReference ()
	Apply reverse rotations to all matrices in vector and fill new matrix with their sum. More...

void	preselectLimitedDirections (double &phi, double &theta)

void	preselectFastSignificant ()

void	expectationSingleImage (Matrix1D< double > &opt_offsets)
	ML-integration over all (or -fast) translations. More...

void	createThreads ()
	Create working threads. More...

void	destroyThreads ()
	Exit threads and free memory. More...

int	getThreadRefnoJob (int &refno)
	Assign refno jobs to threads. More...

void	awakeThreads (ThreadTask task, int start_refno, int load=1)
	Awake threads for different tasks. More...

void	doThreadRotateReferenceRefno ()
	Thread code to parallelize refno loop in rotateReference. More...

void	doThreadReverseRotateReferenceRefno ()
	Thread code to parallelize refno loop in reverseRotateReference. More...

void	doThreadPreselectFastSignificantRefno ()
	Thread code to parallelize refno loop in preselectFastSignificant. More...

void	doThreadExpectationSingleImageRefno ()
	Thread code to parallelize refno loop in expectationSingleImage. More...

void	doThreadESIUpdateRefno ()
	Thread code to parallelize update loop in ESI. More...

virtual void	iteration ()
	Perform an iteration. More...

void	maximizeModel (ModelML2D &model)
	Update all model parameters. More...

virtual void	maximization ()
	Update all model parameters, adapted for IEM blocks use. More...

void	correctScaleAverage ()
	Correct references scale. More...

virtual void	addPartialDocfileData (const MultidimArray< double > &data, size_t first, size_t last)
	Add docfiledata to docfile. More...

virtual void	readModel (ModelML2D &model, int block)
	Read model from file. More...

FileName	getBaseName (String suffix="", int number=-1)
	Get base name based on fn_root and some number. More...

Public Member Functions inherited from ML2DBaseProgram
void	initSamplingStuff ()

	ML2DBaseProgram ()

virtual void	randomizeImagesOrder ()
	Randomize initial images order, only once. More...

virtual bool	checkConvergence ()

virtual void	run ()
	Main function of the program. More...

virtual void	defineBasicParams (XmippProgram *prog)

virtual void	defineAdditionalParams (XmippProgram prog, const char sectionLine)

virtual void	defineHiddenParams (XmippProgram *prog)

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 (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 MpiML2DBase< MpiProgML2D >
void	readMpi (int argc, char **argv)

	MpiML2DBase (MpiProgML2D *prm)

	MpiML2DBase (MpiProgML2D prm, MpiNode node)

	MpiML2DBase (const MpiML2DBase &)=delete

	MpiML2DBase (const MpiML2DBase &&)=delete

	~MpiML2DBase ()

MpiML2DBase &	operator= (const MpiML2DBase &)=delete

MpiML2DBase &	operator= (const MpiML2DBase &&)=delete

void	sendDocfile (const MultidimArray< double > &data)

Additional Inherited Members
Public Attributes inherited from ProgML2D
bool	no_iem

MultidimArray< int >	mask

MultidimArray< int >	omask

int	threadTask

barrier_t	barrier

barrier_t	barrier2

barrier_t	barrier3

pthread_t *	th_ids

structThreadTasks *	threads_d

double	LL

double	sumfracweight

double	wsum_sigma_noise

double	wsum_sigma_offset

double	sumw_allrefs

std::vector< double >	sumw

std::vector< double >	sumw2

std::vector< double >	sumwsc

std::vector< double >	sumwsc2

std::vector< double >	sumw_mirror

std::vector< MultidimArray< double > >	wsum_Mref

MultidimArray< int >	Msignificant

MultidimArray< double >	Mimg

std::vector< double >	allref_offsets

std::vector< double >	pdf_directions

std::vector< MultidimArray< double > >	mref

std::vector< MultidimArray< std::complex< double > > >	fref

std::vector< MultidimArray< std::complex< double > > >	wsumimgs

int	opt_refno

int	iopt_psi

int	iopt_flip

double	trymindiff

double	opt_scale

double	bgmean

double	opt_psi

double	fracweight

double	maxweight2

double	dLL

std::vector< MultidimArray< std::complex< double > > >	Fimg_flip

std::vector< MultidimArray< std::complex< double > > >	mysumimgs

std::vector< double >	refw

std::vector< double >	refw2

std::vector< double >	refwsc2

std::vector< double >	refw_mirror

std::vector< double >	sumw_refpsi

double	wsum_corr

double	sum_refw

double	sum_refw2

double	maxweight

double	wsum_sc

double	wsum_sc2

double	wsum_offset

double	old_bgmean

double	mindiff

size_t	sigdim

int	ioptx

int	iopty

std::vector< int >	ioptx_ref

std::vector< int >	iopty_ref

std::vector< int >	ioptflip_ref

double	pfs_mindiff

MultidimArray< double >	pfs_maxweight

MultidimArray< double >	pfs_weight

int	pfs_count

std::vector< double >	A2

double	Xi2

size_t	refno_index

size_t	refno_load_param

int	refno_load

int	refno_count

int	mygroup

Public Attributes inherited from ML2DBaseProgram
FileName	fn_img

FileName	fn_ref

FileName	fn_root

FileName	fn_frac

FileName	fn_sig

FileName	fn_doc

FileName	fn_oext

FileName	fn_scratch

FileName	fn_control

String	cline

bool	do_mirror

bool	fix_fractions

bool	fix_sigma_offset

bool	fix_sigma_noise

int	istart

int	iter

int	Niter

size_t	dim

size_t	dim2

size_t	hdim

double	ddim2

size_t	nr_psi

size_t	nr_flip

double	psi_step

double	psi_max

size_t	nr_nomirror_flips

size_t	nr_images_global

size_t	nr_images_local

size_t	myFirstImg

size_t	myLastImg

double	eps

MetaDataDb	MDimg

MetaDataDb	MDref

MetaDataDb	MDlog

std::vector< Matrix2D< double > >	F

std::vector< Image< double > >	Iold

MultidimArray< double >	P_phi

MultidimArray< double >	Mr2

bool	fast_mode

double	C_fast

std::vector< Matrix1D< double > >	Vtrans

bool	zero_offsets

bool	limit_rot

double	search_rot

bool	save_mem1

bool	save_mem2

bool	save_mem3

std::vector< double >	imgs_oldphi

std::vector< double >	imgs_oldtheta

bool	do_ML3D

bool	do_generate_refs

std::vector< std::vector< double > >	imgs_offsets

double	trymindiff_factor

double	df

double	df2

double	dfsigma2

bool	do_norm
	Re-normalize internally. More...

std::vector< double >	imgs_scale

std::vector< double >	imgs_bgmean

std::vector< double >	imgs_trymindiff

std::vector< int >	imgs_optrefno

double	average_scale

int	factor_nref

int	refs_per_class

std::vector< double >	conv

size_t	current_image

ModelML2D	model

ModelML2D *	current_model

size_t	blocks

size_t	current_block

std::vector< size_t >	img_id

MultidimArray< double >	docfiledata

bool	do_restart

bool	referenceExclusive

bool	allowFastOption

bool	allowThreads

bool	allowIEM

bool	allowRestart

String	defaultRoot

int	defaultNiter

int	defaultStartingIter

int	threads

String	outRefsMd

MultidimArray< double >	spectral_signal

int	seed

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 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 MpiML2DBase< MpiProgML2D >
MpiNode *	node

bool	created_node

MpiProgML2D *	program

Detailed Description

Class to parallelize the ML 2D alignment program

Definition at line 94 of file mpi_ml_align2d.h.

Constructor & Destructor Documentation

◆ MpiProgML2D() [1/2]

MpiProgML2D::MpiProgML2D ( )

Default constructor

Definition at line 86 of file mpi_ml_align2d.cpp.

86 :MpiML2DBase(this)

87 {}

MpiML2DBase< MpiProgML2D >::MpiML2DBase

MpiML2DBase(MpiProgML2D *prm)

Definition: mpi_ml_align2d.cpp:34

◆ MpiProgML2D() [2/2]

MpiProgML2D::MpiProgML2D ( MpiNode * node )

Constructor passing the MpiNode

Definition at line 89 of file mpi_ml_align2d.cpp.

89 :MpiML2DBase(this, node)

90 {}

MpiML2DBase< MpiProgML2D >::MpiML2DBase

MpiML2DBase(MpiProgML2D *prm)

Definition: mpi_ml_align2d.cpp:34

Member Function Documentation

◆ endIteration()

void MpiProgML2D::endIteration ( )

virtual

Redefine endIteration for some synchronization.

Reimplemented from ML2DBaseProgram.

Definition at line 155 of file mpi_ml_align2d.cpp.

 {
     // Write output files
     sendDocfile(docfiledata);
     writeOutputFiles(model, OUT_ITER);
 }

◆ expectation()

void MpiProgML2D::expectation ( )

virtual

After normal ML2D expectation, data must be collected from nodes.

Reimplemented from ProgML2D.

Definition at line 108 of file mpi_ml_align2d.cpp.

 {
     MultidimArray<double> Maux;
     double aux;
     Maux.resize(dim, dim);
     Maux.setXmippOrigin();
 
     ProgML2D::expectation();
     //After expectation, collect data from all nodes
     // Here MPI_allreduce of all wsums,LL and sumfracweight !!!
     MPI_Allreduce(&LL, &aux, 1, MPI_DOUBLE, MPI_SUM,
                   MPI_COMM_WORLD);
     LL = aux;
     MPI_Allreduce(&sumfracweight, &aux, 1, MPI_DOUBLE, MPI_SUM,
                   MPI_COMM_WORLD);
     sumfracweight = aux;
     MPI_Allreduce(&wsum_sigma_noise, &aux, 1, MPI_DOUBLE,
                   MPI_SUM, MPI_COMM_WORLD);
     wsum_sigma_noise = aux;
     MPI_Allreduce(&wsum_sigma_offset, &aux, 1, MPI_DOUBLE,
                   MPI_SUM, MPI_COMM_WORLD);
     wsum_sigma_offset = aux;
     for (int refno = 0; refno < model.n_ref * factor_nref; refno++)
     {
         MPI_Allreduce(MULTIDIM_ARRAY(wsum_Mref[refno]),
                       MULTIDIM_ARRAY(Maux),
                       MULTIDIM_SIZE(wsum_Mref[refno]), MPI_DOUBLE,
                       MPI_SUM, MPI_COMM_WORLD);
         wsum_Mref[refno] = Maux;
         MPI_Allreduce(&sumw[refno], &aux, 1, MPI_DOUBLE,
                       MPI_SUM, MPI_COMM_WORLD);
         sumw[refno] = aux;
         MPI_Allreduce(&sumwsc2[refno], &aux, 1, MPI_DOUBLE,
                       MPI_SUM, MPI_COMM_WORLD);
         sumwsc2[refno] = aux;
         MPI_Allreduce(&sumw_mirror[refno], &aux, 1, MPI_DOUBLE,
                       MPI_SUM, MPI_COMM_WORLD);
         sumw_mirror[refno] = aux;
         MPI_Allreduce(&sumw2[refno], &aux, 1, MPI_DOUBLE,
                       MPI_SUM, MPI_COMM_WORLD);
         sumw2[refno] = aux;
         MPI_Allreduce(&sumwsc[refno], &aux, 1, MPI_DOUBLE,
                       MPI_SUM, MPI_COMM_WORLD);
         sumwsc[refno] = aux;
     }
 }//end of expectation

◆ printModel()

void MpiProgML2D::printModel	(	const String &	msg,
		const ModelML2D &	model
	)

virtual

Reimplemented from ProgML2D.

Definition at line 176 of file mpi_ml_align2d.cpp.

 {
     if (node->isMaster())
         ProgML2D::printModel(msg, model);
 }

◆ produceSideInfo2()

void MpiProgML2D::produceSideInfo2 ( )

virtual

All mpi nodes should syncronize at this point that's why the need of override the implementation.

Reimplemented from ProgML2D.

Definition at line 100 of file mpi_ml_align2d.cpp.

 {
     node->barrierWait();
     ProgML2D::produceSideInfo2();
     //Also sync after finishing produceSideInfo2
     node->barrierWait();
 }

◆ setNumberOfLocalImages()

void MpiProgML2D::setNumberOfLocalImages ( )

virtual

Only take a part of images for process

Reimplemented from ML2DBaseProgram.

Definition at line 94 of file mpi_ml_align2d.cpp.

 {
     nr_images_local = divide_equally(nr_images_global, node->size, node->rank, myFirstImg,
                                      myLastImg);
 }

◆ usage()

void MpiProgML2D::usage ( int verb = 0 ) const

virtual

Print the usage of the program, reduced version

Reimplemented from XmippProgram.

Definition at line 182 of file mpi_ml_align2d.cpp.

 {
     if (node->isMaster())
         ProgML2D::usage();
 }

◆ writeOutputFiles()

void MpiProgML2D::writeOutputFiles	(	const ModelML2D &	model,
		OutputType	outputType = `OUT_FINAL`
	)

virtual

Write model parameters.

Reimplemented from ProgML2D.

Definition at line 162 of file mpi_ml_align2d.cpp.

 {
     //All nodes should arrive to writeOutput files at same time
     node->barrierWait();
     //Only master write files
     if (node->isMaster())
         ProgML2D::writeOutputFiles(model, outputType);
     else if (outputType == OUT_REFS)
         outRefsMd = FN_CLASSES_MD(getIterExtraPath(fn_root, iter));
     //All nodes wait until files are written
     node->barrierWait();
 }

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

xmipp/libraries/parallel/mpi_ml_align2d.h
xmipp/libraries/parallel/mpi_ml_align2d.cpp

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MpiProgML2D() [1/2]

◆ MpiProgML2D() [2/2]

Member Function Documentation

◆ endIteration()

◆ expectation()

◆ printModel()

◆ produceSideInfo2()

◆ setNumberOfLocalImages()

◆ usage()

◆ writeOutputFiles()