#include <mpi_ml_align2d.h>

Inheritance diagram for MpiProgMLF2D:

Collaboration diagram for MpiProgMLF2D:

Public Member Functions
	MpiProgMLF2D ()

	MpiProgMLF2D (MpiNode *node)

void	produceSideInfo ()

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...

Public Member Functions inherited from ProgMLF2D
	ProgMLF2D (int nr_vols=0, int rank=0, int size=1)

void	defineParams ()
	Params definition. More...

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

void	show (bool ML3D=false)
	Show. More...

virtual void	defineBasicParams (XmippProgram *prog)
	Some redefinitions of the basic and additional params. More...

virtual void	defineAdditionalParams (XmippProgram prog, const char sectionLine)

void	estimateInitialNoiseSpectra ()

void	updateWienerFilters (const MultidimArray< double > &spectral_signal, std::vector< double > &sumw_defocus, int iter)

void	setCurrentSamplingRates (double current_probres_limit)
	Vary in-plane and translational sampling rates with resolution. More...

void	generateInitialReferences ()
	Generate initial references from random subset averages. More...

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

void	appendFTtoVector (const MultidimArray< std::complex< double > > &Fin, std::vector< double > &out)

void	getFTfromVector (const std::vector< double > &in, const int start_point, MultidimArray< std::complex< double > > &out, bool only_real=false)

void	rotateReference (std::vector< double > &out)
	Fill vector of matrices with all rotations of reference. More...

void	reverseRotateReference (const std::vector< double > &in, std::vector< MultidimArray< double > > &out)
	Apply reverse rotations to all matrices in vector and fill new matrix with their sum. More...

void	preselectDirections (float &phi, float &theta, std::vector< double > &pdf_directions)

void	preselect_significant_model_phi (MultidimArray< double > &Mimg, std::vector< double > &offsets, std::vector< std::vector< MultidimArray< double > > > &Mref, MultidimArray< int > &Msignificant, std::vector< double > &pdf_directions)

void	fourierTranslate2D (const std::vector< double > &in, MultidimArray< double > &trans, std::vector< double > &out, int point_start=0)

void	calculateFourierOffsets (const MultidimArray< double > &Mimg, const std::vector< double > &offsets, std::vector< double > &out, MultidimArray< int > &Moffsets, MultidimArray< int > &Moffsets_mirror)

void	processOneImage (const MultidimArray< double > &Mimg, size_t focus, bool apply_ctf, double &fracweight, double &maxweight2, double &sum_refw2, double &opt_scale, size_t &opt_refno, double &opt_psi, size_t &opt_ipsi, size_t &opt_iflip, MultidimArray< double > &opt_offsets, std::vector< double > &opt_offsets_ref, std::vector< double > &pdf_directions, bool do_kstest, bool write_histograms, FileName fn_img, double &KSprob)
	Perform expectation step for a single image. More...

double	performKSTest (MultidimArray< double > &Mimg, const int focus, bool apply_ctf, FileName &fn_img, bool write_histogram, std::vector< std::vector< MultidimArray< std::complex< double > > > > &Fref, double &opt_scale, int &opt_refno, int &opt_ipsi, int &opt_iflip, MultidimArray< double > &opt_offsets)
	Perform Kolmogorov-Smirnov test. More...

void	iteration ()
	One iteration of the process. More...

void	expectation ()
	Integrate over all experimental images. More...

void	maximization ()
	Update all model parameters (maximization step) More...

void	endIteration ()
	Redefine endIteration to update Wiener filters. More...

void	writeNoiseFile (const FileName &fn_base, int ifocus)
	Write noise estimation per resolution. More...

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

Public Member Functions inherited from ML2DBaseProgram
void	initSamplingStuff ()

	ML2DBaseProgram ()

virtual void	setNumberOfLocalImages ()
	Set the number of images, this function is useful only for MPI. More...

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

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

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

virtual bool	checkConvergence ()

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

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 (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 MpiML2DBase< MpiProgMLF2D >
void	readMpi (int argc, char **argv)

	MpiML2DBase (MpiProgMLF2D *prm)

	MpiML2DBase (MpiProgMLF2D 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 ProgMLF2D
double	sigma_offset

std::vector< double >	alpha_k

std::vector< double >	mirror_fraction

size_t	max_nr_psi

bool	do_variable_psi

bool	do_variable_trans

std::vector< Image< double > >	Ictf

bool	limit_trans

size_t	nr_trans

size_t	zero_trans

int	search_shift

int	offsets_keepdir

bool	do_ctf_correction

double	sampling

std::vector< int >	count_defocus

bool	phase_flipped

MultidimArray< size_t >	Mresol_int

std::vector< MultidimArray< double > >	Vsig

std::vector< MultidimArray< double > >	Vctf

std::vector< MultidimArray< double > >	Vdec

double	reduce_snr

size_t	nr_focus

double	lowres_limit

double	highres_limit

double	ini_highres_limit

bool	first_iter_noctf

bool	do_divide_ctf

bool	do_include_allfreqs

double	fix_high

std::vector< int >	pointer_2d

std::vector< int >	pointer_i

std::vector< int >	pointer_j

size_t	nr_points_prob

size_t	nr_points_2d

size_t	dnr_points_2d

size_t	current_highres_limit

bool	do_student
	IN DEVELOPMENT. More...

bool	do_student_sigma_trick

bool	do_kstest
	Statistical analysis of the noise distributions. More...

int	iter_write_histograms

Histogram1D	sumhist

std::vector< Histogram1D >	resolhist

std::vector< double >	refs_avgscale

int	rank

int	size

int	nr_vols

double	LL

double	sumcorr

double	wsum_sigma_offset

double	sumw_allrefs

std::vector< MultidimArray< double > >	wsum_Mref

std::vector< MultidimArray< double > >	wsum_ctfMref

std::vector< std::vector< double > >	Mwsum_sigma2

std::vector< double >	sumw

std::vector< double >	sumw2

std::vector< double >	sumwsc

std::vector< double >	sumwsc2

std::vector< double >	sumw_mirror

std::vector< double >	sumw_defocus

std::vector< double >	Fref

std::vector< double >	Fwsum_imgs

std::vector< double >	Fwsum_ctfimgs

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< MpiProgMLF2D >
MpiNode *	node

bool	created_node

MpiProgMLF2D *	program

Detailed Description

Class to parallelize the MLF 2D alignment program

Definition at line 124 of file mpi_ml_align2d.h.

Constructor & Destructor Documentation

◆ MpiProgMLF2D() [1/2]

MpiProgMLF2D::MpiProgMLF2D ( )

Default constructor

Definition at line 190 of file mpi_ml_align2d.cpp.

190 :MpiML2DBase(this)

191 {}

MpiML2DBase< MpiProgMLF2D >::MpiML2DBase

MpiML2DBase(MpiProgMLF2D *prm)

Definition: mpi_ml_align2d.cpp:34

◆ MpiProgMLF2D() [2/2]

MpiProgMLF2D::MpiProgMLF2D ( MpiNode * node )

Constructor passing the MpiNode

Definition at line 193 of file mpi_ml_align2d.cpp.

193 :MpiML2DBase(this, node)

194 {}

MpiML2DBase< MpiProgMLF2D >::MpiML2DBase

MpiML2DBase(MpiProgMLF2D *prm)

Definition: mpi_ml_align2d.cpp:34

Member Function Documentation

◆ endIteration()

void MpiProgMLF2D::endIteration ( )

virtual

Redefine endIteration for some synchronization.

Reimplemented from ML2DBaseProgram.

Definition at line 278 of file mpi_ml_align2d.cpp.

 {
     // Write output files
     LOG("MpiProgMLF2D::endIteration : before sendDocfile");
     sendDocfile(docfiledata);
     LOG("MpiProgMLF2D::endIteration : before writeOutputFiles");
     writeOutputFiles(model, OUT_ITER);
     LOG("MpiProgMLF2D::endIteration : before updateWienerFilters");
     updateWienerFilters(spectral_signal, sumw_defocus, iter);
     LOG("MpiProgMLF2D::endIteration : before barrierWait");
     node->barrierWait();
 }

◆ expectation()

void MpiProgMLF2D::expectation ( )

virtual

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

Implements ML2DBaseProgram.

Definition at line 196 of file mpi_ml_align2d.cpp.

 {
     MultidimArray<double> Maux, Vaux;
     double aux;
     Maux.resize(dim, dim);
     Maux.setXmippOrigin();
 
     ProgMLF2D::expectation();
     MPI_Allreduce(&LL, &aux, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
     LL = aux;
     MPI_Allreduce(&sumcorr, &aux, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
     sumcorr = aux;
     MPI_Allreduce(&wsum_sigma_offset, &aux, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
     wsum_sigma_offset = aux;
     if (do_kstest)
     {
         Vaux.resize(sumhist);
         MPI_Allreduce(MULTIDIM_ARRAY(sumhist), MULTIDIM_ARRAY(Vaux),
                       MULTIDIM_SIZE(sumhist), MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
         FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(Vaux)
         DIRECT_MULTIDIM_ELEM(sumhist, n) = DIRECT_MULTIDIM_ELEM(Vaux, n);
         for (size_t ires = 0; ires < hdim; ires++)
         {
             Vaux.resize(sumhist);
             MPI_Allreduce(MULTIDIM_ARRAY(resolhist[ires]), MULTIDIM_ARRAY(Vaux),
                           MULTIDIM_SIZE(resolhist[ires]), MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
             FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(Vaux)
             DIRECT_MULTIDIM_ELEM(resolhist[ires], n) = DIRECT_MULTIDIM_ELEM(Vaux, n);
         }
     }
     for (int refno = 0;refno < model.n_ref; 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;
         if (do_ctf_correction)
         {
             MPI_Allreduce(MULTIDIM_ARRAY(wsum_ctfMref[refno]), MULTIDIM_ARRAY(Maux),
                           MULTIDIM_SIZE(wsum_ctfMref[refno]), MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
             wsum_ctfMref[refno] = Maux;
         }
         MPI_Allreduce(&sumw[refno], &aux, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
         sumw[refno] = aux;
         MPI_Allreduce(&sumw2[refno], &aux, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
         sumw2[refno] = aux;
         MPI_Allreduce(&sumwsc2[refno], &aux, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
         sumwsc2[refno] = aux;
         MPI_Allreduce(&sumwsc[refno], &aux, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
         sumwsc[refno] = aux;
         MPI_Allreduce(&sumw_mirror[refno], &aux, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
         sumw_mirror[refno] = aux;
     }
     for (size_t ifocus = 0;ifocus < nr_focus;ifocus++)
     {
         for (size_t ii = 0; ii <  Mwsum_sigma2[ifocus].size(); ii++)
         {
             MPI_Allreduce(&Mwsum_sigma2[ifocus][ii], &aux, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
             Mwsum_sigma2[ifocus][ii] = aux;
         }
         if (do_student)
         {
             MPI_Allreduce(&sumw_defocus[ifocus], &aux, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
             sumw_defocus[ifocus] = aux;
         }
     }
 }//end of expectation

◆ produceSideInfo()

void MpiProgMLF2D::produceSideInfo ( )

virtual

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

Reimplemented from ProgMLF2D.

Definition at line 271 of file mpi_ml_align2d.cpp.

 {
     SET_RANK_AND_SIZE();
     ProgMLF2D::produceSideInfo();
 }

◆ produceSideInfo2()

void MpiProgMLF2D::produceSideInfo2 ( )

virtual

Read reference images in memory & set offset vectors (This produceSideInfo is Selfile-dependent!)

Reimplemented from ProgMLF2D.

Definition at line 263 of file mpi_ml_align2d.cpp.

 {
     node->barrierWait();
     ProgMLF2D::produceSideInfo2();
     //Also sync after finishing produceSideInfo2
     node->barrierWait();
 }

◆ writeOutputFiles()

void MpiProgMLF2D::writeOutputFiles	(	const ModelML2D &	model,
		OutputType	outputType = `OUT_FINAL`
	)

virtual

Write model parameters.

Reimplemented from ProgMLF2D.

Definition at line 291 of file mpi_ml_align2d.cpp.

 {
     //All nodes should arrive to writeOutput files at same time
     LOG("MpiProgMLF2D::writeOutputFiles : waiting before writing");
     node->barrierWait();
     //Only master write files
     if (node->isMaster())
     {
         ProgMLF2D::writeOutputFiles(model, outputType);
         LOG("MpiProgMLF2D::writeOutputFiles : master writing ");
     }
     else if (outputType == OUT_REFS)
     {
       outRefsMd = FN_CLASSES_MD(getIterExtraPath(fn_root, iter));
       LOG(formatString("MpiProgMLF2D::writeOutputFiles : slave setting outRefsMd = %s", outRefsMd.c_str()).c_str());
     }
     //All nodes wait until files are written
     LOG("MpiProgMLF2D::writeOutputFiles : waiting after writing");
     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

◆ MpiProgMLF2D() [1/2]

◆ MpiProgMLF2D() [2/2]

Member Function Documentation

◆ endIteration()

◆ expectation()

◆ produceSideInfo()

◆ produceSideInfo2()

◆ writeOutputFiles()