#include <mpi_image_rotational_pca.h>

Inheritance diagram for MpiProgImageRotationalPCA:

Collaboration diagram for MpiProgImageRotationalPCA:

Public Member Functions
	MpiProgImageRotationalPCA (int argc, char **argv)
	Empty constructor. More...

virtual void	selectPartFromMd (MetaData &MDin)

virtual void	comunicateMatrix (Matrix2D< double > &W)

virtual void	createMutexes (size_t Nimgs)

virtual void	allReduceApplyT (Matrix2D< double > &Wnode_0)

virtual void	comunicateQrDim (int &qrDim)

virtual void	mapMatrix (int qrDim)

virtual void	applySVD ()

virtual void	copyHtoF (int block)

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

	~ProgImageRotationalPCA ()
	Destructor. More...

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

void	show ()
	Show. More...

void	defineParams ()
	Usage. More...

void	produceSideInfo ()
	Produce side info. More...

void	writeToHBuffer (int idx, double *dest)

void	flushHBuffer ()

void	clearHbuffer ()

void	applyT ()

void	applyTt ()

int	QR ()

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
std::shared_ptr< MpiNode >	node

Public Attributes inherited from ProgImageRotationalPCA
FileName	fnIn

FileName	fnRoot

int	Neigen

int	Nits

double	psi_step

double	max_shift_change

double	shift_step

int	maxNimgs

int	Nthreads

int	rank

std::vector< MetaDataVec >	MD

size_t	Nimg

int	Nangles

int	Nshifts

size_t	Xdim

int	Npixels

std::vector< double * >	Hbuffer

std::vector< double * >	HbufferDestination

std::unique_ptr< Mutex >	fileMutex

std::unique_ptr< Mutex >	threadMutex

Matrix2D< double >	H

Matrix2D< double >	F

std::vector< Image< double > >	I

std::vector< MultidimArray< double > >	Iaux

std::vector< Matrix2D< double > >	A

std::vector< Matrix2D< double > >	Hblock

std::vector< Matrix2D< double > >	Wnode

Matrix2D< double >	Wtranspose

MultidimArray< unsigned char >	mask

std::unique_ptr< ThreadTaskDistributor >	taskDistributor

std::unique_ptr< ThreadManager >	thMgr

std::vector< size_t >	objId

Public Attributes inherited from XmippProgram
bool	doRun

bool	runWithoutArgs

int	verbose
	Verbosity level. More...

int	debug

Additional Inherited Members
Static Public Attributes inherited from ProgImageRotationalPCA
static const int	HbufferMax =20

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

Rotational invariant PCA parameters.

Definition at line 36 of file mpi_image_rotational_pca.h.

Constructor & Destructor Documentation

◆ MpiProgImageRotationalPCA()

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

Empty constructor.

Definition at line 33 of file mpi_image_rotational_pca.cpp.

 {
     node = std::make_shared<MpiNode>(argc, argv);
     rank = node->rank;
     if (!IS_MASTER)
         verbose = 0;
 }

Member Function Documentation

◆ allReduceApplyT()

void MpiProgImageRotationalPCA::allReduceApplyT ( Matrix2D< double > & Wnode_0 )

virtual

Last part of function applyT

Reimplemented from ProgImageRotationalPCA.

Definition at line 72 of file mpi_image_rotational_pca.cpp.

 {
     MPI_Allreduce(MPI_IN_PLACE, MATRIX2D_ARRAY(Wnode_0), MAT_XSIZE(Wnode_0)*MAT_YSIZE(Wnode_0),
         MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
 }

◆ applySVD()

void MpiProgImageRotationalPCA::applySVD ( )

virtual

Apply SVD

Reimplemented from ProgImageRotationalPCA.

Definition at line 101 of file mpi_image_rotational_pca.cpp.

 {
   if (IS_MASTER)
     ProgImageRotationalPCA::applySVD();
   node->barrierWait();
 }

◆ comunicateMatrix()

void MpiProgImageRotationalPCA::comunicateMatrix ( Matrix2D< double > & W )

virtual

Comunicate matrix, only meanful for MPI

Reimplemented from ProgImageRotationalPCA.

Definition at line 59 of file mpi_image_rotational_pca.cpp.

 {
     MPI_Bcast(&MAT_ELEM(W,0,0),MAT_XSIZE(W)*MAT_YSIZE(W),MPI_DOUBLE,0,MPI_COMM_WORLD);
 }

◆ comunicateQrDim()

void MpiProgImageRotationalPCA::comunicateQrDim ( int & qrDim )

virtual

Comunicate int param

Reimplemented from ProgImageRotationalPCA.

Definition at line 78 of file mpi_image_rotational_pca.cpp.

 {
   if (IS_MASTER)
     ProgImageRotationalPCA::comunicateQrDim(qrDim);
   node->barrierWait();
   MPI_Bcast(&qrDim,1,MPI_INT,0,MPI_COMM_WORLD);
 }

◆ copyHtoF()

void MpiProgImageRotationalPCA::copyHtoF ( int block )

virtual

Copy H to F.

Reimplemented from ProgImageRotationalPCA.

Definition at line 109 of file mpi_image_rotational_pca.cpp.

 {
   if (IS_MASTER)
     ProgImageRotationalPCA::copyHtoF(block);
   node->barrierWait();
 }

◆ createMutexes()

void MpiProgImageRotationalPCA::createMutexes ( size_t Nimgs )

virtual

Create mutexes and distributor

Reimplemented from ProgImageRotationalPCA.

Definition at line 64 of file mpi_image_rotational_pca.cpp.

 {
   fileMutex = std::make_unique<MpiFileMutex>(node);
   threadMutex = std::make_unique<Mutex>();
   taskDistributor = std::make_unique<MpiTaskDistributor>(Nimgs, XMIPP_MAX(1,Nimgs/(5*node->size)), node);
 }

◆ mapMatrix()

void MpiProgImageRotationalPCA::mapMatrix ( int qrDim )

virtual

Map matrix

Reimplemented from ProgImageRotationalPCA.

Definition at line 86 of file mpi_image_rotational_pca.cpp.

 {
 // Load the first qrDim columns of F in matrix H
   if (IS_MASTER)
   {
     ProgImageRotationalPCA::mapMatrix(qrDim);
     node->barrierWait();
   }
   else
   {
     node->barrierWait();
     H.mapToFile(fnRoot+"_matrixH.raw",MAT_XSIZE(F),qrDim);
   }
 }

◆ selectPartFromMd()

void MpiProgImageRotationalPCA::selectPartFromMd ( MetaData & MDin )

virtual

Read input images

Reimplemented from ProgImageRotationalPCA.

Definition at line 41 of file mpi_image_rotational_pca.cpp.

 {
   if (IS_MASTER)
   {
     ProgImageRotationalPCA::selectPartFromMd(MDin);
     MDin.write(fnRoot + "_temp.xmd");
     node->barrierWait();
     node->barrierWait();
     unlink((fnRoot + "_temp.xmd").c_str());
   }
   else
   {
     node->barrierWait();
     MDin.read(fnRoot + "_temp.xmd");
     node->barrierWait();
   }
 }

Member Data Documentation

◆ node

std::shared_ptr<MpiNode> MpiProgImageRotationalPCA::node

Definition at line 40 of file mpi_image_rotational_pca.h.

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

xmipp/libraries/parallel/mpi_image_rotational_pca.h
xmipp/libraries/parallel/mpi_image_rotational_pca.cpp

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MpiProgImageRotationalPCA()

Member Function Documentation

◆ allReduceApplyT()

◆ applySVD()

◆ comunicateMatrix()

◆ comunicateQrDim()

◆ copyHtoF()

◆ createMutexes()

◆ mapMatrix()

◆ selectPartFromMd()

Member Data Documentation

◆ node