#include <mpi_subtomo_subtraction.h>

Inheritance diagram for MpiProgSubtomoSubtraction:

Collaboration diagram for MpiProgSubtomoSubtraction:

Public Member Functions
void	defineParams () override

void	readParams () override

void	read (int argc, char **argv, bool reportErrors=true) override

void	preProcess () override

void	startProcessing () override

void	showProgress () override

bool	getImageToProcess (size_t &objId, size_t &objIndex) override

void	finishProcessing () override

void	wait () override
	Wait for the distributor to finish. More...

Public Member Functions inherited from ProgSubtomoSubtraction
void	POCSmask (const MultidimArray< double > &, MultidimArray< double > &)
	Processing methods. More...

void	POCSnonnegative (MultidimArray< double > &)

void	POCSFourierAmplitude (const MultidimArray< double > &, MultidimArray< std::complex< double >> &, double)

void	POCSFourierAmplitudeRadAvg (MultidimArray< std::complex< double >> &, double, const MultidimArray< double > &, int, int, int)

void	POCSMinMax (MultidimArray< double > &, double, double)

void	POCSFourierPhase (const MultidimArray< std::complex< double >> &, MultidimArray< std::complex< double >> &)

void	extractPhase (MultidimArray< std::complex< double >> &) const

void	computeEnergy (MultidimArray< double > &, const MultidimArray< double > &) const

void	centerFFTMagnitude (MultidimArray< double > &, MultidimArray< std::complex< double >> &, MultidimArray< double > &) const

void	radialAverage (const MultidimArray< double > &, const MultidimArray< double > &, MultidimArray< double > &)

MultidimArray< double >	computeRadQuotient (const MultidimArray< double > &, const MultidimArray< double > &, const MultidimArray< double > &, const MultidimArray< double > &)

void	createFilter (FourierFilter &, double)

Image< double >	subtraction (Image< double >, Image< double > &, const MultidimArray< double > &, const FileName &, const FileName &, FourierFilter &, double)

MultidimArray< double >	computeMagnitude (MultidimArray< double > &)

MultidimArray< double >	createMask (const Image< double > &, const FileName &, const FileName &)

void	filterMask (MultidimArray< double > &) const

MultidimArray< std::complex< double > >	computePhase (MultidimArray< double > &)

MultidimArray< double >	getSubtractionMask (const FileName &, MultidimArray< double >)

	ProgSubtomoSubtraction ()
	Empty constructor. More...

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

void	show () const override
	Show. More...

void	defineParams () override
	Define parameters. More...

void	readParticle (const MDRow &rowIn)
	Read and write methods. More...

void	writeParticle (MDRow &rowOut, FileName, Image< double > &)

void	preProcess () override
	MPI methods. More...

void	processImage (const FileName &fnImg, const FileName &fnImgOut, const MDRow &rowIn, MDRow &rowOut) override

void	postProcess () override

Public Member Functions inherited from XmippMetadataProgram
MetaData *	getInputMd ()

MetaDataVec &	getOutputMd ()

	XmippMetadataProgram ()
	Empty constructor. More...

virtual int	tryRead (int argc, const char **argv, bool reportErrors=true)

virtual void	init ()

virtual void	setup (MetaData *md, const FileName &o="", const FileName &oroot="", bool applyGeo=false, MDLabel label=MDL_IMAGE)

virtual	~XmippMetadataProgram ()

void	setMode (WriteModeMetaData _mode)

void	setupRowOut (const FileName &fnImgIn, const MDRow &rowIn, const FileName &fnImgOut, MDRow &rowOut) const
	Prepare rowout. More...

virtual void	checkPoint ()
	For very long programs, it may be needed to write checkpoints. More...

virtual void	run ()
	Run over all images. 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

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)

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	read (int argc, const 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)

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 ProgSubtomoSubtraction
FileName	fnVolMd

FileName	fnVolRef

FileName	fnVol2

FileName	fnOut

FileName	fnMask1

FileName	fnMask2

FileName	fnMaskSub

FileName	fnVol1F

FileName	fnVol2A

bool	computeE

size_t	iter

double	v1min

double	v1max

bool	performSubtraction

int	sigma

double	cutFreq

double	lambda

bool	radavg

bool	subtomos

MetaDataVec	mdParticles

MDRowVec	row

Matrix1D< double >	roffset

struct Angles	part_angles

Image< double >	V

Image< double >	V1

Image< double >	padv

double	pad

double	std1

size_t	n

FourierTransformer	transformer2

MultidimArray< std::complex< double > >	V2Fourier

MultidimArray< double >	V1FourierMag

MultidimArray< double >	mask

Image< double >	Vdiff

FourierFilter	filter2

int	rank

Public Attributes inherited from XmippMetadataProgram
FileName	fn_in
	Filenames of input and output Metadata. More...

FileName	fn_out

FileName	baseName

FileName	pathBaseName

FileName	oextBaseName

bool	apply_geo
	Apply geo. More...

size_t	ndimOut
	Output dimensions. More...

size_t	zdimOut

size_t	ydimOut

size_t	xdimOut

DataType	datatypeOut

size_t	mdInSize
	Number of input elements. More...

Public Attributes inherited from XmippProgram
bool	doRun

bool	runWithoutArgs

int	verbose
	Verbosity level. More...

int	debug

Protected Member Functions inherited from XmippMetadataProgram
virtual void	initComments ()

void	show () const override

virtual void	writeOutput ()

virtual void	defineLabelParam ()

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 XmippMetadataProgram
WriteModeMetaData	mode
	Metadata writing mode: OVERWRITE, APPEND. More...

FileName	oext
	Output extension and root. More...

FileName	oroot

MDLabel	image_label
	MDLabel to be used to read/write images, usually will be MDL_IMAGE. More...

bool	produces_an_output
	Indicate that a unique final output is produced. More...

bool	produces_a_metadata
	Indicate that the unique final output file is a Metadata. More...

bool	each_image_produces_an_output
	Indicate that an output is produced for each image in the input. More...

bool	allow_apply_geo

bool	decompose_stacks
	Input Metadata will treat a stack file as a set of images instead of a unique file. More...

bool	delete_output_stack
	Delete previous output stack file prior to process images. More...

bool	get_image_info
	Get the input image file dimensions to further operations. More...

bool	save_metadata_stack
	Save the associated output metadata when output file is a stack. More...

bool	track_origin
	Include the original input image filename in the output stack. More...

bool	keep_input_columns
	Keep input metadata columns. More...

bool	remove_disabled
	Remove disabled images from the input selfile. More...

bool	allow_time_bar
	Show process time bar. More...

bool	input_is_metadata
	Input is a metadata. More...

bool	single_image
	Input is a single image. More...

bool	input_is_stack
	Input is a stack. More...

bool	output_is_stack
	Output is a stack. More...

bool	create_empty_stackfile

bool	delete_mdIn

size_t	time_bar_step
	Some time bar related counters. More...

size_t	time_bar_size

size_t	time_bar_done

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 31 of file mpi_subtomo_subtraction.h.

Member Function Documentation

◆ defineParams()

void MpiProgSubtomoSubtraction::defineParams ( )

overridevirtual

Function in which the param of each Program are defined.

Reimplemented from XmippMetadataProgram.

Definition at line 28 of file mpi_subtomo_subtraction.cpp.

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

◆ finishProcessing()

void MpiProgSubtomoSubtraction::finishProcessing ( )

overridevirtual

finishProcessing

Reimplemented from MpiMetadataProgram.

Definition at line 69 of file mpi_subtomo_subtraction.cpp.

 {
     node->gatherMetadatas(getOutputMd(), fn_out);
     MetaDataVec MDaux;
     MDaux.sort(getOutputMd(), MDL_GATHER_ID);
     MDaux.removeLabel(MDL_GATHER_ID);
     getOutputMd() = MDaux;
     if (node->isMaster())
         ProgSubtomoSubtraction::finishProcessing();
 }

◆ getImageToProcess()

bool MpiProgSubtomoSubtraction::getImageToProcess	(	size_t &	objId,
		size_t &	objIndex
	)

inlineoverridevirtual

Reimplemented from XmippMetadataProgram.

Definition at line 41 of file mpi_subtomo_subtraction.h.

     {
         return getTaskToProcess(objId, objIndex);
     }

◆ preProcess()

void MpiProgSubtomoSubtraction::preProcess ( )

overridevirtual

Preprocess

Reimplemented from MpiMetadataProgram.

Definition at line 42 of file mpi_subtomo_subtraction.cpp.

 {
     rank = (int)node->rank;
     ProgSubtomoSubtraction::preProcess();
     MetaData &mdIn = *getInputMd();
     mdIn.addLabel(MDL_GATHER_ID);
     mdIn.fillLinear(MDL_GATHER_ID, 1, 1);
     createTaskDistributor(mdIn, blockSize);
 }

◆ read()

void MpiProgSubtomoSubtraction::read	(	int	argc,
		char **	argv,
		bool	reportErrors = `true`
	)

overridevirtual

Read the command line arguments A convenience wrapper

Reimplemented from XmippProgram.

Definition at line 38 of file mpi_subtomo_subtraction.cpp.

 {
     MpiMetadataProgram::read(argc, argv);
 }

◆ readParams()

void MpiProgSubtomoSubtraction::readParams ( )

overridevirtual

Function in which each program will read parameters that it need. If some error occurs the usage will be printed out.

Reimplemented from XmippMetadataProgram.

Definition at line 33 of file mpi_subtomo_subtraction.cpp.

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

◆ showProgress()

void MpiProgSubtomoSubtraction::showProgress ( )

overridevirtual

Reimplemented from XmippMetadataProgram.

Definition at line 60 of file mpi_subtomo_subtraction.cpp.

 {
     if (node->rank == 1)
     {
         time_bar_done = first + 1;
         ProgSubtomoSubtraction::showProgress();
     }
 }

◆ startProcessing()

void MpiProgSubtomoSubtraction::startProcessing ( )

overridevirtual

Do some stuff before starting processing in a parallel environment usually this only be executed by master.

Reimplemented from XmippMetadataProgram.

Definition at line 51 of file mpi_subtomo_subtraction.cpp.

 {
     if (node->rank == 1)
     {
         verbose = 1;
         ProgSubtomoSubtraction::startProcessing();
     }
     node->barrierWait();
 }

◆ wait()

void MpiProgSubtomoSubtraction::wait ( )

overridevirtual

Wait for the distributor to finish.

Reimplemented from XmippMetadataProgram.

Definition at line 79 of file mpi_subtomo_subtraction.cpp.

 {
     distributor->wait();
 }

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

xmipp/libraries/parallel/mpi_subtomo_subtraction.h
xmipp/libraries/parallel/mpi_subtomo_subtraction.cpp

Public Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ defineParams()

◆ finishProcessing()

◆ getImageToProcess()

◆ preProcess()

◆ read()

◆ readParams()

◆ showProgress()

◆ startProcessing()

◆ wait()