Inheritance diagram for MpiProgAngularSphAlignment:

Collaboration diagram for MpiProgAngularSphAlignment:

Public Member Functions
void	defineParams ()

void	readParams ()

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

void	showProgress ()

void	createWorkFiles () override

void	startProcessing ()

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

void	finishProcessing ()

void	writeImageParameters (const FileName &fnImg)

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

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

	~ProgAngularSphAlignment ()
	Destructor. More...

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

void	show ()
	Show. More...

void	defineParams ()
	Define parameters. More...

void	preProcess ()

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

void	numCoefficients (int l1, int l2, int &nc) const
	Length of coefficients vector. More...

void	minimizepos (int l2, Matrix1D< double > &steps) const
	Determine the positions to be minimize of a vector containing spherical harmonic coefficients. More...

void	fillVectorTerms (int l1, int l2)
	Zernike and SPH coefficients allocation. More...

void	deformVol (MultidimArray< double > &mVD, const MultidimArray< double > &mV, double &def, double rot, double tilt, double psi)
	Deform a volumen using Zernike-Spherical harmonic basis. More...

void	applyCTFImage (double const &deltaDefocusU, double const &deltaDefocusV, double const &deltaDefocusAngle)

void	updateCTFImage (double defocusU, double defocusV, double angle)

double	tranformImageSph (double *pclnm, double rot, double tilt, double psi, double deltaDefocusU, double deltaDefocusV, double deltaDefocusAngle)

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)

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 ProgAngularSphAlignment
FileName	fnVolR

FileName	fnMaskR

FileName	fnOutDir
	Output directory. More...

int	L1

int	L2

Matrix1D< int >	vL1

Matrix1D< int >	vN

Matrix1D< int >	vL2

Matrix1D< int >	vM

double	maxShift

double	maxAngularChange

double	maxResol

double	Ts

int	Rmax

bool	optimizeAlignment

bool	optimizeDeformation

bool	optimizeDefocus

bool	ignoreCTF

bool	optimizeRadius

bool	phaseFlipped

double	lambda

int	RmaxDef

Matrix1D< double >	p

int	flagEnabled

bool	resume

MultidimArray< int >	mask2D

MultidimArray< int >	V_mask

size_t	Xdim

Image< double >	V

Image< double >	Vdeformed

Image< double >	I

Image< double >	Ip

Image< double >	Ifiltered

Image< double >	Ifilteredp

Image< double >	P

FourierFilter	filter

Matrix2D< double >	A

double	old_rot

double	old_tilt

double	old_psi

double	old_shiftX

double	old_shiftY

bool	old_flip

bool	hasCTF

double	old_defocusU

double	old_defocusV

double	old_defocusAngle

double	currentDefocusU

double	currentDefocusV

double	currentAngle

CTFDescription	ctf

FourierFilter	FilterCTF

int	vecSize

Matrix1D< double >	clnm

Matrix1D< double >	steps_cp

double	totalDeformation

double	sumV

double	sumVd

bool	showOptimization

double	correlation

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 ()

virtual void	postProcess ()

void	show () const override

virtual void	writeOutput ()

virtual void	defineLabelParam ()

Protected Member Functions inherited from XmippProgram
void	defineCommons ()

Protected Member Functions inherited from Rerunable
	Rerunable (const FileName &fn)

virtual void	createWorkFiles (bool resume, MetaData *md)

const FileName &	getFileName () const

void	setFileName (const FileName &fn)

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_angular_sph_alignment.cpp.

Member Function Documentation

◆ createWorkFiles()

void MpiProgAngularSphAlignment::createWorkFiles ( )

inlineoverridevirtual

Reimplemented from ProgAngularSphAlignment.

Definition at line 65 of file mpi_angular_sph_alignment.cpp.

     {
         //Master node should prepare some stuff before start working
         MetaData &mdIn = *getInputMd(); //get a reference to input metadata
 
         if (node->isMaster())
         {
             ProgAngularSphAlignment::createWorkFiles();
             mdIn.write(fnOutDir + "/sphTodo.xmd");
         }
         node->barrierWait();//Sync all before start working
         mdIn.read(fnOutDir + "/sphTodo.xmd");
         mdIn.findObjects(imgsId);//get objects ids
         distributor = new MpiTaskDistributor(mdIn.size(), 1, node);
     }

◆ defineParams()

void MpiProgAngularSphAlignment::defineParams ( )

inlinevirtual

Function in which the param of each Program are defined.

Reimplemented from XmippMetadataProgram.

Definition at line 40 of file mpi_angular_sph_alignment.cpp.

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

◆ finishProcessing()

void MpiProgAngularSphAlignment::finishProcessing ( )

inlinevirtual

finishProcessing

Reimplemented from MpiMetadataProgram.

Definition at line 107 of file mpi_angular_sph_alignment.cpp.

     {
         distributor->wait();
 
         //All nodes wait for each other
         node->barrierWait();
         if (node->isMaster())
             ProgAngularSphAlignment::finishProcessing();
         node->barrierWait();
     }

◆ getImageToProcess()

virtual bool MpiProgAngularSphAlignment::getImageToProcess	(	size_t &	objId,
		size_t &	objIndex
	)

inlineoverridevirtual

Reimplemented from XmippMetadataProgram.

Definition at line 89 of file mpi_angular_sph_alignment.cpp.

     {
         //return getTaskToProcess(objId, objIndex);
         size_t first, last;
         bool moreTasks = distributor->getTasks(first, last);
 
         if (moreTasks)
         {
             time_bar_done = first + 1;
             objIndex = first;
             objId = imgsId[first];
             return true;
         }
         time_bar_done = getInputMd()->size();
         objId = BAD_OBJID;
         objIndex = BAD_INDEX;
         return false;
     }

◆ read()

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

inlinevirtual

Read the command line arguments A convenience wrapper

Reimplemented from XmippProgram.

Definition at line 50 of file mpi_angular_sph_alignment.cpp.

     {
         //AJ new
         fileMutex = new MpiFileMutex(node);
         //END AJ
         MpiMetadataProgram::read(argc,argv);
     }

◆ readParams()

void MpiProgAngularSphAlignment::readParams ( )

inlinevirtual

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 45 of file mpi_angular_sph_alignment.cpp.

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

◆ showProgress()

void MpiProgAngularSphAlignment::showProgress ( )

inlinevirtual

Reimplemented from XmippMetadataProgram.

Definition at line 57 of file mpi_angular_sph_alignment.cpp.

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

◆ startProcessing()

void MpiProgAngularSphAlignment::startProcessing ( )

inlinevirtual

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

Reimplemented from XmippMetadataProgram.

Definition at line 80 of file mpi_angular_sph_alignment.cpp.

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

◆ wait()

void MpiProgAngularSphAlignment::wait ( )

inlinevirtual

Wait for the distributor to finish.

Reimplemented from XmippMetadataProgram.

Definition at line 125 of file mpi_angular_sph_alignment.cpp.

     {
         distributor->wait();
     }

◆ writeImageParameters()

void MpiProgAngularSphAlignment::writeImageParameters ( const FileName & fnImg )

inlinevirtual

Write the parameters found for one image

Reimplemented from ProgAngularSphAlignment.

Definition at line 118 of file mpi_angular_sph_alignment.cpp.

     {
         fileMutex->lock();
         ProgAngularSphAlignment::writeImageParameters(fnImg);
         fileMutex->unlock();
     }

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

xmipp/libraries/parallel/mpi_angular_sph_alignment.cpp

Public Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ createWorkFiles()

◆ defineParams()

◆ finishProcessing()

◆ getImageToProcess()

◆ read()

◆ readParams()

◆ showProgress()

◆ startProcessing()

◆ wait()

◆ writeImageParameters()