#include <movie_alignment_correlation_gpu.h>

Inheritance diagram for ProgMovieAlignmentCorrelationGPU< T >:

Collaboration diagram for ProgMovieAlignmentCorrelationGPU< T >:

Protected Member Functions
void	defineParams ()
	Define parameters. More...

void	show ()
	Show. More...

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

Protected Member Functions inherited from AProgMovieAlignmentCorrelation< T >
Dimensions	getMovieSizeRaw ()

Dimensions	getMovieSize ()

AlignmentResult< T >	computeAlignment (Matrix1D< T > &bX, Matrix1D< T > &bY, Matrix2D< T > &A, const core::optional< size_t > &refFrame, size_t N, int verbose)

int	findReferenceImage (size_t N, const Matrix1D< T > &shiftX, const Matrix1D< T > &shiftY)

void	computeTotalShift (int iref, int j, const Matrix1D< T > &shiftX, const Matrix1D< T > &shiftY, T &totalShiftX, T &totalShiftY)

MultidimArray< T >	createLPF (T Ts, const Dimensions &dims)

void	loadFrame (const MetaData &movie, const Image< T > &dark, const Image< T > &igain, size_t objId, Image< T > &out) const

void	storeResults (const LocalAlignmentResult< T > &alignment)

float	getPixelResolution (float scaleFactor) const

float	getScaleFactor () const

std::pair< size_t, size_t >	getRequestedPatchSize () const

auto	getBinning () const

bool	applyBinning () const

Protected Member Functions inherited from XmippProgram
void	defineCommons ()

Additional Inherited Members
Public Member Functions inherited from AProgMovieAlignmentCorrelation< T >
void	run ()
	Run. 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

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 inherited from XmippProgram
bool	doRun

bool	runWithoutArgs

int	verbose
	Verbosity level. More...

int	debug

Protected Attributes inherited from AProgMovieAlignmentCorrelation< T >
int	nfirst

int	nlast

float	maxShift

FileName	fnAligned

FileName	fnAvg

int	nfirstSum

int	nlastSum

FileName	fnInitialAvg

std::pair< size_t, size_t >	localAlignPatches

Dimensions	localAlignmentControlPoints = Dimensions(0)

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

Static Protected Attributes inherited from AProgMovieAlignmentCorrelation< T >
static constexpr int	solverIterations = 2

Detailed Description

template<typename T>
class ProgMovieAlignmentCorrelationGPU< T >

Definition at line 38 of file movie_alignment_correlation_gpu.h.

Member Function Documentation

◆ defineParams()

template<typename T >

void ProgMovieAlignmentCorrelationGPU< T >::defineParams ( )

protectedvirtual

Define parameters.

Reimplemented from AProgMovieAlignmentCorrelation< T >.

Definition at line 36 of file movie_alignment_correlation_gpu.cpp.

                                                        {
     AProgMovieAlignmentCorrelation<T>::defineParams();
     this->addParamsLine("  [--device <dev=0>]                 : GPU device to use. 0th by default");
     this->addParamsLine("  [--storage <fn=\"\">]              : Path to file that can be used to store results of the benchmark");
     this->addParamsLine("  [--patchesAvg <avg=3>]             : Number of near frames used for averaging a single patch");
     this->addExampleLine(
                 "xmipp_cuda_movie_alignment_correlation -i movie.xmd --oaligned alignedMovie.stk --oavg alignedMicrograph.mrc --device 0");
     this->addSeeAlsoLine("xmipp_movie_alignment_correlation");
 }

◆ readParams()

template<typename T >

void ProgMovieAlignmentCorrelationGPU< T >::readParams ( )

protectedvirtual

Read argument from command line.

Reimplemented from AProgMovieAlignmentCorrelation< T >.

Definition at line 55 of file movie_alignment_correlation_gpu.cpp.

                                                      {
     AProgMovieAlignmentCorrelation<T>::readParams();
 
     // read GPU
     int device = this->getIntParam("--device");
     if (device < 0) REPORT_ERROR(ERR_ARG_INCORRECT, "Invalid GPU device");
     mGpu = core::optional<GPU>(device);
     mGpu.value().set();
 
     // read permanent storage
     storage = this->getParam("--storage");
 
     // read patch averaging
     patchesAvg = this->getIntParam("--patchesAvg");
     if (patchesAvg < 1) REPORT_ERROR(ERR_ARG_INCORRECT, "Patch averaging has to be at least 1 (one).");
 }

◆ show()

template<typename T >

void ProgMovieAlignmentCorrelationGPU< T >::show ( )

protectedvirtual

Show.

Reimplemented from AProgMovieAlignmentCorrelation< T >.

Definition at line 47 of file movie_alignment_correlation_gpu.cpp.

                                                {
     AProgMovieAlignmentCorrelation<T>::show();
     std::cout << "Device:              " << mGpu.value().device() << " (" << mGpu.value().getUUID() << ")" << "\n";
     std::cout << "Benchmark storage    " << (storage.empty() ? "Default" : storage) << "\n";
     std::cout << "Patches avg:         " << patchesAvg << "\n";
 }

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

xmipp/libraries/reconstruction_adapt_cuda/movie_alignment_correlation_gpu.h
xmipp/libraries/reconstruction_adapt_cuda/movie_alignment_correlation_gpu.cpp

Protected Member Functions

Additional Inherited Members

Detailed Description

template<typename T> class ProgMovieAlignmentCorrelationGPU< T >

Member Function Documentation

◆ defineParams()

◆ readParams()

◆ show()

template<typename T>
class ProgMovieAlignmentCorrelationGPU< T >