#include <multireference_aligneability.h>

Inheritance diagram for MultireferenceAligneability:

Collaboration diagram for MultireferenceAligneability:

Public Member Functions
	MultireferenceAligneability ()

void	readParams ()

void	defineParams ()

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
FileName	fnDir

FileName	fnSym

FileName	fin

FileName	finRef

FileName	fnInit

FileName	fnGallery

FileName	fnParticles

FileName	fnParticlesRef

bool	donNotUseWeights

bool	check_mirror

SymList	SL

size_t	rank

size_t	Nprocessors

MetaDataDb	mdPartialParticles

Public Attributes inherited from XmippProgram
bool	doRun

bool	runWithoutArgs

int	verbose
	Verbosity level. More...

int	debug

Additional Inherited Members
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

Definition at line 43 of file multireference_aligneability.h.

Constructor & Destructor Documentation

◆ MultireferenceAligneability()

MultireferenceAligneability::MultireferenceAligneability ( )

Sampling rate of the volume and projections

Definition at line 37 of file multireference_aligneability.cpp.

 {
     rank=0;
     Nprocessors=1;
 }

Member Function Documentation

◆ defineParams()

void MultireferenceAligneability::defineParams ( )

virtual

Function in which the param of each Program are defined.

Reimplemented from XmippProgram.

Definition at line 58 of file multireference_aligneability.cpp.

 {
     addUsageLine("This function takes a volume and a set of projections with orientations. The volume is projected into the set of projection directions defining the "
             "the reference projections. Thus, using the projections and references, calculation of the particle alignment precision and accuracy is carried out");
     addParamsLine("  [ -i <md_file> ]  : Input metadata with images and their angles to be validated against the volume");
     addParamsLine("  [ -i2 <md_file> ] : Input metadata of reference particles obtained projecting the volume at the same orientations that the input particles");
     addParamsLine("  [--volume <md_file=\"\">]    : Input volume to be validated");
     addParamsLine("  [--angles_file <file=\".\">]     : Input metadata with particle projections at several orientations from (usually) Significant");
     addParamsLine("  [--angles_file_ref <file=\".\">] : Input reference metadata with projections and orientations obtained projecting the volume at the several orientations from (usually) Significant");
     addParamsLine("  [--gallery <file=\".\">]         : Reference Gallery of projections ");
     addParamsLine("  [--sym <symfile=c1>]         : Enforce symmetry in projections"); //TODO the input will be two doc files one from the exp and the other from refs
     addParamsLine("  [--odir <outputDir=\".\">]   : Output directory");
     addParamsLine("  [--check_mirrors]            : Correct for mirrors in the alignment precision and accuracy estimation. In this case the precision of the projection axis without direction is computed");
     addParamsLine("  [--dontUseWeights]           : Do not use the particle weigths in the clusterability calculation ");
 
 }

◆ readParams()

void MultireferenceAligneability::readParams ( )

virtual

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

Reimplemented from XmippProgram.

Definition at line 43 of file multireference_aligneability.cpp.

 {
     fnParticles = getParam("-i");
     fnParticlesRef = getParam("-i2");
     fnInit = getParam("--volume");
     fin = getParam("--angles_file");
     finRef = getParam("--angles_file_ref");
     fnGallery = getParam("--gallery");
     fnSym = getParam("--sym");
     fnDir = getParam("--odir");
     donNotUseWeights= checkParam("--dontUseWeights");
     check_mirror = false;
     check_mirror = checkParam("--check_mirrors");
 }

◆ run()

void MultireferenceAligneability::run ( )

virtual

This function will be start running the program. it also should be implemented by derived classes.

Reimplemented from XmippProgram.

Definition at line 75 of file multireference_aligneability.cpp.

 {
     //xmipp_multireference_aligneability --volume 1BRD.vol --sym c3 --odir testMultiReference/ --angles_file testMultiReference/angles_iter001_00.xmd --angles_file_ref testMultiReference/gallery_alignment/angles_iter001_00.xmd &
     randomize_random_generator();
 
     MetaDataVec mdOutQ;
     MetaDataDb mdExp, mdExpSort, mdProj, mdGallery, mdInputParticles, mdInputParticlesRef;
     size_t maxNImg;
     FileName fnOutCL, fnOutQ;
     fnOutCL = fnDir+"/pruned_particles_alignability.xmd";
     fnOutQ = fnDir+"/validationAlignability.xmd";
 
     SL.readSymmetryFile(fnSym.c_str());
 
     mdInputParticles.read(fnParticles);
     mdInputParticlesRef.read(fnParticles);
     mdProj.read(finRef);
     mdExp.read(fin);
     mdGallery.read(fnGallery);
 
     mdExpSort.sort(mdExp,MDL_IMAGE_IDX,true,-1,0);
     size_t sz = mdExp.size();
     mdExpSort.getValue(MDL_IMAGE_IDX,maxNImg,sz);
 
     String expression;
     MDRowSql row,rowInput,rowInputRef;
 
     double validationAlignabilityPrecision, validationAlignabilityAccuracy, validationAlignability, validationMirror;
     validationAlignabilityPrecision = 0;
     validationAlignabilityAccuracy = 0;
     validationAlignability = 0;
     validationMirror = 0;
 
     if (rank==0)
         init_progress_bar(maxNImg);
 
     MetaDataVec tempMdExp, tempMdProj;
     double sum_w_exp;
     double sum_w_proj;
     double sum_noise;
     double error_mirror_exp;
     double error_mirror_proj;
 
     sum_w_exp = 0;
     sum_w_proj = 0;
     sum_noise = 0;
     error_mirror_exp = 0;
     error_mirror_proj = 0;
 
     expression = formatString("imageIndex == %lu",maxNImg);
     tempMdExp.importObjects(mdExp, MDExpression(expression));
     size_t numProjs = tempMdExp.size();
     tempMdExp.clear();
 
     //Noise
     calc_sumw2(numProjs, sum_noise, mdGallery);
 
     double rankPrec = 0.;
     double rankAccNoMirror = 0.;
     double rankAccMirror = 0.;
 
     double accuracy = 0.;
     double accuracyRef = 0.;
     double accuracyMirror = 0.;
     double accuracyMirrorRef = 0.;
 
     FileName imagePath;
 
     for (size_t i=0; i<=maxNImg;i++)
     {
         if ((i+1)%Nprocessors==rank)
         {
             expression = formatString("imageIndex == %lu",i);
             tempMdExp.importObjects(mdExp, MDExpression(expression));
             tempMdProj.importObjects(mdProj, MDExpression(expression));
             mdInputParticles.getRow(rowInput,i+1);
             mdInputParticles.getRow(rowInputRef,i+1);
 
 
             if ( (tempMdExp.size()==0) || (tempMdProj.size()==0))
                 continue;
 
             calc_sumu(tempMdExp, sum_w_exp, error_mirror_exp);
             calc_sumu(tempMdProj, sum_w_proj, error_mirror_proj);
 
             obtainAngularAccuracy(tempMdExp, rowInput, accuracy, accuracyMirror);
             obtainAngularAccuracy(tempMdProj, rowInputRef, accuracyRef, accuracyMirrorRef);
 
 #ifdef DEBUG
 
             std::cout << " " << std::endl;
             std::cout << "accuracy "    << accuracy << std::endl;
             std::cout << "accuracyRef " << accuracyRef << std::endl;
             std::cout << "accuracy2f " << accuracyRef/accuracy << std::endl;
 
 
 
 #endif
 #undef DEBUG
 
             rankPrec = 1/(sum_w_proj-sum_noise)*(sum_w_exp-sum_noise);
             rankAccMirror = 1/(accuracyRef-sum_noise)*(accuracy-sum_noise);
             rankAccNoMirror = 1/(accuracyMirrorRef-sum_noise)*(accuracyMirror-sum_noise);
 
             tempMdExp.getValue(MDL_IMAGE,imagePath,1);
             rowInput.setValue(MDL_IMAGE,imagePath);
             rowInput.setValue(MDL_IMAGE_IDX,i);
             rowInput.setValue(MDL_SCORE_BY_ALIGNABILITY_PRECISION, rankPrec);
             rowInput.setValue(MDL_SCORE_BY_ALIGNABILITY_ACCURACY, rankAccMirror);
             rowInput.setValue(MDL_SCORE_BY_MIRROR, rankAccNoMirror);
             rowInput.setValue(MDL_SCORE_BY_ALIGNABILITY_PRECISION_EXP,sum_w_exp);
             rowInput.setValue(MDL_SCORE_BY_ALIGNABILITY_PRECISION_REF,sum_w_proj);
             rowInput.setValue(MDL_SCORE_BY_ALIGNABILITY_ACCURACY_EXP,accuracy);
             rowInput.setValue(MDL_SCORE_BY_ALIGNABILITY_ACCURACY_REF,accuracyRef);
             rowInput.setValue(MDL_SCORE_BY_ALIGNABILITY_NOISE,sum_noise);
 
             mdPartialParticles.addRow(rowInput);
 
             rowInput.clear();
             rowInputRef.clear();
             tempMdExp.clear();
             tempMdProj.clear();
 
             if (rank==0)
                 progress_bar(i+1);
         }
     }
 
     synchronize();
     gatherResults();
 
 
     if (rank == 0)
     {
         mdPartialParticles.write(fnOutCL);
         row.clear();
 
         for (size_t objId : mdPartialParticles.ids())
         {
             mdPartialParticles.getValue(MDL_SCORE_BY_ALIGNABILITY_PRECISION,rankPrec,objId);
             mdPartialParticles.getValue(MDL_SCORE_BY_ALIGNABILITY_ACCURACY,rankAccMirror,objId);
             mdPartialParticles.getValue(MDL_SCORE_BY_MIRROR,rankAccNoMirror,objId);
 
             validationAlignabilityPrecision += (rankPrec>0.5);
             validationAlignabilityAccuracy += (rankAccMirror > 0.5);
             validationAlignability += ( (rankAccMirror > 0.5) && (rankPrec>0.5));
             validationMirror += (rankAccNoMirror> 0.5);
 
         }
 
         validationAlignabilityPrecision /= (maxNImg+1);
         validationAlignabilityAccuracy /= (maxNImg+1);
         validationAlignability /= (maxNImg+1);
         validationMirror /= (maxNImg+1);
 
         row.setValue(MDL_IMAGE,fnInit);
         row.setValue(MDL_WEIGHT_PRECISION_ALIGNABILITY,validationAlignabilityPrecision);
         row.setValue(MDL_WEIGHT_ACCURACY_ALIGNABILITY,validationAlignabilityAccuracy);
         row.setValue(MDL_WEIGHT_ALIGNABILITY,validationAlignability);
         row.setValue(MDL_WEIGHT_PRECISION_MIRROR,validationMirror);
 
         mdOutQ.addRow(row);
         mdOutQ.write(fnOutQ);
 
     }
 
 }