#include <pdb_construct_dictionary.h>

Inheritance diagram for ProgPDBDictionary:

Collaboration diagram for ProgPDBDictionary:

Public Member Functions
virtual void	defineParams ()

virtual void	readParams ()

virtual void	show ()

virtual void	run ()=0

void	extractPatch (const MultidimArray< double > &V, MultidimArray< double > &patch, int k, int i, int j)

void	insertPatch (MultidimArray< double > &Vhigh, MultidimArray< double > &weightHigh, const MultidimArray< double > &patchHigh, int k, int i, int j, double R2)

void	constructRotationGroup2D ()

void	constructRotationGroup3D ()

void	constructRotationGroup ()

size_t	canonicalOrientation2D (const MultidimArray< double > &patch, MultidimArray< double > &canonicalPatch, Matrix1D< double > &patchSignature)

size_t	canonicalOrientation3D (const MultidimArray< double > &patch, MultidimArray< double > &canonicalPatch, Matrix1D< double > &patchSignature)

bool	notInDictionary (const MultidimArray< double > &candidatePatch, MultidimArray< double > &canonicalPatch, Matrix1D< double > &canonicalSignature, size_t &canonicalIdx)

void	selectDictionaryPatches (const MultidimArray< double > &lowResolutionPatch, Matrix1D< double > &lowResolutionPatchSignature, std::vector< size_t > &selectedPatchesIdx, std::vector< double > &weight)

double	approximatePatch (const MultidimArray< double > &lowResolutionPatch, std::vector< size_t > &selectedPatchesIdx, std::vector< double > &weight, Matrix1D< double > &alpha)

void	reconstructPatch (size_t idxTransf, std::vector< size_t > &selectedPatchesIdx, Matrix1D< double > &alpha, MultidimArray< double > &highResolutionPatch)

void	loadDictionaries ()

void	saveDictionaries () const

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	fnRoot

int	patchSize

double	stdThreshold

double	angleThreshold

double	lambda

int	iterations

int	mode

std::vector< MultidimArray< double > >	dictionaryLow

std::vector< MultidimArray< double > >	dictionaryHigh

std::vector< Matrix1D< double > >	dictionarySignature

std::vector< Matrix2D< double > >	rotationGroup

MultidimArray< double >	auxPatch

Matrix1D< double >	auxSignature

Matrix2D< double >	Ui

Matrix2D< double >	UitUi

Matrix1D< double >	wi

Matrix1D< double >	v1

Matrix1D< double >	v2

Matrix1D< double >	y

Matrix1D< double >	yp

Matrix1D< double >	Uity

int	patchSize_2

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

Generic class to handle PDB Low and High resolution dictionary

Definition at line 38 of file pdb_construct_dictionary.h.

Member Function Documentation

◆ approximatePatch()

double ProgPDBDictionary::approximatePatch	(	const MultidimArray< double > &	lowResolutionPatch,
		std::vector< size_t > &	selectedPatchesIdx,
		std::vector< double > &	weight,
		Matrix1D< double > &	alpha
	)

Approximate patch. It returns the R2 of the approximation.

Definition at line 215 of file pdb_construct_dictionary.cpp.

 {
     Ui.initZeros(MULTIDIM_SIZE(lowResolutionPatch),selectedPatchesIdx.size());
 
     // Prepare Ui
     for (size_t j=0; j<MAT_XSIZE(Ui); ++j)
     {
         const double *ptr=MULTIDIM_ARRAY(dictionaryLow[selectedPatchesIdx[j]]);
         for (size_t i=0; i<MAT_YSIZE(Ui); ++i, ++ptr)
             MAT_ELEM(Ui,i,j)=*ptr;
     }
     matrixOperation_AtA(Ui,UitUi);
 
     // Prepare y
     y.resizeNoCopy(MULTIDIM_SIZE(lowResolutionPatch));
     memcpy(&VEC_ELEM(y,0),&DIRECT_MULTIDIM_ELEM(lowResolutionPatch,0),MULTIDIM_SIZE(lowResolutionPatch)*sizeof(double));
     matrixOperation_Atx(Ui,y,Uity);
 
     // Solve Least Squares problem
     solveBySVD(UitUi,Uity,alpha,1e-6);
 
     // Calculate R2
     matrixOperation_Ax(Ui,alpha,yp);
     double diff2=0.0, norm2=0.0;
     double ymean=y.computeMean();
     FOR_ALL_ELEMENTS_IN_MATRIX1D(y)
     {
         double diff=VEC_ELEM(y,i)-VEC_ELEM(yp,i);
         diff2+=diff*diff;
         diff=VEC_ELEM(y,i)-ymean;
         norm2+=diff*diff;
     }
     double R2=1-diff2/norm2;
     return R2;
 }

◆ canonicalOrientation2D()

size_t ProgPDBDictionary::canonicalOrientation2D	(	const MultidimArray< double > &	patch,
		MultidimArray< double > &	canonicalPatch,
		Matrix1D< double > &	patchSignature
	)

Orient canonically a patch

Definition at line 467 of file pdb_construct_dictionary.cpp.

 {
     patchSignature.resizeNoCopy(4);
     size_t nmax=rotationGroup.size();
     double bestMoment=-1e38;
     size_t bestIdx=0;
     for (size_t n=0; n<nmax; ++n)
     {
         applyGeometry(xmipp_transformation::LINEAR,auxPatch,patch,rotationGroup[n],xmipp_transformation::IS_INV,xmipp_transformation::DONT_WRAP);
         // Calculate gradients
         double momentX=0, momentY=0, momentXmY=0, momentXY=0;
         auxPatch.setXmippOrigin();
         FOR_ALL_ELEMENTS_IN_ARRAY2D(auxPatch)
         {
             double val=A2D_ELEM(auxPatch,i,j);
             double jval=j*val;
             double ival=i*val;
             momentX+=jval;
             momentY+=ival;
             momentXmY+=jval-ival;
             momentXY+=jval+ival;
         }
         double moment=momentX+momentY;
         if (moment>bestMoment)
         {
             bestMoment=moment;
             bestIdx=n;
             canonicalPatch=auxPatch;
             VEC_ELEM(patchSignature,0)=momentX;
             VEC_ELEM(patchSignature,1)=momentY;
             VEC_ELEM(patchSignature,2)=momentXmY;
             VEC_ELEM(patchSignature,3)=momentXY;
         }
     }
     patchSignature.selfNormalize();
     return bestIdx;
 }

◆ canonicalOrientation3D()

size_t ProgPDBDictionary::canonicalOrientation3D	(	const MultidimArray< double > &	patch,
		MultidimArray< double > &	canonicalPatch,
		Matrix1D< double > &	patchSignature
	)

Orient canonically a patch

Definition at line 506 of file pdb_construct_dictionary.cpp.

 {
     patchSignature.resizeNoCopy(3);
     size_t nmax=rotationGroup.size();
     double bestMoment=-1e38;
     size_t bestIdx=0;
     for (size_t n=0; n<nmax; ++n)
     {
         applyGeometry(xmipp_transformation::LINEAR,auxPatch,patch,rotationGroup[n],xmipp_transformation::IS_INV,xmipp_transformation::DONT_WRAP);
         // Calculate gradients
         double momentX=0, momentY=0, momentZ=0;
         auxPatch.setXmippOrigin();
         FOR_ALL_ELEMENTS_IN_ARRAY3D(auxPatch)
         {
             double val=A3D_ELEM(auxPatch,k,i,j);
             momentX+=j*val;
             momentY+=i*val;
             momentZ+=k*val;
         }
         double moment=momentX+momentY+momentZ;
         if (moment>bestMoment)
         {
             bestMoment=moment;
             bestIdx=n;
             canonicalPatch=auxPatch;
             XX(patchSignature)=momentX;
             YY(patchSignature)=momentY;
             ZZ(patchSignature)=momentZ;
         }
     }
     patchSignature.selfNormalize();
     return bestIdx;
 }

◆ constructRotationGroup()

void ProgPDBDictionary::constructRotationGroup ( )

Construct rotation group

Definition at line 439 of file pdb_construct_dictionary.cpp.

 {
     Matrix2D<double> B;
     bool finished;
     do
     {
         finished=true;
         for (size_t i=0; i<rotationGroup.size(); ++i)
             for (size_t j=0; j<rotationGroup.size(); ++j)
             {
                 B=rotationGroup[i]*rotationGroup[j];
                 bool found=false;
                 for (size_t k=0; k<rotationGroup.size(); ++k)
                     if (rotationGroup[k].equal(B))
                     {
                         found=true;
                         break;
                     }
                 if (!found)
                 {
                     rotationGroup.push_back(B);
                     finished=false;
                 }
             }
     } while (!finished);
     std::cout << "Size of rotation group=" << rotationGroup.size() << std::endl;
 }

◆ constructRotationGroup2D()

void ProgPDBDictionary::constructRotationGroup2D ( )

Construct rotation group 2D

Definition at line 389 of file pdb_construct_dictionary.cpp.

 {
     Matrix2D<double> A(3,3);
     A.initIdentity();
     rotationGroup.push_back(A);
 
     A.initZeros();
     A(0,0)=-1; A(1,1)=1; A(2,2)=1;
     rotationGroup.push_back(A);
 
     A.initZeros();
     A(0,0)=1; A(1,1)=-1; A(2,2)=1;
     rotationGroup.push_back(A);
 
     A.initZeros();
     A(0,1)=1; A(1,0)=-1; A(2,2)=1;
     rotationGroup.push_back(A);
 
     constructRotationGroup();
 }

◆ constructRotationGroup3D()

void ProgPDBDictionary::constructRotationGroup3D ( )

Construct rotation group 3D

Definition at line 410 of file pdb_construct_dictionary.cpp.

 {
     Matrix2D<double> A(4,4);
     A.initIdentity();
     rotationGroup.push_back(A);
 
     A.initZeros();
     A(0,1)=A(2,2)=1; A(1,0)=-1; A(3,3)=1;
     rotationGroup.push_back(A);
 
     A.initZeros();
     A(2,0)=1; A(1,1)=1; A(0,2)=1; A(3,3)=1;
     rotationGroup.push_back(A);
 
     A.initZeros();
     A(0,0)=1; A(1,2)=-1; A(2,1)=1; A(3,3)=1;
     rotationGroup.push_back(A);
 
     A.initZeros();
     A(0,0)=-1; A(2,2)=1; A(1,1)=1; A(3,3)=1;
     rotationGroup.push_back(A);
 
     A.initZeros();
     A(0,0)=1; A(1,1)=-1; A(2,2)=1; A(3,3)=1;
     rotationGroup.push_back(A);
 
     constructRotationGroup();
 }

◆ defineParams()

void ProgPDBDictionary::defineParams ( )

virtual

Function in which the param of each Program are defined.

Reimplemented from XmippProgram.

Reimplemented in ProgConstructPDBDictionary, and ProgRestoreWithPDBDictionary.

Definition at line 35 of file pdb_construct_dictionary.cpp.

 {
     // Parameters
     addParamsLine(" [--stdThreshold <s=0.25>] : Threshold on the standard deviation to include a patch");
     addParamsLine(" [--angleThreshold <s=20>] : Threshold in degrees on the angle to consider a patch");
     addParamsLine(" [--regularization <lambda=0.01>] : Regularization factor for the approximation phase");
     addParamsLine(" [--iter <s=50>] : Number of iterations");
     addParamsLine(" [--mode <m=\"3D\">] : 3D, 2Dx, 2Dy, 2Dz mode");
 }

◆ extractPatch()

void ProgPDBDictionary::extractPatch	(	const MultidimArray< double > &	V,
		MultidimArray< double > &	patch,
		int	k,
		int	i,
		int	j
	)

Extract Patch from volume

Definition at line 323 of file pdb_construct_dictionary.cpp.

 {
     if (mode==0)
         V.window(patch,k-patchSize_2,i-patchSize_2,j-patchSize_2,k+patchSize_2,i+patchSize_2,j+patchSize_2);
     else if (mode==1)
     {
         for (int kk=-patchSize_2; kk<=patchSize_2; ++kk)
             for (int ii=-patchSize_2; ii<=patchSize_2; ++ii)
                 A2D_ELEM(patch,kk,ii)=A3D_ELEM(V,k+kk,i+ii,j);
     }
     else if (mode==2)
     {
         for (int kk=-patchSize_2; kk<=patchSize_2; ++kk)
             for (int jj=-patchSize_2; jj<=patchSize_2; ++jj)
                 A2D_ELEM(patch,kk,jj)=A3D_ELEM(V,k+kk,i,j+jj);
     }
     else if (mode==3)
     {
         for (int ii=-patchSize_2; ii<=patchSize_2; ++ii)
             for (int jj=-patchSize_2; jj<=patchSize_2; ++jj)
                 A2D_ELEM(patch,ii,jj)=A3D_ELEM(V,k,i+ii,j+jj);
     }
 }

◆ insertPatch()

void ProgPDBDictionary::insertPatch	(	MultidimArray< double > &	Vhigh,
		MultidimArray< double > &	weightHigh,
		const MultidimArray< double > &	patchHigh,
		int	k,
		int	i,
		int	j,
		double	R2
	)

Insert Patch into volume

Definition at line 347 of file pdb_construct_dictionary.cpp.

 {
     if (mode==0)
     {
         for (int kk=-patchSize_2; kk<=patchSize_2; ++kk)
             for (int ii=-patchSize_2; ii<=patchSize_2; ++ii)
                 for (int jj=-patchSize_2; jj<=patchSize_2; ++jj)
                 {
                     A3D_ELEM(Vhigh,k+kk,i+ii,j+jj)+=R2*A3D_ELEM(patchHigh,kk,ii,jj);
                     A3D_ELEM(weightHigh,k+kk,i+ii,j+jj)+=R2;
                 }
     }
     else if (mode==1)
     {
         for (int kk=-patchSize_2; kk<=patchSize_2; ++kk)
             for (int ii=-patchSize_2; ii<=patchSize_2; ++ii)
             {
                 A3D_ELEM(Vhigh,k+kk,i+ii,j)+=R2*A2D_ELEM(patchHigh,kk,ii);
                 A3D_ELEM(weightHigh,k+kk,i+ii,j)+=R2;
             }
     }
     else if (mode==2)
     {
         for (int kk=-patchSize_2; kk<=patchSize_2; ++kk)
             for (int jj=-patchSize_2; jj<=patchSize_2; ++jj)
             {
                 A3D_ELEM(Vhigh,k+kk,i,j+jj)+=R2*A2D_ELEM(patchHigh,kk,jj);
                 A3D_ELEM(weightHigh,k+kk,i,j+jj)+=R2;
             }
     }
     else if (mode==3)
     {
         for (int ii=-patchSize_2; ii<=patchSize_2; ++ii)
             for (int jj=-patchSize_2; jj<=patchSize_2; ++jj)
             {
                 A3D_ELEM(Vhigh,k,i+ii,j+jj)+=R2*A2D_ELEM(patchHigh,ii,jj);
                 A3D_ELEM(weightHigh,k,i+ii,j+jj)+=R2;
             }
     }
 }

◆ loadDictionaries()

void ProgPDBDictionary::loadDictionaries ( )

Load dictionaries

Definition at line 265 of file pdb_construct_dictionary.cpp.

 {
     std::cout << "Loading dictionaries .." << std::endl;
     size_t Xdim, Ydim, Zdim, Ndim;
     FileName fnLow=fnRoot+"_low.mrcs";
     FileName fnHigh=fnRoot+"_high.mrcs";
     FileName fnSignature=fnRoot+"_signature.raw";
     getImageSize(fnLow, Xdim, Ydim, Zdim, Ndim);
     patchSize=Xdim;
     dictionaryLow.reserve(Ndim);
     dictionaryHigh.reserve(Ndim);
     FILE *fhSignature=fopen(fnSignature.c_str(),"r");
     Image<double> aux;
     Matrix1D<double> auxSignature(3);
     if (Zdim==1)
         auxSignature.resizeNoCopy(4);
     for (size_t n=0; n<Ndim; ++n)
     {
         aux.read(fnLow,DATA,n+1);
         dictionaryLow.push_back(aux());
         aux.read(fnHigh,DATA,n+1);
         dictionaryHigh.push_back(aux());
         size_t sizeRead=fread(MATRIX1D_ARRAY(auxSignature),sizeof(double),VEC_XSIZE(auxSignature),fhSignature);
         if (sizeRead==VEC_XSIZE(auxSignature))
             dictionarySignature.push_back(auxSignature);
     }
     fclose(fhSignature);
     if (dictionarySignature.size()!=dictionaryLow.size())
         REPORT_ERROR(ERR_INDEX_OUTOFBOUNDS,"The dictionary is corrupted: the number of signatures does not correspond to the number of patches");
 }

◆ notInDictionary()

bool ProgPDBDictionary::notInDictionary	(	const MultidimArray< double > &	candidatePatch,
		MultidimArray< double > &	canonicalPatch,
		Matrix1D< double > &	canonicalSignature,
		size_t &	canonicalIdx
	)

True if the patch is not already in the low resolution dictionary

Definition at line 74 of file pdb_construct_dictionary.cpp.

 {
     if (mode==0)
         canonicalIdx=canonicalOrientation3D(candidatePatch,canonicalPatch,canonicalSignature);
     else
         canonicalIdx=canonicalOrientation2D(candidatePatch,canonicalPatch,canonicalSignature);
     size_t imax=dictionaryLow.size();
 
     for (size_t i=0; i<imax; ++i)
     {
         const Matrix1D<double> &dictSignature=dictionarySignature[i];
         double dotProduct=0;
         for (size_t j=0; j<VEC_XSIZE(dictSignature); ++j)
            dotProduct+=VEC_ELEM(canonicalSignature,j)*VEC_ELEM(dictSignature,j);
         if (dotProduct>angleThreshold)
         {
             const MultidimArray<double> &dictionaryPatch=dictionaryLow[i];
             dotProduct=0;
             FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(dictionaryPatch)
                 dotProduct+=DIRECT_MULTIDIM_ELEM(dictionaryPatch,n)*DIRECT_MULTIDIM_ELEM(canonicalPatch,n);
             if (dotProduct>angleThreshold)
                 return false;
         }
     }
     return true;
 }

◆ readParams()

void ProgPDBDictionary::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.

Reimplemented in ProgConstructPDBDictionary, and ProgRestoreWithPDBDictionary.

Definition at line 45 of file pdb_construct_dictionary.cpp.

 {
     stdThreshold=getDoubleParam("--stdThreshold");
     angleThreshold=cos(DEG2RAD(getDoubleParam("--angleThreshold")));
     lambda=getDoubleParam("--regularization");
     iterations=getIntParam("--iter");
     String modeStr=getParam("--mode");
     if (modeStr=="3D")
         mode=0;
     else if (modeStr=="2Dx")
         mode=1;
     else if (modeStr=="2Dy")
         mode=2;
     else if (modeStr=="2Dz")
         mode=3;
 }

◆ reconstructPatch()

void ProgPDBDictionary::reconstructPatch	(	size_t	idxTransf,
		std::vector< size_t > &	selectedPatchesIdx,
		Matrix1D< double > &	alpha,
		MultidimArray< double > &	highResolutionPatch
	)

Reconstruct patch

Definition at line 252 of file pdb_construct_dictionary.cpp.

 {
     const Matrix2D<double> &A=rotationGroup[idxTransf];
     for (size_t j=0; j<VEC_XSIZE(alpha); ++j)
     {
         applyGeometry(xmipp_transformation::LINEAR,auxPatch,dictionaryHigh[selectedPatchesIdx[j]],A,xmipp_transformation::IS_NOT_INV,xmipp_transformation::DONT_WRAP);
         const double *ptr=MULTIDIM_ARRAY(auxPatch);
         for (size_t n=0; n<MULTIDIM_SIZE(highResolutionPatch); ++n, ++ptr)
             DIRECT_MULTIDIM_ELEM(highResolutionPatch,n)+=VEC_ELEM(alpha,j)*(*ptr);
     }
 }

◆ run()

virtual void ProgPDBDictionary::run ( )

pure virtual

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

Reimplemented from XmippProgram.

Implemented in ProgConstructPDBDictionary, and ProgRestoreWithPDBDictionary.

◆ saveDictionaries()

void ProgPDBDictionary::saveDictionaries ( ) const

Save dictionaries

Definition at line 296 of file pdb_construct_dictionary.cpp.

 {
     std::cout << "Saving dictionaries ..." << std::endl;
     size_t imax=dictionaryLow.size();
     FileName fnLow=fnRoot+"_low.mrcs";
     FileName fnHigh=fnRoot+"_high.mrcs";
     FileName fnSignature=fnRoot+"_signature.raw";
     int Zdim;
     if (mode==0)
         Zdim=patchSize;
     else
         Zdim=1;
     createEmptyFile(fnLow,patchSize,patchSize,Zdim,imax,true);
     createEmptyFile(fnHigh,patchSize,patchSize,Zdim,imax,true);
     Image<double> aux;
     FILE *fhSignature=fopen(fnSignature.c_str(),"wb");
     for (size_t i=0; i<imax; ++i)
     {
         aux()=dictionaryLow[i];
         aux.write(fnLow,i+1,true,WRITE_REPLACE);
         aux()=dictionaryHigh[i];
         aux.write(fnHigh,i+1,true,WRITE_REPLACE);
         fwrite(MATRIX1D_ARRAY(dictionarySignature[i]),sizeof(double),VEC_XSIZE(dictionarySignature[i]),fhSignature);
     }
     fclose(fhSignature);
 }

◆ selectDictionaryPatches()

void ProgPDBDictionary::selectDictionaryPatches	(	const MultidimArray< double > &	lowResolutionPatch,
		Matrix1D< double > &	lowResolutionPatchSignature,
		std::vector< size_t > &	selectedPatchesIdx,
		std::vector< double > &	weight
	)

Select dictionary patches for a low resolution patch

Definition at line 103 of file pdb_construct_dictionary.cpp.

 {
     selectedPatchesIdx.clear();
     weight.clear();
     size_t imax=dictionaryLow.size();
     for (size_t i=0; i<imax; ++i)
     {
         const Matrix1D<double> &dictSignature=dictionarySignature[i];
         double dotProduct=0;
         for (size_t j=0; j<VEC_XSIZE(dictSignature); ++j)
            dotProduct+=VEC_ELEM(lowResolutionPatchSignature,j)*VEC_ELEM(dictSignature,j);
         if (dotProduct>angleThreshold)
         {
             const double *ptrDictionaryPatch=MULTIDIM_ARRAY(dictionaryLow[i]);
             dotProduct=0;
             FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(lowResolutionPatch)
                 dotProduct+=(*ptrDictionaryPatch++)*DIRECT_MULTIDIM_ELEM(lowResolutionPatch,n);
             if (dotProduct>angleThreshold)
             {
                 if (dotProduct>1)
                     dotProduct=1;
                 selectedPatchesIdx.push_back(i);
                 weight.push_back(1/dotProduct);
     #ifdef DEBUG
                 Image<double> save;
                 save()=lowResolutionPatch;
                 save.write("PPPexperimentalPatch.vol");
                 memcpy(&DIRECT_MULTIDIM_ELEM(save(),0),MULTIDIM_ARRAY(dictionaryLow[i]),
                         MULTIDIM_SIZE(lowResolutionPatch)*sizeof(double));
                 save.write("PPPdictionaryPatch.vol");
                 std::cout << RAD2DEG(acos(dotProduct)) << ". Press any key" << std::endl;
                 char c; std::cin >> c;
     #endif
             }
         }
     }
 #ifdef DEBUG
     std::cout << "Size idx=" << selectedPatchesIdx.size() << std::endl;
     std::cout << "Weights=";
     for (size_t i=0; i<weight.size(); ++i)
         std::cout << weight[i] << " ";
     std::cout << std::endl;
 #endif
 }

◆ show()

void ProgPDBDictionary::show ( )

virtual

Reimplemented in ProgConstructPDBDictionary, and ProgRestoreWithPDBDictionary.

Definition at line 62 of file pdb_construct_dictionary.cpp.

 {
     if (verbose)
         std::cout
         << "Std threshold:       " << stdThreshold   << std::endl
         << "Angle threshold:     " << angleThreshold << std::endl
         << "Iterations:          " << iterations     << std::endl
         << "Regularization:      " << lambda         << std::endl
         << "Mode:                " << mode           << std::endl
         ;
 }

Member Data Documentation

◆ angleThreshold

double ProgPDBDictionary::angleThreshold

Definition at line 50 of file pdb_construct_dictionary.h.

◆ auxPatch

MultidimArray<double> ProgPDBDictionary::auxPatch

Auxiliary patch

Definition at line 72 of file pdb_construct_dictionary.h.

◆ auxSignature

Matrix1D<double> ProgPDBDictionary::auxSignature

Signature

Definition at line 75 of file pdb_construct_dictionary.h.

◆ dictionaryHigh

std::vector< MultidimArray<double> > ProgPDBDictionary::dictionaryHigh

Definition at line 63 of file pdb_construct_dictionary.h.

◆ dictionaryLow

std::vector< MultidimArray<double> > ProgPDBDictionary::dictionaryLow

Low resolution and high resolution dictionary

Definition at line 63 of file pdb_construct_dictionary.h.

◆ dictionarySignature

std::vector< Matrix1D<double> > ProgPDBDictionary::dictionarySignature

Signature dictionary

Definition at line 66 of file pdb_construct_dictionary.h.

◆ fnRoot

FileName ProgPDBDictionary::fnRoot

Dictionary rootname

Definition at line 42 of file pdb_construct_dictionary.h.

◆ iterations

int ProgPDBDictionary::iterations

Definition at line 56 of file pdb_construct_dictionary.h.

◆ lambda

double ProgPDBDictionary::lambda

Definition at line 53 of file pdb_construct_dictionary.h.

◆ mode

int ProgPDBDictionary::mode

Definition at line 59 of file pdb_construct_dictionary.h.

◆ patchSize

int ProgPDBDictionary::patchSize

Patch is of size size x size x size

Definition at line 45 of file pdb_construct_dictionary.h.

◆ patchSize_2

int ProgPDBDictionary::patchSize_2

Definition at line 80 of file pdb_construct_dictionary.h.

◆ rotationGroup

std::vector< Matrix2D<double> > ProgPDBDictionary::rotationGroup

Rotation group

Definition at line 69 of file pdb_construct_dictionary.h.

◆ stdThreshold

double ProgPDBDictionary::stdThreshold

A patch is candidate if its standard deviation is at least this factor of the total standard deviation

Definition at line 48 of file pdb_construct_dictionary.h.

◆ Ui

Matrix2D<double> ProgPDBDictionary::Ui

Definition at line 78 of file pdb_construct_dictionary.h.

◆ UitUi

Matrix2D<double> ProgPDBDictionary::UitUi

Definition at line 78 of file pdb_construct_dictionary.h.

◆ Uity

Matrix1D<double> ProgPDBDictionary::Uity

Definition at line 79 of file pdb_construct_dictionary.h.

◆ v1

Matrix1D<double> ProgPDBDictionary::v1

Definition at line 79 of file pdb_construct_dictionary.h.

◆ v2

Matrix1D<double> ProgPDBDictionary::v2

Definition at line 79 of file pdb_construct_dictionary.h.

◆ wi

Matrix1D<double> ProgPDBDictionary::wi

Definition at line 79 of file pdb_construct_dictionary.h.

◆ y

Matrix1D<double> ProgPDBDictionary::y

Definition at line 79 of file pdb_construct_dictionary.h.

◆ yp

Matrix1D<double> ProgPDBDictionary::yp

Definition at line 79 of file pdb_construct_dictionary.h.

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

xmipp/legacy/libraries/reconstruction/pdb_construct_dictionary.h
xmipp/legacy/libraries/reconstruction/pdb_construct_dictionary.cpp

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ approximatePatch()

◆ canonicalOrientation2D()

◆ canonicalOrientation3D()

◆ constructRotationGroup()

◆ constructRotationGroup2D()

◆ constructRotationGroup3D()

◆ defineParams()

◆ extractPatch()

◆ insertPatch()

◆ loadDictionaries()

◆ notInDictionary()

◆ readParams()

◆ reconstructPatch()

◆ run()

◆ saveDictionaries()

◆ selectDictionaryPatches()

◆ show()

Member Data Documentation

◆ angleThreshold

◆ auxPatch

◆ auxSignature

◆ dictionaryHigh

◆ dictionaryLow

◆ dictionarySignature

◆ fnRoot

◆ iterations

◆ lambda

◆ mode

◆ patchSize

◆ patchSize_2

◆ rotationGroup

◆ stdThreshold

◆ Ui

◆ UitUi

◆ Uity

◆ v1

◆ v2

◆ wi

◆ y

◆ yp