#include <pdb_restore_with_dictionary.h>

Inheritance diagram for ProgRestoreWithPDBDictionary:

Collaboration diagram for ProgRestoreWithPDBDictionary:

Public Member Functions
void	defineParams ()

void	readParams ()

void	show ()

void	run ()

Public Member Functions inherited from ProgPDBDictionary
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	fnIn

FileName	fnOut

Public Attributes inherited from ProgPDBDictionary
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

Restore with Low and High resolution dictionary

Definition at line 34 of file pdb_restore_with_dictionary.h.

Member Function Documentation

◆ defineParams()

void ProgRestoreWithPDBDictionary::defineParams ( )

virtual

Function in which the param of each Program are defined.

Reimplemented from ProgPDBDictionary.

Definition at line 30 of file pdb_restore_with_dictionary.cpp.

 {
     // Usage
     addUsageLine("This program takes a set of PDB files at low and high resolution and constructs a dictionary for them.");
 
     // Parameters
     addParamsLine(" -i <volume>      : Volume to restore");
     addParamsLine(" [-o <volume=\"\">] : Restored volume");
     addParamsLine(" [--root <root=dictionary>] : Rootname of the dictionary");
     ProgPDBDictionary::defineParams();
 }

◆ readParams()

void ProgRestoreWithPDBDictionary::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 ProgPDBDictionary.

Definition at line 42 of file pdb_restore_with_dictionary.cpp.

 {
     fnIn=getParam("-i");
     fnOut=getParam("-o");
     if (fnOut=="")
         fnOut=fnIn;
     fnRoot=getParam("--root");
     ProgPDBDictionary::readParams();
 }

◆ run()

void ProgRestoreWithPDBDictionary::run ( )

virtual

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

Implements ProgPDBDictionary.

Definition at line 66 of file pdb_restore_with_dictionary.cpp.

 {
     show();
     loadDictionaries();
     constructRotationGroup3D();
 
     Image<double> V, Vhigh;
     MultidimArray<double> weightHigh;
     V.read(fnIn);
     const MultidimArray<double> &mV=V();
     double min, max, mean, std=0;
     mV.computeStats(mean,std,min,max);
 
     MultidimArray<double> patchLow, patchLowNormalized, canonicalPatch, patchHigh;
     patchSize_2=patchSize/2;
     if (mode==0)
         patchLow.resizeNoCopy(patchSize,patchSize,patchSize);
     else
         patchLow.resizeNoCopy(patchSize,patchSize);
     patchLow.setXmippOrigin();
     size_t Npatches=0, NcandidatePatches=0;
 
     std::vector< size_t > selectedPatchesIdx;
     std::vector<double> weight;
     Matrix1D<double> alpha, canonicalSignature;
     init_progress_bar(ZSIZE(mV));
     Vhigh().initZeros(mV);
     weightHigh.initZeros(mV);
     MultidimArray<double> &mVhigh=Vhigh();
     for (int k=patchSize_2; k<(int)ZSIZE(mV)-patchSize_2; ++k)
     {
         for (int i=patchSize_2; i<(int)ZSIZE(mV)-patchSize_2; ++i)
             for (int j=patchSize_2; j<(int)ZSIZE(mV)-patchSize_2; ++j)
             {
                  ++Npatches;
                  extractPatch(mV,patchLow,k,i,j);
 
                 double minPatchLow, maxPatchLow, meanPatchLow, stdPatchLow=0;
                 patchLow.computeStats(meanPatchLow,stdPatchLow,minPatchLow,maxPatchLow);
                 double R2=0;
                 patchHigh.initZeros(patchLow);
 
                 if (stdPatchLow > stdThreshold*std)
                 {
                     ++NcandidatePatches;
                     patchLowNormalized=patchLow;
                     double norm=sqrt(patchLow.sum2());
                     patchLowNormalized*=1.0/norm;
                     size_t idxTransf=0;
                     if (mode==0)
                         idxTransf=canonicalOrientation3D(patchLowNormalized,canonicalPatch,canonicalSignature);
                     else
                         idxTransf=canonicalOrientation2D(patchLowNormalized,canonicalPatch,canonicalSignature);
                     selectDictionaryPatches(canonicalPatch, canonicalSignature, selectedPatchesIdx, weight);
                     if (selectedPatchesIdx.size()>0)
                     {
                         R2=approximatePatch(canonicalPatch,selectedPatchesIdx,weight,alpha);
                         reconstructPatch(idxTransf,selectedPatchesIdx,alpha,patchHigh);
                         patchHigh*=norm;
                         R2*=norm;
 //                      Image<double> save;
 //                      save()=patchLow;
 //                      save.write("PPPlow.vol");
 //                      save()=patchHigh;
 //                      save.write("PPPhigh.vol");
 //                      std::cout << "R2=" << R2 << " alpha=" << alpha << std::endl;
 //                      std::cout << "Press any key" << std::endl;
 //                      char c; std::cin >> c;
                     }
                 }
                 // Insert patchHigh in Vhigh
                 insertPatch(mVhigh,weightHigh,patchHigh,k,i,j,R2);
             }
         progress_bar(k);
     }
     progress_bar(ZSIZE(mV));
 
     // Correct by the Vhigh weights
 //  Image<double> save;
 //  save()=weightHigh;
 //  save.write("PPPweightHigh.vol");
 //  save()=mVhigh;
 //  save.write("PPPVHigh.vol");
     FOR_ALL_ELEMENTS_IN_ARRAY3D(mVhigh)
     if (A3D_ELEM(weightHigh,k,i,j)>0)
         A3D_ELEM(mVhigh,k,i,j)/=A3D_ELEM(weightHigh,k,i,j);
 
     Vhigh.write(fnOut);
 }

◆ show()

void ProgRestoreWithPDBDictionary::show ( )

virtual

Reimplemented from ProgPDBDictionary.

Definition at line 53 of file pdb_restore_with_dictionary.cpp.

 {
     if (verbose)
     {
         std::cout
         << "Input volume:        " << fnIn              << std::endl
         << "Output volume:       " << fnOut             << std::endl
         ;
         ProgPDBDictionary::show();
     }
 }

Member Data Documentation

◆ fnIn

FileName ProgRestoreWithPDBDictionary::fnIn

Input and output volume names

Definition at line 38 of file pdb_restore_with_dictionary.h.

◆ fnOut

FileName ProgRestoreWithPDBDictionary::fnOut

Definition at line 38 of file pdb_restore_with_dictionary.h.

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

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

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ defineParams()

◆ readParams()

◆ run()

◆ show()

Member Data Documentation

◆ fnIn

◆ fnOut