#include <analyze_cluster.h>

Inheritance diagram for ProgAnalyzeCluster:

Collaboration diagram for ProgAnalyzeCluster:

Public Member Functions
void	readParams ()
	Read argument from command line. More...

void	show ()
	Show. More...

void	defineParams ()
	Define parameters. More...

void	produceSideInfo (MDLabel image_label=MDL_IMAGE)
	Produce side info. More...

void	produceBasis (MultidimArray< double > &basis)
	Produce basis. More...

void	run ()
	Main routine. 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
FileName	fnSel

FileName	fnRef

FileName	fnOut

FileName	fnOutBasis

int	NPCA

int	Niter

double	distThreshold

bool	dontMask

bool	basis

MetaDataVec	SFin

MetaDataVec	SFout

MultidimArray< int >	mask

PCAMahalanobisAnalyzer	pcaAnalyzer

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

Analyze cluster parameters.

Definition at line 38 of file analyze_cluster.h.

Member Function Documentation

◆ defineParams()

void ProgAnalyzeCluster::defineParams ( )

virtual

Define parameters.

Reimplemented from XmippProgram.

Definition at line 66 of file analyze_cluster.cpp.

 {
     addUsageLine("Score the images in a cluster according to their PCA projection");
     addUsageLine("It is assumed that the cluster is aligned as is the case of the output of CL2D or ML2D");
     addParamsLine("   -i <metadatafile>             : metadata file  with images assigned to the cluster");
     addParamsLine("   -o <metadatafile>             : output metadata");
     addParamsLine("  [--ref <img=\"\">]             : if an image is provided, differences are computed with respect to it");
     addParamsLine("  [--basis <stackName>]          : write the average (image 1), standard deviation (image 2)");
     addParamsLine("                                 : and basis of the PCA in a stack");
     addParamsLine("  [--NPCA <dim=2>]               : PCA dimension");
     addParamsLine("  [--iter <N=10>]                : Number of iterations");
     addParamsLine("  [--maxDist <d=3>]              : Maximum distance");
     addParamsLine("                                 : Set to -1 if you don't want to filter images");
     addParamsLine("  [--dontMask]                   : Don't use a circular mask");
     addExampleLine("xmipp_classify_analyze_cluster -i images.sel --ref referenceImage.xmp -o sortedImages.xmd --basis basis.stk");
 }

◆ produceBasis()

void ProgAnalyzeCluster::produceBasis ( MultidimArray< double > & basis )

Produce basis.

Definition at line 189 of file analyze_cluster.cpp.

 {
     int iimax=pcaAnalyzer.PCAbasis.size();
     basis.initZeros(iimax,1,YSIZE(mask),XSIZE(mask));
     for (size_t ii=0; ii<pcaAnalyzer.PCAbasis.size(); ii++)
     {
         int idx=0;
         double *ptrBasis=&DIRECT_NZYX_ELEM(basis, ii, 0, 0, 0);
         const MultidimArray<double> &PCAbasis_ii=pcaAnalyzer.PCAbasis[ii];
         FOR_ALL_DIRECT_ELEMENTS_IN_ARRAY2D(mask)
         if (DIRECT_A2D_ELEM(mask,i,j))
             ptrBasis[i*XSIZE(mask)+j]=A1D_ELEM(PCAbasis_ii,idx++);
     }
 }

◆ produceSideInfo()

void ProgAnalyzeCluster::produceSideInfo ( MDLabel image_label = MDL_IMAGE )

Produce side info.

Definition at line 85 of file analyze_cluster.cpp.

 {
     basis = fnOutBasis!="";
 
     // Read input selfile and reference
     if (SFin.size()==0)
     {
         SFin.read(fnSel);
         if (SFin.size()==0)
             return;
         if (SFin.containsLabel(MDL_ENABLED))
             SFin.removeObjects(MDValueEQ(MDL_ENABLED, -1));
         MetaDataVec SFaux;
         SFaux.removeDuplicates(SFin,MDL_IMAGE);
         SFin=SFaux;
     }
     bool subtractRef=false;
     Image<double> Iref;
     if (fnRef!="")
     {
         subtractRef=true;
         Iref.read(fnRef);
         Iref().setXmippOrigin();
     }
 
     // Prepare mask
     size_t Xdim;
     size_t Ydim;
     size_t Zdim;
     size_t Ndim;
     getImageSize(SFin,Xdim,Ydim,Zdim,Ndim,image_label);
     mask.resize(Ydim,Xdim);
     mask.setXmippOrigin();
     if (dontMask)
         mask.initConstant(1);
     else
         BinaryCircularMask(mask,Xdim/2, INNER_MASK);
     auto Npixels=(int)mask.sum();
 
     // Read all images in the class and subtract the mean
     // once aligned
     Image<double> I;
     Image<double> Iaux;
     pcaAnalyzer.clear();
     pcaAnalyzer.reserve(SFin.size());
     if (verbose>0)
     {
         std::cerr << "Processing cluster ...\n";
         init_progress_bar(SFin.size());
     }
     int n=0;
     MultidimArray<float> v(Npixels);
     const MultidimArray<double> &mIref=Iref();
     MultidimArray<double> Ialigned;
     MultidimArray<double> ImirrorAligned;
     Matrix2D<double> M;
     AlignmentAux aux;
     CorrelationAux aux2;
     RotationalCorrelationAux aux3;
     FileName fnImg;
     for (size_t objId : SFin.ids())
     {
         SFin.getValue(image_label,fnImg, objId);
         I.readApplyGeo( fnImg, SFin, objId);
         if (XSIZE(I())!=Xdim || YSIZE(I())!=Ydim)
             REPORT_ERROR(ERR_MULTIDIM_SIZE,"All images must be of the same size");
         I().setXmippOrigin();
         int idx=0;
         if (subtractRef)
         {
             // Choose between this image and its mirror
             Ialigned=I();
             ImirrorAligned=Ialigned;
             ImirrorAligned.selfReverseX();
             ImirrorAligned.setXmippOrigin();
             alignImages(mIref,Ialigned,M,xmipp_transformation::WRAP,aux,aux2,aux3);
             alignImages(mIref,ImirrorAligned,M,xmipp_transformation::WRAP,aux,aux2,aux3);
             double corr=correlationIndex(mIref,Ialigned,&mask);
             double corrMirror=correlationIndex(mIref,ImirrorAligned,&mask);
             if (corr>corrMirror)
                 I()=Ialigned;
             else
                 I()=ImirrorAligned;
 
             FOR_ALL_ELEMENTS_IN_ARRAY2D(mask)
             if (A2D_ELEM(mask,i,j))
                 A1D_ELEM(v,idx++)=IMGPIXEL(I,i,j)-A2D_ELEM(mIref,i,j);
         }
         else
         {
             FOR_ALL_ELEMENTS_IN_ARRAY2D(mask)
             if (A2D_ELEM(mask,i,j))
                 A1D_ELEM(v,idx++)=IMGPIXEL(I,i,j);
         }
         pcaAnalyzer.addVector(v);
         if ((++n)%10==0 && verbose>0)
             progress_bar(n);
     }
     if (verbose>0)
         progress_bar(SFin.size());
 }

◆ readParams()

void ProgAnalyzeCluster::readParams ( )

virtual

Read argument from command line.

Reimplemented from XmippProgram.

Definition at line 36 of file analyze_cluster.cpp.

 {
     fnSel = getParam("-i");
     fnRef = getParam("--ref");
     fnOut = getParam("-o");
     if (checkParam("--basis"))
         fnOutBasis = getParam("--basis");
     NPCA  = getIntParam("--NPCA");
     Niter  = getIntParam("--iter");
     distThreshold = getDoubleParam("--maxDist");
     dontMask = checkParam("--dontMask");
 }

◆ run()

void ProgAnalyzeCluster::run ( )

virtual

Main routine.

Reimplemented from XmippProgram.

Definition at line 205 of file analyze_cluster.cpp.

 {
     show();
     produceSideInfo();
     size_t N=SFin.size();
 
     // Output
     SFout=SFin;
     if (N>Nmin)
     {
         pcaAnalyzer.evaluateZScore(NPCA, Niter);
 
         for (size_t n=0; n<N; n++)
         {
             int trueIdx=pcaAnalyzer.getSorted(n);
             double zscore=pcaAnalyzer.getSortedZscore(n);
             SFout.setValue(MDL_ZSCORE, zscore, SFout.getRowId(trueIdx));
             if (zscore<distThreshold || distThreshold<0)
                 SFout.setValue(MDL_ENABLED,1, SFout.getRowId(trueIdx));
             else
                 SFout.setValue(MDL_ENABLED,-1, SFout.getRowId(trueIdx));
         }
     }
     SFout.write(fnOut,MD_APPEND);
     if (basis && N>Nmin)
     {
         fnOutBasis.deleteFile();
         Image<double> basis;
         produceBasis(basis());
         basis.write(fnOutBasis);
     }
 }

◆ show()

void ProgAnalyzeCluster::show ( )

Show.

Definition at line 50 of file analyze_cluster.cpp.

 {
     if (verbose>0)
         std::cerr
         << "Input metadata file:    " << fnSel         << std::endl
         << "Reference:              " << fnRef         << std::endl
         << "Output metadata:        " << fnOut         << std::endl
         << "Output basis stack:     " << fnOutBasis    << std::endl
         << "PCA dimension:          " << NPCA          << std::endl
         << "Iterations:             " << Niter         << std::endl
         << "Maximum distance:       " << distThreshold << std::endl
         << "Don't mask:             " << dontMask      << std::endl
         ;
 }

Member Data Documentation

◆ basis

bool ProgAnalyzeCluster::basis

Definition at line 66 of file analyze_cluster.h.

◆ distThreshold

double ProgAnalyzeCluster::distThreshold

Distance Threshold

Definition at line 60 of file analyze_cluster.h.

◆ dontMask

bool ProgAnalyzeCluster::dontMask

Don't mask

Definition at line 63 of file analyze_cluster.h.

◆ fnOut

FileName ProgAnalyzeCluster::fnOut

Output metadata

Definition at line 48 of file analyze_cluster.h.

◆ fnOutBasis

FileName ProgAnalyzeCluster::fnOutBasis

Output basis stack

Definition at line 51 of file analyze_cluster.h.

◆ fnRef

FileName ProgAnalyzeCluster::fnRef

Filename reference image

Definition at line 45 of file analyze_cluster.h.

◆ fnSel

FileName ProgAnalyzeCluster::fnSel

Filename selection file containing the images

Definition at line 42 of file analyze_cluster.h.

◆ mask

MultidimArray<int> ProgAnalyzeCluster::mask

Definition at line 73 of file analyze_cluster.h.

◆ Niter

int ProgAnalyzeCluster::Niter

Number of iterations

Definition at line 57 of file analyze_cluster.h.

◆ NPCA

int ProgAnalyzeCluster::NPCA

PCA dimension

Definition at line 54 of file analyze_cluster.h.

◆ pcaAnalyzer

PCAMahalanobisAnalyzer ProgAnalyzeCluster::pcaAnalyzer

Definition at line 76 of file analyze_cluster.h.

◆ SFin

MetaDataVec ProgAnalyzeCluster::SFin

Definition at line 69 of file analyze_cluster.h.

◆ SFout

MetaDataVec ProgAnalyzeCluster::SFout

Definition at line 70 of file analyze_cluster.h.

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

xmipp/libraries/classification/analyze_cluster.h
xmipp/libraries/classification/analyze_cluster.cpp

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ defineParams()

◆ produceBasis()

◆ produceSideInfo()

◆ readParams()

◆ run()

◆ show()

Member Data Documentation

◆ basis

◆ distThreshold

◆ dontMask

◆ fnOut

◆ fnOutBasis

◆ fnRef

◆ fnSel

◆ mask

◆ Niter

◆ NPCA

◆ pcaAnalyzer

◆ SFin

◆ SFout