#include <volume_pca.h>

Inheritance diagram for ProgVolumePCA:

Collaboration diagram for ProgVolumePCA:

Public Member Functions
void	readParams ()
	Read arguments. More...

void	show () const
	Show. More...

void	defineParams ()
	Define parameters. More...

void	produce_side_info ()

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	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	fnVols
	Input set of volumes. More...

FileName	fnVolsOut
	Output set of volumes. More...

int	NPCA
	Number of PCA bases. More...

Mask	mask
	Mask. More...

FileName	fnBasis
	Output basis. More...

StringVector	listOfPercentiles
	List of percentiles to generate volumes. More...

FileName	fnAvgVol
	Average volume. More...

FileName	fnOutStack
	Output PCA stack. More...

MetaDataVec	mdVols

Image< double >	V

PCAMahalanobisAnalyzer	analyzer

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

Volume PCA parameters.

Definition at line 38 of file volume_pca.h.

Member Function Documentation

◆ defineParams()

void ProgVolumePCA::defineParams ( )

virtual

Define parameters.

Reimplemented from XmippProgram.

Definition at line 65 of file volume_pca.cpp.

 {
     addUsageLine("Compute the PCA of a set of volumes, within a mask (optional).");
     addParamsLine("   -i <volumes>             : Metadata with aligned volumes");
     addParamsLine("  [-o <volumes=\"\">]       : Output metadata with PCA projections");
     addParamsLine("  [--Npca <N=1>]            : Number of PCA bases");
     addParamsLine("  [--saveBasis <stack=\"\">]: Save the bases as a stack of volumes");
     addParamsLine("  [--generatePCAVolumes <...>]: List of percentiles (typically, \"10 90\"), to generate volumes along the 1st PCA basis");
     addParamsLine("  [--avgVolume <volume=\"\">] : Volume on which to add the PCA basis");
     addParamsLine("  [--opca <stack=\"\">]     : Stack of generated volumes");
     mask.defineParams(this,INT_MASK);
 }

◆ produce_side_info()

void ProgVolumePCA::produce_side_info ( )

Produce side info.

Definition at line 79 of file volume_pca.cpp.

 {
     mdVols.read(fnVols);
     mdVols.removeDisabled();
 
     size_t Xdim, Ydim, Zdim, Ndim;
     getImageSize(mdVols, Xdim, Ydim, Zdim, Ndim);
     if (mask.type!=NO_MASK)
         mask.generate_mask(Zdim,Ydim,Xdim);
     else
     {
         mask.imask.resizeNoCopy(Zdim,Ydim,Xdim);
         mask.imask.initConstant(1);
     }
 }

◆ readParams()

void ProgVolumePCA::readParams ( )

virtual

Read arguments.

Reimplemented from XmippProgram.

Definition at line 31 of file volume_pca.cpp.

 {
     fnVols = getParam("-i");
     fnVolsOut = getParam("-o");
     NPCA = getIntParam("--Npca");
     fnBasis = getParam("--saveBasis");
     fnAvgVol = getParam("--avgVolume");
     fnOutStack = getParam("--opca");
     if (checkParam("--generatePCAVolumes"))
         getListParam("--generatePCAVolumes",listOfPercentiles);
     if (checkParam("--mask"))
         mask.readParams(this);
 }

◆ run()

void ProgVolumePCA::run ( )

virtual

Run

Reimplemented from XmippProgram.

Definition at line 95 of file volume_pca.cpp.

 {
     show();
     produce_side_info();
 
     const MultidimArray<int> &imask=mask.imask;
     size_t Nvoxels=imask.sum();
     MultidimArray<float> v;
     v.initZeros(Nvoxels);
 
     // Add all volumes to the analyzer
     FileName fnVol;
     for (size_t objId : mdVols.ids())
     {
         mdVols.getValue(MDL_IMAGE,fnVol,objId);
         V.read(fnVol);
 
         // Construct vector
         const MultidimArray<double> &mV=V();
         size_t idx=0;
         FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(mV)
         {
             if (DIRECT_MULTIDIM_ELEM(imask,n))
                 DIRECT_MULTIDIM_ELEM(v,idx++)=DIRECT_MULTIDIM_ELEM(mV,n);
         }
 
         analyzer.addVector(v);
     }
 
     // Construct PCA basis
     analyzer.subtractAvg();
     analyzer.learnPCABasis(NPCA,100);
 
     // Project onto the PCA basis
     Matrix2D<double> proj;
     analyzer.projectOnPCABasis(proj);
     std::vector<double> dimredProj;
     dimredProj.resize(NPCA);
     int i=0;
     for (size_t objId : mdVols.ids())
     {
         memcpy(&dimredProj[0],&MAT_ELEM(proj,i,0),NPCA*sizeof(double));
         mdVols.setValue(MDL_DIMRED,dimredProj,objId);
         i++;
     }
     if (fnVolsOut!="")
         mdVols.write(fnVolsOut);
     else
         mdVols.write(fnVols);
 
     // Save the basis
     const MultidimArray<double> &mV=V();
     for (int i=NPCA-1; i>=0; --i)
     {
         V().initZeros();
         size_t idx=0;
         const MultidimArray<double> &mPCA=analyzer.PCAbasis[i];
         FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(mV)
         {
             if (DIRECT_MULTIDIM_ELEM(imask,n))
                 DIRECT_MULTIDIM_ELEM(mV,n)=DIRECT_MULTIDIM_ELEM(mPCA,idx++);
         }
         if (fnBasis!="")
             V.write(fnBasis,i+1,true,WRITE_OVERWRITE);
     }
 
     // Generate the PCA volumes
     if (listOfPercentiles.size()>0 && fnOutStack!="" && fnAvgVol!="")
     {
         Image<double> Vavg;
         if (fnAvgVol!="")
             Vavg.read(fnAvgVol);
         else
             Vavg().initZeros(V());
 
         Matrix1D<double> p;
         proj.toVector(p);
         Matrix1D<double> psorted=p.sort();
 
         Image<double> Vpca;
         Vpca()=Vavg();
         createEmptyFile(fnOutStack,(int)XSIZE(Vavg()),(int)YSIZE(Vavg()),(int)ZSIZE(Vavg()),listOfPercentiles.size());
         std::cout << "listOfPercentiles.size()=" << listOfPercentiles.size() << std::endl;
         for (size_t i=0; i<listOfPercentiles.size(); i++)
         {
             auto idx=(int)round(textToFloat(listOfPercentiles[i].c_str())/100.0*VEC_XSIZE(p));
             std::cout << "Percentile " << listOfPercentiles[i] << " -> idx=" << idx << " p(idx)=" << psorted(idx) << std::endl;
             Vpca()+=psorted(idx)*V();
             Vpca.write(fnOutStack,i+1,true,WRITE_REPLACE);
         }
     }
 }

◆ show()

void ProgVolumePCA::show ( ) const

virtual

Show.

Reimplemented from XmippProgram.

Definition at line 46 of file volume_pca.cpp.

 {
     if (verbose==0)
         return;
     std::cout << "Input volumes:  " << fnVols     << std::endl
               << "Output metadata:" << fnVolsOut  << std::endl
               << "Number of PCAs: " << NPCA       << std::endl
               << "Basis:          " << fnBasis    << std::endl
               << "Avg. volume:    " << fnAvgVol   << std::endl
               << "Output PCA vols:" << fnOutStack << std::endl;
     std::cout << "Percentiles:    ";
     for (size_t i=0; i<listOfPercentiles.size(); i++)
         std::cout << listOfPercentiles[i] << " ";
     std::cout << std::endl;
     if (mask.type!=NO_MASK)
         mask.show();
 }

Member Data Documentation

◆ analyzer

PCAMahalanobisAnalyzer ProgVolumePCA::analyzer

Definition at line 65 of file volume_pca.h.

◆ fnAvgVol

FileName ProgVolumePCA::fnAvgVol

Average volume.

Definition at line 54 of file volume_pca.h.

◆ fnBasis

FileName ProgVolumePCA::fnBasis

Output basis.

Definition at line 50 of file volume_pca.h.

◆ fnOutStack

FileName ProgVolumePCA::fnOutStack

Output PCA stack.

Definition at line 56 of file volume_pca.h.

◆ fnVols

FileName ProgVolumePCA::fnVols

Input set of volumes.

Definition at line 42 of file volume_pca.h.

◆ fnVolsOut

FileName ProgVolumePCA::fnVolsOut

Output set of volumes.

Definition at line 44 of file volume_pca.h.

◆ listOfPercentiles

StringVector ProgVolumePCA::listOfPercentiles

List of percentiles to generate volumes.

Definition at line 52 of file volume_pca.h.

◆ mask

Mask ProgVolumePCA::mask

Mask.

Definition at line 48 of file volume_pca.h.

◆ mdVols

MetaDataVec ProgVolumePCA::mdVols

Definition at line 59 of file volume_pca.h.

◆ NPCA

int ProgVolumePCA::NPCA

Number of PCA bases.

Definition at line 46 of file volume_pca.h.

◆ V

Image<double> ProgVolumePCA::V

Definition at line 62 of file volume_pca.h.

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

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

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ defineParams()

◆ produce_side_info()

◆ readParams()

◆ run()

◆ show()

Member Data Documentation

◆ analyzer

◆ fnAvgVol

◆ fnBasis

◆ fnOutStack

◆ fnVols

◆ fnVolsOut

◆ listOfPercentiles

◆ mask

◆ mdVols

◆ NPCA

◆ V