#include <classify_first_split.h>

Inheritance diagram for ProgClassifyFirstSplit:

Collaboration diagram for ProgClassifyFirstSplit:

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

void	show ()
	Show. More...

void	defineParams ()
	Define parameters. More...

void	run ()
	Run. More...

void	updateWithNewVolume (const MultidimArray< double > &V)
	Update with new volume. More...

void	volumeToVector (const MultidimArray< double > &V, MultidimArray< double > &v)

void	vectorToVolume (const MultidimArray< double > &v, MultidimArray< double > &V)

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	fnClasses

FileName	fnRoot

int	Nrec

int	Nsamples

FileName	fnSym

bool	externalMask

Mask	mask

double	alpha

MultidimArray< double >	v

int	Nvols

size_t	maskSize

PCAonline	pca

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

Classification First Split Parameters.

Definition at line 37 of file classify_first_split.h.

Member Function Documentation

◆ defineParams()

void ProgClassifyFirstSplit::defineParams ( )

virtual

Define parameters.

Reimplemented from XmippProgram.

Definition at line 61 of file classify_first_split.cpp.

 {
     addUsageLine("Produce a first volume split from a set of directional classes");
     addParamsLine("   -i <metadata>               : Metadata with the list of directional classes with angles");
     addParamsLine("  [--oroot <fnroot=split>]     : Rootname for the output");
     addParamsLine("  [--Nrec <n=100>]             : Number of reconstructions");
     addParamsLine("  [--Nsamples <n=8>]           : Number of images in each reconstruction");
     addParamsLine("  [--sym <sym=c1>]             : Symmetry");
     addParamsLine("  [--alpha <a=0.05>]           : Alpha for the generation of the two separated volumes");
     mask.defineParams(this,INT_MASK);
 }

◆ readParams()

void ProgClassifyFirstSplit::readParams ( )

virtual

Read argument from command line.

Reimplemented from XmippProgram.

Definition at line 32 of file classify_first_split.cpp.

 {
     fnClasses = getParam("-i");
     fnRoot = getParam("--oroot");
     Nrec = getIntParam("--Nrec");
     Nsamples = getIntParam("--Nsamples");
     fnSym = getParam("--sym");
     alpha = getDoubleParam("--alpha");
     mask.allowed_data_types = INT_MASK;
     if ((externalMask=checkParam("--mask")))
         mask.readParams(this);
 }

◆ run()

void ProgClassifyFirstSplit::run ( )

virtual

Run.

Reimplemented from XmippProgram.

Definition at line 73 of file classify_first_split.cpp.

 {
     show();
 
     MetaDataDb md, mdRec;
     md.read(fnClasses);
 
     // Generate the mean
     std::cerr << "Reconstructing average" << std::endl;
     String command=formatString("xmipp_reconstruct_fourier -i %s -o %s_avg.vol --max_resolution 0.25 --sym %s -v 0",fnClasses.c_str(),fnRoot.c_str(), fnSym.c_str());
     int retval=system(command.c_str());
     Image<double> Vavg;
     Vavg.read(fnRoot+"_avg.vol");
     Vavg().setXmippOrigin();
 
     SymList SL;
     SL.readSymmetryFile(fnSym);
     int Nsym=SL.symsNo()+1;
     Matrix2D<double> E, L, R;
 
     FileName fnSubset=fnRoot+"_subset.xmd";
     FileName fnSubsetVol=fnRoot+"_subset.vol";
     command=formatString("xmipp_reconstruct_fourier -i %s -o %s --max_resolution 0.25 -v 0",fnSubset.c_str(),fnSubsetVol.c_str());
 
     Image<double> V;
     Nvols = 0;
     std::cerr << "Generating reconstructions from random subsets ...\n";
     init_progress_bar(Nrec);
     MultidimArray<double> zn(Nrec);
     pca.maxzn=2; // Skip outliers
     for (int n=0; n<Nrec; n++)
     {
         // Generate random subset and randomize angles according to symmetry
         mdRec.selectRandomSubset(md,Nsamples);
         if (Nsym>1)
         {
             double rot, tilt, psi, rotp, tiltp, psip;
             for (size_t objId : mdRec.ids())
             {
                 int idx=round(rnd_unif(0,Nsym));
                 if (idx>0)
                 {
                     mdRec.getValue(MDL_ANGLE_ROT, rot, objId);
                     mdRec.getValue(MDL_ANGLE_TILT, tilt, objId);
                     mdRec.getValue(MDL_ANGLE_PSI, psi, objId);
 
                     SL.getMatrices(idx - 1, L, R, false);
                     Euler_apply_transf(L, R, rot, tilt, psi, rotp, tiltp, psip);
 
                     mdRec.setValue(MDL_ANGLE_ROT, rotp, objId);
                     mdRec.setValue(MDL_ANGLE_TILT, tiltp, objId);
                     mdRec.setValue(MDL_ANGLE_PSI, psip, objId);
                 }
             }
         }
         mdRec.write(fnSubset);
 
         // Perform reconstruction
         retval=system(command.c_str());
         V.read(fnSubsetVol);
         V().setXmippOrigin();
 //      V.write(formatString("%s_%05d.vol",fnRoot.c_str(),n));
         V()-=Vavg();
 //      V.write(formatString("%s_%05d_diff.vol",fnRoot.c_str(),n));
         updateWithNewVolume(V());
         zn(n)=pca.getCurrentProjection();
 //      std::cout << "zn=" << zn(n) << std::endl;
 //      char c; std::cin >> c;
 
         progress_bar(n);
     }
     progress_bar(Nrec);
     deleteFile(fnSubset);
     deleteFile(fnSubsetVol);
 
     // Save average and first principal component
     Image<double> V1, V2, Vdiff;
     vectorToVolume(pca.c1,V1());
     V1.write(fnRoot+"_pc1.vol");
     vectorToVolume(pca.ysum,V1());
     V1()/=pca.N;
     V1()+=Vavg();
     V2()=V1();
 
     // Analyze now the projections
     MultidimArray<double> znSorted;
     zn.sort(znSorted);
     double z1=znSorted(int(alpha/2*Nrec));
     double z2=znSorted(int((1-alpha/2)*Nrec));
     std::cout << "z1=" << z1 << " z2=" << z2 << std::endl;
 
     v=pca.c1;
     v*=z1;
     vectorToVolume(v,Vdiff());
     V1()+=Vdiff();
     V1.write(fnRoot+"_v1.vol");
 
     v=pca.c1;
     v*=z2;
     vectorToVolume(v,Vdiff());
     V2()+=Vdiff();
     V2.write(fnRoot+"_v2.vol");
 
     // Check if the mirrored volume is better
     double corr=correlationIndex(V1(),V2());
     V2().selfReverseX();
     V2.write(fnRoot+"_v2mirrored.vol");
     command="xmipp_volume_align --i1 "+fnRoot+"_v1.vol --i2 "+fnRoot+"_v2mirrored.vol --rot 0 360 15 --tilt 0 360 15 --psi 0 360 15 --apply";
     std::cout << command << std::endl;
     int ok=system(command.c_str());
     command="xmipp_volume_align --i1 "+fnRoot+"_v1.vol --i2 "+fnRoot+"_v2mirrored.vol --local --apply";
     std::cout << command << std::endl;
     ok=system(command.c_str());
     V2.read(fnRoot+"_v2mirrored.vol");
     double corrM=correlationIndex(V1(),V2());
     std::cout << "Correlation unmirrored: " << corr << std::endl;
     std::cout << "Correlation   mirrored: " << corrM << std::endl;
     if (corrM>corr)
         copyImage(fnRoot+"_v2mirrored.vol",fnRoot+"_v2.vol");
     deleteFile(fnRoot+"_v2mirrored.vol");
 
     V2.read(fnRoot+"_v2.vol");
     V1().setXmippOrigin();
     V2().setXmippOrigin();
     Vdiff()=V1();
     Vdiff()-=V2();
     Vdiff.write(fnRoot+"_pc1.vol");
 }

◆ show()

void ProgClassifyFirstSplit::show ( )

Show.

Definition at line 46 of file classify_first_split.cpp.

 {
     if (!verbose)
         return;
     std::cout
     << "Input classes:       " << fnClasses          << std::endl
     << "Output root:         " << fnRoot             << std::endl
     << "N. reconstructions:  " << Nrec               << std::endl
     << "N. samples:          " << Nsamples           << std::endl
     << "Symmetry:            " << fnSym              << std::endl
     << "Alpha:               " << alpha              << std::endl
     ;
 }

◆ updateWithNewVolume()

void ProgClassifyFirstSplit::updateWithNewVolume ( const MultidimArray< double > & V )

Update with new volume.

Definition at line 222 of file classify_first_split.cpp.

 {
     if (Nvols==0)
     {
         if (!externalMask)
         {
             mask.type = BINARY_CIRCULAR_MASK;
             mask.mode = INNER_MASK;
             mask.R1 = XSIZE(V)/2;
         }
         mask.generate_mask(V);
 
         // Resize some internal variables
         maskSize=(size_t) mask.get_binary_mask().sum();
     }
 
     volumeToVector(V,v);
     pca.addVector(v);
     Nvols++;
 }

◆ vectorToVolume()

void ProgClassifyFirstSplit::vectorToVolume	(	const MultidimArray< double > &	v,
		MultidimArray< double > &	V
	)

Definition at line 212 of file classify_first_split.cpp.

 {
     const MultidimArray<int> &mmask = mask.get_binary_mask();
     V.initZeros(mmask);
     size_t idx=0;
     FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(mmask)
     if (DIRECT_MULTIDIM_ELEM(mmask,n))
         DIRECT_MULTIDIM_ELEM(V,n)=DIRECT_MULTIDIM_ELEM(v,idx++);
 }

◆ volumeToVector()

void ProgClassifyFirstSplit::volumeToVector	(	const MultidimArray< double > &	V,
		MultidimArray< double > &	v
	)

Definition at line 202 of file classify_first_split.cpp.

 {
     v.resizeNoCopy(maskSize);
     const MultidimArray<int> &mmask = mask.get_binary_mask();
     size_t idx=0;
     FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(mmask)
     if (DIRECT_MULTIDIM_ELEM(mmask,n))
         DIRECT_MULTIDIM_ELEM(v,idx++)=DIRECT_MULTIDIM_ELEM(V,n);
 }

Member Data Documentation

◆ alpha

double ProgClassifyFirstSplit::alpha

Alpha

Definition at line 55 of file classify_first_split.h.

◆ externalMask

bool ProgClassifyFirstSplit::externalMask

External mask

Definition at line 51 of file classify_first_split.h.

◆ fnClasses

FileName ProgClassifyFirstSplit::fnClasses

Directional classes

Definition at line 41 of file classify_first_split.h.

◆ fnRoot

FileName ProgClassifyFirstSplit::fnRoot

Rootname

Definition at line 43 of file classify_first_split.h.

◆ fnSym

FileName ProgClassifyFirstSplit::fnSym

Symmetry

Definition at line 49 of file classify_first_split.h.

◆ mask

Mask ProgClassifyFirstSplit::mask

Mask

Definition at line 53 of file classify_first_split.h.

◆ maskSize

size_t ProgClassifyFirstSplit::maskSize

Definition at line 80 of file classify_first_split.h.

◆ Nrec

int ProgClassifyFirstSplit::Nrec

Number of reconstructions

Definition at line 45 of file classify_first_split.h.

◆ Nsamples

int ProgClassifyFirstSplit::Nsamples

Number of samples per reconstruction

Definition at line 47 of file classify_first_split.h.

◆ Nvols

int ProgClassifyFirstSplit::Nvols

Definition at line 79 of file classify_first_split.h.

◆ pca

PCAonline ProgClassifyFirstSplit::pca

Definition at line 81 of file classify_first_split.h.

◆ v

MultidimArray<double> ProgClassifyFirstSplit::v

Definition at line 78 of file classify_first_split.h.

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

xmipp/libraries/reconstruction/classify_first_split.h
xmipp/libraries/reconstruction/classify_first_split.cpp

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ defineParams()

◆ readParams()

◆ run()

◆ show()

◆ updateWithNewVolume()

◆ vectorToVolume()

◆ volumeToVector()

Member Data Documentation

◆ alpha

◆ externalMask

◆ fnClasses

◆ fnRoot

◆ fnSym

◆ mask

◆ maskSize

◆ Nrec

◆ Nsamples

◆ Nvols

◆ pca

◆ v