#include <angular_assignment_mag.h>

Inheritance diagram for ProgAngularAssignmentMag:

Collaboration diagram for ProgAngularAssignmentMag:

Public Member Functions
void	defineParams () override

void	readParams () override

void	show () const override

void	preProcess () override

void	processImage (const FileName &fnImg, const FileName &fnImgOut, const MDRow &rowIn, MDRow &rowOut) override

void	postProcess () override

	ProgAngularAssignmentMag ()

	~ProgAngularAssignmentMag ()

void	applyRotation (const MultidimArray< double > &, double &, MultidimArray< double > &) const

void	applyShiftAndRotation (const MultidimArray< double > &MDaRef, double &rot, double &tx, double &ty, MultidimArray< double > &MDaRefRot) const

virtual void	synchronize ()
	Synchronize with other processors. More...

Public Member Functions inherited from XmippMetadataProgram
MetaData *	getInputMd ()

MetaDataVec &	getOutputMd ()

	XmippMetadataProgram ()
	Empty constructor. More...

virtual int	tryRead (int argc, const char **argv, bool reportErrors=true)

virtual void	init ()

virtual void	setup (MetaData *md, const FileName &o="", const FileName &oroot="", bool applyGeo=false, MDLabel label=MDL_IMAGE)

virtual	~XmippMetadataProgram ()

void	setMode (WriteModeMetaData _mode)

void	setupRowOut (const FileName &fnImgIn, const MDRow &rowIn, const FileName &fnImgOut, MDRow &rowOut) const
	Prepare rowout. More...

virtual void	wait ()
	Wait for the distributor to finish. More...

virtual void	checkPoint ()
	For very long programs, it may be needed to write checkpoints. More...

virtual void	run ()
	Run over all images. 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)

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
size_t	rank

size_t	Nprocessors

Public Attributes inherited from XmippMetadataProgram
FileName	fn_in
	Filenames of input and output Metadata. More...

FileName	fn_out

FileName	baseName

FileName	pathBaseName

FileName	oextBaseName

bool	apply_geo
	Apply geo. More...

size_t	ndimOut
	Output dimensions. More...

size_t	zdimOut

size_t	ydimOut

size_t	xdimOut

DataType	datatypeOut

size_t	mdInSize
	Number of input elements. More...

Public Attributes inherited from XmippProgram
bool	doRun

bool	runWithoutArgs

int	verbose
	Verbosity level. More...

int	debug

Additional Inherited Members
Protected Member Functions inherited from XmippMetadataProgram
virtual void	initComments ()

virtual bool	getImageToProcess (size_t &objId, size_t &objIndex)

void	show () const override

virtual void	startProcessing ()

virtual void	finishProcessing ()

virtual void	writeOutput ()

virtual void	showProgress ()

virtual void	defineLabelParam ()

Protected Member Functions inherited from XmippProgram
void	defineCommons ()

Protected Attributes inherited from XmippMetadataProgram
WriteModeMetaData	mode
	Metadata writing mode: OVERWRITE, APPEND. More...

FileName	oext
	Output extension and root. More...

FileName	oroot

MDLabel	image_label
	MDLabel to be used to read/write images, usually will be MDL_IMAGE. More...

bool	produces_an_output
	Indicate that a unique final output is produced. More...

bool	produces_a_metadata
	Indicate that the unique final output file is a Metadata. More...

bool	each_image_produces_an_output
	Indicate that an output is produced for each image in the input. More...

bool	allow_apply_geo

bool	decompose_stacks
	Input Metadata will treat a stack file as a set of images instead of a unique file. More...

bool	delete_output_stack
	Delete previous output stack file prior to process images. More...

bool	get_image_info
	Get the input image file dimensions to further operations. More...

bool	save_metadata_stack
	Save the associated output metadata when output file is a stack. More...

bool	track_origin
	Include the original input image filename in the output stack. More...

bool	keep_input_columns
	Keep input metadata columns. More...

bool	remove_disabled
	Remove disabled images from the input selfile. More...

bool	allow_time_bar
	Show process time bar. More...

bool	input_is_metadata
	Input is a metadata. More...

bool	single_image
	Input is a single image. More...

bool	input_is_stack
	Input is a stack. More...

bool	output_is_stack
	Output is a stack. More...

bool	create_empty_stackfile

bool	delete_mdIn

size_t	time_bar_step
	Some time bar related counters. More...

size_t	time_bar_size

size_t	time_bar_done

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

Angular_Assignment_mag parameters.

Definition at line 49 of file angular_assignment_mag.h.

Constructor & Destructor Documentation

◆ ProgAngularAssignmentMag()

ProgAngularAssignmentMag::ProgAngularAssignmentMag ( )

Definition at line 39 of file angular_assignment_mag.cpp.

                                                   {
     produces_a_metadata = true;
     each_image_produces_an_output = false;
     rank=0;
     Nprocessors=1;
 }

◆ ~ProgAngularAssignmentMag()

ProgAngularAssignmentMag::~ProgAngularAssignmentMag ( )

default

Member Function Documentation

◆ applyRotation()

void ProgAngularAssignmentMag::applyRotation	(	const MultidimArray< double > &	MDaRef,
		double &	rot,
		MultidimArray< double > &	MDaRefRot
	)		const

Definition at line 993 of file angular_assignment_mag.cpp.

                                                {
     // Transform matrix
     Matrix2D<double> A(3, 3);
     A.initIdentity();
     double ang = DEG2RAD(rot);
     double cosine = cos(ang);
     double sine = sin(ang);
 
     // rotation
     MAT_ELEM(A,0, 0) = cosine;
     MAT_ELEM(A,0, 1) = sine;
     MAT_ELEM(A,1, 0) = -sine;
     MAT_ELEM(A,1, 1) = cosine;
 
     // Shift
     MAT_ELEM(A,0, 2) = 0.;
     MAT_ELEM(A,1, 2) = 0.;
 
     applyGeometry(xmipp_transformation::LINEAR, MDaRefRot, MDaRef, A, xmipp_transformation::IS_NOT_INV, xmipp_transformation::DONT_WRAP);
 }

◆ applyShiftAndRotation()

void ProgAngularAssignmentMag::applyShiftAndRotation	(	const MultidimArray< double > &	MDaRef,
		double &	rot,
		double &	tx,
		double &	ty,
		MultidimArray< double > &	MDaRefRot
	)		const

Definition at line 1043 of file angular_assignment_mag.cpp.

                                                             {
     // Transform matrix
     Matrix2D<double> A(3, 3);
     A.initIdentity();
     double ang = DEG2RAD(rot);
     double cosine = cos(ang);
     double sine = sin(ang);
 
     // rotate in opposite direction
     double realTx = cosine * tx + sine * ty;
     double realTy = -sine * tx + cosine * ty;
 
     // rotation
     MAT_ELEM(A,0, 0) = cosine;
     MAT_ELEM(A,0, 1) = sine;
     MAT_ELEM(A,1, 0) = -sine;
     MAT_ELEM(A,1, 1) = cosine;
 
     // Shift
     MAT_ELEM(A,0, 2) = realTx;
     MAT_ELEM(A,1, 2) = realTy;
 
     applyGeometry(xmipp_transformation::LINEAR, MDaRefRot, MDaRef, A, xmipp_transformation::IS_NOT_INV, xmipp_transformation::DONT_WRAP);
 }

◆ defineParams()

void ProgAngularAssignmentMag::defineParams ( )

overridevirtual

Function in which the param of each Program are defined.

Reimplemented from XmippMetadataProgram.

Definition at line 48 of file angular_assignment_mag.cpp.

                                             {
     XmippMetadataProgram::defineParams();
     //usage
     addUsageLine( "Generates a list of candidates for angular assignment for each experimental image");
     addParamsLine("   -ref <md_file>             : Metadata file with input reference projections");
     addParamsLine("  [-odir <outputDir=\".\">]   : Output directory");
     addParamsLine("  [--sym <symfile=c1>]         : Enforce symmetry in projections");
     addParamsLine("  [-sampling <sampling=1.>]   : sampling");
     addParamsLine("  [-angleStep <angStep=3.>]   : angStep");
     addParamsLine("  [--maxShift <maxShift=-1.>]  : Maximum shift allowed (+-this amount)");
     addParamsLine("  [--Nsimultaneous <Nprocessors=1>]  : Nsimultaneous");
     addParamsLine("  [--refVol <refVolFile=NULL>]  : reference volume to be reprojected when comparing with previous alignment");
     addParamsLine("  [--useForValidation] : Use the program for validation");
     addParamsLine("  [--thr <threads=4>]           : How many threads to use");
 }

◆ postProcess()

void ProgAngularAssignmentMag::postProcess ( )

overridevirtual

Reimplemented from XmippMetadataProgram.

Definition at line 643 of file angular_assignment_mag.cpp.

                                            {
     // from angularContinousAssign2
     MetaData &ptrMdOut = getOutputMd();
 
     ptrMdOut.removeDisabled();
     double maxCC = -1.;
     int j = 0;
     for (size_t objId : ptrMdOut.ids())
     {
         double thisMaxCC;
         ptrMdOut.getValue(MDL_MAXCC, thisMaxCC, objId);
         if (thisMaxCC > maxCC)
             maxCC = thisMaxCC;
         if (thisMaxCC == 0.0)
             ptrMdOut.removeObject(objId);
         j++;
     }
     for (size_t objId : ptrMdOut.ids())
     {
         double thisMaxCC;
         ptrMdOut.getValue(MDL_MAXCC, thisMaxCC, objId);
         ptrMdOut.setValue(MDL_WEIGHT, thisMaxCC / maxCC, objId);
         ptrMdOut.setValue(MDL_WEIGHT_SIGNIFICANT, thisMaxCC / maxCC,
                 objId);
     }
     ptrMdOut.write(XmippMetadataProgram::fn_out.replaceExtension("xmd"));
 }

◆ preProcess()

void ProgAngularAssignmentMag::preProcess ( )

overridevirtual

Reimplemented from XmippMetadataProgram.

Definition at line 290 of file angular_assignment_mag.cpp.

                                           {
 
     mdIn.read(XmippMetadataProgram::fn_in);
     mdRef.read(fnRef);
 
     // size of images
     size_t Zdim;
     size_t Ndim;
     getImageSize(mdIn, Xdim, Ydim, Zdim, Ndim);
 
     // some constants
     n_rad = size_t((double)Xdim / 2.);
     startBand = size_t((sampling * (double) Xdim) / 80.);
     finalBand = size_t((sampling * (double) Xdim) / (sampling * 3));
     n_bands = finalBand - startBand;
     n_ang = size_t(180);
     n_ang2 = 2 * n_ang;
     if (maxShift==-1.){
         maxShift = .10 * (double)Xdim;
     }
 
     // read reference images
     FileName fnImgRef;
     sizeMdRef = (int)mdRef.size();
 
     // how many input images
     sizeMdIn = (int)mdIn.size();
 
     computeCircular(); //pre-compute circular mask
 
     checkStorageSpace();
 
     processGallery(fnImgRef); // process reference gallery
 
     computeEigenvectors();  // eigenvectors for graph-signal-processing
 
     // Symmetry List
     if (fnSym != "") {
         SL.readSymmetryFile(fnSym);
         for (int sym = 0; sym < SL.symsNo(); sym++) {
             Matrix2D<double> auxL, auxR;
             SL.getMatrices(sym, auxL, auxR);
             auxL.resize(3, 3);
             auxR.resize(3, 3);
             L.push_back(auxL);
             R.push_back(auxR);
         }
     } // */
 
     if(useForValidation){
         // read reference volume to be re-projected when comparing previous assignment
         // If there is no reference available, exit
         refVol.read(inputReference_volume);
 
         refVol().setXmippOrigin();
         refXdim = (int)XSIZE(refVol());
         refYdim = (int)YSIZE(refVol());
         refZdim = (int)ZSIZE(refVol());
     }
 }

◆ processImage()

void ProgAngularAssignmentMag::processImage	(	const FileName &	fnImg,
		const FileName &	fnImgOut,
		const MDRow &	rowIn,
		MDRow &	rowOut
	)

overridevirtual

Implements XmippMetadataProgram.

Definition at line 371 of file angular_assignment_mag.cpp.

                                            {
 
     // experimental image related
     Image<double> ImgIn;
     MultidimArray<double> MDaIn((int)Ydim, (int)Xdim);
     MultidimArray<std::complex<double> > MDaInF;
     MultidimArray<std::complex<double> > MDaInF2;
     MultidimArray<double> MDaInFM;
     MultidimArray<double> MDaInFMs;
     MultidimArray<double> MDaInFMs_polarPart((int)n_bands, (int)n_ang2);
     MultidimArray<std::complex<double> > MDaInFMs_polarF;
 
     // processing experimental input image
     ImgIn.read(fnImg);
     MDaIn = ImgIn();
     MDaIn.setXmippOrigin();
     transformerImage.FourierTransform(MDaIn, MDaInF, true);
     transformerImage.getCompleteFourier(MDaInF2);
     FFT_magnitude(MDaInF2, MDaInFM);
     completeFourierShift(MDaInFM, MDaInFMs);
     MDaInFMs_polarPart = imToPolar(MDaInFMs, startBand, finalBand);
     transformerPolarImage.FourierTransform(MDaInFMs_polarPart, MDaInFMs_polarF, true);
 
     // variables for an initial screening of possible "good" references
     double psi;
     double cc_coeff;
     double Tx;
     double Ty;
     int maxAccepted = 8;
 
     std::vector<unsigned int> Idx(sizeMdRef, 0);
 
     Matrix1D<double> ccvec;
     ccvec.initZeros(sizeMdRef);
 
     std::vector<double> bestTx(sizeMdRef, 0);
     std::vector<double> bestTy(sizeMdRef, 0);
     std::vector<double> bestPsi(sizeMdRef, 0);
 
     MultidimArray<double> ccMatrixRot;
     MultidimArray<double> ccVectorRot;
 
     // loop over all reference images. Screening of possible "good" references
     for (int k = 0; k < sizeMdRef; ++k) {
         // computing relative rotation and shift
         ccMatrix(MDaInFMs_polarF, vecMDaRefFMs_polarF[k], ccMatrixRot, ccMatrixProcessImageTransformer);
         maxByColumn(ccMatrixRot, ccVectorRot);
         peaksFound = 0;
         std::vector<double> cand(maxAccepted, 0.);
         psiCandidates(ccVectorRot, cand, XSIZE(ccMatrixRot));
         bestCand(MDaIn, MDaInF, vecMDaRef[k], cand, psi, Tx, Ty, cc_coeff);
         // all results are storage for posterior partial_sort
         Idx[k] = k; // for sorting
         VEC_ELEM(ccvec,k) = cc_coeff;
         bestTx[k] = Tx;
         bestTy[k] = Ty;
         bestPsi[k] = psi;
     }
 
     // variables for second loop. Selection of "best" reference image
     std::vector<double> bestTx2(sizeMdRef, 0.);
     std::vector<double> bestTy2(sizeMdRef, 0.);
     std::vector<double> bestPsi2(sizeMdRef, 0.);
 
     MultidimArray<double> &MDaInAux = ImgIn();
     MDaInAux.setXmippOrigin();
     MultidimArray<double> mCurrentImageAligned;
     double corr, scale;
     bool flip;
 
     double minval, maxval;
     ccvec.computeMinMax(minval, maxval);
     double thres = 0.;
     if (SL.symsNo()<=4)
         thres = maxval - (maxval - minval) / 3.;
     else
         thres = maxval - (maxval - minval) / 2.;
 
     // loop over "good" reference images
     for(int k = 0; k < sizeMdRef; ++k) {
         if(VEC_ELEM(ccvec,k)>thres){
             // find rotation and shift using alignImages
             Matrix2D<double> M;
             mCurrentImageAligned = MDaInAux;
             mCurrentImageAligned.setXmippOrigin();
             corr = alignImages(vecMDaRef[k], mCurrentImageAligned, M, xmipp_transformation::DONT_WRAP);
             M = M.inv();
             transformationMatrix2Parameters2D(M, flip, scale, Tx, Ty, psi);
 
             if (maxShift>0 && (fabs(Tx)>maxShift || fabs(Ty)>maxShift))
                 corr /= 3;
 
             VEC_ELEM(ccvec, k) = corr;
             bestTx2[k] = Tx;
             bestTy2[k] = Ty;
             bestPsi2[k] = psi;
 
         }
         else{
             bestTx2[k] = bestTx[k];
             bestTy2[k] = bestTy[k];
             bestPsi2[k] = bestPsi[k];
         }
     }
 
     // === Graph Filter Process after best reference selection ========
     Matrix1D<double> ccvec_filt;
     graphFourierFilter(ccvec,ccvec_filt);
 
     // choose best of the candidates after 2nd loop
     int idx = ccvec.maxIndex();
 
     // choose best candidate direction from graph filtered ccvect signal
     int idxfilt = ccvec_filt.maxIndex();
 
     // angular distance between this two directions
     Matrix1D<double> dirj;
     Matrix1D<double> dirjp;
     double sphericalDistance= angDistance(idx, idxfilt, dirj, dirjp);
 
     // set output alignment parameters values
     double rotRef = referenceRot.at(idx);
     double tiltRef = referenceTilt.at(idx);
     double shiftX = bestTx2[idx];
     double shiftY = bestTy2[idx];
     double anglePsi = bestPsi2[idx];
     corr = ccvec[idx];
 
     //save metadata of images with angles
     rowOut.setValue(MDL_IMAGE, fnImgOut);
     rowOut.setValue(MDL_ENABLED, 1);
     rowOut.setValue(MDL_MAXCC, corr);
     rowOut.setValue(MDL_ANGLE_ROT, rotRef);
     rowOut.setValue(MDL_ANGLE_TILT, tiltRef);
     rowOut.setValue(MDL_ANGLE_PSI, realWRAP(anglePsi, -180., 180.));
     rowOut.setValue(MDL_SHIFT_X, -shiftX);
     rowOut.setValue(MDL_SHIFT_Y, -shiftY);
     rowOut.setValue(MDL_WEIGHT, 1.);
     rowOut.setValue(MDL_WEIGHT_SIGNIFICANT, 1.);
     rowOut.setValue(MDL_GRAPH_DISTANCE2MAX, sphericalDistance);
 
     // validate angular assignment
     validateAssignment(idx, idxfilt, rotRef, tiltRef, rowIn, rowOut, MDaIn, dirjp);
 }

◆ readParams()

void ProgAngularAssignmentMag::readParams ( )

overridevirtual

Function in which each program will read parameters that it need. If some error occurs the usage will be printed out.

Reimplemented from XmippMetadataProgram.

Definition at line 65 of file angular_assignment_mag.cpp.

                                           {
     XmippMetadataProgram::readParams();
     fnRef = getParam("-ref");
     fnDir = getParam("-odir");
     sampling = getDoubleParam("-sampling");
     angStep= getDoubleParam("-angleStep");
     XmippMetadataProgram::oroot = fnDir;
     fnSym = getParam("--sym");
     maxShift = getDoubleParam("--maxShift");
     inputReference_volume = getParam("--refVol");
     useForValidation=checkParam("--useForValidation");
     threads = getIntParam("--thr");
     threadPool.resize(threads);
     transformersForImages.resize(threads);
     ccMatrixBestCandidTransformers.resize(threads);
     ccMatrixShifts.resize(threads);
 }

◆ show()

void ProgAngularAssignmentMag::show ( ) const

overridevirtual

Show parameters

Reimplemented from XmippProgram.

Definition at line 84 of file angular_assignment_mag.cpp.

                                           {
     if (verbose > 0) {
         printf("%d reference images of %d x %d\n",int(sizeMdRef),int(Xdim),int(Ydim));
         printf("%d exp images of %d x %d in this group\n", int(sizeMdIn),int(Xdim), int(Ydim));
         std::cout << "Sampling: " << sampling << std::endl;
         std::cout << "Angular step: " << angStep << std::endl;
         std::cout << "Maximum shift: " << maxShift << std::endl;
         std::cout << "threads: " << threads << std::endl;
         if(useForValidation){
             std::cout << "ref vol size: " << refXdim <<" x "<< refYdim <<" x "<< refZdim << std::endl;
             std::cout << "useForValidation            : "  << useForValidation << std::endl;
         }
         XmippMetadataProgram::show();
         std::cout << "Input references: " << fnRef << std::endl;
     }
 }

◆ synchronize()

virtual void ProgAngularAssignmentMag::synchronize ( )

inlinevirtual

Synchronize with other processors.

Reimplemented in MpiProgAngularAssignmentMag.

Definition at line 64 of file angular_assignment_mag.h.

64 {}

Member Data Documentation

◆ Nprocessors

size_t ProgAngularAssignmentMag::Nprocessors

Definition at line 67 of file angular_assignment_mag.h.

◆ rank

size_t ProgAngularAssignmentMag::rank

Definition at line 66 of file angular_assignment_mag.h.

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

xmipp/libraries/reconstruction/angular_assignment_mag.h
xmipp/libraries/reconstruction/angular_assignment_mag.cpp

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ProgAngularAssignmentMag()

◆ ~ProgAngularAssignmentMag()

Member Function Documentation

◆ applyRotation()

◆ applyShiftAndRotation()

◆ defineParams()

◆ postProcess()

◆ preProcess()

◆ processImage()

◆ readParams()

◆ show()

◆ synchronize()

Member Data Documentation

◆ Nprocessors

◆ rank