#include <angular_continuous_assign2.h>

Inheritance diagram for ProgAngularContinuousAssign2:

Collaboration diagram for ProgAngularContinuousAssign2:

Public Member Functions
	ProgAngularContinuousAssign2 ()
	Empty constructor. More...

	~ProgAngularContinuousAssign2 ()
	Destructor. More...

void	readParams ()
	Read argument from command line. More...

void	show ()
	Show. More...

void	defineParams ()
	Define parameters. More...

void	startProcessing ()

void	preProcess ()

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

void	updateCTFImage (double defocusU, double defocusV, double angle)

void	postProcess ()

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
FileName	fnVol

FileName	fnResiduals

FileName	fnProjections

double	maxShift

double	maxScale

double	maxAngularChange

double	maxResol

double	maxDefocusChange

double	maxA

double	maxB

double	Ts

int	Rmax

int	pad

bool	optimizeGrayValues

bool	optimizeShift

bool	optimizeScale

bool	optimizeAngles

bool	optimizeDefocus

bool	ignoreCTF

String	originalImageLabel

bool	phaseFlipped

bool	sameDefocus

int	rank

MultidimArray< int >	mask2D

double	iMask2Dsum

FourierProjector *	projector

size_t	Xdim

Image< double >	I

Image< double >	Ip

Image< double >	E

Image< double >	Ifiltered

Image< double >	Ifilteredp

Projection	P

FourierFilter	filter

Matrix2D< double >	A

double	old_rot

double	old_tilt

double	old_psi

double	old_shiftX

double	old_shiftY

bool	old_flip

double	old_grayA

double	old_grayB

bool	hasCTF

double	old_defocusU

double	old_defocusV

double	old_defocusAngle

CTFDescription	ctf

Matrix2D< double >	C0

Matrix2D< double >	C

double	Istddev

int	contCost

double	currentDefocusU

double	currentDefocusV

double	currentAngle

MultidimArray< double > *	ctfImage

std::unique_ptr< MultidimArray< double > >	ctfEnvelope

FourierTransformer	fftTransformer

MultidimArray< std::complex< double > >	fftE

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	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

Predict Continuous Parameters.

Definition at line 46 of file angular_continuous_assign2.h.

Constructor & Destructor Documentation

◆ ProgAngularContinuousAssign2()

ProgAngularContinuousAssign2::ProgAngularContinuousAssign2 ( )

Empty constructor.

Definition at line 33 of file angular_continuous_assign2.cpp.

 {
     produces_a_metadata = true;
     each_image_produces_an_output = true;
     projector = nullptr;
     ctfImage = nullptr;
     rank = 0;
 }

◆ ~ProgAngularContinuousAssign2()

ProgAngularContinuousAssign2::~ProgAngularContinuousAssign2 ( )

Destructor.

Definition at line 42 of file angular_continuous_assign2.cpp.

 {
     delete projector;
     delete ctfImage;
 }

Member Function Documentation

◆ defineParams()

void ProgAngularContinuousAssign2::defineParams ( )

virtual

Define parameters.

Reimplemented from XmippMetadataProgram.

Definition at line 112 of file angular_continuous_assign2.cpp.

 {
     addUsageLine("Make a continuous angular assignment");
     defaultComments["-i"].clear();
     defaultComments["-i"].addComment("Metadata with initial alignment");
     defaultComments["-o"].clear();
     defaultComments["-o"].addComment("Stack of images prepared for 3D reconstruction");
     XmippMetadataProgram::defineParams();
     addParamsLine("   --ref <volume>              : Reference volume");
     addParamsLine("  [--max_shift <s=-1>]         : Maximum shift allowed in pixels");
     addParamsLine("  [--max_scale <s=0.02>]       : Maximum scale change");
     addParamsLine("  [--max_angular_change <a=5>] : Maximum angular change allowed (in degrees)");
     addParamsLine("  [--max_defocus_change <d=500>] : Maximum defocus change allowed (in Angstroms)");
     addParamsLine("  [--max_resolution <f=4>]     : Maximum resolution (A)");
     addParamsLine("  [--max_gray_scale <a=0.05>]  : Maximum gray scale change");
     addParamsLine("  [--max_gray_shift <b=0.05>]  : Maximum gray shift change as a factor of the image standard deviation");
     addParamsLine("  [--sampling <Ts=1>]          : Sampling rate (A/pixel)");
     addParamsLine("  [--Rmax <R=-1>]              : Maximum radius (px). -1=Half of volume size");
     addParamsLine("  [--padding <p=2>]            : Padding factor");
     addParamsLine("  [--optimizeGray]             : Optimize gray values");
     addParamsLine("  [--optimizeShift]            : Optimize shift");
     addParamsLine("  [--optimizeScale]            : Optimize scale");
     addParamsLine("  [--optimizeAngles]           : Optimize angles");
     addParamsLine("  [--optimizeDefocus]          : Optimize defocus");
     addParamsLine("  [--ignoreCTF]                : Ignore CTF");
     addParamsLine("  [--applyTo <label=image>]    : Which is the source of images to apply the final transformation");
     addParamsLine("  [--phaseFlipped]             : Input images have been phase flipped");
     // addParamsLine("  [--penalization <l=100>]     : Penalization for the average term");
     addParamsLine("  [--sameDefocus]              : Force defocusU = defocusV");
     addParamsLine("  [--oresiduals <stack=\"\">]  : Output stack for the residuals");
     addParamsLine("  [--oprojections <stack=\"\">] : Output stack for the projections");
     addExampleLine("A typical use is:",false);
     addExampleLine("xmipp_angular_continuous_assign2 -i anglesFromDiscreteAssignment.xmd --ref reference.vol -o assigned_angles.stk");
 }

◆ postProcess()

void ProgAngularContinuousAssign2::postProcess ( )

virtual

Post process

Reimplemented from XmippMetadataProgram.

Definition at line 688 of file angular_continuous_assign2.cpp.

 {
     MetaData &ptrMdOut = getOutputMd();
     ptrMdOut.removeDisabled();
     if (contCost==CONTCOST_L1)
     {
         double minCost=1e38;
         for (size_t objId : ptrMdOut.ids())
         {
             double cost;
             ptrMdOut.getValue(MDL_COST,cost,objId);
             if (cost<minCost)
                 minCost=cost;
         }
         for (size_t objId : ptrMdOut.ids())
         {
             double cost;
             ptrMdOut.getValue(MDL_COST,cost,objId);
             ptrMdOut.setValue(MDL_WEIGHT_CONTINUOUS2,minCost/cost,objId);
         }
     }
     else
     {
         double maxCost=-1e38;
         for (size_t objId : ptrMdOut.ids())
         {
             double cost;
             ptrMdOut.getValue(MDL_COST,cost,objId);
             if (cost>maxCost)
                 maxCost=cost;
         }
         for (size_t objId : ptrMdOut.ids())
         {
             double cost;
             ptrMdOut.getValue(MDL_COST,cost,objId);
             ptrMdOut.setValue(MDL_WEIGHT_CONTINUOUS2,cost/maxCost,objId);
         }
     }
 
     ptrMdOut.write(fn_out.replaceExtension("xmd"));
 }

◆ preProcess()

void ProgAngularContinuousAssign2::preProcess ( )

virtual

Produce side info. An exception is thrown if any of the files is not found

Reimplemented from XmippMetadataProgram.

Definition at line 157 of file angular_continuous_assign2.cpp.

 {
     // Read the reference volume
     Image<double> V;
     if (rank==0)
     {
         V.read(fnVol);
         V().setXmippOrigin();
         Xdim=XSIZE(V());
     }
     else
     {
         size_t ydim, zdim, ndim;
         getImageSize(fnVol, Xdim, ydim, zdim, ndim);
     }
 
     Ip().initZeros(Xdim,Xdim);
     E().initZeros(Xdim,Xdim);
     Ifilteredp().initZeros(Xdim,Xdim);
     Ifilteredp().setXmippOrigin();
 
     // Construct mask
     if (Rmax<0)
         Rmax=Xdim/2;
     Mask mask;
     mask.type = BINARY_CIRCULAR_MASK;
     mask.mode = INNER_MASK;
     mask.R1 = Rmax;
     mask.generate_mask(Xdim,Xdim);
     mask2D=mask.get_binary_mask();
     iMask2Dsum=1.0/mask2D.sum();
 
     // Construct reference covariance
     FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(mask2D)
     if (DIRECT_MULTIDIM_ELEM(mask2D,n))
         DIRECT_MULTIDIM_ELEM(E(),n)=rnd_gaus(0,1);
     covarianceMatrix(E(),C0);
     FOR_ALL_ELEMENTS_IN_MATRIX2D(C0)
     {
         double val=MAT_ELEM(C0,i,j);
         if (val<0.5)
             MAT_ELEM(C0,i,j)=0;
         else
             MAT_ELEM(C0,i,j)=1;
     }
 
     // Construct projector
     if (rank==0)
         projector = new FourierProjector(V(),pad,Ts/maxResol,xmipp_transformation::BSPLINE3);
     else
         projector = new FourierProjector(pad,Ts/maxResol,xmipp_transformation::BSPLINE3);
 
     // Low pass filter
     filter.FilterBand=LOWPASS;
     filter.w1=Ts/maxResol;
     filter.raised_w=0.02;
 
     // Transformation matrix
     A.initIdentity(3);
 
     // Continuous cost
     if (optimizeGrayValues)
         contCost = CONTCOST_L1;
     else
         contCost = CONTCOST_CORR;
 }

◆ processImage()

void ProgAngularContinuousAssign2::processImage	(	const FileName &	fnImg,
		const FileName &	fnImgOut,
		const MDRow &	rowIn,
		MDRow &	rowOut
	)

virtual

Predict angles and shift. At the input the pose parameters must have an initial guess of the parameters. At the output they have the estimated pose.

Implements XmippMetadataProgram.

Definition at line 399 of file angular_continuous_assign2.cpp.

 {
     // Read input image and initial parameters
 //  ApplyGeoParams geoParams;
 //  geoParams.only_apply_shifts=false;
 //  geoParams.wrap=DONT_WRAP;
 
     //AJ some definitions
     double corrIdx=0.0;
     double corrMask = 0.0;
     double corrWeight = 0.0;
     double imedDist = 0.0;
 
     if (verbose>=2)
         std::cout << "Processing " << fnImg << std::endl;
     I.read(fnImg);
     I().setXmippOrigin();
     Istddev=I().computeStddev();
 
     Ifiltered()=I();
     filter.applyMaskSpace(Ifiltered());
 
     old_rot = rowIn.getValueOrDefault(MDL_ANGLE_ROT, 0.);
     old_tilt = rowIn.getValueOrDefault(MDL_ANGLE_TILT, 0.);
     old_psi = rowIn.getValueOrDefault(MDL_ANGLE_PSI, 0.);
     old_shiftX = rowIn.getValueOrDefault(MDL_SHIFT_X, 0.);
     old_shiftY = rowIn.getValueOrDefault(MDL_SHIFT_Y, 0.);
     old_flip = rowIn.getValueOrDefault(MDL_FLIP, false);
     double old_scaleX=0, old_scaleY=0, old_scaleAngle=0;
     old_grayA=1;
     old_grayB=0;
     if (rowIn.containsLabel(MDL_CONTINUOUS_SCALE_X))
     {
         old_scaleX = rowIn.getValue<double>(MDL_CONTINUOUS_SCALE_X);
         old_scaleY = rowIn.getValue<double>(MDL_CONTINUOUS_SCALE_Y);
         if (rowIn.containsLabel(MDL_CONTINUOUS_SCALE_ANGLE))
             old_scaleAngle = rowIn.getValue<double>(MDL_CONTINUOUS_SCALE_ANGLE);
         old_shiftX = rowIn.getValue<double>(MDL_CONTINUOUS_X);
         old_shiftY = rowIn.getValue<double>(MDL_CONTINUOUS_Y);
         old_flip = rowIn.getValue<bool>(MDL_CONTINUOUS_FLIP);
     }
 
     if (optimizeGrayValues && rowIn.containsLabel(MDL_CONTINUOUS_GRAY_A))
     {
         old_grayA = rowIn.getValue<double>(MDL_CONTINUOUS_GRAY_A);
         old_grayB = rowIn.getValue<double>(MDL_CONTINUOUS_GRAY_B);
     }
 
     if ((rowIn.containsLabel(MDL_CTF_DEFOCUSU) || rowIn.containsLabel(MDL_CTF_MODEL)) && !ignoreCTF)
     {
         hasCTF=true;
         ctf.readFromMdRow(rowIn);
         ctf.produceSideInfo();
         old_defocusU=ctf.DeltafU;
         old_defocusV=ctf.DeltafV;
         old_defocusAngle=ctf.azimuthal_angle;
         updateCTFImage(old_defocusU,old_defocusV,old_defocusAngle);
         fftTransformer.FourierTransform(Ifiltered(),fftE,false);
         FOR_ALL_DIRECT_ELEMENTS_IN_ARRAY2D(fftE)
             DIRECT_A2D_ELEM(fftE,i,j)*=DIRECT_A2D_ELEM(*ctfEnvelope,i,j);
         fftTransformer.inverseFourierTransform();
     }
     else
         hasCTF=false;
 
     Matrix1D<double> p(13), steps(13);
     // COSS: Gray values are optimized in transform_image_adjust_gray_values
     if (optimizeGrayValues)
     {
         p(0)=old_grayA; // a in I'=a*I+b
         p(1)=old_grayB; // b in I'=a*I+b
     }
     else
     {
         p(0)=1; // a in I'=a*I+b
         p(1)=0; // b in I'=a*I+b
     }
     p(4)=old_scaleX;
     p(5)=old_scaleY;
     p(6)=old_scaleAngle;
 
     // default values
     if (fnResiduals != "") {
       rowOut.setValue<String>(MDL_IMAGE_RESIDUAL, "");
     }
     if (fnProjections != "") {
       rowOut.setValue<String>(MDL_IMAGE_REF, "");
     }
 
     // Optimize
     double cost=-1;
     if (fabs(old_scaleX)>maxScale || fabs(old_scaleY)>maxScale)
         rowOut.setValue(MDL_ENABLED,-1);
     else
     {
         try
         {
             cost=1e38;
             int iter;
             steps.initZeros();
             if (optimizeGrayValues)
                 steps(0)=steps(1)=1.;
             if (optimizeShift)
                 steps(2)=steps(3)=1.;
             if (optimizeScale)
                 steps(4)=steps(5)=steps(6)=1.;
             if (optimizeAngles)
                 steps(7)=steps(8)=steps(9)=1.;
             if (optimizeDefocus) {
                 if (sameDefocus)
                     steps(10)=steps(12)=1.; 
                 else {
                     steps(10)=steps(11)=steps(12)=1.;
                     if (hasCTF)
                     {
                         currentDefocusU = old_defocusU;
                         currentDefocusV = old_defocusV;
                         currentAngle = old_defocusAngle;
                     }
                     else
                         currentDefocusU = currentDefocusV = currentAngle = 0;
                 }
             }
             powellOptimizer(p, 1, 13, &continuous2cost, this, 0.01, cost, iter, steps, verbose>=2);
             if (cost>1e30 || (cost>0 && contCost==CONTCOST_CORR))
             {
                 rowOut.setValue(MDL_ENABLED,-1);
                 p.initZeros();
                 if (optimizeGrayValues)
                 {
                     p(0)=old_grayA; // a in I'=a*I+b
                     p(1)=old_grayB; // b in I'=a*I+b
                 }
                 else
                 {
                     p(0)=1;
                     p(1)=0;
                 }
                 p(4)=old_scaleX;
                 p(5)=old_scaleY;
                 p(6)=old_scaleAngle;
             }
             else
             {
                 //Calculating several similarity measures between P and Ifilteredp (correlations and imed)
                 corrIdx = correlationIndex(P(), Ifilteredp());
                 corrMask = correlationMasked(P(), Ifilteredp());
                 corrWeight = correlationWeighted(P(), Ifilteredp());
                 imedDist = imedDistance(P(), Ifilteredp());
 
                 if (fnResiduals!="")
                 {
                     FileName fnResidual;
                     fnResidual.compose(fnImgOut.getPrefixNumber(),fnResiduals);
                     E.write(fnResidual);
                     rowOut.setValue(MDL_IMAGE_RESIDUAL,fnResidual);
                 }
                 if (fnProjections!="")
                 {
                     FileName fnProjection;
                     fnProjection.compose(fnImgOut.getPrefixNumber(),fnProjections);
                     P.write(fnProjection);
                     rowOut.setValue(MDL_IMAGE_REF,fnProjection);
                 }
             }
             if (contCost==CONTCOST_CORR)
                 cost=-cost;
             if (verbose>=2)
                 std::cout << "I'=" << p(0) << "*I" << "+" << p(1) << " Dshift=(" << p(2) << "," << p(3) << ") "
                           << "scale=(" << 1+p(4) << "," << 1+p(5) << ", angle=" << p(6) << ") Drot=" << p(7) << " Dtilt=" << p(8)
                           << " Dpsi=" << p(9) << " DU=" << p(10) << " DV=" << p(11) << " Dalpha=" << p(12) << std::endl;
             // Apply
             FileName fnOrig;
             rowIn.getValue(MDL::str2Label(originalImageLabel),fnOrig);
             I.read(fnImg);
             if (XSIZE(Ip())!=XSIZE(I()))
             {
                 scaleToSize(xmipp_transformation::BSPLINE3,Ip(),I(),XSIZE(Ip()),YSIZE(Ip()));
                 I()=Ip();
             }
             A(0,2)=p(2)+old_shiftX;
             A(1,2)=p(3)+old_shiftY;
             double scalex=p(4);
             double scaley=p(5);
             double scaleAngle=p(6);
             double sin2_t=sin(scaleAngle)*sin(scaleAngle);
             double sin_2t=sin(2*scaleAngle);
             A(0,0)=1+scalex+(scaley-scalex)*sin2_t;
             A(0,1)=0.5*(scaley-scalex)*sin_2t;
             A(1,0)=A(0,1);
             A(1,1)=1+scaley-(scaley-scalex)*sin2_t;
 //          A(0,0)=1+p(4);
 //          A(1,1)=1+p(5);
 
             if (old_flip)
             {
                 MAT_ELEM(A,0,0)*=-1;
                 MAT_ELEM(A,0,1)*=-1;
                 MAT_ELEM(A,0,2)*=-1;
             }
             applyGeometry(xmipp_transformation::BSPLINE3,Ip(),I(),A,xmipp_transformation::IS_NOT_INV,xmipp_transformation::DONT_WRAP);
             if (optimizeGrayValues)
             {
                 MultidimArray<double> &mIp=Ip();
                 double ia=1.0/p(0);
                 double b=p(1);
                 FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(mIp)
                 {
                     if (DIRECT_MULTIDIM_ELEM(mask2D,n))
                         DIRECT_MULTIDIM_ELEM(mIp,n)=ia*(DIRECT_MULTIDIM_ELEM(mIp,n)-b);
                     else
                         DIRECT_MULTIDIM_ELEM(mIp,n)=0.0;
                 }
             }
             Ip.write(fnImgOut);
         }
         catch (XmippError &XE)
         {
             std::cerr << XE.what() << std::endl;
             std::cerr << "Warning: Cannot refine " << fnImg << std::endl;
             rowOut.setValue(MDL_ENABLED,-1);
         }
     }
     rowOut.setValue(MDL_IMAGE_ORIGINAL, fnImg);
     rowOut.setValue(MDL_IMAGE, fnImgOut);
     rowOut.setValue(MDL_ANGLE_ROT,  old_rot+p(7));
     rowOut.setValue(MDL_ANGLE_TILT, old_tilt+p(8));
     rowOut.setValue(MDL_ANGLE_PSI,  old_psi+p(9));
     rowOut.setValue(MDL_SHIFT_X,    0.);
     rowOut.setValue(MDL_SHIFT_Y,    0.);
     rowOut.setValue(MDL_FLIP,       false);
     rowOut.setValue(MDL_COST,       cost);
     if (optimizeGrayValues)
     {
         rowOut.setValue(MDL_CONTINUOUS_GRAY_A,p(0));
         rowOut.setValue(MDL_CONTINUOUS_GRAY_B,p(1));
     }
     rowOut.setValue(MDL_CONTINUOUS_SCALE_X,p(4));
     rowOut.setValue(MDL_CONTINUOUS_SCALE_Y,p(5));
     rowOut.setValue(MDL_CONTINUOUS_SCALE_ANGLE,p(6));
     rowOut.setValue(MDL_CONTINUOUS_X,p(2)+old_shiftX);
     rowOut.setValue(MDL_CONTINUOUS_Y,p(3)+old_shiftY);
     rowOut.setValue(MDL_CONTINUOUS_FLIP,old_flip);
     if (hasCTF)
     {
         rowOut.setValue(MDL_CTF_DEFOCUSU,old_defocusU+p(10));
         if (sameDefocus)
             rowOut.setValue(MDL_CTF_DEFOCUSV,old_defocusU+p(10)); 
         else
             rowOut.setValue(MDL_CTF_DEFOCUSV,old_defocusV+p(11));
         rowOut.setValue(MDL_CTF_DEFOCUS_ANGLE,old_defocusAngle+p(12));
         if (sameDefocus)
             rowOut.setValue(MDL_CTF_DEFOCUS_CHANGE,0.5*(p(10)+p(10)));
         else
             rowOut.setValue(MDL_CTF_DEFOCUS_CHANGE,0.5*(p(10)+p(11)));
         if (old_defocusU+p(10)<0 || old_defocusU+p(11)<0)
             rowOut.setValue(MDL_ENABLED,-1);
     }
     //Saving correlation and imed values in the metadata
     rowOut.setValue(MDL_CORRELATION_IDX, corrIdx);
     rowOut.setValue(MDL_CORRELATION_MASK, corrMask);
     rowOut.setValue(MDL_CORRELATION_WEIGHT, corrWeight);
     rowOut.setValue(MDL_IMED, imedDist);
 
 
 #ifdef DEBUG
     std::cout << "p=" << p << std::endl;
     MetaDataVec MDaux;
     MDaux.addRow(rowOut);
     MDaux.write("PPPmd.xmd");
     Image<double> save;
     save()=P();
     save.write("PPPprojection.xmp");
     save()=I();
     save.write("PPPexperimental.xmp");
     //save()=C;
     //save.write("PPPC.xmp");
     Ip.write("PPPexperimentalp.xmp");
     Ifiltered.write("PPPexperimentalFiltered.xmp");
     Ifilteredp.write("PPPexperimentalFilteredp.xmp");
     E.write("PPPresidual.xmp");
     std::cout << A << std::endl;
     std::cout << fnImgOut << " rewritten\n";
     std::cout << "Press any key" << std::endl;
     char c; std::cin >> c;
 #endif
 }

◆ readParams()

void ProgAngularContinuousAssign2::readParams ( )

virtual

Read argument from command line.

Reimplemented from XmippMetadataProgram.

Definition at line 49 of file angular_continuous_assign2.cpp.

 {
     XmippMetadataProgram::readParams();
     fnVol = getParam("--ref");
     maxShift = getDoubleParam("--max_shift");
     maxScale = getDoubleParam("--max_scale");
     maxDefocusChange = getDoubleParam("--max_defocus_change");
     maxAngularChange = getDoubleParam("--max_angular_change");
     maxResol = getDoubleParam("--max_resolution");
     maxA = getDoubleParam("--max_gray_scale");
     maxB = getDoubleParam("--max_gray_shift");
     Ts = getDoubleParam("--sampling");
     Rmax = getIntParam("--Rmax");
     pad = getIntParam("--padding");
     optimizeGrayValues = checkParam("--optimizeGray");
     optimizeShift = checkParam("--optimizeShift");
     optimizeScale = checkParam("--optimizeScale");
     optimizeAngles = checkParam("--optimizeAngles");
     optimizeDefocus = checkParam("--optimizeDefocus");
     ignoreCTF = checkParam("--ignoreCTF");
     originalImageLabel = getParam("--applyTo");
     phaseFlipped = checkParam("--phaseFlipped");
     // penalization = getDoubleParam("--penalization");
     fnResiduals = getParam("--oresiduals");
     fnProjections = getParam("--oprojections");
     sameDefocus = checkParam("--sameDefocus");
     keep_input_columns = true; // each output metadata row is a deep copy of the input metadata row
 }

◆ show()

void ProgAngularContinuousAssign2::show ( )

Show.

Definition at line 79 of file angular_continuous_assign2.cpp.

 {
     if (!verbose)
         return;
     XmippMetadataProgram::show();
     std::cout
     << "Reference volume:    " << fnVol              << std::endl
     << "Max. Shift:          " << maxShift           << std::endl
     << "Max. Scale:          " << maxScale           << std::endl
     << "Max. Angular Change: " << maxAngularChange   << std::endl
     << "Max. Resolution:     " << maxResol           << std::endl
     << "Max. Defocus Change: " << maxDefocusChange   << std::endl
     << "Max. Gray Scale:     " << maxA               << std::endl
     << "Max. Gray Shift:     " << maxB               << std::endl
     << "Sampling:            " << Ts                 << std::endl
     << "Max. Radius:         " << Rmax               << std::endl
     << "Padding factor:      " << pad                << std::endl
     << "Optimize gray:       " << optimizeGrayValues << std::endl
     << "Optimize shifts:     " << optimizeShift      << std::endl
     << "Optimize scale:      " << optimizeScale      << std::endl
     << "Optimize angles:     " << optimizeAngles     << std::endl
     << "Optimize defocus:    " << optimizeDefocus    << std::endl
     << "Ignore CTF:          " << ignoreCTF          << std::endl
     << "Apply to:            " << originalImageLabel << std::endl
     << "Phase flipped:       " << phaseFlipped       << std::endl
     // << "Penalization:        " << penalization       << std::endl
     << "Force same defocus:  " << sameDefocus        << std::endl
     << "Output residuals:    " << fnResiduals        << std::endl
     << "Output projections:  " << fnProjections      << std::endl
     ;
 }

◆ startProcessing()

void ProgAngularContinuousAssign2::startProcessing ( )

virtual

Start processing

Reimplemented from XmippMetadataProgram.

Definition at line 147 of file angular_continuous_assign2.cpp.

 {
     XmippMetadataProgram::startProcessing();
     if (fnResiduals!="")
         createEmptyFile(fnResiduals, xdimOut, ydimOut, zdimOut, mdInSize, true, WRITE_OVERWRITE);
     if (fnProjections!="")
         createEmptyFile(fnProjections, xdimOut, ydimOut, zdimOut, mdInSize, true, WRITE_OVERWRITE);
 }

◆ updateCTFImage()

void ProgAngularContinuousAssign2::updateCTFImage	(	double	defocusU,
		double	defocusV,
		double	angle
	)

Update CTF image

Definition at line 225 of file angular_continuous_assign2.cpp.

 {
     ctf.K=1; // get pure CTF with no envelope
     currentDefocusU=ctf.DeltafU=defocusU;
     currentDefocusV=ctf.DeltafV=defocusV;
     currentAngle=ctf.azimuthal_angle=angle;
     ctf.produceSideInfo();
     if (ctfImage==nullptr)
     {
         ctfImage = new MultidimArray<double>();
         ctfImage->resizeNoCopy(I());
         STARTINGY(*ctfImage)=STARTINGX(*ctfImage)=0;
 
         ctfEnvelope = std::make_unique<MultidimArray<double>>();
         ctfEnvelope->resizeNoCopy(I());
         STARTINGY(*ctfEnvelope)=STARTINGX(*ctfEnvelope)=0;
     }
     ctf.generateCTF((int)YSIZE(I()),(int)XSIZE(I()),*ctfImage,Ts);
     ctf.generateEnvelope((int)YSIZE(I()),(int)XSIZE(I()),*ctfEnvelope,Ts);
     if (phaseFlipped)
         FOR_ALL_ELEMENTS_IN_ARRAY2D(*ctfImage)
             A2D_ELEM(*ctfImage,i,j)=fabs(A2D_ELEM(*ctfImage,i,j));
 }

Member Data Documentation

◆ A

Matrix2D<double> ProgAngularContinuousAssign2::A

Definition at line 116 of file angular_continuous_assign2.h.

◆ C

Matrix2D<double> ProgAngularContinuousAssign2::C

Definition at line 132 of file angular_continuous_assign2.h.

◆ C0

Matrix2D<double> ProgAngularContinuousAssign2::C0

Definition at line 132 of file angular_continuous_assign2.h.

◆ contCost

int ProgAngularContinuousAssign2::contCost

Definition at line 136 of file angular_continuous_assign2.h.

◆ ctf

CTFDescription ProgAngularContinuousAssign2::ctf

Definition at line 130 of file angular_continuous_assign2.h.

◆ ctfEnvelope

std::unique_ptr<MultidimArray<double> > ProgAngularContinuousAssign2::ctfEnvelope

Definition at line 141 of file angular_continuous_assign2.h.

◆ ctfImage

MultidimArray<double>* ProgAngularContinuousAssign2::ctfImage

Definition at line 140 of file angular_continuous_assign2.h.

◆ currentAngle

double ProgAngularContinuousAssign2::currentAngle

Definition at line 138 of file angular_continuous_assign2.h.

◆ currentDefocusU

double ProgAngularContinuousAssign2::currentDefocusU

Definition at line 138 of file angular_continuous_assign2.h.

◆ currentDefocusV

double ProgAngularContinuousAssign2::currentDefocusV

Definition at line 138 of file angular_continuous_assign2.h.

◆ E

Image<double> ProgAngularContinuousAssign2::E

Definition at line 110 of file angular_continuous_assign2.h.

◆ fftE

MultidimArray< std::complex<double> > ProgAngularContinuousAssign2::fftE

Definition at line 145 of file angular_continuous_assign2.h.

◆ fftTransformer

FourierTransformer ProgAngularContinuousAssign2::fftTransformer

Definition at line 143 of file angular_continuous_assign2.h.

◆ filter

FourierFilter ProgAngularContinuousAssign2::filter

Definition at line 114 of file angular_continuous_assign2.h.

◆ fnProjections

FileName ProgAngularContinuousAssign2::fnProjections

Filename of projections

Definition at line 54 of file angular_continuous_assign2.h.

◆ fnResiduals

FileName ProgAngularContinuousAssign2::fnResiduals

Filename of residuals

Definition at line 52 of file angular_continuous_assign2.h.

◆ fnVol

FileName ProgAngularContinuousAssign2::fnVol

Filename of the reference volume

Definition at line 50 of file angular_continuous_assign2.h.

◆ hasCTF

bool ProgAngularContinuousAssign2::hasCTF

Definition at line 126 of file angular_continuous_assign2.h.

◆ I

Image<double> ProgAngularContinuousAssign2::I

Definition at line 110 of file angular_continuous_assign2.h.

◆ Ifiltered

Image<double> ProgAngularContinuousAssign2::Ifiltered

Definition at line 110 of file angular_continuous_assign2.h.

◆ Ifilteredp

Image<double> ProgAngularContinuousAssign2::Ifilteredp

Definition at line 110 of file angular_continuous_assign2.h.

◆ ignoreCTF

bool ProgAngularContinuousAssign2::ignoreCTF

Definition at line 86 of file angular_continuous_assign2.h.

◆ iMask2Dsum

double ProgAngularContinuousAssign2::iMask2Dsum

Definition at line 104 of file angular_continuous_assign2.h.

◆ Ip

Image<double> ProgAngularContinuousAssign2::Ip

Definition at line 110 of file angular_continuous_assign2.h.

◆ Istddev

double ProgAngularContinuousAssign2::Istddev

Definition at line 134 of file angular_continuous_assign2.h.

◆ mask2D

MultidimArray<int> ProgAngularContinuousAssign2::mask2D

Definition at line 102 of file angular_continuous_assign2.h.

◆ maxA

double ProgAngularContinuousAssign2::maxA

Maximum gray scale change

Definition at line 66 of file angular_continuous_assign2.h.

◆ maxAngularChange

double ProgAngularContinuousAssign2::maxAngularChange

Maximum angular change allowed

Definition at line 60 of file angular_continuous_assign2.h.

◆ maxB

double ProgAngularContinuousAssign2::maxB

Maximum gray shift change

Definition at line 68 of file angular_continuous_assign2.h.

◆ maxDefocusChange

double ProgAngularContinuousAssign2::maxDefocusChange

Maximum defocus change (A)

Definition at line 64 of file angular_continuous_assign2.h.

◆ maxResol

double ProgAngularContinuousAssign2::maxResol

Maximum frequency (A)

Definition at line 62 of file angular_continuous_assign2.h.

◆ maxScale

double ProgAngularContinuousAssign2::maxScale

Maximum scale allowed

Definition at line 58 of file angular_continuous_assign2.h.

◆ maxShift

double ProgAngularContinuousAssign2::maxShift

Maximum shift allowed

Definition at line 56 of file angular_continuous_assign2.h.

◆ old_defocusAngle

double ProgAngularContinuousAssign2::old_defocusAngle

Definition at line 128 of file angular_continuous_assign2.h.

◆ old_defocusU

double ProgAngularContinuousAssign2::old_defocusU

Definition at line 128 of file angular_continuous_assign2.h.

◆ old_defocusV

double ProgAngularContinuousAssign2::old_defocusV

Definition at line 128 of file angular_continuous_assign2.h.

◆ old_flip

bool ProgAngularContinuousAssign2::old_flip

Definition at line 122 of file angular_continuous_assign2.h.

◆ old_grayA

double ProgAngularContinuousAssign2::old_grayA

Definition at line 124 of file angular_continuous_assign2.h.

◆ old_grayB

double ProgAngularContinuousAssign2::old_grayB

Definition at line 124 of file angular_continuous_assign2.h.

◆ old_psi

double ProgAngularContinuousAssign2::old_psi

Definition at line 118 of file angular_continuous_assign2.h.

◆ old_rot

double ProgAngularContinuousAssign2::old_rot

Definition at line 118 of file angular_continuous_assign2.h.

◆ old_shiftX

double ProgAngularContinuousAssign2::old_shiftX

Definition at line 120 of file angular_continuous_assign2.h.

◆ old_shiftY

double ProgAngularContinuousAssign2::old_shiftY

Definition at line 120 of file angular_continuous_assign2.h.

◆ old_tilt

double ProgAngularContinuousAssign2::old_tilt

Definition at line 118 of file angular_continuous_assign2.h.

◆ optimizeAngles

bool ProgAngularContinuousAssign2::optimizeAngles

Definition at line 82 of file angular_continuous_assign2.h.

◆ optimizeDefocus

bool ProgAngularContinuousAssign2::optimizeDefocus

Definition at line 84 of file angular_continuous_assign2.h.

◆ optimizeGrayValues

bool ProgAngularContinuousAssign2::optimizeGrayValues

Definition at line 76 of file angular_continuous_assign2.h.

◆ optimizeScale

bool ProgAngularContinuousAssign2::optimizeScale

Definition at line 80 of file angular_continuous_assign2.h.

◆ optimizeShift

bool ProgAngularContinuousAssign2::optimizeShift

Definition at line 78 of file angular_continuous_assign2.h.

◆ originalImageLabel

String ProgAngularContinuousAssign2::originalImageLabel

Definition at line 88 of file angular_continuous_assign2.h.

◆ P

Projection ProgAngularContinuousAssign2::P

Definition at line 112 of file angular_continuous_assign2.h.

◆ pad

int ProgAngularContinuousAssign2::pad

Padding factor

Definition at line 74 of file angular_continuous_assign2.h.

◆ phaseFlipped

bool ProgAngularContinuousAssign2::phaseFlipped

Definition at line 90 of file angular_continuous_assign2.h.

◆ projector

FourierProjector* ProgAngularContinuousAssign2::projector

Definition at line 106 of file angular_continuous_assign2.h.

◆ rank

int ProgAngularContinuousAssign2::rank

Definition at line 99 of file angular_continuous_assign2.h.

◆ Rmax

int ProgAngularContinuousAssign2::Rmax

Maximum radius

Definition at line 72 of file angular_continuous_assign2.h.

◆ sameDefocus

bool ProgAngularContinuousAssign2::sameDefocus

Definition at line 95 of file angular_continuous_assign2.h.

◆ Ts

double ProgAngularContinuousAssign2::Ts

Sampling rate

Definition at line 70 of file angular_continuous_assign2.h.

◆ Xdim

size_t ProgAngularContinuousAssign2::Xdim

Definition at line 108 of file angular_continuous_assign2.h.

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

xmipp/libraries/reconstruction/angular_continuous_assign2.h
xmipp/libraries/reconstruction/angular_continuous_assign2.cpp

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ProgAngularContinuousAssign2()

◆ ~ProgAngularContinuousAssign2()

Member Function Documentation

◆ defineParams()

◆ postProcess()

◆ preProcess()

◆ processImage()

◆ readParams()

◆ show()

◆ startProcessing()

◆ updateCTFImage()

Member Data Documentation

◆ A

◆ C

◆ C0

◆ contCost

◆ ctf

◆ ctfEnvelope

◆ ctfImage

◆ currentAngle

◆ currentDefocusU

◆ currentDefocusV

◆ E

◆ fftE

◆ fftTransformer

◆ filter

◆ fnProjections

◆ fnResiduals

◆ fnVol

◆ hasCTF

◆ I

◆ Ifiltered

◆ Ifilteredp

◆ ignoreCTF

◆ iMask2Dsum

◆ Ip

◆ Istddev

◆ mask2D

◆ maxA

◆ maxAngularChange

◆ maxB

◆ maxDefocusChange

◆ maxResol

◆ maxScale

◆ maxShift

◆ old_defocusAngle

◆ old_defocusU

◆ old_defocusV

◆ old_flip

◆ old_grayA

◆ old_grayB

◆ old_psi

◆ old_rot

◆ old_shiftX

◆ old_shiftY

◆ old_tilt

◆ optimizeAngles

◆ optimizeDefocus

◆ optimizeGrayValues

◆ optimizeScale

◆ optimizeShift

◆ originalImageLabel

◆ P

◆ pad

◆ phaseFlipped

◆ projector

◆ rank

◆ Rmax

◆ sameDefocus

◆ Ts

◆ Xdim