#include <forward_art_zernike3d_subtomos.h>

Inheritance diagram for ProgForwardArtZernike3DSubtomos:

Collaboration diagram for ProgForwardArtZernike3DSubtomos:

Public Types
enum	Mode { Mode::Proj, Mode::Vol }

Public Member Functions
	ProgForwardArtZernike3DSubtomos ()
	Empty constructor. More...

	~ProgForwardArtZernike3DSubtomos ()
	Destructor. More...

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

void	show ()
	Show. More...

void	defineParams ()
	Define parameters. More...

void	preProcess ()

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

void	numCoefficients (int l1, int l2, int &vecSize)
	Length of coefficients vector. More...

void	fillVectorTerms (int l1, int l2, Matrix1D< int > &vL1, Matrix1D< int > &vN, Matrix1D< int > &vL2, Matrix1D< int > &vM)
	Zernike and SPH coefficients allocation. More...

void	deformVol (MultidimArray< double > &mP, MultidimArray< double > &mW, const MultidimArray< double > &mV, double rot, double tilt, double psi)
	Deform a volumen using Zernike-Spherical harmonic basis. More...

void	recoverVol ()

virtual void	finishProcessing ()

void	applyMissingWedge (MultidimArray< double > &mV)

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...

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	fnVolR

FileName	fnMaskR

FileName	fnVolO

FileName	fnOutDir
	Output directory. More...

int	L1

int	L2

Matrix1D< int >	vL1

Matrix1D< int >	vN

Matrix1D< int >	vL2

Matrix1D< int >	vM

double	Ts

int	RmaxDef

bool	phaseFlipped

bool	ignoreCTF

double	lambda

int	save_iter

bool	useCTF

bool	useZernike

int	flagEnabled

double	t1

double	t2

bool	resume

int	niter

int	sort_last_N

MultidimArray< int >	mask2D

size_t	Xdim

Image< double >	V

Image< double >	Vrefined

Image< double >	Vout

Image< double >	Ifilteredp

Image< double >	I

MultidimArray< int >	Vmask

Image< double >	P

Image< double >	W

Image< double >	Idiff

Matrix2D< double >	A

double	rot

double	tilt

double	psi

double	shiftX

double	shiftY

double	shiftZ

bool	flip

bool	hasCTF

double	defocusU

double	defocusV

double	defocusAngle

CTFDescription	ctf

FourierFilter	FilterCTF

int	vecSize

std::vector< double >	clnm

bool	showOptimization

MultidimArray< size_t >	ordered_list

int	current_save_iter

int	num_images

int	current_iter

int	initX

int	endX

int	initY

int	endY

int	initZ

int	endZ

int	loop_step

struct blobtype	blob

double	blob_r

double	sigma

double	sigma4

MultidimArray< double >	gaussian3d

MultidimArray< double >	gaussian_mw

FourierTransformer	transformer

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 void	postProcess ()

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

void	show () const override

virtual void	startProcessing ()

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 40 of file forward_art_zernike3d_subtomos.h.

Member Enumeration Documentation

◆ Mode

enum ProgForwardArtZernike3DSubtomos::Mode

strong

Enumerator
Proj
Vol

Definition at line 143 of file forward_art_zernike3d_subtomos.h.

143 { Proj, Vol };

Constructor & Destructor Documentation

◆ ProgForwardArtZernike3DSubtomos()

ProgForwardArtZernike3DSubtomos::ProgForwardArtZernike3DSubtomos ( )

Empty constructor.

Definition at line 35 of file forward_art_zernike3d_subtomos.cpp.

 {
     resume = false;
     produces_a_metadata = true;
     each_image_produces_an_output = false;
     showOptimization = false;
 }

◆ ~ProgForwardArtZernike3DSubtomos()

ProgForwardArtZernike3DSubtomos::~ProgForwardArtZernike3DSubtomos ( )

default

Destructor.

Member Function Documentation

◆ applyMissingWedge()

void ProgForwardArtZernike3DSubtomos::applyMissingWedge ( MultidimArray< double > & mV )

Definition at line 913 of file forward_art_zernike3d_subtomos.cpp.

 {
     // gaussian_mw = gaussian3d;
     // gaussian_mw.setXmippOrigin();
     MultidimArray<std::complex<double>> fg, Fourier;
     MultidimArray<int> maskWedge;
     Matrix2D<double> R;
     R.initIdentity(3);
     // Euler_angles2matrix(static_cast<double>(rot), static_cast<double>(tilt), static_cast<double>(psi), R, false);
     transformer.FourierTransform(mV, fg, false);
     transformer.getFourierAlias(Fourier);
     maskWedge.initZeros(Fourier);
     maskWedge.setXmippOrigin();
     BinaryWedgeMask(maskWedge, t1, t2, R, true);
     FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(fg)
     DIRECT_MULTIDIM_ELEM(fg,n) *= DIRECT_MULTIDIM_ELEM(maskWedge,n);
     transformer.inverseFourierTransform();
 }

◆ defineParams()

void ProgForwardArtZernike3DSubtomos::defineParams ( )

virtual

Define parameters.

Reimplemented from XmippMetadataProgram.

Definition at line 98 of file forward_art_zernike3d_subtomos.cpp.

 {
     addUsageLine("Template-based canonical volume reconstruction through Zernike3D coefficients");
     defaultComments["-i"].clear();
     defaultComments["-i"].addComment("Metadata with initial alignment");
     defaultComments["-o"].clear();
     defaultComments["-o"].addComment("Refined volume");
     XmippMetadataProgram::defineParams();
     addParamsLine("  [--ref <volume=\"\">]        : Reference volume");
     addParamsLine("  [--mask <m=\"\">]            : Mask reference volume");
     addParamsLine("  [--odir <outputDir=\".\">]   : Output directory");
     addParamsLine("  [--sampling <Ts=1>]          : Sampling rate (A/pixel)");
     addParamsLine("  [--RDef <r=-1>]              : Maximum radius of the deformation (px). -1=Half of volume size");
     addParamsLine("  [--l1 <l1=3>]                : Degree Zernike Polynomials=1,2,3,...");
     addParamsLine("  [--l2 <l2=2>]                : Harmonical depth of the deformation=1,2,3,...");
     addParamsLine("  [--blobr <b=4>]              : Blob radius for forward mapping splatting");
     addParamsLine("  [--step <step=1>]            : Voxel index step");
     addParamsLine("  [--sigma <step=0.25>]        : Gaussian sigma");
     addParamsLine("  [--useZernike]               : Correct heterogeneity with Zernike3D coefficients");
     addParamsLine("  [--useCTF]                   : Correct CTF during ART reconstruction");
     addParamsLine("  [--phaseFlipped]             : Input images have been phase flipped");
     addParamsLine("  [--regularization <l=0.01>]  : ART regularization weight");
     addParamsLine("  [--niter <n=1>]              : Number of ART iterations");
     addParamsLine("  [--save_iter <s=0>]          : Save intermidiate volume after #save_iter iterations");
     addParamsLine("  [--sort_last <N=2>]          : The algorithm sorts projections in the most orthogonally possible way. ");
     addParamsLine("                               : The most orthogonal way is defined as choosing the projection which maximizes the ");
     addParamsLine("                               : dot product with the N previous inserted projections. Use -1 to sort with all  ");
     addParamsLine("                               : previous projections");
     addParamsLine("  [--t1 <t1=-60>]              : First tilt angle range");
     addParamsLine("  [--t2 <t2=60>]               : Second tilt angle range");
     addParamsLine("  [--resume]                   : Resume processing");
     addExampleLine("A typical use is:", false);
     addExampleLine("xmipp_art_zernike3d -i anglesFromContinuousAssignment.xmd --ref reference.vol -o assigned_anglesAndDeformations.xmd --l1 3 --l2 2");
 }

◆ deformVol()

void ProgForwardArtZernike3DSubtomos::deformVol	(	MultidimArray< double > &	mP,
		MultidimArray< double > &	mW,
		const MultidimArray< double > &	mV,
		double	rot,
		double	tilt,
		double	psi
	)

Deform a volumen using Zernike-Spherical harmonic basis.

◆ fillVectorTerms()

void ProgForwardArtZernike3DSubtomos::fillVectorTerms	(	int	l1,
		int	l2,
		Matrix1D< int > &	vL1,
		Matrix1D< int > &	vN,
		Matrix1D< int > &	vL2,
		Matrix1D< int > &	vM
	)

Zernike and SPH coefficients allocation.

Definition at line 371 of file forward_art_zernike3d_subtomos.cpp.

 {
     int idx = 0;
     vL1.initZeros(vecSize);
     vN.initZeros(vecSize);
     vL2.initZeros(vecSize);
     vM.initZeros(vecSize);
     for (int h = 0; h <= l2; h++)
     {
         int totalSPH = 2 * h + 1;
         int aux = std::floor(totalSPH / 2);
         for (int l = h; l <= l1; l += 2)
         {
             for (int m = 0; m < totalSPH; m++)
             {
                 VEC_ELEM(vL1, idx) = l;
                 VEC_ELEM(vN, idx) = h;
                 VEC_ELEM(vL2, idx) = h;
                 VEC_ELEM(vM, idx) = m - aux;
                 idx++;
             }
         }
     }
 }

◆ finishProcessing()

void ProgForwardArtZernike3DSubtomos::finishProcessing ( )

virtual

Reimplemented from XmippMetadataProgram.

Definition at line 275 of file forward_art_zernike3d_subtomos.cpp.

 {
     // XmippMetadataProgram::finishProcessing();
     recoverVol();
     Vout.write(fnVolO);
 }

◆ numCoefficients()

void ProgForwardArtZernike3DSubtomos::numCoefficients	(	int	l1,
		int	l2,
		int &	vecSize
	)

Length of coefficients vector.

Definition at line 353 of file forward_art_zernike3d_subtomos.cpp.

 {
     for (int h = 0; h <= l2; h++)
     {
         int numSPH = 2 * h + 1;
         int count = l1 - h + 1;
         int numEven = (count >> 1) + (count & 1 && !(h & 1));
         if (h % 2 == 0)
         {
             vecSize += numSPH * numEven;
         }
         else
         {
             vecSize += numSPH * (l1 - h + 1 - numEven);
         }
     }
 }

◆ preProcess()

void ProgForwardArtZernike3DSubtomos::preProcess ( )

virtual

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

Reimplemented from XmippMetadataProgram.

Definition at line 148 of file forward_art_zernike3d_subtomos.cpp.

 {
 
     // Check that metadata has all information neede
     if (!getInputMd()->containsLabel(MDL_ANGLE_ROT) ||
         !getInputMd()->containsLabel(MDL_ANGLE_TILT) ||
         !getInputMd()->containsLabel(MDL_ANGLE_PSI))
     {
         REPORT_ERROR(ERR_MD_MISSINGLABEL, "Input metadata projection angles are missing. Exiting...");
     }
 
     if (fnVolR != "")
     {
         V.read(fnVolR);
     }
     else
     {
         FileName fn_first_image;
         Image<double> first_image;
         getInputMd()->getRow(1)->getValue(MDL_IMAGE, fn_first_image);
         first_image.read(fn_first_image);
         size_t Xdim_first = XSIZE(first_image());
         V().initZeros(Xdim_first, Xdim_first, Xdim_first);
     }
     V().setXmippOrigin();
 
     Xdim = XSIZE(V());
 
     Vout().initZeros(V());
     Vout().setXmippOrigin();
 
     if (resume && fnVolO.exists())
     {
         Vrefined.read(fnVolO);
     }
     else
     {
         Vrefined() = V();
     }
     // Vrefined().initZeros(V());
     Vrefined().setXmippOrigin();
 
     if (RmaxDef < 0)
         RmaxDef = Xdim / 2;
 
     // Transformation matrix
     A.initIdentity(4);
 
     // CTF Filter
     FilterCTF.FilterBand = CTFINV;
     FilterCTF.FilterShape = RAISED_COSINE;
     FilterCTF.ctf.enable_CTFnoise = false;
     FilterCTF.ctf.enable_CTF = true;
     // FilterCTF.ctf.produceSideInfo();
 
     // Area where Zernike3D basis is computed (and volume is updated)
     // Read Reference mask if avalaible (otherwise sphere of radius RmaxDef is used)
     Mask mask;
     mask.type = BINARY_CIRCULAR_MASK;
     mask.mode = INNER_MASK;
     if (fnMaskR != "")
     {
         Image<double> aux;
         aux.read(fnMaskR);
         typeCast(aux(), Vmask);
         Vmask.setXmippOrigin();
         double Rmax2 = RmaxDef * RmaxDef;
         for (int k = STARTINGZ(Vmask); k <= FINISHINGZ(Vmask); k++)
         {
             for (int i = STARTINGY(Vmask); i <= FINISHINGY(Vmask); i++)
             {
                 for (int j = STARTINGX(Vmask); j <= FINISHINGX(Vmask); j++)
                 {
                     double r2 = k * k + i * i + j * j;
                     if (r2 >= Rmax2)
                         A3D_ELEM(Vmask, k, i, j) = 0;
                 }
             }
         }
     }
     else
     {
         mask.R1 = RmaxDef;
         mask.generate_mask(V());
         Vmask = mask.get_binary_mask();
         Vmask.setXmippOrigin();
     }
 
     // Area Zernike3D in 2D
     mask.R1 = RmaxDef;
     mask.generate_mask(XSIZE(V()), XSIZE(V()));
     mask2D = mask.get_binary_mask();
     mask2D.setXmippOrigin();
 
     vecSize = 0;
     numCoefficients(L1, L2, vecSize);
     fillVectorTerms(L1, L2, vL1, vN, vL2, vM);
 
     // createWorkFiles();
     initX = STARTINGX(Vrefined());
     endX = FINISHINGX(Vrefined());
     initY = STARTINGY(Vrefined());
     endY = FINISHINGY(Vrefined());
     initZ = STARTINGZ(Vrefined());
     endZ = FINISHINGZ(Vrefined());
 
     sigma4 = 4 * sigma;  // Test 3
     double size_vg = CEIL(sigma4 * sqrt(2) * 50);
     gaussian3d.initZeros(size_vg, size_vg, size_vg);
     gaussian3d.setXmippOrigin();
     FOR_ALL_ELEMENTS_IN_ARRAY3D(gaussian3d)
     A3D_ELEM(gaussian3d, k, i, j) = gaussian1D(sqrt(k*k + i*i + j*j) / 50.0, sigma);
     gaussian3d *= gaussian1D(0, sigma);
 
     // This could also be a valid option, but we need a large volume to enclose the gaussian + 
     // its missing wedge properly. Since the convolution is a linear operator, it is better to apply 
     // it once the volume has been formed by standard gaussians
     // Needed gaussian dimensions CEIL(sigma4 * 2.5 * 50)
     // applyMissingWedge(gaussian3d);
 
     Image<double> W;
     W() = gaussian3d;
     FileName fnMask=fnOutDir+"gaussian_mw.mrc";
     W.write(fnMask);
 
 }

◆ processImage()

void ProgForwardArtZernike3DSubtomos::processImage	(	const FileName &	fnImg,
		const FileName &	fnImgOut,
		const MDRow &	rowIn,
		MDRow &	rowOut
	)

virtual

Create the processing working files. The working files are: nmaTodo.xmd for images to process (nmaTodo = mdIn - nmaDone) nmaDone.xmd image already processed (could exists from a previous run)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 284 of file forward_art_zernike3d_subtomos.cpp.

 {
     flagEnabled = 1;
 
     int img_enabled;
     rowIn.getValue(MDL_ENABLED, img_enabled);
     if (img_enabled == -1) return;
 
     // double auxRot, auxTilt, auxPsi, auxShiftX, auxShiftY;
     rowIn.getValue(MDL_ANGLE_ROT, rot);
     rowIn.getValue(MDL_ANGLE_TILT, tilt);
     rowIn.getValue(MDL_ANGLE_PSI, psi);
     rowIn.getValueOrDefault(MDL_SHIFT_X, shiftX, 0.0);
     rowIn.getValueOrDefault(MDL_SHIFT_Y, shiftY, 0.0);
     rowIn.getValueOrDefault(MDL_SHIFT_Z, shiftZ, 0.0);
     std::vector<double> vectortemp;
     if (useZernike)
     {
         rowIn.getValue(MDL_SPH_COEFFICIENTS, vectortemp);
         std::vector<double> vec(vectortemp.begin(), vectortemp.end());
         clnm = vec;
     }
     rowIn.getValueOrDefault(MDL_FLIP, flip, false);
 
     if ((rowIn.containsLabel(MDL_CTF_DEFOCUSU) || rowIn.containsLabel(MDL_CTF_MODEL)) && useCTF)
     {
         // std::cout << "Applying CTF" << std::endl;
         hasCTF = true;
         FilterCTF.ctf.readFromMdRow(rowIn, false);
         FilterCTF.ctf.Tm = Ts;
         FilterCTF.ctf.produceSideInfo();
     }
     else
         hasCTF = false;
     MAT_ELEM(A, 0, 3) = shiftX;
     MAT_ELEM(A, 1, 3) = shiftY;
     MAT_ELEM(A, 2, 3) = shiftZ;
     MAT_ELEM(A, 0, 0) = 1;
     MAT_ELEM(A, 0, 1) = 0;
     MAT_ELEM(A, 0, 2) = 0;
     MAT_ELEM(A, 1, 0) = 0;
     MAT_ELEM(A, 1, 1) = 1;
     MAT_ELEM(A, 1, 2) = 0;
     MAT_ELEM(A, 2, 0) = 0;
     MAT_ELEM(A, 2, 1) = 0;
     MAT_ELEM(A, 2, 2) = 1;
 
 
     if (verbose >= 2)
         std::cout << "Processing " << fnImg << std::endl;
 
     I.read(fnImg);
     I().setXmippOrigin();
 
     // Forward Model
     artModel<Direction::Forward>();
     // forwardModel();
 
     // ART update
     artModel<Direction::Backward>();
     // updateART();
 }

◆ readParams()

void ProgForwardArtZernike3DSubtomos::readParams ( )

virtual

Read argument from command line.

Reimplemented from XmippMetadataProgram.

Definition at line 46 of file forward_art_zernike3d_subtomos.cpp.

 {
     XmippMetadataProgram::readParams();
     fnVolR = getParam("--ref");
     fnMaskR = getParam("--mask");
     fnOutDir = getParam("--odir");
     RmaxDef = getIntParam("--RDef");
     phaseFlipped = checkParam("--phaseFlipped");
     useCTF = checkParam("--useCTF");
     Ts = getDoubleParam("--sampling");
     L1 = getIntParam("--l1");
     L2 = getIntParam("--l2");
     t1 = getDoubleParam("--t1");
     t2 = getDoubleParam("--t2");
     blob_r = getDoubleParam("--blobr");
     loop_step = getIntParam("--step");
     sigma = getDoubleParam("--sigma");
     useZernike = checkParam("--useZernike");
     lambda = getDoubleParam("--regularization");
     resume = checkParam("--resume");
     niter = getIntParam("--niter");
     save_iter = getIntParam("--save_iter");
     sort_last_N = getIntParam("--sort_last");
     // fnDone = fnOutDir + "/sphDone.xmd";
     fnVolO = fnOutDir + "/Refined.vol";
 }

◆ recoverVol()

void ProgForwardArtZernike3DSubtomos::recoverVol ( )

Definition at line 473 of file forward_art_zernike3d_subtomos.cpp.

 {
     // Find the part of the volume that must be updated
     auto &mVout = Vout();
     const auto &mV = Vrefined();
     mVout.initZeros(mV);
 
     const auto lastZ = FINISHINGZ(mV);
     const auto lastY = FINISHINGY(mV);
     const auto lastX = FINISHINGX(mV);
     // const int step = DIRECTION == Direction::Forward ? loop_step : 1;
     const int step = loop_step;
     auto pos = std::array<double, 3>{};
 
     for (int k = STARTINGZ(mV); k <= lastZ; k++)
     {
         for (int i = STARTINGY(mV); i <= lastY; i++)
         {
             for (int j = STARTINGX(mV); j <= lastX; j++)
             {
                 if (A3D_ELEM(Vmask, k, i, j) == 1)
                 {
                     pos[0] = j;
                     pos[1] = i;
                     pos[2] = k;
                     updateVoxel(pos, A3D_ELEM(mV, k, i, j), mVout);
                 }
             }
         }
     }
 }

◆ show()

void ProgForwardArtZernike3DSubtomos::show ( )

Show.

Definition at line 74 of file forward_art_zernike3d_subtomos.cpp.

 {
     if (!verbose)
         return;
     XmippMetadataProgram::show();
     std::cout
         << "Output directory:          " << fnOutDir << std::endl
         << "Reference volume:          " << fnVolR << std::endl
         << "Reference mask:            " << fnMaskR << std::endl
         << "Sampling:                  " << Ts << std::endl
         << "Max. Radius Deform.        " << RmaxDef << std::endl
         << "Zernike Degree:            " << L1 << std::endl
         << "SH Degree:                 " << L2 << std::endl
         << "Blob radius:               " << blob_r << std::endl
         << "Step:                      " << loop_step << std::endl
         << "Correct CTF:               " << useCTF << std::endl
         << "Correct heretogeneity:     " << useZernike << std::endl
         << "Phase flipped:             " << phaseFlipped << std::endl
         << "Regularization:            " << lambda << std::endl
         << "Number of iterations:      " << niter << std::endl
         << "Save every # iterations:   " << save_iter << std::endl;
 }

Member Data Documentation

◆ A

Matrix2D<double> ProgForwardArtZernike3DSubtomos::A

Definition at line 102 of file forward_art_zernike3d_subtomos.h.

◆ blob

struct blobtype ProgForwardArtZernike3DSubtomos::blob

Definition at line 135 of file forward_art_zernike3d_subtomos.h.

◆ blob_r

double ProgForwardArtZernike3DSubtomos::blob_r

Definition at line 136 of file forward_art_zernike3d_subtomos.h.

◆ clnm

std::vector<double> ProgForwardArtZernike3DSubtomos::clnm

Definition at line 120 of file forward_art_zernike3d_subtomos.h.

◆ ctf

CTFDescription ProgForwardArtZernike3DSubtomos::ctf

Definition at line 114 of file forward_art_zernike3d_subtomos.h.

◆ current_iter

int ProgForwardArtZernike3DSubtomos::current_iter

Definition at line 130 of file forward_art_zernike3d_subtomos.h.

◆ current_save_iter

int ProgForwardArtZernike3DSubtomos::current_save_iter

Definition at line 126 of file forward_art_zernike3d_subtomos.h.

◆ defocusAngle

double ProgForwardArtZernike3DSubtomos::defocusAngle

Definition at line 112 of file forward_art_zernike3d_subtomos.h.

◆ defocusU

double ProgForwardArtZernike3DSubtomos::defocusU

Definition at line 112 of file forward_art_zernike3d_subtomos.h.

◆ defocusV

double ProgForwardArtZernike3DSubtomos::defocusV

Definition at line 112 of file forward_art_zernike3d_subtomos.h.

◆ endX

int ProgForwardArtZernike3DSubtomos::endX

Definition at line 132 of file forward_art_zernike3d_subtomos.h.

◆ endY

int ProgForwardArtZernike3DSubtomos::endY

Definition at line 132 of file forward_art_zernike3d_subtomos.h.

◆ endZ

int ProgForwardArtZernike3DSubtomos::endZ

Definition at line 132 of file forward_art_zernike3d_subtomos.h.

◆ FilterCTF

FourierFilter ProgForwardArtZernike3DSubtomos::FilterCTF

Definition at line 116 of file forward_art_zernike3d_subtomos.h.

◆ flagEnabled

int ProgForwardArtZernike3DSubtomos::flagEnabled

Definition at line 74 of file forward_art_zernike3d_subtomos.h.

◆ flip

bool ProgForwardArtZernike3DSubtomos::flip

Definition at line 108 of file forward_art_zernike3d_subtomos.h.

◆ fnMaskR

FileName ProgForwardArtZernike3DSubtomos::fnMaskR

Filename of the reference volume mask

Definition at line 46 of file forward_art_zernike3d_subtomos.h.

◆ fnOutDir

FileName ProgForwardArtZernike3DSubtomos::fnOutDir

Output directory.

Definition at line 50 of file forward_art_zernike3d_subtomos.h.

◆ fnVolO

FileName ProgForwardArtZernike3DSubtomos::fnVolO

Filename of the refined volume

Definition at line 48 of file forward_art_zernike3d_subtomos.h.

◆ fnVolR

FileName ProgForwardArtZernike3DSubtomos::fnVolR

Filename of the reference volume

Definition at line 44 of file forward_art_zernike3d_subtomos.h.

◆ gaussian3d

MultidimArray<double> ProgForwardArtZernike3DSubtomos::gaussian3d

Definition at line 139 of file forward_art_zernike3d_subtomos.h.

◆ gaussian_mw

MultidimArray<double> ProgForwardArtZernike3DSubtomos::gaussian_mw

Definition at line 139 of file forward_art_zernike3d_subtomos.h.

◆ hasCTF

bool ProgForwardArtZernike3DSubtomos::hasCTF

Definition at line 110 of file forward_art_zernike3d_subtomos.h.

◆ I

Image<double> ProgForwardArtZernike3DSubtomos::I

Definition at line 92 of file forward_art_zernike3d_subtomos.h.

◆ Idiff

Image<double> ProgForwardArtZernike3DSubtomos::Idiff

Definition at line 100 of file forward_art_zernike3d_subtomos.h.

◆ Ifilteredp

Image<double> ProgForwardArtZernike3DSubtomos::Ifilteredp

Definition at line 90 of file forward_art_zernike3d_subtomos.h.

◆ ignoreCTF

bool ProgForwardArtZernike3DSubtomos::ignoreCTF

Definition at line 64 of file forward_art_zernike3d_subtomos.h.

◆ initX

int ProgForwardArtZernike3DSubtomos::initX

Definition at line 132 of file forward_art_zernike3d_subtomos.h.

◆ initY

int ProgForwardArtZernike3DSubtomos::initY

Definition at line 132 of file forward_art_zernike3d_subtomos.h.

◆ initZ

int ProgForwardArtZernike3DSubtomos::initZ

Definition at line 132 of file forward_art_zernike3d_subtomos.h.

◆ L1

int ProgForwardArtZernike3DSubtomos::L1

Degrees of Zernike polynomials and spherical harmonics

Definition at line 54 of file forward_art_zernike3d_subtomos.h.

◆ L2

int ProgForwardArtZernike3DSubtomos::L2

Definition at line 54 of file forward_art_zernike3d_subtomos.h.

◆ lambda

double ProgForwardArtZernike3DSubtomos::lambda

Definition at line 66 of file forward_art_zernike3d_subtomos.h.

◆ loop_step

int ProgForwardArtZernike3DSubtomos::loop_step

Definition at line 134 of file forward_art_zernike3d_subtomos.h.

◆ mask2D

MultidimArray<int> ProgForwardArtZernike3DSubtomos::mask2D

Definition at line 86 of file forward_art_zernike3d_subtomos.h.

◆ niter

int ProgForwardArtZernike3DSubtomos::niter

Definition at line 82 of file forward_art_zernike3d_subtomos.h.

◆ num_images

int ProgForwardArtZernike3DSubtomos::num_images

Definition at line 128 of file forward_art_zernike3d_subtomos.h.

◆ ordered_list

MultidimArray<size_t> ProgForwardArtZernike3DSubtomos::ordered_list

Definition at line 124 of file forward_art_zernike3d_subtomos.h.

◆ P

Image<double> ProgForwardArtZernike3DSubtomos::P

Definition at line 96 of file forward_art_zernike3d_subtomos.h.

◆ phaseFlipped

bool ProgForwardArtZernike3DSubtomos::phaseFlipped

Definition at line 62 of file forward_art_zernike3d_subtomos.h.

◆ psi

double ProgForwardArtZernike3DSubtomos::psi

Definition at line 104 of file forward_art_zernike3d_subtomos.h.

◆ resume

bool ProgForwardArtZernike3DSubtomos::resume

Resume computations

Definition at line 80 of file forward_art_zernike3d_subtomos.h.

◆ RmaxDef

int ProgForwardArtZernike3DSubtomos::RmaxDef

Maximum radius

Definition at line 60 of file forward_art_zernike3d_subtomos.h.

◆ rot

double ProgForwardArtZernike3DSubtomos::rot

Definition at line 104 of file forward_art_zernike3d_subtomos.h.

◆ save_iter

int ProgForwardArtZernike3DSubtomos::save_iter

Definition at line 68 of file forward_art_zernike3d_subtomos.h.

◆ shiftX

double ProgForwardArtZernike3DSubtomos::shiftX

Definition at line 106 of file forward_art_zernike3d_subtomos.h.

◆ shiftY

double ProgForwardArtZernike3DSubtomos::shiftY

Definition at line 106 of file forward_art_zernike3d_subtomos.h.

◆ shiftZ

double ProgForwardArtZernike3DSubtomos::shiftZ

Definition at line 106 of file forward_art_zernike3d_subtomos.h.

◆ showOptimization

bool ProgForwardArtZernike3DSubtomos::showOptimization

Definition at line 122 of file forward_art_zernike3d_subtomos.h.

◆ sigma

double ProgForwardArtZernike3DSubtomos::sigma

Definition at line 137 of file forward_art_zernike3d_subtomos.h.

◆ sigma4

double ProgForwardArtZernike3DSubtomos::sigma4

Definition at line 137 of file forward_art_zernike3d_subtomos.h.

◆ sort_last_N

int ProgForwardArtZernike3DSubtomos::sort_last_N

Definition at line 84 of file forward_art_zernike3d_subtomos.h.

◆ t1

double ProgForwardArtZernike3DSubtomos::t1

Definition at line 76 of file forward_art_zernike3d_subtomos.h.

◆ t2

double ProgForwardArtZernike3DSubtomos::t2

Definition at line 76 of file forward_art_zernike3d_subtomos.h.

◆ tilt

double ProgForwardArtZernike3DSubtomos::tilt

Definition at line 104 of file forward_art_zernike3d_subtomos.h.

◆ transformer

FourierTransformer ProgForwardArtZernike3DSubtomos::transformer

Definition at line 141 of file forward_art_zernike3d_subtomos.h.

◆ Ts

double ProgForwardArtZernike3DSubtomos::Ts

Sampling rate

Definition at line 58 of file forward_art_zernike3d_subtomos.h.

◆ useCTF

bool ProgForwardArtZernike3DSubtomos::useCTF

Definition at line 70 of file forward_art_zernike3d_subtomos.h.

◆ useZernike

bool ProgForwardArtZernike3DSubtomos::useZernike

Definition at line 72 of file forward_art_zernike3d_subtomos.h.

◆ V

Image<double> ProgForwardArtZernike3DSubtomos::V

Definition at line 90 of file forward_art_zernike3d_subtomos.h.

◆ vecSize

int ProgForwardArtZernike3DSubtomos::vecSize

Definition at line 118 of file forward_art_zernike3d_subtomos.h.

◆ vL1

Matrix1D<int> ProgForwardArtZernike3DSubtomos::vL1

Zernike and SPH coefficients vectors

Definition at line 56 of file forward_art_zernike3d_subtomos.h.

◆ vL2

Matrix1D<int> ProgForwardArtZernike3DSubtomos::vL2

Definition at line 56 of file forward_art_zernike3d_subtomos.h.

◆ vM

Matrix1D<int> ProgForwardArtZernike3DSubtomos::vM

Definition at line 56 of file forward_art_zernike3d_subtomos.h.

◆ Vmask

MultidimArray<int> ProgForwardArtZernike3DSubtomos::Vmask

Definition at line 94 of file forward_art_zernike3d_subtomos.h.

◆ vN

Matrix1D<int> ProgForwardArtZernike3DSubtomos::vN

Definition at line 56 of file forward_art_zernike3d_subtomos.h.

◆ Vout

Image<double> ProgForwardArtZernike3DSubtomos::Vout

Definition at line 90 of file forward_art_zernike3d_subtomos.h.

◆ Vrefined

Image<double> ProgForwardArtZernike3DSubtomos::Vrefined

Definition at line 90 of file forward_art_zernike3d_subtomos.h.

◆ W

Image<double> ProgForwardArtZernike3DSubtomos::W

Definition at line 98 of file forward_art_zernike3d_subtomos.h.

◆ Xdim

size_t ProgForwardArtZernike3DSubtomos::Xdim

Definition at line 88 of file forward_art_zernike3d_subtomos.h.

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

xmipp/libraries/reconstruction/forward_art_zernike3d_subtomos.h
xmipp/libraries/reconstruction/forward_art_zernike3d_subtomos.cpp

Public Types

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ Mode

Constructor & Destructor Documentation

◆ ProgForwardArtZernike3DSubtomos()

◆ ~ProgForwardArtZernike3DSubtomos()

Member Function Documentation

◆ applyMissingWedge()

◆ defineParams()

◆ deformVol()

◆ fillVectorTerms()

◆ finishProcessing()

◆ numCoefficients()

◆ preProcess()

◆ processImage()

◆ readParams()

◆ recoverVol()

◆ show()

Member Data Documentation

◆ A

◆ blob

◆ blob_r

◆ clnm

◆ ctf

◆ current_iter

◆ current_save_iter

◆ defocusAngle

◆ defocusU

◆ defocusV

◆ endX

◆ endY

◆ endZ

◆ FilterCTF

◆ flagEnabled

◆ flip

◆ fnMaskR

◆ fnOutDir

◆ fnVolO

◆ fnVolR

◆ gaussian3d

◆ gaussian_mw

◆ hasCTF

◆ I

◆ Idiff

◆ Ifilteredp

◆ ignoreCTF

◆ initX

◆ initY

◆ initZ

◆ L1

◆ L2

◆ lambda

◆ loop_step

◆ mask2D

◆ niter

◆ num_images

◆ ordered_list

◆ P

◆ phaseFlipped

◆ psi

◆ resume

◆ RmaxDef

◆ rot

◆ save_iter

◆ shiftX

◆ shiftY

◆ shiftZ

◆ showOptimization

◆ sigma

◆ sigma4

◆ sort_last_N

◆ t1

◆ t2

◆ tilt

◆ transformer

◆ Ts