#include <parallel_forward_art_zernike3d.h>

Inheritance diagram for ProgParallelForwardArtZernike3D:

Collaboration diagram for ProgParallelForwardArtZernike3D:

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

Public Member Functions
	ProgParallelForwardArtZernike3D ()
	Empty constructor. More...

	~ProgParallelForwardArtZernike3D ()
	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 ()

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	fnMaskRF

FileName	fnMaskRB

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

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 >	VRecMaskF

MultidimArray< int >	VRecMaskB

std::vector< Image< double > >	P

std::vector< Image< double > >	W

std::vector< std::unique_ptr< std::atomic< double * > > >	p_busy_elem

std::vector< std::unique_ptr< std::atomic< double * > > >	w_busy_elem

Image< double >	Idiff

Matrix2D< double >	A

double	rot

double	tilt

double	psi

double	shiftX

double	shiftY

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

size_t	num_images

size_t	current_image

int	current_iter

int	initX

int	endX

int	initY

int	endY

int	initZ

int	endZ

int	loop_step

std::vector< double >	sigma

FourierFilter	filter

FourierFilter	filter2

ctpl::thread_pool	m_threadPool

int	threads

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 42 of file parallel_forward_art_zernike3d.h.

Member Enumeration Documentation

◆ Mode

enum ProgParallelForwardArtZernike3D::Mode

strong

Enumerator
Proj
Vol

Definition at line 148 of file parallel_forward_art_zernike3d.h.

148 { Proj, Vol };

Constructor & Destructor Documentation

◆ ProgParallelForwardArtZernike3D()

ProgParallelForwardArtZernike3D::ProgParallelForwardArtZernike3D ( )

Empty constructor.

Definition at line 38 of file parallel_forward_art_zernike3d.cpp.

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

◆ ~ProgParallelForwardArtZernike3D()

ProgParallelForwardArtZernike3D::~ProgParallelForwardArtZernike3D ( )

default

Destructor.

Member Function Documentation

◆ defineParams()

void ProgParallelForwardArtZernike3D::defineParams ( )

virtual

Define parameters.

Reimplemented from XmippMetadataProgram.

Definition at line 120 of file parallel_forward_art_zernike3d.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("  [--maskf <m=\"\">]           : ART forward model reconstruction mask");
     addParamsLine("  [--maskb <m=\"\">]           : ART backward model reconstruction mask");
     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 <Matrix1D=\"2\">]   : 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("  [--resume]                   : Resume processing");
     addParamsLine("  [--thr <N=-1>]                      : Maximal number of the processing CPU threads");
     addExampleLine("A typical use is:", false);
     addExampleLine("xmipp_parallel_forward_art_zernike3d -i anglesFromContinuousAssignment.xmd --ref reference.vol -o assigned_anglesAndDeformations.xmd --l1 3 --l2 2");
 }

◆ deformVol()

void ProgParallelForwardArtZernike3D::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 ProgParallelForwardArtZernike3D::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 386 of file parallel_forward_art_zernike3d.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 ProgParallelForwardArtZernike3D::finishProcessing ( )

virtual

Reimplemented from XmippMetadataProgram.

Definition at line 310 of file parallel_forward_art_zernike3d.cpp.

 {
     recoverVol();
     Vout.write(fnVolO);
 }

◆ numCoefficients()

void ProgParallelForwardArtZernike3D::numCoefficients	(	int	l1,
		int	l2,
		int &	vecSize
	)

Length of coefficients vector.

Definition at line 368 of file parallel_forward_art_zernike3d.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 ProgParallelForwardArtZernike3D::preProcess ( )

virtual

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

Reimplemented from XmippMetadataProgram.

Definition at line 155 of file parallel_forward_art_zernike3d.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());
 
     p_busy_elem.resize(Xdim*Xdim);
     for (auto& p : p_busy_elem) {
         p = std::make_unique<std::atomic<double*>>(nullptr);
     }
 
     w_busy_elem.resize(Xdim*Xdim);
     for (auto& p : w_busy_elem) {
         p = std::make_unique<std::atomic<double*>>(nullptr);
     }
     
     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(3);
 
     // CTF Filter
     FilterCTF.FilterBand = CTFINV;
     FilterCTF.FilterShape = RAISED_COSINE;
     FilterCTF.ctf.enable_CTFnoise = false;
     FilterCTF.ctf.enable_CTF = true;
 
     // 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 (fnMaskRF != "")
     {
         Image<double> aux;
         aux.read(fnMaskRF);
         typeCast(aux(), VRecMaskF);
         VRecMaskF.setXmippOrigin();
         double Rmax2 = RmaxDef * RmaxDef;
         for (int k = STARTINGZ(VRecMaskF); k <= FINISHINGZ(VRecMaskF); k++)
         {
             for (int i = STARTINGY(VRecMaskF); i <= FINISHINGY(VRecMaskF); i++)
             {
                 for (int j = STARTINGX(VRecMaskF); j <= FINISHINGX(VRecMaskF); j++)
                 {
                     double r2 = k * k + i * i + j * j;
                     if (r2 >= Rmax2)
                         A3D_ELEM(VRecMaskF, k, i, j) = 0;
                 }
             }
         }
     }
     else
     {
         mask.R1 = RmaxDef;
         mask.generate_mask(V());
         VRecMaskF = mask.get_binary_mask();
         VRecMaskF.setXmippOrigin();
     }
 
 
     // Mask determining reconstruction area
     if (fnMaskRB != "")
     {
         Image<double> aux;
         aux.read(fnMaskRB);
         typeCast(aux(), VRecMaskB);
         VRecMaskB.setXmippOrigin();
         double Rmax2 = RmaxDef * RmaxDef;
         for (int k = STARTINGZ(VRecMaskB); k <= FINISHINGZ(VRecMaskB); k++)
         {
             for (int i = STARTINGY(VRecMaskB); i <= FINISHINGY(VRecMaskB); i++)
             {
                 for (int j = STARTINGX(VRecMaskB); j <= FINISHINGX(VRecMaskB); j++)
                 {
                     double r2 = k * k + i * i + j * j;
                     if (r2 >= Rmax2)
                         A3D_ELEM(VRecMaskB, k, i, j) = 0;
                 }
             }
         }
     }
     else
     {
         mask.R1 = RmaxDef;
         mask.generate_mask(V());
         VRecMaskB = mask.get_binary_mask();
         VRecMaskB.setXmippOrigin();
     }
 
     // Init P and W vector of images
     P.resize(sigma.size());
     W.resize(sigma.size());
 
     // 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());
 
     filter.FilterBand=LOWPASS;
     filter.FilterShape=REALGAUSSIANZ;
     filter2.FilterBand=LOWPASS;
     filter2.FilterShape=REALGAUSSIANZ2;
 }

◆ processImage()

void ProgParallelForwardArtZernike3D::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 317 of file parallel_forward_art_zernike3d.cpp.

 {
     flagEnabled = 1;
 
     int img_enabled;
     rowIn.getValue(MDL_ENABLED, img_enabled);
     if (img_enabled == -1) return;
 
     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);
     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)
     {
         hasCTF = true;
         FilterCTF.ctf.readFromMdRow(rowIn, false);
         FilterCTF.ctf.Tm = Ts;
         FilterCTF.ctf.produceSideInfo();
     }
     else
         hasCTF = false;
     MAT_ELEM(A, 0, 2) = shiftX;
     MAT_ELEM(A, 1, 2) = shiftY;
     MAT_ELEM(A, 0, 0) = 1;
     MAT_ELEM(A, 0, 1) = 0;
     MAT_ELEM(A, 1, 0) = 0;
     MAT_ELEM(A, 1, 1) = 1;
 
     if (verbose >= 2)
         std::cout << "Processing " << fnImg << std::endl;
 
     I.read(fnImg);
     I().setXmippOrigin();
 
     // Forward Model
     artModel<Direction::Forward>();
 
     // ART update
     artModel<Direction::Backward>();
 }

◆ readParams()

void ProgParallelForwardArtZernike3D::readParams ( )

virtual

Read argument from command line.

Reimplemented from XmippMetadataProgram.

Definition at line 49 of file parallel_forward_art_zernike3d.cpp.

 {
     XmippMetadataProgram::readParams();
     fnVolR = getParam("--ref");
     fnMaskRF = getParam("--maskf");
     fnMaskRB = getParam("--maskb");
     fnOutDir = getParam("--odir");
     RmaxDef = getIntParam("--RDef");
     phaseFlipped = checkParam("--phaseFlipped");
     useCTF = checkParam("--useCTF");
     Ts = getDoubleParam("--sampling");
     L1 = getIntParam("--l1");
     L2 = getIntParam("--l2");
     loop_step = getIntParam("--step");
     useZernike = checkParam("--useZernike");
     lambda = getDoubleParam("--regularization");
     resume = checkParam("--resume");
     niter = getIntParam("--niter");
     save_iter = getIntParam("--save_iter");
     sort_last_N = getIntParam("--sort_last");
     FileName outPath = getParam("-o");
     outPath = outPath.afterLastOf("/");
     fnVolO = fnOutDir + "/" + outPath;
 
     std::string aux;
     aux = getParam("--sigma");
     // Transform string of values separated by white spaces into substrings stored in a vector
     std::stringstream ss(aux);
     std::istream_iterator<std::string> begin(ss);
     std::istream_iterator<std::string> end;
     std::vector<std::string> vstrings(begin, end);
     sigma.resize(vstrings.size());
     std::transform(vstrings.begin(), vstrings.end(), sigma.begin(), [](const std::string& val)
     {
         return std::stod(val);
     });
 
     // Parallelization
     int threads = getIntParam("--thr");
     if (0 >= threads)
     {
         threads = CPU::findCores();
     }
     m_threadPool.resize(threads);
 }

◆ recoverVol()

void ProgParallelForwardArtZernike3D::recoverVol ( )

Definition at line 433 of file parallel_forward_art_zernike3d.cpp.

 {
     // Find the part of the volume that must be updated
     auto &mVout = Vout();
     const auto &mV = Vrefined();
     mVout.initZeros(mV);
     mVout = mV;
 }

◆ show()

void ProgParallelForwardArtZernike3D::show ( )

Show.

Definition at line 96 of file parallel_forward_art_zernike3d.cpp.

 {
     if (!verbose)
         return;
     XmippMetadataProgram::show();
     std::cout
         << "Output directory:          " << fnOutDir << std::endl
         << "Reference volume:          " << fnVolR << std::endl
         << "Forward model mask:        " << fnMaskRF << std::endl
         << "Backward model mask:       " << fnMaskRB << std::endl
         << "Sampling:                  " << Ts << std::endl
         << "Max. Radius Deform.        " << RmaxDef << std::endl
         << "Zernike Degree:            " << L1 << std::endl
         << "SH Degree:                 " << L2 << 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> ProgParallelForwardArtZernike3D::A

Definition at line 104 of file parallel_forward_art_zernike3d.h.

◆ clnm

std::vector<double> ProgParallelForwardArtZernike3D::clnm

Definition at line 122 of file parallel_forward_art_zernike3d.h.

◆ ctf

CTFDescription ProgParallelForwardArtZernike3D::ctf

Definition at line 116 of file parallel_forward_art_zernike3d.h.

◆ current_image

size_t ProgParallelForwardArtZernike3D::current_image

Definition at line 130 of file parallel_forward_art_zernike3d.h.

◆ current_iter

int ProgParallelForwardArtZernike3D::current_iter

Definition at line 132 of file parallel_forward_art_zernike3d.h.

◆ current_save_iter

int ProgParallelForwardArtZernike3D::current_save_iter

Definition at line 128 of file parallel_forward_art_zernike3d.h.

◆ defocusAngle

double ProgParallelForwardArtZernike3D::defocusAngle

Definition at line 114 of file parallel_forward_art_zernike3d.h.

◆ defocusU

double ProgParallelForwardArtZernike3D::defocusU

Definition at line 114 of file parallel_forward_art_zernike3d.h.

◆ defocusV

double ProgParallelForwardArtZernike3D::defocusV

Definition at line 114 of file parallel_forward_art_zernike3d.h.

◆ endX

int ProgParallelForwardArtZernike3D::endX

Definition at line 134 of file parallel_forward_art_zernike3d.h.

◆ endY

int ProgParallelForwardArtZernike3D::endY

Definition at line 134 of file parallel_forward_art_zernike3d.h.

◆ endZ

int ProgParallelForwardArtZernike3D::endZ

Definition at line 134 of file parallel_forward_art_zernike3d.h.

◆ filter

FourierFilter ProgParallelForwardArtZernike3D::filter

Definition at line 141 of file parallel_forward_art_zernike3d.h.

◆ filter2

FourierFilter ProgParallelForwardArtZernike3D::filter2

Definition at line 141 of file parallel_forward_art_zernike3d.h.

◆ FilterCTF

FourierFilter ProgParallelForwardArtZernike3D::FilterCTF

Definition at line 118 of file parallel_forward_art_zernike3d.h.

◆ flagEnabled

int ProgParallelForwardArtZernike3D::flagEnabled

Definition at line 74 of file parallel_forward_art_zernike3d.h.

◆ flip

bool ProgParallelForwardArtZernike3D::flip

Definition at line 110 of file parallel_forward_art_zernike3d.h.

◆ fnMaskRB

FileName ProgParallelForwardArtZernike3D::fnMaskRB

Definition at line 48 of file parallel_forward_art_zernike3d.h.

◆ fnMaskRF

FileName ProgParallelForwardArtZernike3D::fnMaskRF

Filename of the reference volume mask

Definition at line 48 of file parallel_forward_art_zernike3d.h.

◆ fnOutDir

FileName ProgParallelForwardArtZernike3D::fnOutDir

Output directory.

Definition at line 52 of file parallel_forward_art_zernike3d.h.

◆ fnVolO

FileName ProgParallelForwardArtZernike3D::fnVolO

Filename of the refined volume

Definition at line 50 of file parallel_forward_art_zernike3d.h.

◆ fnVolR

FileName ProgParallelForwardArtZernike3D::fnVolR

Filename of the reference volume

Definition at line 46 of file parallel_forward_art_zernike3d.h.

◆ hasCTF

bool ProgParallelForwardArtZernike3D::hasCTF

Definition at line 112 of file parallel_forward_art_zernike3d.h.

◆ I

Image<double> ProgParallelForwardArtZernike3D::I

Definition at line 90 of file parallel_forward_art_zernike3d.h.

◆ Idiff

Image<double> ProgParallelForwardArtZernike3D::Idiff

Definition at line 102 of file parallel_forward_art_zernike3d.h.

◆ Ifilteredp

Image<double> ProgParallelForwardArtZernike3D::Ifilteredp

Definition at line 88 of file parallel_forward_art_zernike3d.h.

◆ ignoreCTF

bool ProgParallelForwardArtZernike3D::ignoreCTF

Definition at line 64 of file parallel_forward_art_zernike3d.h.

◆ initX

int ProgParallelForwardArtZernike3D::initX

Definition at line 134 of file parallel_forward_art_zernike3d.h.

◆ initY

int ProgParallelForwardArtZernike3D::initY

Definition at line 134 of file parallel_forward_art_zernike3d.h.

◆ initZ

int ProgParallelForwardArtZernike3D::initZ

Definition at line 134 of file parallel_forward_art_zernike3d.h.

◆ L1

int ProgParallelForwardArtZernike3D::L1

Degrees of Zernike polynomials and spherical harmonics

Definition at line 54 of file parallel_forward_art_zernike3d.h.

◆ L2

int ProgParallelForwardArtZernike3D::L2

Definition at line 54 of file parallel_forward_art_zernike3d.h.

◆ lambda

double ProgParallelForwardArtZernike3D::lambda

Definition at line 66 of file parallel_forward_art_zernike3d.h.

◆ loop_step

int ProgParallelForwardArtZernike3D::loop_step

Definition at line 136 of file parallel_forward_art_zernike3d.h.

◆ m_threadPool

ctpl::thread_pool ProgParallelForwardArtZernike3D::m_threadPool

Definition at line 144 of file parallel_forward_art_zernike3d.h.

◆ mask2D

MultidimArray<int> ProgParallelForwardArtZernike3D::mask2D

Definition at line 84 of file parallel_forward_art_zernike3d.h.

◆ niter

int ProgParallelForwardArtZernike3D::niter

Definition at line 80 of file parallel_forward_art_zernike3d.h.

◆ num_images

size_t ProgParallelForwardArtZernike3D::num_images

Definition at line 130 of file parallel_forward_art_zernike3d.h.

◆ ordered_list

MultidimArray<size_t> ProgParallelForwardArtZernike3D::ordered_list

Definition at line 126 of file parallel_forward_art_zernike3d.h.

◆ P

std::vector<Image<double> > ProgParallelForwardArtZernike3D::P

Definition at line 94 of file parallel_forward_art_zernike3d.h.

◆ p_busy_elem

std::vector<std::unique_ptr<std::atomic<double*> > > ProgParallelForwardArtZernike3D::p_busy_elem

Definition at line 98 of file parallel_forward_art_zernike3d.h.

◆ phaseFlipped

bool ProgParallelForwardArtZernike3D::phaseFlipped

Definition at line 62 of file parallel_forward_art_zernike3d.h.

◆ psi

double ProgParallelForwardArtZernike3D::psi

Definition at line 106 of file parallel_forward_art_zernike3d.h.

◆ resume

bool ProgParallelForwardArtZernike3D::resume

Resume computations

Definition at line 78 of file parallel_forward_art_zernike3d.h.

◆ RmaxDef

int ProgParallelForwardArtZernike3D::RmaxDef

Maximum radius

Definition at line 60 of file parallel_forward_art_zernike3d.h.

◆ rot

double ProgParallelForwardArtZernike3D::rot

Definition at line 106 of file parallel_forward_art_zernike3d.h.

◆ save_iter

int ProgParallelForwardArtZernike3D::save_iter

Definition at line 68 of file parallel_forward_art_zernike3d.h.

◆ shiftX

double ProgParallelForwardArtZernike3D::shiftX

Definition at line 108 of file parallel_forward_art_zernike3d.h.

◆ shiftY

double ProgParallelForwardArtZernike3D::shiftY

Definition at line 108 of file parallel_forward_art_zernike3d.h.

◆ showOptimization

bool ProgParallelForwardArtZernike3D::showOptimization

Definition at line 124 of file parallel_forward_art_zernike3d.h.

◆ sigma

std::vector<double> ProgParallelForwardArtZernike3D::sigma

Definition at line 138 of file parallel_forward_art_zernike3d.h.

◆ sort_last_N

int ProgParallelForwardArtZernike3D::sort_last_N

Definition at line 82 of file parallel_forward_art_zernike3d.h.

◆ threads

int ProgParallelForwardArtZernike3D::threads

Definition at line 145 of file parallel_forward_art_zernike3d.h.

◆ tilt

double ProgParallelForwardArtZernike3D::tilt

Definition at line 106 of file parallel_forward_art_zernike3d.h.

◆ Ts

double ProgParallelForwardArtZernike3D::Ts

Sampling rate

Definition at line 58 of file parallel_forward_art_zernike3d.h.

◆ useCTF

bool ProgParallelForwardArtZernike3D::useCTF

Definition at line 70 of file parallel_forward_art_zernike3d.h.

◆ useZernike

bool ProgParallelForwardArtZernike3D::useZernike

Definition at line 72 of file parallel_forward_art_zernike3d.h.

◆ V

Image<double> ProgParallelForwardArtZernike3D::V

Definition at line 88 of file parallel_forward_art_zernike3d.h.

◆ vecSize

int ProgParallelForwardArtZernike3D::vecSize

Definition at line 120 of file parallel_forward_art_zernike3d.h.

◆ vL1

Matrix1D<int> ProgParallelForwardArtZernike3D::vL1

Zernike and SPH coefficients vectors

Definition at line 56 of file parallel_forward_art_zernike3d.h.

◆ vL2

Matrix1D<int> ProgParallelForwardArtZernike3D::vL2

Definition at line 56 of file parallel_forward_art_zernike3d.h.

◆ vM

Matrix1D<int> ProgParallelForwardArtZernike3D::vM

Definition at line 56 of file parallel_forward_art_zernike3d.h.

◆ vN

Matrix1D<int> ProgParallelForwardArtZernike3D::vN

Definition at line 56 of file parallel_forward_art_zernike3d.h.

◆ Vout

Image<double> ProgParallelForwardArtZernike3D::Vout

Definition at line 88 of file parallel_forward_art_zernike3d.h.

◆ VRecMaskB

MultidimArray<int> ProgParallelForwardArtZernike3D::VRecMaskB

Definition at line 92 of file parallel_forward_art_zernike3d.h.

◆ VRecMaskF

MultidimArray<int> ProgParallelForwardArtZernike3D::VRecMaskF

Definition at line 92 of file parallel_forward_art_zernike3d.h.

◆ Vrefined

Image<double> ProgParallelForwardArtZernike3D::Vrefined

Definition at line 88 of file parallel_forward_art_zernike3d.h.

◆ W

std::vector<Image<double> > ProgParallelForwardArtZernike3D::W

Definition at line 96 of file parallel_forward_art_zernike3d.h.

◆ w_busy_elem

std::vector<std::unique_ptr<std::atomic<double*> > > ProgParallelForwardArtZernike3D::w_busy_elem

Definition at line 99 of file parallel_forward_art_zernike3d.h.

◆ Xdim

size_t ProgParallelForwardArtZernike3D::Xdim

Definition at line 86 of file parallel_forward_art_zernike3d.h.

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

xmipp/libraries/reconstruction/parallel_forward_art_zernike3d.h
xmipp/libraries/reconstruction/parallel_forward_art_zernike3d.cpp

Public Types

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ Mode

Constructor & Destructor Documentation

◆ ProgParallelForwardArtZernike3D()

◆ ~ProgParallelForwardArtZernike3D()

Member Function Documentation

◆ defineParams()

◆ deformVol()

◆ fillVectorTerms()

◆ finishProcessing()

◆ numCoefficients()

◆ preProcess()

◆ processImage()

◆ readParams()

◆ recoverVol()

◆ show()

Member Data Documentation

◆ A

◆ clnm

◆ ctf

◆ current_image

◆ current_iter

◆ current_save_iter

◆ defocusAngle

◆ defocusU

◆ defocusV

◆ endX

◆ endY

◆ endZ

◆ filter

◆ filter2

◆ FilterCTF

◆ flagEnabled

◆ flip

◆ fnMaskRB

◆ fnMaskRF

◆ fnOutDir

◆ fnVolO

◆ fnVolR

◆ hasCTF

◆ I

◆ Idiff

◆ Ifilteredp

◆ ignoreCTF

◆ initX

◆ initY

◆ initZ

◆ L1

◆ L2

◆ lambda

◆ loop_step

◆ m_threadPool

◆ mask2D

◆ niter

◆ num_images

◆ ordered_list

◆ P

◆ p_busy_elem

◆ phaseFlipped

◆ psi

◆ resume

◆ RmaxDef

◆ rot

◆ save_iter

◆ shiftX

◆ shiftY

◆ showOptimization

◆ sigma

◆ sort_last_N

◆ threads

◆ tilt

◆ Ts

◆ useCTF

◆ useZernike

◆ V