#include <reconstruct_art_xray.h>

Inheritance diagram for ProgReconsXrayART:

Collaboration diagram for ProgReconsXrayART:

Public Member Functions
	ProgReconsXrayART ()

	~ProgReconsXrayART ()

void	setIO (const FileName &fn_in, const FileName &fn_out)
	Functions of common reconstruction interface. More...

void	defineParams ()

void	readParams ()

void	show ()

void	run ()

void	preProcess (Image< double > &volVoxels)

void	postProcess ()

double	singleStep (MultidimArray< double > &muVol, const Projection &projExp, double rot, double tilt, double psi)

Public Member Functions inherited from ProgReconsBase
virtual	~ProgReconsBase ()

Public Member Functions inherited from XmippProgram
const char *	getParam (const char *param, int arg=0)

const char *	getParam (const char param, const char subparam, int arg=0)

int	getIntParam (const char *param, int arg=0)

int	getIntParam (const char param, const char subparam, int arg=0)

double	getDoubleParam (const char *param, int arg=0)

double	getDoubleParam (const char param, const char subparam, int arg=0)

float	getFloatParam (const char *param, int arg=0)

float	getFloatParam (const char param, const char subparam, int arg=0)

void	getListParam (const char *param, StringVector &list)

int	getCountParam (const char *param)

bool	checkParam (const char *param)

bool	existsParam (const char *param)

void	addParamsLine (const String &line)

void	addParamsLine (const char *line)

ParamDef *	getParamDef (const char *param) const

virtual void	quit (int exit_code=0) const

virtual int	tryRun ()

void	initProgress (size_t total, size_t stepBin=60)

void	setProgress (size_t value=0)

void	endProgress ()

void	processDefaultComment (const char param, const char left)

void	setDefaultComment (const char param, const char comment)

virtual void	initComments ()

void	setProgramName (const char *name)

void	addUsageLine (const char *line, bool verbatim=false)

void	clearUsage ()

void	addExampleLine (const char *example, bool verbatim=true)

void	addSeeAlsoLine (const char *seeAlso)

void	addKeywords (const char *keywords)

const char *	name () const

virtual void	usage (int verb=0) const

virtual void	usage (const String &param, int verb=2)

int	version () const

virtual void	show () const

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

virtual void	read (int argc, char **argv, bool reportErrors=true)

void	read (const String &argumentsLine)

	XmippProgram ()

	XmippProgram (int argc, const char **argv)

virtual	~XmippProgram ()

Public Attributes
FileName	fnDoc
	Selfile with the input images. More...

FileName	fnOut
	Output filename. More...

FileName	fnPSF
	psf Filename More...

FileName	fnStart
	Start Volume Filename. More...

double	lambdaART
	Lambda. More...

int	Nit
	Number of iterations. More...

double	psfThr
	threshold for psfSlabs More...

double	sampling
	Sampling rate. More...

MetaDataVec	MDin
	Metadata with projections info. More...

Basis	basis
	Basis function. By default, blobs. More...

XRayPSF	psf
	Microscope parameters. More...

MultidimArray< double >	IgeoVol
	Vol with the Igeometrical distribution along specimen volume. More...

int	projXdim
	Projection X dimension. More...

int	projYdim
	Projection Y dimension. More...

int	nThreads

ThreadManager *	thMgr

Public Attributes inherited from XmippProgram
bool	doRun

bool	runWithoutArgs

int	verbose
	Verbosity level. More...

int	debug

Protected Attributes
bool	isMpi

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

Additional Inherited Members
Protected Member Functions inherited from XmippProgram
void	defineCommons ()

Detailed Description

Definition at line 39 of file reconstruct_art_xray.h.

Constructor & Destructor Documentation

◆ ProgReconsXrayART()

ProgReconsXrayART::ProgReconsXrayART ( )

inline

Definition at line 77 of file reconstruct_art_xray.h.

78 {}

◆ ~ProgReconsXrayART()

ProgReconsXrayART::~ProgReconsXrayART ( )

inline

Definition at line 79 of file reconstruct_art_xray.h.

80 {}

Member Function Documentation

◆ defineParams()

void ProgReconsXrayART::defineParams ( )

virtual

Function in which the param of each Program are defined.

Basis parameters are forced to be voxels

Reimplemented from XmippProgram.

Definition at line 38 of file reconstruct_art_xray.cpp.

 {
     addUsageLine("Generate 3D reconstructions from projections using ART on x-ray tomograms.");
     addUsageLine("+This program reconstructs based on irregular grids given by pseudo atomic structures. ");
     addUsageLine("+In case of regular grids, please refer to other programs as reconstruct_art ");
     addUsageLine("+or reconstruct_fourier. Optionally, a deformation file generated by Nodal Mode ");
     addUsageLine("+Alignment (NMA) can be passed with --nma parameter.");
 
     //    addSeeAlsoLine("volume_to_pseudoatoms, nma_alignment");
 
     addParamsLine("   -i <md_file>          : Metadata file with input projections");
     addParamsLine("   [-o <volume_file=\"rec_xray_art.vol\">]  : Filename for output volume.");
     addParamsLine("   --psf <psf_param_file>  : XRay-Microscope parameters file");
     addParamsLine("   [--start <basisvolume_file=\"\">]  : Start from this basis volume. The reconstruction is performed in the same grid as the one ");
     addParamsLine("                                      : in which the basis volume was stored (any -FCC or -CC or grid size value are useless)");
     addParamsLine("  [--sampling_rate <Ts=1>]  : Pixel size (Angstrom)");
     addParamsLine("  alias -s;");
     addParamsLine("  [--threshold <thr=0.05>]  : Normalized Threshold relative to maximum of PSF to reduce the volume into slabs");
     addParamsLine("  [-l <lambda=0.1>]         : Relaxation factor");
     addParamsLine("  [-n <N=1>]                : Number of iterations");
     addParamsLine("  [--thr <N=1>]             : Number of threads to use. NOTE: Not available when using MPI.");
 
     //    addParamsLine(" == Basis Parameters ==");
     //    Basis::defineParams(this);
 
 }

◆ postProcess()

void ProgReconsXrayART::postProcess ( )

◆ preProcess()

void ProgReconsXrayART::preProcess ( Image< double > & volVoxels )

Setting initial volume

Definition at line 86 of file reconstruct_art_xray.cpp.

 {
     MDin.read(fnDoc);
 
     ImageInfo imgInfo;
     getImageInfo(MDin,imgInfo);
     projXdim = imgInfo.adim.xdim;
     projYdim = imgInfo.adim.ydim;
 
     psf.calculateParams(sampling*1.e-9, -1, psfThr); // sampling is read in nm
     psf.nThr = nThreads;
 
     if ( fnStart.empty() )
     {
         volVoxels().resize(1, projXdim, projYdim, projXdim, false);
         volVoxels().initZeros();
     }
     else
         volVoxels.read(fnStart);
 
     volVoxels().setXmippOrigin();
 
     //Create threads to start working
     thMgr = new ThreadManager(nThreads);
 
 }

◆ readParams()

void ProgReconsXrayART::readParams ( )

virtual

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

Reimplemented from XmippProgram.

Definition at line 67 of file reconstruct_art_xray.cpp.

 {
     fnDoc = getParam("-i");
     fnOut = getParam("-o");
     fnPSF = getParam("--psf");
     fnStart = getParam("--start");
     sampling = getDoubleParam("--sampling_rate");
     lambdaART = getDoubleParam("-l");
     Nit = getIntParam("-n");
     psfThr = getDoubleParam("--threshold");
     nThreads = getIntParam("--thr");
 
     // Basis parameters
     //    basis.readParams(this);
 
     psf.read(fnPSF);
 
 }

◆ run()

void ProgReconsXrayART::run ( )

virtual

This function will be start running the program. it also should be implemented by derived classes.

Reimplemented from XmippProgram.

Definition at line 210 of file reconstruct_art_xray.cpp.

 {
     //    show();
 
     Image<double> volVoxels;
 
 
     preProcess(volVoxels);
     Projection projExp;
     for (int it=0; it<Nit; it++)
     {
         //        preIteration();
         double itError=0;
         for (size_t objId : MDin.ids())
         {
             FileName fnExp;
             MDin.getValue( MDL_IMAGE, fnExp,objId);
             double rot;
             MDin.getValue( MDL_ANGLE_ROT, rot,objId);
             double tilt;
             MDin.getValue( MDL_ANGLE_TILT, tilt,objId);
             double psi;
             MDin.getValue( MDL_ANGLE_PSI, psi,objId);
             double shiftX;
             MDin.getValue( MDL_SHIFT_X, shiftX,objId);
             double shiftY;
             MDin.getValue( MDL_SHIFT_Y, shiftY,objId);
 
             projExp.read(fnExp);
             projExp().setXmippOrigin();
             projExp.setAngles(rot, tilt, psi);
 
             itError += singleStep(MULTIDIM_ARRAY(volVoxels), projExp, rot, tilt, psi);
         }
         //        postIteration();
 
         if (MDin.size()>0)
             itError/=MDin.size();
         std::cerr << "Error at iteration " << it << " = " << itError << std::endl;
     }
 
     volVoxels.write(fnOut);
 }

◆ setIO()

void ProgReconsXrayART::setIO	(	const FileName &	fn_in,
		const FileName &	fn_out
	)

inlinevirtual

Functions of common reconstruction interface.

Implements ProgReconsBase.

Definition at line 83 of file reconstruct_art_xray.h.

84 {}

◆ show()

void ProgReconsXrayART::show ( )

◆ singleStep()

double ProgReconsXrayART::singleStep	(	MultidimArray< double > &	muVol,
		const Projection &	projExp,
		double	rot,
		double	tilt,
		double	psi
	)

ART single step

Calculation of IgeoVol to optimize process

Forward projection

Definition at line 114 of file reconstruct_art_xray.cpp.

 {
     //    muVol.setXmippOrigin();
 
     size_t iniXdim, iniYdim, iniZdim, newXdim, newYdim, newZdim;
 
     iniXdim = XSIZE(muVol);
     iniYdim = YSIZE(muVol);
     iniZdim = ZSIZE(muVol);
 
     Projection projTheo, projNorm;
     MultidimArray<double> Idiff;
     const MultidimArray<double> &mdaProjExp = projExp();
     MultidimArray<double> &mdaProjTheo = projTheo();
     MultidimArray<double> &mdaProjNorm = projNorm();
 
     mdaProjTheo.initZeros(mdaProjExp);
     projTheo.setAngles(projExp.rot(), projExp.tilt(), projExp.psi());
 
     mdaProjNorm.initZeros(mdaProjExp);
 
     newXdim = iniXdim;
     newYdim = iniYdim;
     newZdim = iniZdim;
 
     MultidimArray<double> rotVol;
 
     rotVol.resizeNoCopy(newZdim, newYdim, newXdim);
     rotVol.setXmippOrigin();
 
     // Rotate volume ....................................................
 
     Matrix2D<double> R;
 
     Euler_angles2matrix(projExp.rot(), projExp.tilt(), projExp.psi(), R, true);
 
     double outside = 0; //phantom.iniVol.getPixel(0,0,0,0);
 
     applyGeometry(xmipp_transformation::LINEAR, rotVol, muVol, R, xmipp_transformation::IS_NOT_INV, xmipp_transformation::DONT_WRAP, outside);
 
     psf.adjustParam(rotVol);
 
     MultidimArray<double> IgeoZb;
     IgeoVol.resize(rotVol, false);
     IgeoZb.resize(1, 1, YSIZE(rotVol), XSIZE(rotVol),false);
     IgeoZb.initConstant(1.);
 
 //    calculateIgeo(rotVol, psf.dzo, IgeoVol, IgeoZb, psf.nThr, thMgr);
 
     Image<double> imTemp;
     imTemp().alias(IgeoVol);
     imTemp.write("IgeoVol.vol");
 
 
     //    projectXrayVolume(rotVol, IgeoVol, psf, projTheo, &mdaProjNorm, thMgr);
     //
     //    projTheo.write("theproj.spi");
     //    projNorm.write("projNorm.spi");
 
     projectXrayGridVolume(muVol, psf, IgeoVol, projTheo, &mdaProjNorm, FORWARD, thMgr);
 
     projTheo.write("theproj.spi");
     projNorm.write("projNorm.spi");
 
 
     //    projectXrayGridVolume(volBasis, basis, IgeoVol, projTheo, projNorm, FORWARD, nThreads);
 
     double mean_error = 0;
     Idiff.initZeros(mdaProjExp);
 
     FOR_ALL_DIRECT_ELEMENTS_IN_ARRAY2D(mdaProjExp)
     {
         // Compute difference image and error
         DIRECT_A2D_ELEM(Idiff, i, j) = DIRECT_A2D_ELEM(mdaProjExp, i, j) - DIRECT_A2D_ELEM(mdaProjTheo, i, j);
         mean_error += DIRECT_A2D_ELEM(Idiff, i, j) * DIRECT_A2D_ELEM(Idiff, i, j);
 
         // Compute the correction image
         DIRECT_A2D_ELEM(mdaProjNorm, i, j) = XMIPP_MAX(DIRECT_A2D_ELEM(mdaProjNorm, i, j), 1);
         DIRECT_A2D_ELEM(mdaProjNorm, i, j) =
             lambdaART * DIRECT_A2D_ELEM(Idiff, i, j) / DIRECT_A2D_ELEM(mdaProjNorm, i, j);
     }
     mean_error /= YXSIZE(mdaProjExp);
 
     projNorm.write("projNorm_2.spi");
 
     imTemp().alias(Idiff);
     imTemp.write("iDiff.spi");
 
     projectXrayGridVolume(muVol, psf, IgeoVol, projTheo, &mdaProjNorm, BACKWARD, thMgr);
 
     return mean_error;
 }

Member Data Documentation

◆ basis

Basis ProgReconsXrayART::basis

Basis function. By default, blobs.

Definition at line 64 of file reconstruct_art_xray.h.

◆ fnDoc

FileName ProgReconsXrayART::fnDoc

Selfile with the input images.

Definition at line 46 of file reconstruct_art_xray.h.

◆ fnOut

FileName ProgReconsXrayART::fnOut

Output filename.

Definition at line 48 of file reconstruct_art_xray.h.

◆ fnPSF

FileName ProgReconsXrayART::fnPSF

psf Filename

Definition at line 50 of file reconstruct_art_xray.h.

◆ fnStart

FileName ProgReconsXrayART::fnStart

Start Volume Filename.

Definition at line 52 of file reconstruct_art_xray.h.

◆ IgeoVol

MultidimArray<double> ProgReconsXrayART::IgeoVol

Vol with the Igeometrical distribution along specimen volume.

Definition at line 68 of file reconstruct_art_xray.h.

◆ isMpi

bool ProgReconsXrayART::isMpi

protected

Definition at line 42 of file reconstruct_art_xray.h.

◆ lambdaART

double ProgReconsXrayART::lambdaART

Lambda.

Definition at line 54 of file reconstruct_art_xray.h.

◆ MDin

MetaDataVec ProgReconsXrayART::MDin

Metadata with projections info.

Definition at line 62 of file reconstruct_art_xray.h.

◆ Nit

int ProgReconsXrayART::Nit

Number of iterations.

Definition at line 56 of file reconstruct_art_xray.h.

◆ nThreads

int ProgReconsXrayART::nThreads

Definition at line 74 of file reconstruct_art_xray.h.

◆ projXdim

int ProgReconsXrayART::projXdim

Projection X dimension.

Definition at line 70 of file reconstruct_art_xray.h.

◆ projYdim

int ProgReconsXrayART::projYdim

Projection Y dimension.

Definition at line 72 of file reconstruct_art_xray.h.

◆ psf

XRayPSF ProgReconsXrayART::psf

Microscope parameters.

Definition at line 66 of file reconstruct_art_xray.h.

◆ psfThr

double ProgReconsXrayART::psfThr

threshold for psfSlabs

Definition at line 58 of file reconstruct_art_xray.h.

◆ sampling

double ProgReconsXrayART::sampling

Sampling rate.

Definition at line 60 of file reconstruct_art_xray.h.

◆ thMgr

ThreadManager* ProgReconsXrayART::thMgr

Definition at line 75 of file reconstruct_art_xray.h.

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

xmipp/legacy/libraries/reconstruction/reconstruct_art_xray.h
xmipp/legacy/libraries/reconstruction/reconstruct_art_xray.cpp

Public Member Functions

Public Attributes

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ProgReconsXrayART()

◆ ~ProgReconsXrayART()

Member Function Documentation

◆ defineParams()

◆ postProcess()

◆ preProcess()

◆ readParams()

◆ run()

◆ setIO()

◆ show()

◆ singleStep()

Member Data Documentation

◆ basis

◆ fnDoc

◆ fnOut

◆ fnPSF

◆ fnStart

◆ IgeoVol

◆ isMpi

◆ lambdaART

◆ MDin

◆ Nit

◆ nThreads

◆ projXdim

◆ projYdim

◆ psf

◆ psfThr

◆ sampling

◆ thMgr