FourierPixelInserter3DMode6 - encapsulates "method 6" for inserting a 2D Fourier slice into a 3D volume See comments in FourierPixelInserter3D for explanations. More...

#include <reconstructor_tools.h>

Inheritance diagram for EMAN::FourierInserter3DMode6:

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Collaboration diagram for EMAN::FourierInserter3DMode6:

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Public Member Functions
	FourierInserter3DMode6 ()

virtual	~FourierInserter3DMode6 ()

virtual bool	insert_pixel (const float &xx, const float &yy, const float &zz, const std::complex< float > dt, const float &weight=1.0)
	Insert a complex pixel [dt[0]+dt[1]i] at (float) coordinate [xx,yy,zz] with weighting into a discrete 3D volume. More...

virtual string	get_name () const
	Get the unique name of this class (especially for factory based instantiation access) More...

virtual string	get_desc () const
	Get a clear, concise description of this class. More...

Public Member Functions inherited from EMAN::FourierPixelInserter3D
	FourierPixelInserter3D ()
	Construct a FourierPixelInserter3D. More...

virtual	~FourierPixelInserter3D ()
	Desctruct a FourierPixelInserter3D. More...

TypeDict	get_param_types () const

virtual void	init ()

Public Member Functions inherited from EMAN::FactoryBase
	FactoryBase ()

virtual	~FactoryBase ()

Dict	get_params () const
	get a copy of the parameters of this class More...

void	set_params (const Dict &new_params)
	Set new parameters. More...

void	set_param (const string key, const EMObject val)

void	insert_params (const Dict &new_params)
	Insert parameters. More...

Dict	copy_relevant_params (const FactoryBase *const that) const

Static Public Member Functions
static FourierPixelInserter3D *	NEW ()

Static Public Attributes
static const string	NAME = "gauss_var"

Private Member Functions
	FourierInserter3DMode6 (const FourierInserter3DMode6 &)

FourierInserter3DMode6 &	operator= (const FourierInserter3DMode6 &)

Additional Inherited Members
Protected Attributes inherited from EMAN::FourierPixelInserter3D
float *	norm
	A pointer to the constructor argument normalize_values. More...

EMData *	data
	A pointer to the constructor argument real_data. More...

int	nx
	Image volume data sizes a convenience variable used here and there. More...

int	ny

int	nz

int	nxyz

int	nx2

int	ny2

int	nz2

int	subx0

int	suby0

int	subz0

int	fullnx

int	fullny

int	fullnz

Protected Attributes inherited from EMAN::FactoryBase
Dict	params
	This is the dictionary the stores the parameters of the object. More...

Detailed Description

FourierPixelInserter3DMode6 - encapsulates "method 6" for inserting a 2D Fourier slice into a 3D volume See comments in FourierPixelInserter3D for explanations.

Definition at line 342 of file reconstructor_tools.h.

Constructor & Destructor Documentation

◆ FourierInserter3DMode6() [1/2]

EMAN::FourierInserter3DMode6::FourierInserter3DMode6 ( )

inline

Definition at line 345 of file reconstructor_tools.h.

345{}

Referenced by NEW().

◆ ~FourierInserter3DMode6()

virtual EMAN::FourierInserter3DMode6::~FourierInserter3DMode6 ( )

inlinevirtual

Definition at line 346 of file reconstructor_tools.h.

346{}

◆ FourierInserter3DMode6() [2/2]

EMAN::FourierInserter3DMode6::FourierInserter3DMode6 ( const FourierInserter3DMode6 & )

private

Member Function Documentation

◆ get_desc()

virtual string EMAN::FourierInserter3DMode6::get_desc ( ) const

inlinevirtual

Get a clear, concise description of this class.

Returns: a clear, concise description of this class

Implements EMAN::FactoryBase.

Definition at line 360 of file reconstructor_tools.h.

                        {
                                return "More exact version of gauss_5";
                        }

◆ get_name()

virtual string EMAN::FourierInserter3DMode6::get_name ( ) const

inlinevirtual

Get the unique name of this class (especially for factory based instantiation access)

Returns: the unique name of this class

Implements EMAN::FactoryBase.

Definition at line 355 of file reconstructor_tools.h.

                        {
                                return NAME;
                        }

References NAME.

◆ insert_pixel()

bool FourierInserter3DMode6::insert_pixel	(	const float &	xx,
		const float &	yy,
		const float &	zz,
		const std::complex< float >	dt,
		const float &	weight = `1.0`
	)

virtual

Insert a complex pixel [dt[0]+dt[1]i] at (float) coordinate [xx,yy,zz] with weighting into a discrete 3D volume.

Parameters

xx	the floating point x coordinate
yy	the floating point y coordinate
zz	the floating point z coordinate
dt	the complex pixel value (dt[0] is real, dt[1] is imaginary)
weight	the weight to given to this complex pixel

Returns: A boolean that indicates the pixel has been inserted (or not)

Implements EMAN::FourierPixelInserter3D.

Definition at line 382 of file reconstructor_tools.cpp.

{
        int x0 = (int) floor(xx-2.5);
        int y0 = (int) floor(yy-2.5);
        int z0 = (int) floor(zz-2.5);
 
        if (subx0<0) {                  // normal full reconstruction
                if (x0<-nx2-4 || y0<-ny2-4 || z0<-nz2-4 || x0>nx2+3 || y0>ny2+3 || z0>nz2+3 ) return false;
 
                // no error checking on add_complex_fast, so we need to be careful here
                int x1=x0+5;
                int y1=y0+5;
                int z1=z0+5;
                if (x0<-nx2) x0=-nx2;
                if (x1>nx2) x1=nx2;
                if (y0<-ny2) y0=-ny2;
                if (y1>ny2) y1=ny2;
                if (z0<-nz2) z0=-nz2;
                if (z1>nz2) z1=nz2;
 
//              float h=2.0/((1.0+pow(Util::hypot3sq(xx,yy,zz),.5))*EMConsts::I2G);
//              float h=1.0f/EMConsts::I5G;
//              float h=1.0f/(Util::hypot3sq(xx/nx2,yy/ny2,zz/nz2)*EMConsts::I5G*2.0+.1);               // gaussian kernel is used as a weight not a kernel. We increase radius of integration with resolution. Changed away from this on 11/10/17
                float h=1.0f/((Util::hypot3sq(xx,yy,zz)/4000)+.15);             // gaussian kernel is used as a weight not a kernel. We increase radius of integration with resolution. Changed away from this on 11/10/17
                h=h<0.1?0.1:h;  // new formula has h from 0.2 to 5
//              if (yy==0 &&zz==0) printf("%0.0f\t%0.0f\t%0.0f\t%g\n",xx,yy,zz,h);
//              printf("%1.0f\t%1.0f\t%1.0f\t%1.4f\n",xx,yy,zz,h);
                float w=weight;
 
//              float h=32.0f/((8.0f+Util::hypot3(xx,yy,zz))*EMConsts::I3G);
//              float w=weight/(1.0f+6.0f*Util::fast_exp(-h)+12*Util::fast_exp(-h*2.0f)+8*Util::fast_exp(-h*3.0f)+
//                      6.0f*Util::fast_exp(-h*4.0f)+24.0f*Util::fast_exp(-h*5.0f)+24.0f*Util::fast_exp(-h*6.0f)+12.0f*Util::fast_exp(-h*8.0f)+
//                      24.0f*Util::fast_exp(-h*9.0f)+8.0f*Util::fast_exp(-h*12.0f));   // approx normalization so higer radii aren't upweighted relative to lower due to wider Gaussian
                //size_t idx;
                float r, gg;
//              int pc=0;
                for (int k = z0 ; k <= z1; k++) {
                        for (int j = y0 ; j <= y1; j++) {
                                for (int i = x0; i <= x1; i ++) {
                                        r = Util::hypot3sq((float) i - xx, j - yy, k - zz);
//                                      gg=weight;
                                        gg = Util::fast_exp(-r *h);
//                                      if (gg<.00001) continue;                // skip tiny weights for speed
//                                      gg = Util::fast_exp(-r / EMConsts::I2G)*weight;
//                                      gg = sqrt(Util::fast_exp(-r / EMConsts::I2G))*weight;
 
                                        size_t off;
                                        off=data->add_complex_at_fast(i,j,k,dt*gg*w);
//                                      if (i==16 && j==7 && k==4) printf("%g\t%g\t%g\t%g\t%g\n",dt.real(),dt.imag(),gg*w,gg,w);
                                        norm[off/2]+=gg*w;              // This would use a Gaussian WEIGHT with square kernel
//                                      norm[off/2]+=w;                 // This would use a Gaussian KERNEL rather than WEIGHT 
 
#ifdef RECONDEBUG
                                        std::complex<double> v1=dt*gg*w,v2=gg*w;
 
                                        if (k<5 && j<5&& i<5&& k>=0 && j>=0 && i>=0) {
                                                int idx=i*2+j*10+k*50;
                                                ddata[idx]+=v1.real();
                                                ddata[idx+1]+=v1.imag();
                                                dnorm[idx]+=v2.real();
                                                dnorm[idx+1]+=v2.imag();
                                        }
#endif
                                }
                        }
                }
                return true;
        }
        printf("region writing not supported in mode 5\n");
        return false;
}

References EMAN::FourierPixelInserter3D::data, EMAN::Util::fast_exp(), EMAN::Util::hypot3sq(), EMAN::FourierPixelInserter3D::norm, EMAN::FourierPixelInserter3D::nx2, EMAN::FourierPixelInserter3D::ny2, EMAN::FourierPixelInserter3D::nz2, and EMAN::FourierPixelInserter3D::subx0.

◆ NEW()

static FourierPixelInserter3D * EMAN::FourierInserter3DMode6::NEW ( )

inlinestatic

Definition at line 350 of file reconstructor_tools.h.

                        {
                                return new FourierInserter3DMode6();
                        }

References FourierInserter3DMode6().

◆ operator=()

FourierInserter3DMode6 & EMAN::FourierInserter3DMode6::operator= ( const FourierInserter3DMode6 & )

private

Member Data Documentation

◆ NAME

const string FourierInserter3DMode6::NAME = "gauss_var"

static

Definition at line 365 of file reconstructor_tools.h.

Referenced by get_name().

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

Public Member Functions

Static Public Member Functions

Static Public Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ FourierInserter3DMode6() [1/2]

◆ ~FourierInserter3DMode6()

◆ FourierInserter3DMode6() [2/2]

Member Function Documentation

◆ get_desc()

◆ get_name()

◆ insert_pixel()

◆ NEW()

◆ operator=()

Member Data Documentation

◆ NAME