#include <reconstructor.h>

Inheritance diagram for EMAN::nn4Reconstructor:

Collaboration diagram for EMAN::nn4Reconstructor:

[legend]

Public Member Functions
	nn4Reconstructor ()

	nn4Reconstructor (const string &symmetry, int size, int npad)

virtual	~nn4Reconstructor ()

virtual void	setup ()
	Initialize the reconstructor. More...

virtual int	insert_slice (const EMData *const slice, const Transform &euler, const float weight)
	Insert an image slice to the reconstructor. More...

virtual EMData *	finish (bool doift=true)
	Finish reconstruction and return the complete model. 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...

virtual TypeDict	get_param_types () const

void	setup (const string &symmetry, int size, int npad)

int	insert_padfft_slice (EMData *padded, const Transform &trans, float mult=1)

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

virtual	~Reconstructor ()

virtual void	setup_seed (EMData *seed, float seed_weight)
	Initialize the reconstructor with a seed volume. More...

virtual void	setup_seedandweights (EMData seed, EMData weight)
	Initialize the reconstructor with a seed volume, as above. More...

virtual EMData *	preprocess_slice (const EMData *const slice, const Transform &t=Transform())
	While you can just insert unprocessed slices, if you call preprocess_slice yourself, and insert the returned slice instead, repeatedly, it can save a fair bit of computation. More...

int	insert_slice (const EMData *const slice, const Transform &euler)

virtual int	determine_slice_agreement (EMData *slice, const Transform &euler, const float weight=1.0, bool sub=true)
	Compares a slice to the current reconstruction volume and computes a normalization factor and quality. More...

virtual EMData *	projection (const Transform &euler, int ret_fourier=1)
	This will create a projection from the current reconstruction. More...

virtual void	clear ()
	set the volume and tmp_volume data to zero, for use in Monte Carlo reconstructors More...

void	print_params () const
	Print the current parameters to std::out. More...

EMObject &	operator[] (const string &key)

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 Reconstructor *	NEW ()

Static Public Attributes
static const string	NAME = "nn4"

Private Member Functions
void	buildFFTVolume ()

void	buildNormVolume ()

void	load_default_settings ()

Private Attributes
EMData *	m_volume

EMData *	m_wptr

string	m_symmetry

int	m_weighting

int	m_vnx

int	m_vny

int	m_vnz

int	m_npad

int	m_nsym

int	m_ndim

int	m_vnzp

int	m_vnyp

int	m_vnxp

int	m_vnzc

int	m_vnyc

int	m_vnxc

float	m_wghta

float	m_wghtb

float	m_osnr

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

Detailed Description

Definition at line 1012 of file reconstructor.h.

Constructor & Destructor Documentation

◆ nn4Reconstructor() [1/2]

nn4Reconstructor::nn4Reconstructor ( )

Definition at line 3164 of file reconstructor.cpp.

{
        m_volume = NULL;
        m_wptr   = NULL;
}

References m_volume, and m_wptr.

Referenced by NEW().

◆ nn4Reconstructor() [2/2]

nn4Reconstructor::nn4Reconstructor	(	const string &	symmetry,
		int	size,
		int	npad
	)

Definition at line 3170 of file reconstructor.cpp.

{
        setup( symmetry, size, npad );
        load_default_settings();
        //print_params();
}

References load_default_settings(), and setup().

◆ ~nn4Reconstructor()

nn4Reconstructor::~nn4Reconstructor ( )

virtual

Definition at line 3177 of file reconstructor.cpp.

{
        //if( m_delete_volume ) checked_delete(m_volume); 
 
        //if( m_delete_weight ) checked_delete( m_wptr );
 
        //checked_delete( m_result );
}

Member Function Documentation

◆ buildFFTVolume()

void nn4Reconstructor::buildFFTVolume ( )

private

Definition at line 3233 of file reconstructor.cpp.

                                      {
        int offset = 2 - m_vnxp%2;
 
        m_volume = params["fftvol"];
 
        if( m_volume->get_xsize() != m_vnxp+offset && m_volume->get_ysize() != m_vnyp && m_volume->get_zsize() != m_vnzp ) {
                m_volume->set_size(m_vnxp+offset,m_vnyp,m_vnzp);
                m_volume->to_zero();
        }
        // ----------------------------------------------------------------
        // Added by Zhengfan Yang on 03/15/07
        // Original author: please check whether my revision is correct and
        // other Reconstructor need similiar revision.
        if ( m_vnxp % 2 == 0 )  m_volume->set_fftodd(0);
        else                    m_volume->set_fftodd(1);
        // ----------------------------------------------------------------
 
        m_volume->set_nxc(m_vnxp/2);
        m_volume->set_complex(true);
        m_volume->set_ri(true);
        m_volume->set_fftpad(true);
        m_volume->set_attr("npad", m_npad);
        m_volume->set_array_offsets(0,1,1);
}

References m_npad, m_vnxp, m_vnyp, m_vnzp, m_volume, and EMAN::FactoryBase::params.

Referenced by setup().

◆ buildNormVolume()

void nn4Reconstructor::buildNormVolume ( )

private

Definition at line 3258 of file reconstructor.cpp.

                                       {
 
        m_wptr = params["weight"];
 
        if( m_wptr->get_xsize() != m_vnxc+1 &&
                m_wptr->get_ysize() != m_vnyp &&
                m_wptr->get_zsize() != m_vnzp ) {
                m_wptr->set_size(m_vnxc+1,m_vnyp,m_vnzp);
                m_wptr->to_zero();
        }
        m_wptr->set_array_offsets(0,1,1);
}

References m_vnxc, m_vnyp, m_vnzp, m_wptr, and EMAN::FactoryBase::params.

Referenced by setup().

◆ finish()

EMData * nn4Reconstructor::finish ( bool doift = true )

virtual

Finish reconstruction and return the complete model.

Parameters

doift A flag indicating whether the returned object should be guaranteed to be in real-space (true) or should be left in whatever space the reconstructor generated

Returns: The result 3D model.

Reimplemented from EMAN::Reconstructor.

Definition at line 3354 of file reconstructor.cpp.

                                     {
 
        if( m_ndim == 3 ) {
                m_volume->symplane0(m_wptr);
        } else {
                for( int i=1; i <= m_vnyp; ++i ) {
 
                        if( (*m_wptr)(0, i, 1)==0.0 ) {
                                int j = m_vnyp + 1 - i;
                                (*m_wptr)(0, i, 1) = (*m_wptr)(0, j, 1);
                                (*m_volume)(0, i, 1) = (*m_volume)(0, j, 1);
                                (*m_volume)(1, i, 1) = (*m_volume)(1, j, 1);
                        }
                }
        }
 
 
        int box = 7;
        int kc = (box-1)/2;
        vector< float > pow_a( m_ndim*kc+1, 1.0 );
        for( unsigned int i=1; i < pow_a.size(); ++i ) pow_a[i] = pow_a[i-1] * exp(m_wghta);
        pow_a.back()=0.0;
 
        float alpha = 0.0;
        if( m_ndim==3) {
                int vol = box*box*box;
                float max = max3d( kc, pow_a );
                alpha = ( 1.0f - 1.0f/(float)vol ) / max;
        } else {
                int ara = box*box;
                float max = max2d( kc, pow_a );
                alpha = ( 1.0f - 1.0f/(float)ara ) / max;
        }
        int ix,iy,iz;
        for (iz = 1; iz <= m_vnzp; iz++) {
                for (iy = 1; iy <= m_vnyp; iy++) {
                        for (ix = 0; ix <= m_vnxc; ix++) {
                                if ( (*m_wptr)(ix,iy,iz) > 0) {//(*v) should be treated as complex!!
                                        float tmp = (-2*((ix+iy+iz)%2)+1)/((*m_wptr)(ix,iy,iz)+m_osnr);
                                        if( m_weighting == ESTIMATE && false) {  // HERE
                                                int cx = ix;
                                                int cy = (iy<=m_vnyc) ? iy - 1 : iy - 1 - m_vnyp;
                                                int cz = (iz<=m_vnzc) ? iz - 1 : iz - 1 - m_vnzp;
                                                float sum = 0.0;
                                                for( int ii = -kc; ii <= kc; ++ii ) {
                                                        int nbrcx = cx + ii;
                                                        if( nbrcx >= m_vnxc ) continue;
                                                        for( int jj= -kc; jj <= kc; ++jj ) {
                                                                int nbrcy = cy + jj;
                                                                if( nbrcy <= -m_vnyc || nbrcy >= m_vnyc ) continue;
 
                                                                int kcz = (m_ndim==3) ? kc : 0;
                                                                for( int kk = -kcz; kk <= kcz; ++kk ) {
                                                                        int nbrcz = cz + kk;
                                                                        if( nbrcz <= -m_vnyc || nbrcz >= m_vnyc ) continue;
                                                                        if( nbrcx < 0 ) {
                                                                                nbrcx = -nbrcx;
                                                                                nbrcy = -nbrcy;
                                                                                nbrcz = -nbrcz;
                                                                        }
                                                                        int nbrix = nbrcx;
                                                                        int nbriy = nbrcy >= 0 ? nbrcy + 1 : nbrcy + 1 + m_vnyp;
                                                                        int nbriz = nbrcz >= 0 ? nbrcz + 1 : nbrcz + 1 + m_vnzp;
                                                                        if( (*m_wptr)( nbrix, nbriy, nbriz ) == 0 ) {
                                                                                int c = m_ndim*kc+1 - std::abs(ii) - std::abs(jj) - std::abs(kk);
                                                                                sum = sum + pow_a[c];
                                                                        }
                                                                }
                                                        }
                                                }
                                                float wght = 1.0f / ( 1.0f - alpha * sum );
                                                tmp = tmp * wght;
                                        }
//cout<<" mvol "<<ix<<"  "<<iy<<"  "<<iz<<"  "<<(*m_volume)(2*ix,iy,iz)<<"  "<<(*m_volume)(2*ix+1,iy,iz)<<"  "<<tmp<<"  "<<m_osnr<<endl;
                                        (*m_volume)(2*ix,iy,iz)   *= tmp;
                                        (*m_volume)(2*ix+1,iy,iz) *= tmp;
                                }
                        }
                }
        }
 
        //if(m_ndim==2) printImage( m_volume );
 
        // back fft
        m_volume->do_ift_inplace();
 
        // EMData* win = m_volume->window_center(m_vnx);
        int npad = m_volume->get_attr("npad");
        m_volume->depad();
        circumfnn( m_volume, npad );
        m_volume->set_array_offsets( 0, 0, 0 );
 
        return 0;
}

References circumfnn(), ESTIMATE, m_ndim, m_osnr, m_vnxc, m_vnyc, m_vnyp, m_vnzc, m_vnzp, m_volume, m_weighting, m_wghta, m_wptr, max2d(), and max3d().

◆ get_desc()

virtual string EMAN::nn4Reconstructor::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 1040 of file reconstructor.h.

                {
                        return "Direct Fourier inversion routine";
                }

◆ get_name()

virtual string EMAN::nn4Reconstructor::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 1035 of file reconstructor.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

virtual TypeDict EMAN::nn4Reconstructor::get_param_types ( ) const

inlinevirtual

Returns: a TypeDict defining and describing the feasible parameters of this class

Implements EMAN::FactoryBase.

Definition at line 1050 of file reconstructor.h.

                {
                        TypeDict d;
                        d.put("size",           EMObject::INT);
                        d.put("npad",           EMObject::INT);
                        d.put("sign",           EMObject::INT);
                        d.put("ndim",           EMObject::INT);
                        d.put("snr",            EMObject::FLOAT);
                        d.put("symmetry",       EMObject::STRING);
                        d.put("snr",            EMObject::FLOAT);
                        d.put("fftvol",         EMObject::EMDATA);
                        d.put("weight",         EMObject::EMDATA);
                        d.put("weighting",  EMObject::INT);
                        return d;
                }

References EMAN::EMObject::EMDATA, EMAN::EMObject::FLOAT, EMAN::EMObject::INT, EMAN::TypeDict::put(), and EMAN::EMObject::STRING.

◆ insert_padfft_slice()

int nn4Reconstructor::insert_padfft_slice	(	EMData *	padded,
		const Transform &	trans,
		float	mult = `1`
	)

Definition at line 3343 of file reconstructor.cpp.

{
        Assert( padfft != NULL );
 
        vector<Transform> tsym = t.get_sym_proj(m_symmetry);
        for (unsigned int isym=0; isym < tsym.size(); isym++)  m_volume->nn( m_wptr, padfft, tsym[isym], weight);
        
        return 0;
}

References Assert, EMAN::Transform::get_sym_proj(), m_symmetry, m_volume, and m_wptr.

Referenced by insert_slice().

◆ insert_slice()

int nn4Reconstructor::insert_slice	(	const EMData *const	slice,
		const Transform &	euler,
		const float	weight
	)

virtual

Insert an image slice to the reconstructor.

To insert multiple image slices, call this function multiple times.

Parameters

slice	Image slice.
euler	Euler angle of this image slice.
weight	A weighting factor for this slice, generally the number of particles in a class-average. May be ignored by some reconstructors

Returns: 0 if OK. 1 if error.

Reimplemented from EMAN::Reconstructor.

Definition at line 3286 of file reconstructor.cpp.

                                                                                                    {
        // sanity checks
        if (!slice) {
                LOGERR("try to insert NULL slice");
                return 1;
        }
 
        int padffted= slice->get_attr_default( "padffted", 0 );
        if( m_ndim==3 ) {
                if ( padffted==0 && (slice->get_xsize()!=slice->get_ysize() || slice->get_xsize()!=m_vnx)  ) {
                        // FIXME: Why doesn't this throw an exception?
                        LOGERR("Tried to insert a slice that is the wrong size.");
                        return 1;
                }
        } else {
                Assert( m_ndim==2 );
                if( slice->get_ysize() !=1 ) {
                        LOGERR( "for 2D reconstruction, a line is excepted" );
                        return 1;
                }
        }
        if( weight > 0.0f )  {
 
                EMData* padfft = padfft_slice( slice, t,  m_npad );
 
                if( m_ndim==3 ) {
                        insert_padfft_slice( padfft, t, weight );
                } else {
                        float alpha = padfft->get_attr( "alpha" );
                        alpha = alpha/180.0f*M_PI;
                        for(int i=0; i < m_vnxc+1; ++i ) {
                                float xnew = i*cos(alpha);
                                float ynew = -i*sin(alpha);
                                float btqr = padfft->get_value_at( 2*i, 0, 0 );
                                float btqi = padfft->get_value_at( 2*i+1, 0, 0 );
                                if( xnew < 0.0 ) {
                                        xnew *= -1;
                                        ynew *= -1;
                                        btqi *= -1;
                                }
 
                                int ixn = int(xnew+0.5+m_vnxp) - m_vnxp;
                                int iyn = int(ynew+0.5+m_vnyp) - m_vnyp;
 
                                if(iyn < 0 ) iyn += m_vnyp;
 
                                (*m_volume)( 2*ixn, iyn+1, 1 )   += btqr * weight;
                                (*m_volume)( 2*ixn+1, iyn+1, 1 ) += btqi * weight;
                                (*m_wptr)(ixn,iyn+1, 1) += weight;
                        }
 
                }
                checked_delete( padfft );
        }
        return 0;
}

References Assert, checked_delete(), insert_padfft_slice(), LOGERR, m_ndim, m_npad, m_vnx, m_vnxc, m_vnxp, m_vnyp, and EMAN::padfft_slice().

◆ load_default_settings()

void EMAN::nn4Reconstructor::load_default_settings ( )

inlineprivate

Definition at line 1088 of file reconstructor.h.

                {
                        //params["use_weights"] = false;
                }

Referenced by nn4Reconstructor().

◆ NEW()

static Reconstructor * EMAN::nn4Reconstructor::NEW ( )

inlinestatic

Definition at line 1045 of file reconstructor.h.

                {
                        return new nn4Reconstructor();
                }

References nn4Reconstructor().

◆ setup() [1/2]

void nn4Reconstructor::setup ( )

virtual

Initialize the reconstructor.

Implements EMAN::Reconstructor.

Definition at line 3187 of file reconstructor.cpp.

{
 
        int size = params["size"];
        int npad = params["npad"];
 
        string symmetry;
        if( params.has_key("symmetry") )  symmetry = params["symmetry"].to_str();
        else                               symmetry = "c1";
 
        if( params.has_key("ndim") )  m_ndim = params["ndim"];
        else                          m_ndim = 3;
 
        if( params.has_key( "snr" ) )  m_osnr = 1.0f/float( params["snr"] );
        else                           m_osnr = 0.0;
 
        setup( symmetry, size, npad );
}

References EMAN::Dict::has_key(), m_ndim, m_osnr, EMAN::FactoryBase::params, and setup().

Referenced by nn4Reconstructor(), and setup().

◆ setup() [2/2]

void nn4Reconstructor::setup	(	const string &	symmetry,
		int	size,
		int	npad
	)

Definition at line 3206 of file reconstructor.cpp.

{
        m_weighting = ESTIMATE;
        m_wghta = 0.2f;
 
        m_symmetry = symmetry;
        m_npad = npad;
        m_nsym = Transform::get_nsym(m_symmetry);
 
        m_vnx = size;
        m_vny = size;
        m_vnz = (m_ndim==3) ? size : 1;
 
        m_vnxp = size*npad;
        m_vnyp = size*npad;
        m_vnzp = (m_ndim==3) ? size*npad : 1;
 
        m_vnxc = m_vnxp/2;
        m_vnyc = m_vnyp/2;
        m_vnzc = (m_ndim==3) ? m_vnzp/2 : 1;
 
        buildFFTVolume();
        buildNormVolume();
 
}

References buildFFTVolume(), buildNormVolume(), ESTIMATE, EMAN::Transform::get_nsym(), m_ndim, m_npad, m_nsym, m_symmetry, m_vnx, m_vnxc, m_vnxp, m_vny, m_vnyc, m_vnyp, m_vnz, m_vnzc, m_vnzp, m_weighting, and m_wghta.

Member Data Documentation

◆ m_ndim

int EMAN::nn4Reconstructor::m_ndim

private

Definition at line 1080 of file reconstructor.h.

Referenced by finish(), insert_slice(), and setup().

◆ m_npad

int EMAN::nn4Reconstructor::m_npad

private

Definition at line 1078 of file reconstructor.h.

Referenced by buildFFTVolume(), insert_slice(), and setup().

◆ m_nsym

int EMAN::nn4Reconstructor::m_nsym

private

Definition at line 1079 of file reconstructor.h.

Referenced by setup().

◆ m_osnr

float EMAN::nn4Reconstructor::m_osnr

private

Definition at line 1087 of file reconstructor.h.

Referenced by finish(), and setup().

◆ m_symmetry

string EMAN::nn4Reconstructor::m_symmetry

private

Definition at line 1075 of file reconstructor.h.

Referenced by insert_padfft_slice(), and setup().

◆ m_vnx

int EMAN::nn4Reconstructor::m_vnx

private

Definition at line 1077 of file reconstructor.h.

Referenced by insert_slice(), and setup().

◆ m_vnxc

int EMAN::nn4Reconstructor::m_vnxc

private

Definition at line 1082 of file reconstructor.h.

Referenced by buildNormVolume(), finish(), insert_slice(), and setup().

◆ m_vnxp

int EMAN::nn4Reconstructor::m_vnxp

private

Definition at line 1081 of file reconstructor.h.

Referenced by buildFFTVolume(), insert_slice(), and setup().

◆ m_vny

int EMAN::nn4Reconstructor::m_vny

private

Definition at line 1077 of file reconstructor.h.

Referenced by setup().

◆ m_vnyc

int EMAN::nn4Reconstructor::m_vnyc

private

Definition at line 1082 of file reconstructor.h.

Referenced by finish(), and setup().

◆ m_vnyp

int EMAN::nn4Reconstructor::m_vnyp

private

Definition at line 1081 of file reconstructor.h.

Referenced by buildFFTVolume(), buildNormVolume(), finish(), insert_slice(), and setup().

◆ m_vnz

int EMAN::nn4Reconstructor::m_vnz

private

Definition at line 1077 of file reconstructor.h.

Referenced by setup().

◆ m_vnzc

int EMAN::nn4Reconstructor::m_vnzc

private

Definition at line 1082 of file reconstructor.h.

Referenced by finish(), and setup().

◆ m_vnzp

int EMAN::nn4Reconstructor::m_vnzp

private

Definition at line 1081 of file reconstructor.h.

Referenced by buildFFTVolume(), buildNormVolume(), finish(), and setup().

◆ m_volume

EMData* EMAN::nn4Reconstructor::m_volume

private

Definition at line 1073 of file reconstructor.h.

Referenced by buildFFTVolume(), finish(), insert_padfft_slice(), and nn4Reconstructor().

◆ m_weighting

int EMAN::nn4Reconstructor::m_weighting

private

Definition at line 1076 of file reconstructor.h.

Referenced by finish(), and setup().

◆ m_wghta

float EMAN::nn4Reconstructor::m_wghta

private

Definition at line 1085 of file reconstructor.h.

Referenced by finish(), and setup().

◆ m_wghtb

float EMAN::nn4Reconstructor::m_wghtb

private

Definition at line 1086 of file reconstructor.h.

◆ m_wptr

EMData* EMAN::nn4Reconstructor::m_wptr

private

Definition at line 1074 of file reconstructor.h.

Referenced by buildNormVolume(), finish(), insert_padfft_slice(), and nn4Reconstructor().

◆ NAME

const string nn4Reconstructor::NAME = "nn4"

static

Definition at line 1070 of file reconstructor.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

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ nn4Reconstructor() [1/2]

◆ nn4Reconstructor() [2/2]

◆ ~nn4Reconstructor()

Member Function Documentation

◆ buildFFTVolume()

◆ buildNormVolume()

◆ finish()

◆ get_desc()

◆ get_name()

◆ get_param_types()

◆ insert_padfft_slice()

◆ insert_slice()

◆ load_default_settings()

◆ NEW()

◆ setup() [1/2]

◆ setup() [2/2]

Member Data Documentation

◆ m_ndim

◆ m_npad

◆ m_nsym

◆ m_osnr

◆ m_symmetry

◆ m_vnx

◆ m_vnxc

◆ m_vnxp

◆ m_vny

◆ m_vnyc

◆ m_vnyp

◆ m_vnz

◆ m_vnzc

◆ m_vnzp

◆ m_volume

◆ m_weighting

◆ m_wghta

◆ m_wghtb

◆ m_wptr

◆ NAME