This class originally added for 2D experimentation and prototying. More...

#include <reconstructor.h>

Inheritance diagram for EMAN::FourierReconstructorSimple2D:

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Collaboration diagram for EMAN::FourierReconstructorSimple2D:

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Public Member Functions
	FourierReconstructorSimple2D ()

virtual	~FourierReconstructorSimple2D ()

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

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

Public Member Functions inherited from EMAN::ReconstructorVolumeData
	ReconstructorVolumeData ()
	Only constructor All member variables are zeroed. More...

virtual	~ReconstructorVolumeData ()
	Destructor safely frees memory. More...

const EMData *	get_emdata ()
	Get the main image pointer, probably redundant (not used) More...

Static Public Member Functions
static Reconstructor *	NEW ()

Static Public Attributes
static const string	NAME = "fouriersimple2D"

Additional Inherited Members
Protected Member Functions inherited from EMAN::ReconstructorVolumeData
void	free_memory ()
	Free allocated memorys The inherited class may have allocated image of tmp_data In either case you can safely call this function to delete either of those pointers, even if they bdb:refine_03::threed_00are NULL. More...

virtual void	normalize_threed (const bool sqrt_damp=false, const bool wiener=false)
	Normalize on the assumption that image is a Fourier volume and that tmp_data is a volume of weights corresponding in size to this Fourier volume. More...

virtual void	zero_memory ()
	Sends the pixels in tmp_data and image to zero Convenience only. More...

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

Protected Attributes inherited from EMAN::ReconstructorVolumeData
EMData *	image
	Inheriting class allocates this, probably in setup(). More...

EMData *	tmp_data
	Inheriting class may allocate this, probably in setup() More...

int	nx

int	nx2

int	ny

int	ny2

int	nz

int	nz2

int	subnx

int	subny

int	subnz

int	subx0

int	suby0

int	subz0

Detailed Description

This class originally added for 2D experimentation and prototying.

It is basically a replica of the FourierReconstructor, but works in 2D

Author: David Woolford and Phil Baldwin

Date: early 2008

Definition at line 302 of file reconstructor.h.

Constructor & Destructor Documentation

◆ FourierReconstructorSimple2D()

EMAN::FourierReconstructorSimple2D::FourierReconstructorSimple2D ( )

inline

Definition at line 305 of file reconstructor.h.

305{}

Referenced by NEW().

◆ ~FourierReconstructorSimple2D()

virtual EMAN::FourierReconstructorSimple2D::~FourierReconstructorSimple2D ( )

inlinevirtual

Definition at line 307 of file reconstructor.h.

307{ }

Member Function Documentation

◆ finish()

EMData * FourierReconstructorSimple2D::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 301 of file reconstructor.cpp.

{
        normalize_threed();
 
        image->process_inplace("xform.fourierorigin.tocorner");
        image->do_ift_inplace();
        image->depad();
        image->process_inplace("xform.phaseorigin.tocenter");
 
        EMData *ret = image;
        image = 0;
        return  ret;
}

References EMAN::ReconstructorVolumeData::image, and EMAN::ReconstructorVolumeData::normalize_threed().

◆ get_desc()

virtual string EMAN::FourierReconstructorSimple2D::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 317 of file reconstructor.h.

317{ return "performs 2D reconstruction"; }

◆ get_name()

virtual string EMAN::FourierReconstructorSimple2D::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 315 of file reconstructor.h.

315{ return NAME; }

EMAN::FourierReconstructorSimple2D::NAME

static const string NAME

Definition: reconstructor.h:333

References NAME.

◆ get_param_types()

virtual TypeDict EMAN::FourierReconstructorSimple2D::get_param_types ( ) const

inlinevirtual

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

Implements EMAN::FactoryBase.

Definition at line 325 of file reconstructor.h.

                        {
                                TypeDict d;
                                d.put("nx", EMObject::INT, "Necessary. The x dimension of the input images.");
//                              d.put("sym", EMObject::STRING, "Symmetry - assumed to be C1 if not specified");
                                return d;
                        }

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

◆ insert_slice()

int FourierReconstructorSimple2D::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 184 of file reconstructor.cpp.

{
 
        // Are these exceptions really necessary? (d.woolford)
        if (!slice) throw NullPointerException("EMData pointer (input image) is NULL");
 
        if ( slice->get_ndim() != 1 ) throw ImageDimensionException("Image dimension must be 1");
 
        // I could also test to make sure the image is the right dimensions...
        if (slice->is_complex()) throw ImageFormatException("The image is complex, expecting real");
 
        EMData* working_slice = slice->process("xform.phaseorigin.tocorner");
 
        // Fourier transform the slice
        working_slice->do_fft_inplace();
 
        float* rdata = image->get_data();
        float* norm = tmp_data->get_data();
        float* dat = working_slice->get_data();
 
        float g[4];
        int offset[4];
        float dt[2];
        offset[0] = 0; offset[1] = 2; offset[2] = nx; offset[3] = nx+2;
 
        float alt = -((float)(euler.get_rotation("2d"))["alpha"])*M_PI/180.0f;
        for (int x = 0; x < working_slice->get_xsize() / 2; x++) {
 
                float rx = (float) x;
 
                float xx = rx*cos(alt);
                float yy = rx*sin(alt);
                float cc = 1.0;
 
                if (xx < 0) {
                        xx = -xx;
                        yy = -yy;
                        cc = -1.0;
                }
 
                yy += ny / 2;
 
 
                dt[0] = dat[2*x];
                dt[1] = cc * dat[2*x+1];
 
                // PHIL IS INTERESTED FROM HERE DOWN
                int x0 = (int) floor(xx);
                int y0 = (int) floor(yy);
 
                int i = 2*x0 + y0*nx;
 
                float dx = xx - x0;
                float dy = yy - y0;
 
                g[0] = Util::agauss(1, dx, dy, 0, EMConsts::I2G);
                g[1] = Util::agauss(1, 1 - dx, dy, 0, EMConsts::I2G);
                g[2] = Util::agauss(1, dx, 1 - dy, 0, EMConsts::I2G);
                g[3] = Util::agauss(1, 1 - dx, 1 - dy, 0, EMConsts::I2G);
 
                // At the extreme we can only do some much...
                if ( x0 == nx-2 ) {
                        int k = i + offset[0];
                        rdata[k] += g[0] * dt[0];
                        rdata[k + 1] += g[0] * dt[1];
                        norm[k/2] += g[0];
 
                        k = i + offset[2];
                        rdata[k] += g[2] * dt[0];
                        rdata[k + 1] += g[2] * dt[1];
                        norm[k/2] += g[2];
                        continue;
 
                }
                // capture and accommodate for periodic boundary conditions in the x direction
                if ( x0 > nx-2 ) {
                        int dif = x0 - (nx-2);
                        x0 -= dif;
                }
                // At the extreme we can only do some much...
                if ( y0 == ny -1 ) {
                        int k = i + offset[0];
                        rdata[k] += g[0] * dt[0];
                        rdata[k + 1] += g[0] * dt[1];
                        norm[k/2] += g[0];
 
                        k = i + offset[1];
                        rdata[k] += g[1] * dt[0];
                        rdata[k + 1] += g[1] * dt[1];
                        norm[k/2] += g[1];
                        continue;
                }
                // capture and accommodate for periodic boundary conditions in the y direction
                if ( y0 > ny-1) {
                        int dif = y0 - (ny-1);
                        y0 -= dif;
                }
 
                if (x0 >= nx - 2 || y0 >= ny - 1) continue;
 
 
 
 
                for (int j = 0; j < 4; j++)
                {
                        int k = i + offset[j];
                        rdata[k] += g[j] * dt[0];
                        rdata[k + 1] += g[j] * dt[1];
                        norm[k/2] += g[j];
 
                }
        }
 
        return 0;
 
}

References EMAN::Util::agauss(), EMAN::Transform::get_rotation(), EMAN::EMConsts::I2G, EMAN::ReconstructorVolumeData::image, ImageDimensionException, ImageFormatException, NullPointerException, EMAN::ReconstructorVolumeData::nx, EMAN::ReconstructorVolumeData::ny, rdata, EMAN::ReconstructorVolumeData::tmp_data, and x.

◆ NEW()

static Reconstructor * EMAN::FourierReconstructorSimple2D::NEW ( )

inlinestatic

Definition at line 319 of file reconstructor.h.

                        {
                                return new FourierReconstructorSimple2D();
                        }

References FourierReconstructorSimple2D().

◆ setup()

void FourierReconstructorSimple2D::setup ( )

virtual

Initialize the reconstructor.

Implements EMAN::Reconstructor.

Definition at line 163 of file reconstructor.cpp.

{
        nx = params.set_default("nx",0);
 
        if ( nx < 0 ) throw InvalidValueException(nx, "nx must be positive");
 
        bool is_fftodd = (nx % 2 == 1);
 
        ny = nx;
        nx += 2-is_fftodd;
 
        image = new EMData();
        image->set_size(nx, ny);
        image->set_complex(true);
        image->set_fftodd(is_fftodd);
        image->set_ri(true);
 
        tmp_data = new EMData();
        tmp_data->set_size(nx/2, nx);
}

References EMAN::ReconstructorVolumeData::image, InvalidValueException, is_fftodd(), EMAN::ReconstructorVolumeData::nx, EMAN::ReconstructorVolumeData::ny, EMAN::FactoryBase::params, EMAN::Dict::set_default(), and EMAN::ReconstructorVolumeData::tmp_data.

Member Data Documentation

◆ NAME

const string FourierReconstructorSimple2D::NAME = "fouriersimple2D"

static

Definition at line 333 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

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ FourierReconstructorSimple2D()

◆ ~FourierReconstructorSimple2D()

Member Function Documentation

◆ finish()

◆ get_desc()

◆ get_name()

◆ get_param_types()

◆ insert_slice()

◆ NEW()

◆ setup()

Member Data Documentation

◆ NAME