FourierPixelInserter3D class defines a way a continuous pixel in 3D is inserted into the discrete 3D volume - there are various schemes for doing this including simply finding the nearest neighbor to more elaborate schemes that involve interpolation using the nearest 8 voxels and so on. More...

#include <reconstructor_tools.h>

Inheritance diagram for EMAN::FourierPixelInserter3D:

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Collaboration diagram for EMAN::FourierPixelInserter3D:

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Public Member Functions
	FourierPixelInserter3D ()
	Construct a FourierPixelInserter3D. More...

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

TypeDict	get_param_types () const

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

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

virtual	~FactoryBase ()

virtual string	get_name () const =0
	Get the unique name of this class (especially for factory based instantiation access) More...

virtual string	get_desc () const =0
	Get a clear, concise description of this class. More...

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

Protected Attributes
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...

Private Member Functions
	FourierPixelInserter3D (const FourierPixelInserter3D &)

FourierPixelInserter3D &	operator= (const FourierPixelInserter3D &)

void	free_memory ()

Detailed Description

FourierPixelInserter3D class defines a way a continuous pixel in 3D is inserted into the discrete 3D volume - there are various schemes for doing this including simply finding the nearest neighbor to more elaborate schemes that involve interpolation using the nearest 8 voxels and so on.

FourierPixelInserter3D class is the base class for all pixel inserters. Each specific pixel inserter class has a unique ID name. This name is used to create a FourierPixelInserter3D instance or do a pixel insertion. Currently these IDs are (strings) 1,2,3,4,5,6,7 - where mode 2 is currently the most popularly used pixel insertion mode as it generally performs well, and was the default mode in EMAN1 - it interpolates to the nearest 8 voxels using a gaussian weighting based on Euclidian distance

All FourierPixelInserter3D classes in EMAN2 are managed by a Factory pattern. So each FourierPixelInserter3D class must define:

a unique name to idenfity itself in the factory.
a static method to register itself in the factory.

Typical usages of FourierPixelInserter3D are as follows:

How to get all the FourierPixelInserter3D names:
vector<string> all_pixel_inserters = Factory<FourierPixeldtInserter3D>::get_list();

EMAN::Factory::get_list
static vector< string > get_list()
Definition: emobject.h:837
- How to use a FourierPixelInserter3D in your code
  // First set up the params correctly this is essential - setting up the params requires
  
  // these 5 parameters (only and always these 5). nx,ny, and nz are the dims of data and
  
  // norm, data is the (Fourier) EMData object, and norm is the associated normalization matrix.
  
  parms["data"] = image;
  
  parms["norm"] = tmp_data->get_data();
  
  // The two is the ID of the FourierInserter3DMode2 in this case.
  
  FourierPixelInserter3D* r = Factory<FourierPixelInserter3D>::get("2", params);
  
  // Then call init - this causes all of the internal data to be stored correctly
  
  r->init()
  
  // Then tell the inserter to insert the pixel with real and imaginary components dt[0] and dt[1] at floating point coords [xx,yy,zz]
  
  // using the given weight - this is typically done for pixels in a set of many slices - see FourierReconstructor::insert_slice
  
  r->insert_pixel(xx, yy, zz, dt, weight)
  
  EMAN::FactoryBase::params
  Dict params
  This is the dictionary the stores the parameters of the object.
  Definition: emobject.h:953
  
  EMAN::Factory::get
  static T * get(const string &instance_name)
  Definition: emobject.h:781
  
  EMAN::FourierPixelInserter3D::FourierPixelInserter3D
  FourierPixelInserter3D()
  Construct a FourierPixelInserter3D.
  Definition: reconstructor_tools.h:99

Definition at line 94 of file reconstructor_tools.h.

Constructor & Destructor Documentation

◆ FourierPixelInserter3D() [1/2]

EMAN::FourierPixelInserter3D::FourierPixelInserter3D ( )

inline

Construct a FourierPixelInserter3D.

Definition at line 99 of file reconstructor_tools.h.

99 : norm(0), data(0), nx(0), ny(0), nz(0), nxyz(0)

100 {}

EMAN::FourierPixelInserter3D::nxyz

int nxyz

Definition: reconstructor_tools.h:142

EMAN::FourierPixelInserter3D::data

EMData * data

A pointer to the constructor argument real_data.

Definition: reconstructor_tools.h:139

EMAN::FourierPixelInserter3D::nx

int nx

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

Definition: reconstructor_tools.h:142

EMAN::FourierPixelInserter3D::ny

int ny

Definition: reconstructor_tools.h:142

EMAN::FourierPixelInserter3D::norm

float * norm

A pointer to the constructor argument normalize_values.

Definition: reconstructor_tools.h:137

EMAN::FourierPixelInserter3D::nz

int nz

Definition: reconstructor_tools.h:142

◆ ~FourierPixelInserter3D()

virtual EMAN::FourierPixelInserter3D::~FourierPixelInserter3D ( )

inlinevirtual

Desctruct a FourierPixelInserter3D.

Definition at line 104 of file reconstructor_tools.h.

                {
                        free_memory();
                }

References free_memory().

◆ FourierPixelInserter3D() [2/2]

EMAN::FourierPixelInserter3D::FourierPixelInserter3D ( const FourierPixelInserter3D & )

private

Member Function Documentation

◆ free_memory()

void EMAN::FourierPixelInserter3D::free_memory ( )

inlineprivate

Definition at line 151 of file reconstructor_tools.h.

152 {

153 }

Referenced by ~FourierPixelInserter3D().

◆ get_param_types()

TypeDict EMAN::FourierPixelInserter3D::get_param_types ( ) const

inlinevirtual

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

Implements EMAN::FactoryBase.

Definition at line 109 of file reconstructor_tools.h.

                {
                        TypeDict d;
                        d.put("data", EMObject::EMDATA);
                        d.put("norm", EMObject::FLOAT_POINTER);
                        return d;
                }

References EMAN::EMObject::EMDATA, EMAN::EMObject::FLOAT_POINTER, and EMAN::TypeDict::put().

◆ init()

void FourierPixelInserter3D::init ( )

virtual

Reimplemented in EMAN::FourierInserter3DMode8.

Definition at line 74 of file reconstructor_tools.cpp.

{
        if ( params.has_key("data") )
        {
                data = params["data"];
                if ( data == 0 )
                        throw NotExistingObjectException("data", "error the data pointer was 0 in FourierPixelInserter3D::init");
        }
        else throw NotExistingObjectException("data", "the data pointer was not defined in FourierPixelInserter3D::init");
 
        if ( params.has_key("norm"))
        {
                norm = params["norm"];
                if ( norm == 0 )
                        throw NotExistingObjectException("norm", "error the norm pointer was 0 in FourierPixelInserter3D::init");
        }
        else throw NotExistingObjectException("norm", "the norm pointer was not defined in FourierPixelInserter3D::init");
 
        nx=data->get_xsize();
        ny=data->get_ysize();
        nz=data->get_zsize();
        nxyz=(size_t)nx*ny*nz;
        nx2=nx/2-1;
        ny2=ny/2;
        nz2=nz/2;
 
        if (data->has_attr("subvolume_x0") && data->has_attr("subvolume_full_nx")) {
                subx0=data->get_attr("subvolume_x0");
                suby0=data->get_attr("subvolume_y0");
                subz0=data->get_attr("subvolume_z0");
                fullnx=data->get_attr("subvolume_full_nx");
                fullny=data->get_attr("subvolume_full_ny");
                fullnz=data->get_attr("subvolume_full_nz");
        }
        else {
                subx0=suby0=subz0=-1;
        }
}

References data, fullnx, fullny, fullnz, EMAN::Dict::has_key(), norm, NotExistingObjectException, nx, nx2, nxyz, ny, ny2, nz, nz2, EMAN::FactoryBase::params, subx0, suby0, and subz0.

Referenced by EMAN::FourierInserter3DMode8::init(), and EMAN::FourierReconstructor::load_inserter().

◆ insert_pixel()

virtual bool EMAN::FourierPixelInserter3D::insert_pixel	(	const float &	xx,
		const float &	yy,
		const float &	zz,
		const std::complex< float >	dt,
		const float &	weight = `1.0`
	)

pure 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)

Implemented in EMAN::FourierInserter3DMode1, EMAN::FourierInserter3DMode2, EMAN::FourierInserter3DMode2l, EMAN::FourierInserter3DMode3, EMAN::FourierInserter3DMode5, EMAN::FourierInserter3DMode6, EMAN::FourierInserter3DMode7, EMAN::FourierInserter3DMode8, EMAN::FourierInserter3DMode9, EMAN::FourierInserter3DMode10, and EMAN::FourierInserter3DMode11.

Referenced by EMAN::WienerFourierReconstructor::do_insert_slice_work(), and EMAN::FourierReconstructor::do_insert_slice_work().

◆ operator=()

FourierPixelInserter3D & EMAN::FourierPixelInserter3D::operator= ( const FourierPixelInserter3D & )

private

Member Data Documentation

◆ data

EMData* EMAN::FourierPixelInserter3D::data

protected

A pointer to the constructor argument real_data.

Definition at line 139 of file reconstructor_tools.h.

◆ fullnx

int EMAN::FourierPixelInserter3D::fullnx

protected

Definition at line 144 of file reconstructor_tools.h.

Referenced by init(), EMAN::FourierInserter3DMode1::insert_pixel(), EMAN::FourierInserter3DMode2::insert_pixel(), EMAN::FourierInserter3DMode2l::insert_pixel(), and EMAN::FourierInserter3DMode8::insert_pixel().

◆ fullny

int EMAN::FourierPixelInserter3D::fullny

protected

Definition at line 144 of file reconstructor_tools.h.

Referenced by init(), EMAN::FourierInserter3DMode1::insert_pixel(), EMAN::FourierInserter3DMode2::insert_pixel(), EMAN::FourierInserter3DMode2l::insert_pixel(), and EMAN::FourierInserter3DMode8::insert_pixel().

◆ fullnz

int EMAN::FourierPixelInserter3D::fullnz

protected

Definition at line 144 of file reconstructor_tools.h.

Referenced by init(), EMAN::FourierInserter3DMode1::insert_pixel(), EMAN::FourierInserter3DMode2::insert_pixel(), EMAN::FourierInserter3DMode2l::insert_pixel(), and EMAN::FourierInserter3DMode8::insert_pixel().

◆ norm

float* EMAN::FourierPixelInserter3D::norm

protected

A pointer to the constructor argument normalize_values.

Definition at line 137 of file reconstructor_tools.h.

◆ nx

int EMAN::FourierPixelInserter3D::nx

protected

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

Definition at line 142 of file reconstructor_tools.h.

Referenced by init().

◆ nx2

int EMAN::FourierPixelInserter3D::nx2

protected

Definition at line 143 of file reconstructor_tools.h.

Referenced by init(), EMAN::FourierInserter3DMode2::insert_pixel(), EMAN::FourierInserter3DMode2l::insert_pixel(), EMAN::FourierInserter3DMode3::insert_pixel(), EMAN::FourierInserter3DMode5::insert_pixel(), EMAN::FourierInserter3DMode6::insert_pixel(), EMAN::FourierInserter3DMode7::insert_pixel(), EMAN::FourierInserter3DMode8::insert_pixel(), EMAN::FourierInserter3DMode9::insert_pixel(), EMAN::FourierInserter3DMode10::insert_pixel(), and EMAN::FourierInserter3DMode11::insert_pixel().

◆ nxyz

int EMAN::FourierPixelInserter3D::nxyz

protected

Definition at line 142 of file reconstructor_tools.h.

Referenced by init(), EMAN::FourierInserter3DMode1::insert_pixel(), EMAN::FourierInserter3DMode2::insert_pixel(), EMAN::FourierInserter3DMode2l::insert_pixel(), and EMAN::FourierInserter3DMode8::insert_pixel().

◆ ny

int EMAN::FourierPixelInserter3D::ny

protected

Definition at line 142 of file reconstructor_tools.h.

Referenced by init().

◆ ny2

int EMAN::FourierPixelInserter3D::ny2

protected

Definition at line 143 of file reconstructor_tools.h.

Referenced by init(), EMAN::FourierInserter3DMode2::insert_pixel(), EMAN::FourierInserter3DMode2l::insert_pixel(), EMAN::FourierInserter3DMode3::insert_pixel(), EMAN::FourierInserter3DMode5::insert_pixel(), EMAN::FourierInserter3DMode6::insert_pixel(), EMAN::FourierInserter3DMode7::insert_pixel(), EMAN::FourierInserter3DMode8::insert_pixel(), EMAN::FourierInserter3DMode9::insert_pixel(), EMAN::FourierInserter3DMode10::insert_pixel(), and EMAN::FourierInserter3DMode11::insert_pixel().

◆ nz

int EMAN::FourierPixelInserter3D::nz

protected

Definition at line 142 of file reconstructor_tools.h.

Referenced by init().

◆ nz2

int EMAN::FourierPixelInserter3D::nz2

protected

Definition at line 143 of file reconstructor_tools.h.

Referenced by init(), EMAN::FourierInserter3DMode2::insert_pixel(), EMAN::FourierInserter3DMode2l::insert_pixel(), EMAN::FourierInserter3DMode3::insert_pixel(), EMAN::FourierInserter3DMode5::insert_pixel(), EMAN::FourierInserter3DMode6::insert_pixel(), EMAN::FourierInserter3DMode7::insert_pixel(), EMAN::FourierInserter3DMode8::insert_pixel(), EMAN::FourierInserter3DMode9::insert_pixel(), EMAN::FourierInserter3DMode10::insert_pixel(), and EMAN::FourierInserter3DMode11::insert_pixel().

◆ subx0

int EMAN::FourierPixelInserter3D::subx0

protected

Definition at line 144 of file reconstructor_tools.h.

◆ suby0

int EMAN::FourierPixelInserter3D::suby0

protected

Definition at line 144 of file reconstructor_tools.h.

Referenced by init(), EMAN::FourierInserter3DMode1::insert_pixel(), EMAN::FourierInserter3DMode2::insert_pixel(), EMAN::FourierInserter3DMode2l::insert_pixel(), and EMAN::FourierInserter3DMode8::insert_pixel().

◆ subz0

int EMAN::FourierPixelInserter3D::subz0

protected

Definition at line 144 of file reconstructor_tools.h.

Referenced by init(), EMAN::FourierInserter3DMode1::insert_pixel(), EMAN::FourierInserter3DMode2::insert_pixel(), EMAN::FourierInserter3DMode2l::insert_pixel(), and EMAN::FourierInserter3DMode8::insert_pixel().

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

Public Member Functions

Protected Attributes

Private Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ FourierPixelInserter3D() [1/2]

◆ ~FourierPixelInserter3D()

◆ FourierPixelInserter3D() [2/2]

Member Function Documentation

◆ free_memory()

◆ get_param_types()

◆ init()

◆ insert_pixel()

◆ operator=()

Member Data Documentation

◆ data

◆ fullnx

◆ fullny

◆ fullnz

◆ norm

◆ nx

◆ nx2

◆ nxyz

◆ ny

◆ ny2

◆ nz

◆ nz2

◆ subx0

◆ suby0

◆ subz0