phantom.cpp File Reference

#include "phantom.h"
#include "core/geometry.h"
#include "core/metadata_label.h"
#include "core/metadata_vec.h"
#include "core/xmipp_error.h"
#include "data/blobs.h"
#include "data/fourier_projection.h"

Include dependency graph for phantom.cpp:

Go to the source code of this file.

Macros
#define	DEF_Sph_Blob_point_inside
#define	DEBUG_SHOW
#define	Vr   A3D_ELEM(V,(int)ZZ(r),(int)YY(r),(int)XX(r))
#define	COPY_COMMON_PART
#define	COPY_ANGLES

Functions
std::ostream &	operator<< (std::ostream &o, const Feature *F)
std::ostream &	operator<< (std::ostream &o, const Sphere &f)
std::ostream &	operator<< (std::ostream &o, const Blob &f)
std::ostream &	operator<< (std::ostream &o, const Gaussian &f)
std::ostream &	operator<< (std::ostream &o, const Cylinder &f)
std::ostream &	operator<< (std::ostream &o, const DCylinder &f)
std::ostream &	operator<< (std::ostream &o, const Cube &f)
std::ostream &	operator<< (std::ostream &o, const Ellipsoid &f)
std::ostream &	operator<< (std::ostream &o, const Cone &f)
std::ostream &	operator<< (std::ostream &o, const Phantom &P)

Macro Definition Documentation

COPY_ANGLES

#define COPY_ANGLES

Value:

f->rot          = rot; \
    f->tilt         = tilt; \
    f->psi          = psi;

Definition at line 1479 of file phantom.cpp.

COPY_COMMON_PART

#define COPY_COMMON_PART

Value:

f->type         = type; \
    f->add_assign   = add_assign; \
    f->density      = density; \
    f->center       = center;

Definition at line 1473 of file phantom.cpp.

DEBUG_SHOW

#define DEBUG_SHOW

Definition at line 843 of file phantom.cpp.

DEF_Sph_Blob_point_inside

#define DEF_Sph_Blob_point_inside

Value:

{\
        /*Express r in the feature coord. system*/\
        V3_MINUS_V3(aux,r,center);\
        /*Check if it is inside*/\
        if (XX(aux)*XX(aux) + YY(aux)*YY(aux) +ZZ(aux)*ZZ(aux) <= radius*radius)\
            return 1;\
        return 0;}

Definition at line 686 of file phantom.cpp.

Vr

#define Vr   A3D_ELEM(V,(int)ZZ(r),(int)YY(r),(int)XX(r))

Definition at line 982 of file phantom.cpp.

Function Documentation

operator<<() [1/10]

std::ostream& operator<<	(	std::ostream &	o,
		const Feature *	F
	)

Show feature not in the standard format but more informatively. This function is based on the std::cout << ... of each subclass. First shows the common part of the feature and then its specific part. Be careful that you must show a pointer to the feature!! \ Ex: Sphere sphere; std::cout << (Feature *) &sphere;

Definition at line 569 of file phantom.cpp.

{
    if (F != nullptr)
    {
        o << "Feature --------" << std::endl;
        o << "   type:        " << F->type << std::endl;
        o << "   add_assign:  " << F->add_assign << std::endl;
        o << "   density:     " << F->density << std::endl;
        o << "   center:      " << F->center.transpose() << std::endl;
        if (F->type == "sph")
            o << *((Sphere *) F);
        else if (F->type == "blo")
            o << *((Blob *) F);
        else if (F->type == "gau")
            o << *((Gaussian *) F);
        else if (F->type == "cyl")
            o << *((Cylinder *) F);
        else if (F->type == "dcy")
            o << *((DCylinder *) F);
        else if (F->type == "cub")
            o << *((Cube *) F);
        else if (F->type == "ell")
            o << *((Ellipsoid *) F);
        else if (F->type == "con")
            o << *((Cone *) F);
    }
    return o;
}

operator<<() [2/10]

std::ostream& operator<<	(	std::ostream &	o,
		const Sphere &	f
	)

Show feature not in the standard format but more informatively. This function only shows the non common part of the feature. Use the << operator of Feature to show the whole feature.

Definition at line 599 of file phantom.cpp.

{
    o << "   Radius: " << f.radius << std::endl;
    return o;
}

operator<<() [3/10]

std::ostream& operator<<	(	std::ostream &	o,
		const Blob &	f
	)

Show feature not in the standard format but more informatively. This function only shows the non common part of the feature. Use the << operator of Feature to show the whole feature.

Definition at line 606 of file phantom.cpp.

{
    o << "   Radius: "  << f.radius << std::endl;
    o << "   Alpha:  "  << f.alpha << std::endl;
    o << "   m:      "  << f.m << std::endl;
    return o;
}

operator<<() [4/10]

std::ostream& operator<<	(	std::ostream &	o,
		const Gaussian &	f
	)

Show feature not in the standard format but more informatively. This function only shows the non common part of the feature. Use the << operator of Feature to show the whole feature.

Definition at line 615 of file phantom.cpp.

{
    o << "   Sigma: "  << f.sigma << std::endl;
    return o;
}

operator<<() [5/10]

std::ostream& operator<<	(	std::ostream &	o,
		const Cylinder &	f
	)

Show feature not in the standard format but more informatively. This function only shows the non common part of the feature. Use the << operator of Feature to show the whole feature.

Definition at line 622 of file phantom.cpp.

{
    o << "   XRadius: " << f.xradius << std::endl;
    o << "   YRadius: " << f.yradius << std::endl;
    o << "   Height:  " << f.height << std::endl;
    o << "   Rot:     " << f.rot << std::endl;
    o << "   Tilt:    " << f.tilt << std::endl;
    o << "   Psi:     " << f.psi << std::endl;
    return o;
}

operator<<() [6/10]

std::ostream& operator<<	(	std::ostream &	o,
		const DCylinder &	f
	)

Show feature not in the standard format but more informatively. This function only shows the non common part of the feature. Use the << operator of Feature to show the whole feature.

Definition at line 634 of file phantom.cpp.

{
    o << "   Radius: " << f.radius << std::endl;
    o << "   Height: " << f.height << std::endl;
    o << "   Separ.: " << f.separation << std::endl;
    o << "   Rot:    " << f.rot << std::endl;
    o << "   Tilt:   " << f.tilt << std::endl;
    o << "   Psi:    " << f.psi << std::endl;
    return o;
}

operator<<() [7/10]

std::ostream& operator<<	(	std::ostream &	o,
		const Cube &	f
	)

Show feature not in the standard format but more informatively. This function only shows the non common part of the feature. Use the << operator of Feature to show the whole feature.

Definition at line 646 of file phantom.cpp.

{
    o << "   Xdim:   " << f.xdim << std::endl;
    o << "   Ydim:   " << f.ydim << std::endl;
    o << "   Zdim:   " << f.zdim << std::endl;
    o << "   Rot:    " << f.rot << std::endl;
    o << "   Tilt:   " << f.tilt << std::endl;
    o << "   Psi:    " << f.psi << std::endl;
    return o;
}

operator<<() [8/10]

std::ostream& operator<<	(	std::ostream &	o,
		const Ellipsoid &	f
	)

Show feature not in the standard format but more informatively. This function only shows the non common part of the feature. Use the << operator of Feature to show the whole feature.

Definition at line 658 of file phantom.cpp.

{
    o << "   Xradius: " << f.xradius << std::endl;
    o << "   Yradius: " << f.yradius << std::endl;
    o << "   Zradius: " << f.zradius << std::endl;
    o << "   Rot:     " << f.rot << std::endl;
    o << "   Tilt:    " << f.tilt << std::endl;
    o << "   Psi:     " << f.psi << std::endl;
    return o;
}

operator<<() [9/10]

std::ostream& operator<<	(	std::ostream &	o,
		const Cone &	f
	)

Show feature not in the standard format but more informatively. This function only shows the non common part of the feature. Use the << operator of Feature to show the whole feature.

Definition at line 670 of file phantom.cpp.

{
    o << "   Radius: " << f.radius << std::endl;
    o << "   Height: " << f.height << std::endl;
    o << "   Rot:    " << f.rot << std::endl;
    o << "   Tilt:   " << f.tilt << std::endl;
    o << "   Psi:    " << f.psi << std::endl;
    return o;
}

operator<<() [10/10]

std::ostream& operator<<	(	std::ostream &	o,
		const Phantom &	P
	)

Show a phantom file. The more descriptive format is used instead of the standard Feature format

Definition at line 2343 of file phantom.cpp.

{
    std::cout << "Phantom ---------------------------------------\n";
    std::cout << "Dimensions: " << P.xdim << " x " << P.ydim << " x " << P.zdim << std::endl;
    std::cout << "Background density: " << P.Background_Density << std::endl;
    std::cout << "phantom_scale : " << P.phantom_scale << std::endl;
    for (size_t i = 0; i < P.VF.size(); i++)
        o << P.VF[i];
    return o;
}