Sphere Class Reference

#include <phantom.h>

Inheritance diagram for Sphere:

Collaboration diagram for Sphere:

Public Member Functions
void	prepare ()
void	assign (const Sphere &F)
int	point_inside (const Matrix1D< double > &r, Matrix1D< double > &aux) const
double	density_inside (const Matrix1D< double > &r, Matrix1D< double > &aux) const
Feature *	scale (double factor) const
	__attribute__ ((deprecated)) void scale(double factor
double	intersection (const Matrix1D< double > &direction, const Matrix1D< double > &passing_point, Matrix1D< double > &r, Matrix1D< double > &u) const
double	volume () const
void	read_specific (char *line)
void	read_specific (const std::vector< double > &vect)
void	feat_printf (FILE *fh) const
void	feat_printm (MetaData &MD, size_t id)
void	init_rnd (double minradius, double maxradius, double minden=1.0, double maxden=1.0, double minx0=0, double maxx0=0, double miny0=0, double maxy0=0, double minz0=0, double maxz0=0)
Public Member Functions inherited from Feature
void	assign (const Feature &F)
virtual void	rotate (const Matrix2D< double > &E)
virtual void	rotate_center (const Matrix2D< double > &E)
int	point_inside (const Matrix1D< double > &r) const
int	voxel_inside (const Matrix1D< double > &r, Matrix1D< double > &aux1, Matrix1D< double > &aux2) const
int	voxel_inside (const Matrix1D< double > &r) const
double	voxel_inside_by_normalized_density (const Matrix1D< double > &r, Matrix1D< double > &aux1, Matrix1D< double > &aux2) const
int	intersects_sphere (const Matrix1D< double > &r, double radius, Matrix1D< double > &aux1, Matrix1D< double > &aux2, Matrix1D< double > &aux3) const
int	intersects_sphere (const Matrix1D< double > &r, double radius) const
Feature *	encircle (double radius=0) const
Feature *	background (int back_mode, double back_param) const
double	intersection (const Matrix1D< double > &direction, const Matrix1D< double > &passing_point) const
void	mean_variance_in_plane (Image< double > *V, double z, double &mean, double &var)
void	project_to (Projection &P, const Matrix2D< double > &VP, const Matrix2D< double > &PV) const
void	corners (const MultidimArray< double > &V, Matrix1D< double > &corner1, Matrix1D< double > &corner2)
void	draw_in (MultidimArray< double > &V, int color_mode=INTERNAL, double colour=-1)
void	sketch_in (MultidimArray< double > &V, double colour=2)
void	shift (double shiftX, double shiftY, double shiftZ)
void	selfApplyGeometry (const Matrix2D< double > &A)
void	readCommon (char *line)
void	readCommon (MDRow &row)
void	read (MDRow &row)

Public Attributes
double	radius
	Sphere radius. More...
Feature **_f	const
Public Attributes inherited from Feature
std::string	type
char	add_assign
double	density
Matrix1D< double >	center
double	max_distance

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

Detailed Description

Spheres. The spheres are defined by its center and a radius. The label is "sph".

A point (r) in the universal coordinate system, where spheres are defined in general, can be expressed (rp) with respect to a system where the sphere is centered at the origin and its radius is unity by

V3_MINUS_V3(rp,r,sph.Center);
V3_BY_CT(rp, rp, 1/radius);

Directions (free vectors) are transformed in the same fashio except that for the first vector subtraction (referring to the origin).

Definition at line 467 of file phantom.h.

Member Function Documentation

__attribute__()

Sphere::__attribute__

(

(deprecated)

)

Another function for return a scaled sphere.

assign()

void Sphere::assign

(

const Sphere &

F

)

Another function for assignment.

Definition at line 108 of file phantom.cpp.

{
    *this = F;
}

density_inside()

double Sphere::density_inside ( const Matrix1D< double > &  r, Matrix1D< double > &  aux  ) const

inlinevirtual

Density inside an Sphere. This function tells you the density of the sphere at point r for constant valued features is trivial

Implements Feature.

Definition at line 488 of file phantom.h.

    {
        return 1.;
    }

feat_printf()

void Sphere::feat_printf ( FILE *  fh ) const

virtual

Print sphere in the standard feature format. \ See {Feature::feat_printf}, Phantoms

Implements Feature.

Definition at line 405 of file phantom.cpp.

{
    fprintf(fh, "sph    %c     %1.4f    % 7.2f   % 7.2f    % 7.2f    % 7.2f\n",
            add_assign, density, XX(center), YY(center), ZZ(center),
            radius);
}

feat_printm()

void Sphere::feat_printm ( MetaData &  MD, size_t  id  )

virtual

Implements Feature.

Definition at line 413 of file phantom.cpp.

{
    std::vector<double> FSVect;
    FSVect.push_back(radius);
    MD.setValue(MDL_PHANTOM_FEATURE_SPECIFIC,FSVect, id);
}

init_rnd()

void Sphere::init_rnd	(	double	minradius,
		double	maxradius,
		double	minden = 1.0,
		double	maxden = 1.0,
		double	minx0 = 0,
		double	maxx0 = 0,
		double	miny0 = 0,
		double	maxy0 = 0,
		double	minz0 = 0,
		double	maxz0 = 0
	)

Generate a random sphere. A sphere is generated randomly within the range of the parameters given. Notice that most of them are set by default. The exact parameters are picked uniformly from the range. The maximum distance is adjusted properly according to the randomly generated feature. 'den' stands for density and (x0,y0,z0) is the center of the feature. The behaviour of the new sphere is always Add

Definition at line 1681 of file phantom.cpp.

{
    randomize_random_generator();
    center.resize(3);
    type           = "sph";
    add_assign     = '+';
    density        = rnd_unif(minden, maxden);
    XX(center)     = rnd_unif(minx0, maxx0);
    YY(center)     = rnd_unif(miny0, maxy0);
    ZZ(center)     = rnd_unif(minz0, maxz0);

    radius         = rnd_unif(minradius, maxradius);

    max_distance   = radius;
}

intersection()

double Sphere::intersection ( const Matrix1D< double > &  direction, const Matrix1D< double > &  passing_point, Matrix1D< double > &  r, Matrix1D< double > &  u  ) const

virtual

Intersection of a ray with a sphere. See Feature::intersection to know more about the parameters meaning.

Implements Feature.

Definition at line 1102 of file phantom.cpp.

{
    // This is done in order to correct the different lengths seen by
    // rays with different "speed". It is related to the jacobian of
    // the transformation from a non-unit direction to a unit one.
    double norm = direction.module();

    // Set the passing point in the ellipsoid coordinate system
    // and normalise to a unit sphere
    V3_MINUS_V3(r, passing_point, center);
    V3_BY_CT(r, r, 1 / radius);
    V3_BY_CT(u, direction, 1 / radius);
    return intersection_unit_sphere(u, r) / norm;
}

point_inside()

int Sphere::point_inside ( const Matrix1D< double > &  r, Matrix1D< double > &  aux  ) const

virtual

Speeded up point inside a sphere. This function tells you if a point is inside the sphere or not. See Feature::point_inside

Implements Feature.

Definition at line 695 of file phantom.cpp.

{
    DEF_Sph_Blob_point_inside
}

prepare()

void Sphere::prepare ( )

virtual

Prepare sphere for work. Computes the maximum distance, in this case, equal to "radius"

Implements Feature.

Definition at line 44 of file phantom.cpp.

{
    max_distance = radius;
}

read_specific() [1/2]

void Sphere::read_specific

(

char *

line

)

Read specific description for a sphere. An exception is thrown if the line doesn't conform the standard specification. See Feature::read_specific

Definition at line 222 of file phantom.cpp.

{
    int stat;
    stat = sscanf(line, "%*s %*c %*f %*f %*f %*f %lf", &radius);
    if (stat != 1)
        REPORT_ERROR(ERR_IO_NOREAD, (std::string)"Error when reading a sphere:" + line);
    prepare();
}

read_specific() [2/2]

void Sphere::read_specific ( const std::vector< double > &  vector )

virtual

Read a feature from a file, VIRTUAL!!!. The format must be the one given in Phantoms, and each subclass must implement its own I/O routines. These routines must fill only the non common part of the feature description, but they receive the whole line with the description.

Implements Feature.

Definition at line 231 of file phantom.cpp.

{
    if (vect.size() != 1)
        REPORT_ERROR(ERR_ARG_MISSING, MDL::label2Str(MDL_PHANTOM_FEATURE_SPECIFIC) + "Error when reading a sphere: empty Feature vector");
    radius = vect[0];
    prepare();
}

scale()

void Sphere::scale ( double  factor ) const

virtual

Return a scaled sphere. The center, density, and behaviour of the new sphere is exactly the same as the actual one. The radius is multiplied by the scale factor and the maximum distance is recalculated for the new sphere.

Implements Feature.

Definition at line 1485 of file phantom.cpp.

{
    Sphere *f;
    f = new Sphere;
    COPY_COMMON_PART;

    f->radius       = factor * radius;
    f->prepare();
    return (Feature *)f;
}

volume()

double Sphere::volume ( ) const

inlinevirtual

Volume of a sphere. This function returns 4/3*PI*radius*radius*radius. See Feature::volume

Implements Feature.

Definition at line 512 of file phantom.h.

    {
        return 4 / 3*PI*radius*radius*radius;
    }

Friends And Related Function Documentation

operator<<

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

friend

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;
}

Member Data Documentation

const

Feature** _f Sphere::const

Definition at line 500 of file phantom.h.

radius

double Sphere::radius

Sphere radius.

Definition at line 471 of file phantom.h.

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

• xmipp/libraries/data/phantom.h
• xmipp/libraries/data/phantom.cpp