Blob Class Reference

#include <phantom.h>

Inheritance diagram for Blob:

Collaboration diagram for Blob:

Public Member Functions
void	prepare ()
void	assign (const Blob &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 minalpha, double maxalpha, double minorder, double maxorder, 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
	Blob radius. More...
double	alpha
	Blob alpha. More...
int	m
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 Blob &f)

Detailed Description

Blobs. The blobs are defined by its center, radius, alpha and m (bessel function order). The label is "blo".

A point (r) in the universal coordinate system, where blobs are defined in general, can be expressed (rp) with respect to a system where the blob 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 fashion except that for the first vector subtraction (referring to the origin).

Definition at line 563 of file phantom.h.

Member Function Documentation

__attribute__()

Blob::__attribute__

(

(deprecated)

)

Another function for return a scaled Blob.

assign()

void Blob::assign

(

const Blob &

F

)

Another function for assignment.

Definition at line 113 of file phantom.cpp.

{
    *this = F;
}

density_inside()

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

virtual

Density inside a blob. This function tells you the density of the blob at point r

Implements Feature.

Definition at line 708 of file phantom.cpp.

{
    /*Express r in the feature coord. system*/
    V3_MINUS_V3(aux, r, center);
    /*Calculate density*/
    return (kaiser_value(aux.module(), radius,  alpha,  m));
}

feat_printf()

void Blob::feat_printf ( FILE *  fh ) const

virtual

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

Implements Feature.

Definition at line 421 of file phantom.cpp.

{
    fprintf(fh, "blo    %c     %1.4f    % 7.2f   % 7.2f    % 7.2f    % 7.2f"
            "    % 7.2f    %1d\n",
            add_assign, density, XX(center), YY(center), ZZ(center),
            radius, alpha, m);
}

feat_printm()

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

virtual

Implements Feature.

Definition at line 430 of file phantom.cpp.

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

init_rnd()

void Blob::init_rnd	(	double	minradius,
		double	maxradius,
		double	minalpha,
		double	maxalpha,
		double	minorder,
		double	maxorder,
		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 blob. 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 1702 of file phantom.cpp.

{
    randomize_random_generator();
    center.resize(3);
    type           = "blo";
    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);
    alpha   = rnd_unif(minalpha, maxalpha);
    m    = (int)(rnd_unif(minorder, maxorder) + 0.5);
    max_distance   = radius;
}

intersection()

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

virtual

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

Implements Feature.

Definition at line 1121 of file phantom.cpp.

{
    return(kaiser_proj(point_line_distance_3D(center, passing_point, direction),
                       radius, alpha, m));
}

point_inside()

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

virtual

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

Implements Feature.

Definition at line 701 of file phantom.cpp.

{
    DEF_Sph_Blob_point_inside
}

prepare()

void Blob::prepare ( )

virtual

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

Implements Feature.

Definition at line 49 of file phantom.cpp.

{
    max_distance = radius;
}

read_specific() [1/2]

void Blob::read_specific

(

char *

line

)

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

Definition at line 239 of file phantom.cpp.

{
    int stat;
    stat = sscanf(line, "%*s %*c %*f %*f %*f %*f %lf %lf %d", &radius, &alpha, &m);
    if (stat != 3)
        REPORT_ERROR(ERR_IO_NOREAD, (std::string)"Error when reading a blob:" + line);
    prepare();
}

read_specific() [2/2]

void Blob::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 248 of file phantom.cpp.

{
    if (vect.size() != 3)
        REPORT_ERROR(ERR_ARG_MISSING, MDL::label2Str(MDL_PHANTOM_FEATURE_SPECIFIC) + "Error when reading a blob");
    radius = vect[0];
    alpha = vect[1];
    m = (int)vect[2];
    prepare();
}

scale()

void Blob::scale ( double  factor ) const

virtual

Return a scaled Blob. The center, density, and behaviour of the new blob 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. Alpha is kept constant

Implements Feature.

Definition at line 1502 of file phantom.cpp.

{
    Blob *f;
    f = new Blob;
    COPY_COMMON_PART;

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

volume()

double Blob::volume ( ) const

virtual

Mass of a Blob. This function returns mass inside a blob. 3 is the dimension See Feature::volume

Implements Feature.

Definition at line 258 of file phantom.cpp.

{
    return basvolume(radius, alpha, m, 3);
}

Friends And Related Function Documentation

operator<<

std::ostream& operator<< ( std::ostream &  o, const Blob &  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 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;
}

Member Data Documentation

alpha

double Blob::alpha

Blob alpha.

Definition at line 572 of file phantom.h.

const

Feature** _f Blob::const

Definition at line 600 of file phantom.h.

m

int Blob::m

Definition at line 574 of file phantom.h.

radius

double Blob::radius

Blob radius.

Definition at line 570 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