#include <phantom.h>

Inheritance diagram for DCylinder:

Collaboration diagram for DCylinder:

Public Member Functions
void	prepare ()

void	assign (const DCylinder &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 minheight, double maxheight, double minsep, double maxsep, 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, double minrot=0, double maxrot=360, double mintilt=0, double maxtilt=180, double minpsi=0, double maxpsi=360)

Public Member Functions inherited from Oriented_Feature
void	prepare_Euler ()

void	assign (const Oriented_Feature &OF)

virtual void	rotate (const Matrix2D< double > &E)

Public Member Functions inherited from Feature
void	assign (const Feature &F)

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
	Cylinder radius. More...

double	height
	Each cylinder height. More...

double	separation
	Separation between cylinders. More...

Feature **_f	const

Public Attributes inherited from Oriented_Feature
double	rot
	First Euler angle. More...

double	tilt
	Second Euler angle. More...

double	psi
	Third Euler angle. More...

Matrix2D< double >	euler
	Euler matrix. More...

Matrix2D< double >	eulert
	Inverse Euler matrix. More...

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 DCylinder &f)

Detailed Description

Double cylinders. A double cylinder is defined by its center, a radius, a height and a set of Euler angles, label="dcy". The double cylinder are two cylinders whose centers are (before rotating) "+separation/2+height/2" and "-separation/2-height/2" respectively. Ie, two cylinders along Z axis of height "height" and separated "separation" units. These two cylinders are placed with its base parallel to XY plane (the base is of radius "radius"), and the cylinder is defined between "-height/2" to "+height/2" starting from their own centers. Then the cylinders, as a block, are rotated after the three Euler angles.

A point (r) in the universal coordinate system, where cylinders are defined in general, can be expressed (rp) with respect to a system where the FIRST cylinder is centered at the origin, its radius is unity and its base is parallel to the XY plane (notice that the height is not transformed) by

V3_MINUS_V3(rp,r,dcy.Center+dcy.);
ZZ(r) -= (separation/2+height/2);
M3x3_BY_V3x1(rp,dcy.euler,rp);
XX(rp) /= dcy.radius;
YY(rp) /= dcy.radius;

and for the SECOND dcyinder

V3_MINUS_V3(rp,r,dcy.Center+dcy.);
ZZ(r) += (separation/2+height/2);     // This is the only one line changing
M3x3_BY_V3x1(rp,dcy.euler,rp);
XX(rp) /= dcy.radius;
YY(rp) /= dcy.radius;

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

Definition at line 890 of file phantom.h.

Member Function Documentation

◆ attribute()

DCylinder::__attribute__ ( (deprecated) )

Another function for return a scaled double cylinder.

◆ assign()

void DCylinder::assign ( const DCylinder & F )

Another function for assignment.

Definition at line 128 of file phantom.cpp.

 {
     *this = F;
 }

◆ density_inside()

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

inlinevirtual

Density inside a double cylinder. This function tells you the density of the double cylinder at point r for constant valued features is trivial

Implements Feature.

Definition at line 920 of file phantom.h.

     {
         return 1.;
     }

◆ feat_printf()

void DCylinder::feat_printf ( FILE * fh ) const

virtual

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

Implements Feature.

Definition at line 478 of file phantom.cpp.

 {
     fprintf(fh, "dcy    %c     %1.4f    % 7.2f   % 7.2f    % 7.2f    % 7.2f    "
             "% 7.2f    % 7.2f    % 7.2f    % 7.2f    % 7.2f\n",
             add_assign, density, XX(center), YY(center), ZZ(center),
             radius, height, separation,
             rot, tilt, psi);
 }

◆ feat_printm()

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

virtual

Implements Feature.

Definition at line 488 of file phantom.cpp.

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

◆ init_rnd()

void DCylinder::init_rnd	(	double	minradius,
		double	maxradius,
		double	minheight,
		double	maxheight,
		double	minsep,
		double	maxsep,
		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`,
		double	minrot = `0`,
		double	maxrot = `360`,
		double	mintilt = `0`,
		double	maxtilt = `180`,
		double	minpsi = `0`,
		double	maxpsi = `360`
	)

Generate a random double cylinder. A double cylinder 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. 'Sep' is the range for the separation

Definition at line 1779 of file phantom.cpp.

 {
     randomize_random_generator();
     center.resize(3);
     type           = "dcy";
     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);
     height         = rnd_unif(minheight, maxheight);
     separation     = rnd_unif(minsep, maxsep);
     rot            = rnd_unif(minrot, maxrot);
     tilt           = rnd_unif(mintilt, maxtilt);
     psi            = rnd_unif(minpsi, maxpsi);
     Euler_angles2matrix(rot, tilt, psi, euler);
     eulert = euler.transpose();
 
     max_distance   = sqrt((height + separation) * (height + separation) / 4
                           + radius * radius);
 }

◆ intersection()

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

virtual

Intersection of a ray with a double cylinder. See Feature::intersection to know more about the parameters meaning. The ray intersection consider both cylinders, of course.

Implements Feature.

Definition at line 1182 of file phantom.cpp.

 {
     double norm = direction.module();
     SPEED_UP_temps012;
 
     // Express also the direction in the cylinder coordinate system
     // and normalise to a unit cylinder
     M3x3_BY_V3x1(u, euler, direction);
     XX(u) /= radius;
     YY(u) /= radius;
     ZZ(u) /= height;
 
     // Top cylinder
     // Set the passing point in the cylinder coordinate system
     // and normalise to a unit cylinder
     V3_MINUS_V3(r, passing_point, center);
     M3x3_BY_V3x1(r, euler, r);
     ZZ(r) -= (separation / 2 + height / 2);
     XX(r) /= radius;
     YY(r) /= radius;
     ZZ(r) /= height;
     double i1 = intersection_unit_cylinder(u, r);
 
     // Bottom cylinder
     // Set the passing point in the cylinder coordinate system
     // and normalise to a unit cylinder
     V3_MINUS_V3(r, passing_point, center);
     M3x3_BY_V3x1(r, euler, r);
     ZZ(r) += (separation / 2 + height / 2);
     XX(r) /= radius;
     YY(r) /= radius;
     ZZ(r) /= height;
     double i2 = intersection_unit_cylinder(u, r);
 
     return (i1 + i2) / norm;
 }

◆ point_inside()

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

virtual

Speeded up point inside a double cylinder. This function tells you if a point is inside any of the cylinders or not. See Feature::point_inside

Implements Feature.

Definition at line 757 of file phantom.cpp.

 {
     SPEED_UP_temps012;
 
     // Express r in the feature coord. system
     V3_MINUS_V3(aux, r, center);
     M3x3_BY_V3x1(aux, euler, aux);
 
     // Check if inside
     if (XX(aux)*XX(aux) + YY(aux)*YY(aux) <= radius*radius)
     {
         double cyl_center = separation / 2 + height / 2;
         if (ABS(ZZ(aux) - cyl_center) <= height / 2)
             return 1;
         else if (ABS(ZZ(aux) + cyl_center) <= height / 2)
             return 1;
     }
     return 0;
 }

◆ prepare()

void DCylinder::prepare ( )

virtual

Prepare double cylinder for work. Computes the maximum distance, in this case, equal to "sqrt((height+separation)*(height+separation)/4+radius*radius)", and computes the Euler and inverse Euler matrices as a function of the Euler angles

Implements Feature.

Definition at line 65 of file phantom.cpp.

 {
     prepare_Euler();
     max_distance = sqrt((height + separation) * (height + separation) / 4 + radius * radius);
 }

◆ read_specific() [1/2]

void DCylinder::read_specific ( char * line )

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

Definition at line 308 of file phantom.cpp.

 {
     int stat;
     stat = sscanf(line, "%*s %*c %*f %*f %*f %*f %lf %lf %lf %lf %lf %lf",
                   &radius, &height, &separation, &rot, &tilt, &psi);
     if (stat != 6)
         REPORT_ERROR(ERR_IO_NOREAD, (std::string)"Error when reading a double cylinder:" + line);
     prepare();
 }

◆ read_specific() [2/2]

void DCylinder::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 319 of file phantom.cpp.

 {
     if (vect.size() != 6)
         REPORT_ERROR(ERR_ARG_MISSING, MDL::label2Str(MDL_PHANTOM_FEATURE_SPECIFIC) + "Error when reading a double cylinder");
     radius = vect[0];
     height = vect[1];
     separation = vect[2];
     rot = vect[3];
     tilt = vect[4];
     psi =  vect[5];
     prepare();
 }

◆ scale()

void DCylinder::scale ( double factor ) const

virtual

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

Implements Feature.

Definition at line 1558 of file phantom.cpp.

 {
     DCylinder *f;
     f = new DCylinder;
     COPY_COMMON_PART;
     COPY_ANGLES;
 
     f->radius       = factor * radius;
     f->height       = factor * height;
     f->separation   = separation - 2 * (factor - 1) * height;
     f->prepare();
 
     return (Feature *)f;
 }

◆ volume()

double DCylinder::volume ( ) const

inlinevirtual

Volume of a double cylinder. This function returns 2* 4/3*PI*radius*radius*height. See Feature::volume

Implements Feature.

Definition at line 946 of file phantom.h.

     {
         return 2* 4 / 3*PI*radius*radius*height;
     }

Friends And Related Function Documentation

◆ operator<<

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

Member Data Documentation

◆ const

Feature** _f DCylinder::const

Definition at line 934 of file phantom.h.

◆ height

double DCylinder::height

Each cylinder height.

Definition at line 897 of file phantom.h.

◆ radius

double DCylinder::radius

Cylinder radius.

Definition at line 894 of file phantom.h.

◆ separation

double DCylinder::separation

Separation between cylinders.

Definition at line 900 of file phantom.h.

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

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

Public Member Functions

Public Attributes

Friends

Detailed Description

Member Function Documentation

◆ __attribute__()

◆ assign()

◆ density_inside()

◆ feat_printf()

◆ feat_printm()

◆ init_rnd()

◆ intersection()

◆ point_inside()

◆ prepare()

◆ read_specific() [1/2]

◆ read_specific() [2/2]

◆ scale()

◆ volume()

Friends And Related Function Documentation

◆ operator<<

Member Data Documentation

◆ const

◆ height

◆ radius

◆ separation

◆ attribute()