#include <phantom.h>

Inheritance diagram for Cylinder:

Collaboration diagram for Cylinder:

Public Member Functions
void	prepare ()

void	assign (const Cylinder &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 minxradius, double maxxradius, double minyradius, double maxyradius, double minheight, double maxheight, 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	xradius
	Cylinder X radius. More...

double	yradius
	Cylinder Y radius. More...

double	height
	Cylinder height. 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 Cylinder &f)

Detailed Description

Cylinder. A cylinder is defined by its center, a radius, a height and a set of Euler angles, label="cyl". The center of the cylinder is at the geometrical center, ie, first the cylinder is 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". Then the cylinder is 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 cylinder is centered at the origin, its radius and height are unity and its base is parallel to the XY plane by

V3_MINUS_V3(rp,r,cyl.Center);
M3x3_BY_V3x1(rp,cyl.euler,rp);
XX(rp) /= cyl.radius;
YY(rp) /= cyl.radius;
ZZ(rp) /= cyl.height;

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

Definition at line 762 of file phantom.h.

Member Function Documentation

◆ attribute()

Cylinder::__attribute__ ( (deprecated) )

Another function for return a scaled cylinder.

◆ assign()

void Cylinder::assign ( const Cylinder & F )

Another function for assignment.

Definition at line 123 of file phantom.cpp.

 {
     *this = F;
 }

◆ density_inside()

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

inlinevirtual

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

Implements Feature.

Definition at line 791 of file phantom.h.

     {
         return 1.;
     }

◆ feat_printf()

void Cylinder::feat_printf ( FILE * fh ) const

virtual

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

Implements Feature.

Definition at line 456 of file phantom.cpp.

 {
     fprintf(fh, "cyl    %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),
             xradius, yradius, height,
             rot, tilt, psi);
 }

◆ feat_printm()

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

virtual

Implements Feature.

Definition at line 466 of file phantom.cpp.

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

◆ init_rnd()

void Cylinder::init_rnd	(	double	minxradius,
		double	maxxradius,
		double	minyradius,
		double	maxyradius,
		double	minheight,
		double	maxheight,
		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 cylinder. A 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

Definition at line 1746 of file phantom.cpp.

 {
     randomize_random_generator();
     center.resize(3);
     type           = "cyl";
     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);
 
     xradius        = rnd_unif(minxradius, maxxradius);
     yradius        = rnd_unif(minyradius, maxyradius);
     height         = rnd_unif(minheight, maxheight);
     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 * height + XMIPP_MAX(xradius * xradius, yradius * yradius));
 }

◆ intersection()

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

virtual

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

Implements Feature.

Definition at line 1143 of file phantom.cpp.

 {
     double norm = direction.module();
     SPEED_UP_temps012;
 
     // 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);
     XX(r) /= xradius;
     YY(r) /= yradius;
     ZZ(r) /= height;
 
     // Express also the direction in the cyilinder coordinate system
     // and normalise to a unit cylinder
     M3x3_BY_V3x1(u, euler, direction);
     XX(u) /= xradius;
     YY(u) /= yradius;
     ZZ(u) /= height;
 
 #ifdef DEBUG
 
     std::cout << "Intersecting .-.-.-.-.-.-.\n";
     std::cout << *this;
     std::cout << "   direction(Univ) = " << direction.transpose() << std::endl;
     std::cout << "   passing  (Univ) = " << passing_point.transpose() << std::endl;
     std::cout << "   direction(Obj.) = " << u.transpose() << std::endl;
     std::cout << "   passing  (Obj.) = " << r.transpose() << std::endl;
     std::cout << "   intersection    = " << intersection_unit_cylinder(u, r) << std::endl;
 #endif
 
     return intersection_unit_cylinder(u, r) / norm;
 }

◆ point_inside()

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

virtual

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

Implements Feature.

Definition at line 738 of file phantom.cpp.

 {
     SPEED_UP_temps012;
     double tx;
     double ty;
 
     // Express r in the feature coord. system
     V3_MINUS_V3(aux, r, center);
     M3x3_BY_V3x1(aux, euler, aux);
 
     // Check if it is inside
     tx = XX(aux) / xradius;
     ty = YY(aux) / yradius;
     if (tx*tx + ty*ty <= 1.0 && fabs(ZZ(aux)) <= height / 2)
         return 1;
     return 0;
 }

◆ prepare()

void Cylinder::prepare ( )

virtual

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

Implements Feature.

Definition at line 59 of file phantom.cpp.

 {
     prepare_Euler();
     max_distance = sqrt(height * height / 4 + XMIPP_MAX(xradius * xradius, yradius * yradius));
 }

◆ read_specific() [1/2]

void Cylinder::read_specific ( char * line )

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

Definition at line 283 of file phantom.cpp.

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

◆ read_specific() [2/2]

void Cylinder::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 294 of file phantom.cpp.

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

◆ scale()

void Cylinder::scale ( double factor ) const

virtual

Return a scaled cylinder. The center, density, angles and behaviour of the new 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 cylinder.

Implements Feature.

Definition at line 1538 of file phantom.cpp.

 {
     Cylinder *f;
     f = new Cylinder;
     COPY_COMMON_PART;
     COPY_ANGLES;
 
     f->xradius      = factor * xradius;
     f->yradius      = factor * yradius;
     f->height       = factor * height;
     f->prepare();
     return (Feature *)f;
 }

◆ volume()

double Cylinder::volume ( ) const

inlinevirtual

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

Implements Feature.

Definition at line 815 of file phantom.h.

     {
         return 4 / 3*PI*xradius*yradius*height;
     }

Friends And Related Function Documentation

◆ operator<<

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

Member Data Documentation

◆ const

Feature** _f Cylinder::const

Definition at line 803 of file phantom.h.

◆ height

double Cylinder::height

Cylinder height.

Definition at line 772 of file phantom.h.

◆ xradius

double Cylinder::xradius

Cylinder X radius.

Definition at line 766 of file phantom.h.

◆ yradius

double Cylinder::yradius

Cylinder Y radius.

Definition at line 769 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

◆ xradius

◆ yradius

◆ attribute()