#include <phantom.h>

Inheritance diagram for Cube:

Collaboration diagram for Cube:

Public Member Functions
void	prepare ()

void	assign (const Cube &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 minXdim, double maxXdim, double minYdim=0, double maxYdim=0, double minZdim=0, double maxZdim=0, 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	xdim
	X dimension before rotating. More...

double	ydim
	Y dimension before rotating. More...

double	zdim
	Z dimension before rotating. 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 Cube &f)

Detailed Description

Cube. A cube is defined by its center, and the length in the 3 dimensions (X, Y and Z, before rotating), label="cub". The center of the cube is at the geometrical center, and the dimensions define the cube from "-Xdim/2" to "Xdim/2", ... around the center. Then the cube is rotated after the three Euler angles. The corresponding Euler matrix is stored in the field "euler" while its inverse is in "eulert".

A point (r) in the universal coordinate system, where cubes are defined in general, can be expressed (rp) with respect to a system where the cube is centered at the origin, all its dimensions are unity and its axes are aligned with XYZ by

V3_MINUS_V3(rp,r,cub.Center);
M3x3_BY_V3x1(rp,cub.euler,rp);
XX(rp) /= cub.xdim;
YY(rp) /= cub.ydim;
ZZ(rp) /= cub.zdim;

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

Definition at line 1010 of file phantom.h.

Member Function Documentation

◆ attribute()

Cube::__attribute__ ( (deprecated) )

Another function for return a scaled cube.

◆ assign()

void Cube::assign ( const Cube & F )

Another function for assignment.

Definition at line 133 of file phantom.cpp.

 {
     *this = F;
 }

◆ density_inside()

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

inlinevirtual

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

Implements Feature.

Definition at line 1039 of file phantom.h.

     {
         return 1.;
     }

◆ feat_printf()

void Cube::feat_printf ( FILE * fh ) const

virtual

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

Implements Feature.

Definition at line 500 of file phantom.cpp.

 {
     fprintf(fh, "cub    %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),
             xdim, ydim, zdim,
             rot, tilt, psi);
 }

◆ feat_printm()

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

virtual

Implements Feature.

Definition at line 510 of file phantom.cpp.

 {
     std::vector<double> FSVect;
     FSVect.push_back(xdim);
     FSVect.push_back(ydim);
     FSVect.push_back(zdim);
     FSVect.push_back(rot);
     FSVect.push_back(tilt);
     FSVect.push_back(psi);
     MD.setValue(MDL_PHANTOM_FEATURE_SPECIFIC,FSVect,id);
 }

◆ init_rnd()

void Cube::init_rnd	(	double	minXdim,
		double	maxXdim,
		double	minYdim = `0`,
		double	maxYdim = `0`,
		double	minZdim = `0`,
		double	maxZdim = `0`,
		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 cube. A cube 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. If Ydim and Zdim ranges are restricted to 0, then it's applied the same range as for Xdim.

Definition at line 1813 of file phantom.cpp.

 {
     randomize_random_generator();
     center.resize(3);
     type           = "cub";
     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);
 
     if (minYdim == 0)
         minYdim = minXdim;
     if (minZdim == 0)
         minZdim = minXdim;
     if (maxYdim == 0)
         maxYdim = maxXdim;
     if (maxZdim == 0)
         maxZdim = maxXdim;
     xdim           = rnd_unif(minXdim, maxXdim);
     ydim           = rnd_unif(minYdim, maxYdim);
     zdim           = rnd_unif(minZdim, maxZdim);
     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(xdim * xdim + ydim * ydim + zdim * zdim);
 }

◆ intersection()

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

virtual

Intersection of a ray with a cube, NOT IMPLEMENTED!!!. See Feature::intersection to know more about the parameters meaning.

Implements Feature.

Definition at line 1223 of file phantom.cpp.

 {
     double norm = direction.module();
     SPEED_UP_temps012;
 
     // Set the passing point in the cube coordinate system
     // and normalise to a unit cube
     V3_MINUS_V3(r, passing_point, center);
     M3x3_BY_V3x1(r, euler, r);
     XX(r) /= xdim;
     YY(r) /= ydim;
     ZZ(r) /= zdim;
 
     // Express also the direction in the cube coordinate system
     // and normalise to a unit cube
     M3x3_BY_V3x1(u, euler, direction);
     XX(u) /= xdim;
     YY(u) /= ydim;
     ZZ(u) /= zdim;
 
     return intersection_unit_cube(u, r) / norm;
 }

◆ point_inside()

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

virtual

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

Implements Feature.

Definition at line 778 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 (ABS(XX(aux)) <= xdim / 2 && ABS(YY(aux)) <= ydim / 2 &&
         ABS(ZZ(aux)) <= zdim / 2)
         return 1;
     return 0;
 }

◆ prepare()

void Cube::prepare ( )

virtual

Prepare cube for work. Computes the maximum distance, in this case, equal to "sqrt(xdim*xdim+ydim*ydim+zdim*zdim)", and computes the Euler and inverse Euler matrices as a function of the Euler angles

Implements Feature.

Definition at line 71 of file phantom.cpp.

 {
     prepare_Euler();
     max_distance = sqrt(xdim * xdim + ydim * ydim + zdim * zdim);
 }

◆ read_specific() [1/2]

void Cube::read_specific ( char * line )

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

Definition at line 332 of file phantom.cpp.

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

◆ read_specific() [2/2]

void Cube::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 343 of file phantom.cpp.

 {
     if (vect.size() != 6)
         REPORT_ERROR(ERR_IO_NOREAD, (std::string)"Error when reading a cube");
     xdim = vect[0];
     ydim = vect[1];
     zdim = vect[2];
     rot = vect[3];
     tilt = vect[4];
     psi =  vect[5];
     prepare();
 }

◆ scale()

void Cube::scale ( double factor ) const

virtual

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

Implements Feature.

Definition at line 1579 of file phantom.cpp.

 {
     Cube *f;
     f = new Cube;
     COPY_COMMON_PART;
     COPY_ANGLES;
 
     f->xdim         = factor * xdim;
     f->ydim         = factor * ydim;
     f->zdim         = factor * zdim;
     f->prepare();
     return (Feature *)f;
 }

◆ volume()

double Cube::volume ( ) const

inlinevirtual

Volume of a cube. This function returns xdim*ydim*zdim. See Feature::volume

Implements Feature.

Definition at line 1063 of file phantom.h.

     {
         return xdim*ydim*zdim;
     }

Friends And Related Function Documentation

◆ operator<<

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

Member Data Documentation

◆ const

Feature** _f Cube::const

Definition at line 1051 of file phantom.h.

◆ xdim

double Cube::xdim

X dimension before rotating.

Definition at line 1014 of file phantom.h.

◆ ydim

double Cube::ydim

Y dimension before rotating.

Definition at line 1017 of file phantom.h.

◆ zdim

double Cube::zdim

Z dimension before rotating.

Definition at line 1020 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

◆ xdim

◆ ydim

◆ zdim

◆ attribute()