Xmipp
v3.23.11-Nereus
|
#include <phantom.h>
Public Member Functions | |
void | prepare () |
void | assign (const Cone &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 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 |
Cone base radius. More... | |
double | height |
Cone 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 Cone &f) |
Cone. A cone is defined by its center, a radius, a height and a set of Euler angles, label="con". The center of the cone is at the geometrical center, ie, first the cone is placed with its base parallel to XY plane (the base is of radius "radius"), and the cone is defined between "-height/2" to "+height/2". Then the cone 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 cones are defined in general, can be expressed (rp) with respect to a system where the cone is centered at the origin, its radius and height is unity and its base is parallel to the XY plane by
Directions (free vectors) are transformed in the same fashion except that for the first vector subtraction (referring the origin).
Cone::__attribute__ | ( | (deprecated) | ) |
Another function for return a scaled cone.
Another function for assignment.
Definition at line 143 of file phantom.cpp.
|
virtual |
Print cone in the standard feature format. \ See {Feature::feat_printf}, Phantoms
Implements Feature.
Definition at line 546 of file phantom.cpp.
|
virtual |
Implements Feature.
Definition at line 556 of file phantom.cpp.
void Cone::init_rnd | ( | double | minradius, |
double | maxradius, | ||
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 cone. A cone 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 1895 of file phantom.cpp.
|
virtual |
Intersection of a ray with a cone, NOT IMPLEMENTED!!!!. See Feature::intersection to know more about the parameters meaning.
Implements Feature.
Definition at line 1277 of file phantom.cpp.
Speeded up point inside a cone. This function tells you if a point is inside the cone or not. See Feature::point_inside
Implements Feature.
Definition at line 815 of file phantom.cpp.
|
virtual |
void Cone::read_specific | ( | char * | line | ) |
Read specific description for a cone. An exception is thrown if the line doesn't conform the standard specification. See Feature::read_specific
Definition at line 382 of file phantom.cpp.
|
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 393 of file phantom.cpp.
|
virtual |
Return a scaled cone. The center, density, angles and behaviour of the new cone 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 cone.
Implements Feature.
Definition at line 1619 of file phantom.cpp.
|
inlinevirtual |
Volume of a cone. This function returns 1/3*PI*radius*radius*height. See Feature::volume
Implements Feature.
Definition at line 1295 of file phantom.h.
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 670 of file phantom.cpp.