Xmipp
v3.23.11-Nereus
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#include <phantom.h>
Public Member Functions | |
void | prepare () |
void | assign (const Ellipsoid &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 minZradius, double maxZradius, 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 |
X radius before rotating. More... | |
double | yradius |
Y radius before rotating. More... | |
double | zradius |
Z radius 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 Ellipsoid &f) |
Ellipsoid. An elliposid is defined by its center, and the radius in the 3 dimensions (X, Y and Z, before rotating), label="ell". The center of the ellipsoid is at the geometrical center, and the dimensions define the elliposid from "-Xradius/2" to "Xradius/2", ... around the center. Then the ellipsoid 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 elliposids are defined in general, can be expressed (rp) with respect to a system where the ellipsoid is centered at the origin, all its radii are unity and its axes are aligned with XYZ by
Directions (free vectors) are transformed in the same fashion except that for the first vector subtraction (referring the origin).
Ellipsoid::__attribute__ | ( | (deprecated) | ) |
Another function for return a scaled elliposoid.
Another function for assignment.
Definition at line 138 of file phantom.cpp.
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Print ellipsoid in the standard feature format. \ See {Feature::feat_printf}, Phantoms
Implements Feature.
Definition at line 523 of file phantom.cpp.
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Implements Feature.
Definition at line 533 of file phantom.cpp.
void Ellipsoid::init_rnd | ( | double | minXradius, |
double | maxXradius, | ||
double | minYradius, | ||
double | maxYradius, | ||
double | minZradius, | ||
double | maxZradius, | ||
double | minden = 1.0 , |
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double | maxden = 1.0 , |
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double | minx0 = 0 , |
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double | maxx0 = 0 , |
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double | miny0 = 0 , |
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double | maxy0 = 0 , |
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double | minz0 = 0 , |
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double | maxz0 = 0 , |
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double | minrot = 0 , |
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double | maxrot = 360 , |
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double | mintilt = 0 , |
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double | maxtilt = 180 , |
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double | minpsi = 0 , |
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double | maxpsi = 360 |
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Generate a random ellipsoid. An ellipsoid 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 1854 of file phantom.cpp.
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Intersection of a ray with an ellipsoid. See Feature::intersection to know more about the parameters meaning.
Implements Feature.
Definition at line 1250 of file phantom.cpp.
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Speeded up point inside an ellipsoid. This function tells you if a point is inside the elliposoid or not. See Feature::point_inside
Implements Feature.
Definition at line 794 of file phantom.cpp.
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void Ellipsoid::read_specific | ( | char * | line | ) |
Read specific description for an ellipsoid. An exception is thrown if the line doesn't conform the standard specification. See Feature::read_specific
Definition at line 357 of file phantom.cpp.
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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 368 of file phantom.cpp.
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Return a scaled elliposoid. The center, density, angles and behaviour of the new ellipsoid 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 ellipsoid.
Implements Feature.
Definition at line 1599 of file phantom.cpp.
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inlinevirtual |
Volume of an ellipsoid. This function returns 4/3*PI*xradius*yradius*zradius. See Feature::volume
Implements Feature.
Definition at line 1180 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 658 of file phantom.cpp.