Xmipp
v3.23.11-Nereus
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Enumerations | |
enum | FP_TYPE { SIMPLY_OPEN_FRINGES, SIMPLY_CLOSED_FRINGES, COMPLEX_OPEN_FRINGES, COMPLEX_CLOSED_FRINGES, SIMPLY_CLOSED_FRINGES_MOD } |
Functions | |
void | simulPattern (MultidimArray< double > &im, enum FP_TYPE type, int xdim, int ydim, double noiseLevel, const double freq, Matrix1D< int > coefs) |
Function to simulate some test fringe patterns. More... | |
void | SPTH (FourierTransformer &ftrans, MultidimArray< double > &im, MultidimArray< std::complex< double > > &imProc) |
void | orMinDer (const MultidimArray< double > &im, MultidimArray< double > &orMap, MultidimArray< double > &orModMap, int wSize, MultidimArray< bool > &ROI) |
void | normalize (FourierTransformer &ftrans, MultidimArray< double > &im, MultidimArray< double > &imN, MultidimArray< double > &imModMap, double R, double S, MultidimArray< bool > &ROI) |
void | normalizeWB (MultidimArray< double > &im, MultidimArray< double > &imN, MultidimArray< double > &imModMap, double rmax, double rmin, MultidimArray< bool > &ROI) |
void | normalizeWB2 (MultidimArray< double > &im, MultidimArray< double > &imN, MultidimArray< double > &imModMap, double rmax, double rmin, MultidimArray< bool > &ROI) |
void | direction (const MultidimArray< double > &orMap, MultidimArray< double > &qualityMap, double lambda, int size, MultidimArray< double > &dirMap, int x, int y) |
void | unwrapping (const MultidimArray< double > &wrappedPhase, MultidimArray< double > &qualityMap, double lambda, int size, MultidimArray< double > &unwrappedPhase) |
void | demodulate (MultidimArray< double > &im, double lambda, int size, int x, int y, int rmin, int rmax, MultidimArray< double > &phase, MultidimArray< double > &mod, Matrix1D< double > &coeffs, int verbose=0) |
void | demodulate2 (MultidimArray< double > &im, double lambda, int size, int rmin, int rmax, Matrix1D< double > &coeffs, int verbose=0) |
void | firsPSDZero (MultidimArray< double > &enhancedPSD, Matrix1D< double > &xPoints, Matrix1D< double > &yPoints, double rmin, double rmax, int numAngles, int verbose=0) |
void | fitEllipse (Matrix1D< double > &xPts, Matrix1D< double > &yPts, double &x0, double &y0, double &majorAxis, double &minorAxis, double &ellipseAngle) |
void | fitEllipse (MultidimArray< double > &normImag, double &x0, double &y0, double &majorAxis, double &minorAxis, double &ellipseAngle, size_t &area) |
void | calculateDefocus (double &defocusU, double &defocusV, double majorAxis, double minorAxis, double Q0, double lambda, double Cs, double imgSize, double Ts) |
enum FP_TYPE |
Types of fringes. This class groups all the fringe processing methods that will be used to process the CTF in the non parametric CTF estimation approach
Enumerator | |
---|---|
SIMPLY_OPEN_FRINGES | |
SIMPLY_CLOSED_FRINGES | |
COMPLEX_OPEN_FRINGES | |
COMPLEX_CLOSED_FRINGES | |
SIMPLY_CLOSED_FRINGES_MOD |
Definition at line 44 of file fringe_processing.h.
void calculateDefocus | ( | double & | defocusU, |
double & | defocusV, | ||
double | majorAxis, | ||
double | minorAxis, | ||
double | Q0, | ||
double | lambda, | ||
double | Cs, | ||
double | imgSize, | ||
double | Ts | ||
) |
Definition at line 1235 of file fringe_processing.cpp.
void demodulate | ( | MultidimArray< double > & | im, |
double | lambda, | ||
int | size, | ||
int | x, | ||
int | y, | ||
int | rmin, | ||
int | rmax, | ||
MultidimArray< double > & | phase, | ||
MultidimArray< double > & | mod, | ||
Matrix1D< double > & | coeffs, | ||
int | verbose = 0 |
||
) |
Definition at line 671 of file fringe_processing.cpp.
void demodulate2 | ( | MultidimArray< double > & | im, |
double | lambda, | ||
int | size, | ||
int | rmin, | ||
int | rmax, | ||
Matrix1D< double > & | coeffs, | ||
int | verbose = 0 |
||
) |
Definition at line 853 of file fringe_processing.cpp.
void direction | ( | const MultidimArray< double > & | orMap, |
MultidimArray< double > & | qualityMap, | ||
double | lambda, | ||
int | size, | ||
MultidimArray< double > & | dirMap, | ||
int | x, | ||
int | y | ||
) |
Definition at line 436 of file fringe_processing.cpp.
void firsPSDZero | ( | MultidimArray< double > & | enhancedPSD, |
Matrix1D< double > & | xPoints, | ||
Matrix1D< double > & | yPoints, | ||
double | rmin, | ||
double | rmax, | ||
int | numAngles, | ||
int | verbose = 0 |
||
) |
Definition at line 1022 of file fringe_processing.cpp.
void fitEllipse | ( | Matrix1D< double > & | xPts, |
Matrix1D< double > & | yPts, | ||
double & | x0, | ||
double & | y0, | ||
double & | majorAxis, | ||
double & | minorAxis, | ||
double & | ellipseAngle | ||
) |
Definition at line 1139 of file fringe_processing.cpp.
void fitEllipse | ( | MultidimArray< double > & | normImag, |
double & | x0, | ||
double & | y0, | ||
double & | majorAxis, | ||
double & | minorAxis, | ||
double & | ellipseAngle, | ||
size_t & | area | ||
) |
Definition at line 1213 of file fringe_processing.cpp.
void normalize | ( | FourierTransformer & | ftrans, |
MultidimArray< double > & | im, | ||
MultidimArray< double > & | imN, | ||
MultidimArray< double > & | imModMap, | ||
double | R, | ||
double | S, | ||
MultidimArray< bool > & | ROI | ||
) |
Definition at line 233 of file fringe_processing.cpp.
void normalizeWB | ( | MultidimArray< double > & | im, |
MultidimArray< double > & | imN, | ||
MultidimArray< double > & | imModMap, | ||
double | rmax, | ||
double | rmin, | ||
MultidimArray< bool > & | ROI | ||
) |
Definition at line 298 of file fringe_processing.cpp.
void normalizeWB2 | ( | MultidimArray< double > & | im, |
MultidimArray< double > & | imN, | ||
MultidimArray< double > & | imModMap, | ||
double | rmax, | ||
double | rmin, | ||
MultidimArray< bool > & | ROI | ||
) |
Definition at line 361 of file fringe_processing.cpp.
void orMinDer | ( | const MultidimArray< double > & | im, |
MultidimArray< double > & | orMap, | ||
MultidimArray< double > & | orModMap, | ||
int | wSize, | ||
MultidimArray< bool > & | ROI | ||
) |
Definition at line 149 of file fringe_processing.cpp.
void simulPattern | ( | MultidimArray< double > & | im, |
enum FP_TYPE | type, | ||
int | xdim, | ||
int | ydim, | ||
double | noiseLevel, | ||
const double | freq, | ||
Matrix1D< int > | coefs | ||
) |
Function to simulate some test fringe patterns.
Definition at line 42 of file fringe_processing.cpp.
void SPTH | ( | FourierTransformer & | ftrans, |
MultidimArray< double > & | im, | ||
MultidimArray< std::complex< double > > & | imProc | ||
) |
Function to simulate some test fringe patterns. sd=SPHT(c) computes the quadrture term of c still affected by the direction phase factor. Therefore for a real c=b*cos(phi) sd=SPHT(c)=i*exp(i*dir)*b*sin(phi) Ref: Kieran G. Larkin, Donald J. Bone, and Michael A. Oldfield, "Natural demodulation of two-dimensional fringe patterns. I. General background of the spiral phase quadrature transform," J. Opt. Soc. Am. A 18, 1862-1870 (2001)
Definition at line 111 of file fringe_processing.cpp.
void unwrapping | ( | const MultidimArray< double > & | wrappedPhase, |
MultidimArray< double > & | qualityMap, | ||
double | lambda, | ||
int | size, | ||
MultidimArray< double > & | unwrappedPhase | ||
) |
Definition at line 552 of file fringe_processing.cpp.