transformations.cpp File Reference

#include "transformations.h"
#include "geometry.h"
#include "bilib/tboundaryconvention.h"
#include "bilib/tsplinebasis.h"
#include "bilib/kerneldiff1.h"
#include "bilib/changebasis.h"
#include "bilib/pyramidtools.h"
#include "xmipp_fft.h"
#include "bilib/kernel.h"
#include <algorithm>
#include "metadata_row_base.h"
#include "utils/half.hpp"

Include dependency graph for transformations.cpp:

Go to the source code of this file.

Macros
#define	ADD_IF_EXIST_NONZERO(label, value)
#define	DELTA_THRESHOLD   10e-7
#define	APPLYGEO(type)
#define	SELFSCALETOSIZE(type)
#define	SCALETOSIZE(type)
#define	SELFPYRAMIDREDUCE(type)
#define	SELFPYRAMIDEXPAND(type)
#define	PYRAMIDEXPAND(type)
#define	PYRAMIDREDUCE(type)

Functions
template<typename T >
void	produceSplineCoefficients (int SplineDegree, MultidimArray< double > &coeffs, const MultidimArray< T > &V1)
template<typename T >
void	produceImageFromSplineCoefficients (int SplineDegree, MultidimArray< T > &img, const MultidimArray< double > &coeffs)
template<typename T >
void	reduceBSpline (int SplineDegree, MultidimArray< double > &V2, const MultidimArray< T > &V1)
template<typename T >
void	expandBSpline (int SplineDegree, MultidimArray< double > &V2, const MultidimArray< T > &V1)
void	geo2TransformationMatrix (const MDRow &imageGeo, Matrix2D< double > &A, bool only_apply_shifts)
void	string2TransformationMatrix (const String &matrixStr, Matrix2D< double > &matrix, size_t dim)
template<typename T >
void	transformationMatrix2Parameters2D (const Matrix2D< T > &A, bool &flip, T &scale, T &shiftX, T &shiftY, T &psi)
template void	transformationMatrix2Parameters2D (const Matrix2D< float > &A, bool &flip, float &scale, float &shiftX, float &shiftY, float &psi)
template void	transformationMatrix2Parameters2D (const Matrix2D< double > &A, bool &flip, double &scale, double &shiftX, double &shiftY, double &psi)
void	transformationMatrix2Parameters3D (const Matrix2D< double > &A, bool &flip, double &scale, double &shiftX, double &shiftY, double &shiftZ, double &rot, double &tilt, double &psi)
void	transformationMatrix2Geo (const Matrix2D< double > &A, MDRow &imageGeo)
template<typename T >
void	rotation2DMatrix (T ang, Matrix2D< T > &result, bool homogeneous)
template void	rotation2DMatrix (float ang, Matrix2D< float > &result, bool homogeneous)
template void	rotation2DMatrix (double ang, Matrix2D< double > &result, bool homogeneous)
template void	translation2DMatrix (const Matrix1D< float > &, Matrix2D< float > &, bool inverse)
template void	translation2DMatrix (const Matrix1D< double > &, Matrix2D< double > &, bool inverse)
template<typename T >
void	translation2DMatrix (const Matrix1D< T > &translation, Matrix2D< T > &resMatrix, bool inverse)
void	rotation3DMatrix (double ang, char axis, Matrix2D< double > &result, bool homogeneous)
void	alignWithZ (const Matrix1D< double > &axis, Matrix2D< double > &result, bool homogeneous)
void	rotation3DMatrix (double ang, const Matrix1D< double > &axis, Matrix2D< double > &result, bool homogeneous)
template void	translation3DMatrix (const Matrix1D< float > &translation, Matrix2D< float > &resMatrix, bool inverse)
template void	translation3DMatrix (const Matrix1D< double > &translation, Matrix2D< double > &resMatrix, bool inverse)
template<typename T >
void	translation3DMatrix (const Matrix1D< T > &translation, Matrix2D< T > &resMatrix, bool inverse)
void	scale3DMatrix (const Matrix1D< double > &sc, Matrix2D< double > &result, bool homogeneous)
bool	getLoopRange (double value, double min, double max, double delta, int loopLimit, int &minIter, int &maxIter)
template<>
void	applyGeometry (int SplineDegree, MultidimArray< std::complex< double > > &V2, const MultidimArray< std::complex< double > > &V1, const Matrix2D< double > &A, bool inv, bool wrap, std::complex< double > outside, MultidimArray< double > *BcoeffsPtr)
template<>
void	selfApplyGeometry (int Splinedegree, MultidimArray< std::complex< double > > &V1, const Matrix2D< double > &A, bool inv, bool wrap, std::complex< double > outside)
void	applyGeometry (int SplineDegree, MultidimArrayGeneric &V2, const MultidimArrayGeneric &V1, const Matrix2D< double > &A, bool inv, bool wrap, double outside)
void	produceSplineCoefficients (int SplineDegree, MultidimArray< double > &coeffs, const MultidimArray< std::complex< double > > &V1)
void	selfScaleToSize (int SplineDegree, MultidimArrayGeneric &V1, int Xdim, int Ydim, int Zdim)
void	scaleToSize (int SplineDegree, MultidimArrayGeneric &V2, const MultidimArrayGeneric &V1, int Xdim, int Ydim, int Zdim)
void	scaleToSize (int SplineDegree, MultidimArray< std::complex< double > > &V2, const MultidimArray< std::complex< double > > &V1, int Xdim, int Ydim, int Zdim)
void	selfScaleToSize (int SplineDegree, MultidimArray< std::complex< double > > &V1, int Xdim, int Ydim, int Zdim)
void	selfPyramidReduce (int SplineDegree, MultidimArrayGeneric &V1, int levels)
void	selfPyramidExpand (int SplineDegree, MultidimArrayGeneric &V1, int levels)
void	pyramidExpand (int SplineDegree, MultidimArrayGeneric &V2, const MultidimArrayGeneric &V1, int levels)
void	pyramidReduce (int SplineDegree, MultidimArrayGeneric &V2, const MultidimArrayGeneric &V1, int levels)
double	interpolatedElementBSplineDiffX (MultidimArray< double > &vol, double x, double y, double z, int SplineDegree)
double	interpolatedElementBSplineDiffY (MultidimArray< double > &vol, double x, double y, double z, int SplineDegree)
double	interpolatedElementBSplineDiffZ (MultidimArray< double > &vol, double x, double y, double z, int SplineDegree)
void	radiallySymmetrize (const MultidimArray< double > &img, MultidimArray< double > &radialImg)
void	rotation3DMatrixFromIcoOrientations (const char *icoFrom, const char *icoTo, Matrix2D< double > &R)
template<typename T >
void	radialAverageNonCubic (const MultidimArray< T > &m, Matrix1D< int > &center_of_rot, MultidimArray< T > &radial_mean, MultidimArray< int > &radial_count, bool rounding)
template void	reduceBSpline< double > (int, MultidimArray< double > &, MultidimArray< double > const &)
template void	expandBSpline< double > (int, MultidimArray< double > &, const MultidimArray< double > &)
template void	produceImageFromSplineCoefficients< double > (int, MultidimArray< double > &, MultidimArray< double > const &)
template void	produceSplineCoefficients< bool > (int, MultidimArray< double > &, MultidimArray< bool > const &)
template void	produceSplineCoefficients< unsigned short > (int, MultidimArray< double > &, MultidimArray< unsigned short > const &)
template void	produceSplineCoefficients< unsigned int > (int, MultidimArray< double > &, MultidimArray< unsigned int > const &)
template void	produceSplineCoefficients< int > (int, MultidimArray< double > &, MultidimArray< int > const &)
template void	produceSplineCoefficients< double > (int, MultidimArray< double > &, MultidimArray< double > const &)
template void	produceSplineCoefficients< unsigned char > (int, MultidimArray< double > &, MultidimArray< unsigned char > const &)
template void	produceSplineCoefficients< short > (int, MultidimArray< double > &, MultidimArray< short > const &)
template void	produceSplineCoefficients< long > (int, MultidimArray< double > &, MultidimArray< long > const &)
template void	produceSplineCoefficients< unsigned long > (int, MultidimArray< double > &, MultidimArray< unsigned long > const &)
template void	produceSplineCoefficients< char > (int, MultidimArray< double > &, MultidimArray< char > const &)
template void	produceSplineCoefficients< float > (int, MultidimArray< double > &, MultidimArray< float > const &)
template void	produceSplineCoefficients< half_float::half > (int, MultidimArray< double > &, MultidimArray< half_float::half > const &)
template void	radialAverageNonCubic< double > (const MultidimArray< double > &m, Matrix1D< int > &center_of_rot, MultidimArray< double > &radial_mean, MultidimArray< int > &radial_count, bool rounding)

Macro Definition Documentation

ADD_IF_EXIST_NONZERO

#define ADD_IF_EXIST_NONZERO	(		label,
			value
	)

Value:

if (imageGeo.containsLabel(label) || \
                                               !XMIPP_EQUAL_ZERO(value))\
                                               imageGeo.setValue(label, value);

Definition at line 327 of file transformations.cpp.

APPLYGEO

#define APPLYGEO

(

type

)

Value:

applyGeometry(SplineDegree,(*(MultidimArray<type>*)(V2.im)), \
                        (*(MultidimArray<type>*)(V1.im)), A, inv, wrap, (type) outside);

DELTA_THRESHOLD

#define DELTA_THRESHOLD   10e-7

Definition at line 602 of file transformations.cpp.

PYRAMIDEXPAND

#define PYRAMIDEXPAND

(

type

)

Value:

pyramidExpand(SplineDegree,MULTIDIM_ARRAY_TYPE(V2,type),\
                                              MULTIDIM_ARRAY_TYPE(V1,type), levels);

PYRAMIDREDUCE

#define PYRAMIDREDUCE

(

type

)

Value:

pyramidReduce(SplineDegree,MULTIDIM_ARRAY_TYPE(V2,type),\
                                              MULTIDIM_ARRAY_TYPE(V1,type), levels);

SCALETOSIZE

#define SCALETOSIZE

(

type

)

Value:

scaleToSize(SplineDegree,MULTIDIM_ARRAY_TYPE(V2,type), \
                          MULTIDIM_ARRAY_TYPE(V1,type),Xdim,Ydim,Zdim);

SELFPYRAMIDEXPAND

#define SELFPYRAMIDEXPAND

(

type

)

Value:

selfPyramidExpand(SplineDegree, \
                                      *((MultidimArray<type>*)(V1.im)), levels);

SELFPYRAMIDREDUCE

#define SELFPYRAMIDREDUCE

(

type

)

Value:

selfPyramidReduce(SplineDegree, \
                                      *((MultidimArray<type>*)(V1.im)), levels);

SELFSCALETOSIZE

#define SELFSCALETOSIZE

(

type

)

Value:

selfScaleToSize(SplineDegree,MULTIDIM_ARRAY_TYPE(V1,type), \
                                                                Xdim,Ydim,Zdim);

Function Documentation

expandBSpline< double >()

template void expandBSpline< double >	(	int	,
		MultidimArray< double > &	,
		const MultidimArray< double > &
	)

produceImageFromSplineCoefficients< double >()

template void produceImageFromSplineCoefficients< double >	(	int	,
		MultidimArray< double > &	,
		MultidimArray< double > const &
	)

produceSplineCoefficients< bool >()

template void produceSplineCoefficients< bool >	(	int	,
		MultidimArray< double > &	,
		MultidimArray< bool > const &
	)

produceSplineCoefficients< char >()

template void produceSplineCoefficients< char >	(	int	,
		MultidimArray< double > &	,
		MultidimArray< char > const &
	)

produceSplineCoefficients< double >()

template void produceSplineCoefficients< double >	(	int	,
		MultidimArray< double > &	,
		MultidimArray< double > const &
	)

produceSplineCoefficients< float >()

template void produceSplineCoefficients< float >	(	int	,
		MultidimArray< double > &	,
		MultidimArray< float > const &
	)

produceSplineCoefficients< half_float::half >()

template void produceSplineCoefficients< half_float::half >	(	int	,
		MultidimArray< double > &	,
		MultidimArray< half_float::half > const &
	)

produceSplineCoefficients< int >()

template void produceSplineCoefficients< int >	(	int	,
		MultidimArray< double > &	,
		MultidimArray< int > const &
	)

produceSplineCoefficients< long >()

template void produceSplineCoefficients< long >	(	int	,
		MultidimArray< double > &	,
		MultidimArray< long > const &
	)

produceSplineCoefficients< short >()

template void produceSplineCoefficients< short >	(	int	,
		MultidimArray< double > &	,
		MultidimArray< short > const &
	)

produceSplineCoefficients< unsigned char >()

template void produceSplineCoefficients< unsigned char >	(	int	,
		MultidimArray< double > &	,
		MultidimArray< unsigned char > const &
	)

produceSplineCoefficients< unsigned int >()

template void produceSplineCoefficients< unsigned int >	(	int	,
		MultidimArray< double > &	,
		MultidimArray< unsigned int > const &
	)

produceSplineCoefficients< unsigned long >()

template void produceSplineCoefficients< unsigned long >	(	int	,
		MultidimArray< double > &	,
		MultidimArray< unsigned long > const &
	)

produceSplineCoefficients< unsigned short >()

template void produceSplineCoefficients< unsigned short >	(	int	,
		MultidimArray< double > &	,
		MultidimArray< unsigned short > const &
	)

radialAverageNonCubic< double >()

template void radialAverageNonCubic< double >	(	const MultidimArray< double > &	m,
		Matrix1D< int > &	center_of_rot,
		MultidimArray< double > &	radial_mean,
		MultidimArray< int > &	radial_count,
		bool	rounding
	)

reduceBSpline< double >()

template void reduceBSpline< double >	(	int	,
		MultidimArray< double > &	,
		MultidimArray< double > const &
	)

rotation2DMatrix() [1/2]

template void rotation2DMatrix	(	float	ang,
		Matrix2D< float > &	result,
		bool	homogeneous
	)

rotation2DMatrix() [2/2]

template void rotation2DMatrix	(	double	ang,
		Matrix2D< double > &	result,
		bool	homogeneous
	)

transformationMatrix2Parameters2D() [1/2]

template void transformationMatrix2Parameters2D	(	const Matrix2D< float > &	A,
		bool &	flip,
		float &	scale,
		float &	shiftX,
		float &	shiftY,
		float &	psi
	)

transformationMatrix2Parameters2D() [2/2]

template void transformationMatrix2Parameters2D	(	const Matrix2D< double > &	A,
		bool &	flip,
		double &	scale,
		double &	shiftX,
		double &	shiftY,
		double &	psi
	)

translation2DMatrix() [1/2]

template void translation2DMatrix	(	const Matrix1D< float > &	,
		Matrix2D< float > &	,
		bool	inverse
	)

translation2DMatrix() [2/2]

template void translation2DMatrix	(	const Matrix1D< double > &	,
		Matrix2D< double > &	,
		bool	inverse
	)

translation3DMatrix() [1/2]

template void translation3DMatrix	(	const Matrix1D< float > &	translation,
		Matrix2D< float > &	resMatrix,
		bool	inverse
	)

translation3DMatrix() [2/2]

template void translation3DMatrix	(	const Matrix1D< double > &	translation,
		Matrix2D< double > &	resMatrix,
		bool	inverse
	)