Namespaces
namespace	analysis

namespace	constants

namespace	path
	Namespace for paths.

namespace	sim

Classes
struct	influenceFunctionGaussianSpec

Functions
template<typename realT >
void	applyPupil2Basis (eigenCube< realT > &modes, const std::string &basisName, const std::string &pupilName, realT fwhm=0)
	Multiply a raw modal basis by a pupil mask.

template<typename realT , typename spectRealT >
int	orthogonalizeBasis (eigenCube< realT > &ortho, Eigen::Array< spectRealT, -1, -1 > &spect, eigenCube< realT > &modes, int method, realT psum=1.0)

template<typename realT >
void	orthogonalizeBasis (const std::string &orthoName, const std::string &basisName, const std::string &pupilName, int method)
	Calculate an orthogonal projection of a basis on a pupil.

template<typename spectRealT , typename realT >
void	normalizeSpectrum (mx::improc::eigenImage< spectRealT > &spectrum, mx::improc::eigenCube< realT > &modes, mx::improc::eigenCube< realT > &ortho, mx::improc::eigenImage< realT > &pupil)

template<typename realT >
int	slaveBasis (const std::string &outputBasisN, const std::string &inputBasisN, const std::string &pupilN, const std::string &dmN, realT fwhm, realT fsmooth, int firstMode=0)

template<typename realT >
int	apodizeBasis (const std::string &outputBasisN, const std::string &inputBasisN, realT tukeyAlpha, realT centralObs, realT overScan, int firstMode)

template<typename realT >
int	subtractBasis (const std::string &basisName, const std::string &basisName1, const std::string &basisName2, const std::string &pupilName, int method)

template<typename realT >
void	makeModfBasis (const std::string &basisName, int dim, int N, realT ang, int nZern=0)
	Make the modified Fourier basis.

template<typename realT >
void	influenceFunctionsGaussian (const std::string &dmName, realT dmSz, int linNAct, realT diameter, realT coupling, realT couplingRange, realT pupilSz=0, bool offsetOdd=false)
	Create a set of Gaussian influence functions (IFs) on a square grid.

template<typename realT >
void	ifPInv (const std::string &dmName, realT maxCondition=-1)
	Calculate the pseudo-inverse and mirror modes for a set of influence functions.

template<typename realT >
void	m2cMatrix (Eigen::Array< realT, -1, -1 > &M2c, Eigen::Array< realT, -1, -1 > &Ap, mx::improc::eigenCube< realT > &M)
	Calculate the modes-to-commands matrix for a set of modes.

template<typename realT >
void	m2cMatrix (const std::string &dmName, const std::string &basisName)
	Calculate the modes-to-commands matrix for a set of modes.

template<typename realT >
void	modalDMM2cMatrix (const std::string &basisName)
	Generate the modes-to-commands matrix for a set of modes on the modal DM.

template<typename realT >
void	modesOnDM (const std::string &dmName, const std::string &basisName)
	Calculate the basis set as it will be reproduced by the DM.

template<typename realT >
void	circularPupil (const std::string &pupilName, realT pupilDiamPixels, realT pupilDiamMeters, realT centralObs=0, realT overscan=0)
	Generate a circular pupil and saves it to disk.

template<typename realT >
void	circularApodizedPupil (const std::string &pupilName, int pupilDiamPixels, realT pupilDiamMeters, realT tukeyAlpha, realT centralObs=0, realT overScan=0)
	Generates a circular apodized pupil and saves it to disk.

template<typename realT >
void	makeZernikeBasis (const std::string &basisName, const std::string &pupilName, int dim, int N)
	Make the Zernike basis.

Function Documentation

◆ apodizeBasis()

template<typename realT >

int mx::AO::apodizeBasis	(	const std::string &	outputBasisN,
		const std::string &	inputBasisN,
		realT	tukeyAlpha,
		realT	centralObs,
		realT	overScan,
		int	firstMode
	)

Definition at line 371 of file basis.hpp.

References mx::AO::path::basis::modes(), and mx::math::six_fifths().

◆ applyPupil2Basis()

template<typename realT >

void mx::AO::applyPupil2Basis	(	eigenCube< realT > &	modes,
		const std::string &	basisName,
		const std::string &	pupilName,
		realT	fwhm = `0`
	)

Multiply a raw modal basis by a pupil mask.

Definition at line 38 of file basis.hpp.

References mx::improc::filterImage(), mx::AO::path::basis::modes(), mx::improc::padImage(), mx::AO::path::pupil::pupilFile(), and mx::math::six_fifths().

Referenced by orthogonalizeBasis().

◆ circularApodizedPupil()

template<typename realT >

void mx::AO::circularApodizedPupil	(	const std::string &	pupilName,
		int	pupilDiamPixels,
		realT	pupilDiamMeters,
		realT	tukeyAlpha,
		realT	centralObs = `0`,
		realT	overScan = `0`
	)

Generates a circular apodized pupil and saves it to disk.

Apodization is with a Tukey window.

Definition at line 62 of file pupil.hpp.

References mx::fits::fitsHeader::append(), mx::AO::path::pupil::pupilFile(), and mx::fits::fitsFile< dataT >::write().

◆ circularPupil()

template<typename realT >

void mx::AO::circularPupil	(	const std::string &	pupilName,
		realT	pupilDiamPixels,
		realT	pupilDiamMeters,
		realT	centralObs = `0`,
		realT	overscan = `0`
	)

Generate a circular pupil and saves it to disk.

Definition at line 28 of file pupil.hpp.

References mx::fits::fitsHeader::append(), mx::wfp::circularPupil(), mx::AO::path::pupil::pupilFile(), and mx::fits::fitsFile< dataT >::write().

◆ ifPInv()

template<typename realT >

void mx::AO::ifPInv	(	const std::string &	dmName,
		realT	maxCondition = `-1`
	)

Calculate the pseudo-inverse and mirror modes for a set of influence functions.

The influence functions are a cube of 2D maps of mirror deformations, and the matrix \( A \) is formed by vectorizing the influence functions. The pseudo inverse is then calculated from the SVD as follows: \( A = U S V^T \) which gives the Moore-Penrose pseudo-inverse: \( A^+ = V S^+ U^T\). The columns of U contain the orthogonal mirror modes, and S contains the singular values. These are both written to disk along with the pseudo-inverse.

Parameters

[in]	dmName	is the name of the deformable mirror.
[in]	maxCondition	[optional] the maximum condition number to accept for the pseudo-inverse. If < 0 [default] then the user is interactively asked what to use.

Template Parameters

realT is the real floating point type in which to do calculations.

Definition at line 366 of file influenceFunctions.hpp.

References mx::fits::fitsHeader::append(), mx::improc::eigenCube< dataT >::asVectors(), mx::improc::eigenCube< dataT >::cols(), mx::math::eigenPseudoInverse(), mx::AO::path::dm::influenceFunctions(), mx::AO::path::dm::mirrorModes(), MX_PINV_ASK, MX_PINV_NO_INTERACT, MX_PINV_PLOT, mx::improc::eigenCube< dataT >::planes(), mx::AO::path::dm::pseudoInverse(), mx::fits::fitsFile< dataT >::read(), mx::improc::eigenCube< dataT >::resize(), mx::improc::eigenCube< dataT >::rows(), mx::AO::path::dm::singularValues(), and mx::fits::fitsFile< dataT >::write().

◆ influenceFunctionsGaussian()

template<typename realT >

void mx::AO::influenceFunctionsGaussian	(	const std::string &	dmName,
		realT	dmSz,
		int	linNAct,
		realT	diameter,
		realT	coupling,
		realT	couplingRange,
		realT	pupilSz = `0`,
		bool	offsetOdd = `false`
	)

Create a set of Gaussian influence functions (IFs) on a square grid.

The width of the IFs is specified by the coupling, which is the height of the IF at 1 actuator separation. For a FWHM = 1 actuator, coupling = 0.0625. The IFs are normalized to a height of 1.

Parameters

[in]	dmName	the name of the deformable mirror (DM) (the mx::AO path will be constructed from this).
[in]	dmSz	the linear size of the DM in pixels.
[in]	linNAct	the linear number of actuators across the DM.
[in]	diameter	is the diameter of the DM, in actuators. If 0 then the DM is a square.
[in]	coupling	is the height of the IF at 1 actuator separation. E.G., for a FWHM = 1 actuator, set this to 0.0625.
[in]	pupilSz	is the size of the pupil, and therefore the size of the maps (pupilSz x pupilSz), Is set to dmSz if 0, can be pupilSz < dmSx for an oversized DM. The pupil is assumed to be centered.

Template Parameters

realT is the real floating point type in which to do calculations.

< Uniform deviate, used in shiftRandom.

Parameters

couplingRange Uniformly distributed uncertainy in coupling, in fraction of the coupling.

Definition at line 230 of file influenceFunctions.hpp.

References mx::AO::path::dm::actuatorPositions(), mx::fits::fitsHeader::append(), mx::math::func::fwhm2sigma(), mx::improc::eigenCube< dataT >::image(), mx::AO::path::dm::influenceFunctions(), mx::math::randomT< typeT, _ranengT, _randistT >::seed(), and mx::fits::fitsFile< dataT >::write().

◆ m2cMatrix() [1/2]

template<typename realT >

void mx::AO::m2cMatrix	(	const std::string &	dmName,
		const std::string &	basisName
	)

Calculate the modes-to-commands matrix for a set of modes.

A wrapper for m2cMatrix, where the various matrices are here specified with names, which in turn generate mx::AO paths

Parameters

[in]	dmName	is the name of the deformable mirror
[in]	basisName	is the name of the modal basis
[in]	pupilName	is the name of the pupil

Template Parameters

realT is the real floating point type in which to do calculations.

Definition at line 470 of file influenceFunctions.hpp.

References mx::AO::path::dm::M2c(), m2cMatrix(), mx::AO::path::basis::modes(), mx::AO::path::dm::pseudoInverse(), mx::fits::fitsFile< dataT >::read(), and mx::fits::fitsFile< dataT >::write().

◆ m2cMatrix() [2/2]

template<typename realT >

void mx::AO::m2cMatrix	(	Eigen::Array< realT, -1, -1 > &	M2c,
		Eigen::Array< realT, -1, -1 > &	Ap,
		mx::improc::eigenCube< realT > &	M
	)

Calculate the modes-to-commands matrix for a set of modes.

Given the pseudo-inverse \( A^+ \) of the influence functions, the commands to the actuators to take a mirror shape \( \vec{s} \) are calculated as

\[ \vec{c} = \mathbf{A^+} \vec{s}. \]

Now given a basis set \( \mathbf{M} \), the mirror shape is specified as

\[ \vec{s}= \sum_i m_i M_i \]

where \( \vec{m} = m_0, m_1, \cdot m_i \cdot \) are the modal coefficients. If the mirror-to-commands matrix, \( \mathbf{M2c} \) gives commands as

\[ \vec{c} = \mathbf{M2c} \vec{m} \]

then we can calculate \( \mathbf{M2c} \) as:

\[ \mathbf{M2c} = \mathbf{A}^{+T} \mathbf{M} \]

Parameters

[out]	M2c	is the M2c matrix, allocated during the calculationg
[in]	Ap	is the pseudo-inverse of the influence function basis set
[in]	M	is the modal basis set, a cube of shapes

Template Parameters

realT is the real floating point type used for all calculations.

Definition at line 453 of file influenceFunctions.hpp.

References mx::improc::eigenCube< dataT >::asVectors().

Referenced by m2cMatrix().

◆ makeModfBasis()

template<typename realT >

void mx::AO::makeModfBasis	(	const std::string &	basisName,
		int	dim,
		int	N,
		realT	ang,
		int	nZern = `0`
	)

Make the modified Fourier basis.

Parameters

[in]	basisName	the name of the basis (not including the mx::AO path)
[in]	dim	the linear size of the maps, that is they will be dimxdim in size.
[in]	N	is the number of degrees of freedom. Number of modes will be (N+1)(N+1) - 1.

Template Parameters

realT the real numeric type for calculations

Definition at line 32 of file fourierBasis.hpp.

References mx::improc::eigenCube< dataT >::image(), mx::sigproc::makeFourierBasis_Rect(), mx::AO::path::basis::modes(), MX_FOURIER_MODIFIED, mx::improc::eigenCube< dataT >::resize(), and mx::fits::fitsFile< dataT >::write().

◆ makeZernikeBasis()

template<typename realT >

void mx::AO::makeZernikeBasis	(	const std::string &	basisName,
		const std::string &	pupilName,
		int	dim,
		int	N
	)

Make the Zernike basis.

Parameters

[in]	basisName	the name of the basis (not including the mx::AO path)
[in]	dim	the linear size of the maps, that is they will be dimxdim in size.
[in]	N	is the number of degrees of freedom. Number of modes will be (N+1)(N+1) - 1.

Template Parameters

realT the real numeric type for calculations

Definition at line 29 of file zernikeBasis.hpp.

References mx::improc::eigenCube< dataT >::image(), mx::AO::path::basis::modes(), mx::improc::eigenCube< dataT >::planes(), mx::AO::path::pupil::pupilFile(), and mx::improc::eigenCube< dataT >::resize().

◆ modalDMM2cMatrix()

template<typename realT >

void mx::AO::modalDMM2cMatrix ( const std::string & basisName )

Generate the modes-to-commands matrix for a set of modes on the modal DM.

Generates an Identity matrix of the appropriate size.

Parameters

[in] basisName is the name of the modal basis

Template Parameters

realT is the real floating point type in which to do calculations.

Definition at line 502 of file influenceFunctions.hpp.

References mx::AO::path::dm::M2c(), mx::AO::path::basis::modes(), mx::improc::eigenCube< dataT >::planes(), mx::fits::fitsFile< dataT >::read(), and mx::fits::fitsFile< dataT >::write().

◆ modesOnDM()

template<typename realT >

void mx::AO::modesOnDM	(	const std::string &	dmName,
		const std::string &	basisName
	)

Calculate the basis set as it will be reproduced by the DM.

The projected modes are written to the path specified by mx::AO::path::dm::projectedModes().

Parameters

[in]	dmName	is the name of the DM.
[in]	basisName	is the name of the basis.

Template Parameters

realT is the real floating point type in which to do calculations.

Definition at line 540 of file influenceFunctions.hpp.

References mx::improc::eigenCube< dataT >::cols(), mx::improc::eigenCube< dataT >::image(), mx::AO::path::dm::influenceFunctions(), mx::AO::path::dm::M2c(), mx::AO::path::dm::projectedModes(), mx::fits::fitsFile< dataT >::read(), mx::improc::eigenCube< dataT >::resize(), mx::improc::eigenCube< dataT >::rows(), mx::improc::eigenCube< dataT >::setZero(), and mx::fits::fitsFile< dataT >::write().

◆ normalizeSpectrum()

template<typename spectRealT , typename realT >

void mx::AO::normalizeSpectrum	(	mx::improc::eigenImage< spectRealT > &	spectrum,
		mx::improc::eigenCube< realT > &	modes,
		mx::improc::eigenCube< realT > &	ortho,
		mx::improc::eigenImage< realT > &	pupil
	)

Definition at line 202 of file basis.hpp.

References mx::improc::eigenCube< dataT >::image(), mx::math::six_fifths(), and mx::math::vectorMedianInPlace().

◆ orthogonalizeBasis() [1/2]

template<typename realT >

void mx::AO::orthogonalizeBasis	(	const std::string &	orthoName,
		const std::string &	basisName,
		const std::string &	pupilName,
		int	method
	)

Calculate an orthogonal projection of a basis on a pupil.

Can use either the stabilized Gramm Schmidt (SGS) procedure, or Singular Value Decomposition (SVD). This calls applyPupil2Basis as a first step..

Parameters

[in]	basisName	the name of the basis to orthogonalize
[in]	pupilName	the name of the pupil on which to orthogonalize.
[in]	method	either MXAO_ORTHO_METHOD_SGS (for SGS) or MXAO_ORTHO_METHOD_SVD (for SVD)

Template Parameters

realT

Definition at line 143 of file basis.hpp.

References applyPupil2Basis(), mx::improc::eigenCube< dataT >::image(), mx::AO::path::basis::modes(), orthogonalizeBasis(), mx::improc::eigenCube< dataT >::planes(), mx::AO::path::pupil::pupilFile(), mx::math::six_fifths(), and mx::AO::path::basis::spectrum().

◆ orthogonalizeBasis() [2/2]

template<typename realT , typename spectRealT >

int mx::AO::orthogonalizeBasis	(	eigenCube< realT > &	ortho,
		Eigen::Array< spectRealT, -1, -1 > &	spect,
		eigenCube< realT > &	modes,
		int	method,
		realT	psum = `1.0`
	)

Definition at line 89 of file basis.hpp.

References mx::improc::eigenCube< dataT >::cols(), mx::improc::eigenCube< dataT >::data(), mx::math::eigenGESDD(), mx::improc::eigenCube< dataT >::planes(), mx::improc::eigenCube< dataT >::resize(), mx::improc::eigenCube< dataT >::rows(), and mx::math::six_fifths().

Referenced by orthogonalizeBasis(), and subtractBasis().

◆ slaveBasis()

template<typename realT >

int mx::AO::slaveBasis	(	const std::string &	outputBasisN,
		const std::string &	inputBasisN,
		const std::string &	pupilN,
		const std::string &	dmN,
		realT	fwhm,
		realT	fsmooth,
		int	firstMode = `0`
	)

Definition at line 266 of file basis.hpp.

References mx::improc::cutPaddedImage(), mx::improc::filterImage(), mx::AO::path::dm::influenceFunctions(), mx::AO::path::basis::modes(), mx::improc::padImage(), mx::AO::path::pupil::pupilFile(), mx::improc::eigenCube< dataT >::resize(), mx::improc::eigenCube< dataT >::rows(), and mx::math::six_fifths().

◆ subtractBasis()

template<typename realT >

int mx::AO::subtractBasis	(	const std::string &	basisName,
		const std::string &	basisName1,
		const std::string &	basisName2,
		const std::string &	pupilName,
		int	method
	)

Definition at line 412 of file basis.hpp.

References mx::improc::eigenCube< dataT >::cols(), mx::improc::cutPaddedImage(), mx::improc::filterImage(), mx::improc::eigenCube< dataT >::image(), mx::AO::path::basis::modes(), orthogonalizeBasis(), mx::improc::padImage(), mx::AO::path::pupil::pupilFile(), mx::improc::eigenCube< dataT >::rows(), and mx::math::six_fifths().

Namespaces

Classes

Functions

Function Documentation

◆ apodizeBasis()

◆ applyPupil2Basis()

◆ circularApodizedPupil()

◆ circularPupil()

◆ ifPInv()

◆ influenceFunctionsGaussian()

◆ m2cMatrix() [1/2]

◆ m2cMatrix() [2/2]

◆ makeModfBasis()

◆ makeZernikeBasis()

◆ modalDMM2cMatrix()

◆ modesOnDM()

◆ normalizeSpectrum()

◆ orthogonalizeBasis() [1/2]

◆ orthogonalizeBasis() [2/2]

◆ slaveBasis()

◆ subtractBasis()