FiberModel Class Reference

Public Types

• typedef Cheby2D_7< double, double > FiberModelPattern
• typedef FiberModelPattern::TPar TPar
• typedef Poly1D< double, double, 7 > FiberThroughput
• typedef FiberThroughput::TPar FiberThroughputPars

Public Member Functions

• FiberModel ()
• FiberModel (const bool fixed_h2, const bool fixed_h3)
• FiberModel (const std::string &filename)
• FiberModel (const FiberModel &other)
• virtual ~FiberModel ()
• void init_from_file (const std::string &filename)
• std::vector< FiberThroughputPars > get_amplitudes () const

  returns an array of amplitudes, index is fiber number
  

• void set_amplitudes (const std::vector< FiberThroughputPars > &amplitudes)

  returns the amplitude of fiber number i
  

• void set_h2 (const FiberModel &other)
• void set_h3 (const FiberModel &other)
• void set_sigma (const FiberModel &other)
• void set_sigma_mult (double multiplier)

  multiply sigma by a multiplication factor
  

• void fit_sigma (MArray< double, 1 > &x, MArray< double, 1 > &y, MArray< double, 1 > &sigma, MArray< double, 1 > &sigma_errors)

  fit sigma and h2 parameters over the whole chip
  

• void fit_h2 (MArray< double, 1 > &x, MArray< double, 1 > &y, MArray< double, 1 > &h2, MArray< double, 1 > &h2_errors)
• void fit_h3 (MArray< double, 1 > &x, MArray< double, 1 > &y, MArray< double, 1 > &h3, MArray< double, 1 > &h3_errors)
• void print_amplitude_coefficients () const

  prettily print the model coefficients
  

• void print_sigma_coefficients () const
• void print_h2_coefficients () const
• void print_h3_coefficients () const
• float get_single_fiberflux (const int x, const int y, const Distortion &D) const

  get amplitudes of fibers, index by fibernumber
  

• float get_single_fiberflux (const double x, const double y, const Distortion &D) const

  return the model flux of the nearest fiber for a position x,y on the chip
  

• float get_single_fiberflux (const double x, const double y, const int fiber, const Distortion &D) const

  return the model flux of a particular fiber for a position x,y on the chip
  

• float get_single_fiberprofile (const int x, const int y, const Distortion &D) const

  return the profile of the nearest fiber normalized to one at the center of the fiber, for a pixel x,y on the chip
  

• float get_single_fiberprofile (const double x, const double y, const Distortion &D) const

  return the profile of the nearest fiber normalized to one at the center of the fiber, for a position x,y on the chip
  

• float get_single_fiberprofile (const int x, const int y, const int fiber, const Distortion &D) const

  return the profile of a fiber normalized to one at the center of the fiber, for a position x,y on the chip
  

• float get_single_fiberprofile (const double x, const double y, const int fiber, const Distortion &D) const

  return the profile of a fiber normalized to one at the center of the fiber, for a position x,y on the chip
  

• float get_cumulative_fiberflux (const int x, const int y, const Distortion &D) const

  return the model flux of all 3 adjacent fibers, for a pixel x,y on the chip
  

• float get_cumulative_fiberflux (const double x, const double y, const Distortion &D) const

  return the model flux of all 3 adjacent fibers, for a position x,y on the chip
  

• float get_xy_amplitude (const float x, const float y, const Distortion &D) const

  get fiber attributes
  

• float get_wf_amplitude (const float w, const int f) const
• float get_fiducial_amplitude (const float w) const
• float get_xy_sigma (const float x, const float y) const
• float get_xy_h2 (const float x, const float y) const
• float get_xy_h3 (const float x, const float y) const
• MArray< float, 2 > flat_from_data (const MArray< float, 2 > &A, const Distortion &D, const int length) const

  create a flat field image from science frame with sky signal. normalized to the fiber model amplitudes
  

• MArray< float, 2 > flat_from_model (const int lx, const int ly, const Distortion &D) const

  create a flat field image from the fiber model
  

• MArray< float, 2 > single_fiber_flat (const int lx, const int ly, const int fiber, const Distortion &D) const

  create a flat field image which contains only a single fiber
  

• MArray< float, 2 > pixelflat (const MArray< float, 2 > &Flat, const Distortion &D) const

  create a pixel-flat by dividing twilight flat by model flat
  

• float interpolate_at_xy (const MArray< float, 2 > &I, const float x, const float y) const

Static Public Attributes

• static string version = "$Id: fibermodel.cpp 1079 2015-11-02 16:11:19Z snigula $"

Protected Member Functions

• int get_fit_parameters (const double x, const double y, const Distortion &D, double *Amp, double *H2, double *H3, double *y0, double *s) const

Protected Attributes

• FiberModelPattern F_

  instance of function
  

• std::vector< FiberThroughputPars > amplitudes_
• TPar sigma_par_

  Parameters of the fit of the variation of sigma over the chip.
  

• TPar sigma_errors_

  Errors of the fit of the variation of sigma over the chip.
  

• TPar h2_par_

  Parameters of the fit of the variation of h2 over the chip.
  

• TPar h2_errors_

  Errors of the fit of the variation of h2 over the chip.
  

• TPar h3_par_

  Parameters of the fit of the variation of h3 over the chip.
  

• TPar h3_errors_

  Errors of the fit of the variation of h3 over the chip.
  

• double sigma_mult_
• int fit_niter_
• int fiducial_fib_

Friends

• std::ostream & operator<< (std::ostream &os, const FiberModel &d)
• std::istream & operator>> (std::istream &is, FiberModel &d)

---

Detailed Description

this class encapsulates all the knowledge about the fiber model pattern of the VIRUS spectrograph.

The form of the spectrum from each fiber is described by a gaussian with second and third hermite polynomials. The variation of fibermodel parameters sigma, h2 and h3 over the chip area are fitted with 7th order Chebychev polynoms.

The amplitudes are fitted for each fiber individually. First the amplitdude profile of the fiducial fiber is fitted with a one dimensional 7th order polynomial. The measured amplitudes of the remaining fibers are divided by the amplitude of the fiducial fiber and the remaining variation again individually fitted with a 7th order polynomial.

Together with Distortion and PsfModel, this forms a complete model of the VIRUS spectrograph.

---

Member Typedef Documentation

typedef Cheby2D_7<double,double> FiberModel::FiberModelPattern

typedef FiberModelPattern::TPar FiberModel::TPar

typedef Poly1D<double, double,7> FiberModel::FiberThroughput

typedef FiberThroughput::TPar FiberModel::FiberThroughputPars

---

Constructor & Destructor Documentation

FiberModel::FiberModel

(

)

References fiducial_fib_, FIDUCIAL_FIBER, fit_niter_, h2_errors_, h2_par_, H2_PARAM, h3_errors_, h3_par_, H3_PARAM, sigma_errors_, sigma_mult_, and sigma_par_.

FiberModel::FiberModel	(	const bool	fixed_h2,
		const bool	fixed_h3
	)

FiberModel::FiberModel

(

const std::string &

filename

)

References init_from_file().

FiberModel::FiberModel

(

const FiberModel &

other

)

References amplitudes_, F_, fiducial_fib_, fit_niter_, h2_errors_, h2_par_, h3_errors_, h3_par_, sigma_errors_, sigma_mult_, and sigma_par_.

virtual FiberModel::~FiberModel

(

)

[inline, virtual]

---

Member Function Documentation

void FiberModel::init_from_file

(

const std::string &

filename

)

References fit_niter_, and sigma_mult_.

Referenced by FiberModel(), main(), plot_data(), VFrame::read_fibermodels(), and refit_models().

std::vector<FiberThroughputPars> FiberModel::get_amplitudes

(

)

const [inline]

References amplitudes_.

void FiberModel::set_amplitudes

(

const std::vector< FiberThroughputPars > &

amplitudes

)

sets the amplitudes of the fibers

References amplitudes_.

Referenced by fit_initial_dist(), main(), and refit_models().

void FiberModel::set_h2

(

const FiberModel &

other

)

References h2_errors_, and h2_par_.

Referenced by main(), and refit_models().

void FiberModel::set_h3

(

const FiberModel &

other

)

References h3_errors_, and h3_par_.

Referenced by main(), and refit_models().

void FiberModel::set_sigma

(

const FiberModel &

other

)

References sigma_errors_, and sigma_par_.

Referenced by main(), and refit_models().

void FiberModel::set_sigma_mult

(

double

multiplier

)

References sigma_mult_.

void FiberModel::fit_sigma	(	MArray< double, 1 > &	x,
		MArray< double, 1 > &	y,
		MArray< double, 1 > &	sigma,
		MArray< double, 1 > &	sigma_errors
	)

References _scalx_, _scaly_, BivariateLinearLsqFit< T, Function >::fit(), fit_niter_, sigma_errors_, and sigma_par_.

Referenced by fit_fibermodel().

void FiberModel::fit_h2	(	MArray< double, 1 > &	x,
		MArray< double, 1 > &	y,
		MArray< double, 1 > &	h2,
		MArray< double, 1 > &	h2_errors
	)

References _scalx_, _scaly_, BivariateLinearLsqFit< T, Function >::fit(), fit_niter_, h2_errors_, and h2_par_.

Referenced by fit_fibermodel().

void FiberModel::fit_h3	(	MArray< double, 1 > &	x,
		MArray< double, 1 > &	y,
		MArray< double, 1 > &	h3,
		MArray< double, 1 > &	h3_errors
	)

References _scalx_, _scaly_, BivariateLinearLsqFit< T, Function >::fit(), fit_niter_, h3_errors_, and h3_par_.

Referenced by fit_fibermodel().

void FiberModel::print_amplitude_coefficients

(

)

const

References amplitudes_, and Poly1D< T, Tpar, N >::prettyPrint().

void FiberModel::print_sigma_coefficients

(

)

const

References Cheby2D_7< double, double >::prettyPrint(), and sigma_par_.

Referenced by fit_fibermodel().

void FiberModel::print_h2_coefficients

(

)

const

References h2_par_, and Cheby2D_7< double, double >::prettyPrint().

Referenced by fit_fibermodel().

void FiberModel::print_h3_coefficients

(

)

const

References h3_par_, and Cheby2D_7< double, double >::prettyPrint().

Referenced by fit_fibermodel().

float FiberModel::get_single_fiberflux	(	const int	x,
		const int	y,
		const Distortion &	D
	)			const

return the model flux of the nearest fiber, for a pixel x,y on the chip

return the flux of the nearest fiber, for a pixel x,y on the chip

Referenced by SourceSimulator::add_continuum_source_to_images(), SourceSimulator::add_sersic_source_to_images(), get_cumulative_fiberflux(), main(), PointSourceDetector::make_image(), single_fiber_flat(), and FiberIterator::single_fiberflux().

float FiberModel::get_single_fiberflux	(	const double	x,
		const double	y,
		const Distortion &	D
	)			const

return the flux of the nearest fiber, for a position x,y on the chip

References get_fit_parameters(), MAX_FIBER_DIST, and sigma_mult_.

float FiberModel::get_single_fiberflux	(	const double	x,
		const double	y,
		const int	fiber,
		const Distortion &	D
	)			const

return the flux of a given fiber, for a position x,y on the chip

References get_fit_parameters(), Distortion::get_reference_f(), Distortion::map_xf_y(), MAX_FIBER_DIST, and sigma_mult_.

float FiberModel::get_single_fiberprofile	(	const int	x,
		const int	y,
		const Distortion &	D
	)			const

Referenced by ProfExtractor::extract_profile_fit(), Continuum::get_continua(), get_single_fiberprofile(), and Continuum::subtract_continuum().

float FiberModel::get_single_fiberprofile	(	const double	x,
		const double	y,
		const Distortion &	D
	)			const

References get_fit_parameters(), MAX_FIBER_DIST, and sigma_mult_.

float FiberModel::get_single_fiberprofile	(	const int	x,
		const int	y,
		const int	fiber,
		const Distortion &	D
	)			const

return the profile of a fiber normalized to one at the center of the fiber, for a pixel x,y on the chip

References get_single_fiberprofile().

float FiberModel::get_single_fiberprofile	(	const double	x,
		const double	y,
		const int	fiber,
		const Distortion &	D
	)			const

References get_fit_parameters(), Distortion::get_reference_f(), Distortion::map_xf_y(), MAX_FIBER_DIST, and sigma_mult_.

float FiberModel::get_cumulative_fiberflux	(	const int	x,
		const int	y,
		const Distortion &	D
	)			const

return the flux of all 3 adjacent fibers, for a pixel x,y on the chip

Referenced by SourceSimulator::addSkyToFrame(), FiberIterator::cumulative_flux(), flat_from_model(), main(), mask_cosmics(), pixelflat(), and refit_models().

float FiberModel::get_cumulative_fiberflux	(	const double	x,
		const double	y,
		const Distortion &	D
	)			const

return the flux of all 3 adjacent fibers, for a position x,y on the chip

References Distortion::get_numfibers(), get_single_fiberflux(), and Distortion::map_xy_fibernum().

float FiberModel::get_xy_amplitude	(	const float	x,
		const float	y,
		const Distortion &	D
	)			const

References get_wf_amplitude(), Distortion::map_xy_fibernum(), and Distortion::map_xy_wavelength().

Referenced by flat_from_data(), get_fit_parameters(), and Measure::remove_spectra().

float FiberModel::get_wf_amplitude	(	const float	w,
		const int	f
	)			const

References _scalw_, and amplitudes_.

Referenced by get_xy_amplitude(), main(), plot_fibermodel(), and Measure::scale_fiberthroughput().

float FiberModel::get_fiducial_amplitude

(

const float

w

)

const

References _scalw_, amplitudes_, and FIDUCIAL_FIBER.

float FiberModel::get_xy_sigma	(	const float	x,
		const float	y
	)			const

References _scalx_, _scaly_, F_, and sigma_par_.

Referenced by fit_fibermodel(), Measure::fit_peaks3H_initial(), Measure::fit_psf1D(), get_fit_parameters(), main(), and plot_fibermodel().

float FiberModel::get_xy_h2	(	const float	x,
		const float	y
	)			const

References _scalx_, _scaly_, F_, and h2_par_.

Referenced by fit_fibermodel(), Measure::fit_peaks3H_initial(), Measure::fit_psf1D(), get_fit_parameters(), main(), and plot_fibermodel().

float FiberModel::get_xy_h3	(	const float	x,
		const float	y
	)			const

References _scalx_, _scaly_, F_, and h3_par_.

Referenced by fit_fibermodel(), Measure::fit_peaks3H_initial(), Measure::fit_psf1D(), get_fit_parameters(), and plot_fibermodel().

MArray< float, 2 > FiberModel::flat_from_data	(	const MArray< float, 2 > &	A,
		const Distortion &	D,
		const int	length
	)			const

create a flat field from science frame with sky signal

References clamp_window(), Distortion::get_reference_f(), get_xy_amplitude(), interpolate_at_xy(), Distortion::map_xf_y(), Distortion::map_xy_fibernum(), Resampler< Interpolator, Transform >::resample_xf_xy(), and Resampler< Interpolator, Transform >::resample_xy_xf().

Referenced by main(), and SuperSky::SuperSky().

MArray< float, 2 > FiberModel::flat_from_model	(	const int	lx,
		const int	ly,
		const Distortion &	D
	)			const

References get_cumulative_fiberflux().

Referenced by main(), and SuperSky::SuperSky().

MArray< float, 2 > FiberModel::single_fiber_flat	(	const int	lx,
		const int	ly,
		const int	fiber,
		const Distortion &	D
	)			const

References get_single_fiberflux().

Referenced by Extractor::extract_core_ac(), Extractor::extract_core_x_ac(), and main().

MArray< float, 2 > FiberModel::pixelflat	(	const MArray< float, 2 > &	Flat,
		const Distortion &	D
	)			const

References get_cumulative_fiberflux(), Distortion::get_reference_f(), interpolate_at_xy(), Distortion::map_xf_y(), and Distortion::map_xy_fibernum().

Referenced by main().

float FiberModel::interpolate_at_xy	(	const MArray< float, 2 > &	I,
		const float	x,
		const float	y
	)			const

interpolate an image at fractional coordinates x,y

References BiCubicInterpolator::interpolate().

Referenced by flat_from_data(), main(), and pixelflat().

int FiberModel::get_fit_parameters	(	const double	x,
		const double	y,
		const Distortion &	D,
		double *	Amp,
		double *	H2,
		double *	H3,
		double *	y0,
		double *	s
	)			const [protected]

References Distortion::get_reference_f(), get_xy_amplitude(), get_xy_h2(), get_xy_h3(), get_xy_sigma(), Distortion::map_xf_y(), and Distortion::map_xy_fibernum().

Referenced by get_single_fiberflux(), and get_single_fiberprofile().

---

Friends And Related Function Documentation

std::ostream& operator<<	(	std::ostream &	os,
		const FiberModel &	d
	)			[friend]

std::istream& operator>>	(	std::istream &	is,
		FiberModel &	d
	)			[friend]

---

Field Documentation

string FiberModel::version = "$Id: fibermodel.cpp 1079 2015-11-02 16:11:19Z snigula $" [static]

Referenced by copy_org_models(), fit_initial_dist(), main(), and refit_models().

FiberModelPattern FiberModel::F_ [protected]

Referenced by FiberModel(), get_xy_h2(), get_xy_h3(), and get_xy_sigma().

std::vector<FiberThroughputPars> FiberModel::amplitudes_ [protected]

Fit of the amplitudes relative to the fiducial fiber see full description above

Referenced by FiberModel(), get_amplitudes(), get_fiducial_amplitude(), get_wf_amplitude(), operator<<(), operator>>(), print_amplitude_coefficients(), and set_amplitudes().

TPar FiberModel::sigma_par_ [protected]

Referenced by FiberModel(), fit_sigma(), get_xy_sigma(), operator<<(), operator>>(), print_sigma_coefficients(), and set_sigma().

TPar FiberModel::sigma_errors_ [protected]

Referenced by FiberModel(), fit_sigma(), operator<<(), operator>>(), and set_sigma().

TPar FiberModel::h2_par_ [protected]

Referenced by FiberModel(), fit_h2(), get_xy_h2(), operator<<(), operator>>(), print_h2_coefficients(), and set_h2().

TPar FiberModel::h2_errors_ [protected]

Referenced by FiberModel(), fit_h2(), operator<<(), operator>>(), and set_h2().

TPar FiberModel::h3_par_ [protected]

Referenced by FiberModel(), fit_h3(), get_xy_h3(), operator<<(), operator>>(), print_h3_coefficients(), and set_h3().

TPar FiberModel::h3_errors_ [protected]

Referenced by FiberModel(), fit_h3(), operator<<(), operator>>(), and set_h3().

double FiberModel::sigma_mult_ [protected]

Multiplicative factor applied to sigma when deriving the fiberflux. usually only by simfmod to simulate different optics / fiberbundles. Defaults to 1.

Referenced by FiberModel(), get_single_fiberflux(), get_single_fiberprofile(), init_from_file(), and set_sigma_mult().

int FiberModel::fit_niter_ [protected]

Number of iterations to do when fitting variation of the fibermodel parameters currently not used and defaults to 1.

Referenced by FiberModel(), fit_h2(), fit_h3(), fit_sigma(), and init_from_file().

int FiberModel::fiducial_fib_ [protected]

Fiducial fiber used for fitting the amplitudes, see full description above default defined in specconf.h

Referenced by FiberModel(), operator<<(), and operator>>().