Measure Class Reference

Public Types

• typedef gauss1D_H< float > FiberProfile
• typedef FiberModel::FiberThroughput FiberThroughput
• typedef FiberThroughput::TPar FiberThroughputPars

Public Member Functions

• Measure (FiberModel &F, float min_slope=0.02, float peak_offset=8., float select_chi=100., float fit_radius=4., int iter=50, float accuracy=1.e-4, int verbose=1, float peak_cutoff=0.1, int fid=FIDUCIAL_FIBER)
• MArray< float, 1 > search (int search_x, const MArray< float, 2 > &Data, const MArray< float, 2 > &Data_error)
• MArray< DistDataTuple, 2 > trace (const MArray< float, 2 > &Data, const MArray< float, 2 > &Data_error, int x, int start, int stop, const MArray< float, 1 > &peakpos)
• MArray< DistDataTuple, 2 > correlate (const MArray< float, 2 > &Data, const MArray< float, 2 > &Data_error, const MArray< DistDataTuple, 2 > &Peaks, const MArray< float, 1 > &fvalue, ArcLineList arcLineList, ltl::FVector< double, 7 > startpar)
• MArray< float, 2 > remove_spectra_ind (const MArray< float, 2 > &Data, const Distortion &D)
• MArray< float, 2 > remove_spectra (const MArray< float, 2 > &Data, const Distortion &D)
• MArray< float, 2 > remove_spectra (const MArray< float, 2 > &Data, const Distortion &D, const FiberModel &F)
• MArray< FiberDataTuple, 2 > measure_fiberpars (const MArray< float, 2 > Data, const Distortion &D, const bool rect_to_wf, const MArray< float, 2 > &sigma_guess, int start, int end, int step, int length, bool fix_h2=false, bool fix_h3=false)
• MArray< float, 1 > measure_at_ref_w (const MArray< float, 2 > &Data, const Distortion &D, const bool rect_to_wf, const MArray< float, 2 > &sigma_guess, const int length, bool fix_h2=false, bool fix_h3=false)
• std::vector
  < Measure::FiberThroughputPars > fit_fiberthroughput (MArray< FiberDataTuple, 2 > &FiberPars, const Distortion &D)
• std::vector
  < Measure::FiberThroughputPars > scale_fiberthroughput (MArray< FiberDataTuple, 2 > &FiberPars, const MArray< float, 1 > &flx5577, const FiberModel &Fold, const Distortion &D, const bool use_5577)
• MArray< float, 2 > rectify_to_xf (const MArray< float, 2 > &A, const Distortion &D) const
• MArray< float, 2 > rectify_to_wf (const MArray< float, 2 > &A, const Distortion &D, float &minw, float &maxw) const
• list< PsfDataTuple > fit_psf1D (const MArray< float, 2 > &I, const MArray< float, 2 > &I_e, const MArray< DistDataTuple, 2 > &ArcPeaks, const Distortion &D, const FiberModel &F, const float kappa)
• list< PsfDataTuple > fit_psf2D (const MArray< float, 2 > &I, const MArray< float, 2 > &I_e, const MArray< DistDataTuple, 2 > &ArcPeaks, const Distortion &D, const float kappa)

Static Public Attributes

• static string version = "$Id: measure.cpp 1032 2015-07-10 18:35:34Z drory $"

Protected Member Functions

• void trace_outwards (const MArray< float, 2 > &Data, const MArray< float, 2 > &Data_error, int start, int stop, const MArray< float, 1 > &peakpos, MArray< DistDataTuple, 2 > &Peaks)
• float interpolate_at_xy (const MArray< float, 2 > &I, const float x, const float y) const
• UnsortFiberData fit_peaks3H_initial (const MArray< float, 1 > &Fguess, const MArray< float, 1 > &x, const MArray< float, 1 > &Data, const MArray< float, 1 > &sigma_guess, const Distortion &D, const float minw, const float dw, const bool wf)

  Fit gaussian hermite polynoms to the fibers of a x column on the chip.
  

• UnsortFiberData fit_peaks3H_final (const UnsortFiberData &initial_fiberdata, const MArray< float, 1 > &Fguess, const MArray< float, 1 > &x, const MArray< float, 1 > &Data, const MArray< float, 1 > &sigma_guess, const Distortion &D, const float minw, const float dw, const bool wf)

  Measure final fiber parameters on a rectified image slice based on the results of fit_peaks3h_initial.
  

• UnsortFiberData fit_peaks3H (const MArray< float, 1 > &Fguess, const float x, const MArray< float, 1 > &Data, const MArray< float, 1 > &Data_err)

  Fit gaussian hermite polynoms to the fibers of a x column on the chip.
  

• float sum2gaussH (float x, const ltl::FVector< float, 10 > &C)

  Subtract the nearest four fibers using model parameters from a column window,.
  

• void fit_gauss2D (const MArray< float, 2 > &Data, const MArray< float, 2 > &Data_error, ltl::FVector< double, 7 > &parameter, ltl::FVector< double, 7 > &errors, double &chi2, const bool norm=false)
• int get_fittype (const MArray< float, 1 > &Fguess, int i)
• template<class Fct , typename TPar , int N> void fit_fiber (ltl::FVector< TPar, N > &P, ltl::FVector< TPar, N > &dP, TPar &chi2, const MArray< TPar, 1 > X, float x, float y, const MArray< TPar, 1 > &A, const MArray< TPar, 1 > &dA, ltl::FVector< bool, N > &ignore, int iter, double tol, int yidx, double ytol, Fct F)
• float integrate_fiber_profile (const MArray< float, 2 > &I, float x, float y, float aperture, int nf)
• void filter_peaks (list< PsfDataTuple > &l, const Distortion &D, const float kappa)

Protected Attributes

• FiberModel F_

  instance of FiberModel
  

• int fiducial_fib_

  number of fiducial fiber
  

• float min_slope_

  minimum normalized slope in normalized flux to be recognized as a fiber
  

• float peak_offset_

  minimum offset of peaks in trace file
  

• float select_chi_

  maximum chi value of a gaussian to be selected as a peak
  

• float fit_radius_

  size of fit window for gaussian fitting in pixel
  

• int iter_

  Number of iterations for fitting.
  

• float accuracy_

  accuracy for fitting
  

• bool fix_h2_

  Fix h2 in fiber profile fitting.
  

• bool fix_h3_

  Fix h3 in fiber profile fitting.
  

• int verbose_

  Control verbosity of output: 0 shut up, 1 normal, 2 chatty.
  

• float peak_cutoff_

---

Detailed Description

Helper class to Distortion, FiberModel, and PsfModel. This class locates the fibers and the arc lamp line images on a flat field and an arc lamp frame. Trace the fibers, measure the arc lines, and provide and fit fitting functions to the fiber profiles and the shapes of the arc lamp images.

---

Member Typedef Documentation

typedef gauss1D_H<float> Measure::FiberProfile

typedef FiberModel::FiberThroughput Measure::FiberThroughput

typedef FiberThroughput::TPar Measure::FiberThroughputPars

---

Constructor & Destructor Documentation

Measure::Measure	(	FiberModel &	F,
		float	min_slope = 0.02,
		float	peak_offset = 8.,
		float	select_chi = 100.,
		float	fit_radius = 4.,
		int	iter = 50,
		float	accuracy = 1.e-4,
		int	verbose = 1,
		float	peak_cutoff = 0.1,
		int	fid = FIDUCIAL_FIBER
	)

References accuracy_, F_, fiducial_fib_, fit_radius_, fix_h2_, fix_h3_, iter_, min_slope_, peak_cutoff_, peak_offset_, select_chi_, and verbose_.

---

Member Function Documentation

MArray< float, 1 > Measure::search	(	int	search_x,
		const MArray< float, 2 > &	Data,
		const MArray< float, 2 > &	Data_error
	)

Look for peaks in a given Data array with peak_offset_ and a slope of at least min_slope_ returns counter number of Peaks

Look for peaks in a given Data array with peak_offset_ and a slope of at least min_slope_ returns counter number of Peaks

Parameters:

	search_x	int column to use to search the peaks
	Data	ltl::MArray() array in which the peaks are searched
	Data_error	ltl::MArray() error array

and work your way down.

References index_of_max(), min_slope_, peak_cutoff_, peak_offset_, SEARCHBORDER, and verbose_.

Referenced by fit_initial_dist(), main(), VirusHealth::validate_min_flux(), and VirusHealth::validate_n_fibers().

MArray< DistDataTuple, 2 > Measure::trace	(	const MArray< float, 2 > &	Data,
		const MArray< float, 2 > &	Data_error,
		int	x,
		int	start,
		int	stop,
		const MArray< float, 1 > &	peakpos
	)

Trace peaks from start to stop going from x to start and x to stop using guess_y as start y position return peaks in TracePeaks

References trace_outwards().

Referenced by fit_initial_dist(), and main().

MArray< DistDataTuple, 2 > Measure::correlate	(	const MArray< float, 2 > &	Data,
		const MArray< float, 2 > &	Data_error,
		const MArray< DistDataTuple, 2 > &	Peaks,
		const MArray< float, 1 > &	fvalue,
		ArcLineList	arcLineList,
		ltl::FVector< double, 7 >	startpar
	)

Correlate position of (trace) Peaks with lines given in configuration file to find arc peak positions in Data file at that position.

References fit_gauss2D(), fit_radius_, ArcLineList::getActivePXpos(), ArcLineList::getActiveWL(), and ArcLineList::getNumActiveLines().

Referenced by fit_initial_dist(), and main().

MArray< float, 2 > Measure::remove_spectra_ind	(	const MArray< float, 2 > &	A,
		const Distortion &	D
	)

Prepare a data frame for processing by measure_fiberpars(). The spectra in the frame are normalized to the interpolated data at the center of each fiber (eliminating any spectral features in the data).

References Distortion::get_reference_f(), interpolate_at_xy(), Distortion::map_wf_x(), Distortion::map_xf_y(), Distortion::map_xy_fibernum(), Distortion::map_xy_wavelength(), maxx(), maxy(), minx(), and miny().

MArray< float, 2 > Measure::remove_spectra	(	const MArray< float, 2 > &	A,
		const Distortion &	D
	)

Prepare a data frame for processing by measure_fiberpars(). The spectra in the frame are normalized to the interpolated data at the center of the fiducial fiber (eliminating any spectral features in the data).

References fiducial_fib_, Distortion::get_reference_f(), integrate_fiber_profile(), Distortion::map_wf_x(), Distortion::map_wf_y(), and Distortion::map_xy_wavelength().

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

MArray< float, 2 > Measure::remove_spectra	(	const MArray< float, 2 > &	A,
		const Distortion &	D,
		const FiberModel &	F
	)

Prepare a data frame for processing by measure_fiberpars(). The spectra in the frame are normalized to the center each fiber using the fiber model (eliminating any spectral features in the data), then normalized to the amplitudes of the FiberModel object.

References Distortion::get_reference_f(), FiberModel::get_xy_amplitude(), integrate_fiber_profile(), Distortion::map_xf_y(), and Distortion::map_xy_fibernum().

MArray< FiberDataTuple, 2 > Measure::measure_fiberpars	(	const MArray< float, 2 >	Data,
		const Distortion &	D,
		const bool	rect_to_wf,
		const MArray< float, 2 > &	sigma_guess,
		int	start,
		int	end,
		int	step,
		int	length,
		bool	fix_h2 = false,
		bool	fix_h3 = false
	)

Measure the fiber profile parameters (using the FiberModel in this class) by fitting it to every fiber and from x-position start to end with step-size step on Data file. The data are assumed to be resampled into x-f space.

References UnsortFiberData::Amplitude, c, clamp_window(), UnsortFiberData::Error, fit_peaks3H_final(), fit_peaks3H_initial(), fix_h2_, fix_h3_, Distortion::get_numfibers(), Distortion::get_reference_f(), UnsortFiberData::H2, UnsortFiberData::H3, Distortion::map_wf_x(), Distortion::map_wf_y(), Distortion::map_xf_y(), Distortion::map_xy_wavelength(), rectify_to_wf(), rectify_to_xf(), UnsortFiberData::Sigma, and UnsortFiberData::Yposition.

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

MArray< float, 1 > Measure::measure_at_ref_w	(	const MArray< float, 2 > &	Data,
		const Distortion &	D,
		const bool	rect_to_wf,
		const MArray< float, 2 > &	sigma_guess,
		const int	length,
		bool	fix_h2 = false,
		bool	fix_h3 = false
	)

Measure the fiber profile parameters (using the FiberModel in this class) by fitting it to every fiber at the reference wavelength only. The data are assumed to be resampled into x-f space.

References c, clamp_window(), fit_peaks3H_final(), fit_peaks3H_initial(), fix_h2_, fix_h3_, Distortion::get_numfibers(), Distortion::get_reference_f(), Distortion::get_reference_wavelength(), Distortion::map_wf_x(), Distortion::map_wf_y(), rectify_to_wf(), and rectify_to_xf().

Referenced by main(), and refit_models().

std::vector< Measure::FiberThroughputPars > Measure::fit_fiberthroughput	(	MArray< FiberDataTuple, 2 > &	FiberPars,
		const Distortion &	D
	)

References _scalw_, a, FIDUCIAL_FIBER, UnivariateLinearLsqFit< T, Function >::fit(), and Distortion::get_numfibers().

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

std::vector< Measure::FiberThroughputPars > Measure::scale_fiberthroughput	(	MArray< FiberDataTuple, 2 > &	FiberPars,
		const MArray< float, 1 > &	flx5577,
		const FiberModel &	Fold,
		const Distortion &	D,
		const bool	use_5577
	)

References _scalw_, a, FIDUCIAL_FIBER, UnivariateLinearLsqFit< T, Function >::fit(), Distortion::get_numfibers(), and FiberModel::get_wf_amplitude().

Referenced by main(), and refit_models().

MArray< float, 2 > Measure::rectify_to_xf	(	const MArray< float, 2 > &	A,
		const Distortion &	D
	)			const

References Resampler< Interpolator, Transform >::resample_xy_xf().

Referenced by measure_at_ref_w(), and measure_fiberpars().

MArray< float, 2 > Measure::rectify_to_wf	(	const MArray< float, 2 > &	A,
		const Distortion &	D,
		float &	minw,
		float &	maxw
	)			const

References Distortion::map_xy_wavelength(), and Resampler< Interpolator, Transform >::resample_wf().

Referenced by measure_at_ref_w(), and measure_fiberpars().

list< PsfDataTuple > Measure::fit_psf1D	(	const MArray< float, 2 > &	I,
		const MArray< float, 2 > &	I_e,
		const MArray< DistDataTuple, 2 > &	ArcPeaks,
		const Distortion &	D,
		const FiberModel &	F,
		const float	kappa
	)

Fit gaussians to arc peaks and return a list of the best-fitting parameters. In this version of fit_psf the PSFs are fitted only in spectral direction. The cross dispersion parameters are taken from the fiber model.

References filter_peaks(), gauss1Dfit(), FiberModel::get_xy_h2(), FiberModel::get_xy_h3(), FiberModel::get_xy_sigma(), interpolate_at_xy(), Distortion::map_wf_x(), Distortion::map_wf_y(), Distortion::map_xf_y(), Distortion::map_xy_fiber(), and Distortion::map_xy_wavelength().

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

list< PsfDataTuple > Measure::fit_psf2D	(	const MArray< float, 2 > &	I,
		const MArray< float, 2 > &	I_e,
		const MArray< DistDataTuple, 2 > &	ArcPeaks,
		const Distortion &	D,
		const float	kappa
	)

Fit gaussians to arc peaks and return a list of the best-fitting parameters. In this version of fit_psf actual bivariate Gaussians are fitted to the PSFs. The Gauss-Hermite moments in PsfDataTuple are zero.

Fit gaussians to arc peaks and return a list of the best-fitting parameters. In this version of fit_psf actual bivariate Gaussians are fitted to the PSFs. The Gauss-Hermite Moments in PsfDataTuple are zero.

References filter_peaks(), fit_gauss2D(), fit_radius_, Distortion::get_position_angle(), Distortion::map_xy_fiber(), and Distortion::map_xy_wavelength().

void Measure::trace_outwards	(	const MArray< float, 2 > &	Data,
		const MArray< float, 2 > &	Data_error,
		int	start,
		int	stop,
		const MArray< float, 1 > &	peakpos,
		MArray< DistDataTuple, 2 > &	Peaks
	)			[protected]

Trace peaks outwards from start to stop return peaks in TracePeaks

References UnsortFiberData::Error, fit_peaks3H(), and UnsortFiberData::Yposition.

Referenced by trace().

float Measure::interpolate_at_xy	(	const MArray< float, 2 > &	I,
		const float	x,
		const float	y
	)			const [protected]

interpolate an image at fractional coordinates x,y

References BiCubicInterpolator::interpolate().

Referenced by fit_psf1D(), integrate_fiber_profile(), and remove_spectra_ind().

UnsortFiberData Measure::fit_peaks3H_initial	(	const MArray< float, 1 > &	Fguess,
		const MArray< float, 1 > &	x,
		const MArray< float, 1 > &	Data,
		const MArray< float, 1 > &	sigma_guess,
		const Distortion &	D,
		const float	minw,
		const float	dw,
		const bool	wf
	)			[protected]

Measure initial fiberparameters on a rectified image slice to be used as initial values for final fit.

References accuracy_, F_, fit_fiber(), fix_h2_, fix_h3_, gauss1D_2H_fit(), gauss1D_3H_fit(), get_fittype(), FiberModel::get_xy_h2(), FiberModel::get_xy_h3(), FiberModel::get_xy_sigma(), iter_, Distortion::map_wf_x(), Distortion::map_wf_y(), Distortion::map_xf_y(), peak_offset_, and verbose_.

Referenced by measure_at_ref_w(), and measure_fiberpars().

UnsortFiberData Measure::fit_peaks3H_final	(	const UnsortFiberData &	initial_fiberdata,
		const MArray< float, 1 > &	Fguess,
		const MArray< float, 1 > &	x,
		const MArray< float, 1 > &	Data,
		const MArray< float, 1 > &	sigma_guess,
		const Distortion &	D,
		const float	minw,
		const float	dw,
		const bool	wf
	)			[protected]

References accuracy_, UnsortFiberData::Amplitude, UnsortFiberData::Error, fit_fiber(), fix_h2_, fix_h3_, gauss1D_H_fit(), get_fittype(), UnsortFiberData::H2, UnsortFiberData::H3, iter_, UnsortFiberData::Sigma, sum2gaussH(), verbose_, and UnsortFiberData::Yposition.

Referenced by measure_at_ref_w(), and measure_fiberpars().

UnsortFiberData Measure::fit_peaks3H	(	const MArray< float, 1 > &	Fguess,
		const float	x,
		const MArray< float, 1 > &	Data,
		const MArray< float, 1 > &	Data_err
	)			[protected]

Fit fiber peaks with gaussians, using blocks of 3 fibers and a sum of 3 gaussians. Inputs are the initial guesses for the Y centroids of the fibers and a column of a trace flat image.

Note that the y values of the fibers are ordered opposite to the data, since we count fiber 1 at the top of the chip and FITS coordinates start at the bottom.

Returns a number-of-fibers x 4 array containing amplitude, centroid, width, goodness flag for each fiber.

References fit_fiber(), gauss1D_2H_fit(), gauss1D_3H_fit(), get_fittype(), and peak_offset_.

Referenced by trace_outwards().

float Measure::sum2gaussH	(	float	x,
		const ltl::FVector< float, 10 > &	C
	)			[protected]

Referenced by fit_peaks3H_final().

void Measure::fit_gauss2D	(	const MArray< float, 2 > &	Data,
		const MArray< float, 2 > &	Data_error,
		ltl::FVector< double, 7 > &	parameter,
		ltl::FVector< double, 7 > &	errors,
		double &	chi2,
		const bool	norm = false
	)			[protected]

References fit_radius_, gauss2Dfit(), and index_of_max().

Referenced by correlate(), and fit_psf2D().

int Measure::get_fittype	(	const MArray< float, 1 > &	Fguess,
		int	i
	)			[protected]

References peak_offset_.

Referenced by fit_peaks3H(), fit_peaks3H_final(), and fit_peaks3H_initial().

template<class Fct , typename TPar , int N>

void Measure::fit_fiber	(	ltl::FVector< TPar, N > &	P,
		ltl::FVector< TPar, N > &	dP,
		TPar &	chi2,
		const MArray< TPar, 1 >	X,
		float	x,
		float	y,
		const MArray< TPar, 1 > &	A,
		const MArray< TPar, 1 > &	dA,
		ltl::FVector< bool, N > &	ignore,
		int	iter,
		double	tol,
		int	yidx,
		double	ytol,
		Fct	F
	)			[inline, protected]

References P, and verbose_.

Referenced by fit_peaks3H(), fit_peaks3H_final(), and fit_peaks3H_initial().

float Measure::integrate_fiber_profile	(	const MArray< float, 2 > &	I,
		float	x,
		float	y,
		float	aperture,
		int	nf
	)			[protected]

References interpolate_at_xy().

Referenced by remove_spectra().

void Measure::filter_peaks	(	list< PsfDataTuple > &	l,
		const Distortion &	D,
		const float	kappa
	)			[protected]

Filter arc peaks: remove peaks with large errors

References a, and b.

Referenced by fit_psf1D(), and fit_psf2D().

---

Field Documentation

string Measure::version = "$Id: measure.cpp 1032 2015-07-10 18:35:34Z drory $" [static]

FiberModel Measure::F_ [protected]

Referenced by fit_peaks3H_initial(), and Measure().

int Measure::fiducial_fib_ [protected]

Referenced by Measure(), and remove_spectra().

float Measure::min_slope_ [protected]

Referenced by Measure(), and search().

float Measure::peak_offset_ [protected]

Referenced by fit_peaks3H(), fit_peaks3H_initial(), get_fittype(), Measure(), and search().

float Measure::select_chi_ [protected]

Referenced by Measure().

float Measure::fit_radius_ [protected]

Referenced by correlate(), fit_gauss2D(), fit_psf2D(), and Measure().

int Measure::iter_ [protected]

Referenced by fit_peaks3H_final(), fit_peaks3H_initial(), and Measure().

float Measure::accuracy_ [protected]

Referenced by fit_peaks3H_final(), fit_peaks3H_initial(), and Measure().

bool Measure::fix_h2_ [protected]

Referenced by fit_peaks3H_final(), fit_peaks3H_initial(), Measure(), measure_at_ref_w(), and measure_fiberpars().

bool Measure::fix_h3_ [protected]

Referenced by fit_peaks3H_final(), fit_peaks3H_initial(), Measure(), measure_at_ref_w(), and measure_fiberpars().

int Measure::verbose_ [protected]

Referenced by fit_fiber(), fit_peaks3H_final(), fit_peaks3H_initial(), Measure(), and search().

float Measure::peak_cutoff_ [protected]

Referenced by Measure(), and search().