fit_lines

pyplatefit.fit_lines(wave, data, std, redshift, *, unit_wave=None, unit_data=None, vac=False, lines=None, line_ratios=None, major_lines=False, fit_all=False, lsf=None, trimm_spec=True, find_lya_vel_offset=True, dble_lyafit=False, mcmc_lya=False, mcmc_all=False, fit_lws=None, minpars={}, mcmcpars={})

Fit lines from a set of arrays (wave, data, std) using lmfit.

This function uses lmfit to perform fit of know lines in a spectrum with a given redshift, to compute the flux and flux uncertainty of each line covered by the spectrum. It must be used on a continuum subtracted spectrum.

The fit are performed by line families, each family is defined by a unique velocity offset and velocity dispersion, plus a list of emission lines. All lines are assumed to be gaussian except for lyman-alpha where an asymetric gaussian model is used.

All the emission lines known by linelist.get_lines are searched for, unless a list of line names or a table of lines is provided with the lines parameter. If trim_spectrum is set to true (default), the fit is done keeping only the parts of the spectrum around the expected lines.

It is possible to add constraints in the ratio of some lines (for instance for doublets). These constraints are given in the line_ratios parameter and are expressed as a list of tuples (line_1 name, line_2 name, line_2 flux / line_1 flux minimum, flux ratio maximum). For instance, to constraint doublet fluxes and discriminate between single lines and doublets in MUSE-UDF, we used:

line_ratios = [(“CIII1907”, “CIII1909”, 0.6, 1.2), (“OII3726”, “OII3729”, 1.0, 2.0)]

That stands for:

0.6 <= OII3729 / OII3726 <= 1.2 1.0 <= CIII1909 / CIII1907 <= 2.0

If the units of the wavelength and data axis are provided, the function will try to determine the unit of the computed fluxes.

The table of the lines found in the spectrum are given in the table lines. The columns are:

  • FAMILY: the line family name (eg balmer)

  • LINE: The name of the line

  • LBDA_REST: The rest-frame position of the line in vacuum

  • DNAME: The display name for the line (set to None for close doublets)

  • VEL: The velocity offset in km/s with respect to the initial redshift (rest frame)

  • VEL_ERR: The error in velocity offset in km/s

  • Z: The fitted redshift in vacuum of the line (note for lyman-alpha the line peak is used)

  • Z_ERR: The error in fitted redshift of the line.

  • Z_INIT: The initial redshift

  • VDISP: The fitted velocity dispersion in km/s (rest frame)

  • VDISP_ERR: The error in fitted velocity dispersion

  • VDINST: The instrumental velocity dispersion in km/s

  • FLUX: Flux in the line. The unit depends on the units of the spectrum.

  • FLUX_ERR: The fitting uncertainty on the flux value.

  • SNR: the SNR of the line

  • SKEW: The skewness parameter of the asymetric line (for Lyman-alpha line only).

  • SKEW_ERR: The uncertainty on the skewness (for Lyman-alpha line only).

  • SEP: The fitted lya rest frame peak separation (in km/s) (for the double lyman-alpha fit only)

  • SEP_ERR: The error in fitted lya rest frame peak separation (in km/s) (for the double lyman-alpha fit only)

  • LBDA_OBS: The fitted position the line peak in the observed frame

  • PEAK_OBS: The fitted peak of the line in the observed frame

  • LBDA_LEFT: The wavelength at the left of the peak with 0.5*peak value

  • LBDA_RIGHT: The wavelength at the rigth of the peak with 0.5*peak value

  • FWHM_OBS: The full width at half maximum of the line in the observed frame

  • NSTD: The log10 of the normalized standard deviation of the line fit

  • LBDA_LNSTD: The wavelength at the left of the range used for NSTD estimation

  • LBDA_RNSTD: The wavelength at the right of the range used for NSTD estimation

  • EQW: The restframe line equivalent width

  • EQW_ERR: The error in EQW

  • CONT_OBS: The continuum mean value in Observed frame

  • CONT: the continuum mean value in rest frame

  • CONT_ERR: the error in rest frame continuum

The redshift table is saved in the table ztable The columns are:

  • FAMILY: the line family name

  • VEL: the velocity offset with respect to the original z in km/s

  • VEL_ERR: the error in velocity offset

  • Z: the fitted redshift (in vacuum)

  • Z_ERR: the error in redshift

  • Z_INIT: The initial redshift

  • VDISP: The fitted velocity dispersion in km/s (rest frame)

  • VDISP_ERR: The error in fitted velocity dispersion

  • LINE: the emission line name with maximum SNR

  • SNRMAX: the maximum SNR

  • SNRSUM: the sum of SNR (all lines)

  • SNRSUM_CLIPPED: the sum of SNR (only lines above a MIN SNR (default 3))

  • NL: number of fitted lines

  • NL_CLIPPED: number of lines with SNR>SNR_MIN

  • NFEV: the number of function evaluation

  • RCHI2: the reduced Chi2 of the family lines fit

Parameters:
wavearray_like of floats

The wavelength axis of the spectrum.

dataarray_like of floats

The data (flux) axis of the spectrum.

stdarray_like of floats

The standard deviation associated to the data. It can be set to None if it’s not available.

redshiftfloat

Expected redshift of the spectrum.

unit_waveastropy.unit.Unit, optional

The unit of the wavelength axis.

unit_dataastropy.unit.Unit, optional

The unit of the data axis.

vacbool, optional

If True, vacuum wavelength are expected; else air wavelength are expected. Default: False.

lineslist of str or astropy.table.Table, optional

To limit the searched for lines, it is possible to use this parameter to pass:

  • a list of line names as in MPDAF line list;

  • or an astropy table with the information on the lines to fit. The table must contain the following columns

    • LINE: the line name

    • FAMILY: the line family (balmer, forbidden, ism)

    • LBDA_REST: the rest frame wavelength in vacuum (Angstroem)

    • DOUBLET: the central wavelength if this is a multiplet (Angstroem)

    • RESONANT: bool, True if the line is resonant

    • ABS: bool, True if the line can be in absorption

    • EMI: bool, True if the line can be in emission

    • DNAME: the line display name (None if no display)

line_ratioslist of (str, str, float, float) tuples or string

List on line ratio constraints (line1 name, line2 name, line2/line1 minimum, line2/line1 maximum.

major_linesbool, optional

If true, the fit is restricted to the major lines as defined in mpdaf line table (used only when lines is None, ) default: False

fit_allbool, optional

if True, use same velocity offset and velocity dispersion for all lines except Lya if False, allow different velocity offsets and velocity disperions between balmer, forbidden and resonnant lines default: false

lsffunction, optional

LSF function LSF to derive FWHM as function of wavelength, otherwise assume no LSF default: True

trimm_specbool, optional

if True, mask unused wavelengths part default : True

find_lya_vel_offset: boolean, optional

if True, compute a starting velocity offset for lya on the data [disabled for dble_lyafit]

dble_lyafitFalse

if True, use a double asymetric gaussian model for the lya line fit

fit_lwsdictionary with some default and bounds parameters
minparsdictionary with minimization method and associate parameters
Returns:
resultDictionary

  • lines (see above)

  • ztable (see above)

  • lmfit_{family} the ResultObject from lmfit for the given family

  • table_spec an astropy table with the following columns

    • RESTWL: restframe wavelength

    • FLUX: resframe data value

    • ERR: stddev of FLUX

    • LINEFIT: final fit value

    • INIT_FIT: init value for the full fit

    • {family}_INIT_FIT: initial value for the fit of the given family

    • {family}_FIT_LSQ: LSQ fit of the given family

Raises:
NoLineError:

when none of the fitted line can be on the spectrum at the given redshift.