SCL Sfit Commands

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valid : summarise current valid SFIT mode/method combinations

method_formal: Compute formal solution for given parameters
method_levenburg: Select Levenburg-Marquardt method
method_amoeba: Select downhill simplex method
method_genetic: Select genetic algorithm method
method_chisq: Locate minimum chi^2 in grid
method_tolerance <tol>: Set tolerance (or convergence criterion)
method_range <w1> <w2>: Set wavelength range for fit

data_spectrum <name> : data in "spectrum" format
data_pamela <name> : data in "pamela" format (w,f,s)
data_flux_units <name> : flux units of data

"norm" for normalised data (default)
anything else and data are currently assumed to be F_lambda

data_flux_scale <scale> : factor to scale observed fluxes (default 1)

In cases where observed fluxes are typically 10^-11 ergs/cm²/s/A, we find numerical errors when inverting the covariance matrices. To avoid this, the data may be scaled by an arbitrary factor in order to improve numerical stability.

data_sigma <sigma> : define mean standard error in data
data_instrument <delta_wl>|<R> : define instrumental broadening FWHM | R

Note two alternate uses of this command -- selected by the value provided. If the argument is >1000, it is assumed to be R = wl / delta_wl, and the data will be broadened as a fn of wavelentgth, otherwise the value is assumed to be a FWHM (in A) and the data will be broadened uniformly.
The command is marked for replacement with "data_resolution"

data_cosmic <threshold> : define rejection threshold (eg cosmic ray)

If any datum exceeds this value (default=10³⁰), it will be assigned a large error (10³⁰) and will thus carry negligible weight in any subsequent fit. If set too low, such that more than 5% of data points are rejected, this threshold will not be applied. To restore defaults, set <threshold> = 0.

data_drift <dv> : define velocity drift through exposure (km/s)
data_line_set | data_lines | dls <wl> <dw>: Defines line to emphasize or include in the fit, by artificially reducing the local error (sigma) by a factor 100. Repeat command to add additional lines. An entry of 0 0 clears all lines. So does dmc
data_mask_set | data_masks | dms <w1> <w2> <sigma>: Defines wavelength interval to emphasize or exclude from fit, by artificially modifying the local error (sigma). Repeat command to add additional mask regions. sigma is the s.d. to apply to the data within the region to be masked. An entry of 0 0 0 clears all regions. but see dmc
data_mask_disp | data_maskd : Display current mask
data_mask_clear | dmc : Clear current mask

cont_reg_set <w1> <w2>, cont_regs <w1> <w2> : Defines wavelength regions to be used in fitting a continuum. Repeat command to add additiona continuum regions. An entry of 0 0 clears all regions. but see cont_reg_clear
cont_reg_disp, cont_regd : Display current continuum regions
cont_reg_clear : Clear current continuum regions
cont_poly <np> : Polynomial of order <np> to fit continuum

An nth order polynomial is fitted to this ratio in those wavelength regions defined by "cmask". The observed spectrum is then multipled by this polynomial to obtain a new spectrum for use by SFIT.

cont_filter <w> : Gaussian filter with FWHM w through ratioed spectrum

A gaussian filter with FWHM = w is passed through the ratioed spectrum. The observed spectrum is then multipled by this filter to obtain a new spectrum for use by SFIT.

cont_special <w> <w2> : Gaussian filter with bad point rejection

a gaussian filter with FWHM = w2 is passed through the ratioed spectrum wavelength. Points more than 3-sigma from this local mean value are deleted. A second gaussian filter with FWHM = w is passed through the result. The observed spectrum is then multipled by this filter to obtain a new spectrum for use by SFIT.

cont_sigma : Computes standard deviation of data in continuum regions and applies it to current data
normalize : Normalizes the current spectrum using the defined continuum

Executes one normalization step and applies it to the current spectrum, using the current parameter estimates, the method defined by cont_poly or cont_filter and the continuum regions defined by cont_reg_set. This command takes no parameters

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Old format commands
[method] {...} : Defines the method to be used in the solution

Old format: subcommands consist of some combination of:
levenburg
amoeba
genetic
chi-squared
range <w1> <w2>
tolerance <tol>
For example, to use amoeba to find the best fit spectrum in the wavelength region 4350 -- 4520, such that the chi-squared minimum is located to within 0.002:

method{ amoeba tolerance 0.002 range 4350 4520 }

[data] {...} : Defines the observational data to be fitted (obsolete)

Old format: subcommands consist of some combination of:
folder<name>; name of folder containing data
spectrum<name>; name of file containing spectrum in "spectrum format 2"

header1
header2
nw
w_1, f_1
w_2, f_2
...
w_nw, f_nw

sigma <sig> : mean standard error on data
pamela<name> : name of file containing spectrum in pamela format ( x, y, s )
instrument <fwhm> : FWHM (A) of instrumental broadening function
cosmic <threshold> : Threshold for rejection of fluxes (e.g. due to cosmic ray spikes)
drift <dv> : velocity drift (km/s) during exposure

[mask] {...} : forces given spectral regions to be omitted from the fit (obsolete)

This is a fixed format command in which the first argument (nmask) is the number of mask regions and the following nmask triples define the start (ms) and end (me) wavelength of each region, and the stastistical weight to apply to that region (ms).

mask{
<n>
<ms_1> <me_1> <mw_1>
<ms_2> <me_2> <mw_2>
...
<ms_n> <me_n> <mw_n> }

"ms" should be a small number if you require the fit procedure to ignore data in the given window. SFIT uses a weighted chi-square minimisation approach. The weights are by default assumed to be the standared errors on each observation. In this command, weights are converted to a pseudo standard error by inversion. Thus a "weight" of 0.1 corresponds to a standard error of 10.
Example - to eliminate cores of HeI 4026 and 4388, and emphasize HeI 4471 in fit, assuming an average s.e of 0.01 on each pixel.

 mask{
3
4020 4032 0.001
4380 4396 0.001
4465 4477 100.0 } 

[continuum] {...}: Defines how a spectrum will be (re-)normalized

Old format: subcommands consist of some combination of:
poly <np>
filter <w>
special <w> <w2>

SFIT allows the observed spectrum to be renormalized either by fitting a polynomial to defined regions of spectrum (normally chosen to be primarily continuum) or by using a given model as an appoximate solution. This method is particularly useful when the true "continuum" is impossible to identify. In fact this is generally the case. NOTE: It must be applied with caution as it is possible that an assumed solution can be used to "lead" the final solution, by overrectifying broad lines, for example.

[cmask] {...} : ( obsolete command )

This is a fixed format command in which the first argument (nc) is the number of continuum regions and the following nc doubles define the start (ms) and end (me) wavelength of each region.

 cregs{
<nc>
<cs_1> <ce_1>
<cs_2> <ce_2>
...
<cs_n> <ce_n> } 

These wavelength regions define regions of spectrum where the continuum level is to be estimated by comparing the current optimum model and the observed spectrum. It does not assume that data in these windows define the continuum per se but rather that the fit is sufficiently good in these regions that the ratio of observed and model spectrum should be close to unity after rectification.