5.1.2.0 sd.scantable.auto_sinusoid_baseline

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sd.scantable.auto_sinusoid_baseline - Function

5.1.2 Perform automatic line finding and baseline subtraction using sinusoidal function
Description

Return a scan which has been baselined (all rows) with sinusoidal functions. Fit will be done with ’sigma-clipping’.

Spectral lines are detected first using linefinder and masked out to avoid them affecting the baseline solution.

If applyfft is set to True, the function performs Fourier analysis to select wave numbers for sinusoidal fitting. Currently, ’fft’ is only available to be used for the analysis. You can specify threshold for selection of wave number using fftthresh parameter. Both float and string is acceptable. Given a float value, the unit is set to sigma. For string values, allowed formats include:

any decimal number plus ’sigma’ (e.g. ’3sigma’)
’top’ plus any decimal number (e.g. ’top10’)

In addition, you can add or reject specific wave numbers from the fit using addwn and rejwn, respectively. You can specify wave numbers as an integer, string, or list of them. For string specification, syntax for those parameters are as follows:

’a-b’ (= a, a+1, a+2, ..., b-1, b)
’<a’ (= 0, 1, ..., a-2, a-1)
’>a’ (= a+1, a+2, ... up to maximum wave number corresponding to the Nyquist frequency)

You can append ’=’ after inequality sign. When both addwn and rejwn are set, rejwn will take priority of addwn.

The edge argument is an optional number of channel to drop at the edge of spectrum. If only one value is specified, the same number will be dropped from both sides of the spectrum. Default is to keep all channels. Nested tuples represent individual edge selection for different IFs (a number of spectral channels can be different).

The threshold and chan_avg_limit arguments are linefinder options. The former is the threshold used by line finder. It is better to keep it large as only strong lines affect the baseline solution. The later is a maximum number of consequtive spectral channels to average during the search of weak and broad lines. The default is no averaging (and no search for weak lines). If such lines can affect the fitted baseline (e.g. a high order polynomial is fitted), increase this parameter (usually values up to 8 are reasonable). Most users of this method should find the default value sufficient. See linefinder for more details on these options.

Note: The best-fit parameter values output in logger and/or blfile are now based on specunit of ’channel’.

Arguments


Inputs
insitu	If False a new scantable is returned
	allowed:	bool
	Default:	None (use default value)
mask	An optional mask retreived from scantable
	allowed:	bool array
	Default:	None (no mask)
applyfft	Perform Fourier analysis to find appropriate sinusoidal component
	allowed:	bool
	Default:	True
fftmethod	Method to find sinusoidal component (currently only ’fft’ is available)
	allowed:	string
	Default:	’fft’
fftthresh	Threshod to select wave number in Fourier analysis
	allowed:	float, string
	Default:	3.0
addwn	Additional wave numbers to be used for fitting
	allowed:	integer, string, any array
	Default:	[]
rejwn	Waver numbers not to be used for fitting
	allowed:	integer, string, any array
	Default:	[]
clipthresh	Clipping threshold in unit of sigma
	allowed:	float
	Default:	3.0
clipniter	Maximum number of iteration of clipping
	allowed:	integer
	Default:	0
edge	An optional number of channel to drop at the edge of spectrum
	allowed:	integer, integer array
	Default:	(0,0)
threshold	The threshold used by line finder
	allowed:	float
	Default:	3
chan_avg_limit	A maximum number of consequtive spectral channels to average during the search
	allowed:	int
	Default:	1
plot	Plot the fit and the residual (currently unavailable)
	allowed:	bool
	Default:	False
getresidual	If False, return best-fit value instead of residual
	allowed:	bool
	Default:	True
showprogress	Show progress status for large data
	allowed:	bool
	Default:	True
minnrow	Minimum number of spectra to show progress status
	allowed:	integer
	Default:	1000
outlog	Output the coefficients of the best-fit function to logger
	allowed:	bool
	Default:	False
blfile	Name of text file in which the best-fit parameter values to be written
	allowed:	string
	Default:	”

Returns
scantable

Example

scan = sd.scantable(’OrionS_rawACSmod_cal’,average=False)
scan2 = scan.auto_sinusoid_baseline(addwn=’<=10’, insitu=False)

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