soxs_nod

The soxs_nod recipe reduces the science frames produced by the NTT and SOXS from a nodding mode observation block.

Usage

The soxs_nod recipe can be run with the following convention:

soxspipe [-Vx] nod <inputFrames> [-o <outputDirectory> -s <pathToSettingsFile>]

To rerun a previously executed soxs_nod recipe, you can find the execution command at the end of the recipe log file (found in the workspace products/soxs_nod directory). Use the -x flag to overwrite the product files if they already exist. For example, from the root of your workspace, you would run a command like:

soxspipe nod sof/20260111T041914_NIR_3_NOD_STD_FLUX_SLIT1_0_150_0S_SOXS.sof -s ./sessions/base/soxspipe.yaml  -x

To adjust the default settings for the soxs_nod recipe, open the soxspipe.yaml file referenced in the command above in a text editor, navigate to the soxs_nod dictionary, save the file and rerun the recipe command. The settings’ descriptions can be found in Table 30.

Product files are written in the products/soxs_nod, and QC plots are in the qc/soxs_nod workspace directory. A report of the product files, QC plots and metrics is also printed to the terminal. The QC metrics calculated for soxs_nod are found in Table 33.

Reduction Tips

Typically, this recipe fails because the object trace is not found or fitted correctly. This may simply be because the object is too faint in the data, but a few settings can be adjusted to try and secure a fit. First, increase slice-length by a few pixels and try the recipe again. If this does not work, adjust poly-fitting-residual-clipping-sigma to both lower and higher levels (by 1 or 2 sigma each time) and rerun the recipe each time.

Parameters

Table 30 The soxs_nod recipe parameters.

Parameter	Description	Type	Entry Point	Related Util
use_flat	divide image by master flat frame	bool	settings file	-
subtract_background	fit and subtract the intra-order background light	bool	settings file	-
save_single_frame_extractions	If True, each A and B stacked frame for each offset is saved as 2D image	bool	settings file	-
use_lacosmic	use la cosmic to remove CRHs before extraction	bool	settings file	-
stacked_clipping_sigma	the sigma clipping limit used when stacking frames into a composite frame	float	settings file	clip_and_stack
stacked_clipping_iterations	the maximum sigma-clipping iterations used when stacking frames into a composite frame	int	settings file	clip_and_stack
horne_extraction_slit_length	the length of the ‘slit’ used to collect object flux (in pixels). Doubles are boxcar extraction aperture size.	int	settings file	horne_extraction
horne_extraction_profile_poly_order	degree of the polynomial used to fit the dispersion-direction profiles of the object.	int	settings file	horne_extraction
horne_extraction_profile_global_clipping_sigma	sigma clipping limit when fitting the object profile (global over the order)	float	settings file	horne_extraction
horne_extraction_profile_clipping_sigma	sigma clipping limit when fitting the dispersion-direction profiles of the object	float	settings file	horne_extraction
horne_extraction_profile_clipping_iteration_count	maximum number of clipping iterations when fitting dispersion-direction profiles	int	settings file	horne_extraction
order_sample_count	number of cross-order slices per order	int	settings file	detect_continuum
slice_length	length of each slice (pixels)	int	settings file	detect_continuum
slice_width	width of each slice (pixels)	int	settings file	detect_continuum
peak_sigma_limit	height gaussian peak must be above median flux to be “detected” by code (std via median absolute deviation)	float	settings file	detect_continuum
order_deg	degree of order-component of global polynomial fit to object trace	int	settings file	detect_continuum
disp_axis_deg	degree of y-component of global polynomial fit to object trace	int	settings file	detect_continuum
poly_fitting_residual_clipping_sigma	clipping limit (median and mad) when fitting global polynomial to object trace	float	settings file	detect_continuum
poly_clipping_iteration_limit	maximum number of clipping iterations when fitting global polynomial to object trace	int	settings file	detect_continuum
background_subtraction: bspline_deg	degree of bsplines used to fit the inter-order background (if subtract_background == True)	int	settings file	subtract_background
background_subtraction: gaussian_blur_sigma	standard deviation of Gaussian kernel used to smooth background image (if subtract_background == True)	int	settings file	subtract_background
response: max_iteration	maximum number of iterations used to fit the polynomial to the response function	int	settings file	response_function
response: poly_order	degree of the polynomial used to fit the response function	int	settings file	response_function

Input

Table 31 Input files for the soxs_nod recipe. The files are typically passed to the soxs_nod recipe via a set-of-file (sof) file listing one file per line.

Data Type	Content	Related OB
FITS Image	Raw science frames of targets observed in nodding mode	SOXS_slt_obs_AutoNodOnSlit, SOXS_slt_cal_TelluricStdNod, SOXS_slt_cal_SpecphotNod
FITS Image	Master flat frame (optional)	-
FITS Table	order location table containing coefficients to the polynomial fits describing the order locations.	-
FITS Table	Dispersion map table giving coefficients of polynomials describing 2D dispersion/spatial solution	-
FITS Image	Dispersion map FITS image with 3-extensions (wavelength, slit-position and echelle order number)	-

Output

Table 32 Output files for the soxs_nod recipe and their respective ESO PRO keywords. Some output file may not be generated depending on the user’s pipeline settings.

Label	Content	Data Type	PRO CATG	PRO TYPE	PRO TECH
EXTRACTED ORDERS TABLE	Table of the extracted source in each order	FITS	SCI_SLIT_FLUX_NIR	REDUCED	ECHELLE,SLIT
EXTRACTED MERGED TABLE	Table of the extracted, order-merged	FITS	SCI_SLIT_FLUX_NIR	REDUCED	ECHELLE,SLIT
EXTRACTED FLUXCAL SPECTRUM	Table of the flux calibrated extracted spectrum	FITS	SCI_SLIT_FLUX_<ARM>	REDUCED	ECHELLE,SLIT
RESPONSE_FUNC	Response function coefficients	FITS	RESP_TAB_<ARM>	REDUCED	ECHELLE,SLIT
EFFICIENCY	Efficiency estimate	FITS	EFFICIENCY_TAB_<ARM>	REDUCED	ECHELLE,SLIT
EXTRACTED MERGED ASCII	Ascii version of extracted source spectrum	TXT	-	-	-
OBJECT TRACE RES	Residuals of the object trace polynomial fit	PDF	-	-	-
BKGROUND	Fitted intra-order image background	PDF	-	-	-
EXTRACTED ORDERS QC PLOT	QC plot of extracted source	PDF	-	-	-
EXTRACTED MERGED QC PLOT	QC plot of extracted order-merged source	PDF	-	-	-
EXTRACTED MERGED FLUXCALIBRATED QC PLOT	QC plot of extracted order-merged, flux-calibrated source	PDF	-	-	-
RESPONSE QC PLOT	Response curve QC plot.	PDF	-	-	-

QC Metrics

Table 33 Quality Control metrics calculated in the soxs_nod recipe. Note that the acceptable ranges are enforced only for standard stars, not for science frames.

Label	Description	Unit	Acceptable Range
BADPIX FRAC	Fraction of bad pixels		VIS: [0.0,0.01], NIR: [-0.001,0.01]
INNER ORDER PIX MEAN	Mean inner-order pixel value	electrons	VIS: [-40,60], NIR: [-40,60]
INNER ORDER PIX SUM	Sum of all inner-order pixel values	electrons	-
BADPIX NUM	Number of bad pixels		-
N ORDERS	Number of orders containing an object trace		VIS: 4 , NIR: 15
SAMPLES DET NUM	Number of samples where a continuum is detected		-
SAMPLES DET FRAC	Fraction of samples where a continuum is detected		VIS: [0.93,1.0] NIR: [0.7,1.0]
SAMPLES TOT NUM	Total number of samples along orders		-
SAMPLES CLIP NUM	Number of continuum sample clipped during solution fitting		-
SAMPLES CLIP FRAC	Fraction of detected continuum samples clipped during solution fitting		VIS: [0.0,0.2], NIR: [0.0,0.3]
X RES MAX	Maximum residual in continuum fit along x-axis	px	-
X RES MIN	Minimum residual in continuum fit along x-axis	px	-
X RES SD	Std-dev of residual continuum fit along x-axis	px	VIS: [0.0,0.2]
Y RES MAX	Maximum residual in continuum fit along y-axis	px	-
Y RES MIN	Minimum residual in continuum fit along y-axis	px	-
Y RES SD	Std-dev of residual continuum fit along y-axis	px	NIR: [0.0,0.5]
EFF MEDIAN	The median efficiency (global)		VIS: [0.04,0.30], NIR: [0.02,0.2]
SNR MEDIAN	The median signal-to-noise ratio across all orders (global)		VIS: [50,1000], NIR: [7,200]
EFF MEDIAN O<N>	The median efficiency (order N)		-
SNR MEDIAN O<N>	The median signal-to-noise ratio across all orders (order N)		-

Fig. 17 The output of the reponse_function utility (used by nodding and stare recipes) used in the reduction of spectroscopic standard star spectra. The third panel shows th fittted response curve, and the final panel shows the overall efficiency of the instrument across the entire wavelength range of the spectrograph arm.