Pipeline Settings

Here is a list of all the pipeline settings:

Table 34 The soxs_mbias recipe parameters.

Parameter	Description	Type	Entry Point	Related Util
frame_clipping_sigma	number of \(\sigma\) from the median frame flux beyond which pixel is added to the bad-pixel mask	float	settings file	clip_and_stack
frame_clipping_iterations	number of \(\sigma\)-clipping iterations to perform when adding pixels to the bad-pixel mask	int	settings file	clip_and_stack
stacked_clipping_sigma	number of \(\sigma\) deviations from the median pixel flux beyond which pixel is excluded from stack	float	settings file	clip_and_stack
stacked_clipping_iterations	number of \(\sigma\)-clipping iterations to perform before stacking	int	settings file	clip_and_stack

Table 35 The soxs_mdark recipe parameters.

Parameter	Description	Type	Entry Point	Related Util
frame_clipping_sigma	number of \(\sigma\) from the median frame flux beyond which pixel is added to the bad-pixel mask	float	settings file	clip_and_stack
frame_clipping_iterations	number of \(\sigma\)-clipping iterations to perform when adding pixels to the bad-pixel mask	int	settings file	clip_and_stack
stacked_clipping_sigma	number of \(\sigma\) deviations from the median pixel flux beyond which pixel is excluded from stack	float	settings file	clip_and_stack
stacked_clipping_iterations	number of \(\sigma\)-clipping iterations to perform before stacking	int	settings file	clip_and_stack

Table 36 The soxs_mflat recipe parameters.

Parameter	Description	Type	Entry Point	Related Util
subtract_background	fit and subtract the intra-order background light	bool	settings file	subtract_background
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
centre_order_window	size of the window (in pixels) used to measure flux in the central band to determine median exposure	int	settings file	-
slice_length_for_edge_detection	length of the cross_dispersion slices used to determine order edges	int	settings file	detect_order_edges
slice_width_for_edge_detection	width of the cross_dispersion slices used to determine order edges	int	settings file	detect_order_edges
min_percentage_threshold_for_edge_detection	minimum value flux can drop to as percentage of central flux and be counted as an order edge	int	settings file	detect_order_edges
max_percentage_threshold_for_edge_detection	maximum value flux can climb to as percentage of central flux and be counted as an order edge	int	settings file	detect_order_edges
disp_axis_deg	degree of y-component of global polynomial fit to order edges	int	settings file or command-line	detect_order_edges
order_deg	degree of echelle order number component of global polynomial fit to order edges	int	settings file or command-line	detect_order_edges
poly_fitting_residual_clipping_sigma	sigma clipping limit when fitting global polynomial to order edges	float	settings file	detect_order_edges
poly_clipping_iteration_limit	maximum number of clipping iterations when fitting global polynomial to order edges	int	settings file	detect_order_edges
low_sensitivity_clipping_sigma	pixels with a flux less than this many sigma (mad) below the median flux level added to the bp map	float	settings file	-
scale_d2_to_qth	scale d2 to qth lamp flats when stitching	bool	settings file	-
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

Table 37 The soxs_disp_solution recipe parameters.

Parameter	Description	Type	Entry Point	Related Util
pixel_window_size	the size of the square window used to search for an arc-lamp emission line, centred on the predicted pixel position of the line	int	settings file	create_dispersion_map
pinhole_detection_thres_sigma	minimum significance required for arc-line to be considered ‘detected’	float	settings file	create_dispersion_map
order_deg	degree of echelle order number component of global polynomial fit to the dispersion solution [x, y]	int/list	settings file or command-line	create_dispersion_map
wavelength_deg	degree of wavelength component of global polynomial fit to the dispersion solution [x, y]	int/list	settings file or command-line	create_dispersion_map
poly_clipping_iteration_limit	number of sigma-clipping iterations to perform before settling on a polynomial fit for the dispersion solution	int	settings file	create_dispersion_map
poly_fitting_residual_clipping_sigma	sigma clipping limit when fitting global polynomial to the dispersion solution	float	settings file	create_dispersion_map

Table 38 The soxs_order_centres recipe parameters.

Parameter	Description	Type	Entry Point	Related Util
order_sample_count	number of cross-order slices per order	int	settings file	detect_continuum utility
slice_length	length of each slice (pixels)	int	settings file	detect_continuum utility
slice_width	width of each slice (pixels)	int	settings file	detect_continuum utility
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 utility
disp_axis_deg	degree of y-component of global polynomial fit to order centres	int	settings file or command-line	detect_continuum utility
order_deg	degree of echelle order number component of global polynomial fit to order centres	int	settings file or command-line	detect_continuum utility
poly_fitting_residual_clipping_sigma	sigma clipping limit when fitting global polynomial to order centres	float	settings file	detect_continuum utility
poly_clipping_iteration_limit	maximum number of clipping iterations when fitting global polynomial to order centres	int	settings file	detect_continuum utility

Table 39 The soxs_spatial_solution recipe parameters.

Parameter	Description	Type	Entry Point	Related Util
use_flat	divide image by master flat frame	bool	settings	-
subtract_background	fit and subtract the intra-order background light	bool	settings	subtract_background
pixel_window_size	the size of the square window used to search for an arc-lamp emission line, centred on the predicted pixel position of the line	int	settings	create_dispersion_map
pinhole_detection_thres_sigma	minimum significance required for arc-line to be considered ‘detected’	float	settings	create_dispersion_map
order_deg	degree of echelle order number component of global polynomial fit to the dispersion solution [x, y]	int/list	settings file or command-line	create_dispersion_map
wavelength_deg	degree of wavelength component of global polynomial fit to the dispersion solution [x, y]	int/list	settings file or command-line	create_dispersion_map
slit_deg	degree of slit position component of global polynomial fit to the dispersion solution [x, y]	int/list	settings file or command-line	create_dispersion_map
poly_clipping_iteration_limit	number of sigma-clipping iterations to perform before settings on a polynomial fit for the dispersion solution	int	settings	create_dispersion_map
poly_fitting_residual_clipping_sigma	sigma clipping limit when fitting global polynomial to the dispersion solution	float	settings	create_dispersion_map
poly_clipping_pinhole_sets	clipping performed on multi-pinhole sets (true) or individual pinholes (false)	bool	settings	create_dispersion_map
map_to_image_displacement_threshold	maximum distance allowed from the pixel centre when calculating wavelength, order and slit-position for 2d disp-sol image	float	settings	create_dispersion_map
mph_line_set_min	full multi-pinholes sets (same arc line) with fewer than mph_line_set_min lines detected get clipped	int	settings	create_dispersion_map
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

Table 40 The soxs_stare 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	-
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

Table 41 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