soxs_mbias

A zero-second exposure will contain only read-noise, and \(\sim\)half of the pixels within this Gaussian distribution centred around zero counts will always contain negative flux. To avoid negative counts, an offset bias voltage is applied at the amplifier stage so that even when no photons are detected, the A/D converter will always register a positive value. This bias-voltage offset must be accounted for in the data reduction process.

The purpose of the soxs_mbias recipe is to provide a master-bias frame that can be subtracted from science/calibration frames to remove the contribution of pixel counts resulting from the bias voltage.

Usage

The soxs_mbias recipe can be run with the following convention:

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

To rerun a previously executed soxs_mbias recipe, you can find the execution command at the end of the recipe log file (found in the workspace products/soxs_mbias 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 mbias sof/20251010T091927_VIS_1X1_1_MBIAS_SOXS.sof -s ./sessions/base/soxspipe.yaml -x

To adjust the default settings for the soxs_mbias recipe, open the soxspipe.yaml file referenced in the command above in a text editor, navigate to the soxs_mbias dictionary, save the file and rerun the recipe command. The settings’ descriptions can be found in Table 1.

Product files are written in the products/soxs_mbias, and QC plots are in the qc/soxs_mbias workspace directory. A report of the product files, QC plots and metrics is also printed to the terminal. The QC metrics calculated for soxs_mbias are found in Table 4.

Reduction Tips

The soxs_mbias recipe is one of the simpler recipes, and therefore, it is typically very robust against failures. To reduce the time it takes to run the recipe (at the expense of allowing a few more outlying pixels into your master bias frame), you can experiment with reducing both frame-clipping-iterations and stacked-clipping-iterations (although speed gains will be very moderate).

Parameters

Table 1 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

Input

Table 2 Input files for the soxs_mbias recipe. The files are typically passed to the soxs_mbias recipe via a set-of-file (sof) file listing one file per line.

Data Type	Content	Related OB	Min. Frame Count
FITS images	raw bias frames (UV-VIS/AC exposures with exptime = 0)	SOXS_img_cal_Bias, SOXS_gen_cal_VISBias	5

Output

Table 3 Output files for the soxs_mbias recipe and their respective ESO PRO keywords.

Label	Content	Data Type	PRO CATG	PRO TYPE	PRO TECH
MBIAS	Master bias frame (frame containing typical bias-voltage applied to the detector)	FITS image	MASTER_BIAS_<ARM>	REDUCED	IMAGE

QC Metrics

Table 4 Quality Control metrics calculated in the soxs_mbias recipe.

Label	Description	Unit	Acceptable Range
BADPIX FRAC	Fraction of bad pixels	-	-
MBIAS MEDIAN	Median flux level of master bias	electrons	VIS: [0, 2000]
BADPIX NUM	Number of bad pixels	-	-
FPN FRACMAX	Maximum periodic pattern noise ratio in raw bias frames	-	VIS: [0,3]
RAW RON	RON in single BIAS	electrons	VIS: [0,15]
MASTER RON	Combined RON in MBIAS	electrons	VIS: [0,10]
STRUCTX	Slope of BIAS in X direction	-	VIS: [-3,1]
STRUCTY	Slope of BIAS in Y direction	-	VIS: [0.0,0.6]