# Description¶

Master background subtraction is one form of background subtraction available for spectroscopic data. See Background Subtraction for an overview of all the available methods and where they occur within the various stages of the calibration pipeline.

The master background subtraction step subtracts background signal from 2-D spectroscopic data using a 1-D master background spectrum. The 1-D master background spectrum is created from one or more input exposures, or can alternatively be supplied by the user. The 1-D background spectrum - surface brightness versus wavelength - is projected into the 2-D space of source data based on the wavelength of each pixel in the 2-D data. The resulting 2-D background signal is then subtracted directly from the 2-D source data.

Logic built into the step checks to see if the exposure-based background subtraction step in the calwebb_spec2 pipeline has already been performed on the input images, based on the value of the S_BKDSUB keyword. If S_BKGSUB is set to “COMPLETE”, the master background step is skipped. If the calwebb_spec2 background step was not applied, the master background step will proceed. The user can override this logic, if desired, by setting the step argument --force_subtract to True, in which case master background subtraction will be applied regardless of the value of S_BKDSUB (see Step Arguments).

Upon successful completion of the step, the S_MSBSUB keyword is set to “COMPLETE” in the output product. The background-subtracted results are returned as a new data model, leaving the input model unchanged.

Note: The application of master background subtraction to NIRSpec Fixed-Slit, IFU, and MOS observations requires special handling, due to unique types of calibrations that are applied to these modes. NIRSpec MOS mode requires even more special handling than NIRSpec Fixed-Slit and IFU. The next several sections pertain primarily to MIRI MRS and LRS Fixed-Slit, and in a general way to NIRSpec Fixed-Slit and IFU modes. Details regarding all NIRSpec modes are given later in NIRSpec Master Background Subtraction.

## Inputs¶

The primary driver of the master background step is usually a spec3 type Association (ASN) file or a ModelContainer data model populated from a spec3 ASN file. This is the same ASN file used as input to the calwebb_spec3 pipeline, which defines a stage 3 combined product and its input members. The list of input members includes both “science” and “background” exposure types. The master background subtraction step uses the input members designated with "exptype": "background" to create the master background spectrum (see example_asn1). These need to be x1d products created from individual exposures at the end of the calwebb_spec2 pipeline, containing spectra of background regions. The master background signal will be subtracted from all input members designated as "exptype": "science" in the ASN, resulting in a new version of each science input. These inputs need to be cal products created from individual exposures by the calwebb_spec2 pipeline.

There are two main observing scenarios that are supported by this step: nodded exposures of point sources and off-source background exposures of extended targets. A third type of operation is performed for NIRSpec MOS observations that include background slits. The details for each mode are explained below.

### Nodded Point Sources¶

If an observation uses a nodding type dither pattern to move a small or point-like source within the field-of-view, it is assumed that part of the field-of-view in each exposure is also suitable for measuring background. Exposures of this type are identified by the pipeline based on their “PATTTYPE” (primary dither pattern type) keyword value. The value will either contain the substring “NOD” somewhere within the name (e.g. “2-POINT-NOD” or “ALONG-SLIT-NOD”), or will be set to “POINT-SOURCE” (for MIRI MRS). The calwebb_spec2 srctype step recognizes these PATTTYPE values and sets the source type to “POINT.”

This in turn causes the extract_1d step at the end of calwebb_spec2 to extract spectra for both source and background regions. For IFU exposures the background region is typically an annulus that is concentric with a circular source region. For slit-like modes, one or more background regions can be defined in the extract1d reference file, flanking the central source region. In both cases, the extraction regions are centered within the image/cube at the RA/Dec of the target. Hence for nodded exposures, the location of the extraction regions follows the movement of the source in each exposure. The extracted data from the source region are stored in the “FLUX” and “SURF_BRIGHT” (surface brightness) columns of the x1d product, while the background extraction is stored in the “BACKGROUND” column. The master_background step uses the data from the “BACKGROUND” column of each background x1d product to create the 1-D master background spectrum.

Below is an example ASN file for a simple 2-point nodded observation consisting of two exposures.

{
"asn_type": "spec3",
"asn_rule": "candidate_Asn_IFU",
"program": "00626",
"asn_id": "c1003",
"target": "t001",
"asn_pool": "jw00626_20190128T194403_pool",
"products": [
{"name": "jw00626-c1003_t001_nrs",
"members": [
{"expname": "jw00626009001_02101_00001_nrs1_cal.fits",
"exptype": "science",
"asn_candidate": "('c1003', 'background')"
},
{"expname": "jw00626009001_02102_00001_nrs1_cal.fits",
"exptype": "science",
"asn_candidate": "('c1003', 'background')"
},
{"expname": "jw00626009001_02101_00001_nrs1_x1d.fits",
"exptype": "background",
"asn_candidate": "('c1003', 'background')"
},
{"expname": "jw00626009001_02102_00001_nrs1_x1d.fits",
"exptype": "background",
"asn_candidate": "('c1003', 'background')"
}
]
}
]
}


As you can see, the same two exposures are defined as being both “science” and “background” members, because they both contain the target of interest and a region of background. The “science” members, which are the cal products created by the calwebb_spec2 pipeline, are the data files that will have the master background subtraction applied, while the “background” members are the x1d spectral products from which the master background spectrum will be created. The combined master background spectrum will be subtracted from each of the two science exposures.

### Extended Source with Dedicated Background Exposures¶

Observations of extended sources must obtain exposures of a separate background target/field in order to measure the background. Exposures of a background target are identified by the keyword “BKGDTARG” set to True in the header. During calwebb_spec2 processing, the srctype step recognizes these and sets their source type to “EXTENDED”, because all dedicated background exposures are to be processed as extended sources.

This in turn causes the extract_1d step at the end of calwebb_spec2 to extract a spectrum in extended source mode, which uses the entire field-of-view (whether it be a slit image or an IFU cube) as the extraction region. The master_background step recognizes which type of background exposure it’s working with and uses the appropriate data from the x1d product to construct the master background spectrum.

Below is an example ASN file for an extended source observation that includes background target exposures, using a 2-point dither for both the science and background targets.

{
"asn_type": "spec3",
"asn_rule": "candidate_Asn_IFU",
"program": "00626",
"asn_id": "c1004",
"target": "t002",
"asn_pool": "jw00626_20190128T194403_pool",
"products": [
{"name": "jw00626-c1004_t002_nrs",
"members": [
{"expname": "jw00626009001_02101_00001_nrs1_cal.fits",
"exptype": "science",
"asn_candidate": "('c1004', 'background')"
},
{"expname": "jw00626009001_02102_00001_nrs1_cal.fits",
"exptype": "science",
"asn_candidate": "('c1004', 'background')"
},
{"expname": "jw00626009001_02103_00001_nrs1_x1d.fits",
"exptype": "background",
"asn_candidate": "('c1004', 'background')"
},
{"expname": "jw00626009001_02104_00001_nrs1_x1d.fits",
"exptype": "background",
"asn_candidate": "('c1004', 'background')"
}
]
}
]
}


In this example there are two exposures of the science target, labeled as “science” members, and two exposures of the background target, labeled as “background” members. As before, the science members use cal products as input and the background members use x1d products as input. The master background step will first combine the data from the two background members into a master background spectrum and then subtract it from each of the two science exposures.

## Creating the 1-D Master Background Spectrum¶

The 1-D master background spectrum is created by combining data contained in the x1d products listed in the input ASN as "exptype": "background" members. As noted above, the background members can be exposures of dedicated background targets or can be a collection of exposures of a point-like source observed in a nod pattern.

When all of the input background spectra have been collected, they are combined using the combine_1d step to produce the 1-D master background spectrum. See the combine_1d step for more details on the processes used to create the combined spectrum.

## Subtracting the Master Background¶

The 1-D master background spectrum is interpolated by wavelength at each pixel of a 2-D source spectrum and subtracted from it. The source data instances can be, for example, a set of NIRSpec or MIRI IFU exposures, a set of NIRSpec fixed-slit 2-D extractions, or a set of nodded MIRI LRS fixed-slit exposures. The subtraction is performed on all data instances within all input science exposures. For example, if there are 3 NIRSpec fixed-slit exposures, each containing data from multiple slits, the subtraction is applied one-by-one to all slit instances in all exposures. For each data instance to be subtracted the following steps are performed:

• Compute a 2-D wavelength grid corresponding to the 2-D source data. For some observing modes, such as NIRSpec MOS and fixed-slit, a 2-D wavelength array is already computed and attached to the data in the calwebb_spec2 pipeline extract_2d step. If such a wavelength array is present, it is used. For modes that don’t have a 2-D wavelength array contained in the data, it is computed on the fly using the WCS object for each source data instance.

• Compute the background signal at each pixel in the 2-D wavelength grid by interpolating within the 1-D master background spectrum as a function of wavelength. Pixels in the 2-D source data with an undefined wavelength (e.g. wavelength array value of NaN) or a wavelength that is beyond the limits of the master background spectrum receive special handling. The interpolated background value is set to zero and a DQ flag of “DO_NOT_USE” is set.

• Subtract the resulting 2-D background image from the 2-D source data. DQ values from the 2-D background image are propagated into the DQ array of the subtracted science data.

## NIRSpec Master Background Corrections¶

The master background subtraction methods and processing flow for NIRSpec Fixed-Slit and IFU modes is largely the same as what’s outlined above, with some additional operations that need to be applied to accommodate some of the unique calibrations applied to NIRSpec data. NIRSpec MOS mode requires even more special handling. This is due to two primary effects of NIRSpec calibration:

• Point sources in MOS and Fixed-Slit mode receive wavelength offset corrections if the source is not centered (along the dispersion direction) within the slit. Hence the wavelength grid assigned to each 2-D slit cutout can be shifted slightly relative to the wavelengths of the background signal contained in the same cutout. And because the flat-field, pathloss, and photom corrections/calibrations are wavelength-dependent, the pixel-level calibrations for the source signal are slightly different than the background.

• Point sources and uniform sources receive different pathloss and bar shadow corrections (in fact point sources don’t receive any bar shadow correction). So the background signal contained within a calibrated point source cutout has received a different pathloss correction and hasn’t received any bar shadow correction. Meanwhile, the master background is created from data that had corrections for a uniform source applied to it and hence there’s a mismatch relative to the point source data.

The 2-D background that’s initially created from the 1-D master background is essentially a perfectly calibrated background signal. However, due to the effects mentioned above, the actual background signal contained within a calibrated point source slit (or IFU image) is not perfect (e.g. it still has the bar shadow effects in it). So all of these effects need to be accounted for in the computed 2-D background before subtracting from the source data.

### NIRSpec IFU Mode¶

For the NIRSpec IFU mode, the overall processing flow is the same as other modes, in that the 1-D master background spectrum is created and applied during calwebb_spec3 processing, as outlined above. No wavelength offset or bar shadow corrections are applied to IFU data, so any differences due to the way those calibrations are applied are not relevant to IFU mode. So the only effect that needs to be accounted for in the 2-D background generated from the master background is the difference between point source and uniform source pathloss corrections. This is accomplished by removing the uniform source pathloss correction from the 2-D background signal and applying the point source pathloss correction to it. It is then in a state where it matches the background signal contained in the point source IFU image from which it will be subtracted. Mathematically, the operation performed on the IFU 2-D background is:

$bkg(corr) = bkg * pathloss(uniform) / pathloss(point)$

The uniform and point source pathloss correction arrays referenced above are retrieved from the cal products used as input to the master background step. They are computed by the pathloss step during calwebb_spec2 processing and stored as extra extensions in the cal products.

### NIRSpec Fixed-Slit Mode¶

NIRSpec fixed slit data receive flat-field, pathloss, and photometric calibrations, all of which are wavelength-dependent, and the pathloss correction is also source type dependent. Fixed slit data do not receive a bar shadow correction. Only slits containing a point source can have a wavelength correction applied, to account for source centering within the slit, hence slits containing uniform sources receive the same flat-field and photometric calibrations as background spectra and therefore don’t require corrections for those two calibrations. Furthermore, the source position in the slit is only known for the primary slit in an exposure, so even if the secondary slits contain point sources, no wavelength correction can be applied, and therefore again the flat-field and photometric calibrations are the same as for background spectra. This means only the pathloss correction difference between uniform and point sources needs to be accounted for in the secondary slits.

Therefore if the primary slit (as given by the FXD_SLIT keyword) contains a point source (as given by the SRCTYPE keyword) the corrections that need to be applied to the 2-D master background for that slit are:

$\begin{split}bkg(corr) = bkg &* [flatfield(uniform) / flatfield(point)]\\ &* [pathloss(uniform) / pathloss(point)]\\ &* [photom(point) / photom(uniform)]\end{split}$

For secondary slits that contain a point source, the correction applied to the 2-D master background is simply:

$bkg(corr) = bkg * pathloss(uniform) / pathloss(point)$

The uniform and point source versions of the flat-field, pathloss, and photom corrections are retrieved from the input cal product. They are computed and stored there during the execution of each of those steps during calwebb_spec2 processing of NIRSpec Fixed-Slit exposures.

### NIRSpec MOS Mode¶

Master background subtraction for NIRSpec MOS mode shares the high-level concepts of other modes, but differs greatly in the details. Most importantly, the source of the master background spectrum does not come from either nodded exposures or exposures of a background target. The background data instead come from designated background MSA slitlets contained with the same exposure as the science targets. Alternatively, a user can supply a master background spectrum to be used, as is the case for all other modes. The master background processing for MOS mode is therefore done within the calwebb_spec2 pipeline when processing individual MOS exposures, rather than in the calwebb_spec3 pipeline. Applying the master background subtraction within the calwebb_spec2 pipeline also has advantages due to the complex series of operations that need to be performed, as described below.

During calwebb_spec2 processing, all source and background slits are first partially calibrated up through the extract_2d and srctype steps of calwebb_spec2, which results in 2D cutouts for each slit with the source type identified. At this point the master_background_nrs_slits step is applied, which is a unique version of the step specifically tailored to NIRSpec MOS mode.

This version of the master background step completes the remaining calibration for all slits, but treats them all as extended sources and saves the correction arrays from each step (e.g. flat-field, pathloss, photom) for each slit, so that they can be used later to apply corrections to the background data. The resulting extracted 1D spectra from the background slits are combined to create the master background spectrum. The master background spectrum is then interpolated into the 2D space of each slit and has the photom, barshadow, pathloss, and flat-field corrections removed from the 2D background arrays, so that the background data now match the partially calibrated slit data from which they’ll be subtracted. Mathematically, the corrections applied to the 2D master background for each MOS slit are:

$\begin{split}bkg(corr) = bkg &* flatfield(uniform) * pathloss(uniform)\\ &* barshadow(uniform) / photom(uniform)\end{split}$

Once the corrected 2D backgrounds have been subtracted from each slit, processing returns to the calwebb_spec2 flow, where all of the remaining calibration steps are applied to each slit, resulting in background-subtracted and fully calibrated 2D cutouts (cal and s2d products) and extracted 1D spectra (x1d products).

The detailed list of operations performed when applying master background subtraction to MOS data during calwebb_spec2 processing is as follows:

1. Process all slitlets in the MOS exposure up through the extract_2d and srctype steps

2. The master_background_nrs_slits step temporarily applies remaining calibration steps up through photom to all slits, treating them all as extended sources (appropriate for background signal), and saving the extended source correction arrays for each slit in an internal copy of the data model

3. If a user-supplied master background spectrum is not given, the resample_spec and extract_1d steps are applied to the calibrated background slits, resulting in extracted 1D background spectra

4. The 1D background spectra are combined, using the combine_1d step, into a master background spectrum

5. If a user-supplied master background is given, steps 3 and 4 are skipped and the user-supplied spectrum is inserted into the processing flow

6. The master background spectrum (either user-supplied or created on-the-fly) is expanded into the 2D space of each slit

7. The 2D background “image” for each slit is processed in inverse mode through the photom, barshadow, pathloss, and flatfield steps, using the correction arrays that were computed in step 2, so that the background data now matches the partially calibrated background signal in each slit

8. The corrected 2D background is subtracted from each slit

9. The background-subtracted slits are processed through all remaining calwebb_spec2 calibration steps, using the corrections appropriate for the source type in each slit