calwebb_spec3: Stage 3 Spectroscopic Processing

Class:: jwst.pipeline.Spec3Pipeline
Alias:: calwebb_spec3

Stage 3 processing for spectroscopic observations is intended for combining the calibrated data from multiple exposures (e.g. a dither/nod pattern) into a single combined 2D or 3D spectral product and a combined 1D spectrum. Before being combined, the exposures may receive additional corrections for the purpose of background matching and subtraction, as well as outlier rejection. The steps applied by the calwebb_spec3 pipeline are shown below. This pipeline is intended for non-TSO spectra only. TSO spectral data should be processed using the calwebb_tso3 pipeline.

Instrument/Mode	NIRSpec			MIRI		NIRISS		NIRCam
Step	FS	MOS	IFU	FS	MRS	SOSS	WFSS	WFSS
assign_mtwcs¹	✓	✓	✓	✓	✓	✓	✓	✓
master_background²	✓		✓	✓	✓
exp_to_source	✓	✓					✓	✓
mrs_imatch					✓
outlier_detection	✓	✓	✓	✓	✓
pixel_replace	✓	✓	✓	✓	✓		✓	✓
resample_spec	✓	✓		✓
cube_build			✓		✓
extract_1d	✓	✓	✓	✓	✓	✓	✓	✓
spectral_leak					✓
combine_1d						✓	✓	✓

¹The assign_mtwcs step is only applied to observations of a moving target (TARGTYPE=’moving’).

²The master background subtraction step is applied to NIRSpec MOS exposures in the calwebb_spec2 pipeline.

WFSS and SOSS Processing

Notice that NIRCam and NIRISS WFSS, as well as NIRISS SOSS data, receive only minimal processing by calwebb_spec3. WFSS 2D input data are reorganized into source-based products by the exp_to_source step (see below), have 1D extracted spectra produced for each source, and then the 1D spectra for each source are combined into a final 1D spectrum. NIRISS SOSS inputs do not go through the exp_to_source step, because they contain data for a single source. Hence the only processing that they receive is to extract a 1D spectrum from each input and then combine those spectra into a final 1D spectrum. This type of processing is intended only for NIRISS SOSS exposures that are not obtained in TSO mode. TSO mode NIRISS SOSS exposures should be processed with the calwebb_tso3 pipeline.

Combined NIRSpec MOS and FS Exposures

It is possible to observe NIRSpec fixed slit targets alongside MSA slitlets in NIRSpec MOS exposures. In this case, the input files produced by the calwebb_spec2 pipeline contain both MOS and FS data. Any master_background corrections applied in this pipeline will operate on the fixed slits only, since background corrections for MOS slitlets should be applied in the calwebb_spec2 pipeline. After the sources are separated in the exp_to_source step, each data product will contain only a fixed slit or a MOS target, so all further processing follows the standard flow for each exposure type.

Arguments

The calwebb_spec3 pipeline does not have any optional arguments.

Inputs

2D calibrated data

Data model:: ImageModel, IFUImageModel, SlitModel, or MultiSlitModel
File suffix:: _cal

The inputs to calwebb_spec3 should be in the form of an ASN file that lists the multiple exposures to be processed into combined output products. The individual exposures should be calibrated the (“_cal”) products from calwebb_spec2 processing.

The member list for each product in the ASN file can also contain exposures of dedicated background targets, which are intended for use in the master_background step. These input exposures must be the “x1d” products (extracted 1-D spectra) of the background target(s) and are usually the “x1d” files produced by the calwebb_spec2 pipeline. They must be listed in the ASN file with “exptype” values of “background” in order to be correctly identified as background exposures. See the master_background for more details.

Outputs

Source-based calibrated data

Data model:: MultiExposureModel
File suffix:: _cal

For NIRSpec fixed-slit, NIRSpec MOS, and NIRCam and NIRISS WFSS, which have a defined set of slits or sources, the data from the input calibrated exposures is reorganized by the exp_to_source step so that all of the instances of data for a particular source/slit are contained in a single product. These are referred to as “source-based” products, as opposed to the input exposure-based products. The source-based collections of data are saved in intermediate files, one per source/slit. The root names of the source-based files contain the source ID as an identifier and use the same “_cal” suffix as the input calibrated exposure files. An example source-based file name is “jw00042-o001_s00000002_niriss_gr150r_f150w_cal.fits”, where “s00000002” is the source id.

The reorganized sets of data are sent to subsequent steps to process and combine all the data for one source at a time.

CR-flagged exposures

Data model:: ImageModel
File suffix:: _crf

If the outlier_detection step is applied, a new version of each input calibrated exposure is created, in which the DQ array has been updated to flag pixels detected as outliers. These files use the “_crf” (CR-Flagged) product type suffix and also includes the association candidate ID as a new field in the original product root name, e.g. “jw96090001001_03101_00001_nrs2_o001_crf.fits.”

2D resampled and combined spectral data

Data model:: SlitModel
File suffix:: _s2d

When processing non-IFU modes, a resampled/rectified 2D product of type “_s2d” is created containing the rectified and combined data for a given slit/source, which is the output of the resample_spec step.

3D resampled and combined spectral data

Data model:: IFUCubeModel
File suffix:: _s3d

When processing IFU exposures, a resampled and combined 3D IFU cube product created by the cube_build step is saved as an “_s3d” file.

1D extracted spectral data

Data model:: MultiSpecModel
File suffix:: _x1d

All types of inputs result in a 1D extracted spectral data product, which is saved as a “_x1d” file, and is normally the result of performing the extract_1d step on the combined “_s2d” or “_s3d” product.

For NIRCam and NIRISS WFSS, as well as NIRISS SOSS data, the extract_1d is performed on the individual unresampled 2D cutout images, resulting in multiple 1-D spectra per source in a “_x1d” product. Those spectra are combined using the subsequent combine_1d step (see below).

1D combined spectral data

Data model:: CombinedSpecModel
File suffix:: _c1d

For NIRCam and NIRISS WFSS, as well as NIRISS SOSS data, the combine_1d combines the multiple 1-D spectra for a given source into a final spectrum, which is saved as a “_c1d” product.