The calwebb_tso3 module is stage 3 of the JWST Science Calibration Pipeline for all TSO data. The inputs to this stage are the calibrated slope images (calwebb_image2 and calwebb_spec2 output "*calints.fits") and the outputs are extracted photometry and spectroscopy as appropriate. The steps are listed in Figure 1 with the flow from the top to the bottom.

This third stage of the pipeline performs some final operations on the data to produce higher-level output products. It does not currently perform any additional calibration steps; as such, the output of the calwebb_spec2 pipeline constitutes the "science-ready" data. The main additional operation is that file segments for segmented exposures are merged into single output products; for example, the extract_1d step returns a single "x1dints.fits" file containing the extracted spectra for all integrations.

Unless otherwise stated, the algorithms described are the baseline version.

A brief description of each of the steps within calwebb_tso3 can be found below, along with links to further details (e.g., the relevant reference files) that can be found on the corresponding ReadTheDocs pages. Note, however, that the reference files themselves are all provided via CRDS. For instrument mode-specific notes on these pipeline steps see the corresponding known issues with JWST data articles.

Steps for all TSO data

Outlier detection

ReadTheDocs documentation: Outlier Detection
Package name: outlier_detection

A 2nd pass at outlier detection is done using the image stack. The majority of the outliers will be due to cosmic rays undetected during the 1st pass at outlier detection done in calwebb_detector1. As of build 11.0, a rolling median in the time domain is applied to detect outliers in TSO multi-integration data. The presence of an outlier results in a DQ pixel flag being set in the output "crfints.fits" files.

Exposure level products

The exposure level products are recreated at this stage to provide the highest quality products that include the results of the ensemble processing (a 2nd pass outlier detection). These products are for the Archive and include the unrectified 2-D images and rectified 2-D images.

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Imaging-specific steps

Extract photometry

ReadTheDocs documentation: TSO Photometry 
Package name: tso_photometry

Aperture photometry with a predefined aperture is performed for each integration providing the time-series photometry, returning a "phot.ecsv" output file tabulating fluxes as a function of julian date of the observation.  Note that unlike for the ordinary imaging pipeline, as of build 11.1 the TSO pipeline will ignore NaN valued-pixels in aperture photometry returned by the tso_photometry step.

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Spectroscopy-specific steps

Spectral extraction

ReadTheDocs documentation: Extract 2D 
Package name: extract_2d

The extraction is done using a boxcar for each integration providing time-series spectroscopy. Exposure segments will be merged, and the spectra are re-extracted as a single product (with the segments merged together), producing a new "x1dints.fits" file.

White-light photometry

ReadTheDocs documentation: White Light Curve Generation 
Package name: white_light

The 1-D extracted spectra are collapsed to create time-series white-light photometry for the spectral observations by integrating the spectra over a particular wavelength range (which can be adjusted in the step parameters), returned in a "whtlt.ecsv" file. 

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