JWST NIRSpec IFU Pipeline Caveats

Some JWST Science Calibration Pipeline features specific to NIRSpec IFU data are described in this article, providing an overview of known issues that users should be aware of for their use of this science mode.

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NIRSpec IFU pipeline

Cube building

See also: Cube Building

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The cube_build step combines the individual 2-D IFU slice images and creates a 3-D spectral cube. The IFU cubes are by default constructed with north pointing up and east to the left. Cube building can be done using either the default 3-D drizzle algorithm, or alternatively Shepard's method of weighting. The current pipeline default is set to use the 3-D drizzle algorithm.

  • Set WEIGHTING = DRIZZLE to use 3-D drizzle; or
  • WEIGHTING = emsm or = msm  to use Shepard's method with exponential or linear weighting.

It is sometimes useful to build a cube in the detector frame (for example, when analyzing the point spread function), rather than in sky coordinates:

  • Set coord_system = ifualign to build the cube in detector coordinates.

Cube building artifacts

There is spatial under-sampling in the IFU that may result in an apparent "ringing" in the spectrum upon resampling during cube building. This is inherent to the cube building process and there is currently no correction in the pipeline for it. Ways to mitigate this effect are currently being investigated. It may help to use a larger spatial extraction region to reduce the amplitude of the effect in extracted 1-D spectra.

Background Subtraction

See also:  Background Subtraction

Background subtraction is automatically applied by the spec3 pipeline for nodded observations or observations with dedicated background or leakage observations. It is not automatically applied for observations that have off-scene background observations that were not linked to the target in APT. Custom background subtraction may be required depending on science use case. In particular, a 1-D master background spectrum may be specified when running the spec3 pipeline.

Leakage of flux through the MSA may be significant in the case of bright extended targets or point sources in stuck-open shutters.  If dedicated leakage observations were obtained at every dither or nod, the pipeline will use them to subtract the leakage signal.  However, if leakage observations were only acquired at one dither or nod, the pipeline may not process the data correctly.  In this case, custom background subtraction may be necessary.

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