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.

On this page

Cube building

ReadTheDocs (External Link): Cube Building

Words in bold are GUI menus/
panels or data software packages; 
bold italics are buttons in GUI
tools or package parameters.

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, the Shepard's method of weighting. The current pipeline default setting is the 3-D drizzle algorithm.

  • To use 3-D drizzle, set WEIGHTING = DRIZZLE
  • To use Shepard's method with exponential or linear weighting, set WEIGHTING = emsm or msm  

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. To build the cube in detector coordinates:

Set coord_system = ifualign

Cube building artifacts

There is spatial undersampling 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

ReadTheDocs (External Link): Background Subtraction

Background subtraction is automatically applied by the calwebb_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 calwebb_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.

Latest updates

Originally published