The saturation step flags saturated pixel values. It loops over all integrations within an exposure, examining each one group-by-group, comparing the pixel values in the SCI array with defined saturation thresholds for each pixel. When it finds a pixel value in a given group that is above the threshold, it sets the “SATURATED” flag in the corresponding location of the “GROUPDQ” array in the science exposure. It also flags all subsequent groups for that pixel as saturated. For example, if there are 10 groups in an integration and group 7 is the first one to cross the saturation threshold for a given pixel, then groups 7 through 10 will all be flagged for that pixel.

NIRSpec data acquired using the “IRS2” readout pattern require special handling in this step, due to the extra reference pixel values that are interleaved within the science data. The saturation reference file data does not contain extra entries for these pixels. The step-by-step process is as follows:

  • Retrieve and load data from the appropriate “SATURATION” reference file from CRDS

  • If the input science exposure used the NIRSpec IRS2 readout pattern:

  • Create a temporary saturation array that is the same size as the IRS2 readout

  • Copy the saturation threshold values from the original reference data into the larger saturation array, skipping over the interleaved reference pixel locations within the array

  • If the input science exposure used a subarray readout, extract the matching subarray from the full-frame saturation reference file data

  • For pixels that contain NaN in the reference file saturation threshold array or are flagged in the reference file with “NO_SAT_CHECK” (no saturation check available), propagate the “NO_SAT_CHECK” flag to the science data PIXELDQ array

  • For each group in the input science data, set the “SATURATION” flag in the “GROUPDQ” array if the pixel value is greater than or equal to the saturation threshold from the reference file

Note that pixels set to NaN or flagged as “NO_SAT_CHECK” in the saturation reference file do not receive any saturation checking by this step. They are simply flagged as “NO_SAT_CHECK” in the output science data.


The saturation step will accept either full-frame or subarray saturation reference files. If only a full-frame reference file is available, the step will extract a subarray to match that of the science exposure. Otherwise, subarray-specific saturation reference files will be used if they are available.