Comment by Greg Sloan on JIRA:

I agree with the reasoning. We should move pixel_replace so that the cal.fits files are saved before pixels are replaced.

Comment by Melanie Clarke on JIRA:

I agree as well - I think this is a good first step toward making missing pixel handling more robust.  This would save interpolation until the last minute possible with the current implementation, and make it much easier to generate products with and without pixel replacement for comparison.

For more future improvements, we might want to consider moving the interpolation even further down in the processing, during spectral extraction and/or resampling.  It might be possible to make a more robust spatial profile to fit, for example, if all input data is available to the algorithm, or if a PSF model is provided for optimal extraction.

Comment by Jane Morrison on JIRA:

Howard Bushouse or Greg Sloan I am updating the regression tests. I updated test_miri_lrs_slit_spec2.py to do the pixel_replacement and not skip it - since that is how the default pipeline is run.
I want to make sure the s2d results are the expected results. When a pixel is a nan in the input to resample it seems that the resulting s2d pixel value is 0 . The CON plane has a value of 0 in this case. I wanted to make sure that to be consistent with other products these pixels should be a NAN. This would be a nice JP-ticket but I thought since I saw this I would ask.

Comment by Greg Sloan on JIRA:

Seems like NaNs should stay NaNs. Zeroes can be interpreted as valid data. But I want to be clear on what is happening. Is pixel_replace writing "0", or is resample_spec doing that?

Comment by Howard Bushouse on JIRA:

Jane Morrison Greg Sloan The issue of zero vs. NaN in resampled images is the subject of the long-standing ticket JP-3281, which was just discussed at the JP coordination meeting yesterday. They come out zero in resampled images because of the setting of the FILLVAL=INDEF parameter in resample. Once the default gets changed for that to NaN, then resampled pixels that have no contribution from inputs will be set to NaN.