clobber_ref

jwst.refpix.irs2_subtract_reference.clobber_ref(data, output, odd_even, mask, ref_flags, is_irs2, scipix_n=16, refpix_r=4)[source]

Set some interleaved reference pixel values to zero.

This is an explanation of the arithmetic for computing ref in the loop over the list of bit numbers that is returned by decode_mask(). Reads of reference pixels are interleaved with reads of science data. The pattern of science pixels (S) and reference pixels (r) looks like this:

SSSSSSSSrrrrSSSSSSSSSSSSSSSSrrrrSSSSSSSSSSSSSSSSrrrr ... rrrrSSSSSSSS

Within each amplifier output, a row starts and ends with 8 (scipix_n / 2) science pixels, and the row contains 32 blocks of 4 reference pixels. There are 20 (scipix_n + refpix_r) pixels from the start of one block of reference pixels to the start of the next. k is an integer between 0 and 31, inclusive, an index to identify the block of reference pixels that we need to modify (we’ll set two of the pixels to zero). odd_even is either 1 or 2, indicating that we should set either the first or the second pair of reference pixels to 0.

The same set of interleaved reference pixels will be set to 0 regardless of integration number, group number, or image line number.

Parameters:

datandarray: The 4-D data array in detector orientation. This includes both the science and interleaved reference pixel values. data will be modified in-place to set some of the reference pixel values to zero. The science data values will not be modified.
outputndarray of int16: A 1-D array of amplifier output numbers, 1, 2, 3, or 4, read from the OUTPUT column in the DQ extension of the CRDS reference file.
odd_evenndarray of int16: A 1-D array of integer values, which may be either 1 or 2, read from the ODD_EVEN column in the DQ extension of the CRDS reference file.
maskndarray of uint32: The MASK column (1-D) read from the CRDS reference file.
ref_flagsndarray of bool: Bad reference pixel flags (1-D) , matching the data row size in detector orientation. True indicates a bad reference pixel.
is_irs2ndarray of bool: A 1-D array matching the data row size in detector orientation. True indicates an interleaved reference pixel.
scipix_nint, optional: Number of regular (science) samples before stepping out to collect reference samples.
refpix_rint, optional: Number of reference samples before stepping back in to collect regular samples.