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JP-2032: Fix bug introduced when adding 4-amp subarray processing in refpix step #5937

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Apr 7, 2021
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JP-2032: Fix bug introduced when adding 4-amp subarray processing in refpix step #5937

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9566d2e
Fix bug introduced when adding 4-amp subarray processing in refpix step
stscirij Apr 7, 2021
2d2c862
Add changelog entry
stscirij Apr 7, 2021
10c4896
Fix typo
stscirij Apr 7, 2021
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2 changes: 2 additions & 0 deletions CHANGES.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -106,6 +106,8 @@ refpix
- Added code to handle NIR subarrays that use 4 readout amplifiers. Uses and applies reference pixel signal from
available amplifiers and side reference pixel regions, including odd-even column separation if requested [#5926]

- Fixed a bug introduced in #5026 that affected refpix calibration of 1-amp NIR subarrays [#5937]

source_catalog
--------------

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4 changes: 2 additions & 2 deletions docs/jwst/refpix/description.rst
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Expand Up @@ -108,7 +108,7 @@ NIR Data
++++++++

For single amplifier readout (NOUTPUTS keyword = 1):
----------------------------------------------------
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

If the odd_even_columns flag is set to True, then the clipped means of all
reference pixels in odd-numbered columns and those in even numbered columns
Expand All @@ -127,7 +127,7 @@ If the science dataset has at least 1 group with no valid reference pixels,
the step is skipped and the S_REFPIX header keyword is set to 'SKIPPED'.

For 4 amplifier readout (NOUTPUTS keyword = 4):
-----------------------------------------------
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

If the NOUTPUTS keyword is 4 for a subarray exposure, then the data are calibrated
the same as for full-frame exposures. The top/bottom reference values are obtained from available
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3 changes: 2 additions & 1 deletion jwst/refpix/reference_pixels.py
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Expand Up @@ -909,12 +909,13 @@ def do_subarray_corrections(self):
# First transform to detector coordinates
#
refdq = dqflags.pixel['REFERENCE_PIXEL']
donotuse = dqflags.pixel['DO_NOT_USE']
#
# This transforms the pixeldq array from DMS to detector coordinates,
# only needs to be done once
self.DMS_to_detector_dq()
# Determined refpix indices to use on each group
refpixindices = np.where(np.bitwise_and(self.pixeldq, refdq) == refdq)
refpixindices = np.where((self.pixeldq & refdq == refdq) & (self.pixeldq & donotuse != donotuse))
nrefpixels = len(refpixindices[0])
if nrefpixels == 0:
self.bad_reference_pixels = True
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