JP-2032: Fix bug introduced when adding 4-amp subarray processing in …

…refpix step (#5937) * Fix bug introduced when adding 4-amp subarray processing in refpix step * Add changelog entry * Fix typo
spacetelescope · Apr 7, 2021 · c5cfcd5 · c5cfcd5
1 parent 2dd780f
commit c5cfcd5
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Showing 3 changed files with 6 additions and 3 deletions.
diff --git a/CHANGES.rst b/CHANGES.rst
@@ -110,6 +110,8 @@ 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 #5926 that affected refpix calibration of 1-amp NIR subarrays [#5937]
+
 source_catalog
 --------------
 

diff --git a/docs/jwst/refpix/description.rst b/docs/jwst/refpix/description.rst
@@ -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
@@ -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

diff --git a/jwst/refpix/reference_pixels.py b/jwst/refpix/reference_pixels.py
@@ -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