JP-3288 use DQ plane in residual_fringe code (spacetelescope#8381)

Co-authored-by: Howard Bushouse <[email protected]>

CHANGES.rst

@@ -45,6 +45,11 @@ ramp_fitting
   to use uint16 instead of uint8, in order to avoid potential
   overflow/wraparound problems. [#8377]
 
+residual_fringe
+---------------
+
+- Use DQ plane to exclude pixels marked as DO_NOT_USE in correction. [#8381]
+
 tweakreg
 --------
 

jwst/regtest/test_miri_residual_fringe.py

@@ -10,7 +10,7 @@
 def test_residual_fringe_cal(rtdata, fitsdiff_default_kwargs):
     """Run residual fringe correction on MIRI IFUShort """
 
-    input_file = 'MIRM108-SHORT-6021192005_1_495_MIRIFUSHORT_cal.fits'
+    input_file = 'jw01523001001_03101_00001_mirifushort_cal.fits'
     rtdata.get_data(f"miri/mrs/{input_file}")
 
     args = [

jwst/residual_fringe/residual_fringe.py

@@ -83,11 +83,13 @@ def do_correction(self):
             raise ErrorNoFringeFlat("The fringe flat step has not been run on file %s",
                                     self.input_model.meta.filename)
 
-        # Remove any NaN values from the data prior to processing
+        # Remove any NaN values and flagged DO_NOT_USE pixels from the data prior to processing
         # Set them to 0 for the residual fringe routine
         # They will be re-added at the end
         output_data = self.model.data.copy()
-        nanval_indx = np.where(~np.isfinite(output_data))
+        DO_NOT_USE = datamodels.dqflags.pixel["DO_NOT_USE"]
+        nanval_indx = np.where(np.logical_or(np.bitwise_and(self.model.dq, DO_NOT_USE).astype(bool),
+                                              ~np.isfinite(output_data)))
         output_data[nanval_indx] = 0
 
         # normalise the output_data to remove units