JP-3587: Clean up NIRSpec IFU flat field SCI/ERR/DQ flagging (spacete…

…lescope#8385)

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

CHANGES.rst

@@ -36,6 +36,12 @@ extract_1d
 
 - Replaced deprecated ``np.trapz`` with ``np.trapezoid()``. [#8415]
 
+flat_field
+----------
+
+- Update the flatfield code for NIRSpec IFU data to ensure that SCI=ERR=NaN and
+  DQ has the DO_NOT_USE flag set outside the footprint of the IFU slices [#8385]
+
 general
 -------
 

jwst/flatfield/flat_field.py

@@ -1627,9 +1627,9 @@ def flat_for_nirspec_ifu(output_model, f_flat_model, s_flat_model, d_flat_model,
     """
     any_updated = False
     exposure_type = output_model.meta.exposure.type
-    flat = np.ones_like(output_model.data)
+    flat = np.ones_like(output_model.data) * np.nan
     flat_dq = np.zeros_like(output_model.dq)
-    flat_err = np.zeros_like(output_model.data)
+    flat_err = np.zeros_like(output_model.data) * np.nan
 
     try:
         list_of_wcs = nirspec.nrs_ifu_wcs(output_model)
@@ -1726,6 +1726,13 @@ def flat_for_nirspec_ifu(output_model, f_flat_model, s_flat_model, d_flat_model,
 
         any_updated = True
 
+    # Ensure consistency between NaN-valued pixels and the DO_NOT_USE flag
+    indx = np.where((flat_dq & dqflags.pixel['DO_NOT_USE']) != 0)
+    flat[indx] = np.nan
+    flat_err[indx] = np.nan
+    indx = np.where(~ np.isfinite(flat))
+    flat_dq[indx] = flat_dq[indx] | dqflags.pixel['DO_NOT_USE']
+
     # That's all folks
     return flat, flat_dq, flat_err, any_updated