8000 JP-4024: Set negative NIRSpec flat fields to NaN and DNU by hayescr · Pull Request #9522 · spacetelescope/jwst · GitHub
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JP-4024: Set negative NIRSpec flat fields to NaN and DNU #9522

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Merged
merged 7 commits into from
Jun 13, 2025
Merged

JP-4024: Set negative NIRSpec flat fields to NaN and DNU #9522

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c5da294
set negative flat to nan and flag
hayescr Jun 4, 2025
b0a6c58
Merge branch 'spacetelescope:main' into jp-4024
hayescr Jun 6, 2025
aedf212
add changelog stub
hayescr Jun 6, 2025
5535a33
Merge branch 'main' into jp-4024
melanieclarke Jun 12, 2025
8e754a0
combine BADFLAT to one line
hayescr Jun 12, 2025
72bd8ed
set fore flat bad data to nan
hayescr Jun 12, 2025
78c0ff3
Merge branch 'main' into jp-4024
melanieclarke Jun 13, 2025
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1 change: 1 addition & 0 deletions changes/9522.flatfield.rst
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Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
Set pixels with negative flat fields to NaN and flag as them DNU for NIRSpec data.
28 changes: 16 additions & 12 deletions jwst/flatfield/flat_field.py
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Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,10 @@
HORIZONTAL = 1
VERTICAL = 2

BADFLAT = (
dqflags.pixel["NO_FLAT_FIELD"] | dqflags.pixel["DO_NOT_USE"] | dqflags.pixel["UNRELIABLE_FLAT"]
)


def do_correction(
input_model,
Expand Down Expand Up @@ -853,9 +857,10 @@
# Find all pixels in the flat that have a DQ value of DO_NOT_USE
flat_bad = np.bitwise_and(f_flat_dq, dqflags.pixel["DO_NOT_USE"])

# Reset the flat value of all bad pixels to 1.0, so that no
# correction is made
f_flat[np.where(flat_bad)] = 1.0
# Set the flat value of all bad pixels to nan. F-flats provide
# flux calibration scaling, so there is no safe default value for bad
# pixels.
f_flat[np.where(flat_bad)] = np.nan
return f_flat, f_flat_dq, f_flat_err


Expand Down Expand Up @@ -1070,9 +1075,6 @@
The 2D DQ array resulting from combining the input DQ arrays via
bitwise OR.
"""
badflat = dqflags.pixel["NO_FLAT_FIELD"] | dqflags.pixel["DO_NOT_USE"]
badflat = badflat | dqflags.pixel["UNRELIABLE_FLAT"]

dq_list = []
if f_flat_dq is not None:
dq_list.append(f_flat_dq)
Expand All @@ -1086,7 +1088,7 @@
# dq array with all BADFLAT bits set
flat_dq = np.zeros(default_shape, dtype=np.uint32)
if n_dq == 0:
flat_dq = np.bitwise_or(flat_dq, badflat)
flat_dq = np.bitwise_or(flat_dq, BADFLAT)

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else:
for dq_component in dq_list:
flat_dq = np.bitwise_or(flat_dq, dq_component)
Expand All @@ -1098,7 +1100,7 @@
# Flag DO_NOT_USE, NO_FLAT_FIELD and UNRELIABLE_FLAT where some or all the
# flats had DO_NOT_USE set
iloc = np.where(np.bitwise_and(flat_dq, dqflags.pixel["DO_NOT_USE"]))
flat_dq[iloc] = np.bitwise_or(flat_dq[iloc], badflat)
flat_dq[iloc] = np.bitwise_or(flat_dq[iloc], BADFLAT)

return flat_dq

Expand Down Expand Up @@ -1720,12 +1722,12 @@
None,
None,
)
flat_2d[nan_flag] = 1.0
mask = flat_2d <= 0.0
nbad = mask.sum(dtype=np.intp)
if nbad > 0:
log.debug("%d flat-field values <= 0", nbad)
flat_2d[mask] = 1.0
flat_2d[mask] = np.nan
flat_dq_2d[mask] = np.bitwise_or(flat_dq_2d[mask], BADFLAT)

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del mask

flat[ystart:ystop, xstart:xstop][good_flag] = flat_2d[good_flag]
Expand Down Expand Up @@ -1859,7 +1861,8 @@
nbad = mask.sum(dtype=np.intp)
if nbad > 0:
log.debug("%d flat-field values <= 0", nbad)
flat_2d[mask] = 1.0
flat_2d[mask] = np.nan
flat_dq_2d[mask] = np.bitwise_or(flat_dq_2d[mask], BADFLAT)

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del mask

flat_dq_2d = flat_dq_2d.astype(output_model.dq.dtype)
Expand Down Expand Up @@ -1984,7 +1987,8 @@
nbad = mask.sum(dtype=np.intp)
if nbad > 0:
log.debug("%d flat-field values <= 0", nbad)
flat_2d[mask] = 1.0
flat_2d[mask] = np.nan
flat_dq_2d[mask] = np.bitwise_or(flat_dq_2d[mask], BADFLAT)
del mask

# Put the computed flat, flat_dq and flat_err into a datamodel
Expand Down
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