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JP-3790 add residual fringe correction to extract1d table #9073

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JP-3790 add residual fringe correction to extract1d table #9073

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5 changes: 2 additions & 3 deletions jwst/extract_1d/extract_1d_step.py
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Original file line number Diff line number Diff line change
Expand Up @@ -88,8 +88,7 @@ class Extract1dStep(Step):

ifu_rfcorr : bool
Switch to select whether or not to apply a 1d residual fringe correction
for MIRI MRS IFU spectra. Default is False.

for MIRI MRS IFU spectra. Default is True.
ifu_set_srctype : str
For MIRI MRS IFU data override srctype and set it to either POINT or EXTENDED.

Expand Down Expand Up @@ -172,7 +171,7 @@ class Extract1dStep(Step):
center_xy = float_list(min=2, max=2, default=None) # IFU extraction x/y center
ifu_autocen = boolean(default=False) # Auto source centering for IFU point source data.
bkg_sigma_clip = float(default=3.0) # background sigma clipping threshold for IFU
ifu_rfcorr = boolean(default=False) # Apply 1d residual fringe correction
ifu_rfcorr = boolean(default=True) # Apply 1d residual fringe correction
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One concern with changing this to True is that it would then require failsafe cases for all non-MRS uses of extract1d, which may have unintended consequences. May be easier to keep as False, since the only purpose of the flag now is to print a message saying how the flag isn't necessary any longer.

ifu_set_srctype = option("POINT", "EXTENDED", None, default=None) # user-supplied source type
ifu_rscale = float(default=None, min=0.5, max=3) # Radius in terms of PSF FWHM to scale extraction radii
ifu_covar_scale = float(default=1.0) # Scaling factor to apply to errors to account for IFU cube covariance
Expand Down
73 changes: 44 additions & 29 deletions jwst/extract_1d/ifu.py
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Expand Up @@ -71,7 +71,7 @@

ifu_rfcorr : bool
Switch to select whether or not to apply a 1d residual fringe correction
for MIRI MRS IFU spectra. Default is False.
for MIRI MRS IFU spectra. Default is True.

ifu_rscale: float
For MRS IFU data a value for changing the extraction radius. The value provided is the number of PSF
Expand Down Expand Up @@ -106,7 +106,8 @@
else:
log.info(f"Source type = {source_type}")

output_model = datamodels.MultiSpecModel()
#output_model = datamodels.MultiSpecModel()
output_model = datamodels.MrsSpecModel()
output_model.update(input_model, only="PRIMARY")

slitname = input_model.meta.exposure.type
Expand Down Expand Up @@ -183,21 +184,21 @@

# Apply residual fringe to the flux array
try:
temp_flux = rfutils.fit_residual_fringes_1d(temp_flux, wavelength, channel=channel,
temp_flux_rf = rfutils.fit_residual_fringes_1d(temp_flux, wavelength, channel=channel,

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dichroic_only=False, max_amp=None)
except Exception:
log.info("Flux residual fringe correction failed- skipping.")

# Apply residual fringe to the surf_bright array
try:
surf_bright = rfutils.fit_residual_fringes_1d(surf_bright, wavelength, channel=channel,
surf_bright_rf = rfutils.fit_residual_fringes_1d(surf_bright, wavelength, channel=channel,

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dichroic_only=False, max_amp=None)
except Exception:
log.info("Surf bright residual fringe correction failed- skipping.")

# Apply residual fringe to the background array
try:
background = rfutils.fit_residual_fringes_1d(background, wavelength, channel=channel,
background_rf = rfutils.fit_residual_fringes_1d(background, wavelength, channel=channel,

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dichroic_only=False, max_amp=None)
except Exception:
log.info("Background residual fringe correction failed- skipping.")
Expand All @@ -208,17 +209,20 @@
"the flux will not be correct.")
pixel_solid_angle = 1.

# Convert flux from MJy / steradian to Jy.
# Convert flux from MJy / steradian to Jy
flux = temp_flux * pixel_solid_angle * 1.e6
flux_rf = temp_flux_rf * pixel_solid_angle * 1.e6

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f_var_poisson *= (pixel_solid_angle ** 2 * 1.e12) # (MJy / sr)**2 --> Jy**2
f_var_rnoise *= (pixel_solid_angle ** 2 * 1.e12) # (MJy / sr)**2 --> Jy**2
f_var_flat *= (pixel_solid_angle ** 2 * 1.e12) # (MJy / sr)**2 --> Jy**2
# surf_bright and background were computed above
del temp_flux
del temp_flux_rf

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error = np.sqrt(f_var_poisson + f_var_rnoise + f_var_flat)
sb_error = np.sqrt(sb_var_poisson + sb_var_rnoise + sb_var_flat)
berror = np.sqrt(b_var_poisson + b_var_rnoise + b_var_flat)
spec_dtype = datamodels.SpecModel().spec_table.dtype
spec_dtype = datamodels.MrsSpecModel().mrs_spec_table.dtype

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# If we only used the Poisson variance array as a vehicle to pass through
# non-differentiated errors, clear it again here so that only the total
Expand Down Expand Up @@ -250,31 +254,38 @@
list(
zip(wavelength, flux, error, f_var_poisson, f_var_rnoise, f_var_flat,
surf_bright, sb_error, sb_var_poisson, sb_var_rnoise, sb_var_flat,
dq, background, berror, b_var_poisson, b_var_rnoise, b_var_flat, npixels)
dq, background, berror, b_var_poisson, b_var_rnoise, b_var_flat, npixels,
flux_rf, surf_bright_rf, background_rf)
),
dtype=spec_dtype
)

spec = datamodels.SpecModel(spec_table=otab)
if ((input_model.meta.instrument.name == 'MIRI') & (extract_params['ifu_rfcorr'] is True)):
spec = datamodels.MrsSpecModel(mrs_spec_table=otab)

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else:
spec = datamodels.SpecModel(spec_table=otab)

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spec.meta.wcs = spec_wcs.create_spectral_wcs(ra, dec, wavelength)
spec.spec_table.columns['wavelength'].unit = 'um'
spec.spec_table.columns['flux'].unit = "Jy"
spec.spec_table.columns['flux_error'].unit = "Jy"
spec.spec_table.columns['flux_var_poisson'].unit = "Jy^2"
spec.spec_table.columns['flux_var_rnoise'].unit = "Jy^2"
spec.spec_table.columns['flux_var_flat'].unit = "Jy^2"
spec.spec_table.columns['surf_bright'].unit = "MJy/sr"
spec.spec_table.columns['sb_error'].unit = "MJy/sr"
spec.spec_table.columns['sb_var_poisson'].unit = "(MJy/sr)^2"
spec.spec_table.columns['sb_var_rnoise'].unit = "(MJy/sr)^2"
spec.spec_table.columns['sb_var_flat'].unit = "(MJy/sr)^2"
spec.spec_table.columns['background'].unit = "MJy/sr"
spec.spec_table.columns['bkgd_error'].unit = "MJy/sr"
spec.spec_table.columns['bkgd_var_poisson'].unit = "(MJy/sr)^2"
spec.spec_table.columns['bkgd_var_rnoise'].unit = "(MJy/sr)^2"
spec.spec_table.columns['bkgd_var_flat'].unit = "(MJy/sr)^2"
spec.mrs_spec_table.columns['wavelength'].unit = 'um'
spec.mrs_spec_table.columns['flux'].unit = "Jy"
spec.mrs_spec_table.columns['flux_error'].unit = "Jy"
spec.mrs_spec_table.columns['flux_var_poisson'].unit = "Jy^2"
spec.mrs_spec_table.columns['flux_var_rnoise'].unit = "Jy^2"
spec.mrs_spec_table.columns['flux_var_flat'].unit = "Jy^2"
spec.mrs_spec_table.columns['surf_bright'].unit = "MJy/sr"
spec.mrs_spec_table.columns['sb_error'].unit = "MJy/sr"
spec.mrs_spec_table.columns['sb_var_poisson'].unit = "(MJy/sr)^2"
spec.mrs_spec_table.columns['sb_var_rnoise'].unit = "(MJy/sr)^2"
spec.mrs_spec_table.columns['sb_var_flat'].unit = "(MJy/sr)^2"
spec.mrs_spec_table.columns['background'].unit = "MJy/sr"
spec.mrs_spec_table.columns['bkgd_error'].unit = "MJy/sr"
spec.mrs_spec_table.columns['bkgd_var_poisson'].unit = "(MJy/sr)^2"
spec.mrs_spec_table.columns['bkgd_var_rnoise'].unit = "(MJy/sr)^2"
spec.mrs_spec_table.columns['bkgd_var_flat'].unit = "(MJy/sr)^2"
spec.mrs_spec_table.columns['rf_flux'].unit = "Jy"
spec.mrs_spec_table.columns['rf_surf_bright'].unit = "MJy/sr"
spec.mrs_spec_table.columns['rf_background'].unit = "MJy/sr"

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spec.slit_ra = ra
spec.slit_dec = dec

if slitname is not None and slitname != "ANY":
spec.name = slitname

Expand Down Expand Up @@ -305,10 +316,14 @@
radius = radius_match[i]
apcorr.find_apcorr_func(i, radius)

apcorr.apply(spec.spec_table)

output_model.spec.append(spec)
apcorr.apply(spec.mrs_spec_table)

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#output_model.spec.append(spec)
output_model = spec
print(spec.mrs_spec_table['FLUX'])
print(spec.mrs_spec_table['RF_FLUX'])
print(spec.mrs_spec_table['RF_SURF_BRIGHT'])
print(spec.mrs_spec_table['RF_BACKGROUND'])

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# See output_model.spec[0].meta.wcs instead.
output_model.meta.wcs = None

Expand Down
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