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Fix coadd2d in sensfunc_blaze_jwst_lists branch #1635

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merged 3 commits into from
Jul 19, 2023
Merged

Fix coadd2d in sensfunc_blaze_jwst_lists branch #1635

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6be5550
fix rms_sn for echelle
debora-pe Jul 18, 2023
724e5c6
fix self.use_weight for echelle
debora-pe Jul 18, 2023
3b4ca61
fix bug
debora-pe Jul 19, 2023
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47 changes: 20 additions & 27 deletions pypeit/coadd2d.py
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Original file line number Diff line number Diff line change
Expand Up @@ -489,11 +489,13 @@ def coadd(self, only_slits=None, interp_dspat=True):
maskdef_dict = self.get_maskdef_dict(slit_idx, ref_trace_stack)

# weights
## JFH I do not understand why this is here and am removing it.
#if not isinstance(self.use_weights, str):
# weights = self.use_weights[slit_idx]
#else:
# weights = self.use_weights
# if this is echelle data and the parset 'weights' is set to 'auto',
# then the weights are computed per order, i.e., every order has a
# different set of weights in each exposure (len(self.use_weights[slit_idx]) = nexp)
if self.pypeline == 'Echelle' and self.weights == 'auto':
_weights = self.use_weights[slit_idx]
else:
_weights = self.use_weights

# Perform the 2d coadd
# NOTE: mask_stack is a gpm, and this is called inmask_stack in
Expand All @@ -507,7 +509,7 @@ def coadd(self, only_slits=None, interp_dspat=True):
self.stack_dict['waveimg_stack'],
self.wave_grid, self.spat_samp_fact,
maskdef_dict=maskdef_dict,
weights=self.use_weights, interp_dspat=interp_dspat)
weights=_weights, interp_dspat=interp_dspat)
coadd_list.append(coadd_dict)

return coadd_list
Expand Down Expand Up @@ -1090,8 +1092,6 @@ def compute_weights(self, weights):
msgs.info('Using uniform weights')
# use uniform weights
self.use_weights = (np.ones(self.nexp) / float(self.nexp)).tolist()
#self.use_weights = 'uniform'


# 3) Bright object exists and parset `weights` is equal to 'auto'
elif (self.objid_bri is not None) and (weights == 'auto'):
Expand Down Expand Up @@ -1348,25 +1348,21 @@ def get_brightest_obj(self, specobjs_list, spat_ids):
# Loop over each exposure, slit, find the brighest object on that slit for every exposure
for iexp, sobjs in enumerate(specobjs_list):
msgs.info("Working on exposure {}".format(iexp))
#nspec_now = self.nspec_array[iexp]
for islit, spat_id in enumerate(spat_ids):
ithis = np.abs(sobjs.SLITID - spat_id) <= self.par['coadd2d']['spat_toler']
#nobj_slit = np.sum(ithis)
if np.any(ithis):
objid_this = sobjs[ithis].OBJID
waves, fluxes, ivars, gpms = [], [], [], []
fluxes, ivars, gpms = [], [], []
for iobj, spec in enumerate(sobjs[ithis]):
# check if OPT_COUNTS is available
if spec.has_opt_ext():
wave_iobj, flux_iobj, ivar_iobj, gpm_iobj = spec.get_opt_ext()
waves.append(wave_iobj)
_, flux_iobj, ivar_iobj, gpm_iobj = spec.get_opt_ext()
fluxes.append(flux_iobj)
ivars.append(ivar_iobj)
gpms.append(gpm_iobj)
# check if BOX_COUNTS is available
elif spec.has_box_ext():
wave_iobj, flux_iobj, ivar_iobj, gpm_iobj = spec.get_box_ext()
waves.append(wave_iobj)
_, flux_iobj, ivar_iobj, gpm_iobj = spec.get_box_ext()
fluxes.append(flux_iobj)
ivars.append(ivar_iobj)
gpms.append(gpm_iobj)
Expand All @@ -1378,7 +1374,7 @@ def get_brightest_obj(self, specobjs_list, spat_ids):
msgs.warn(f'Optimal and Boxcar extraction not available for obj {spec.OBJID} in slit {spat_id}.')
#remove_indx.append(iobj)
# if there are objects on this slit left, we can proceed with computing rms_sn
if len(waves) > 0:
if len(fluxes) > 0:
rms_sn, weights = coadd.sn_weights(fluxes, ivars, gpms, const_weights=True)
imax = np.argmax(rms_sn)
slit_snr_max[islit, iexp] = rms_sn[imax]
Expand Down Expand Up @@ -1594,12 +1590,10 @@ def compute_weights(self, weights):
if (self.objid_bri is not None) and (weights == 'auto'):
# computing a list of weights for all the slitord_ids that we than parse in coadd
slitord_ids = self.stack_dict['slits_list'][0].slitord_id
use_weights = []
for id in slitord_ids:
_, iweights = self.optimal_weights(id, self.objid_bri)
use_weights.append(iweights)
# Commenting this out since self.use_weights needs to be a list or a string
#self.use_weights = np.array(use_weights)
self.use_weights = []
for idx in slitord_ids:
_, iweights = self.optimal_weights(idx, self.objid_bri)
self.use_weights.append(iweights)
if self.par['coadd2d']['user_obj'] is not None:
msgs.info('Weights computed using a unique reference object provided by the user')
else:
Expand Down Expand Up @@ -1628,7 +1622,6 @@ def get_brightest_obj(self, specobjs_list, nslits):

objid = np.zeros(nexp, dtype=int)
snr_bar = np.zeros(nexp)
# norders = specobjs_list[0].ech_orderindx.max() + 1
for iexp, sobjs in enumerate(specobjs_list):
msgs.info("Working on exposure {}".format(iexp))
uni_objid = np.unique(sobjs.ECH_OBJID)
Expand All @@ -1637,22 +1630,22 @@ def get_brightest_obj(self, specobjs_list, nslits):
bpm = np.ones((nslits, nobjs), dtype=bool)
for iord in range(nslits):
for iobj in range(nobjs):
flux = None
ind = (sobjs.ECH_ORDERINDX == iord) & (sobjs.ECH_OBJID == uni_objid[iobj])
# check if OPT_COUNTS is available
if sobjs[ind][0].has_opt_ext():
wave, flux, ivar, mask = sobjs[ind][0].get_opt_ext()
_, flux, ivar, mask = sobjs[ind][0].get_opt_ext()
# check if BOX_COUNTS is available
elif sobjs[ind][0].has_box_ext():
wave, flux, ivar, mask = sobjs[ind][0].get_box_ext()
_, flux, ivar, mask = sobjs[ind][0].get_box_ext()
msgs.warn(f'Optimal extraction not available for object {sobjs[ind][0].ECH_OBJID} '
f'in order {sobjs[ind][0].ECH_ORDER}. Using box extraction.')
else:
flux = None
msgs.warn(f'Optimal and Boxcar extraction not available for '
f'object {sobjs[ind][0].ECH_OBJID} in order {sobjs[ind][0].ECH_ORDER}.')
continue
if flux is not None:
rms_sn, weights = coadd.sn_weights(wave, flux, ivar, mask, const_weights=True)
rms_sn, weights = coadd.sn_weights([flux], [ivar], [mask], const_weights=True)
order_snr[iord, iobj] = rms_sn
bpm[iord, iobj] = False

Expand Down
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