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working version - spectroscopy
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@moustakas
moustakas committed Oct 30, 2024
1 parent 82cbe63 commit 615b769
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121 changes: 73 additions & 48 deletions py/fastspecfit/continuum.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1504,6 +1504,7 @@ def continuum_fastspec(redshift, objflam, objflamivar, CTools,
specflux = np.hstack(data['flux'])
specivar_nolinemask = np.hstack(data['ivar'])
specivar = specivar_nolinemask * np.logical_not(np.hstack(data['linemask'])) # mask emission lines
npix = len(specwave)

if np.all(specivar == 0.) or np.any(specivar < 0.):
errmsg = 'All pixels are masked or some inverse variances are negative!'
Expand All @@ -1519,11 +1520,17 @@ def continuum_fastspec(redshift, objflam, objflamivar, CTools,
snrmsg += f" S/N_{data['cameras'][icam]}={data['snr'][icam]:.2f}"
log.info(snrmsg)

ebv_ivar = 0.
vdisp_ivar = 0.
dn4000_model_ivar = 0.
coeff_monte = None
sedmodel_monte = None
sedmodel_nolines_monte = None

if templates.use_legacy_fitting:
ebv = 0.
ebvivar = 0.
ebv = None
(coeff, rchi2_cont, rchi2_phot, median_apercorr, apercorrs,
vdisp, vdispivar, sedmodel, sedmodel_nolines) = \
vdisp, vdisp_ivar, sedmodel, sedmodel_nolines) = \
_continuum_fastspec_legacy(redshift, specwave, specflux, specivar,
objflam, objflamivar, CTools,
debug_plots=debug_plots)
Expand Down Expand Up @@ -1617,18 +1624,30 @@ def continuum_fastspec(redshift, objflam, objflamivar, CTools,
f'[rchi2_cont={rchi2_cont:.1f}, ndof={ndof_cont:.0f}; ' + \
f'rchi2_phot={rchi2_phot:.1f}, ndof={ndof_phot:.0f}].')

# Monte Carlo here to get ebvivar, vdispivar, and coeff_monte.
if np.all(coeff == 0.):
log.warning('Continuum coefficients are all zero.')
sedmodel = np.zeros(len(templates.wave))
sedmodel_nolines = np.zeros(len(templates.wave))
dn4000_model = 0.
rchi2_cont = 0.
rchi2_phot = 0.
else:
# get the best-fitting model with and without line-emission
sedmodel = CTools.optimizer_saved_contmodel
sedmodel_nolines = CTools.build_stellar_continuum(
input_templateflux_nolines, coeff, ebv=ebv,
vdisp=(vdisp if compute_vdisp else None),
conv_pre=input_conv_pre_nolines, dust_emission=False)

# Monte Carlo here to get ebv_ivar, vdisp_ivar, and coeff_monte.
# --Capture case where vdisp (and also maybe ebv) hits its bounds.
# --delta-chi2 test for solving for velocity dispersion.
ebvivar = 0.
vdispivar = 0.
coeff_monte = None
if nmonte is not None and nmonte > 0 and (ndof_cont > 0 or ndof_phot > 0):
if nmonte > 0 and (ndof_cont > 0 or ndof_phot > 0):
if ndof_cont > 0:
specstd = np.zeros_like(specistd)
I = specistd > 0.
specstd[I] = 1. / specistd[I]
specflux_monte = rng.normal(loc=specflux[:, np.newaxis], scale=specstd[:, np.newaxis],
specflux_monte = rng.normal(specflux[:, np.newaxis], specstd[:, np.newaxis],
size=(len(specflux), nmonte))
else:
specflux_monte = np.repeat(specflux[:, np.newaxis], nmonte, axis=1)
Expand All @@ -1637,13 +1656,17 @@ def continuum_fastspec(redshift, objflam, objflamivar, CTools,
objflamstd = np.zeros_like(objflamistd)
I = objflamistd > 0.
objflamstd[I] = 1. / objflamistd[I]
objflam_monte = rng.normal(loc=objflam[:, np.newaxis], scale=objflamstd[:, np.newaxis], size=(len(objflam), nmonte))
objflam_monte = rng.normal(objflam[:, np.newaxis], objflamstd[:, np.newaxis],
size=(len(objflam), nmonte))
else:
objflam_monte = np.repeat(objflam[:, np.newaxis], nmonte, axis=1)

ebv_monte = np.zeros(nmonte)
vdisp_monte = np.zeros(nmonte)
dn4000_model_monte = np.zeros(nmonte)
coeff_monte = np.zeros((nage, nmonte))
sedmodel_monte = np.zeros((templates.npix, nmonte))
sedmodel_nolines_monte = np.zeros((templates.npix, nmonte))
for imonte in range(nmonte):
ebv1, vdisp1, coeff1, _ = CTools.fit_stellar_continuum(
input_templateflux, # [npix,nage]
Expand All @@ -1654,45 +1677,42 @@ def continuum_fastspec(redshift, objflam, objflamivar, CTools,
specflux=specflux_monte[:, imonte]*median_apercorr,
specistd=specistd/median_apercorr,
synthphot=True, synthspec=True)
coeff_monte[:, imonte] = coeff1
ebv_monte[imonte] = ebv1
vdisp_monte[imonte] = vdisp1
coeff_monte[:, imonte] = coeff1

ebvvar = np.var(ebv_monte)
vdispvar = np.var(vdisp_monte)
if ebvvar > 0.:
ebvivar = 1. / ebvvar
if vdispvar > 0.:
vdispivar = 1. / vdispvar
sedmodel_monte[:, imonte] = CTools.optimizer_saved_contmodel
sedmodel_nolines_monte[:, imonte] = CTools.build_stellar_continuum(
input_templateflux_nolines, coeff1, ebv=ebv1,
vdisp=(vdisp1 if compute_vdisp else None),
conv_pre=input_conv_pre_nolines, dust_emission=False)

dn4000_model1, _ = Photometry.get_dn4000(
templates.wave, sedmodel_nolines_monte[:, imonte], rest=True)
dn4000_model_monte[imonte] = dn4000_model1

ebv_var = np.var(ebv_monte)
vdisp_var = np.var(vdisp_monte)
dn4000_model_var = np.var(dn4000_model_monte)
if ebv_var > 0.:
ebv_ivar = 1. / ebv_var
if vdisp_var > 0.:
vdisp_ivar = 1. / vdisp_var
if dn4000_model_var > 0.:
dn4000_model_ivar = 1. / dn4000_model_var
#import matplotlib.pyplot as plt
#plt.clf()
#plt.hist(vdisp_monte, bins=20)
#plt.savefig('junk.png')

if np.all(coeff == 0.):
log.warning('Continuum coefficients are all zero.')
sedmodel = np.zeros(len(templates.wave))
dn4000_model = 0.
rchi2_cont = 0.
rchi2_phot = 0.
else:
var_msg = f'+/-{1./np.sqrt(ebvivar):.3f}' if ebvivar > 0. else ''
ebv_msg = f'E(B-V)={ebv:.3f}{var_msg} mag'

if compute_vdisp and vdispivar > 0.:
var_msg = f'+/-{1./np.sqrt(vdispivar):.1f}' if vdispivar > 0. else ''
vdisp_msg = f'vdisp={vdisp:.1f}{var_msg} km/s'
var_msg = f'+/-{1./np.sqrt(ebv_ivar):.3f}' if ebv_ivar > 0. else ''
ebv_msg = f'E(B-V)={ebv:.3f}{var_msg} mag'

log.info(f'{ebv_msg}, {vdisp_msg}.')
if compute_vdisp and vdisp_ivar > 0.:
var_msg = f'+/-{1./np.sqrt(vdisp_ivar):.1f}' if vdisp_ivar > 0. else ''
vdisp_msg = f'vdisp={vdisp:.1f}{var_msg} km/s'
log.info(f'{ebv_msg}, {vdisp_msg}.')

# get the best-fitting model with and without line-emission
sedmodel = CTools.optimizer_saved_contmodel
sedmodel_nolines = CTools.build_stellar_continuum(
input_templateflux_nolines, coeff, ebv=ebv,
vdisp=(vdisp if compute_vdisp else None),
conv_pre=input_conv_pre_nolines, dust_emission=False)

import pdb ; pdb.set_trace()
desimodel_nolines = CTools.continuum_to_spectroscopy(sedmodel_nolines)

# Get DN(4000).
Expand All @@ -1704,7 +1724,8 @@ def continuum_fastspec(redshift, objflam, objflamivar, CTools,

var_msg = f'+/-{1./np.sqrt(dn4000_ivar):.3f}' if dn4000_ivar > 0. else ''
msg = [f'Spectroscopic DN(4000)={dn4000:.3f}{var_msg}']
msg.append(f'model Dn(4000)={dn4000_model:.3f}')
var_msg = f'+/-{1./np.sqrt(dn4000_model_ivar):.3f}' if dn4000_model_ivar > 0. else ''
msg.append(f'model Dn(4000)={dn4000_model:.3f}{var_msg}')
log.info(', '.join(msg))

# Get the smooth continuum.
Expand Down Expand Up @@ -1743,9 +1764,10 @@ def continuum_fastspec(redshift, objflam, objflamivar, CTools,
corr = np.mean(1 - _smoothcontinuum[ss:ee][I] / specflux[ss:ee][I])
smoothstats[icam] = corr

return (coeff, rchi2_cont, rchi2_phot, median_apercorr, apercorrs,
ebv, ebvivar, vdisp, vdispivar, dn4000, dn4000_ivar, dn4000_model,
sedmodel, sedmodel_nolines, continuummodel, smoothcontinuum, smoothstats)
return (coeff, coeff_monte, rchi2_cont, rchi2_phot, median_apercorr, apercorrs,
ebv, ebv_ivar, vdisp, vdisp_ivar, dn4000, dn4000_ivar, dn4000_model,
dn4000_model_ivar, sedmodel, sedmodel_monte, sedmodel_nolines,
sedmodel_nolines_monte, continuummodel, smoothcontinuum, smoothstats)


def continuum_specfit(data, result, templates, igm, phot,
Expand Down Expand Up @@ -1801,13 +1823,14 @@ def continuum_specfit(data, result, templates, igm, phot,

if fastphot:
# Photometry-only fitting.
coeff, rchi2_phot, ebv, ebvivar, vdisp, dn4000_model, sedmodel, sedmodel_nolines = \
coeff, rchi2_phot, ebv, ebv_ivar, vdisp, dn4000_model, sedmodel, sedmodel_nolines = \
continuum_fastphot(redshift, objflam, objflamivar, CTools,
nmonte=nmonte, rng=rng, debug_plots=debug_plots)
else:
(coeff, rchi2_cont, rchi2_phot, median_apercorr, apercorrs,
ebv, ebvivar, vdisp, vdispivar, dn4000, dn4000_ivar, dn4000_model,
sedmodel, sedmodel_nolines, continuummodel, smoothcontinuum, smoothstats) = \
(coeff, coeff_monte, rchi2_cont, rchi2_phot, median_apercorr, apercorrs,
ebv, ebv_ivar, vdisp, vdisp_ivar, dn4000, dn4000_ivar, dn4000_model,
dn4000_model_ivar, sedmodel, sedmodel_monte, sedmodel_nolines,
sedmodel_nolines_monte, continuummodel, smoothcontinuum, smoothstats) = \
continuum_fastspec(redshift, objflam, objflamivar, CTools,
nmonte=nmonte, rng=rng, debug_plots=debug_plots,
no_smooth_continuum=no_smooth_continuum)
Expand All @@ -1829,9 +1852,11 @@ def continuum_specfit(data, result, templates, igm, phot,
result['RCHI2_PHOT'] = rchi2_phot
result['VDISP'] = vdisp # * u.kilometer/u.second

import pdb ; pdb.set_trace()

if not fastphot:
result['RCHI2_CONT'] = rchi2_cont
result['VDISP_IVAR'] = vdispivar # * (u.second/u.kilometer)**2
result['VDISP_IVAR'] = vdisp_ivar # * (u.second/u.kilometer)**2

result['APERCORR'] = median_apercorr
for iband, band in enumerate(phot.synth_bands):
Expand Down
1 change: 1 addition & 0 deletions py/fastspecfit/templates.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -92,6 +92,7 @@ def __init__(self, template_file=None, template_version=None, imf=None,
self.wave = templatewave[keeplo:keephi]
self.flux = templateflux[keeplo:keephi, :]
self.flux_nolines = self.flux - templatelineflux[keeplo:keephi, :]
self.npix = len(self.wave)

# dust attenuation curve
self.dust_klambda = Templates.klambda(self.wave)
Expand Down

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