def fit_dlogM_mw(tab, sfrsd_tab, mltype='ring', mlb='i'):
merge_tab = t.join(tab, sfrsd_tab, 'plateifu')
is_agn = m.mask_from_maskbits(merge_tab['mngtarg3'], [1, 2, 3, 4])
mlb_ix = totalmass.StellarMass.bands_ixs[mlb]
absmag_sun_mlb = totalmass.StellarMass.absmag_sun[mlb_ix]
logmass_in_ifu = merge_tab['mass_in_ifu'].to(u.dex(u.Msun))
logmass_in_ifu_lw = merge_tab['ml_fluxwt'] + merge_tab[f'logsollum_in_ifu_{mlb}']
merge_tab['dlogmass_lw'] = logmass_in_ifu - logmass_in_ifu_lw
std_atten_mwtd = merge_tab['std_atten_mwtd']
mean_atten_mwtd = merge_tab['mean_atten_mwtd']
ha_corr = np.exp(merge_tab['mean_atten_mwtd'] * (6563 / 5500)**-1.3)
sfrsd = merge_tab['sigma_sfr'] * ha_corr * u.Msun / u.yr / u.pc**2
outer_mass = (merge_tab[f'outerml_{mltype}'] + \
merge_tab[f'logsollum_outer_{mlb}']).to(u.Msun)
mass_pca = merge_tab['mass_in_ifu'].to(u.Msun) + outer_mass
ssfrsd = sfrsd / mass_pca
merge_tab['log_ssfrsd'] = ssfrsd.to(u.dex(ssfrsd.unit))
merge_tab['log_ssfrsd'][~np.isfinite(merge_tab['log_ssfrsd'])] = np.nan * merge_tab['log_ssfrsd'].unit
ols = OLS(
endog=np.array(merge_tab['dlogmass_lw'][~is_agn]),
exog=sm_add_constant(
t.Table(merge_tab['mean_atten_mwtd', 'std_atten_mwtd', 'log_ssfrsd'])[~is_agn].to_pandas(),
prepend=False),
hasconst=True, missing='drop')
olsfit = ols.fit()
return olsfit
def fit_dlogM_mw(tab, sfrsd_tab, mltype='ring', mlb='i'):
merge_tab = t.join(tab, sfrsd_tab, 'plateifu')
is_agn = m.mask_from_maskbits(merge_tab['mngtarg3'], [1, 2, 3, 4])
mlb_ix = totalmass.StellarMass.bands_ixs[mlb]
absmag_sun_mlb = totalmass.StellarMass.absmag_sun[mlb_ix]
logmass_in_ifu = merge_tab['mass_in_ifu'].to(u.dex(u.Msun))
logmass_in_ifu_lw = merge_tab['ml_fluxwt'] + merge_tab['ifu_absmag'][:, mlb_ix].to(
u.dex(m.bandpass_sol_l_unit), totalmass.bandpass_flux_to_solarunits(absmag_sun_mlb))
merge_tab['dlogmass_lw'] = logmass_in_ifu - logmass_in_ifu_lw
ha_corr = np.exp(merge_tab['mean_atten_mwtd'] * (6563 / 5500)**-1.3)
sfrsd = merge_tab['sigma_sfr'] * ha_corr * u.Msun / u.yr / u.pc**2
mass_pca = merge_tab['mass_in_ifu'] + merge_tab['outer_mass_{}'.format(mltype)]
ssfrsd = sfrsd / mass_pca
merge_tab['log_ssfrsd'] = ssfrsd.to(u.dex(ssfrsd.unit))
merge_tab['log_ssfrsd'][~np.isfinite(merge_tab['log_ssfrsd'])] = np.nan * merge_tab['log_ssfrsd'].unit
ols = OLS(
endog=np.array(merge_tab['dlogmass_lw'][~is_agn]),
exog=sm_add_constant(
t.Table(merge_tab['mean_atten_mwtd', 'std_atten_mwtd', 'log_ssfrsd'])[~is_agn].to_pandas(),
prepend=False),
hasconst=True, missing='drop')
olsfit = ols.fit()
return olsfit
def compare_missing_mass(tab, mlb='i', cb1='g', cb2='r'):
'''make figure showing effect of aperture correction on total mass
Figure shows P+ (red) and S (blue) samples,
with their integrated color, difference between aperture-corrected
masses using CMLR and ring method
Parameters
----------
tab : astropy.table.Table
full aggregation results table
mlb : {str}, optional
bandpass for mass-to-light ratio
(the default is 'i', which [default_description])
cb1 : {str}, optional
bluer bandpass for color (the default is 'g', SDSS g band)
cb2 : {str}, optional
redder bandpass for color (the default is 'r', SDSS r band)
'''
cb1_nsa_mag = tab[f'mag_nsa_{cb1}']
cb2_nsa_mag = tab[f'mag_nsa_{cb2}']
broadband_color = cb1_nsa_mag - cb2_nsa_mag
outermass_cmlr = (tab[f'logsollum_outer_{mlb}'] + tab['outerml_cmlr']).to(
u.Msun)
mass_cmlr = (tab['mass_in_ifu'].to(u.Msun) + outermass_cmlr)
outermass_ring = (tab[f'logsollum_outer_{mlb}'] + tab['outerml_ring']).to(
u.Msun)
mass_ring = (tab['mass_in_ifu'].to(u.Msun) + outermass_ring)
dlogmass_cmlr_ring = mass_cmlr.to(u.dex(u.Msun)) - mass_ring.to(u.dex(u.Msun))
primarysample = m.mask_from_maskbits(tab['mngtarg1'], [10])
secondarysample = m.mask_from_maskbits(tab['mngtarg1'], [11])
fig, main_ax, hist_ax = make_panel_hist(top=0.9, left=.225)
valid = np.isfinite(dlogmass_cmlr_ring)
for selection, label, marker, color in zip(
[primarysample, secondarysample], ['Primary', 'Secondary'],
['o', 'D'], ['r', 'b']):
main_ax.scatter(
x=broadband_color[selection * valid], y=dlogmass_cmlr_ring[selection * valid],
c=color, edgecolor='None', s=3., marker=marker, label=label,
alpha=0.5)
hist_ax.hist(dlogmass_cmlr_ring[selection * valid], color=color, density=True, bins='auto',
histtype='step', orientation='horizontal', linewidth=0.75)
main_ax.set_xlim(np.percentile(broadband_color[valid], [5., 99.]))
main_ax.set_ylim(np.percentile(dlogmass_cmlr_ring[valid], [5., 99.]))
main_ax.legend(loc='best', prop={'size': 'xx-small'})
main_ax.tick_params(labelsize='xx-small')
main_ax.set_xlabel(r'${}-{}$'.format(cb1, cb2), size='x-small')
main_ax.set_ylabel(r'$\log \frac{M^{\rm tot}_{\rm CMLR}}{M^{\rm tot}_{\rm ring}}$',
size='x-small')
fig.suptitle(r'Impact of aperture-correction on $M^{\rm tot}$', size='small')
fig.savefig(os.path.join(csp_basedir, 'lib_diags/', 'mtot_compare_cmlr_ring.png'))
def test_cds_function_units(reader_cls):
data_and_readme = 'data/cdsFunctional.dat'
reader = ascii.get_reader(reader_cls)
table = reader.read(data_and_readme)
assert table['logg'].unit == u.dex(u.cm / u.s**2)
assert table['logTe'].unit == u.dex(u.K)
assert table['Mass'].unit == u.Msun
assert table['e_Mass'].unit == u.Msun
assert table['Age'].unit == u.Myr
assert table['e_Age'].unit == u.Myr
def test_cds_function_units():
from astropy.units import dex
data_and_readme = 'data/cdsFunctional.dat'
reader = ascii.get_reader(ascii.Cds)
table = reader.read(data_and_readme)
assert table['logg'].unit == u.dex(u.cm / u.s**2)
assert table['logTe'].unit == u.dex(u.K)
assert table['Mass'].unit == u.Msun
assert table['e_Mass'].unit == u.Msun
assert table['Age'].unit == u.Myr
assert table['e_Age'].unit == u.Myr
def test_cds_function_units2(reader_cls):
# This one includes some dimensionless dex.
data_and_readme = 'data/cdsFunctional2.dat'
reader = ascii.get_reader(reader_cls)
table = reader.read(data_and_readme)
assert table['Teff'].unit == u.K
assert table['logg'].unit == u.dex(u.cm / u.s**2)
assert table['vturb'].unit == u.km / u.s
assert table['[Fe/H]'].unit == u.dex(u.one)
assert table['e_[Fe/H]'].unit == u.dex(u.one)
assert_almost_equal(table['[Fe/H]'].to(u.one),
10.**(np.array([-2.07, -1.50, -2.11, -1.64])))
def test_to_funcunit_quantity(self, Column):
"""
Tests for #8424, check if function-unit can be retrieved from column.
"""
d = Column([1, 2, 3], name='a', dtype="f8", unit="dex(AA)")
assert np.all(d.quantity == ([1, 2, 3] * u.dex(u.AA)))
assert np.all(d.quantity.value == ([1, 2, 3] * u.dex(u.AA)).value)
assert np.all(d.quantity == d.to("dex(AA)"))
assert np.all(d.quantity.value == d.to("dex(AA)").value)
# make sure, casting to linear unit works
q = [10, 100, 1000] * u.AA
np.testing.assert_allclose(d.to(u.AA), q)
def make_stdtauV_vs_dMass_ssfrsd_fig(tab, sfrsd_tab, mltype='ring', mlb='i'):
merge_tab = t.join(tab, sfrsd_tab, 'plateifu')
mlb_ix = totalmass.StellarMass.bands_ixs[mlb]
absmag_sun_mlb = totalmass.StellarMass.absmag_sun[mlb_ix]
fig, ax, cax, hist_ax = make_panel_hcb_hist(figsize=(3, 3), dpi=300, top=.8)
logmass_in_ifu = merge_tab['mass_in_ifu'].to(u.dex(u.Msun))
logmass_in_ifu_lw = merge_tab['ml_fluxwt'] + merge_tab['ifu_absmag'][:, mlb_ix].to(
u.dex(m.bandpass_sol_l_unit), totalmass.bandpass_flux_to_solarunits(absmag_sun_mlb))
std_atten_mwtd = merge_tab['std_atten_mwtd']
mean_atten_mwtd = merge_tab['mean_atten_mwtd']
ha_corr = np.exp(merge_tab['mean_atten_mwtd'] * (6563 / 5500)**-1.3)
sfrsd = merge_tab['sigma_sfr'] * ha_corr * u.Msun / u.yr / u.pc**2
mass_pca = merge_tab['mass_in_ifu'] + merge_tab['outer_mass_{}'.format(mltype)]
ssfrsd = sfrsd / mass_pca
sc = ax.scatter(
x=std_atten_mwtd, y=(logmass_in_ifu - logmass_in_ifu_lw),
c=ssfrsd.to(u.dex(ssfrsd.unit)),
edgecolor='k', linewidths=.125, s=2., cmap='viridis_r',
vmin=-15., vmax=-10.)
cb = colorbartop(fig, sc, cax)
cb.set_label(r'$\log \frac{{\Sigma}^{\rm SFR}_{R<R_e}}{M^*_{\rm tot}}$', size='xx-small')
ax.tick_params(which='major', labelsize='xx-small')
ax.tick_params(which='minor', labelbottom=False, labelleft=False)
ax.set_xscale('log')
ax.set_xlabel(r'$\sigma_{\tau_V}$', size='x-small')
ax.set_ylabel(r'$\log{ \frac{M^*}{M^*_{\rm LW}} ~ {\rm [dex]} }$', size='x-small')
hist_ax.hist(np.ma.masked_invalid(logmass_in_ifu - logmass_in_ifu_lw).compressed(),
bins='auto', histtype='step', orientation='horizontal', linewidth=.5,
density=True, color='k')
for yloc, lw, ls, c in zip(
np.percentile(np.ma.masked_invalid(logmass_in_ifu - logmass_in_ifu_lw).compressed(),
[16., 50., 84.]),
[.5, 1., .5], ['--', '-', '--'], ['gray', 'k', 'gray']):
hist_ax.axhline(yloc, linestyle=ls, linewidth=lw, color=c)
fig.suptitle('Mass excess from luminosity-weighting', size='x-small')
fig.savefig(
os.path.join(basedir, 'lib_diags/', 'stdtauV_dMglobloc_ssfrsd.png'),
dpi=fig.dpi)
def update_mass_table(drpall, mass_table_old=None, limit=None, mlband='i'):
'''
'''
# what galaxies are available to aggregate?
res_fnames = glob(os.path.join(basedir, 'results/*-*/*-*_res.fits'))[:limit]
# filter out whose that have not been done
if mass_table_old is None:
already_aggregated = [False for _ in range(len(res_fnames))]
else:
already_aggregated = [os.path.split(fn)[1].split('_')[0] in old_mass_table['plateifu']
for fn in res_fnames]
res_fnames = [fn for done, fn in zip(already_aggregated, res_fnames)]
# aggregate individual galaxies, and stack them
mass_tables_new = list(ProgressBar.map(
partial(mass_agg_onegal, mlband=mlband), res_fnames, multiprocess=False, step=5))
mass_table_new = t.vstack(mass_tables_new)
# if there was an old mass table, stack it with the new one
if mass_table_old is None:
mass_table = mass_table_new
else:
mass_table = t.vstack([mass_table_old, mass_table_new], join_type='inner')
cmlr = totalmass.cmlr_kwargs
missing_flux = (mass_table['nsa_absmag'].to(m.Mgy) - \
mass_table['ifu_absmag'].to(m.Mgy)).clip(
a_min=0.*m.Mgy, a_max=np.inf*m.Mgy)
mag_missing_flux = missing_flux.to(u.ABmag)
cb1, cb2 = cmlr['cb1'], cmlr['cb2']
color_missing_flux = mag_missing_flux[:, totalmass.StellarMass.bands_ixs[cb1]] - \
mag_missing_flux[:, totalmass.StellarMass.bands_ixs[cb2]]
color_missing_flux[~np.isfinite(color_missing_flux)] = np.inf
mass_table['outer_ml_cmlr'] = np.polyval(cmlr['cmlr_poly'], color_missing_flux.value) * \
u.dex(m.m_to_l_unit)
mass_table['outer_lum'] = mag_missing_flux.to(
u.dex(m.bandpass_sol_l_unit),
totalmass.bandpass_flux_to_solarunits(totalmass.StellarMass.absmag_sun))
mass_table['outer_mass_ring'] = \
(mass_table['outer_lum'][:, totalmass.StellarMass.bands_ixs['i']] + \
mass_table['outer_ml_ring']).to(u.Msun)
mass_table['outer_mass_cmlr'] = \
(mass_table['outer_lum'][:, totalmass.StellarMass.bands_ixs['i']] + \
mass_table['outer_ml_cmlr']).to(u.Msun)
return mass_table
def sollum_bands(self):
with catch_warnings():
simplefilter('ignore', category=RuntimeWarning)
sollum = self.absmag_bands.to(
u.dex(m.bandpass_sol_l_unit),
bandpass_flux_to_solarunits(self.absmag_sun[..., None, None]))
return sollum
def test_str(self):
"""Do some spot checks that str, repr, etc. work as expected."""
lu1 = u.mag(u.Jy)
assert str(lu1) == 'mag(Jy)'
assert repr(lu1) == 'Unit("mag(Jy)")'
assert lu1.to_string('generic') == 'mag(Jy)'
with pytest.raises(ValueError):
lu1.to_string('fits')
with pytest.raises(ValueError):
lu1.to_string(format='cds')
lu2 = u.dex()
assert str(lu2) == 'dex'
assert repr(lu2) == 'Unit("dex(1)")'
assert lu2.to_string() == 'dex(1)'
lu3 = u.MagUnit(u.Jy, function_unit=2 * u.mag)
assert str(lu3) == '2 mag(Jy)'
assert repr(lu3) == 'MagUnit("Jy", unit="2 mag")'
assert lu3.to_string() == '2 mag(Jy)'
lu4 = u.mag(u.ct)
assert lu4.to_string('generic') == 'mag(ct)'
assert lu4.to_string('latex') == ('$\\mathrm{mag}$$\\mathrm{\\left( '
'\\mathrm{ct} \\right)}$')
assert lu4._repr_latex_() == lu4.to_string('latex')
def __init__(self, results, pca_system, drp, dap, drpall_row, cosmo, mlband='i'):
self.results = results
self.pca_system = pca_system
self.drp = drp
self.dap = dap
self.drpall_row = drpall_row
self.cosmo = cosmo
self.mlband = mlband
with catch_warnings():
simplefilter('ignore')
self.results.setup_photometry(pca_system)
self.s2p = results.spec2phot
# stellar mass to light ratio
self.ml0 = results.cubechannel('ML{}'.format(mlband), 0)
self.badpdf = results.cubechannel('GOODFRAC', 2) < 1.0e-4
self.ml_mask = np.logical_or.reduce((self.results.mask, self.badpdf))
# infer values in interior spaxels affected by one of the following:
# bad PDF, foreground star, dead fiber
self.low_or_no_cov = m.mask_from_maskbits(
self.drp['MASK'].data, [0, 1]).mean(axis=0) > .3
self.drp3dmask_interior = m.mask_from_maskbits(
self.drp['MASK'].data, [2, 3]).mean(axis=0) > .3
self.interior_mask = np.logical_or.reduce((self.badpdf, self.drp3dmask_interior))
self.logml_final = infer_masked(
q_trn=self.ml0, bad_trn=self.ml_mask,
infer_here=self.interior_mask) * u.dex(m.m_to_l_unit)
def sollum_bands(self):
with catch_warnings():
simplefilter('ignore', category=RuntimeWarning)
sollum = self.absmag_bands.to(
u.dex(m.bandpass_sol_l_unit),
bandpass_flux_to_solarunits(self.absmag_sun[..., None, None]))
return sollum
def test_using_quantity_class(self):
"""Check that we can use Quantity if we have subok=True"""
# following issue #5851
lu = u.dex(u.AA)
with pytest.raises(u.UnitTypeError):
u.Quantity(1., lu)
q = u.Quantity(1., lu, subok=True)
assert type(q) is lu._quantity_class
def test_using_quantity_class(self):
"""Check that we can use Quantity if we have subok=True"""
# following issue #5851
lu = u.dex(u.AA)
with pytest.raises(u.UnitTypeError):
u.Quantity(1., lu)
q = u.Quantity(1., lu, subok=True)
assert type(q) is lu._quantity_class
def test_inequality():
"""Check __ne__ works (regression for #5342)."""
lu1 = u.mag(u.Jy)
lu2 = u.dex(u.Jy)
lu3 = u.mag(u.Jy**2)
lu4 = lu3 - lu1
assert lu1 != lu2
assert lu1 != lu3
assert lu1 == lu4
def test_inequality():
"""Check __ne__ works (regresssion for #5342)."""
lu1 = u.mag(u.Jy)
lu2 = u.dex(u.Jy)
lu3 = u.mag(u.Jy**2)
lu4 = lu3 - lu1
assert lu1 != lu2
assert lu1 != lu3
assert lu1 == lu4
def cmlr_equivalency(slope, intecept):
'''
'''
def color_to_logml(c):
return slope * c + intercept
def logml_to_color(logml):
return (logml - intercept) / slope
return [(u.mag, u.dex(m.m_to_l_unit), color_to_logml, logml_to_color)]
def cmlr_equivalency(slope, intercept):
'''
'''
def color_to_logml(c):
return slope * c + intercept
def logml_to_color(logml):
return (logml - intercept) / slope
return [(u.mag, u.dex(m.m_to_l_unit), color_to_logml, logml_to_color)]
def compare_mtot_pca_nsa(tab, jhu_mpa, mltype='ring', mlb='i', cb1='g', cb2='r'):
jointab = t.join(tab, jhu_mpa, 'plateifu')
cb1_nsa_mag = jointab[f'mag_nsa_{cb1}']
cb2_nsa_mag = jointab[f'mag_nsa_{cb2}']
broadband_color = cb1_nsa_mag - cb2_nsa_mag
outer_mass = (jointab[f'outerml_{mltype}'] + \
jointab[f'logsollum_outer_{mlb}']).to(u.dex(u.Msun))
mass_pca = jointab['mass_in_ifu'].to(u.Msun) + outer_mass.to(u.Msun)
nsa_h = 1.
mass_nsa = (jointab['nsa_elpetro_mass'] * u.Msun * (nsa_h * u.littleh)**-2).to(
u.Msun, u.with_H0(cosmo.H0))
jhumpa_h = 1. / .7
chabrier_to_kroupa_dex = .05
mass_jhumpa = (10.**(jointab['LOG_MSTAR'] + chabrier_to_kroupa_dex) * \
u.Msun * (jhumpa_h * u.littleh)**-2.).to(u.Msun, u.with_H0(cosmo.H0))
lowess_grid = np.linspace(np.nanmin(broadband_color), np.nanmax(broadband_color), 100).value
lowess_pca_nsa, swt_nsa = smooth(
x=broadband_color.value, y=np.log10(mass_pca / mass_nsa).value,
xgrid=lowess_grid, bw=.01)
lowess_pca_jhumpa, swt_jhumpa = smooth(
x=broadband_color.value, y=np.log10(mass_pca / mass_jhumpa).value,
xgrid=lowess_grid, bw=.01)
swt_th = .2 * swt_nsa.max()
good_lowess_nsa = (swt_nsa >= swt_th)
good_lowess_jhumpa = (swt_jhumpa >= swt_th)
fig, ax = plt.subplots(1, 1, figsize=(3, 3), dpi=300)
ax.scatter(broadband_color, np.log10(mass_pca / mass_nsa),
s=2., edgecolor='None', c='C0', label='NSA')
ax.plot(lowess_grid[good_lowess_nsa], lowess_pca_nsa[good_lowess_nsa], linewidth=0.5, c='k', linestyle='-')
ax.scatter(broadband_color, np.log10(mass_pca / mass_jhumpa),
s=2., edgecolor='None', c='C1', label='JHU-MPA')
ax.plot(lowess_grid[good_lowess_jhumpa], lowess_pca_jhumpa[good_lowess_jhumpa],
linewidth=0.5, c='k', linestyle='--')
ax.set_ylim([-.2, .5]);
ax.set_xlim([-.1, 1.])
ax.legend(loc='best', prop={'size': 'xx-small'})
ax.tick_params(labelsize='xx-small')
ax.set_xlabel(r'${}-{}$'.format(cb1, cb2), size='x-small')
ax.set_ylabel(r'$\log \frac{M^*_{\rm PCA}}{M^*_{\rm catalog}}$',
size='x-small')
fig.tight_layout()
fig.subplots_adjust(top=.95, left=.21, right=.97)
fig.savefig(os.path.join(csp_basedir, 'lib_diags/', 'dMasses.png'), dpi=fig.dpi)
def make_stdtauV_vs_ssfrsd_dMass_fig(tab, sfrsd_tab, mltype='ring', mlb='i'):
merge_tab = t.join(tab, sfrsd_tab, 'plateifu')
mlb_ix = totalmass.StellarMass.bands_ixs[mlb]
absmag_sun_mlb = totalmass.StellarMass.absmag_sun[mlb_ix]
fig, ax = plt.subplots(1, 1, figsize=(3, 3), dpi=300)
logmass_in_ifu = merge_tab['mass_in_ifu'].to(u.dex(u.Msun))
logmass_in_ifu_lw = merge_tab['ml_fluxwt'] + merge_tab[f'logsollum_in_ifu_{mlb}']
std_atten_mwtd = merge_tab['std_atten_mwtd']
mean_atten_mwtd = merge_tab['mean_atten_mwtd']
ha_corr = np.exp(merge_tab['mean_atten_mwtd'] * (6563 / 5500)**-1.3)
sfrsd = merge_tab['sigma_sfr'] * ha_corr * u.Msun / u.yr / u.pc**2
outer_mass = (merge_tab[f'outerml_{mltype}'] + \
merge_tab[f'logsollum_outer_{mlb}']).to(u.Msun)
mass_pca = merge_tab['mass_in_ifu'].to(u.Msun) + outer_mass
ssfrsd = sfrsd / mass_pca
sc = ax.scatter(
x=np.log10(std_atten_mwtd), c=(logmass_in_ifu - logmass_in_ifu_lw),
y=ssfrsd.to(u.dex(ssfrsd.unit)),
edgecolor='k', linewidths=.125, s=1., cmap='viridis_r', alpha=0.5,
vmin=.01, vmax=.12)
cb = fig.colorbar(sc, ax=ax, extend='both')
cb.set_label(r'$\log{ \frac{M^*}{M^*_{\rm LW}} ~ {\rm [dex]} }$', size='xx-small')
cb.ax.tick_params(labelsize='xx-small')
ax.tick_params(which='major', labelsize='xx-small')
ax.tick_params(which='minor', labelbottom=False, labelleft=False)
ax.set_xlabel(r'$\log \sigma_{\tau_V}$', size='x-small')
ax.set_ylabel(r'$\log \frac{{\Sigma}^{\rm SFR}_{R<R_e}}{M^*_{\rm tot}}$', size='x-small')
fig.tight_layout()
fig.suptitle('Mass excess from luminosity-weighting', size='x-small')
fig.subplots_adjust(left=.225, bottom=.125, right=.9, top=.925)
fig.savefig(
os.path.join(csp_basedir, 'lib_diags/', 'stdtauV_ssfrsd_dMglobloc.png'),
dpi=fig.dpi)
def to_table(self):
'''
make table of stellar-mass results
'''
tab = t.QTable()
tab['plateifu'] = [self.drpall_row['plateifu']]
# tabulate mass in IFU
tab['mass_in_ifu'] = self.mstar_in_ifu[
None, ...][:, self.bands_ixs[self.mlband]]
nsa_absmag = self.nsa_absmags_cosmocorr
#tab['nsa_absmag'].meta['bands'] = self.bands
ifu_absmag = (self.ifu_flux_bands.to(u.ABmag) - self.distmod)
#tab['ifu_absmag'].meta['bands'] = self.bands
missing_flux = ((nsa_absmag + self.distmod).to(m.Mgy) -
(ifu_absmag + self.distmod).to(m.Mgy)).clip(
a_min=0. * m.Mgy, a_max=np.inf * m.Mgy)
for i, b in enumerate(self.bands):
outer_flux = missing_flux[i]
if outer_flux <= 0. * m.Mgy:
tab['outer_absmag_{}'.format(b)] = np.inf * u.ABmag
tab['outer_lum_{}'.format(b)] = -np.inf * u.dex(
m.bandpass_sol_l_unit)
else:
tab['outer_absmag_{}'.format(b)] = outer_flux.to(
u.ABmag) - self.distmod
tab['outer_lum_{}'.format(b)] = tab['outer_absmag_{}'.format(
b)].to(
u.dex(m.bandpass_sol_l_unit),
bandpass_flux_to_solarunits(StellarMass.absmag_sun[i]))
tab['outer_ml_ring'] = self.ml_ring()
#tab['outer_ml_ring'].meta['band'] = self.mlband
tab['ml_fluxwt'] = self.logml_fnuwt
#tab['ml_fluxwt'].meta['band'] = self.mlband
tab['distmod'] = self.distmod[None, ...]
return tab
def logspace(start, stop, *args, **kwargs):
from astropy.units import LogQuantity, dex
if (not isinstance(start, LogQuantity)
or not isinstance(stop, LogQuantity)):
raise NotImplementedError
# Get unit from end point as for linspace.
stop = stop.to(dex(stop.unit.physical_unit))
start = start.to(stop.unit)
unit = stop.unit.physical_unit
return (start.value, stop.value) + args, kwargs, unit, None
def compare_missing_mass(tab, mlb='i', cb1='g', cb2='r'):
mlb_ix = totalmass.StellarMass.bands_ixs[mlb]
cb1_ix = totalmass.StellarMass.bands_ixs[cb1]
cb2_ix = totalmass.StellarMass.bands_ixs[cb2]
absmag_sun_mlb = totalmass.StellarMass.absmag_sun[mlb_ix]
broadband_color = (tab['nsa_absmag'][:, cb1_ix] - tab['nsa_absmag'][:, cb2_ix])
outerlum_frac = tab['outer_lum'][:, mlb_ix].to(m.bandpass_sol_l_unit) / \
tab['nsa_absmag'][:, mlb_ix].to(m.bandpass_sol_l_unit,
totalmass.bandpass_flux_to_solarunits(absmag_sun_mlb))
dlogmass_cmlr_ring = ((tab['mass_in_ifu'] + tab['outer_mass_cmlr']).to(u.dex(u.Msun)) - \
(tab['mass_in_ifu'] + tab['outer_mass_ring']).to(u.dex(u.Msun)))
primarysample = m.mask_from_maskbits(tab['mngtarg1'], [10])
secondarysample = m.mask_from_maskbits(tab['mngtarg1'], [11])
fig, main_ax, hist_ax = make_panel_hist(top=0.9, left=.225)
valid = np.isfinite(dlogmass_cmlr_ring)
for selection, label, marker, color in zip(
[primarysample, secondarysample], ['Primary', 'Secondary'],
['o', 'D'], ['r', 'b']):
main_ax.scatter(
x=broadband_color[selection * valid], y=dlogmass_cmlr_ring[selection * valid],
c=color, edgecolor='None', s=5., marker=marker, label=label)
hist_ax.hist(dlogmass_cmlr_ring[selection * valid], color=color, density=True, bins='auto',
histtype='step', orientation='horizontal', linewidth=0.75)
main_ax.set_xlim(np.percentile(broadband_color[valid], [1., 99.]))
main_ax.set_ylim(np.percentile(dlogmass_cmlr_ring[valid], [1., 99.]))
main_ax.legend(loc='best', prop={'size': 'xx-small'})
main_ax.tick_params(labelsize='xx-small')
main_ax.set_xlabel(r'${}-{}$'.format(cb1, cb2), size='x-small')
main_ax.set_ylabel(r'$\log \frac{M^{\rm tot}_{\rm CMLR}}{M^{\rm tot}_{\rm ring}}$',
size='x-small')
fig.suptitle(r'Impact of aperture-correction on $M^{\rm tot}$', size='small')
fig.savefig(os.path.join(basedir, 'lib_diags/', 'mtot_compare_cmlr_ring.png'))
def make_stdtauV_vs_ssfrsd_dMass_fig(tab, sfrsd_tab, mltype='ring', mlb='i'):
merge_tab = t.join(tab, sfrsd_tab, 'plateifu')
mlb_ix = totalmass.StellarMass.bands_ixs[mlb]
absmag_sun_mlb = totalmass.StellarMass.absmag_sun[mlb_ix]
fig, ax = plt.subplots(1, 1, figsize=(3, 3), dpi=300)
logmass_in_ifu = merge_tab['mass_in_ifu'].to(u.dex(u.Msun))
logmass_in_ifu_lw = merge_tab['ml_fluxwt'] + merge_tab['ifu_absmag'][:, mlb_ix].to(
u.dex(m.bandpass_sol_l_unit), totalmass.bandpass_flux_to_solarunits(absmag_sun_mlb))
std_atten_mwtd = merge_tab['std_atten_mwtd']
mean_atten_mwtd = merge_tab['mean_atten_mwtd']
ha_corr = np.exp(merge_tab['mean_atten_mwtd'] * (6563 / 5500)**-1.3)
sfrsd = merge_tab['sigma_sfr'] * ha_corr * u.Msun / u.yr / u.pc**2
mass_pca = merge_tab['mass_in_ifu'] + merge_tab['outer_mass_{}'.format(mltype)]
ssfrsd = sfrsd / mass_pca
sc = ax.scatter(
x=np.log10(std_atten_mwtd), c=(logmass_in_ifu - logmass_in_ifu_lw),
y=ssfrsd.to(u.dex(ssfrsd.unit)),
edgecolor='k', linewidths=.125, s=2., cmap='viridis_r',
vmin=.01, vmax=.12)
cb = fig.colorbar(sc, ax=ax, extend='both')
cb.set_label(r'$\log{ \frac{M^*}{M^*_{\rm LW}} ~ {\rm [dex]} }$', size='xx-small')
cb.ax.tick_params(labelsize='xx-small')
ax.tick_params(which='major', labelsize='xx-small')
ax.tick_params(which='minor', labelbottom=False, labelleft=False)
ax.set_xlabel(r'$\log \sigma_{\tau_V}$', size='x-small')
ax.set_ylabel(r'$\log \frac{{\Sigma}^{\rm SFR}_{R<R_e}}{M^*_{\rm tot}}$', size='x-small')
fig.tight_layout()
fig.suptitle('Mass excess from luminosity-weighting', size='x-small')
fig.subplots_adjust(left=.2, bottom=.125, right=.9, top=.925)
fig.savefig(
os.path.join(basedir, 'lib_diags/', 'stdtauV_ssfrsd_dMglobloc.png'),
dpi=fig.dpi)
def make_stdtauV_vs_dMass_ba_fig(tab, mlb='i'):
mlb_ix = totalmass.StellarMass.bands_ixs[mlb]
absmag_sun_mlb = totalmass.StellarMass.absmag_sun[mlb_ix]
fig, ax, cax, hist_ax = make_panel_hcb_hist(figsize=(3, 3), dpi=300)
logmass_in_ifu = tab['mass_in_ifu'].to(u.dex(u.Msun))
logmass_in_ifu_lw = tab['ml_fluxwt'] + tab['ifu_absmag'][:, mlb_ix].to(
u.dex(m.bandpass_sol_l_unit), totalmass.bandpass_flux_to_solarunits(absmag_sun_mlb))
std_atten_mwtd = tab['std_atten_mwtd']
mean_atten_mwtd = tab['mean_atten_mwtd']
ba = tab['nsa_elpetro_ba']
sc = ax.scatter(
x=std_atten_mwtd, y=(logmass_in_ifu - logmass_in_ifu_lw), c=ba,
edgecolor='k', linewidths=.125, s=2., cmap='viridis_r',
vmin=.15, vmax=.8)
cb = colorbartop(fig, sc, cax)
cb.set_label(r'$\frac{b}{a}$', size='x-small', labelpad=0)
ax.set_xlabel(r'$\sigma_{\tau_V}$', size='x-small')
ax.set_ylabel(r'$\log{ \frac{M^*}{M^*_{\rm LW}} ~ {\rm [dex]} }$', size='x-small')
hist_ax.hist(np.ma.masked_invalid(logmass_in_ifu - logmass_in_ifu_lw).compressed(),
bins='auto', histtype='step', orientation='horizontal', linewidth=.5,
density=True, color='k')
for yloc, lw, ls, c in zip(
np.percentile(np.ma.masked_invalid(logmass_in_ifu - logmass_in_ifu_lw).compressed(),
[16., 50., 84.]),
[.5, 1., .5], ['--', '-', '--'], ['gray', 'k', 'gray']):
hist_ax.axhline(yloc, linestyle=ls, linewidth=lw, color=c)
fig.suptitle('Mass excess from luminosity-weighting', size='x-small')
fig.savefig(
os.path.join(basedir, 'lib_diags/', 'stdtauV_dMglobloc_ba.png'),
dpi=fig.dpi)
def make_stdtauV_vs_dMass_ba_fig(tab, mlb='i'):
'''global-local plot: mean tau, dmass, b/a
make figure plotting mass deficit on y,
mass weighted atten on x, colored by NSA b/a
Parameters
----------
tab : astropy.table.Table
full aggregation results table
mlb : {str}, optional
mass-to-light bandpass (the default is 'i', SDSS i-band)
'''
fig, ax, cax, hist_ax = make_panel_hcb_hist(figsize=(3, 3), dpi=300)
logmass_in_ifu = tab['mass_in_ifu'].to(u.dex(u.Msun))
logmass_in_ifu_lw = tab['ml_fluxwt'] + tab[f'logsollum_in_ifu_{mlb}']
std_atten_mwtd = tab['std_atten_mwtd']
mean_atten_mwtd = tab['mean_atten_mwtd']
ba = tab['nsa_elpetro_ba']
sc = ax.scatter(
x=std_atten_mwtd, y=(logmass_in_ifu - logmass_in_ifu_lw), c=ba,
edgecolor='k', linewidths=.125, s=1., cmap='viridis_r', alpha=0.5,
vmin=.15, vmax=.8)
ax.set_ylim([-.1, 0.3])
cb = colorbartop(fig, sc, cax)
cb.set_label(r'$\frac{b}{a}$', size='x-small', labelpad=0)
ax.set_xlabel(r'$\sigma_{\tau_V}$', size='x-small')
ax.set_ylabel(r'$\log{ \frac{M^*}{M^*_{\rm LW}} ~ {\rm [dex]} }$', size='x-small')
hist_ax.hist(np.ma.masked_invalid(logmass_in_ifu - logmass_in_ifu_lw).compressed(),
bins='auto', histtype='step', orientation='horizontal', linewidth=.5,
density=True, color='k')
for yloc, lw, ls, c in zip(
np.percentile(np.ma.masked_invalid(logmass_in_ifu - logmass_in_ifu_lw).compressed(),
[16., 50., 84.]),
[.5, 1., .5], ['--', '-', '--'], ['gray', 'k', 'gray']):
hist_ax.axhline(yloc, linestyle=ls, linewidth=lw, color=c)
fig.suptitle('Mass excess from luminosity-weighting', size='x-small')
fig.savefig(
os.path.join(csp_basedir, 'lib_diags/', 'stdtauV_dMglobloc_ba.png'),
dpi=fig.dpi)
def p_main(p):
'''
main : factor combined_units
| combined_units
| OPEN_BRACKET combined_units CLOSE_BRACKET
| factor
'''
from astropy.units.core import Unit
from astropy.units import dex
if len(p) == 3:
p[0] = Unit(p[1] * p[2])
elif len(p) == 4:
p[0] = dex(p[2])
else:
p[0] = Unit(p[1])
def update_mass_table(res_fnames, mlband='i'):
'''
'''
# filter out whose that have not been done
if mass_table_old is None:
already_aggregated = [False for _ in range(len(res_fnames))]
else:
already_aggregated = [
os.path.split(fn)[1].split('_')[0] in mass_table_old['plateifu']
for fn in res_fnames
]
res_fnames = [fn for done, fn in zip(already_aggregated, res_fnames)]
# aggregate individual galaxies, and stack them
mass_tables_new = list(
ProgressBar.map(partial(mass_agg_onegal, mlband=mlband),
res_fnames,
multiprocess=False,
step=5))
mass_table_new = t.vstack(mass_tables_new)
# if there was an old mass table, stack it with the new one
if mass_table_old is None:
mass_table = mass_table_new
else:
mass_table = t.vstack([mass_table_old, mass_table_new],
join_type='inner')
cmlr = cmlr_kwargs
cb1, cb2 = cmlr['cb1'], cmlr['cb2']
color_missing_flux = mass_table['outer_absmag_{}'.format(cb1)] - \
mass_table['outer_absmag_{}'.format(cb2)]
mass_table['outer_ml_cmlr'] = np.polyval(
cmlr['cmlr_poly'], color_missing_flux.value) * u.dex(m.m_to_l_unit)
mass_table['outer_mass_ring'] = \
(mass_table['outer_lum_{}'.format(mlband)] + \
mass_table['outer_ml_ring']).to(u.Msun)
mass_table['outer_mass_cmlr'] = \
(mass_table['outer_lum_{}'.format(mlband)] + \
mass_table['outer_ml_cmlr']).to(u.Msun)
return mass_table['plateifu', 'mass_in_ifu', 'outer_mass_cmlr',
'outer_mass_ring']
def make_meanstdtauV_vs_dMass_fig(tab, mlb='i'):
'''global-local plot: sig tau, mean tau, dmass
make figure plotting mass weighted atten on x,
std of mass weighted atten on y, colored by mass deficit
Parameters
----------
tab : astropy.table.Table
full aggregation results table
mlb : {str}, optional
mass-to-light bandpass (the default is 'i', SDSS i-band)
'''
fig, ax, cax, hist_ax = make_panel_hcb_hist(figsize=(3, 3), dpi=300)
logmass_in_ifu = tab['mass_in_ifu'].to(u.dex(u.Msun))
logmass_in_ifu_lw = tab['ml_fluxwt'] + tab[f'logsollum_in_ifu_{mlb}']
std_atten_mwtd = tab['std_atten_mwtd']
mean_atten_mwtd = tab['mean_atten_mwtd']
sc = ax.scatter(
y=std_atten_mwtd, x=mean_atten_mwtd, c=(logmass_in_ifu - logmass_in_ifu_lw),
edgecolor='k', linewidths=.125, s=1., cmap='viridis_r', alpha=0.5,
vmin=.005, vmax=.15)
cb = colorbartop(fig, sc, cax)
cb.set_label(r'$\log \frac{M^*}{M_{\rm LW}}$', size='x-small', labelpad=0)
ax.set_ylabel(r'$\sigma_{\tau_V}$', size='x-small')
ax.set_xlabel(r'$\bar{\tau_V}$', size='x-small')
hist_ax.hist(std_atten_mwtd, bins='auto', histtype='step', range=[0.1, 1.5],
orientation='horizontal', linewidth=.5, density=True, color='k')
for yloc, lw, ls, c in zip(
np.percentile(std_atten_mwtd[np.isfinite(std_atten_mwtd)], [16., 50., 84.]),
[.5, 1., .5], ['--', '-', '--'], ['gray', 'k', 'gray']):
hist_ax.axhline(yloc, linestyle=ls, linewidth=lw, color=c)
fig.suptitle('Mass excess from luminosity-weighting', size='x-small')
fig.savefig(
os.path.join(csp_basedir, 'lib_diags/', 'mean+stdtauV_dMglobloc.png'),
dpi=fig.dpi)
class TestRoundtripCDS(RoundtripBase):
format_ = 'cds'
@pytest.mark.parametrize('unit', [
unit for unit in u_format.CDS._units.values()
if (isinstance(unit, core.UnitBase) and
not isinstance(unit, core.PrefixUnit))])
def test_roundtrip(self, unit):
self.check_roundtrip(unit)
if unit == u.mag:
# Skip mag: decomposes into dex, which is unknown to CDS.
return
self.check_roundtrip_decompose(unit)
@pytest.mark.parametrize('unit', [u.dex(unit) for unit in
(u.cm/u.s**2, u.K, u.Lsun)])
def test_roundtrip_dex(self, unit):
string = unit.to_string(format='cds')
recovered = u.Unit(string, format='cds')
assert recovered == unit
def __init__(self,
results,
pca_system,
drp,
dap,
drpall_row,
cosmo,
mlband='i'):
self.results = results
self.pca_system = pca_system
self.drp = drp
self.dap = dap
self.drpall_row = drpall_row
self.cosmo = cosmo
self.mlband = mlband
with catch_warnings():
simplefilter('ignore')
self.results.setup_photometry(pca_system)
self.s2p = results.spec2phot
# stellar mass to light ratio
self.ml0 = results.cubechannel('ML{}'.format(mlband), 0)
self.badpdf = results.cubechannel('GOODFRAC', 2) < 1.0e-4
self.ml_mask = np.logical_or.reduce((self.results.mask, self.badpdf))
# infer values in interior spaxels affected by one of the following:
# bad PDF, foreground star, dead fiber
self.low_or_no_cov = m.mask_from_maskbits(self.drp['MASK'].data,
[0, 1]).mean(axis=0) > .3
self.drp3dmask_interior = m.mask_from_maskbits(
self.drp['MASK'].data, [2, 3]).mean(axis=0) > .3
self.interior_mask = np.logical_or.reduce(
(self.badpdf, self.drp3dmask_interior))
self.logml_final = infer_masked(q_trn=self.ml0,
bad_trn=self.ml_mask,
infer_here=self.interior_mask) * u.dex(
m.m_to_l_unit)
def test_qtable_column_conversion():
"""
Ensures that a QTable that gets assigned a unit switches to be Quantity-y
"""
qtab = table.QTable([[1, 2], [3, 4.2]], names=['i', 'f'])
assert isinstance(qtab['i'], table.column.Column)
assert isinstance(qtab['f'], table.column.Column)
qtab['i'].unit = 'km/s'
assert isinstance(qtab['i'], u.Quantity)
assert isinstance(qtab['f'], table.column.Column)
# should follow from the above, but good to make sure as a #4497 regression test
assert isinstance(qtab['i'][0], u.Quantity)
assert isinstance(qtab[0]['i'], u.Quantity)
assert not isinstance(qtab['f'][0], u.Quantity)
assert not isinstance(qtab[0]['f'], u.Quantity)
# Regression test for #5342: if a function unit is assigned, the column
# should become the appropriate FunctionQuantity subclass.
qtab['f'].unit = u.dex(u.cm/u.s**2)
assert isinstance(qtab['f'], u.Dex)
def test_qtable_column_conversion():
"""
Ensures that a QTable that gets assigned a unit switches to be Quantity-y
"""
qtab = table.QTable([[1, 2], [3, 4.2]], names=['i', 'f'])
assert isinstance(qtab['i'], table.column.Column)
assert isinstance(qtab['f'], table.column.Column)
qtab['i'].unit = 'km/s'
assert isinstance(qtab['i'], u.Quantity)
assert isinstance(qtab['f'], table.column.Column)
# should follow from the above, but good to make sure as a #4497 regression test
assert isinstance(qtab['i'][0], u.Quantity)
assert isinstance(qtab[0]['i'], u.Quantity)
assert not isinstance(qtab['f'][0], u.Quantity)
assert not isinstance(qtab[0]['f'], u.Quantity)
# Regression test for #5342: if a function unit is assigned, the column
# should become the appropriate FunctionQuantity subclass.
qtab['f'].unit = u.dex(u.cm / u.s**2)
assert isinstance(qtab['f'], u.Dex)
def test_str(self):
"""Do some spot checks that str, repr, etc. work as expected."""
lu1 = u.mag(u.Jy)
assert str(lu1) == 'mag(Jy)'
assert repr(lu1) == 'Unit("mag(Jy)")'
assert lu1.to_string('generic') == 'mag(Jy)'
with pytest.raises(ValueError):
lu1.to_string('fits')
lu2 = u.dex()
assert str(lu2) == 'dex'
assert repr(lu2) == 'Unit("dex(1)")'
assert lu2.to_string() == 'dex(1)'
lu3 = u.MagUnit(u.Jy, function_unit=2*u.mag)
assert str(lu3) == '2 mag(Jy)'
assert repr(lu3) == 'MagUnit("Jy", unit="2 mag")'
assert lu3.to_string() == '2 mag(Jy)'
lu4 = u.mag(u.ct)
assert lu4.to_string('generic') == 'mag(ct)'
assert lu4.to_string('latex') == ('$\\mathrm{mag}$$\\mathrm{\\left( '
'\\mathrm{ct} \\right)}$')
assert lu4._repr_latex_() == lu4.to_string('latex')
'tm':
tm,
'dt':
TimeDelta([1, 2] * u.day),
'sc':
sc,
'scc':
scc,
'scd':
SkyCoord([1, 2], [3, 4], [5, 6],
unit='deg,deg,m',
frame='fk4',
obstime=['J1990.5', 'J1991.5']),
'x': [1, 2] * u.m,
'qdb': [10, 20] * u.dB(u.mW),
'qdex': [4.5, 5.5] * u.dex(u.cm / u.s**2),
'qmag': [21, 22] * u.ABmag,
'lat':
Latitude([1, 2] * u.deg),
'lon':
Longitude([1, 2] * u.deg, wrap_angle=180. * u.deg),
'ang':
Angle([1, 2] * u.deg),
'el2':
el2,
}
time_attrs = ['value', 'shape', 'format', 'scale', 'location']
compare_attrs = {
'c1': ['data'],
'c2': ['data'],
return olsfit
if __name__ == '__main__':
mlband = 'i'
mass_table = update_mass_table(drpall, mass_table_old=None, limit=None, mlband=mlband)
drpall.keep_columns(['plateifu', 'mangaid', 'objra', 'objdec', 'ebvgal',
'mngtarg1', 'mngtarg2', 'mngtarg3', 'nsa_iauname', 'ifudesignsize',
'nsa_z', 'nsa_zdist', 'nsa_nsaid', 'nsa_elpetro_ba', 'nsa_elpetro_mass'])
full_table = t.join(mass_table, drpall, 'plateifu')
mlband_ix = totalmass.StellarMass.bands_ixs[mlband]
mlband_absmag_sun = totalmass.StellarMass.absmag_sun[mlband_ix]
mass_deficit = full_table['mass_in_ifu'].to(u.dex(u.Msun)) - \
(full_table['ml_fluxwt'] + full_table['ifu_absmag'][:, mlband_ix].to(
u.dex(m.bandpass_sol_l_unit), totalmass.bandpass_flux_to_solarunits(
mlband_absmag_sun)))
mass_deficit_order = np.argsort(mass_deficit)[::-1]
compare_outerml_ring_cmlr(full_table)
compare_missing_mass(full_table)
make_missing_mass_fig(full_table, mltype='ring')
make_missing_mass_fig(full_table, mltype='cmlr')
make_missing_flux_fig(full_table)
compare_mtot_pca_nsa(full_table, jhumpa, mltype='ring')
#compare_mtot_pca_nsa(full_table, jhumpa, mltype='cmlr')
make_meanstdtauV_vs_dMass_fig(full_table)
make_stdtauV_vs_dMass_ba_fig(full_table)
"M_E": u.M_earth, "Earth Mass": u.M_earth, "M_J": u.M_jupiter, "Jupiter Mass": u.M_jupiter, "R_Earth": u.R_earth, # Add u.R_jupiter "Earth Radius": u.R_earth, "Jupiter Radius": u.R_jupiter, "R_Sun": u.R_sun, "Rstar": u.R_sun, "a_perp": u.au, "arc-sec/year": u.arcsec / u.yr, "cm/s**2": u.cm / u.s**2, "g/cm**3": u.g / u.cm**3, "days": u.day, "degrees": u.deg, "dexincgs": u.dex(u.cm / u.s**2), "hours": u.hr, "hrs": u.hr, "kelvin": u.K, "logLsun": u.dex(u.L_sun), "log(Solar)": u.dex(u.L_sun), "mags": u.mag, "microas": u.uas, "perc": u.percent, "pi_E": None, "pi_EE": None, "pi_EN": None, "pi_rel": None, "ppm": cds.ppm, "seconds": u.s, "Solar mass": u.M_sun,
def __init__(self, fitfilename, sedfilename):
"""
potato potato potato
"""
fitfile = open(fitfilename)
sedfile = open(sedfilename)
fitinfo = fitfile.readlines()
sedinfo = sedfile.readlines()
fitfile.close()
sedfile.close()
#strip out newline characters
for i in range(len(fitinfo)):
fitinfo[i] = fitinfo[i].strip()
for i in range(len(sedinfo)):
sedinfo[i] = sedinfo[i].strip()
#first go through fitinfo
filternames = fitinfo[1].strip("#")
filternames = filternames.split()
flux = np.array(fitinfo[2].split(), dtype=float) * u.Jy
fluxerr = np.array(fitinfo[3].split(), dtype=float) * u.Jy
predicted = np.array(fitinfo[12].split(), dtype=float) * u.Jy
self.obs_filters = filternames
self.obs_flux = flux
self.obs_flux_err = fluxerr
self.obs_predict = predicted
bestfitmodel = fitinfo[8].split()
self.bestfit_i_sfh = int(bestfitmodel[0])
self.bestfit_i_ir = int(bestfitmodel[1])
self.bestfit_chi2 = float(bestfitmodel[2])
self.bestfit_redshift = float(bestfitmodel[3])
bestfitparams = fitinfo[9].strip('.#')
bestfitparams = re.split('\.+', bestfitparams)
bestfitresults = list(map(float, fitinfo[10].split()))
assert len(bestfitparams) == len(bestfitresults)
for i, paramname in enumerate(bestfitparams):
setattr(self, self.clean_param_names(paramname), bestfitresults[i])
#now working on the marginal PDF histograms for each parameter
marginalpdfs = fitinfo[15:]
#first, need to split the pdfs into each parameter
self.marginal_pdfs = {}
self.marginal_percentiles = {}
hash_idx = []
for i in range(len(marginalpdfs)):
if '#' in marginalpdfs[i]:
hash_idx.append(i)
assert len(hash_idx) % 2 == 0
for i in range(len(hash_idx) // 2):
param = marginalpdfs[hash_idx[2 * i]].strip(' #.')
marginal = marginalpdfs[hash_idx[2 * i] + 1:hash_idx[2 * i + 1]]
marginal = np.array([j.split() for j in marginal], dtype=float)
percentile = np.array(marginalpdfs[hash_idx[2 * i + 1] +
1].split(),
dtype=float)
self.marginal_pdfs[self.clean_param_names(param)] = marginal
self.marginal_percentiles[self.clean_param_names(
param)] = percentile
#now time for the SED file
self.sed_model_params = {}
#there are model names and params on lines 2 & 3 and 5 & 6
modelparams = sedinfo[2].strip('.#')
modelparams = re.split('\.+', modelparams)
model_vals = list(map(float, sedinfo[3].split()))
assert len(modelparams) == len(model_vals)
for i, paramname in enumerate(modelparams):
self.sed_model_params[self.clean_param_names(
paramname)] = model_vals[i]
modelparams = sedinfo[5].strip('.#')
modelparams = re.split('\.+', modelparams)
model_vals = list(map(float, sedinfo[6].split()))
assert len(modelparams) == len(model_vals)
for i, paramname in enumerate(modelparams):
self.sed_model_params[self.clean_param_names(
paramname)] = model_vals[i]
#sed is from line 10 to the end.
#three columns, log lambda, log L_lam attenuated, log L_lam unattenuated
model_sed = sedinfo[10:]
model_sed = [i.split() for i in model_sed]
self.sed_model = np.array(model_sed, dtype=float)
self.sed_model_logwaves = self.sed_model[:, 0] * u.dex(u.AA)
self.sed_model_logluminosity_lambda = self.sed_model[:, 1] * u.dex(
u.Lsun / u.AA)
import sys
# Related third party imports.
from astropy import units as u
from astropy.io import ascii
import pandas
from math import isnan
import matplotlib.pyplot as plt
import numpy
from scipy.interpolate import interp1d
#import splat
from splat import SPLAT_PATH, SPLAT_URL
EVOLUTIONARY_MODEL_FOLDER = '/reference/EvolutionaryModels/'
EMODELS = ['baraffe','burrows','saumon']
EPARAMETERS = ['mass','age','temperature','gravity','luminosity','radius']
EPARAMETER_UNITS = {'mass': u.solMass, 'age': u.Gyr, 'temperature': u.K, 'gravity': u.dex(u.cm / u.s**2),\
'luminosity': u.dex(u.solLum), 'radius': u.solRad}
# change the command prompt
sys.ps1 = 'splat evolve> '
###############################################################################
###############################################################################
def readModel(*model,**kwargs):
"""
:Description: This class reads in evolutionary models that are defined
in the methods below, and their data is acquired `here
<http://pono.ucsd.edu/~adam/splat/EvolutionaryModels/>`_.
Units are the following: masses are in M/Msun,
luminosities in log L/Lsun, radius in R/Rsun, surface
def test_cds_log10_dimensionless():
assert u.Unit('[-]', format='cds') == u.dex(u.dimensionless_unscaled)
assert u.dex(u.dimensionless_unscaled).to_string(format='cds') == "[-]"
(["uarcmin"], u.uarcmin),
(["uarcsec"], u.uarcsec),
(["kbarn"], u.kbarn),
(["Gbit"], u.Gbit),
(["Gibit"], 2 ** 30 * u.bit),
(["kbyte"], u.kbyte),
(["mRy"], 0.001 * u.Ry),
(["mmag"], u.mmag),
(["Mpc"], u.Mpc),
(["Gyr"], u.Gyr),
(["°"], u.degree),
(["°/s"], u.degree / u.s),
(["Å"], u.AA),
(["Å/s"], u.AA / u.s),
(["\\h"], si.h),
(["[cm/s2]"], dex(u.cm / u.s ** 2)),
(["[K]"], dex(u.K)),
(["[-]"], dex(u.dimensionless_unscaled))])
def test_cds_grammar(strings, unit):
for s in strings:
print(s)
unit2 = u_format.CDS.parse(s)
assert unit2 == unit
@pytest.mark.parametrize('string', [
'0.1 nm',
'solMass(3/2)',
'km / s',
'km s-1',
'pix0.1nm',
def __init__(self, fitfilename, sedfilename):
"""
potato potato potato
"""
fitfile = open(fitfilename)
sedfile = open(sedfilename)
fitinfo = fitfile.readlines()
sedinfo = sedfile.readlines()
fitfile.close()
sedfile.close()
#strip out newline characters
for i in range(len(fitinfo)):
fitinfo[i] = fitinfo[i].strip()
for i in range(len(sedinfo)):
sedinfo[i] = sedinfo[i].strip()
#first go through fitinfo
filternames = fitinfo[1].strip("#")
filternames = filternames.split()
flux = np.array(fitinfo[2].split(), dtype=float) * u.Jy
fluxerr = np.array(fitinfo[3].split(), dtype=float) * u.Jy
predicted = np.array(fitinfo[12].split(), dtype=float) * u.Jy
self.obs_filters = filternames
self.obs_flux = flux
self.obs_flux_err = fluxerr
self.obs_predict = predicted
bestfitmodel = fitinfo[8].split()
self.bestfit_i_sfh = int(bestfitmodel[0])
self.bestfit_i_ir = int(bestfitmodel[1])
self.bestfit_chi2 = float(bestfitmodel[2])
self.bestfit_redshift = float(bestfitmodel[3])
bestfitparams = fitinfo[9].strip('.#')
bestfitparams = re.split('\.+',bestfitparams)
bestfitresults = list(map(float,fitinfo[10].split()))
assert len(bestfitparams) == len(bestfitresults)
for i,paramname in enumerate(bestfitparams):
setattr(self,self.clean_param_names(paramname),bestfitresults[i])
#now working on the marginal PDF histograms for each parameter
marginalpdfs = fitinfo[15:]
#first, need to split the pdfs into each parameter
self.marginal_pdfs = {}
self.marginal_percentiles = {}
hash_idx = []
for i in range(len(marginalpdfs)):
if '#' in marginalpdfs[i]:
hash_idx.append(i)
assert len(hash_idx) % 2 == 0
for i in range(len(hash_idx)//2):
param = marginalpdfs[hash_idx[2*i]].strip(' #.')
marginal = marginalpdfs[hash_idx[2*i]+1:hash_idx[2*i+1]]
marginal = np.array([j.split() for j in marginal],dtype=float)
percentile = np.array(marginalpdfs[hash_idx[2*i+1]+1].split(),dtype=float)
self.marginal_pdfs[self.clean_param_names(param)] = marginal
self.marginal_percentiles[self.clean_param_names(param)] = percentile
#now time for the SED file
self.sed_model_params = {}
#there are model names and params on lines 2 & 3 and 5 & 6
modelparams = sedinfo[2].strip('.#')
modelparams = re.split('\.+',modelparams)
model_vals = list(map(float,sedinfo[3].split()))
assert len(modelparams) == len(model_vals)
for i,paramname in enumerate(modelparams):
self.sed_model_params[self.clean_param_names(paramname)] = model_vals[i]
modelparams = sedinfo[5].strip('.#')
modelparams = re.split('\.+',modelparams)
model_vals = list(map(float,sedinfo[6].split()))
assert len(modelparams) == len(model_vals)
for i,paramname in enumerate(modelparams):
self.sed_model_params[self.clean_param_names(paramname)] = model_vals[i]
#sed is from line 10 to the end.
#three columns, log lambda, log L_lam attenuated, log L_lam unattenuated
model_sed = sedinfo[10:]
model_sed = [i.split() for i in model_sed]
self.sed_model = np.array(model_sed,dtype=float)
self.sed_model_logwaves = self.sed_model[:,0] * u.dex(u.AA)
self.sed_model_logluminosity_lambda = self.sed_model[:,1] * u.dex(u.Lsun / u.AA)
UNIT_MAPPER = {
"--": None,
"BJD": None, # TODO: optionally supprot mapping columns to Time objects
"BKJD": None, # TODO: optionally supprot mapping columns to Time objects
"D_L": u.pc,
"D_S": u.pc,
"Earth flux": None, # TODO: Include Earth insolation units
"Fearth": None, # TODO: Include Earth insolation units
"M_E": u.M_earth,
"M_J": u.M_jupiter,
"R_Earth": u.R_earth,
"R_Sun": u.R_sun,
"Rstar": u.R_sun,
"a_perp": u.au,
"arc-sec/year": u.arcsec / u.yr,
"cm/s**2": u.dex(u.dm / u.s**2),
"days": u.day,
"degrees": u.deg,
"dexincgs": u.dex(u.cm / u.s**2),
"hours": u.hr,
"hrs": u.hr,
"kelvin": u.K,
"logLsun": u.dex(u.L_sun),
"mags": u.mag,
"microas": u.uas,
"perc": u.percent,
"pi_E": None,
"pi_EE": None,
"pi_EN": None,
"pi_rel": None,
"ppm": cds.ppm,
def mag_to_dexmasstolight(q, cmlr_poly):
qmag = q.to('mag')
return np.polyval(cmlr_poly, qmag.value) * u.dex(m.m_to_l_unit)
def test_pickle():
lu1 = u.dex(u.cm/u.s**2)
s = pickle.dumps(lu1)
lu2 = pickle.loads(s)
assert lu1 == lu2
def make_stdtauV_vs_dMass_ssfrsd_fig(tab, sfrsd_tab, mltype='ring', mlb='i'):
'''global-local plot: sig tau, dmass, ssfrsd
[description]
Parameters
----------
tab : astropy.table.Table
full aggregation results table
sfrsd_tab : astropy.table.Table
specific star formation rate table
mlb : {str}, optional
mass-to-light bandpass (the default is 'i', SDSS i-band)
mltype : {str}
'ring' or 'cmlr', the M/L applied to the ouside flux
(the default is 'ring')
'''
merge_tab = t.join(tab, sfrsd_tab, 'plateifu')
fig, ax, cax, hist_ax = make_panel_hcb_hist(figsize=(3, 3), dpi=300, top=.8)
logmass_in_ifu = merge_tab['mass_in_ifu'].to(u.dex(u.Msun))
logmass_in_ifu_lw = merge_tab['ml_fluxwt'] + merge_tab[f'logsollum_in_ifu_{mlb}']
std_atten_mwtd = merge_tab['std_atten_mwtd']
mean_atten_mwtd = merge_tab['mean_atten_mwtd']
ha_corr = np.exp(merge_tab['mean_atten_mwtd'] * (6563 / 5500)**-1.3)
sfrsd = merge_tab['sigma_sfr'] * ha_corr * u.Msun / u.yr / u.pc**2
outer_mass = (merge_tab[f'outerml_{mltype}'] + \
merge_tab[f'logsollum_outer_{mlb}']).to(u.Msun)
mass_pca = merge_tab['mass_in_ifu'].to(u.Msun) + outer_mass
ssfrsd = sfrsd / mass_pca
sc = ax.scatter(
x=std_atten_mwtd, y=(logmass_in_ifu - logmass_in_ifu_lw),
c=ssfrsd.to(u.dex(ssfrsd.unit)),
edgecolor='k', linewidths=.125, s=1., cmap='viridis_r', alpha=0.5,
vmin=-15., vmax=-10.)
ax.set_ylim([-.1, 0.3])
cb = colorbartop(fig, sc, cax)
cb.set_label(r'$\log \frac{{\Sigma}^{\rm SFR}_{R<R_e}}{M^*_{\rm tot}}$', size='xx-small')
ax.tick_params(which='major', labelsize='xx-small')
ax.tick_params(which='minor', labelbottom=False, labelleft=False)
ax.set_xscale('log')
ax.set_xlabel(r'$\sigma_{\tau_V}$', size='x-small')
ax.set_ylabel(r'$\log{ \frac{M^*}{M^*_{\rm LW}} ~ {\rm [dex]} }$', size='x-small')
hist_ax.hist(np.ma.masked_invalid(logmass_in_ifu - logmass_in_ifu_lw).compressed(),
bins='auto', histtype='step', orientation='horizontal', linewidth=.5,
density=True, color='k')
for yloc, lw, ls, c in zip(
np.percentile(np.ma.masked_invalid(logmass_in_ifu - logmass_in_ifu_lw).compressed(),
[16., 50., 84.]),
[.5, 1., .5], ['--', '-', '--'], ['gray', 'k', 'gray']):
hist_ax.axhline(yloc, linestyle=ls, linewidth=lw, color=c)
fig.suptitle('Mass excess from luminosity-weighting', size='x-small')
fig.subplots_adjust(left=0.25)
fig.savefig(
os.path.join(csp_basedir, 'lib_diags/', 'stdtauV_dMglobloc_ssfrsd.png'),
dpi=fig.dpi)
# 'morley12': 'Morley et al. (2012)',\
# 'morley14': 'Morley et al. (2014)',\
# 'saumon12': 'Saumon et al. (2012)',\
# 'drift': 'Witte et al. (2011)'}
SPECTRAL_MODELS = {\
'burrows06': {'name': 'Burrows et al. (2006)', 'bibcode': '2006ApJ...640.1063B', 'altnames': ['burrows','burrows2006'], 'rawfolder': HOME_FOLDER+'/models/burrows/burrows06/'}, \
'btsettl08': {'name': 'BT-Settl (2008)', 'bibcode': '2012RSPTA.370.2765A', 'altnames': ['allard','allard12','allard2012','btsettl','btsettled','btsettl08','btsettl2008','BTSettl2008'], 'rawfolder': HOME_FOLDER+'/models/allard/cifist2011/'}, \
'madhusudhan11': {'name': 'Madhusudhan et al. (2011)', 'bibcode': '2011ApJ...737...34M', 'altnames': ['madhu','madhusudhan','madhu11','madhu2011','madhusudhan2011'], 'rawfolder': HOME_FOLDER+'/models/burrows/burrows11/all/'}, \
'morley12': {'name': 'Morley et al. (2012)', 'bibcode': '2012ApJ...756..172M', 'altnames': ['morley','morley2012'], 'rawfolder': HOME_FOLDER+'/models/ames/Morley12/'}, \
'morley14': {'name': 'Morley et al. (2014)', 'bibcode': '2014ApJ...787...78M', 'altnames': ['morley2014'], 'rawfolder': HOME_FOLDER+'/models/ames/Morley14/'}, \
'saumon12': {'name': 'Saumon et al. (2012)', 'bibcode': '2012ApJ...750...74S', 'altnames': ['saumon','saumon2012'], 'rawfolder': HOME_FOLDER+'/models/ames/Saumon12/'}, \
'drift': {'name': 'Witte et al. (2011)', 'bibcode': '2011A&A...529A..44W', 'altnames': ['witte','witte11','witte2011','helling'], 'rawfolder': HOME_FOLDER+'/models/drift/'}}
SPECTRAL_MODEL_PARAMETERS_INORDER = ['teff','logg','z','fsed','cld','kzz']
SPECTRAL_MODEL_PARAMETERS = {\
'teff': {'unit': u.K, 'default': 1000.0, 'title': '$T_{eff}$'}, \
'logg': {'unit': u.dex(u.cm/u.s/u.s), 'default': 5.0, 'title': '$\log{g}$'}, \
'z': {'unit': u.dex(), 'default': 0., 'title': '$[M/H]$'}, \
'fsed': {'unit': u.m/u.m, 'default': 'nc', 'title': '$f_{sed}$'}, \
'cld': {'unit': u.m/u.m, 'default': 'nc', 'title': '$cld$'}, \
'kzz': {'unit': u.m/u.m, 'default': 'eq', 'title': '$log\ \kappa_{zz}$'}}
# 'kzz': u.dex(u.cm*u.cm/u.s), \
# 'slit': {'unit': u.arcsec, 'default': 0.5, 'title': 'slit'}}
SPECTRAL_MODEL_FLUX_UNIT = u.erg/(u.s*u.micron*(u.cm**2))
SPECTRAL_MODEL_WAVE_UNIT = u.micron
#DEFINED_MODEL_BIBCODES = {\
# 'BTSettl2008': '', \
# 'burrows06': '2006ApJ...640.1063B',\
# 'morley12': '2012ApJ...756..172M',\
# 'morley14': '2014ApJ...787...78M',\
# 'saumon12': '2012ApJ...750...74S',\
# 'drift': '2011A&A...529A..44W'}
