def phxCompare(star, wlim=None, maxpow=None, mindw=None, ax=None):
if ax is None: ax = plt.gca()
xf = db.findfiles('ir', 'phx', star, fullpaths=True)
pf = db.panpath(star)
phx = io.read(xf)[0]
pan = io.read(pf)[0]
normfac = pan['normfac'][-1]
if wlim is not None:
phx, pan = utils.keepranges(phx, wlim), utils.keepranges(pan, wlim)
if maxpow or mindw:
pan = utils.fancyBin(pan, maxpow=maxpow, mindw=mindw)
phx = utils.fancyBin(phx, maxpow=maxpow, mindw=mindw)
Fbol = utils.bolo_integral(star)
pan['normflux'] = pan['flux'] / Fbol
pan['normerr'] = pan['error'] / Fbol
phx['normflux'] = phx['flux'] * normfac / Fbol
line = specstep(pan, key='normflux', label='Panspec', ax=ax)
specstep(pan,
key='normerr',
label='Panspec Error',
ax=ax,
color=line.get_color(),
ls=':')
specstep(phx, key='normflux', label='Phoenix', ax=ax, color='r', alpha=0.5)
ax.set_xlim(wlim)
ax.legend(loc='best')
def compare_v20_v10(stars=None, plot=False):
if stars is None:
stars = mlstars
oldfile_template = '/Users/rolo7566/Datasets/MUSCLES/products/archive/panspecs v10/p_msl_pan_-----_{}_panspec_native_resolution.fits'
hlspfile_template = '/Users/rolo7566/Google Drive/Grad School/PhD Work/muscles/share/hlsp/archive/hlsp_muscles_multi_multi_{}_broadband_v10_var-res-sed.fits'
compare_template = '/Users/rolo7566/Google Drive/Grad School/PhD Work/muscles/scratchwork/v10 - v20 comparisons/{' \
'} v20 vs v10 ratio.fits'
for star in stars:
p = io.readpan(star)
op, = io.read(oldfile_template.format(star))
hp, = io.read(hlspfile_template.format(star))
op = red.splice(op, utils.keepranges(hp, 100., 1169.))
p, op = [utils.keepranges(spec, 0, 10000.) for spec in [p, op]]
cs = utils.compare_specs(p, op, savetxt=compare_template.format(star))
cf = compare_template.format(star)
cs.write(cf, overwrite=True)
if plot:
plt.figure()
ss(cs, key='ratio')
plt.title(star)
plt.xlabel('Wavelength $\AA$')
plt.ylabel('Ratio of v20 to v10 SED')
def vetnormfacs(spec, panspec, normfac, normranges):
"""Check the normalization of files by plotting normalized and unnormalieze
versions. Called from reduce.panspec"""
name = spec.meta['NAME']
oranges = utils.overlap_ranges(spec, panspec)
if normranges is None:
normranges = oranges
else:
normranges = mnp.rangeset_intersect(normranges, oranges)
# construct bins from lower res in each normrange
overbins = []
for normrange in normranges:
getbins = lambda s: utils.wbins(utils.keepranges(s, normrange))
possible_bins = map(getbins, [spec, panspec])
bins = min(possible_bins, key=lambda b: len(b))
overbins.append(bins)
overbins = np.vstack(overbins)
# rebin each spec to the lowest res within the overlap
def coarsebin(s):
overspec = utils.rebin(s, overbins)
return red.splice(s, overspec)
spec, panspec = map(coarsebin, [spec, panspec])
# plot the spectrum being normalized, highlighting the normranges
plt.figure()
# ax = plt.axes()
inranges, _ = utils.argoverlap(spec, normranges)
specin = spec[inranges]
specout = spec[~inranges]
kwargs = {'err': False}
line1 = specstep(specout, alpha=0.3, linestyle='--', **kwargs)
kwargs['color'] = line1.get_color()
line2 = specstep(specin, alpha=0.3, **kwargs)
specin['flux'] *= normfac
specout['flux'] *= normfac
line3 = specstep(specout, linestyle='--', **kwargs)
line4 = specstep(specin, **kwargs)
plt.legend((line2, line4), ('original', 'normalized'))
# plot panspec
fullrange = spec['w0'][0], spec['w1'][-1]
panspec = utils.keepranges(panspec, fullrange)
# ymax = np.max(panspec['flux'])
piecespec(panspec, err=False)
normed = panspec['normfac'] != 1.0
if np.any(normed):
normspec = panspec[normed]
normspec['flux'] /= normspec['normfac']
specstep(normspec, color='k', linestyle='--', alpha=0.5, err=False)
# ax.set_ylim(-0.05 * ymax, 1.05 * ymax)
plt.title('{} normalization'.format(name))
def phxFit(star='gj832', ax=None):
if ax is None: ax = plt.gca()
ax.autoscale(axis='x', tight=True)
ax.set_yscale('log')
pan = io.readpan(star)
bolo = utils.bolo_integral(star)
xf = db.findfiles('ir', 'phx', star, fullpaths=True)
phx = io.read(xf)[0]
phx['flux'] *= pan['normfac'][-1]
pan = pan[pan['instrument'] != pan['instrument'][-1]]
fmin = np.min(pan['error'][pan['error'] > 0]) / bolo
rng = [phx['w0'][0], 6000.]
phx, pan = [
utils.keepranges(spec, rng, ends='loose') for spec in [phx, pan]
]
phx, pan = [utils.fancyBin(s, mindw=10.0) for s in [phx, pan]]
pan['flux'][pan['flux'] < pan['error'] / 2.0] = np.nan
pan['normflux'] = pan['flux'] / bolo
phx['normflux'] = phx['flux'] / bolo
ymax = 10**np.ceil(np.log10(np.max(phx['normflux'])))
ymin = 10**np.floor(np.log10(fmin) - 3)
ax.set_ylim(ymin, ymax)
pline = plot.specstep(pan, ax=ax, color='k', err=False, key='normflux')
xline = plot.specstep(phx, ax=ax, color='gray', err=False, key='normflux')
ax.legend((pline, xline), ('$HST$ Data', 'PHOENIX Model'),
loc='lower right')
def splitSpec(spec, ax=None, wsplit=3000., scale_fac=50.):
ax1 = plt.gca() if ax is None else ax
ax2 = ax1.twinx()
leftspec = utils.keepranges(spec, 0.0, wsplit)
rightspec = utils.keepranges(spec, wsplit, np.inf)
step = lambda spec, ax: plot.specstep(
spec, err=False, ax=ax, color='k', autolabel=False)
leftline = step(leftspec, ax1)
rightline = step(rightspec, ax2)
ax2.set_ylim(0.0, None)
ax1.set_ylim(0.0, ax2.get_ylim()[1] / scale_fac)
ax1.axvline(wsplit, ls=':')
return (ax1, leftline), (ax2, rightline)
def fuv_cont_stats(star):
"""
Get stats on FUV continuum flux:
- avg flux
- avg flux error
- raito of FUV continuum to total flux in the FUV assuming flat continuum
- error on ratio
"""
pan = io.readpan(star)
cont = utils.keepranges(pan, rc.contbands, ends='exact')
dw = cont['w1'] - cont['w0']
# assume flat continuum
# Fcont_avg = np.sum(cont['flux'] * dw)/np.sum(dw)
# Fcont_avg_err = mnp.quadsum(cont['error'] * dw)/np.sum(dw)
# dw_fuv = rc.fuv[1] - rc.fuv[0]
# Fall_FUV, Fall_FUV_err = utils.flux_integral(pan, *rc.fuv)
# ratio = Fcont_avg * dw_fuv / Fall_FUV
# ratio_err = abs(ratio)*np.sqrt((Fall_FUV_err/Fall_FUV)**2 + (Fcont_avg_err/Fcont_avg)**2)
# just do continuum actual measured, ignore "in-between" continuumFcont_avg
Fcont = np.sum(cont['flux'] * dw)
Fcont_err = mnp.quadsum(cont['error'] * dw)
Fall_FUV, Fall_FUV_err = utils.flux_integral(pan, cont['w0'][0], cont['w1'][-1])
ratio = Fcont / Fall_FUV
ratio_err = abs(ratio)*np.sqrt((Fall_FUV_err/Fall_FUV)**2 + (Fcont_err/Fcont)**2)
return Fcont, Fcont_err, ratio, ratio_err
def lya_splices(stars='all'):
if stars == 'all':
stars = rc.stars[:11]
stars.remove('gj551')
dw = 0.05
for star in stars:
pan = io.readpan(star)
pan = utils.keepranges(pan, 1100, 1300)
pan = utils.evenbin(pan, dw)
sf = db.findfiles('u', star, 'coadd', 'cos_g130m')
spec, = io.read(sf)
spec = utils.evenbin(spec, dw)
lf = db.findfiles('u', star, 'mod', 'lya')
lya, = io.read(lf)
plt.figure()
[ss(s, err=False) for s in [pan, spec, lya]]
plt.xlim(1210, 1222)
up, _ = utils.flux_integral(spec, 1217, 1220)
plt.ylim(0, up * 4)
plt.legend(['pan', 'cos', 'lya'], loc='best')
plt.savefig(
os.path.join(rc.scratchpath, 'lya splices',
'{} linear.pdf'.format(star)))
mx = spec['flux'].max()
plt.ylim(mx / 1e7, mx)
plt.yscale('log')
plt.savefig(
os.path.join(rc.scratchpath, 'lya splices',
'{} log.pdf'.format(star)))
def plotspec(version, ax):
f, = db.findfiles(rc.hlsppath, star, 'broadband', version, res)
spec, = io.read(f)
spec = utils.keepranges(spec, 0, maxw)
spec = utils.evenbin(spec, binto)
plt.axes(ax)
piecespec(spec)
plt.text(0.05, 0.9, version, transform=ax.transAxes)
def vetpanspec(pan_or_star, constant_dw=None, redlim=8000.0):
"""Plot unnormalized components of the panspec with the panspec to see that
all choices were good. Phoenix spectrum is excluded because it is too big."""
if type(pan_or_star) is str:
star = pan_or_star
panspec = io.read(db.panpath(star))[0]
else:
panspec = pan_or_star
star = panspec.meta['STAR']
files = db.panfiles(star)[0]
panspec = utils.keepranges(panspec, 0.0, redlim)
if constant_dw is None:
plotfun = specstep
else:
panspec = utils.evenbin(panspec, constant_dw)
wbins = utils.wbins(panspec)
def plotfun(spec, **kwargs):
s = utils.rebin(spec, wbins)
return specstep(s, **kwargs)
for f in files:
if 'phx' in f: continue
specs = io.read(f)
for spec in specs:
p = plotfun(spec, err=True)[0]
x = (spec['w0'][0] + spec['w0'][-1]) / 2.0
y = np.mean(spec['flux'])
inst = db.parse_instrument(spec.meta['NAME'])
plt.text(x,
y,
inst,
bbox={
'facecolor': 'w',
'alpha': 0.5,
'color': p.get_color()
},
ha='center',
va='center')
plotfun(panspec, color='k', alpha=0.5)
ymax = np.max(utils.keepranges(panspec, 3000.0, 8000.0)['flux'])
plt.gca().set_ylim(-0.01 * ymax, 1.05 * ymax)
plt.draw()
def stackpans(range=[1310, 1350],
keeprange=[1100, 2000],
xlim=None,
norm=True,
offfac=1.0):
if xlim is None: xlim = keeprange
pans = []
for star in rc.observed:
p = io.read(db.panpath(star))[0]
pans.append(utils.keepranges(p, *keeprange))
stackspecs(pans, range, norm=norm, offfac=offfac, xlim=xlim)
def fuv_cont_spec(star):
"""Get just the continuum flux regions of a star's panspec."""
spec = io.readpan(star)
return utils.keepranges(spec, rc.contbands, ends='exact')