def fluxResPlot(input='OUTPUT/photz.out',outplot='fluxres.pdf'):
sed = eazy.getEazySED(idnum, MAIN_OUTPUT_FILE='photz', OUTPUT_DIRECTORY='./OUTPUT',
CACHE_FILE='Same', scale_flambda=True, verbose=False,
individual_templates=False)
lambdaz, temp_sed, lci, obs_sed, fobs, efobs = sed
def plotResult(idnum,catalog,save=False):
id=str(idnum)
obsData=Table.read(catalog).to_pandas()
rmag=-2.5*np.log10(obsData['fRauto'][idnum])+23.9
axes = eazy.plotExampleSED(idx=idnum, writePNG=False, MAIN_OUTPUT_FILE='photz',
OUTPUT_DIRECTORY='OUTPUT', CACHE_FILE='Same', lrange=[3800, 3.e4],
axes=None, individual_templates=False, fnu=False)
sed = eazy.getEazySED(idnum, MAIN_OUTPUT_FILE='photz', OUTPUT_DIRECTORY='./OUTPUT',
CACHE_FILE='Same', scale_flambda=True, verbose=False,
individual_templates=False)
lambdaz, temp_sed, lci, obs_sed, fobs, efobs = sed
zgrid, pzi, prior = eazy.getEazyPz(idnum, MAIN_OUTPUT_FILE='photz', OUTPUT_DIRECTORY='./OUTPUT',
CACHE_FILE='Same', binaries=None, get_prior=True)
axes[1].plot(zgrid, pzi, color='black')
axes[1].plot(zgrid, prior/prior.max()*pzi.max(), color='purple')
axes[1].set_xlim([0.,1.])
axes[0].text(5500.,axes[0].get_ylim()[1]*0.1,r'$m_{R}$ = '+str(rmag)[:5]+' mag')
if save == True:
plt.savefig('OUTPUT/'+id+'.pdf',format='pdf',dpi=6000)
plt.clf()
else:
plt.show()
plt.close()
lo, hi = stack.min(), stack.max() stack -= lo stack /= (hi - lo) stack *= 2 hinds = pylab.where(stack > 1) stack[hinds] = 1 rgb.set_data(stack) ### sed subplot sed = eazyPy.getEazySED(i, MAIN_OUTPUT_FILE=version, OUTPUT_DIRECTORY='./EAZY') lambdaz, temp_sed, lci, temp_obs, fobs, efobs = sed lambdaz, lci = lambdaz / 10.**4, lci / 10.**4 sp_sed.loglog(lambdaz, temp_sed, color='r', lw=1, zorder=1) # sp_sed.errorbar(lci, temp_obs, ls='', marker='s', ms=8, mew=2, mec='r', mfc='r', zorder=2) sp_sed.errorbar(lci, fobs, yerr=efobs, ls='', marker='o', ms=12, mew=2, mfc='none', mec='k', ecolor='k', zorder=3) indspos = pylab.find(fobs > 0) fmin = min(fobs[indspos]) fmax = max(fobs[indspos]) sp_sed.set_xlim(2*10**-1, 1.7*10**1) sp_sed.set_ylim(fmin/5, fmax*5) sp_sed = restore_logaxes_labels(sp_sed)
################################################
#### Example object. `idx` is zero-indexed
################################################
axes = eazy.plotExampleSED(idx=17, writePNG=False, MAIN_OUTPUT_FILE='photz',
OUTPUT_DIRECTORY='OUTPUT', CACHE_FILE='Same', lrange=[3800, 3.e4],
axes=None, individual_templates=True, fnu=False)
plt.savefig('eazy_fit.png'); plt.close()
################################################
#### Pull out data from the BINARY_OUTPUTS files
################################################
## SED, data & fit
sed = eazy.getEazySED(17, MAIN_OUTPUT_FILE='photz', OUTPUT_DIRECTORY='./OUTPUT',
CACHE_FILE='Same', scale_flambda=True, verbose=False,
individual_templates=False)
lambdaz, temp_sed, lci, obs_sed, fobs, efobs = sed
axes[0].scatter(lci, obs_sed, color='orange', zorder=2)
axes[0].scatter(lci, fobs, color='green', marker='s', s=150, zorder=2)
## p(z)
zgrid, pzi, prior = eazy.getEazyPz(17, MAIN_OUTPUT_FILE='photz', OUTPUT_DIRECTORY='./OUTPUT',
CACHE_FILE='Same', binaries=None, get_prior=True)
axes[1].plot(zgrid, pzi, color='black')
axes[1].plot(zgrid, prior/prior.max()*pzi.max(), color='purple')
plt.savefig('eazy_fit_2.png')
################################################
def specphot_acs_and_wfc3(id=69, grism_root='ibhm45030',
MAIN_OUTPUT_FILE = 'cosmos-1.v4.6',
OUTPUT_DIRECTORY = '/Users/gbrammer/research/drg/PHOTZ/EAZY/NEWFIRM/v4.6/OUTPUT_KATE/',
CACHE_FILE = 'Same', Verbose=False,
SPC = None, cat=None, grismCat = None,
zout = None, fout = None, OUT_PATH='/tmp/', OUT_FILE_FORMAT=True,
OUT_FILE='junk.png', GET_SPEC_ONLY=False, GET_WFC3=False, WFC3_DIR='/3DHST/Spectra/Release/v2.0/GOODS-S'):
"""
specphot_acs_and_wfc3(id)
Get photometry/SED fit as well as WFC3 spectrum when available and overplot G141 spectrum.
This is different from unicorn.analysis.specphot() which does not get the WFC3 spectrum.
"""
import threedhst.eazyPy as eazy
import threedhst.catIO as catIO
import pyfits
#### Get G141 spectrum
if Verbose:
print 'Read SPC'
if SPC is None:
SPC = threedhst.plotting.SPCFile(grism_root+'_2_opt.SPC.fits',
axe_drizzle_dir='DRIZZLE_G141')
spec = SPC.getSpec(id)
if spec is False:
return False
xmin = 3000
xmax = 2.4e4
lam = spec.field('LAMBDA')
flux = spec.field('FLUX')
ffix = flux-spec.field('CONTAM')
ferr = spec.field('FERROR') #*0.06/0.128254
if Verbose:
print 'Read grism catalog'
#### Read the grism catalog and get coords of desired object
if grismCat is None:
grismCat = threedhst.sex.mySexCat('DATA/'+grism_root+'_drz.cat')
#### Source size
R = np.sqrt(np.cast[float](grismCat.A_IMAGE)*np.cast[float](grismCat.B_IMAGE))
grism_idx = np.where(grismCat.id == id)[0][0]
Rmatch = R[grism_idx]*1.
ra0 = grismCat.ra[grismCat.id == id][0]
de0 = grismCat.dec[grismCat.id == id][0]
#### Read EAZY outputs and get info for desired object
if cat is None:
cat = catIO.ReadASCIICat(OUTPUT_DIRECTORY+'../'+MAIN_OUTPUT_FILE+'.cat')
dr = np.sqrt((cat.ra-ra0)**2*np.cos(de0/360.*2*np.pi)**2+(cat.dec-de0)**2)*3600.
photom_idx = np.where(dr == np.min(dr))[0][0]
drMatch = dr[photom_idx]*1.
if drMatch > 2:
return False
if Verbose:
print 'Read zout'
if zout is None:
zout = catIO.ReadASCIICat(OUTPUT_DIRECTORY+'/'+MAIN_OUTPUT_FILE+'.zout')
if fout is None:
fout = catIO.ReadASCIICat(OUTPUT_DIRECTORY+'/../cosmos-1.m05.v4.6.fout')
if Verbose:
print 'Read binaries'
lambdaz, temp_sed, lci, obs_sed, fobs, efobs = \
eazy.getEazySED(photom_idx, MAIN_OUTPUT_FILE=MAIN_OUTPUT_FILE, \
OUTPUT_DIRECTORY=OUTPUT_DIRECTORY, \
CACHE_FILE = CACHE_FILE)
try:
lambdaz, temp_sed_sm = unicorn.analysis.convolveWithThumb(id, lambdaz, temp_sed, SPC)
except:
temp_sed_sm = temp_sed*1.
wfc3_exist = False
if GET_WFC3:
wfc3_file_path = WFC3_DIR+"/*/1D/FITS/*%05d.1D.fits" %(cat.id[photom_idx])
wfc3_file = glob.glob(wfc3_file_path)
if wfc3_file != []:
wfc3_spec = pyfits.open(wfc3_file[0])
wfc3_exist = True
else:
print 'No WFC3 spectrum.'
if Verbose:
print 'Normalize spectrum'
q = np.where((lam > 0.55e4) & (lam < 1.0e4) & (flux > 0))[0]
if len(q) == 0:
return False
yint = np.interp(lam[q], lambdaz, temp_sed_sm)
anorm = np.sum(yint*ffix[q])/np.sum(ffix[q]**2)
if np.isnan(anorm):
anorm=1.
total_err = np.sqrt((ferr)**2+(1.0*spec.field('CONTAM'))**2)*anorm
if GET_SPEC_ONLY:
if drMatch > 1:
return False
else:
return lam, ffix*anorm, total_err, lci, fobs, efobs, photom_idx
if Verbose:
print 'Start plot'
#### Make the plot
threedhst.plotting.defaultPlotParameters()
xs=5.8
ys = xs/4.8*3.2
if USE_PLOT_GUI:
fig = plt.figure(figsize=[xs,ys],dpi=100)
else:
fig = Figure(figsize=[xs,ys], dpi=100)
fig.subplots_adjust(wspace=0.2,hspace=0.2,left=0.13*4.8/xs, bottom=0.15*4.8/xs,right=1.-0.02*4.8/xs,top=1-0.10*4.8/xs)
ax = fig.add_subplot(111)
ymax = np.max((ffix[q])*anorm)
if Verbose:
print 'Make the plot'
ax.plot(lambdaz, temp_sed_sm, color='red')
ax.plot(lam[q],ffix[q]*anorm, color='blue', alpha=0.2, linewidth=1)
#### Show own extraction
sp1d = threedhst.spec1d.extract1D(id, root=grism_root, path='./HTML', show=False, out2d=False)#, GRISM_NAME='G800L')
lam = sp1d['lam']
flux = sp1d['flux']
ffix = sp1d['flux']-sp1d['contam']
ferr = sp1d['error']
anorm = np.sum(yint*ffix[q])/np.sum(ffix[q]**2)
ax.plot(lam[q],ffix[q]*anorm, color='blue', alpha=0.6, linewidth=1)
#### Show photometry + eazy template
ax.errorbar(lci, fobs, yerr=efobs, color='orange', marker='o', markersize=10, linestyle='None', alpha=0.4)
ax.plot(lambdaz, temp_sed_sm, color='red', alpha=0.4)
if wfc3_exist:
q_wfc3 = np.where((wfc3_spec[1].data.wave > 1.08e4) & (wfc3_spec[1].data.wave < 1.68e4) & (wfc3_spec[1].data.flux > 0))[0]
yint_wfc3 = np.interp(wfc3_spec[1].data.wave[q_wfc3], lambdaz, temp_sed_sm)
spec_wfc3 = (wfc3_spec[1].data.flux-wfc3_spec[1].data.contam)/wfc3_spec[1].data.sensitivity
anorm_wfc3 = np.sum(yint_wfc3*spec_wfc3[q_wfc3])/np.sum(spec_wfc3[q_wfc3]**2)
if np.isnan(anorm_wfc3): anorm_wfc3 = 1.
print 'Scaling factors: ', anorm, anorm_wfc3
ax.plot(wfc3_spec[1].data.wave[q_wfc3], spec_wfc3[q_wfc3]*anorm_wfc3, color='blue',alpha=0.6, linewidth=1)
ax.set_ylabel(r'$f_{\lambda}$')
if plt.rcParams['text.usetex']:
ax.set_xlabel(r'$\lambda$ [\AA]')
ax.set_title('%s: \#%d, z=%4.1f'
%(SPC.filename.split('_2_opt')[0].replace('_','\_'),id,
zout.z_peak[photom_idx]))
else:
ax.set_xlabel(r'$\lambda$ [$\AA$]')
ax.set_title('%s: #%d, z=%4.1f'
%(SPC.filename.split('_2_opt')[0].replace('_','\_'),id,
zout.z_peak[photom_idx]))
#kmag = 25-2.5*np.log10(cat.ktot[photom_idx])
kmag = cat.kmag[photom_idx]
##### Labels
label = 'ID='+r'%s K=%4.1f $\log M$=%4.1f' %(np.int(cat.id[photom_idx]),
kmag, fout.field('lmass')[photom_idx])
ax.text(5e3,1.08*ymax, label, horizontalalignment='left',
verticalalignment='bottom')
label = 'R=%4.1f"' %(drMatch)
if drMatch > 1.1:
label_color = 'red'
else:
label_color = 'black'
ax.text(2.2e4,1.08*ymax, label, horizontalalignment='right',
color=label_color, verticalalignment='bottom')
ax.set_xlim(xmin,xmax)
ax.set_ylim(-0.1*ymax,1.2*ymax)
if Verbose:
print 'Save the plot'
if OUT_FILE_FORMAT:
out_file = '%s_%05d_SED.png' %(grism_root, id)
else:
out_file = OUT_FILE
if USE_PLOT_GUI:
fig.savefig(OUT_PATH+'/'+out_file,dpi=100,transparent=False)
plt.close()
else:
canvas = FigureCanvasAgg(fig)
canvas.print_figure(OUT_PATH+'/'+out_file, dpi=100, transparent=False)
print unicorn.noNewLine+OUT_PATH+'/'+out_file
if Verbose:
print 'Close the plot window'
def specphot_acs_and_wfc3(
id=69,
grism_root='ibhm45030',
MAIN_OUTPUT_FILE='cosmos-1.v4.6',
OUTPUT_DIRECTORY='/Users/gbrammer/research/drg/PHOTZ/EAZY/NEWFIRM/v4.6/OUTPUT_KATE/',
CACHE_FILE='Same',
Verbose=False,
SPC=None,
cat=None,
grismCat=None,
zout=None,
fout=None,
OUT_PATH='/tmp/',
OUT_FILE_FORMAT=True,
OUT_FILE='junk.png',
GET_SPEC_ONLY=False,
GET_WFC3=False,
WFC3_DIR='/3DHST/Spectra/Release/v2.0/GOODS-S'):
"""
specphot_acs_and_wfc3(id)
Get photometry/SED fit as well as WFC3 spectrum when available and overplot G141 spectrum.
This is different from unicorn.analysis.specphot() which does not get the WFC3 spectrum.
"""
import threedhst.eazyPy as eazy
import threedhst.catIO as catIO
import pyfits
#### Get G141 spectrum
if Verbose:
print 'Read SPC'
if SPC is None:
SPC = threedhst.plotting.SPCFile(grism_root + '_2_opt.SPC.fits',
axe_drizzle_dir='DRIZZLE_G141')
spec = SPC.getSpec(id)
if spec is False:
return False
xmin = 3000
xmax = 2.4e4
lam = spec.field('LAMBDA')
flux = spec.field('FLUX')
ffix = flux - spec.field('CONTAM')
ferr = spec.field('FERROR') #*0.06/0.128254
if Verbose:
print 'Read grism catalog'
#### Read the grism catalog and get coords of desired object
if grismCat is None:
grismCat = threedhst.sex.mySexCat('DATA/' + grism_root + '_drz.cat')
#### Source size
R = np.sqrt(np.cast[float](grismCat.A_IMAGE) *
np.cast[float](grismCat.B_IMAGE))
grism_idx = np.where(grismCat.id == id)[0][0]
Rmatch = R[grism_idx] * 1.
ra0 = grismCat.ra[grismCat.id == id][0]
de0 = grismCat.dec[grismCat.id == id][0]
#### Read EAZY outputs and get info for desired object
if cat is None:
cat = catIO.ReadASCIICat(OUTPUT_DIRECTORY + '../' + MAIN_OUTPUT_FILE +
'.cat')
dr = np.sqrt((cat.ra - ra0)**2 * np.cos(de0 / 360. * 2 * np.pi)**2 +
(cat.dec - de0)**2) * 3600.
photom_idx = np.where(dr == np.min(dr))[0][0]
drMatch = dr[photom_idx] * 1.
if drMatch > 2:
return False
if Verbose:
print 'Read zout'
if zout is None:
zout = catIO.ReadASCIICat(OUTPUT_DIRECTORY + '/' + MAIN_OUTPUT_FILE +
'.zout')
if fout is None:
fout = catIO.ReadASCIICat(OUTPUT_DIRECTORY +
'/../cosmos-1.m05.v4.6.fout')
if Verbose:
print 'Read binaries'
lambdaz, temp_sed, lci, obs_sed, fobs, efobs = \
eazy.getEazySED(photom_idx, MAIN_OUTPUT_FILE=MAIN_OUTPUT_FILE, \
OUTPUT_DIRECTORY=OUTPUT_DIRECTORY, \
CACHE_FILE = CACHE_FILE)
try:
lambdaz, temp_sed_sm = unicorn.analysis.convolveWithThumb(
id, lambdaz, temp_sed, SPC)
except:
temp_sed_sm = temp_sed * 1.
wfc3_exist = False
if GET_WFC3:
wfc3_file_path = WFC3_DIR + "/*/1D/FITS/*%05d.1D.fits" % (
cat.id[photom_idx])
wfc3_file = glob.glob(wfc3_file_path)
if wfc3_file != []:
wfc3_spec = pyfits.open(wfc3_file[0])
wfc3_exist = True
else:
print 'No WFC3 spectrum.'
if Verbose:
print 'Normalize spectrum'
q = np.where((lam > 0.55e4) & (lam < 1.0e4) & (flux > 0))[0]
if len(q) == 0:
return False
yint = np.interp(lam[q], lambdaz, temp_sed_sm)
anorm = np.sum(yint * ffix[q]) / np.sum(ffix[q]**2)
if np.isnan(anorm):
anorm = 1.
total_err = np.sqrt((ferr)**2 + (1.0 * spec.field('CONTAM'))**2) * anorm
if GET_SPEC_ONLY:
if drMatch > 1:
return False
else:
return lam, ffix * anorm, total_err, lci, fobs, efobs, photom_idx
if Verbose:
print 'Start plot'
#### Make the plot
threedhst.plotting.defaultPlotParameters()
xs = 5.8
ys = xs / 4.8 * 3.2
if USE_PLOT_GUI:
fig = plt.figure(figsize=[xs, ys], dpi=100)
else:
fig = Figure(figsize=[xs, ys], dpi=100)
fig.subplots_adjust(wspace=0.2,
hspace=0.2,
left=0.13 * 4.8 / xs,
bottom=0.15 * 4.8 / xs,
right=1. - 0.02 * 4.8 / xs,
top=1 - 0.10 * 4.8 / xs)
ax = fig.add_subplot(111)
ymax = np.max((ffix[q]) * anorm)
if Verbose:
print 'Make the plot'
ax.plot(lambdaz, temp_sed_sm, color='red')
ax.plot(lam[q], ffix[q] * anorm, color='blue', alpha=0.2, linewidth=1)
#### Show own extraction
sp1d = threedhst.spec1d.extract1D(id,
root=grism_root,
path='./HTML',
show=False,
out2d=False) #, GRISM_NAME='G800L')
lam = sp1d['lam']
flux = sp1d['flux']
ffix = sp1d['flux'] - sp1d['contam']
ferr = sp1d['error']
anorm = np.sum(yint * ffix[q]) / np.sum(ffix[q]**2)
ax.plot(lam[q], ffix[q] * anorm, color='blue', alpha=0.6, linewidth=1)
#### Show photometry + eazy template
ax.errorbar(lci,
fobs,
yerr=efobs,
color='orange',
marker='o',
markersize=10,
linestyle='None',
alpha=0.4)
ax.plot(lambdaz, temp_sed_sm, color='red', alpha=0.4)
if wfc3_exist:
q_wfc3 = np.where((wfc3_spec[1].data.wave > 1.08e4)
& (wfc3_spec[1].data.wave < 1.68e4)
& (wfc3_spec[1].data.flux > 0))[0]
yint_wfc3 = np.interp(wfc3_spec[1].data.wave[q_wfc3], lambdaz,
temp_sed_sm)
spec_wfc3 = (wfc3_spec[1].data.flux -
wfc3_spec[1].data.contam) / wfc3_spec[1].data.sensitivity
anorm_wfc3 = np.sum(yint_wfc3 * spec_wfc3[q_wfc3]) / np.sum(
spec_wfc3[q_wfc3]**2)
if np.isnan(anorm_wfc3): anorm_wfc3 = 1.
print 'Scaling factors: ', anorm, anorm_wfc3
ax.plot(wfc3_spec[1].data.wave[q_wfc3],
spec_wfc3[q_wfc3] * anorm_wfc3,
color='blue',
alpha=0.6,
linewidth=1)
ax.set_ylabel(r'$f_{\lambda}$')
if plt.rcParams['text.usetex']:
ax.set_xlabel(r'$\lambda$ [\AA]')
ax.set_title(
'%s: \#%d, z=%4.1f' % (SPC.filename.split('_2_opt')[0].replace(
'_', '\_'), id, zout.z_peak[photom_idx]))
else:
ax.set_xlabel(r'$\lambda$ [$\AA$]')
ax.set_title(
'%s: #%d, z=%4.1f' % (SPC.filename.split('_2_opt')[0].replace(
'_', '\_'), id, zout.z_peak[photom_idx]))
#kmag = 25-2.5*np.log10(cat.ktot[photom_idx])
kmag = cat.kmag[photom_idx]
##### Labels
label = 'ID=' + r'%s K=%4.1f $\log M$=%4.1f' % (np.int(
cat.id[photom_idx]), kmag, fout.field('lmass')[photom_idx])
ax.text(5e3,
1.08 * ymax,
label,
horizontalalignment='left',
verticalalignment='bottom')
label = 'R=%4.1f"' % (drMatch)
if drMatch > 1.1:
label_color = 'red'
else:
label_color = 'black'
ax.text(2.2e4,
1.08 * ymax,
label,
horizontalalignment='right',
color=label_color,
verticalalignment='bottom')
ax.set_xlim(xmin, xmax)
ax.set_ylim(-0.1 * ymax, 1.2 * ymax)
if Verbose:
print 'Save the plot'
if OUT_FILE_FORMAT:
out_file = '%s_%05d_SED.png' % (grism_root, id)
else:
out_file = OUT_FILE
if USE_PLOT_GUI:
fig.savefig(OUT_PATH + '/' + out_file, dpi=100, transparent=False)
plt.close()
else:
canvas = FigureCanvasAgg(fig)
canvas.print_figure(OUT_PATH + '/' + out_file,
dpi=100,
transparent=False)
print unicorn.noNewLine + OUT_PATH + '/' + out_file
if Verbose:
print 'Close the plot window'
axes=None,
individual_templates=True,
fnu=False)
plt.savefig('eazy_fit.png')
plt.close()
################################################
#### Pull out data from the BINARY_OUTPUTS files
################################################
## SED, data & fit
sed = eazy.getEazySED(17,
MAIN_OUTPUT_FILE='photz',
OUTPUT_DIRECTORY='./OUTPUT',
CACHE_FILE='Same',
scale_flambda=True,
verbose=False,
individual_templates=False)
lambdaz, temp_sed, lci, obs_sed, fobs, efobs = sed
axes[0].scatter(lci, obs_sed, color='orange', zorder=2)
axes[0].scatter(lci, fobs, color='green', marker='s', s=150, zorder=2)
## p(z)
zgrid, pzi, prior = eazy.getEazyPz(17,
MAIN_OUTPUT_FILE='photz',
OUTPUT_DIRECTORY='./OUTPUT',
CACHE_FILE='Same',
binaries=None,
get_prior=True)