location=None, xcorV=None, chivel=None, veloffset=0.,

wavemin=3800., wavemax=6800., maskBalm=False,

plotblue=False, smoothkern=0):

flux_factor = 1e17

dhdu = pyfits.open(datafile)[0]

data = dhdu.data

head = dhdu.header

error = pyfits.open(errorfile)[0].data

numfibers, wavesize = data.shape

cdelt = head['CDELT1']

crval = head['CRVAL1']

crpix = head['CRPIX1']

print 'CDELT1 = ', cdelt

print 'CRVAL1 = ', crval

print 'CRPIX1 = ', crpix

wave = (np.arange(wavesize) - (crpix-1)) * cdelt + crval

idx = np.where((wave >= wavemin) & (wave <= wavemax))[0]

restwl = wave[idx]

if location is not None:

fiber_radii, rkpc, zkpc = np.loadtxt(location,

usecols=(1,4,5),

unpack=True)

sizeidx = [0.937,1.406,1.875,2.344,2.812]

m = pyfits.open(model)[1].data[0]

nmodels = m['FLUX'].shape[0]

numZ = np.unique(m['Z'][:,0]).size

numAge = np.unique(m['AGE'][:,0]).size

big_w = np.zeros((numZ,numAge))

if output is None:

output = '.'.join(fitfile.split('.')[0:-1])+'.pdf'

if plotblue:

output = '.'.join(output.split('.')[0:-1])+'.blue.pdf'

if veloffset != 0:

output = '.'.join(output.split('.')[0:-1])+'.voff.pdf'

if smoothkern > 0:

output = '.'.join(output.split('.')[0:-1])+'.smooth.pdf'

pp = PDF(output)

if xcorV is not None:

xcorVd = np.loadtxt(xcorV,usecols=(1,),unpack=True)

if chivel is not None:

vel_arr = pyfits.open(chivel)[1].data

coef_arr = pyfits.open(coeffile)[1].data

yfits = pyfits.open(fitfile)[0].data

size_borders = [19, 43, 62, 87, 109] # The last one is needed to prevent indexing errors

size_switch = 0

redidx = np.where(restwl >= 5400)

blueidx = np.where(restwl < 5400)

hklow = 3920

hkhigh = 4000

hkidx = np.where((restwl > hklow) & (restwl < hkhigh))

npix = restwl.size

TT_chi = np.zeros((numfibers, npix))

for i in range(numfibers):

flux = data[i,idx]*flux_factor

err = error[i,idx]*flux_factor

yfit = yfits[i,:] * flux_factor

coefs = coef_arr[i]

if np.mean(yfit) == 0.0:

print "No data in aperture", i+1

continue

if xcorV is None:

VSYS = coefs['VSYS']

else:

VSYS = xcorVd[i]

if chivel is not None:

print 'loading chisq velocity'

VSYS += vel_arr[i]['VSYS']

if veloffset != 0:

print 'Applying manual velocity offset of {} km/s'.format(veloffset)

VSYS += veloffset

if location is not None:

vdidx = np.where(sizeidx == fiber_radii[i])[0][0]

plotlabel = 'Aperture {:n}, r={:6.2f}, z={:5.2f}'.\

format(i+1,rkpc[i],zkpc[i])

else:

if i == size_borders[0]:

size_switch += 1

size_borders = size_borders[1:]

vdidx = size_switch

plotlabel = 'Fiber {:n}'.format(i+1)

print plotlabel

quality = np.ones(npix)

bad = np.where((err == 0) | (np.isnan(flux)) | (np.isnan(err)))

quality[bad] = 0

outside_model = np.where((restwl < m['WAVE'].min()) |\

(restwl > m['WAVE'].max()))

quality[outside_model] = 0

sk = np.array([6300., 5890., 5683.8, 5577., 5461., 5199., 4983., 4827.32, 4665.69, 4420.23, 4358., 4165.68, 4047.0])

sknam = ['[OI] (atm)', 'NaD', 'NaI', 'OI (atm)', 'HgI', 'NI (atm)', 'NaI', 'HgI', 'NaI', 'NaI', 'HgI', 'NaI', 'HgI']

sk2 = np.array([6300., 5890., 5577.])

# em2 = np.array([6563.8, 6716.0, 6583.41, 6548.04])

em2 = np.array([6563.8, 4959., 5006.8, 6716.0, 6583.41, 6548.04])

em = np.array([6563.8, 6716.0, 6583.41, 6548.04, 4959., 5006.8])

emnam = [r'H$\alpha$', 'S2', 'NII', 'NII', '[OIII]', '[OIII]']

ab = np.array([3820.4, 3835.4, 3889.0, 3933.7, 3968.5, 3970.18, 4304.4, 4341., 5175.3, 5894.0, 4861., 4102., 3820.4])

absnam = ['L', r'H$\eta$', r'H$\zeta$', 'K', 'H' , r'H$\epsilon$', 'G', r'H$\gamma$', 'Mg', 'Na', r'H$\beta$', r'H$\delta$', 'L']

balm = 1.*np.array([6563, 4861, 4341, 4102, 3970])

try:

dz = coefs['EMMASKW']/3e5

print 'Loading emmaskw = {}'.format(coefs['EMMASKW'])

except KeyError:

dz = 1000. / 3e5

dzsk = 1500. / 3e5

try:

if 'FIXEDVBOOL' in coef_arr.names:

em2 *= (coefs['VSYS']/3e5 + 1.)

balm *= (coefs['VSYS']/3e5 + 1.)

else:

em2 *= (coefs['VELSTART']/3e5 + 1.)

balm *= (coefs['VELSTART']/3e5 + 1.)

except KeyError:

pass

for ee in em2:

maskout = np.where((restwl > ee*(1-dz)) & (restwl < ee*(1+dz)))

quality[maskout] = 0

for ss in sk2:

maskout = np.where((restwl > ss*(1-dzsk)) & (restwl < ss*(1+dzsk)))

quality[maskout] = 0

if maskBalm:

for b in balm:

maskout = np.where((restwl > b*(1-dz)) & (restwl < b*(1+dz)))

quality[maskout] = 0

ok = quality == 1

# Interpolate models to data wavelength grid

custom_lib = np.zeros((nmodels, npix))

for ii in range(nmodels):

custom_lib[ii,:] = np.interp(restwl,

m['WAVE'], m['FLUX'][ii,:,vdidx])

custom_lib[:,outside_model] = 0

############################

############################

if plotblue:

pidx = np.where(restwl < 4500.)

bidx = np.where((restwl > 5000.) & (restwl < 5330.))

bwave = restwl[bidx]

bxmin = bwave.min() - 20.

bxmax = bwave.max() + 20.

fbox = [0.1,0.25,0.56,0.69]

bbox = [0.67,0.25,0.28,0.69]

else:

pidx = np.where(restwl == restwl)

fbox = [0.1,0.25,0.85,0.69]

pwave = restwl[pidx]

xmin = pwave.min() - 20.

xmax = pwave.max() + 20.

fig = plt.figure(figsize=(11,8))

fax = fig.add_axes(fbox)

fax.set_xticklabels([])

fax.set_ylabel('Log Flux + 17 [erg/s/cm$^2$/$\AA$]')

fax.set_xlim(xmin,xmax)

fax.set_ylim(-0.49, 2.6)

fax.axvline(x=5400, color='k', ls=':', alpha=0.3)

fax.axvline(x=hklow, color='k', ls=':', alpha=0.3)

fax.axvline(x=hkhigh, color='k', ls=':', alpha=0.3)

if plotblue:

bax = fig.add_axes(bbox)

bax.set_xticks([5000,5100,5200,5300])

bax.set_xticklabels([])

bax.set_yticklabels([])

bax.set_xlim(bxmin,bxmax)

bax.set_ylim(*fax.get_ylim())

bax.spines['left'].set_visible(False)

bax.yaxis.tick_right()

fax.spines['right'].set_visible(False)

fax.yaxis.tick_left()

yfit *= 0.0

for j in range(coefs['LIGHT_FRAC'].size):

xred = restwl * (VSYS/3e5 + 1)

yi = coefs['LIGHT_FRAC'][j] * custom_lib[j,:] *\

np.exp(-1 * coefs['TAUV']*(restwl/5500.)**(-0.7))

yi = np.interp(restwl, xred, yi)

yfit += yi

fax.plot(pwave,

np.log10(spnd.filters.gaussian_filter1d(yi,smoothkern))[pidx],

color='b',alpha=0.4)

if plotblue:

bax.plot(bwave,

np.log10(spnd.filters.gaussian_filter1d(yi,smoothkern))[bidx],

color='b',alpha=0.4)

textloc = np.log10(spnd.filters.gaussian_filter1d(yi,smoothkern))[bidx][-1]

if np.isfinite(textloc):

bax.text(bwave[-1] + 30, textloc, j+1, color='b',

va='center', ha='center', fontsize=8)

else:

textloc = np.log10(spnd.filters.gaussian_filter1d(yi,smoothkern))[pidx][-1]

if np.isfinite(textloc):

fax.text(pwave[-1] + 50, textloc, j+1, color='b',

va='center', ha='center', fontsize=8)

TT_chi[i,:] = (flux - yfit)/err

galfit = np.zeros(flux.size) + yfit

galfit[ok] = flux[ok]

plotgal = spnd.filters.gaussian_filter1d(galfit,smoothkern)

galfit[~ok] = np.NAN

plotgal[~ok] = np.NAN

masked = spnd.filters.gaussian_filter1d(flux,smoothkern)

masked[ok] = np.NAN

plotfit = spnd.filters.gaussian_filter1d(yfit,smoothkern)

fax.plot(pwave,np.log10(plotgal)[pidx],color='k')

fax.plot(pwave,np.log10(masked)[pidx],color='c',lw=1)

fax.plot(pwave,np.log10(plotfit)[pidx],color='r')

fax.fill_between(pwave,

np.log10(plotgal -

spnd.filters.gaussian_filter1d(

err,smoothkern*2))[pidx],

np.log10(plotgal +

spnd.filters.gaussian_filter1d(

err,smoothkern*2))[pidx],

color='k', alpha=0.2)

if plotblue:

bax.plot(bwave,np.log10(plotgal)[bidx],color='k')

bax.plot(bwave,np.log10(masked)[bidx],color='c',lw=1)

bax.plot(bwave,np.log10(plotfit)[bidx],color='r')

bax.fill_between(bwave,

np.log10(plotgal -

spnd.filters.gaussian_filter1d(

err,smoothkern*2))[bidx],

np.log10(plotgal +

spnd.filters.gaussian_filter1d(

err,smoothkern*2))[bidx],

color='k', alpha=0.2)

###################################

###################################

Z = VSYS/3e5 + 1

tlim1 = xmin + 20

tlim2 = xmax - 20

if plotblue:

btlim1 = bxmin + 20

btlim2 = bxmax - 20

ypos = 1

for s, sn in zip(sk, sknam):

tidx = np.where((restwl >= s - 10) & (restwl <= s + 10.))

try:

ypos = np.log10(np.nanmax(np.r_[flux[tidx],yfit[tidx]])) + 0.1

except ValueError:

pass

if s < tlim2 and s > tlim1:

fax.text(s, ypos, sn, fontsize=8,

ha='center', va='center')

if plotblue:

if s < tlim2 and s > tlim1:

fax.axvline(s, color='k', ls=':', alpha=0.7)

if s < btlim2 and s > btlim1:

bax.text(s, ypos, sn, fontsize=8,

ha='center', va='center')

bax.axvline(s, color='k', ls=':', alpha=0.7)

else:

fax.plot((s,s), (ypos-0.04,ypos-0.1), color='k', alpha=0.8)

prevy = 99

for a, an in zip(ab*Z, absnam):

tidx = np.where((restwl >= a - 10) & (restwl <= a + 10.))

try:

ypos = np.log10(np.nanmin(np.r_[flux[tidx],yfit[tidx]])) - 0.1

except ValueError:

pass

if (an == r'H$\gamma$' or

an == r'H$\eta$' or

an == r'H$\epsilon$') and np.abs(ypos - prevy) <= 0.04:

ypos += 0.06

prevy = ypos

if np.isnan(ypos) or ypos < -0.4:

ypos = -0.4

if a > tlim1 and a < tlim2:

fax.text(a, ypos, an, color='r', fontsize=8,

ha='center', va='center')

if plotblue:

if a > tlim1 and a < tlim2:

fax.axvline(a, color='r', ls=':', alpha=0.7)

if a > btlim1 and a < btlim2:

bax.text(a, ypos, an, color='r', fontsize=8,

ha='center', va='center')

bax.axvline(a, color='r', ls=':', alpha=0.7)

else:

fax.plot((a,a), (ypos+0.04,ypos+0.1), color='r', alpha=0.8)

for e, en in zip(em*Z, emnam):

tidx = np.where((restwl >= e - 10) & (restwl <= e + 10.))

try:

ypos = np.log10(np.nanmax(np.r_[flux[tidx],yfit[tidx]])) + 0.1

except ValueError:

pass

if en == '[OIII]': ypos += 0.2

if e > tlim1 and e < tlim2:

fax.text(e, ypos, en, color='b', fontsize=8,

ha='center', va='center')

if plotblue:

if e > tlim1 and e < tlim2:

fax.axvline(e, color='b', ls=':', alpha=0.7)

if e > btlim1 and e < btlim2:

bax.text(e, ypos, en, color='b', fontsize=8,

ha='center', va='center')

bax.axvline(e, color='b', ls=':', alpha=0.7)

else:

fax.plot((e,e), (ypos-0.04,ypos-0.1), color='b', alpha=0.8)

############################################

############################################

chivec = (flux - yfit)/err

plotchi = spnd.filters.gaussian_filter1d(chivec,smoothkern)

maskedchi = plotchi * 1.0

maskedchi[ok] = np.NAN

eax = fig.add_axes([0.1,0.1,fbox[2],0.15])

eax.set_xlabel('Wavelength [$\AA$]')

eax.set_ylabel('Residuals/error')

eax.set_xlim(fax.get_xlim())

eax.set_ylim(-6,6)

eax.set_yticks([-5,0,5])

eax.plot(pwave, plotchi[pidx], color='k')

eax.plot(pwave, maskedchi[pidx], color='c', lw=1)

if plotblue:

beax = fig.add_axes([bbox[0],0.1,bbox[2],0.15])

beax.set_yticklabels([])

beax.set_xlim(bax.get_xlim())

beax.set_ylim(eax.get_ylim())

beax.set_yticks([-5,0,5])

beax.set_xticks([5000,5100,5200,5300])

beax.plot(bwave, plotchi[bidx], color='k')

beax.plot(bwave, maskedchi[bidx], color='c', lw=1)

beax.spines['left'].set_visible(False)

beax.yaxis.tick_right()

eax.spines['right'].set_visible(False)

eax.yaxis.tick_left()

eax.set_xlabel('')

eax.text(0.76, -0.3, 'Wavelength [$\AA$]',

ha='center', va='center', transform=eax.transAxes)

###########################################

###########################################

fs = 10

fig.text(0.15, 0.92, plotlabel, fontsize=fs)

fig.text(0.15, 0.89, 'SNR = {:8.2f}'.format(coefs['SNR']), fontsize=fs)

fig.text(0.15, 0.87, 'V = {:8.2f} km/s'.format(VSYS),

fontsize=fs)

if chivel is not None:

fig.text(0.15, 0.85, r'$\Delta$V$_{{fit}}$ = {:8.2f}'.format(vel_arr[i]['VSYS']),

fontsize=fs)

fig.text(0.15, 0.83, "V_disp = {}'' fiber".format(vdidx+2),

fontsize=fs)

fig.text(0.15, 0.81, r'$\tau_V$ = {:8.2f}'.format(coefs['tauv']),

fontsize=fs)

else:

fig.text(0.15, 0.85, "V_disp = {}'' fiber".format(vdidx+2),

fontsize=fs)

fig.text(0.15, 0.83, r'$\tau_V$ = {:8.2f}'.format(coefs['tauv']),

fontsize=fs)

fig.text(0.35, 0.89, 'MLWA = {:8.2f}'.format(coefs['MLWA']),

fontsize=fs)

fig.text(0.35, 0.87, 'MMWA = {:8.2f}'.format(coefs['MMWA']),

fontsize=fs)

fig.text(0.35, 0.85, 'MLWZ = {:8.2f}'.format(coefs['MLWZ']),

fontsize=fs)

fig.text(0.35, 0.83, 'MMWZ = {:8.2f}'.format(coefs['MMWZ']),

fontsize=fs)

fig.text(0.55, 0.89, r'$\chi^2$ = {:8.2f}'.format(coefs['chisq']),

fontsize=fs)

fig.text(0.55, 0.87, r'$\chi^2_\mathrm{{red}}$ = {:8.2f}'.\

format(coefs['redchi']), fontsize=fs)

fig.text(0.55, 0.85, r'$\chi^2_\mathrm{{blue}}$ = {:8.2f}'.\

format(coefs['bluechi']), fontsize=fs)

fig.text(0.55, 0.83, r'$\chi^2_\mathrm{{HK}}$ = {:8.2f}'.\

format(coefs['hkchi']), fontsize=fs)

######################

######################

wax = fig.add_axes([0.70,0.83,0.2,0.1])

wdata = coefs['LIGHT_FRAC'].reshape(numZ,numAge)

wax.imshow(wdata,origin='lower',cmap='Blues',interpolation='none')

wax.set_xticks(range(numAge))

wax.set_xticklabels(m['AGE'][:numAge,0]/1e9, rotation=90, fontsize=7)

wax.set_yticks(range(numZ))

wax.set_yticklabels(m['Z'][::numAge,0],fontsize=7)

for l in range(numZ):

wax.text(wax.get_xlim()[1]+1, l, numAge*(l + 1), va='center',

ha='center', fontsize=7, color='b')

big_w += wdata/np.max(wdata)

fig.suptitle(time.asctime())

pp.savefig(fig)

plt.close(fig)

bwax = plt.figure().add_subplot(111)

bwax.imshow(big_w,origin='lower',cmap='Blues',interpolation='none')

bwax.set_xlabel('SSP Age [Gyr]')

bwax.set_xticks(range(numAge))

bwax.set_xticklabels(m['AGE'][:numAge,0]/1e9)

bwax.set_ylabel(r'$Z/Z_{\odot}$')

bwax.set_yticks(range(numZ))

bwax.set_yticklabels(m['Z'][::numAge,0])

pp.savefig(bwax.figure)

plt.close(bwax.figure)

pp.close()

#pyfits.PrimaryHDU(TT_chi).writeto(output.split('.pdf')[0]+'_tmpchi.fits', clobber=True)

coeffile = inputlist[0]

fitfile = inputlist[1]

datafile = inputlist[2]

errorfile = inputlist[3]

modelfile = inputlist[4]

kwar = {}

i = 5

while i < len(inputlist):

if inputlist[i] == '-o':

kwar['output'] = inputlist[i+1]

i += 1

if inputlist[i] == '-v':

kwar['veloffset'] = float(inputlist[i+1])

i += 1

if inputlist[i] == '-l':

kwar['location'] = inputlist[i+1]

i += 1

if inputlist[i] == '-w':

kwar['wavemin'] = inputlist[i+1]

kwar['wavemax'] = inputlist[i+2]

i += 2

if inputlist[i] == '-x':

kwar['xcorV'] = inputlist[i+1]

i += 1

if inputlist[i] == '-c':

kwar['chivel'] = inputlist[i+1]

i += 1

if inputlist[i] == '-s':

kwar['smoothkern'] = int(inputlist[i+1])

i += 1

if inputlist[i] == '-b':

kwar['plotblue'] = True

if inputlist[i] == '-n':

import nice_plots

nice_plots.format_plots(False)

if inputlist[i] == '-H':

kwar['maskBalm'] = True

i += 1