'''

Run a cure command

Parameter suppress_output is used to quiet down. (default)

Return the value of os.system(command)

'''

# store info in log?

if debug:

print('Running: \'%s\'' % command)

if not suppress_output:

return os.system(op.join(CUREBIN, command) +' 1>>output.log 2>> error.log')

else:

command = ('fiberextract %s -d %s -f %s -o "%s" %s'

%(opts, distmodel, fibermodel, outname, filename))

run_cure_command(command, 0)

nifu = len(Felist)

nw = len(Felist[0][0].data[0,:])

xp = np.linspace(0, 1, num=nw)

nbspline = 12

a = np.linspace(0, 1, nbspline)

knots = np.hstack([0,0,np.vstack([a,a]).T.ravel(),1,1])

b = Bspline(knots, 3)

basis = np.array([b(xi) for xi in xp])

B = np.zeros((nifu,nw))

for i in xrange(nifu):

spec = biweight_location(Felist[i][0].data,axis=(0,))

mask = np.where((~np.isnan(spec))*(~np.isinf(spec))*(spec!=0))[0]

sol = np.linalg.lstsq(basis[mask,:], spec[mask])[0]

B[i,:] = np.dot(basis,sol)

# if args.plot:

# pltfile = op.join(args.outfolder, 'spectrum_%i.pdf' %i)

# fig = plt.figure(figsize=(8, 6))

# plt.plot(xp, spec)

# plt.plot(xp, B[i,:],'r--')

# plt.xticks([])

# plt.xlabel('Wavelength')

# plt.ylabel('Arbitrary Units')

# plt.xlim([0, 1])

# fig.savefig(pltfile, dpi=150)

# plt.close()

if args.plot:

norm = plt.Normalize()

colors = plt.cm.viridis(norm(np.arange(nifu)+1))

pltfile = op.join(args.outfolder, 'IFU_average_spectra.pdf')

fig = plt.figure(figsize=(8, 6))

avgB = biweight_location(B,axis=(0,))

for i in xrange(nifu):

with np.errstate(divide='ignore'):

plt.plot(xp, B[i,:]/avgB, color=colors[i,0:3], alpha=0.9)

plt.xticks([])

plt.xlabel('Wavelength')

plt.ylabel('Normalized Units')

plt.xlim([0, 1])

plt.ylim([0.5,1.5])

fig.savefig(pltfile, dpi=150)

plt.close()

nifu = len(Fiblist)

wave = np.arange(header_tup[0]) * header_tup[2] + header_tup[1]

for i in xrange(nifu):

F = FiberModel(Fiblist[i])

nfib, nw = Felist[i][0].data.shape

through = A[i] * B[i,:] / avgB

for j in xrange(nfib):

if args.debug:

t1 = time.time()

print("Working on Fibermodel, fiber: %i, %i" %(i,j))

mask = np.where(np.isfinite(through[j,:]))[0]

basis = np.vstack([F.amplitudes[j].get_basis(F._scal_w(w))

for w in wave])

x = through[j,mask]

x[-1] = x[-2]

y = basis[mask,:]

ax,ay = y.shape

lb = -1.*np.ones((ay,))

lb[-1]=-10.

ub = 1.*np.ones((ay,))

ub[-1]=10.

sol = lsq_linear(np.array(basis[mask,:]), np.array(x), bounds=(lb,ub))

F.amplitudes[j].A = sol['x'][:-1]

F.amplitudes[j].mean = sol['x'][-1]

filename = Fiblist[i][:-6]+'adjpy_'+Fiblist[i][-6]+'.fmod'

if args.debug:

print("Writing out %s" % filename)

F.writeto(op.join(args.outfolder, filename))

if args.debug:

t2=time.time()

nifu = len(Felist)

for i in xrange(nifu):

outfile = op.join(op.dirname(Fenames[i]),'n'+op.basename(Fenames[i]))

outfile_e = op.join(op.dirname(Fenames[i]),'e.n'+op.basename(Fenames[i]))

outfile_t = op.join(op.dirname(Fenames[i]),'t'+op.basename(Fenames[i]))

with np.errstate(divide='ignore'):

norm = np.where(B[i,:]!=0., Felist[i][0].data / B[i,:] * avgB, 0.)

norm_e = np.where(B[i,:]!=0., Fe_e_list[i][0].data / B[i,:] * avgB, 0.)

through = np.where(B[i,:]!=0., A[i] * B[i,:] / avgB, 0.)

Felist[i][0].data = norm

Fe_e_list[i][0].data = norm_e

Felist[i][0].header['HISTORY'] = 'Divided by Smoothed Average IFU Spectrum'

Fe_e_list[i][0].header['HISTORY'] = 'Divided by Smoothed Average IFU Spectrum'

Felist[i].writeto(outfile, clobber=True)

Fe_e_list[i].writeto(outfile_e, clobber=True)

Felist[i][0].data = through

nifu = len(Fiblist)

wave = np.arange(header_tup[0]) * header_tup[2] + header_tup[1]

A = []

for i in xrange(nifu):

if args.debug:

t1 = time.time()

print("Working on IFU %i" %i)

F = FiberModel(Fiblist[i])

nfib, nw = Felist[i][0].data.shape

a = np.zeros((nfib, nw))

for j, w in enumerate(wave):

for k in xrange(1, nfib+1):

a[k-1, j] = F.get_wf_amplitude(w, k)

A.append(a)

if args.debug:

t2=time.time()

print("Time Taken to get amplitudes for IFU %i: %0.2f" %(i,t2-t1))

fig = plt.figure(figsize=(12, 9))

p = fits.open(fibextract)[0].data

crval1 = fits.open(fibextract)[0].header['CRVAL1']

cdelt1 = fits.open(fibextract)[0].header['CDELT1']

plots = [1, 2, 3, 4, 5, 6, 7, 8, 9]

solar = np.loadtxt(op.join(virus_config, 'solar_spec', 'sun.spec'))

pos = 0

xs = p.shape[1]

nfib = p.shape[0]

wave = cdelt1 * np.arange(xs) + crval1

for i in [1, 0.5, 0]:

for j in [0, 0.5, 1]:

minx = int(j*xs - j*psize)

maxx = minx + psize

minf = int(i*nfib - i*fsize)

maxf = minf + fsize

minw = wave[minx]

maxw = wave[maxx-1]

miny = np.max([0,np.min(p[minf:maxf, minx:maxx])])

maxy = np.max(p[minf:maxf, minx:maxx])

solminx = np.searchsorted(solar[:,0],minw)

solmaxx = np.searchsorted(solar[:,0],maxw,side='right')

po = np.polyfit(wave[minx:maxx],

np.median(p[minf:maxf,minx:maxx],axis=0),3)

ps = np.polyfit(solar[solminx:solmaxx,0],

solar[solminx:solmaxx,1],3)

sub = fig.add_subplot(3, 3, plots[pos])

sub.set_xticks(np.arange(int(minw/50)*50, int(maxw/50 + 1)*50, 50))

sub.set_yticks(np.linspace(miny,maxy,5))

mult = np.polyval(po, solar[solminx:solmaxx,0])

div = np.polyval(ps, solar[solminx:solmaxx,0])

sub.plot(solar[solminx:solmaxx,0],

solar[solminx:solmaxx,1] * mult / div,

color=[0.35,0.23,0.35],linewidth=2)

for k in xrange(minf,maxf):

sub.plot(wave[minx:maxx], p[k,minx:maxx],

color=[1.0,0.23,0.35], alpha=0.5)

xran = maxw-minw

yran = maxy-miny

sub.text(0.1*xran+minw,0.85*yran+miny,

'Fibers: %03d - %03d' %(minf+1,maxf), color='red')

sub.set_xlim([minw, maxw])

sub.set_ylim([miny, maxy])

pos += 1

plt.tight_layout()

fig.savefig(outfile)

"""

Command line parser

Parameters

----------

argv: list of strings

list to be parsed

output

------

namespace:

Parsed arguments

"""

p = ap.ArgumentParser(formatter_class=ap.ArgumentDefaultsHelpFormatter)

p.add_argument('-F', '--folder', dest='folder', default=None,

help="""Folder for skyframes""")

p.add_argument('-C', '--calfolder', dest='calfolder', default=None,

help="""Folder for twighlights and cals""")

p.add_argument('-O', '--outfolder', dest='outfolder', default=None,

help="""Folder for twighlights and cals""")

p.add_argument('-o', '--options', dest='opts',

default="-n 1032 -W 3500,5500 -P",

help="""Fiberextract options.""")

p.add_argument('-w', '--overwrite', dest='overwrite', default=0,

action="count", help="""Overwrite the existing Fe* file?""")

p.add_argument('-p', '--plot', dest='plot',

action="count", default=0,

help="""Plot Fiber extracted twighlights vs. solar spectrum.""")

p.add_argument('-D', '--debug', dest='debug',

action="count", default=0,

help="""Debug.""")

p.add_argument('-T', '--twi', dest='twi',

action="count", default=0,

help="""Twighlight Frames? Otherwise Sky frames are used.""")

args = p.parse_args(args=args)

if not args.twi:

if not args.folder:

msg = ('If not running on twis, '

'you need to provide a folder for the sky frames')

p.error(msg)

if not args.calfolder:

msg = ('You need to provide a cal folder for the twis, dist, and fib.')

p.error(msg)

if not args.outfolder:

msg = ('You need to provide an out folder for the (n,t)Fe files.')

p.error(msg)

if args.twi:

sky_fn = op.join(args.calfolder, 'mastertrace_twi_%s_%s.fits' %(specid, side))

else:

sky_fn = op.join(args.folder,'c%s' %specid, 'sci', 'Sky*%s_sci_%s.fits' %(

specid_to_ifuslot(specid), side))

skyfiles = glob.glob(sky_fn)

distfile = op.join(args.calfolder, 'mastertrace_twi_%s_%s.dist' %(specid, side))

fibfile = op.join(args.calfolder, 'mastertrace_twi_%s_%s.fmod' %(specid, side))

# parse the command line

args = parse_arg(sys.argv[1:])

Felist = []

Fe_e_list = []

Fiblist = []

Fenames = []

if args.debug:

t1 = time.time()

for uca in ucam:

for sp in SIDE:

skyfiles, distfile, fibfile = make_sky_filenames(args, uca, sp)

if not op.exists(distfile):

print("%s does not exist" %distfile)

continue

if not op.exists(fibfile):

print("%s does not exist" %fibfile)

continue

for sky in skyfiles:

FeFile = op.join(args.outfolder,'Fe%s' %(op.basename(sky)))

FeFile_e = op.join(args.outfolder,'e.Fe%s' %(op.basename(sky)))

Fiblist.append(fibfile)

Fenames.append(FeFile)

if not op.exists(FeFile) or args.overwrite:

fiberextract(sky, distfile, fibfile,

op.join(args.outfolder, "%s" %(op.basename(sky))),

args.opts)

Felist.append(fits.open(FeFile))

Fe_e_list.append(fits.open(FeFile_e))

#outfile = op.join(args.outfolder, 'FePlot_cam%s_%s.pdf'

# %(uca, sp))

#if args.plot:

# plot_fiberextract(FeFile, args.psize, args.fsize,

# outfile)

if args.debug:

t2 = time.time()

print("Time Taken Extracting Fibers and/or Gathering Data: %0.2f" %(t2-t1))

outfile = op.join(args.outfolder, 'Avg_IFU_spectrum.fits')

if args.debug:

t1 = time.time()

B, avgB = throughput_fiberextract(Felist, args)

if args.debug:

t2 = time.time()

print("Time Taken fitting splines to Fe files: %0.2f" %(t2-t1))

header_tup = (Felist[0][0].header['NAXIS1'],

Felist[0][0].header['CRVAL1'],

Felist[0][0].header['CDELT1'])

if args.debug:

t1 = time.time()

A = get_fiber_amps(Fiblist, Felist, header_tup, args)

if args.debug:

t2 = time.time()

print("Time Taken getting fiber amps: %0.2f" %(t2-t1))

hdu = fits.PrimaryHDU(np.array(avgB))

hdu.header['CRVAL1'] = Felist[0][0].header['CRVAL1']

hdu.header['CDELT1'] = Felist[0][0].header['CDELT1']

hdu.writeto(outfile, clobber=True)

if args.debug:

t1 = time.time()

normalize_fiberextract(Felist, Fe_e_list, Fenames, B, avgB, A, args)

if args.debug:

t2 = time.time()

print("Time Taken normalizing Fe files: %0.2f" %(t2-t1))

if args.debug:

t1 = time.time()

edit_fibermodel(Felist, Fiblist, header_tup, B, avgB, A, args)

if args.debug:

t2 = time.time()