spectrum = np.genfromtxt('{}/{}'.format(directory,specfile), usecols=(0,1), dtype= 'string')

DtoE(spectrum[:,0])

DtoE(spectrum[:,1])

spectrum = np.array(spectrum, dtype=float)

spectrum[:,1] = spectrum[:,1][np.argsort(spectrum[:,0])]

spectrum[:,0] = np.sort(spectrum[:,0])

spectrum[:,1] = 10.0**(spectrum[:,1])

'''

Loads the normalized spectra created with the Normalize_Phoenix program.

'''

spectrum = np.genfromtxt('{}/{}'.format(directory,specfile), dtype='string')

spectrum = np.array(spectrum,dtype=float)

allspec = ('%(allspec)s' %{'allspec' : specfile})

contspec = ('%(cont)s' %{'cont' : continuum})

scalefactor = [0.995,1.02,0.997,1.02,0.997,1.02]

a = specfile.split('-')

#Calls in the file from the directory

spectrum = load_spec(allspec,'PHOENIX')

conspec = load_spec(contspec, 'PHOENIXcont')

newgrid = np.arange(3000,12000,0.01)

conspecflux = np.interp(newgrid, conspec[:,0], conspec[:,1])

specflux = np.interp(newgrid, spectrum[:,0], spectrum[:,1])

macroturb = 6

spectrograph = 2

conspecflux2 = convolve(conspecflux, macroturb,0.01) #Macroturbulence

conspecflux3 = convolve(conspecflux2, spectrograph,0.01) #Spectrograph resolution

specflux2 = convolve(specflux, FWHM,0.01)

specflux3 = convolve(specflux2, FWHM2, 0.01)

divflux = specflux3/conspecflux3

plt.title('Observed Arcturus Spectrum \n With 4250K Alpha enhanced model comparison \n Smoothed by convolution with gaussian curve FWHM = 5/150 Angstroms')

plt.xlabel('Wavelength ($\AA$)')

plt.ylabel('Normalized Flux (unitless)')

plt.grid(True)

plt.plot(newgrid, divflux/scalefactor[i], label = '%(type)s, $T_{eff}$ = %(metal)sK' %{ 'type' :a[0], 'metal' :a[1]})

plt.xlim(7149,7150.8)

modspec = '{}'.format(model)

contspec = '{}'.format(continuum)

a = model.split('-')

b = continuum.split('-')

#print 'Normalizing {}-{}K model with {}K continuum.'.format(a[0],a[1],b[1])

#Calls in the file from the directory

spectrum = load_spec(modspec,'PHOENIX')

conspec = load_spec(contspec,'PHOENIXcont')

newgrid = np.arange(3000,12000,0.01)

conspecflux = np.interp(newgrid, conspec[:,0], conspec[:,1])

specflux = np.interp(newgrid, spectrum[:,0], spectrum[:,1])

divflux = specflux/conspecflux

#print 'Normalization complete.'

arc_list =list()

for file in os.listdir('Arcturus'):

if 'ar' in file:

arc_list.append(file)

Arcturus = []

for line in arc_list:

arcspecfile = ('Arcturus/{}'.format(line) )

ArcSpec = np.genfromtxt(arcspecfile,dtype=float)

ArcSpec = np.array(ArcSpec,dtype=float)

Arcturus.append(ArcSpec)

Arc = np.vstack(Arcturus)

Arc[:,1] = Arc[:,1][np.argsort(Arc[:,0])]

Arc[:,2] = Arc[:,2][np.argsort(Arc[:,0])]

Arc[:,3] = Arc[:,3][np.argsort(Arc[:,0])]

Arc[:,0] = np.sort(Arc[:,0])

Arc[:,0] = pyasl.airtovac2(Arc[:,0])

np.savetxt('ArcturusSpectrum.txt',Arc)

Arc = Arc[(Arc[:,1] > 0.) & (Arc[:,3] > 0.)]

scales = [0.995,1.02,0.997,1.02,0.997,1.02]

ModelSpec = array(Spec_Normalize(file_list[i],cont_file[i//2])).T

Arcturus = arcturus_link()

a = file_list[i].split('-')

#Modelspecfile = ('PHOENIX/%(allspec)s' %{'allspec' : model})

specgrid = np.arange(xmin, xmax, 0.01)

Arcturus = Arcturus[(Arcturus[:,0] >= xmin) & (Arcturus[:,0] <= xmax)]

ModelSpec = ModelSpec[(ModelSpec[:,0] >= xmin) &

(ModelSpec[:,0] <= xmax) ]

ModelSpecFlux = np.interp(specgrid, ModelSpec[:,0], ModelSpec[:,1])

ArcturusFlux = np.interp(specgrid, Arcturus[:,0] , Arcturus[:,1])

ModelSpec2 = convolve(ModelSpecFlux, 6 , 0.01)

RelativeSpec = 100.*(ModelSpec2/scales[i] - ArcturusFlux)/ArcturusFlux

Unity = array((specgrid, RelativeSpec )).T

#Unity = Unity[(Unity[:,1] <= 1000 ) & (Unity[:,1] >= -1000)]

plt.plot(Unity[:,0], Unity[:,1], label = 'Type: {}, T = {}K'.format(a[0],a[1]))

plt.ylim(-100,1000)

plt.grid(True)

plt.legend()

plt.ylabel('Relative Flux')

plt.xlabel('Wavelength, ($\AA$)')

#Arc = arcturus_link()

('ion' ,'a2'),

('wavelength' ,'f8'),

('potential' ,'f8'),

('oscillator' ,'f8')])

temperature2 = [4250,4000,4500]

file_list = list() #Defines an empty list to put spectra filenames in.

for file in os.listdir('PHOENIX'): #My spectra are in this directory.

for i in range(0,len(temperature2)):

if file.endswith('.spec.7') and ('%(teff)s-2.0-%(feh)s' %{'teff' : temperature2[i] ,'feh' : 0.5}) in file and 'lines' not in file and 'lte-4250-2.0-0.5.sph.no_rad.ames.spec.7' not in file:

file_list.append(file)

file_list.sort(key = lambda x: x.split('-')[1] )

global file_list

cont_file = list()

for file in os.listdir('PHOENIXcont'):

if file.endswith('.cont.7') and '4000-2.0-0.5'in file or '4250-2.0-0.5' in file or '4000-2.0-0.5' in file:

cont_file.append(file)

global cont_file

ltelist= list()

for i in range(0,len(file_list)):

if '.sph.no_rad.ames.spec.7' in file_list[i]:

ltelist.append(file_list[i])

#nltelist= list()

for i in range(0,len(file_list)):

if '.sph.spec.7' in file_list[i] or 'sph.alpha.spec.7' in file_list[i]:

ltelist.append(file_list[i])

Arc = arcturus_link()

z = -0.00001666

Arc[:,0] = Arc[:,0]/(z+1)

plt.grid(True)

plt.plot(Arc[:,0],Arc[:,1], label = 'Arcturus', linewidth = 2.0, c = 'b')

plt.plot(Arc[:,0],Arc[:,1]/Arc[:,3], label = 'Telluric', linewidth = 2.0, c = 'k')

plt.plot(Arc[:,0], Arc[:,2], label = 'Sol', linestyle = '--', c='k')

plt.legend()

plt.xlim(3000,9000)

colourstring = ['k','c','y','m','pink','orange','brown' ]

for i in range(0,len(file_list)):

Relative_spec(3900,9300,i)

for i in range(0,len(file_list)):

regular_spectrum_graph(file_list[i],cont_file[i//2],colourstring[i],scales[i])