def hydrogen(nu,nl, vacuum=True):
"""
Compute the rest wavelength of Hydrogen recombination lines in angstroms
"""
rydberg = 10973731.6 # m^-1
protontoelectron = 1836.15266 # ratio
lvac = 1.0/rydberg * 1./(1/float(nl)**2 - 1/float(nu)**2) * 1e10 * (1.0+1.0/protontoelectron)
if not vacuum:
import ref_index
return ref_index.vac2air(lvac/10)*10
else:
return lvac
def get_telluric_lines(wavelength_array, telluric_linelist_file, vacuum=True): """ This will load the telluric line list Reading the telluric line list using astropy Table function Inputs ------ wavelength_array: array This is the wavelength array that you want checked against the given telluric line list telluric_linelist_file: string This is the location of the telluric line list file you would like to use. vacuum: Boolean (default is True) Is the telleric line list given in vacuum. Most line lists I've seen are provided in vacuum, but it might not always be the case. Returns ------ telluric_lines_centres: array The array containing the telluric lines Examples ------ """ import ref_index line_list_file = telluric_linelist_file data = Table.read(line_list_file) Telluric_Line_List_Wavelength_centre = data['wavelength'] # Trim the telluric line list to only be within the same # wavelength range as the input waveleangth array # This saves a lot of time when trying to fit Gaussians Above_Min_Wavelength = (Telluric_Line_List_Wavelength_centre > np.min(wavelength_array)) Below_Max_Wavelength = (Telluric_Line_List_Wavelength_centre < np.max(wavelength_array)) telluric_lines_centres = Telluric_Line_List_Wavelength_centre[np.where((Below_Max_Wavelength*Above_Min_Wavelength) == True)] if vacuum: telluric_lines_centres = ref_index.vac2air(telluric_lines_centres) else: pass return telluric_lines_centres
def vac_to_air(wavelengths):
"""
convert wavelengths in air to vacuum using ref_index
INPUT: wavelengths - in angstroms
OUTPUT: wavelengths - in angstroms
"""
print('wavelengths.min: ', wavelengths.min())
new_wavelengths = wavelengths / 10.
new_wavelengths = ref_index.vac2air(
new_wavelengths) * 10. #back to angstroms
print('new_wavelengths.min():', new_wavelengths.min())
return new_wavelengths
def hydrogen(nu, nl, vacuum=True):
"""
Compute the rest wavelength of Hydrogen recombination lines in angstroms
"""
rydberg = 10973731.6 # m^-1
protontoelectron = 1836.15266 # ratio
lvac = 1.0 / rydberg * 1. / (1 / float(nl)**2 - 1 / float(nu)**2
) * 1e10 * (1.0 + 1.0 / protontoelectron)
if not vacuum:
import ref_index
return ref_index.vac2air(lvac / 10) * 10
else:
return lvac
def fit_hdelta(
sp,
date,
xmin=3900,
xmax=4300,
ymin=0.8,
ymax=1.405,
#exclude=[3601,3846,3869.37,3913,3956,3984.59,4013.4,4045.81,4081.81,4117.82,4230,4396,4460,4482],
exclude=[3600, 4035, 4089, 4114, 4150, 4600],
guesses=[
0.1,
ref_index.vac2air(
pyspeckitmodels.hydrogen.hydrogen.wavelength['balmerd'] * 1e3)
* 10, 5, 2
],
fittype='voigt'):
sp.plotter(xmin=xmin, xmax=xmax, ymin=ymin, ymax=ymax)
sp.baseline(xmin=xmin,
xmax=xmax,
exclude=exclude,
subtract=False,
reset_selection=True,
highlight_fitregion=True,
order=1)
sp.specfit(guesses=guesses, fittype=fittype)
sp.specfit.xmin, sp.specfit.xmax = sp.specfit.get_model_xlimits()
sp.specfit.parinfo.tableprint()
sp.baseline.highlight_fitregion()
sp.specfit.plot_components(add_baseline=True, component_yoffset=-0.1)
sp.specfit.plotresiduals(axis=sp.plotter.axis,
clear=False,
yoffset=ymin + 0.1,
label=False)
sp.plotter.savefig("SN2009ip_UT" + str(date) + "_hdelta.png")
print " ".join([
"%15s" % x for x in ('Center Wavelength', 'Peak', 'Integral', 'FWHM')
])
print " ".join([
"%15g" % x
for x in (sp.specfit.parinfo.SHIFT0.value,
(sp.data - sp.baseline.basespec)[sp.specfit.get_full_model(
add_baseline=False) > sp.error].max(),
sp.specfit.integral(direct=True),
sp.specfit.measure_approximate_fwhm(plot=True,
interpolate_factor=100))
])
def fit_hdelta(sp, date, xmin=3900,xmax=4300,ymin=0.8,ymax=1.405,
#exclude=[3601,3846,3869.37,3913,3956,3984.59,4013.4,4045.81,4081.81,4117.82,4230,4396,4460,4482],
exclude=[3600,4035,4089,4114,4150,4600],
guesses=[0.1,ref_index.vac2air(pyspeckitmodels.hydrogen.hydrogen.wavelength['balmerd']*1e3)*10,5,2],
fittype='voigt'):
sp.plotter(xmin=xmin,xmax=xmax,ymin=ymin,ymax=ymax)
sp.baseline(xmin=xmin, xmax=xmax, exclude=exclude, subtract=False,
reset_selection=True, highlight_fitregion=True, order=1)
sp.specfit(guesses=guesses,
fittype=fittype)
sp.specfit.xmin, sp.specfit.xmax = sp.specfit.get_model_xlimits()
sp.specfit.parinfo.tableprint()
sp.baseline.highlight_fitregion()
sp.specfit.plot_components(add_baseline=True,component_yoffset=-0.1)
sp.specfit.plotresiduals(axis=sp.plotter.axis,clear=False,yoffset=ymin+0.1,label=False)
sp.plotter.savefig("SN2009ip_UT"+str(date)+"_hdelta.png")
print " ".join(["%15s" % x for x in ('Center Wavelength','Peak','Integral','FWHM')])
print " ".join(["%15g" % x for x in (sp.specfit.parinfo.SHIFT0.value, (sp.data-sp.baseline.basespec)[sp.specfit.get_full_model(add_baseline=False) > sp.error].max(),sp.specfit.integral(direct=True),sp.specfit.measure_approximate_fwhm(plot=True,interpolate_factor=100)) ])
def halpha(sp):
#return pyspeckitmodels.hydrogen.hydrogen.wavelength['balmera'] * 1e4
HA = ref_index.vac2air(pyspeckitmodels.hydrogen.hydrogen.wavelength['balmera']*1e3)
return line(sp, 6562.7715) # NIST
return line(sp, HA)
def brgamma(sp):
#return pyspeckitmodels.hydrogen.hydrogen.wavelength['balmerg'] * 1e4
HG = ref_index.vac2air(pyspeckitmodels.hydrogen.hydrogen.wavelength['brackettg']*1e3)
#return line(sp, 4340.471)
return line(sp, HG)
def padelta(sp):
#return pyspeckitmodels.hydrogen.hydrogen.wavelength['balmerg'] * 1e4
HG = ref_index.vac2air(pyspeckitmodels.hydrogen.hydrogen.wavelength['paschend']*1e3)
#return line(sp, 4340.471)
return line(sp, HG)
def hbeta(sp):
#return pyspeckitmodels.hydrogen.hydrogen.wavelength['balmerb'] * 1e4
HB = ref_index.vac2air(pyspeckitmodels.hydrogen.hydrogen.wavelength['balmerb']*1e3)
return line(sp, 4861.128) # NIST
return line(sp, HB)
def hgamma(sp):
HG = ref_index.vac2air(
pyspeckitmodels.hydrogen.hydrogen.wavelength['balmerg'] * 1e3)
return line(sp, 4340.471)
return line(sp, HG)
def hbeta(sp):
HB = ref_index.vac2air(
pyspeckitmodels.hydrogen.hydrogen.wavelength['balmerb'] * 1e3)
return line(sp, 4861.128) # NIST
return line(sp, HB)
def halpha(sp):
HA = ref_index.vac2air(
pyspeckitmodels.hydrogen.hydrogen.wavelength['balmera'] * 1e3)
return line(sp, 6562.7715) # NIST
return line(sp, HA)
def makemyplots(errstyle=None,units=None,xRange=200):
spectra = ['UT120830_DIS.final.txt','UT120830_DIS.final.txt','UT121002_DIS.final.txt','UT121009_DIS.final.txt']
eng_to_grk = {'g':'gamma',
'a':'alpha',
'b':'beta',
'd':'delta'}
figure(0); clf();
rcParams['font.size']=18
nx = len(spectra)
ny = len(eng_to_grk)
for ii,spname in enumerate(spectra):
sp = pyspeckit.Spectrum(spname,skiplines=1,xarrkwargs={'xtype':'wavelength','unit':'angstroms'})
if ii == 1:
sp.data *= 10
sp.error *= 10
sp.baseline(order=5,highlight_fitregion=False,
exclude=[a for x in [4101,4340,4863,5879,6562.8,6850,7067,7575]
for a in [x-50,x+50]])
sp.specname=spname[:8]
if ii==1: sp.specname+="$\\times$10"
sp.xarr.units='angstroms'
sp.xarr.xtype='wavelength'
sp.units = '10$^{-14}$ erg s$^{-1}$ cm$^{-2}$ $\\AA^{-1}$'
for jj,line in enumerate(['a','b','g','d']):
name = 'balmer'+line
wavelength = pyspeckitmodels.hydrogen.wavelength[name]
airwave = ref_index.vac2air(wavelength*1e3)*10
sp.xarr.refX = airwave
sp.xarr.refX_units = 'angstroms'
if units is not None:
sp.xarr.convert_to_unit(units)
ax = subplot(ny,nx,ii+jj*ny+1)
sp.plotter.axis=ax
if units is None:
sp.plotter(axis=ax,xmin=airwave-xRange/2, xmax=airwave+xRange/2,
offset=0.1*(jj==0), ymin=-0.1, errstyle=errstyle)
elif units == 'Mm/s':
sp.plotter(axis=ax,xmin=-xRange/2, xmax=+xRange/2,
offset=0.1*(jj==0), ymin=-0.1, errstyle=errstyle)
print name,"y limits: ",sp.plotter.ymin,sp.plotter.ymax
ax.set_ylabel('')
ax.set_xlabel('')
ax.yaxis.set_major_locator(MaxNLocator(5))
ax.yaxis.set_tick_params(labelsize=14)
ax.xaxis.set_major_locator(MaxNLocator(5))
ax.xaxis.set_tick_params(labelsize=14)
if ii != 0:
ax.set_yticklabels([])
else:
ax.set_ylabel('H$\\'+eng_to_grk[line]+"$")
if jj == 0:
pass
#sp.plotter.axis.set_ylabel('H$\\'+eng_to_grk[line]+"$\\n"+sp.units)
else:
sp.plotter.axis.set_title("")
#if ii != 2:
# sp.plotter.axis.set_xticklabels([])
if units is not None:
sp.xarr.convert_to_unit('angstroms')
for ii,spname in enumerate(spectra):
for jj,line in enumerate(['a','b','g','d']):
ax = subplot(ny,nx,ii+jj*nx+1)
yl = subplot(ny,nx,(nx-1)+jj*nx+1).get_ylim()
ax.set_ylim(-0.1,yl[1])
tight_layout(pad=2.2,h_pad=0.175,w_pad=0)
#subplots_adjust(hspace=0.175,wspace=0)
figtext(0.03,0.5,sp.units,rotation='vertical',va='center',ha='center')
if units is None:
figtext(0.5,0.03,"Wavelength ($\\AA$)")
elif units == 'Mm/s':
figtext(0.5,0.03,"Velocity (1000 km s$^{-1}$)")
if errstyle is not None:
if units is not None:
savefig('SN2009ip_hlines_grid_errbar_velocity.png')
savefig('SN2009ip_hlines_grid_errbar_velocity.eps')
else:
savefig('SN2009ip_hlines_grid_errbar.png')
savefig('SN2009ip_hlines_grid_errbar.eps')
elif units is not None:
savefig('SN2009ip_hlines_grid_velocity.png')
savefig('SN2009ip_hlines_grid_velocity.eps')
else:
savefig('SN2009ip_hlines_grid.png')
savefig('SN2009ip_hlines_grid.eps')
show()
def brgamma(sp):
#return pyspeckitmodels.hydrogen.hydrogen.wavelength['balmerg'] * 1e4
HG = ref_index.vac2air(
pyspeckitmodels.hydrogen.hydrogen.wavelength['brackettg'] * 1e3)
#return line(sp, 4340.471)
return line(sp, HG)
def padelta(sp):
#return pyspeckitmodels.hydrogen.hydrogen.wavelength['balmerg'] * 1e4
HG = ref_index.vac2air(
pyspeckitmodels.hydrogen.hydrogen.wavelength['paschend'] * 1e3)
#return line(sp, 4340.471)
return line(sp, HG)