def print_elemvar_table(table,outname):
# Write the table
elems= ['C','N','O','Na','Mg','Al','Si','S','K','Ca','Ti','V','Mn','Fe',
'Ni']
with open(outname,'w') as outfile:
cnt= 0
for elemc in elems:
# First write total
tline= '%s ' % elemc
ref= table[elems.index(elemc)][cnt]
for ii,elem in enumerate(elems):
if elem == elemc:
tline+= '& %.3f' % (table[ii][cnt])
else:
tline+= '& %i' % (int(round(100.*table[ii][cnt]/ref)))
outfile.write(tline+'\\\\\n')
cnt+= 1
if _NO_INDIV_WINDOWS: continue
# Now do each individual window
for jj in range(apwindow.num(elemc,pad=0)):
tline= '%s%i ' % (elemc,jj+1)
ref= table[elems.index(elemc)][cnt]
for ii,elem in enumerate(elems):
if elem == elemc:
tline+= '& %.3f' % (table[ii][cnt])
else:
tline+= '& %i' % (100.*table[ii][cnt]/ref)
outfile.write(tline+'\\\\\n')
cnt+= 1
return None
def parse_elemvar():
table= calc_elemvar_table.calc_elemvar_table('elemVariations_DR12_M67.sav')
# Parse the table for easier use
out1= {}
out2= {}
cnt= 0
for elemc in elems:
ref= {}
others= {}
cnt+= 1
for jj in range(apwindow.num(elemc,pad=0)):
ref[jj]= table[elems.index(elemc)][cnt]
tothers= []
for ii,elem in enumerate(elems):
if elem == elemc:
continue
else:
tothers.append(100.*table[ii][cnt]/ref[jj])
others[jj]= tothers
cnt+= 1
out1[elemc]= ref
out2[elemc]= others
return (out1,out2)
def windows(*args, **kwargs):
"""
NAME:
windows
PURPOSE:
plot the spectral windows for a given element
INPUT:
Either:
(a) wavelength, spectrum (\AA,spectrum units)
(b) spectrum (assumed on standard APOGEE re-sampled wavelength grid)
(c) location ID, APOGEE ID (default loads aspcapStar, loads extension ext(=1); apStar=True loads apStar spectrum)
+element string (e.g., 'Al'); Adding 1 and 2 splits the windows into two
KEYWORDS:
plot_weights= (False) if True, also plot the weights for the windows (assumes that the spectrum is on the apStarWavegrid)
markLines= mark the location of 'lines' (see apogee.spec.window.lines)
apogee.spec.plot.waveregions keywords
OUTPUT:
plot to output
The final axes allow one to put additional labels on the plot, e.g., for adding the APOGEE ID:
bovy_plot.bovy_text(r'$\mathrm{%s}$' % '2M02420597+0837017',top_left=True)
Note that an ID (e.g., the apogee ID) and Teff, logg, metallicity, and alpha-enhancement labels can be added using the keywords label* above
HISTORY:
2015-01-26 - Written (based on older code) - Bovy (IAS)
"""
pad = kwargs.pop('pad', 3)
try:
si, ei = apwindow.waveregions(args[2], pad=pad, asIndex=True)
except IOError:
try:
si, ei = apwindow.waveregions(args[2][:-1], pad=pad, asIndex=True)
except IOError:
raise IOError(
"Windows for element %s could not be loaded, please specify an existing APOGEE element"
% ((args[2].lower().capitalize())))
if args[2][-1] == '1':
si = si[:len(si) // 2]
ei = ei[:len(ei) // 2]
else:
si = si[len(si) // 2:]
ei = ei[len(ei) // 2:]
# Remove the number from the element
newargs = (args[0], args[1], args[2][:-1])
for ii in range(len(args) - 3):
newargs = newargs + (args[ii + 3], )
args = newargs
# Also get the number and total width of all of the windows
dlam = apwindow.total_dlambda(args[2], pad=pad)
numw = apwindow.num(args[2])
# Set spacing between windows
if numw > 20:
kwargs['skipdx'] = 0.003
kwargs['_noskipdiags'] = True
elif numw > 15:
kwargs['skipdx'] = 0.01
# Set initial space to zero
kwargs['_startendskip'] = 0
# Set initial figure width
if not kwargs.get('overplot', False) and not 'fig_width' in kwargs:
if dlam > 150.:
kwargs['fig_width'] = 8.4
else:
kwargs['fig_width'] = 4.2
# Don't tick x
kwargs['_noxticks'] = True
# Label the largest wavelength in angstrom
kwargs['_labelwav'] = True
# Don't label the lines unless explicitly asked for
kwargs['labelLines'] = kwargs.get('labelLines', False)
# Plot the weights as well
if kwargs.pop('plot_weights', False):
kwargs['_plotw'] = apwindow.read(args[2], apStarWavegrid=True)
if kwargs.get('apStar', False):
kwargs['yrange'] = kwargs.get('yrange',
[0., 1.1 * numpy.nanmax(args[1])])
else:
kwargs['yrange'] = kwargs.get('yrange', [0., 1.2])
# mark the 'lines'
markLines = kwargs.get('markLines', not 'overplot' in kwargs)
if markLines and not '_markwav' in kwargs:
kwargs['_markwav'] = apwindow.lines(args[2])
# Plot
waveregions(args[0],
args[1],
startindxs=si,
endindxs=ei,
*args[3:],
**kwargs)
# Add label
bovy_plot.bovy_text(r'$\mathrm{%s}$' % ((args[2].lower().capitalize())),
top_left=True,
fontsize=10,
backgroundcolor='w')
return None
def windows(*args,**kwargs):
"""
NAME:
windows
PURPOSE:
plot the spectral windows for a given element
INPUT:
Either:
(a) wavelength, spectrum (\AA,spectrum units)
(b) spectrum (assumed on standard APOGEE re-sampled wavelength grid)
(c) location ID, APOGEE ID (default loads aspcapStar, loads extension ext(=1); apStar=True loads apStar spectrum)
+element string (e.g., 'Al'); Adding 1 and 2 splits the windows into two
KEYWORDS:
plot_weights= (False) if True, also plot the weights for the windows (assumes that the spectrum is on the apStarWavegrid)
markLines= mark the location of 'lines' (see apogee.spec.window.lines)
apogee.spec.plot.waveregions keywords
OUTPUT:
plot to output
The final axes allow one to put additional labels on the plot, e.g., for adding the APOGEE ID:
bovy_plot.bovy_text(r'$\mathrm{%s}$' % '2M02420597+0837017',top_left=True)
Note that an ID (e.g., the apogee ID) and Teff, logg, metallicity, and alpha-enhancement labels can be added using the keywords label* above
HISTORY:
2015-01-26 - Written (based on older code) - Bovy (IAS)
"""
pad= kwargs.pop('pad',3)
try:
si,ei= apwindow.waveregions(args[2],pad=pad,asIndex=True)
except IOError:
try:
si, ei= apwindow.waveregions(args[2][:-1],pad=pad,asIndex=True)
except IOError:
raise IOError("Windows for element %s could not be loaded, please specify an existing APOGEE element" % ((args[2].lower().capitalize())))
if args[2][-1] == '1':
si= si[:len(si)//2]
ei= ei[:len(ei)//2]
else:
si= si[len(si)//2:]
ei= ei[len(ei)//2:]
# Remove the number from the element
newargs= (args[0],args[1],args[2][:-1])
for ii in range(len(args)-3):
newargs= newargs+(args[ii+3],)
args= newargs
# Also get the number and total width of all of the windows
dlam= apwindow.total_dlambda(args[2],pad=pad)
numw= apwindow.num(args[2])
# Set spacing between windows
if numw > 20:
kwargs['skipdx']= 0.003
kwargs['_noskipdiags']= True
elif numw > 15:
kwargs['skipdx']= 0.01
# Set initial space to zero
kwargs['_startendskip']= 0
# Set initial figure width
if not kwargs.get('overplot',False) and not 'fig_width' in kwargs:
if dlam > 150.:
kwargs['fig_width']= 8.4
else:
kwargs['fig_width']= 4.2
# Don't tick x
kwargs['_noxticks']= True
# Label the largest wavelength in angstrom
kwargs['_labelwav']= True
# Don't label the lines unless explicitly asked for
kwargs['labelLines']= kwargs.get('labelLines',False)
# Plot the weights as well
if kwargs.pop('plot_weights',False):
kwargs['_plotw']= apwindow.read(args[2],apStarWavegrid=True)
if kwargs.get('apStar',False):
kwargs['yrange']= kwargs.get('yrange',
[0.,1.1*numpy.nanmax(args[1])])
else:
kwargs['yrange']= kwargs.get('yrange',[0.,1.2])
# mark the 'lines'
markLines= kwargs.get('markLines',not 'overplot' in kwargs)
if markLines and not '_markwav' in kwargs:
kwargs['_markwav']= apwindow.lines(args[2])
# Plot
waveregions(args[0],args[1],startindxs=si,endindxs=ei,
*args[3:],**kwargs)
# Add label
bovy_plot.bovy_text(r'$\mathrm{%s}$' % ((args[2].lower().capitalize())),
top_left=True,fontsize=10,backgroundcolor='w')
return None