Optical Plotting - Echelle spectrum of Vega (in color!)

import pyspeckit
from pylab import *

if 'wav2rgb' not in globals():
    # this is to deal with python3 not being able to execfile
    import wav2rgb

if not 'interactive' in globals():
    interactive=False
if not 'savedir' in globals():
    savedir = ''


speclist = pyspeckit.wrappers.load_IRAF_multispec('evega.0039.rs.ec.dispcor.fits')

for spec in speclist:
    spec.unit="Counts"

SP = pyspeckit.Spectra(speclist)
SPa = pyspeckit.Spectra(speclist,xunit='angstrom',quiet=False)

SP.plotter(figure=figure(1))
SPa.plotter(figure=figure(2))

figure(3)
clf()
figure(4)
clf()

#clr = [list(clr) for clr in matplotlib.cm.brg(linspace(0,1,len(speclist)))]
clr = [wav2rgb.wav2RGB(c) + [1.0] for c in linspace(380,780,len(speclist))]
for ii,(color,spec) in enumerate(zip(clr[::-1],speclist)):
    spec.plotter(figure=figure(3), clear=False, reset=False, color=color,
            refresh=False) 

    fig4=figure(4)
    fig4.subplots_adjust(hspace=0.35,top=0.97,bottom=0.03)
    spec.plotter(axis=subplot(10,1,ii%10+1), clear=False, reset=False,
            color=color, refresh=False) 
    spec.plotter.axis.yaxis.set_major_locator(matplotlib.ticker.MaxNLocator(4)) 

    if ii % 10 == 9: 
        spec.plotter.refresh()
        spec.plotter.savefig(savedir+'vega_subplots_%03i.png' % (ii/10+1))
        clf()

draw() # refresh all
figure(3)
savefig(savedir+'vega_colorized.png')

#[s.plotter() for s in splist[:5]]
#[s.plotter() for s in speclist[:5]]
#[(subplot(5,1,ii),s.plotter()) for ii,s in enumerate(speclist[:5])]
#[(subplot(5,1,ii),s.plotter()) for ii,s in enumerate(speclist[:5])]
#[(subplot(5,1,ii),s.plotter(axis=subplot(5,1,ii))) for ii,s in enumerate(speclist[:5])]
#[(subplot(5,1,ii),s.plotter(axis=subplot(15,1,ii))) for ii,s in enumerate(speclist[:15])]
#len (speclist)
#subpot
#[(s.plotter(axis=subplot(15,1,ii))) for ii,s in enumerate(speclist[:15])]
#[(s.plotter(axis=subplot(15,1,ii+1))) for ii,s in enumerate(speclist[:15])]
#s.units
#for s in speclist: s.units='counts' 
#[(s.plotter(axis=subplot(15,1,ii+1))) for ii,s in enumerate(speclist[:15])]
#savefig('vega_echelle_example.png')
#get_ipython().system(u"open ./")

Modifying and saving echelle orders

load_IRAF_multispec returns a list of Spectrum objects, one per echelle order. There is no writer for the IRAF multispec format itself, but each order can be modified and written out as a standard (linear-wavelength) 1D FITS spectrum with Spectrum.write:

import pyspeckit

orders = pyspeckit.wrappers.load_IRAF_multispec('evega.0039.rs.ec.dispcor.fits')

# modify the flux of each order however you like, e.g.:
for sp in orders:
    sp.data = sp.data * 2

# save each order to its own FITS file
for ii, sp in enumerate(orders):
    sp.write('vega_order{0:03d}.fits'.format(ii), type='fits')

# the saved files are standard 1D spectra; they can be re-loaded with
sp10 = pyspeckit.Spectrum('vega_order010.fits')

By default the error spectrum is written as a second row in the output file; pass errspecnum=1 to pyspeckit.Spectrum to recover it when re-loading, or write_error=False to Spectrum.write to write only the flux.

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