import AstroUtils
fig = pyplot.figure(0)
fig.clear()
ax = fig.add_axes([0.1, 0.1, 0.8, 0.8])
baseName = sys.argv[1]
arcturusConfig = AstroUtils.parse_config(baseName + "_Solar.cfg")
solarConfig = AstroUtils.parse_config(baseName + "_Arcturus.cfg")
originalConfig = arcturusConfig.copy()
arcturusConfig["applyCorrections"] = True
solarConfig["applyCorrections"] = True
arcturus = MoogTools.LineList(None, arcturusConfig)
solar = MoogTools.LineList(None, solarConfig)
original = MoogTools.LineList(None, originalConfig)
orig = []
sol = []
arc = []
diff = []
dsol = []
darc = []
species = []
expot = []
wl = []
for i in range(original.nStrong):
orig.append(original.strongLines[i].loggf)
fig = pyplot.figure(0)
ax = fig.add_axes([0.1, 0.1, 0.8, 0.8])
ax.plot(S)
hdu = pyfits.PrimaryHDU(CM)
hdu.writeto('CommandMatrix.fits', clobber=True)
hdu = pyfits.PrimaryHDU(factor)
hdu.writeto('scalingfactor.fits', clobber=True)
configFile = 'CMStudent.cfg'
#diffplot = True
diffplot = False
Synth = MoogTools.Moog(configFile)
Synth.lineList.writeLineLists()
Synth.parameterFile.writeParFile()
solarWave = Synth.solarSpectrum.wave + 0.1
solarFlux = Synth.solarSpectrum.flux + 0.001 + numpy.random.randn(
len(solarWave)) * 0.001
continuum = 0.0
wlOffset = 0.0
resolution = 45000
nominalWavelength, nominalSpectrum = Synth.run()
wave, spectrum = SpectralTools.resample(nominalWavelength, nominalSpectrum,
resolution)
#solar = Moog960.ObservedMelody.fromFile(filename='SolarSpectrum.fits')
#solar.loadData()
solar = Moog960.Score(observed='SolarSpectrum.fits')
arcturus = Moog960.Score(observed='ArcturusSpectrum.fits')
wlStart = 17000
wlStop = 17100
observed = solar.getLabels(keySignature='OBSERVED')
for obs in observed:
obs.Spectrum.plot(ax=ax, color='g')
observed = arcturus.getLabels(keySignature='OBSERVED')
for obs in observed:
obs.Spectrum.plot(ax=ax, color='b')
ArcSynth = MoogTools.MoogStokes('Arcturus.cfg', wlStart=wlStart, wlStop=wlStop)
SolarSynth = MoogTools.MoogStokes('Solar.cfg', wlStart=wlStart, wlStop=wlStop)
SolarSynth.run()
ArcSynth.run()
SolarSynth.Spectra[0].plot(ax=ax, color='r')
SolarSynth.Spectra[1].plot(ax=ax, color='m')
ax.set_xbound(wlStart, wlStop)
ax.set_ybound(0.0, 1.0)
fig.show()
# 'India', 'Juliett', 'Kilo', 'Lima', 'Mike', 'November', 'Oscar']
baseNames = ['Charlie']
arcGfDiff = []
solGfDiff = []
arcEWs = []
arcEWDiffSelf = []
arcEWDiffOther = []
solEWs = []
solEWDiffSelf = []
solEWDiffOther = []
for baseName in baseNames:
#Original
arcturus = MoogTools.MoogStokes(baseName + "_Arcturus.cfg",
moogInstance='ALPHA',
fileBase="arcold")
solar = MoogTools.MoogStokes(baseName + "_Solar.cfg",
moogInstance='BRAVO',
fileBase="solold")
#New gfs determined by self
arcturusNew = MoogTools.MoogStokes(baseName + "_Arcturus.cfg",
moogInstance='CHARLIE',
fileBase="arcnew")
solarNew = MoogTools.MoogStokes(baseName + "_Solar.cfg",
moogInstance='DELTA',
fileBase="solnew")
#New gfs determined by other
#arcSol = MoogTools.MoogStokes(baseName+"_Arcturus.cfg", moogInstance = 'CHARLIE', fileBase="arcsol")
#solArc = MoogTools.MoogStokes(baseName+"_Solar.cfg", moogInstance = 'DELTA', fileBase="solarc")
contFloat = bool(sys.argv[4]== 'True')
except:
contFloat = False
try:
rotFloat = bool(sys.argv[5] == 'True')
except:
rotFloat = False
f1 = pyplot.figure(0)
f1.clear()
ax1 = f1.add_axes([0.1, 0.1, 0.8, 0.8])
diffplot = True
diffplot = False
Synth = MoogTools.MoogStokes(configFile, moogInstance=moogInstance, fileBase=''.join(random.choice(string.ascii_letters)
for _ in range(3)))
#Synth.lineList.writeLineLists()
#Synth.parameterFile.writeParFile()
outFile = Synth.config["outputDir"] + Synth.config["baseName"]+'_results.dat'
inFile = Synth.config["inFile"]
solarSpectrum = Moog960.ObservedMelody.fromFile(filename=inFile)
solarSpectrum.loadData()
wlRange = [Synth.config["wlStart"], Synth.config["wlStop"]]
solarSpectrum.selectPhrases(wlRange=wlRange)
observed, labels = solarSpectrum.perform()
continuum = 0.00
wlOffset = Synth.config["wlShift"]
import AstroUtils
fig1 = pyplot.figure(0)
fig1.clear()
ax1 = fig1.add_axes([0.1, 0.1, 0.8, 0.8])
fig2 = pyplot.figure(1)
fig2.clear()
ax2 = fig2.add_axes([0.1, 0.1, 0.8, 0.8])
baseName = sys.argv[1]
arcConfig = baseName + ".arcturus.cfg"
solConfig = baseName + ".solar.cfg"
arcturus = MoogTools.MoogStokes(arcConfig, moogInstance="ALPHA")
solar = MoogTools.MoogStokes(solConfig, moogInstance="BRAVO")
solarSpectrum = Moog960.ObservedMelody.fromFile(
filename=solar.config["inFile"])
arcturusSpectrum = Moog960.ObservedMelody.fromFile(
filename=arcturus.config["inFile"])
solarSpectrum.loadData()
arcturusSpectrum.loadData()
wlRange = [solar.config["wlStart"], solar.config["wlStop"]]
solarSpectrum.selectPhrases(wlRange=wlRange)
obsSol, labels = solarSpectrum.perform()
arcturusSpectrum.selectPhrases(wlRange=wlRange)
obsArc, labels = arcturusSpectrum.perform()
import MoogTools
baseNames = ['Alpha', 'Bravo', 'Charlie', 'Delta', 'Echo', 'Foxtrot', 'Golf',
'Hotel', 'India', 'Juliett', 'Kilo', 'Lima', 'Mike', 'November', 'Oscar']
outName = '/home/deen/MoogPyData/AbsorptionLines/corrections/compositeCorrected.dat'
inDir = './Output/'
solar = []
arcturus = []
for baseName in baseNames:
inFile = inDir+baseName+'_Solar_results.dat'
for line in open(inFile, 'r'):
solar.append(MoogTools.MOOG_Line(line))
inFile = inDir+baseName+'_Arcturus_results.dat'
for line in open(inFile, 'r'):
arcturus.append(MoogTools.MOOG_Line(line))
for arc in arcturus:
if arc in solar:
if arc.expot_lo < 3.0:
index = solar.index(arc)
solar[index].loggf = arc.loggf
solar[index].VdW = arc.VdW
else:
solar.append(arc)
import numpy
import scipy
import matplotlib.pyplot as pyplot
import AstroUtils
import MoogTools
import Moog960
import SpectralTools
import pyfits
configFile = 'CMTeacher.cfg'
Synth = MoogTools.MoogStokes(configFile, moogInstance='ALPHA')
Synth.lineList.writeLineLists()
Synth.parameterFile.writeParFile()
Synth.run()
nominal = Synth.Spectra[0]
smoothed = nominal.resample(R=80000)
resampled = nominal.resample(R=80000, nyquist=True)
phrases = []
parameters = {}
parameters["LABEL"] = "CM Teacher"
parameters["TEFF"] = 5770
parameters["LOGG"] = 4.43
parameters["BFIELD"] = 0.0
parameters["SELECTED"] = False
parameters["WLSTART"] = resampled.wl[0]
parameters["WLSTOP"] = resampled.wl[-1]
header = resampled.header
def generateLineList(b_dir, prefix, wl_start, wl_stop, Bfield, **kwargs):
''' This subroutine generates Zeeman-split MOOG line lists (both
strong and weak) '''
staging_dir = 'stage_'+prefix+'/'
print "Feature : ", prefix, ' ', b_dir
try:
os.makedirs(os.path.join(staging_dir,'Parfiles',b_dir))
os.makedirs(os.path.join(staging_dir,'Output', b_dir))
os.makedirs(os.path.join(staging_dir,'Linelists', b_dir))
except:
pass
MoogTools.write_par_file(wl_start, wl_stop, staging_dir, b_dir, prefix,
mode='gridstokes', strongLines=True, **kwargs)
# Load in configuration file
config = AstroUtils.parse_config('counterpoint.cfg')
weak_file = config['weak_file']
strong_file = config['strong_file']
molecules = config['molecules']
VALD_list = config['VALD_file']
gf_corrections = config['gf_file']
strongLines, weakLines = MoogTools.parse_VALD(VALD_list, strong_file,
wl_start, wl_stop, Bfield, gf_corrections)
# CO
weakLines = numpy.append(weakLines, MoogTools.parse_HITRAN(
molecules+'05_HITEMP2010new.par', wl_start, wl_stop, Bfield,
gf_corrections, weedout=2.5))
# OH
weakLines = numpy.append(weakLines, MoogTools.parse_HITRAN(
molecules+'13_HITEMP2010.par', wl_start, wl_stop, Bfield,
gf_corrections))
# CN
weakLines = numpy.append(weakLines, MoogTools.parse_Plez_CN(
molecules+'CN_Plez_linelist.dat', wl_start, wl_stop, Bfield,
gf_corrections))
sfn = os.path.join(staging_dir, 'Linelists', b_dir,
prefix+'_strong_linelist.stokes')
outfile = open(sfn, 'w')
for strongLine in strongLines:
strongLine.dump(out=outfile, mode='MOOGSTOKES')
outfile.close()
sort_file(sfn)
wfn = os.path.join(staging_dir, 'Linelists', b_dir,
prefix+'_weak_linelist.stokes')
weakfile = open(wfn, 'w')
for weakLine in weakLines:
weakLine.dump(out=weakfile, mode='MOOGSTOKES')
weakfile.close()
sort_file(wfn, weak=True)
if Bfield==0.0:
MoogTools.write_par_file(wl_start, wl_stop, staging_dir, b_dir,
prefix, mode='gridsyn', strongLines=True, **kwargs)
sfn = os.path.join(staging_dir, 'Linelists', b_dir,
prefix+'_strong_linelist.scalar')
outfile = open(sfn, 'w')
for strongLine in strongLines:
strongLine.dump(out=outfile, mode='MOOGSCALAR')
outfile.close()
sort_file(sfn)
wfn = os.path.join(staging_dir, 'Linelists', b_dir,
prefix+'_weak_linelist.scalar')
outfile = open(wfn, 'w')
for weakLine in weakLines:
weakLine.dump(out=outfile, mode='MOOGSCALAR')
outfile.close()
sort_file(wfn, weak=True)