def __init__(self, **kwargs):
self.Envi = rfm.Environment()
self.rfm_exe = self.Envi.exe_file
self.outname = 'rfm.tra'
def __init__(self,
ObsFilename=None,
ModelFilename=None,
wave_min=None,
wave_max=None,
cull=50,
am=1.0,
H2O_scale=1.0,
CO_scale=1.0,
CH4_scale=1.0,
CO2_scale=1.0,
vrad=0.0,
vbary=0.0):
## SETUP MODEL ATMOSPHERE ##
Envi = rfm.Environment()
A = rfm.Atmosphere(filename=Envi.atm_file)
A.scaleProf('H2O', H2O_scale)
A.scaleProf('CO', CO_scale)
A.scaleProf('CH4', CH4_scale)
A.scaleProf('CO2', CO2_scale)
A.writeAll('tmp.atm')
self.A = A
M = Model()
M.RFM(atm_files=['tmp.atm'],
wmin=1e4 / wave_max,
wmax=1e4 / wave_min,
am=am)
M.blur(rpower=25000.)
self.M = M
## GET MODEL SKY SPECTRUM ##
ModInfo = M.getSpec()
self.WaveMod = ModInfo['wavelength']
self.SkyRadMod = ModInfo['Radiance'] / np.amax(ModInfo['Radiance'])
self.SkyRadMod = 1 - self.SkyRadMod
scale = np.amax(self.SkyRadMod)
## GET MODEL STELLAR SPECTRUM ##
a = np.loadtxt(ModelFilename, skiprows=1)
StellWL, StellFlux = 1e4 / a[:, 0], a[:, 1]
plt.plot(StellWL, StellFlux)
if np.all(np.diff(StellWL) > 0) != True:
StellWL = np.flip(StellWL, 0)
StellFlux = np.flip(StellFlux, 0)
## BROADEN STELLAR SPECTRUM ##
StellFlux_Broad = self.blur_function(StellWL, StellFlux, 25000.)
print StellFlux_Broad
plt.plot(StellWL, StellFlux_Broad)
plt.show()
## SHIFT STELLAR SPECTRUM ##
StellWave_Shift = self.shift_wavelength(StellWL, vrad - vbary)
print StellWL
print StellWave_Shift
## INTERPOLATE STELLAR SPECTRUM ONTO COMMON WAVELENGTH GRID ##
self.StellFlux_Interp = np.interp(self.WaveMod, StellWave_Shift,
StellFlux_Broad)
## COMBINE STELLAR AND TELLURIC SPECTRA ##
assert (np.shape(self.StellFlux_Interp) == np.shape(self.SkyRadMod))
self.StellFlux_Interp = self.StellFlux_Interp / np.median(
self.StellFlux_Interp)
self.SkyRadMod = self.SkyRadMod / np.median(self.SkyRadMod)
self.ModSpec = 1.0 * self.StellFlux_Interp + 0.8 * self.SkyRadMod ####change these to change ratios - SkyRadMod = telluric
self.ModSpec = self.ModSpec / np.median(self.ModSpec)
## colors combined model to show tell vs stell contributions
self.color = self.colorinmodel(self.StellFlux_Interp, self.SkyRadMod)
plt.figure()
plt.plot(self.WaveMod, self.StellFlux_Interp, label='stell')
plt.plot(self.WaveMod, self.SkyRadMod, label='tell')
#plt.plot(self.WaveMod, self.ModSpec, label='stell+tell')
self.plot_multicolored_lines(self.WaveMod,
self.ModSpec,
self.color,
label='stell(c)+tell(k)')
plt.legend(loc=0)
## GET OBSERVED SKY ##
ObsInfo = nt.WaveOrder(ObsFilename).getData()
WaveObsPos = np.array(ObsInfo['wl_pos'])
# SkyObsPos = np.array(ObsInfo['sky_pos']) / np.median(ObsInfo['sky_pos']) # L BAND
SkyObsPos = np.array(ObsInfo['flux_pos']) / np.median(
ObsInfo['flux_pos']) # K BAND
WaveObsNeg = np.array(ObsInfo['wl_neg'])
# SkyObsNeg = np.array(ObsInfo['sky_neg']) / np.median(ObsInfo['sky_neg']) # L BAND
SkyObsNeg = np.array(ObsInfo['flux_neg']) / np.median(
ObsInfo['flux_neg']) # K BAND
## FIT OUT CONTINUUM ## (DP 21 JAN 16)
wn_data_all = [WaveObsPos, WaveObsNeg]
flux_data_all = [SkyObsPos, SkyObsNeg]
merp = 16 #64 ##32 #16
factor = 64 #16 #32# 64
posneg = 0
baseline_pos, baseline_neg = np.ones(np.size(WaveObsPos)), np.ones(
np.size(WaveObsNeg))
# SkyObsPos_contrmv, SkyObsNeg_contrmv = np.array(np.size(SkyObsPos)), np.array(np.size(SkyObsNeg))
for wn_data, flux_data in zip(wn_data_all, flux_data_all):
points_flux, points_wn, points_count = np.zeros(merp), np.zeros(
merp), np.arange(merp)
for count in points_count:
startpoint = count * factor
endpoint = (count + 1) * factor
if count == 0: startpoint = 14
if count == 15: endpoint = 1024 - 30
# if count==63 : endpoint = 1024-14
points_flux[count] = np.max(flux_data[startpoint:endpoint])
loc = np.argmax(flux_data[startpoint:endpoint])
# points_wn[count]=wn_data[loc+startpoint]
points_wn[count] = loc + startpoint
coeff = np.polyfit(points_wn, points_flux, 2)
# coeff = np.polyfit(points_wn, points_flux, 4)
print coeff
# if posneg == 0 : baseline_pos = coeff[1] + coeff[0]*wn_data# + coeff[1]*wn_data**2 + coeff[0]*wn_data**3
# if posneg == 1 : baseline_neg = coeff[1] + coeff[0]*wn_data# + coeff[1]*wn_data**2 + coeff[0]*wn_data**3
if posneg == 0:
baseline_pos = coeff[2] + coeff[1] * np.arange(1024) + coeff[
0] * np.arange(1024)**2 # + coeff[0]*np.arange(1024)**3
if posneg == 1:
baseline_neg = coeff[2] + coeff[1] * np.arange(1024) + coeff[
0] * np.arange(1024)**2 # + coeff[0]*np.arange(1024)**3
# if posneg == 0 : baseline_pos = coeff[4] + coeff[3]*np.arange(1024) + coeff[2]*np.arange(1024)**2 + coeff[1]*np.arange(1024)**3 + coeff[0]*np.arange(1024)**4# + coeff[0]*np.arange(1024)**3
# if posneg == 1 : baseline_neg = coeff[4] + coeff[3]*np.arange(1024) + coeff[2]*np.arange(1024)**2 + coeff[1]*np.arange(1024)**3 + coeff[0]*np.arange(1024)**4# + coeff[0]*np.arange(1024)**3
posneg += 1
SkyObsPos_contrmv, SkyObsNeg_contrmv = SkyObsPos / baseline_pos, SkyObsNeg / baseline_neg
self.ModSpec = 1 - self.ModSpec
plt.figure()
plt.plot(SkyObsPos, hold=True)
plt.plot(baseline_pos, hold=True)
plt.show()
plt.figure()
plt.plot(SkyObsNeg, hold=True)
plt.plot(baseline_neg, hold=True)
plt.show()
self.ObsLabelPN = ['pos', 'neg']
### break spec into 4 pieces
#fourth = int(len(WaveObsPos)/4)
#Wavepos = []
#Waveneg = []
#for val in range(fourth):
# Wavepos.append(WaveObsPos[val])
# Waveneg.append(WaveObsNeg[val])
self.WaveObsPN = [WaveObsPos, WaveObsNeg]
SkyObsPos_contrmv_scaled = (1 - SkyObsPos_contrmv)
SkyObsNeg_contrmv_scaled = (1 - SkyObsNeg_contrmv)
self.Pixels = [np.arange(len(WaveObsPos)), np.arange(len(WaveObsNeg))]
self.SkyObsPN_orig = [SkyObsPos, SkyObsNeg]
self.SkyObsPN = [SkyObsPos_contrmv_scaled, SkyObsNeg_contrmv_scaled]
self.GoodFit = [False, False]
self.Coefs, self.WaveObsPN = self.FitInitDS(self.WaveObsPN,
self.ObsLabelPN)
secs = ['one', 'two', 'three', 'four']
for sec in secs:
sec = 'full'
print "======================"
print "======================"
print 'QUARTER', sec
print "======================"
print "======================"
while (True):
RawInput = raw_input('>> ').replace(" ", "").lower()
if (RawInput == 'quit'):
break
if (RawInput == 'pos'):
RawInput2 = raw_input("Pos. Coefficients?: ").split(",")
self.Coefs[0] = np.array(RawInput2, dtype=np.float)
self.WaveObsPN[0] = self.DSFunc(self.Pixels[0],
self.Coefs[0])
modflux, newfl_obs = self.comparemodelanddata(
self.WaveMod, self.ModSpec, self.WaveObsPN[0],
self.SkyObsPN[0])
if sec == 'full':
self.PlotModObs(self.WaveMod, modflux,
self.WaveObsPN[0], newfl_obs,
self.ObsLabelPN[0])
else:
wvm, fm, wvo, fo = self.Breakintofour(
self.WaveMod,
modflux,
self.WaveObsPN[0],
newfl_obs,
section=sec)
self.PlotModObs(wvm, fm, wvo, fo, self.ObsLabelPN[0])
if (RawInput == 'neg'):
RawInput2 = raw_input("Neg. Coefficients?: ").split(",")
self.Coefs[1] = np.array(RawInput2, dtype=np.float)
self.WaveObsPN[1] = self.DSFunc(self.Pixels[1],
self.Coefs[1])
modflux, newfl_obs = self.comparemodelanddata(
self.WaveMod, self.ModSpec, self.WaveObsPN[1],
self.SkyObsPN[1])
if sec == 'full':
self.PlotModObs(self.WaveMod, modflux,
self.WaveObsPN[1], newfl_obs,
self.ObsLabelPN[1])
else:
wvm, fm, wvo, fo = self.Breakintofour(
self.WaveMod,
modflux,
self.WaveObsPN[1],
newfl_obs,
section=sec)
self.PlotModObs(wvm, fm, wvo, fo, self.ObsLabelPN[1])
if (RawInput == 'fit'):
for i in range(0, len(self.Coefs)):
if (self.GoodFit[i] != True):
#self.Coefs[i], self.WaveObsPN[i] = self.FitDS(self.WaveMod, self.ModSpec, self.SkyObsPN[i], self.Coefs[i])
modflux, newfl_obs = self.comparemodelanddata(
self.WaveMod, self.ModSpec, self.WaveObsPN[i],
self.SkyObsPN[i])
if sec == 'full':
self.Coefs[i], self.WaveObsPN[i] = self.FitDS(
self.WaveMod, modflux, newfl_obs,
self.Coefs[i])
self.PlotModObs(self.WaveMod, modflux,
self.WaveObsPN[i], newfl_obs,
self.ObsLabelPN[i])
else:
wvm, fm, wvo, fo = self.Breakintofour(
self.WaveMod,
modflux,
self.WaveObsPN[i],
newfl_obs,
section=sec)
self.Coefs[i], self.WaveObsPN[i] = self.FitDS(
wvm, fm, fo, self.Coefs[i])
self.PlotModObs(wvm, fm, self.WaveObsPN[i], fo,
self.ObsLabelPN[i])
RawInput2 = raw_input(
"Good Fit? (yes/no): ").replace(" ",
"").lower()
while (True):
if (RawInput2 == 'yes'):
self.GoodFit[i] = True
break
if (RawInput2 == 'no'):
break
else:
print "Please type yes or no."
break
else:
print ''
print '## Dispersion Solution for ' + self.ObsLabelPN[
i] + ' position is good.'
if (RawInput == 'pf'):
self.PrintCoefs()
if sec == 'full':
break
def __init__(self, ObsFilename=None, wave_min=None, wave_max=None, cull=50, am=1.0, H2O_scale=0.5, CO_scale=1.0):
## SETUP MODEL ATMOSPHERE ##
Envi = rfm.Environment()
A = rfm.Atmosphere(filename=Envi.atm_file)
A.scaleProf('H2O', H2O_scale)
A.scaleProf('CO', CO_scale)
# A.scaleProf('CH4', 1.0)
# A.scaleProf('CO2', 1.0)
A.writeAll('tmp.atm')
self.A = A
M = Model()
M.RFM(atm_files=['tmp.atm'],wmin=1e4/wave_max,wmax=1e4/wave_min, am=am)
M.blur(rpower=25000.)
self.M = M
# plt.figure()
# plt.plot(self.M.spectrum['wavelength'], self.M.spectrum['Transmission']/np.mean(self.M.spectrum['Transmission']))
# print self.M.spectrum['Transmission']
# assert(0==1)
## GET MODEL SKY SPECTRA ##
ModInfo = M.getSpec()
self.WaveMod = ModInfo['wavelength']
# self.SkyRadMod = ModInfo['Radiance'] / np.median(ModInfo['Radiance'])
self.SkyRadMod = ModInfo['Radiance'] / np.amax(ModInfo['Radiance'])
scale = np.amax(self.SkyRadMod)
## GET OBSERVED SKY ##
ObsInfo = nt.WaveOrder(ObsFilename).getData()
WaveObsPos = np.array(ObsInfo['wl_pos'])
SkyObsPos = np.array(ObsInfo['sky_pos']) #/ np.median(ObsInfo['sky_pos']) # L BAND
# SkyObsPos = np.array(ObsInfo['flux_pos']) / np.median(ObsInfo['flux_pos']) # K BAND
WaveObsNeg = np.array(ObsInfo['wl_neg'])
SkyObsNeg = np.array(ObsInfo['sky_neg']) / np.median(ObsInfo['sky_neg']) # L BAND
# SkyObsNeg = np.array(ObsInfo['flux_neg']) / np.median(ObsInfo['flux_neg']) # K BAND
#plt.plot(WaveObsPos, SkyObsPos)
#plt.show()
## FIT OUT CONTINUUM ## (DP 21 JAN 16)
wn_data_all = [WaveObsPos, WaveObsNeg]
flux_data_all = [SkyObsPos, SkyObsNeg]
merp = 16
factor = 64
posneg = 0
baseline_pos, baseline_neg = np.ones(np.size(WaveObsPos)), np.ones(np.size(WaveObsNeg))
# SkyObsPos_contrmv, SkyObsNeg_contrmv = np.array(np.size(SkyObsPos)), np.array(np.size(SkyObsNeg))
for wn_data, flux_data in zip(wn_data_all, flux_data_all) :
points_flux, points_wn, points_count =np.zeros(merp), np.zeros(merp), np.arange(merp)
for count in points_count :
startpoint = count*factor
endpoint = (count+1)*factor
if count == 0 : startpoint = 10
if count == 15 : endpoint = 1024-10
points_flux[count]=np.min(flux_data[startpoint:endpoint])
loc=np.argmax(flux_data[startpoint:endpoint])
# points_wn[count]=wn_data[loc+startpoint]
points_wn[count]=loc+startpoint
coeff = np.polyfit(points_wn, points_flux, 1)
print coeff
# if posneg == 0 : baseline_pos = coeff[1] + coeff[0]*wn_data# + coeff[1]*wn_data**2 + coeff[0]*wn_data**3
# if posneg == 1 : baseline_neg = coeff[1] + coeff[0]*wn_data# + coeff[1]*wn_data**2 + coeff[0]*wn_data**3
if posneg == 0 : baseline_pos = coeff[1] + coeff[0]*np.arange(1024)# + coeff[1]*np.arange(1024)**2 + coeff[0]*np.arange(1024)**3
if posneg == 1 : baseline_neg = coeff[1] + coeff[0]*np.arange(1024)# + coeff[1]*np.arange(1024)**2 + coeff[0]*np.arange(1024)**3
posneg += 1
# SkyObsPos_contrmv, SkyObsNeg_contrmv = SkyObsPos / baseline_pos, SkyObsNeg / baseline_neg
SkyObsPos_contrmv, SkyObsNeg_contrmv = SkyObsPos, SkyObsNeg
# plt.figure()
# plt.plot(SkyObsPos, hold=True)
# plt.plot(baseline_pos, hold=True)
# plt.show()
# plt.figure()
# plt.plot(SkyObsNeg, hold=True)
# plt.plot(baseline_neg, hold=True)
# plt.show()
self.ObsLabelPN = ['pos', 'neg']
self.WaveObsPN = [WaveObsPos, WaveObsNeg]
SkyObsPos_contrmv_scaled = SkyObsPos_contrmv / np.amax(SkyObsPos_contrmv) #scale * SkyObsPos_contrmv
SkyObsNeg_contrmv_scaled = SkyObsNeg_contrmv / np.amax(SkyObsNeg_contrmv) #scale * SkyObsNeg_contrmv
self.Pixels = [np.arange(len(WaveObsPos)), np.arange(len(WaveObsNeg))]
self.SkyObsPN_orig = [SkyObsPos, SkyObsNeg]
self.SkyObsPN = [SkyObsPos_contrmv_scaled, SkyObsNeg_contrmv_scaled]
# print np.shape(self.SkyObsPN_orig)
# print np.shape(SkyObsPos), np.shape(SkyObsNeg)
# print np.shape(SkyObsPos_contrmv_scaled), np.shape(SkyObsNeg_contrmv_scaled)
# print np.shape(self.SkyObsPN)
# plt.figure()
# plt.plot(SkyObsPos_contrmv_scaled)
# plt.plot(self.SkyRadMod)
# plt.show()
self.GoodFit = [False, False]
self.Coefs, self.WaveObsPN = self.FitInitDS(self.WaveObsPN, self.ObsLabelPN)
while(True):
RawInput = raw_input('>> ').replace(" ", "").lower()
if (RawInput == 'quit'):
break
if (RawInput == 'pos'):
RawInput2 = raw_input("Pos. Coefficients?: ").split(",")
self.Coefs[0] = np.array(RawInput2, dtype=np.float)
self.WaveObsPN[0] = self.DSFunc(self.Pixels[0], self.Coefs[0])
self.PlotModObs(self.WaveMod, self.SkyRadMod, self.WaveObsPN[0], self.SkyObsPN[0], self.ObsLabelPN[0])
if (RawInput == 'neg'):
RawInput2 = raw_input("Neg. Coefficients?: ").split(",")
self.Coefs[1] = np.array(RawInput2, dtype=np.float)
self.WaveObsPN[1] = self.DSFunc(self.Pixels[1], self.Coefs[1])
self.PlotModObs(self.WaveMod, self.SkyRadMod, self.WaveObsPN[1], self.SkyObsPN[1], self.ObsLabelPN[1])
if (RawInput == 'fit'):
for i in range(0,len(self.Coefs)):
if (self.GoodFit[i] != True):
self.Coefs[i], self.WaveObsPN[i] = self.FitDS(self.WaveMod, self.SkyRadMod, self.SkyObsPN[i], self.Coefs[i])
self.PlotModObs(self.WaveMod, self.SkyRadMod, self.WaveObsPN[i], self.SkyObsPN[i], self.ObsLabelPN[i])
RawInput2 = raw_input("Good Fit? (yes/no): ").replace(" ", "").lower()
while (True):
if (RawInput2 == 'yes'):
self.GoodFit[i] = True
break
if (RawInput2 == 'no'):
break
else:
print "Please type yes or no."
break
else:
print ''
print '## Dispersion Solution for ' + self.ObsLabelPN[i] + ' position is good.'
if (RawInput == 'pf'):
self.PrintCoefs()