Examples¶
Running doppler¶
The simplest way to run Doppler is with the command-line script doppler. The only required argument is the name of a spectrum fits file.
doppler spectrum.fits
This will create an output file called spectrum_doppler.fits.
By default, Doppler doesn’t print anything to the screen. So let’s set the --verbose or -v parameter.
doppler spectrum.fits -v
spectrum.fits S/N= 85.1
Fitting Cannon model to spectrum with parameters: Teff, logg, [Fe/H], RV
Masked 103 outlier or negative pixels
TEFF LOGG FEH VREL CCPEAK CHISQ
3500.00 4.80 -0.50 -13.67 0.23 7.87
4000.00 4.80 -0.50 -15.37 0.39 5.41
5000.00 4.60 -0.50 -16.56 0.50 3.85
6000.00 4.40 -0.50 -16.77 0.48 5.16
7500.00 4.00 -0.50 -16.90 0.16 7.65
15000.00 4.00 -0.50 989.79 0.03 8.32
25000.00 4.00 -0.50 -999.68 0.05 8.81
40000.00 4.00 -0.50 -308.33 0.08 8.96
3500.00 0.50 -0.50 -15.19 0.34 13.01
4300.00 1.00 -0.50 -16.22 0.45 6.58
4700.00 2.00 -0.50 -16.55 0.50 4.68
5200.00 3.00 -0.50 -16.81 0.50 4.45
Initial RV fit:
Teff = 5000.00 K
logg = 4.60
[Fe/H] = -0.50
Vrel = -16.56 +/- 0.136 km/s
Initial Cannon stellar parameters using initial RV
Teff = 5074.34 K
logg = 4.86
[Fe/H] = 0.10
Masked 48 discrepant pixels
Initial Cannon stellar parameters using initial RV and Tweaking the normalization
Teff = 5049.52 K
logg = 4.98
[Fe/H] = 0.14
Improved RV and Cannon stellar parameters:
Teff = 5049.52 K
logg = 4.98
[Fe/H] = 0.14
Vrel = -16.78 +/- 0.117 km/s
Least Squares RV and stellar parameters:
Teff = 5049.52 K
logg = 4.98
[Fe/H] = 0.14
Vrel = -16.78 km/s
chisq = 1.96
Fine grid best RV = -16.98 km/s
chisq = 1.96
Final parameters:
Teff = 5049.52 +/- 3.158 K
logg = 4.98 +/- 0.003
[Fe/H] = 0.14 +/- 0.001
Vhelio = -18.02 +/- 0.01 km/s
BC = -1.04 km/s
chisq = 1.96
dt = 3.40 sec.
Writing output to spectrum_doppler.fits
You can also have it save a figure of the spectrum and the best-fit model using the --plot or -p parameter.
doppler spectrum.fits -v -p
spectrum.fits S/N= 85.1
Fitting Cannon model to spectrum with parameters: Teff, logg, [Fe/H], RV
Masked 103 outlier or negative pixels
TEFF LOGG FEH VREL CCPEAK CHISQ
3500.00 4.80 -0.50 -13.67 0.23 7.87
...
chisq = 1.96
Figure saved to spectrum_dopfit.png
dt = 4.08 sec.
Writing output to spectrum_doppler.fits
By default, the figure filename is spectrum_dopfit.png, but the figure filename can be set with the
--figfile parameter. Note that you can set the figure type with the extension. For example,
to get a PDF just use --figfile spectrum_dopfit.pdf.
Using a Payne Model¶
By default, Doppler uses a Cannon model fitting Teff, logg, [Fe/H] and RV. To use a Payne model instead,
just set the --payne parameter.
doppler spectrum.fits -v --payne
spectrum.fits S/N= 85.1
Fitting Payne model to spectrum with parameters: TEFF, LOGG, FE_H, ALPHA_H, RV
Masked 103 outlier or negative pixels
TEFF LOGG FEH ALPHAFE VREL CCPEAK CHISQ
3500 4.80 -1.50 0.00 -13.86 0.13 8.67
4000 4.80 -1.50 0.00 -15.52 0.17 8.21
5000 4.60 -1.50 0.00 -17.53 0.33 7.89
6000 4.40 -1.50 0.00 -17.57 0.28 8.25
7500 4.00 -1.50 0.00 -17.97 0.04 8.20
15000 4.00 -1.50 0.00 994.28 0.02 8.57
25000 4.00 -1.50 0.00 -1004.90 0.01 8.83
40000 4.00 -1.50 0.00 -1004.90 0.01 9.08
3500 0.50 -1.50 0.00 -14.79 0.25 9.16
4300 1.00 -1.50 0.00 -16.82 0.40 6.60
4700 2.00 -1.50 0.00 -17.12 0.37 7.29
5200 3.00 -1.50 0.00 -17.31 0.33 7.77
3500 4.80 -0.50 0.00 -13.67 0.16 7.96
4000 4.80 -0.50 0.00 -15.71 0.30 6.23
5000 4.60 -0.50 0.00 -16.92 0.45 4.19
6000 4.40 -0.50 0.00 -17.03 0.43 6.11
7500 4.00 -0.50 0.00 -16.94 0.15 7.54
15000 4.00 -0.50 0.00 996.77 0.02 8.60
25000 4.00 -0.50 0.00 -1004.90 0.01 8.85
40000 4.00 -0.50 0.00 -1004.90 0.01 9.08
3500 0.50 -0.50 0.00 -15.56 0.30 12.90
4300 1.00 -0.50 0.00 -16.60 0.43 6.51
4700 2.00 -0.50 0.00 -16.81 0.46 4.95
5200 3.00 -0.50 0.00 -16.99 0.45 5.27
3500 4.80 -1.50 0.30 -13.75 0.11 8.59
4000 4.80 -1.50 0.30 -16.02 0.20 8.17
5000 4.60 -1.50 0.30 -17.21 0.32 7.58
6000 4.40 -1.50 0.30 -17.37 0.28 8.06
7500 4.00 -1.50 0.30 -17.60 0.05 8.14
15000 4.00 -1.50 0.30 994.34 0.02 8.57
25000 4.00 -1.50 0.30 -1004.90 0.01 8.83
40000 4.00 -1.50 0.30 -1004.90 0.01 9.08
3500 0.50 -1.50 0.30 -14.96 0.27 8.73
4300 1.00 -1.50 0.30 -16.75 0.40 6.43
4700 2.00 -1.50 0.30 -17.03 0.37 7.13
5200 3.00 -1.50 0.30 -17.19 0.33 7.60
3500 4.80 -0.50 0.30 -13.92 0.18 7.74
4000 4.80 -0.50 0.30 -15.63 0.32 5.93
5000 4.60 -0.50 0.30 -16.78 0.43 3.98
6000 4.40 -0.50 0.30 -16.96 0.41 5.84
7500 4.00 -0.50 0.30 -16.88 0.16 7.45
15000 4.00 -0.50 0.30 997.53 0.02 8.59
25000 4.00 -0.50 0.30 -1004.90 0.01 8.85
40000 4.00 -0.50 0.30 -998.83 0.01 9.08
3500 0.50 -0.50 0.30 -15.62 0.31 12.53
4300 1.00 -0.50 0.30 -16.51 0.42 6.98
4700 2.00 -0.50 0.30 -16.74 0.45 4.99
5200 3.00 -0.50 0.30 -16.93 0.45 5.05
Initial RV fit:
Teff = 5000.00 K
logg = 4.60
[Fe/H] = -0.50
[alpha/Fe] = 0.30
Vrel = -16.78 +/- 0.093 km/s
chisq = 3.98
Least Squares RV and stellar parameters:
TEFF = 4828.16
LOGG = 4.68
FE_H = -0.03
ALPHA_H = -0.23
RV = -17.05
chisq = 2.15
Fine grid best RV = -17.08 km/s
chisq = 2.15
Final parameters:
TEFF = 4828.16 +/- 12.276
LOGG = 4.68 +/- 0.016
FE_H = -0.03 +/- 0.005
ALPHA_H = -0.23 +/- 0.008
RV = -17.08 +/- 0.045
Vhelio = -18.12 +/- 0.04 km/s
BC = -1.04 km/s
chisq = 2.15
dt = 11.10 sec.
Writing output to spectrum_doppler.fits
By default, Doppler fits the parameters Teff, logg, [Fe/H], [alpha/H], and RV with a Payne model.
But the parameters can be set using the --fitpars parameter with a comma-separated list of parameter
names (with no spaces). Note that all abundance names need to end with _h such as fe_h,
alpha_h and c_h. To fit the carbon abundance as well, you would do,
doppler spectrum.fits -v --payne --fitpars teff,logg,fe_h,alpha_h,c_h,rv
spectrum.fits S/N= 85.1
Fitting Payne model to spectrum with parameters: TEFF, LOGG, FE_H, ALPHA_H, RV
Masked 103 outlier or negative pixels
TEFF LOGG FEH ALPHAFE VREL CCPEAK CHISQ
3500 4.80 -1.50 0.00 -13.86 0.13 8.67
...
Least Squares RV and stellar parameters:
TEFF = 4860.69
LOGG = 4.72
FE_H = -0.03
ALPHA_H = -0.24
C_H = 0.08
RV = -17.03
chisq = 2.13
Fine grid best RV = -17.06 km/s
chisq = 2.13
Final parameters:
TEFF = 4860.69 +/- 16.727
LOGG = 4.72 +/- 0.019
FE_H = -0.03 +/- 0.007
ALPHA_H = -0.24 +/- 0.010
C_H = 0.08 +/- 0.010
RV = -17.06 +/- 0.045
Vhelio = -18.10 +/- 0.05 km/s
BC = -1.04 km/s
chisq = 2.13
dt = 11.00 sec.
The current Payne model has 33 labels (Teff, logg, Vmicro, [C/H], [N/H], [O/H], [Na/H], [Mg/H], [Al/H], [Si/H], [P/H], [S/H], [K/H], [Ca/H], [Ti/H], [V/H], [Cr/H], [Mn/H], [Fe/H], [Co/H], [Ni/H], [Cu/H], [Ni/H], [Cu/H], [Ge/H], [Ce/H], [Nd/H], [Ba/H], [Eu/H], [La/H], [Y/H], [Sc/H], [Zr/H], [Pr/H], [Yb/H]). Besides RV, Vsini and Vmacro can also be fit with a Payne model.
Jointly fitting spectra¶
Doppler can fit mulitple spectra of the same star simultaneously. It will fit a single set of labels and separate
RVs for each spectrum. To use this option, set the --joint or j parameters. You also need to give the
names of the mulitiple spectrum files. You can give these on the command list, e.g. doppler spectrum1.fits spectrum2.fits -j,
or you can put the names of the files in an ASCII list file (one per line) and give that to Doppler. To use a list, be sure
to also set the --list or -l parameter.
doppler speclist.txt -v -j -l
--- Running Doppler Jointfit on 3 spectra ---
Loading the spectra
Spectrum 1: apVisit-r13-9289-58006-107.fits S/N= 102.4
Spectrum 2: apVisit-r13-9289-58028-113.fits S/N= 74.5
Spectrum 3: apVisit-r13-9289-58054-107.fits S/N= 72.4
Jointly fitting Cannon model to 3 spectra with parameters: Teff, logg, [Fe/H] and RV for each spectrum
Step #1: Fitting the individual spectra
Fitting spectrum 1
apVisit-r13-9289-58006-107.fits
Fitting Cannon model to spectrum with parameters: Teff, logg, [Fe/H], RV
...
Final parameters:
Teff = 4658.20 +/- 1.463 K
logg = 2.62 +/- 0.002
[Fe/H] = -0.16 +/- 0.001
Vhelio = -82.05 +/- 0.01 km/s
BC = 14.38 km/s
chisq = 2.26
dt = 4.16 sec.
Fitting spectrum 2
apVisit-r13-9289-58028-113.fits
Fitting Cannon model to spectrum with parameters: Teff, logg, [Fe/H], RV
...
Final parameters:
Teff = 4666.10 +/- 1.498 K
logg = 2.56 +/- 0.002
[Fe/H] = -0.15 +/- 0.001
Vhelio = -82.03 +/- 0.01 km/s
BC = 8.07 km/s
chisq = 1.88
dt = 3.37 sec.
Fitting spectrum 3
apVisit-r13-9289-58054-107.fits
Fitting Cannon model to spectrum with parameters: Teff, logg, [Fe/H], RV
...
Final parameters:
Teff = 4657.61 +/- 1.624 K
logg = 2.59 +/- 0.002
[Fe/H] = -0.16 +/- 0.001
Vhelio = -82.10 +/- 0.01 km/s
BC = -1.02 km/s
chisq = 1.70
dt = 3.28 sec.
Step #2: Getting weighted stellar parameters
Initial weighted parameters are:
Teff = 4660.75 K
logg = 2.59
[Fe/H] = -0.16
Vrel = -82.06 km/s
Step #3: Fitting all spectra simultaneously
Parameters:
Teff = 4660.97 K
logg = 2.59
[Fe/H] = -0.16
Vhelio = -82.05 +/- 0.01 km/s
Vscatter = 0.017 km/s
[-82.04650497 -82.03479767 -82.10112727]
Step #4: Tweaking continuum and masking outliers
Masked 4 discrepant pixels
Masked 3 discrepant pixels
Masked 1 discrepant pixels
Step #5: Re-fitting all spectra simultaneously
Final parameters:
Teff = 4661.19 K
logg = 2.59
[Fe/H] = -0.16
Vhelio = -82.05 +/- 0.01 km/s
Vscatter = 0.017 km/s
[-82.04650497 -82.03479767 -82.10112727]
dt = 13.05 sec.
Writing output to apVisit-r13-9289-58006-107_doppler.fits
Doppler first fits each spectrum separately. Then it finds weighted stellar parameters and Vhelio. Finally, it fits a single set of stellar parameters and an RV for each spectrum to all spectra simultaneously.
Running Doppler from python¶
All of the Doppler functionality is also available directory from python.
First, import Doppler and read in the example spectrum.
import doppler
spec = doppler.read('spectrum.fits')
Print out it’s properties:
spec
<class 'doppler.spec1d.Spec1D'>
APOGEE spectrum
File = spectrum.fits
S/N = 85.06
Dimensions: [2048,3]
Flux = [[3.6705207e-15 3.8983997e-15 4.8754683e-15]
[3.6727666e-15 3.9004448e-15 4.8746174e-15]
[3.6702780e-15 3.9016904e-15 4.8737662e-15]
...
[4.3078719e-15 4.5482637e-15 5.8845268e-15]
[4.3102292e-15 4.5506604e-15 5.8881089e-15]
[4.3116611e-15 4.5502703e-15 5.8918320e-15]]
Err = [[1.5879806e-08 2.8263509e-08 3.4794638e-08]
[1.5880362e-08 2.8273581e-08 3.4788567e-08]
[1.5881179e-08 2.8282614e-08 3.4782488e-08]
...
[2.7037721e-08 3.5628904e-08 3.2013901e-08]
[2.7046704e-08 3.5624442e-08 3.2033391e-08]
[2.7055689e-08 3.5619223e-08 3.2053357e-08]]
Wave = [[16953.30940492 16433.71888594 15808.37977415]
[16953.09701271 16433.45786229 15808.07341694]
[16952.88459753 16433.19681725 15807.76703994]
...
[16471.98020599 15856.26367213 15141.55733694]
[16471.72234417 15855.96043257 15141.21203183]
[16471.46446085 15855.65717311 15140.86670842]]
Now fit the spectrum:
out,model,specm = doppler.rv.fit(spec)
The output will be a table with the final results, the best-fitting model spectrum, and the masked and tweaked version of the observed spectrum used internall by Doppler for the fitting.
To jointly fit spectra, you want to load all of the spectra into a list and then run jointfit().
import doppler
from dlnpyutils import utils as dln
# Read in the list of files
files = dln.readlines(.txt')
speclist = []
for i in range(len(files)):
spec = doppler.read(files[i]
speclist.append(spec)
# Now run jointfit()
sumstr,final,bmodel,specmlist = doppler.rv.jointfit_payne(speclist)
The outputs are a summary file of the best-fit values (sumstr), final best-fit values for each individual spectrum (final), list of best-fitting model spectra (bmodel), and the list of the masked and tweaked observed spectra (specmlist).