TelFit Documentation. Release Kevin Gullikson

Transcription

1 TelFit Documentation Release Kevin Gullikson June 23, 2015

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3 Contents 1 Introduction to Telluric Modeling with TelFit 3 2 Installation 5 3 TelFit Tutorial Generating a Telluric Model with TelFit Simple Model Fitting API for TelFit API for TelluricFitter API for MakeModel Updating the Atmosphere profile 11 6 Indices and tables 17 i

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5 Contents: Contents 1

6 2 Contents

7 CHAPTER 1 Introduction to Telluric Modeling with TelFit Do you have spectra observed from Earth? Do you hate needing to spend precious telescope time just to observe a telluric standard star? If so, TelFit might work for you! TelFit is a Python code written specifically to model and fit the telluric absorption spectrum in astronomical data. It is essentially a wrapper around the LBLRTM FORTRAN code, and provides an easy to use, object-oriented interface to the code. TelFit vastly simplifies the process of gnerating a telluric model, and can efficiently remove the telluric absorption lines in high-resolution optical or near-infrared spectra. 3

8 4 Chapter 1. Introduction to Telluric Modeling with TelFit

9 CHAPTER 2 Installation This code requires the following packages: matplotlib numpy v1.6 or greater scipy v0.13 or greater astropy v0.2 or greater lockfile pysynphot v0.7 or greater fortranformat cython requests The bolded entries are required before installation, so make sure you get them from pip, apt-get/yum, or conda (depending on your OS and linux distribution). The setup script will attempt to install the rest if you don t have them, but I suggest doing it yourself just to make sure nothing goes wrong. Once you have the dependencies, simply type pip install TelFit to install TelFit. It may take a while, as it needs to build the LBLRTM code and some of its standard input files. 5

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11 CHAPTER 3 TelFit Tutorial After installation, there should a few usage examples in ~/.TelFit/examples. We go into a bit more detail on what the examples are doing here. 3.1 Generating a Telluric Model with TelFit Making a telluric model used to be hard. With TelFit, it is just a few lines of code. from telfit import Modeler # Set the start and end wavelength, in nm wavestart = waveend = # Make the model modeler = Modeler() model = modeler.makemodel(humidity=50.0, lowfreq=1e7/waveend, highfreq=1e7/wavestart) 3.2 Simple Model Fitting Alright making a model is pretty simple, but you probably want to go further and find the best model for your data. This is a more complicated thing, so requires a bit more code. The rest of this tutorial will assume that you have imported a few modules: import numpy as np import matplotlib.pyplot as plt from telfit import TelluricFitter, DataStructures The first thing we need to do is make an instance of the TelluricFitter class, and set some basic information about your observatory. fitter = TelluricFitter() observatory = {"latitude": 30.5, "altitude": 2.5} fitter.setobservatory(observatory) You just need to give the TelluricFitter class a latitude and altitude. For your convenience, there are a few common observatories already loaded into TelFit, so you can also set the observatory with 7

12 fitter.setobservatory(obsname) where obsname is one of the following: McDonald CTIO Mauna Kea La Silla Paranal You can easily add your own observatory if you wish by editing the source code for the SetObservatory method. Alright, now that we have initialized the fitter class we need to tell it how what variables to fit and give their initial values. In this example, we will just fit the relative humidity and oxygen mixing ratio. You should be able to get an initial value for the humidity from your fits header or archived weather data; if not, guess with something like 50%. We will also set some constant values that are important. fitter.fitvariable({'h2o': humidity_guess, 'o2': 2.12e5}) # This is a good initial guess for the O2 abundance fitter.adjustvalue({"angle": angle, "pressure": pressure, "resolution": resolution, "wavestart": data.x[0] , "waveend": data.x[-1] }) You will notice that the input for both of the methods is a dictionary with parameter name and value. For the FitVariable method, the value is an initial guess. For the AdjustValue method, the value you give it is fixed (with the exception of detector resolution).now let s set some bounds on the fitted parameters as well. You can set bounds on any parameter, but it will be ignored if it is a constant. fitter.setbounds({'h2o': [1.0, 99.0], 'o2': [5e4, 1e6], 'resolution': , }) You will notice that we set bounds on the resolution parameter as well. The detector resolution is always fit, and you should always give it bounds that are pretty close to the true value. Finally, we can perform the fit. This will take quite some time to run, so go get some coffee if you are following along... model = fitter.fit(data=data) There are lots of options to Fit to control how it does everything. Check the API if the defaults aren t working for you. The data object you pass to Fit must be an object of type DataStructures.xypoint, which you can create with the following code (assuming you have your data in numpy arrays called wave, flux, and continuum ) data = DataStructures.xypoint(x=wave, y=flux, cont=continuum) The continuum does not need to be great, since TelFit estimates that as well after dividing out the telluric model. 8 Chapter 3. TelFit Tutorial

13 CHAPTER 4 API for TelFit 4.1 API for TelluricFitter 4.2 API for MakeModel 9

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15 CHAPTER 5 Updating the Atmosphere profile An atmosphere profile gives the pressure, temperature, and various molecular mixing ratios as a function of height in the atmosphere. TelFit comes with a default atmosphere profile suitable for mid-latitudes at nighttime that works pretty well, but you can do better by using a profile tailored to your observatory. There isn t a particularly easy way to do this, so I will outline the steps I use to get an updated atmosphere profile from the Global Data Assimilation System below. I have included screenshots of the various stages to aid you in your journey, but you are on your own if the website changes between now and when you are reading this! First, go to the GDAS website. Enter the latitude and longitude of your observatory, and click continue. In the Sounding row, choose the entry titled GDAS (0.5 deg, 3 hourly, Global). Hit the Go button in the sounding row. 11

16 Choose the appropriate UT date: On the next page, use the following settings. Choose the appropriate UT time Choose Text only in the Output Options row. Choose Text listing in the Graphics row. Complete the captcha (this is why I can t make it easy on you!) hit Get Sounding 12 Chapter 5. Updating the Atmosphere profile

17 After all this, you should get a page with a bunch of information. You want to copy-paste the second block into a text file. It should look something like this. PRESS HGT(MSL) TEMP DEW PT WND DIR WND SPD HPA M C C DEG M/S E = Estimated Surface Height E E E E E E E E E E E E E E E E E E E E E E E E E

18 E E E E E E E E E E E E E E E E E E E E E E E E E E E E E E E We are finally ready to do some Python! Read that text file in using your favorite method (I using numpy.loadtxt). You might need to go through and delete the E on every line, and probably delete the first row since it doesn t have all the information. import numpy as np Pres, height, Temp, dew = np.loadtxt(atmosphere_filename, usecols=(0, 1, 2, 3), unpack=true) You could concievably do something with the wind information, but TelFit doesn t use that so you are on your own. Now, we need to convert the units so that TelFit does the right thing. Here is some sample code for doing so. Most of it is pretty self-explanatory except for the conversion from dew point to mixing ratio in ppmv. The equation and constants were taken from a compilation of formulas for humidity, available here (hopefully). # Sort the arrays by height. sorter = numpy.argsort(height) height = height[sorter] Pres = Pres[sorter] Temp = Temp[sorter] dew = dew[sorter] #Convert dew point temperature to ppmv Pw = * 10**( *Temp/(Temp )) h2o = Pw / (Pres-Pw) * 1e6 #Unit conversion 14 Chapter 5. Updating the Atmosphere profile

19 height /= Temp += Now, you can tell TelFit about the new atmosphere with the following commands. I ll assume fitter is an instance of the TelluricFitter class. The Modeler class has the same method if you just want to make a model. fitter.editatmosphereprofile("temperature", height, Temp) fitter.editatmosphereprofile("pressure", height, Pres) fitter.editatmosphereprofile("h2o", height, h2o) 15

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21 CHAPTER 6 Indices and tables genindex modindex search 17