Doing a li6le astronomy with. Python. Ryan Cooke (K16) These slides & examples:

Transcription

1 Doing a li6le astronomy with Python Ryan Cooke (K16) These slides & examples:

2 An aside Let s begin by installing ATLAS: (AutomaIcally Tuned Linear Algebra SoKware) > cd ~! > mkdir local! You need to idenify a directory where you can keep your sokware. A datadisk would be ideal if you already have one, if not, your home directory is fine (i.e. /home/<your name>). Go to this directory. > mkdir software! > cd software! > mkdir python! > cd python! > mkdir bin py-lib scripts numpy scipy pymc examples!

3 Now open your.mytcshrc file > emacs.mytcshrc &! An aside and include the following code: # Settings for PYTHON! setenv PYDIR /usr/local/lib/python2.6! setenv MYPYDIR /home/rcooke/software/python! setenv PYTHONPATH $MYPYDIR/scripts! setenv PYTHONPATH ${PYTHONPATH}:$MYPYDIR/py-lib! setenv PATH ${PATH}:$MYPYDIR/bin! setenv BLAS /home/rcooke/local/lib/libf77blas.a! setenv LAPACK /home/rcooke/local/lib/liblapack.a!

4 Now open your.mytcshrc file > emacs.mytcshrc &! An aside and include the following code: # Settings for PYTHON! setenv PYDIR /usr/local/lib/python2.6! setenv MYPYDIR /home/rcooke/software/python! setenv PYTHONPATH $MYPYDIR/scripts! setenv PYTHONPATH ${PYTHONPATH}:$MYPYDIR/py-lib! setenv PATH ${PATH}:$MYPYDIR/bin! setenv BLAS /home/rcooke/local/lib/libf77blas.a! setenv LAPACK /home/rcooke/local/lib/liblapack.a! To save some Ime, go to to get a copy this text, and just change the red highlighted text from the file install_notes.txt to your sevngs.

5 An aside Now go into the packages directory, which is located: and download the atlas package into the sokware directory. Type the following command: > bunzip2 c atlas tar.bz2 tar xfm -! > cd ATLAS! Now download the lapack package and put it in this ATLAS directory. Type the following into the command line: > mkdir BUILD! > cd BUILD! >../configure (see install_notes.txt for full command)! > make! ~10 mins Let s get started!!!

6 Before I begin Here are some great slides which describe the correct programming technique: Some thoughts on coding with Python Andrew Pontzen These slides & examples

7 Python vs IDL Open source (free) Widely used Clean Syntax Loads of Packages 1/20 Astronomers Creates nice GUIs Commercial (costs money) Astronomers (almost) only! Syntax is crap(ish) Loads of Astro Packages 18.9/20 Astronomers Forget about it!!! Which should you pick?

8 Which should you pick You will probably use what your Ph.D. supervisor uses which is likely to be IDL (or Fortran/C in some cases). Python is officially THE language supported by the University CompuIng Service you can ask them for help! There are some great Python courses offered through the University and they re free! Go to the following website and enter the search term: python h6p:// You should pick the language you feel most comfortable with.

9 Recommended Python Packages Science/Numerical SciPy, NumPy PloVng Matplotlib, Veusz Astro Tools Astropysics, AstroLib, PyRAF FiVng Tools mpfit, pymc GUIs pygtk, PyQT Arbitrary Precision mpmath Fits files PyFITS (We ll start by installing the bold packages today) See the AstroPython website for useful notes: h6p://

10 The Aim of this Lecture Course Set you up with Python at the IoA. Teach you the easy way to set yourself up with Python! Do a li6le useful Astronomy Create fake data Fit this data with our models using two methods: Markov chain Monte Carlo (MCMC) χ 2 - minimisaion

11 GeVng you setup with Python There are 4 ways you can do this!!! Be the IoA administrator which you re not! Mac OS X User installaion virtual- python Tradi8onal approach PYTHONPATH

12 Let s coninue with our install The last command we gave was make. Now do the following: > cd lib! > make shared! > make ptshared! > cd../! > make install! check that this worked by typing the following: > echo $BLAS! > echo $LAPACK! Great! Now go to: and download a copy numpy, scipy, and pymc. Put these three packages in your python directory ($MYPYDIR)

13 We re almost there! Now type the following command into a terminal: > emacs ~/.pydistutils.cfg &! This file should be blank. Enter the following text in this file: [install]! install_lib = $MYPYDIR/py-lib! install_scripts = $MYPYDIR/bin! Close this file and then install numpy by entering the following into a terminal > cd $MYPYDIR! > gunzip numpy tar.gz! > tar xvf numpy tar! > cd numpy-1.6.1! > python setup.py build --fcompiler=gnu95! > python setup.py install! ~1 min

14 We re almost there! Now install scipy in much the same way: > cd $MYPYDIR! > gunzip scipy b2.tar.gz! > tar xvf scipy b2.tar! > cd scipy b2! > python setup.py build --fcompiler=gnu95! > python setup.py install! ~5 mins and again for pymc: > cd $MYPYDIR! > unzip pymc-devs-pymc-raked_sandbox-159-g28953e9.zip! > cd pymc-devs-pymc-28953e9! > python setup.py config_fc --fcompiler=gnu95 build! ~30 s > python setup.py install! FantasIc! These have all been installed in $MYPYDIR/py-lib/

15 Now let s do it the easy way! Download a copy of setuptools from the packages directory. Place this in your python directory (i.e. $MYPYDIR/py-lib/). Issue the following commands: > cd $MYPYDIR! > sh setuptools-0.6c11-py2.6.egg! We are now ready to use easy_install! Try this: > easy_install numexpr! > easy_install matplotlib! That s easy! These have all been installed in $MYPYDIR/py-lib/ There are some other useful scripts that we will use in this course. To make use of these, download mpfit.py and MCMC_errors.py from the packages directory and put them in your python scripts directory (i.e. $MYPYDIR/scripts/). These scripts are just single.py files (not packages) and handle a few tasks, or have a handful of useful funcions.

16 How do we do Python? Write a script and execute it with the python command in a terminal > python myscript.py! ! >! Use Python on the command line > python! >>> import numpy as np! >>> print np.pi! ! Use ipython on the command line (much, much be6er) > ipython! In [1]: import numpy as np! In [2]: print np.pi! Out[2]: !

17 How do we do Python? We ll be wriing python scripts (i.e. filename.py files). Here s a crash course: # A hash symbol (#) indicates a comment line! # We can use the packages we have just! # installed with the import command:! import numpy! # To print text to a terminal use the print command:! print The number pi is equal to, numpy.pi! # We can also rename numpy to np! import numpy as np! print The number pi is equal to, np.pi! # or just import the function pi:! from numpy import pi! print The number pi is equal to, pi!

18 How do we do Python? # Here s an example of how to create a number array! import numpy as np! numbers = np.array([1,2,3,4,5])! # Or you could use! # (start at 1, end at 6, separate numbers by 1):! numbers = np.arange(1,6,1)! # We can write simple definitions (or functions)! # to perform certain tasks:! import numpy as np! def info(thing):! # Note that we now have to indent!! print This array has, len(thing), elements! print thing[0], thing[1]! somearray = np.array([np.pi, 2*np.pi, 3*np.pi])! info(somearray) # Call the definition!

19 What we are going to do Go to your python directory and cd into the examples folder (cd $MYPYDIR/ examples). Open a file called gen_fakedata.py (gedit gen_fakedata.py &) Import numpy, and pyplot (part of the matplotlib package) Create a definiion for a Gaussian (use numpy.exp for the exponenial) Be sure to allow four free parameters (offset, amplitude, mean, dispersion). Generate a wavelength array between Å with 1Å increments. Create an array with four elements these numbers will be the parameters of the Gaussian emission line we will synthesise (set the mean to ). Generate a Gaussian emission line! Add some noise to the flux nothing is ever perfect Create an error array that stores this noise value at each wavelength. Write this generated data to a file called my_fakedata.dat Plot the data you have created! That s it for now! Next Lesson we ll a6empt to fit this data with a Gaussian model.