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Intro_to_Pyton_for_Astronomers.html
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Intro_to_Pyton_for_Astronomers.html
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<!DOCTYPE html>
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<title>Intro_to_Pyton_for_Astronomers</title>
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<h2 id="A-quick-introduction-to-Python-for-Astronomers">A quick introduction to Python for Astronomers<a class="anchor-link" href="#A-quick-introduction-to-Python-for-Astronomers">¶</a></h2><p>Written for the Practical Introduction to Research Class at UT Austin in Fall 2015</p>
<p>Updated for TAURUS sumemr research program in June 2016</p>
<p>Emma Yu</p>
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<h3 id="1.-Backgroud">1. Backgroud<a class="anchor-link" href="#1.-Backgroud">¶</a></h3>
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<p>After a few weeks working with IDL, many of you are already IDL ninjas. Now let's have a look at another language in which a lot of Astronomy packages are now available - <a href="https://www.python.org/">Python</a>.</p>
<p>Python is an object-orientied, dynamic, general-purpose language. Unlike C and Fortran, it's an <a href="https://en.wikipedia.org/wiki/Interpreted_language">interpreted language</a>, which means the code is interpreted at runtime, and one does not need to compile the code ahead of time. Python is an free and <a href="https://en.wikipedia.org/wiki/Free_and_open-source_software">open source software</a>, which means one does not need to pay anything to use it, and everyone is welcome to contribute and to make the software better!</p>
<p>The language was first develoted by <a href="https://www.python.org/~guido/">Guido van Rossum</a>, and the first version appearred in <a href="https://en.wikipedia.org/wiki/Python_(programming_language">1991</a>). There are a few popular distributions available for easy installation and package management. I personally recomend <a href="https://store.continuum.io/cshop/anaconda/">Anoconda</a> - with which one can install and manage libraraies all in one place and easily create different working environments.</p>
<p>This tutorial is written in <a href="http://jupyter.org">Jupyter notebook</a>, which allows one to write programs in a browser, and save all the instructions, code, and plots in the same notebook. It's great for writing a tutorial like this, but may not be optimal for writing a large project.</p>
<p>This tutorial is based on Python 2.7 because at the time when this tutorial was first written, many Astronomy packages were not available in Python 3 yet. For a comparison between the two versions, please see this <a href="https://wiki.python.org/moin/Python2orPython3">wiki article</a>.</p>
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<h3 id="2.-A-few-practical-differences-between-Python-and-IDL">2. A few practical differences between Python and IDL<a class="anchor-link" href="#2.-A-few-practical-differences-between-Python-and-IDL">¶</a></h3>
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<h4 id="Similarities:">Similarities:<a class="anchor-link" href="#Similarities:">¶</a></h4><ul>
<li>the data type is dynamic - it can be changed in the code.</li>
<li>index starts from 0.</li>
<li>Note that "copy" only generates a new view and does not actually copy the data!!!!</li>
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<h4 id="Differences:">Differences:<a class="anchor-link" href="#Differences:">¶</a></h4><ul>
<li>Python uses indentation to denote the structure of the code. </li>
<li>Things are organized as objects in Python.</li>
<li>The basic Python does not usually support what we want to do. One needs to load several packages for example to manipulate multi-dimensional arrays.</li>
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<h3 id="3.-Array-basics">3. Array basics<a class="anchor-link" href="#3.-Array-basics">¶</a></h3><p>For the purposes of this tutorial, we will mostly use the <a href="http://www.numpy.org/">Numpy</a> package to manipulate array-based data.</p>
<p>First, let load the package by:</p>
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<div class=" highlight hl-ipython2"><pre><span class="kn">import</span> <span class="nn">numpy</span> <span class="kn">as</span> <span class="nn">np</span>
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<p>Numpy supports the array data type just as the arrays we've previously seen in IDL. Similar to 'findgen', one can generate an array with indics by:</p>
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<div class=" highlight hl-ipython2"><pre><span class="n">a</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">15</span><span class="p">)</span>
<span class="k">print</span> <span class="n">a</span>
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<pre>[ 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14]
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<p>"a" is a numpy array object. Numpy array provides a range of a lot of default precedures called "methods" that can be applied to numpy array objects. One can use "dir()" to find out what methods are avialible.</p>
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<div class=" highlight hl-ipython2"><pre><span class="k">print</span> <span class="nb">type</span><span class="p">(</span><span class="n">a</span><span class="p">)</span>
<span class="k">print</span> <span class="nb">dir</span><span class="p">(</span><span class="n">a</span><span class="p">)</span>
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<pre><type 'numpy.ndarray'>
['T', '__abs__', '__add__', '__and__', '__array__', '__array_finalize__', '__array_interface__', '__array_prepare__', '__array_priority__', '__array_struct__', '__array_wrap__', '__class__', '__contains__', '__copy__', '__deepcopy__', '__delattr__', '__delitem__', '__delslice__', '__div__', '__divmod__', '__doc__', '__eq__', '__float__', '__floordiv__', '__format__', '__ge__', '__getattribute__', '__getitem__', '__getslice__', '__gt__', '__hash__', '__hex__', '__iadd__', '__iand__', '__idiv__', '__ifloordiv__', '__ilshift__', '__imod__', '__imul__', '__index__', '__init__', '__int__', '__invert__', '__ior__', '__ipow__', '__irshift__', '__isub__', '__iter__', '__itruediv__', '__ixor__', '__le__', '__len__', '__long__', '__lshift__', '__lt__', '__mod__', '__mul__', '__ne__', '__neg__', '__new__', '__nonzero__', '__oct__', '__or__', '__pos__', '__pow__', '__radd__', '__rand__', '__rdiv__', '__rdivmod__', '__reduce__', '__reduce_ex__', '__repr__', '__rfloordiv__', '__rlshift__', '__rmod__', '__rmul__', '__ror__', '__rpow__', '__rrshift__', '__rshift__', '__rsub__', '__rtruediv__', '__rxor__', '__setattr__', '__setitem__', '__setslice__', '__setstate__', '__sizeof__', '__str__', '__sub__', '__subclasshook__', '__truediv__', '__xor__', 'all', 'any', 'argmax', 'argmin', 'argpartition', 'argsort', 'astype', 'base', 'byteswap', 'choose', 'clip', 'compress', 'conj', 'conjugate', 'copy', 'ctypes', 'cumprod', 'cumsum', 'data', 'diagonal', 'dot', 'dtype', 'dump', 'dumps', 'fill', 'flags', 'flat', 'flatten', 'getfield', 'imag', 'item', 'itemset', 'itemsize', 'max', 'mean', 'min', 'nbytes', 'ndim', 'newbyteorder', 'nonzero', 'partition', 'prod', 'ptp', 'put', 'ravel', 'real', 'repeat', 'reshape', 'resize', 'round', 'searchsorted', 'setfield', 'setflags', 'shape', 'size', 'sort', 'squeeze', 'std', 'strides', 'sum', 'swapaxes', 'take', 'tobytes', 'tofile', 'tolist', 'tostring', 'trace', 'transpose', 'var', 'view']
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<p>Now let's try to use the reshape method to reshape the array!
In general, one can apply a method to an object by using "arrayname dot nameofthemethod".</p>
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<div class=" highlight hl-ipython2"><pre><span class="c"># For example, to rearrange it</span>
<span class="n">a</span> <span class="o">=</span> <span class="n">a</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="mi">3</span><span class="p">,</span><span class="mi">5</span><span class="p">)</span>
<span class="k">print</span> <span class="n">a</span>
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<pre>[[ 0 1 2 3 4]
[ 5 6 7 8 9]
[10 11 12 13 14]]
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<div class=" highlight hl-ipython2"><pre><span class="c"># To find out the shape</span>
<span class="n">a</span><span class="o">.</span><span class="n">shape</span>
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<pre>(3, 5)</pre>
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<div class=" highlight hl-ipython2"><pre><span class="c"># To find out the type of data contained in the array</span>
<span class="n">a</span><span class="o">.</span><span class="n">dtype</span><span class="o">.</span><span class="n">name</span>
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<pre>'int64'</pre>
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<p>As we've seen in the examples, "#" denotes comments in Python, and the line after the # sign will not be executed.</p>
<p>One can also create arrays by specifying the elements.</p>
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<div class=" highlight hl-ipython2"><pre><span class="n">b</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([[</span><span class="mi">4</span><span class="p">,</span><span class="mi">6</span><span class="p">,</span><span class="mi">2</span><span class="p">,</span><span class="mi">6</span><span class="p">],[</span><span class="mi">5</span><span class="p">,</span><span class="mi">7</span><span class="p">,</span><span class="mi">2</span><span class="p">,</span><span class="mi">8</span><span class="p">]])</span>
<span class="k">print</span> <span class="n">b</span>
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<pre>[[4 6 2 6]
[5 7 2 8]]
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<p>Similar to IDL, a function to the array can be broadcasted to every element. So unlike in C and Fortran, one doesn't have to loop through every element.</p>
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<div class=" highlight hl-ipython2"><pre><span class="k">print</span> <span class="n">b</span><span class="o">*</span><span class="mi">2</span>
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<pre>[[ 8 12 4 12]
[10 14 4 16]]
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<div class=" highlight hl-ipython2"><pre><span class="k">print</span> <span class="n">b</span><span class="o">**</span><span class="mi">2</span>
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<pre>[[16 36 4 36]
[25 49 4 64]]
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<p>To slice the array or access individual elements, one can select by location just as in IDL, and the index start from 0 as well.</p>
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<div class=" highlight hl-ipython2"><pre><span class="k">print</span> <span class="n">b</span><span class="p">[</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">:</span><span class="mi">2</span><span class="p">]</span>
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<pre>[4 6]
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<p>":" means everything, just like "*" in IDL.</p>
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<div class=" highlight hl-ipython2"><pre><span class="k">print</span> <span class="n">b</span><span class="p">[</span><span class="mi">0</span><span class="p">,:]</span>
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<pre>[4 6 2 6]
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<h3 id="4.-Control-Structure">4. Control Structure<a class="anchor-link" href="#4.-Control-Structure">¶</a></h3>
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<li>The if statement in Python looks like:</li>
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<div class=" highlight hl-ipython2"><pre><span class="n">x</span> <span class="o">=</span> <span class="mi">3</span>
<span class="k">if</span> <span class="n">x</span> <span class="o"><</span> <span class="mi">0</span><span class="p">:</span>
<span class="k">print</span> <span class="s">'x is negative!'</span>
<span class="k">elif</span> <span class="n">x</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="k">print</span> <span class="s">'x is zero!'</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">print</span> <span class="s">'x is positive!'</span>
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<pre>x is positive!
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<p>Note that the begining and end of the statement is marked by indentation, and there is the ":" after each control statement.</p>
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<li>A for loop looks like this in Python:</li>
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<div class=" highlight hl-ipython2"><pre><span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">10</span><span class="p">):</span>
<span class="k">print</span> <span class="n">i</span>
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<pre>0
1
2
3
4
5
6
7
8
9
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<div class=" highlight hl-ipython2"><pre><span class="n">words</span> <span class="o">=</span> <span class="p">[</span><span class="s">'cat'</span><span class="p">,</span> <span class="s">'window'</span><span class="p">,</span> <span class="s">'defenestrate'</span><span class="p">]</span>
<span class="k">for</span> <span class="n">w</span> <span class="ow">in</span> <span class="n">words</span><span class="p">:</span>
<span class="k">print</span> <span class="n">w</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">w</span><span class="p">)</span>
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<pre>cat 3
window 6
defenestrate 12
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<h3 id="5.-User-defined-functions">5. User defined functions<a class="anchor-link" href="#5.-User-defined-functions">¶</a></h3>
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<h4 id="Example-1:-define-a-function-to-print-out-the-user's-name-and-age-in-a-nice-format">Example 1: define a function to print out the user's name and age in a nice format<a class="anchor-link" href="#Example-1:-define-a-function-to-print-out-the-user's-name-and-age-in-a-nice-format">¶</a></h4>
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<div class=" highlight hl-ipython2"><pre><span class="k">def</span> <span class="nf">printinfo</span><span class="p">(</span> <span class="n">name</span><span class="p">,</span> <span class="n">age</span> <span class="p">):</span>
<span class="s">"This prints a passed info into this function"</span>
<span class="k">print</span> <span class="s">"Name: "</span><span class="p">,</span> <span class="n">name</span>
<span class="k">print</span> <span class="s">"Age: "</span><span class="p">,</span> <span class="n">age</span>
<span class="k">return</span>
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<p>Now we can call printinfo function:</p>
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<div class=" highlight hl-ipython2"><pre><span class="n">printinfo</span><span class="p">(</span> <span class="s">"Eva"</span><span class="p">,</span> <span class="mi">22</span> <span class="p">)</span>
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<pre>Name: Eva
Age: 22
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<p>One can specify variable names, and put them in arbitrary order:</p>
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<div class=" highlight hl-ipython2"><pre><span class="n">printinfo</span><span class="p">(</span> <span class="n">age</span><span class="o">=</span> <span class="mi">18</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="s">"Tom"</span> <span class="p">)</span>
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<pre>Name: Tom
Age: 18
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<h4 id="Example-2:-Apply-the-same-function-to-all-array-elements">Example 2: Apply the same function to all array elements<a class="anchor-link" href="#Example-2:-Apply-the-same-function-to-all-array-elements">¶</a></h4>
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<div class=" highlight hl-ipython2"><pre><span class="k">def</span> <span class="nf">addminus</span><span class="p">(</span><span class="n">a</span><span class="p">,</span><span class="n">b</span><span class="p">):</span>
<span class="k">if</span> <span class="n">a</span> <span class="o">></span> <span class="n">b</span><span class="p">:</span>
<span class="k">return</span> <span class="n">a</span> <span class="o">-</span> <span class="n">b</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="n">a</span> <span class="o">+</span> <span class="n">b</span>
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<p>A function can be very useful when we want to apply the same procedure again and again:</p>
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<div class=" highlight hl-ipython2"><pre><span class="n">a</span> <span class="o">=</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span><span class="mi">3</span><span class="p">,</span><span class="mi">6</span><span class="p">,</span><span class="mi">9</span><span class="p">]</span>
<span class="n">b</span> <span class="o">=</span> <span class="p">[</span><span class="mi">1</span><span class="p">,</span><span class="mi">3</span><span class="p">,</span><span class="mi">5</span><span class="p">,</span><span class="mi">7</span><span class="p">]</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">4</span><span class="p">):</span>
<span class="k">print</span> <span class="s">'a= '</span><span class="p">,</span> <span class="n">a</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="s">', b= '</span><span class="p">,</span> <span class="n">b</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="s">', result= '</span><span class="p">,</span> <span class="n">addminus</span><span class="p">(</span><span class="n">a</span><span class="p">[</span><span class="n">i</span><span class="p">],</span><span class="n">b</span><span class="p">[</span><span class="n">i</span><span class="p">])</span>
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<pre>a= 0 , b= 1 , result= 1
a= 3 , b= 3 , result= 6
a= 6 , b= 5 , result= 1
a= 9 , b= 7 , result= 2
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<h3 id="6.-Basic-plotting">6. Basic plotting<a class="anchor-link" href="#6.-Basic-plotting">¶</a></h3>
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<h4 id="Example-1:-A-simple-scatter-plot-of-the-data-above:">Example 1: A simple scatter plot of the data above:<a class="anchor-link" href="#Example-1:-A-simple-scatter-plot-of-the-data-above:">¶</a></h4>
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<div class=" highlight hl-ipython2"><pre><span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="kn">as</span> <span class="nn">plt</span>
<span class="o">%</span><span class="k">matplotlib</span> inline
<span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">a</span><span class="p">,</span><span class="n">b</span><span class="p">,</span><span class="s">'o'</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">xlabel</span><span class="p">(</span><span class="s">'a'</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">ylabel</span><span class="p">(</span><span class="s">'b'</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">title</span><span class="p">(</span><span class="s">'A simple scatter plot'</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">axis</span><span class="p">([</span><span class="o">-</span><span class="mi">2</span><span class="p">,</span><span class="mi">12</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">10</span><span class="p">])</span> <span class="c">#set the range of axis</span>
<span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
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