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.highlight .hll { background-color: #ffffcc }
.highlight { background: #f8f8f8; }
.highlight .c { color: #408080; font-style: italic } /* Comment */
.highlight .err { border: 1px solid #FF0000 } /* Error */
.highlight .k { color: #008000; font-weight: bold } /* Keyword */
.highlight .o { color: #666666 } /* Operator */
.highlight .cm { color: #408080; font-style: italic } /* Comment.Multiline */
.highlight .cp { color: #BC7A00 } /* Comment.Preproc */
.highlight .c1 { color: #408080; font-style: italic } /* Comment.Single */
.highlight .cs { color: #408080; font-style: italic } /* Comment.Special */
.highlight .gd { color: #A00000 } /* Generic.Deleted */
.highlight .ge { font-style: italic } /* Generic.Emph */
.highlight .gr { color: #FF0000 } /* Generic.Error */
.highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */
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.highlight .go { color: #888888 } /* Generic.Output */
.highlight .gp { color: #000080; font-weight: bold } /* Generic.Prompt */
.highlight .gs { font-weight: bold } /* Generic.Strong */
.highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */
.highlight .gt { color: #0044DD } /* Generic.Traceback */
.highlight .kc { color: #008000; font-weight: bold } /* Keyword.Constant */
.highlight .kd { color: #008000; font-weight: bold } /* Keyword.Declaration */
.highlight .kn { color: #008000; font-weight: bold } /* Keyword.Namespace */
.highlight .kp { color: #008000 } /* Keyword.Pseudo */
.highlight .kr { color: #008000; font-weight: bold } /* Keyword.Reserved */
.highlight .kt { color: #B00040 } /* Keyword.Type */
.highlight .m { color: #666666 } /* Literal.Number */
.highlight .s { color: #BA2121 } /* Literal.String */
.highlight .na { color: #7D9029 } /* Name.Attribute */
.highlight .nb { color: #008000 } /* Name.Builtin */
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.highlight .ni { color: #999999; font-weight: bold } /* Name.Entity */
.highlight .ne { color: #D2413A; font-weight: bold } /* Name.Exception */
.highlight .nf { color: #0000FF } /* Name.Function */
.highlight .nl { color: #A0A000 } /* Name.Label */
.highlight .nn { color: #0000FF; font-weight: bold } /* Name.Namespace */
.highlight .nt { color: #008000; font-weight: bold } /* Name.Tag */
.highlight .nv { color: #19177C } /* Name.Variable */
.highlight .ow { color: #AA22FF; font-weight: bold } /* Operator.Word */
.highlight .w { color: #bbbbbb } /* Text.Whitespace */
.highlight .mb { color: #666666 } /* Literal.Number.Bin */
.highlight .mf { color: #666666 } /* Literal.Number.Float */
.highlight .mh { color: #666666 } /* Literal.Number.Hex */
.highlight .mi { color: #666666 } /* Literal.Number.Integer */
.highlight .mo { color: #666666 } /* Literal.Number.Oct */
.highlight .sb { color: #BA2121 } /* Literal.String.Backtick */
.highlight .sc { color: #BA2121 } /* Literal.String.Char */
.highlight .sd { color: #BA2121; font-style: italic } /* Literal.String.Doc */
.highlight .s2 { color: #BA2121 } /* Literal.String.Double */
.highlight .se { color: #BB6622; font-weight: bold } /* Literal.String.Escape */
.highlight .sh { color: #BA2121 } /* Literal.String.Heredoc */
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</style>
<style type="text/css">
/* Overrides of notebook CSS for static HTML export */
body {
overflow: visible;
padding: 8px;
}
div#notebook {
overflow: visible;
border-top: none;
}
@media print {
div.cell {
display: block;
page-break-inside: avoid;
}
div.output_wrapper {
display: block;
page-break-inside: avoid;
}
div.output {
display: block;
page-break-inside: avoid;
}
}
</style>
<!-- Custom stylesheet, it must be in the same directory as the html file -->
<link rel="stylesheet" href="custom.css">
<!-- Loading mathjax macro -->
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<script src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS_HTML"></script>
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<script type="text/x-mathjax-config">
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tex2jax: {
inlineMath: [ ['$','$'], ["\\(","\\)"] ],
displayMath: [ ['$$','$$'], ["\\[","\\]"] ],
processEscapes: true,
processEnvironments: true
},
// Center justify equations in code and markdown cells. Elsewhere
// we use CSS to left justify single line equations in code cells.
displayAlign: 'center',
"HTML-CSS": {
styles: {'.MathJax_Display': {"margin": 0}},
linebreaks: { automatic: true }
}
});
</script>
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</head>
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<div class=" highlight hl-ipython2"><pre><span class="o">%</span><span class="k">load_ext</span> load_style
<span class="o">%</span><span class="k">load_style</span> talk.css
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<h2 id="Overview-of-the-IPython-notebook">Overview of the IPython notebook<a class="anchor-link" href="#Overview-of-the-IPython-notebook">¶</a></h2>
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<div class=" highlight hl-ipython2"><pre><span class="kn">import</span> <span class="nn">addutils.toc</span> <span class="p">;</span> <span class="n">addutils</span><span class="o">.</span><span class="n">toc</span><span class="o">.</span><span class="n">js</span><span class="p">(</span><span class="n">ipy_notebook</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
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<div class=" highlight hl-ipython2"><pre><span class="kn">from</span> <span class="nn">IPython.display</span> <span class="kn">import</span> <span class="n">display</span><span class="p">,</span> <span class="n">HTML</span>
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<p>Python ships with a basic interactive interpreter ... not much fun here</p>
<div align="center">
<img src="images/python_console.png" width="700">
</div>
<p><a href="www.ipython.org">IPython</a> is an enhanced interactive interpreter, developped for scientific development, adding e.g. history, tab-completion, interactive help, and lots and lots of goodies:</p>
<div align="center">
<img src="images/ipython_console.png" width="700">
</div>
<p>The <a href="http://ipython.org/ipython-doc/2/interactive/qtconsole.html">IPython qtconsole</a> provides a number of enhancements only possible in a GUI, such as inline figures, proper multiline editing with syntax highlighting, graphical calltips, and much more. To lauch it:</p>
<pre><code>$ ipython qtconsole</code></pre>
<div align="center">
<img src="images/qtconsole.png" width="700">
</div>
<hr>
<p>Since 2005, the IPython development team has introduced the <strong>IPython notebook</strong>. This is a web application, running in the browser, that is connected to a Python kernel running in the background.</p>
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<div class=" highlight hl-ipython2"><pre><span class="kn">from</span> <span class="nn">IPython.display</span> <span class="kn">import</span> <span class="n">HTML</span>
<span class="n">HTML</span><span class="p">(</span><span class="s">'<iframe src=http://ipython.org/notebook.html width=900 height=350></iframe>'</span><span class="p">)</span>
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<p>in 2014, at the Scipy 2014 conference, the IPython development team announced the split of the project
into <a href="https://jupyter.org/">Project Jupyter</a> (all the language-agnostic components of the notebook) and IPython
(the Python language specific component, including the interactive prompt and the qtconsole)</p>
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<p>It behaves as an <strong>interactive notebook</strong>, in which you can weave Python code and outputs, figures generated from Python / matplotlib, images (either local and remote), websites, videos and richly formatted comments using <a href="wikipedia/markdown">markdown</a>, which is a superset of HTML with a very simple syntax (see <a href="www.markdown.com">here</a> for more)</p>
<p>It is structured into executable cells, into which by default you can run arbitrary python code</p>
<p>It has a sophisticated tab completion and help system</p>
<p>The power of IPython comes in part because of its numerous extensions and <em>magic</em> functions</p>
<p>And finally you can <em>export</em> a notebook in different formats, including HTML and Latex (and PDF).</p>
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<p>Recently the IPython notebook as been featured in the <strong>toolbox</strong> section of <a href="http://www.nature.com">Nature</a></p>
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<div class=" highlight hl-ipython2"><pre><span class="kn">from</span> <span class="nn">IPython.display</span> <span class="kn">import</span> <span class="n">HTML</span>
<span class="n">HTML</span><span class="p">(</span><span class="s">'<iframe src=http://www.nature.com/news/interactive-notebooks-sharing-the-code-1.16261 width=900 height=350></iframe>'</span><span class="p">)</span>
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<h2 id="Using-the-IPython-notebook">Using the IPython notebook<a class="anchor-link" href="#Using-the-IPython-notebook">¶</a></h2>
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<p>To start an IPython notebook session open a command prompt, navigate to a desired working directory then issue the following command:</p>
<p><code>$ ipython notebook</code></p>
<p>A new window open in your browser where you can open an existing notebook or start a new one.</p>
<p>it should look like</p>
<div align="center">
<img src="images/ipython_dashboard.png" width="800">
</div>
<p>Notebooks are organized with cells. You may have a code cell for inputing commands followed by its result cell which contains the output of the code. You may also have a text cell, such as this one you're reading right now. Cell type can be changed in the above dropdown menu.</p>
<p>There is the menubar above for navigating a notebook but you will find the following shortcuts helpful:</p>
<ul>
<li><code>Enter</code> : Enter the edit mode of a cell</li>
<li><code>Esc</code> : Leave the edit mode and get into the <em>control</em> mode (see icons on the right of the menu bar)</li>
<li><code>Shift + Enter</code> : Execute cell and advance to next cell</li>
<li><code>Alt + Enter</code> : Execute cell and insert an empty cell below</li>
<li><code>Ctrl + Enter</code> : Execute cell in place (do not advance to the next cell)</li>
<li>Press <code>esc</code> (command mode) then <code>h</code> to display keyboard shortcuts</li>
</ul>
<p>At times you might run code that gets stuck in an infinite loop or simply you want to clear all your workspace variables and start over. To do that you can do:</p>
<p><code>Kernel -> Interrupt</code></p>
<p><code>Kernel -> Restart</code></p>
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<div class=" highlight hl-ipython2"><pre><span class="c">### This is a code cell, containing python code, it is executed by <shift>-<enter> or <alt>-<enter></span>
<span class="k">def</span> <span class="nf">func</span><span class="p">(</span><span class="n">x</span><span class="p">):</span>
<span class="k">return</span> <span class="n">x</span><span class="o">**</span><span class="mi">3</span>
<span class="p">[</span><span class="n">func</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="nb">xrange</span><span class="p">(</span><span class="mi">10</span><span class="p">)]</span>
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<h3 id="Getting-help">Getting help<a class="anchor-link" href="#Getting-help">¶</a></h3>
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<p>IPython has a sophisticated help and tab completion system, which allows <strong>introspection</strong>: i.e.
If you want details regarding the properties and functionality of any Python objects currently loaded into IPython, you can use the <code>?</code> to reveal any details that are available:</p>
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<div class=" highlight hl-ipython2"><pre><span class="n">some_dict</span> <span class="o">=</span> <span class="p">{}</span>
<span class="n">some_dict</span><span class="o">?</span>
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<div class=" highlight hl-ipython2"><pre><span class="kn">from</span> <span class="nn">numpy</span> <span class="kn">import</span> <span class="n">random</span>
<span class="n">random</span><span class="o">.</span><span class="n">randn</span><span class="o">?</span>
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<div class=" highlight hl-ipython2"><pre><span class="kn">import</span> <span class="nn">numpy</span>
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<div class=" highlight hl-ipython2"><pre><span class="n">help</span><span class="p">(</span><span class="n">numpy</span><span class="o">.</span><span class="n">random</span><span class="p">)</span>
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<h3 id="Tab-completion">Tab completion<a class="anchor-link" href="#Tab-completion">¶</a></h3>
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<p>Because IPython allows for introspection, it is able to afford the user the ability to tab-complete commands or objects that have been partially typed. This is done by pressing the <code><tab></code> key at any point during the process of typing a command:</p>
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<div class=" highlight hl-ipython2"><pre><span class="n">listA</span> <span class="o">=</span> <span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mf">2.</span><span class="p">,</span> <span class="s">'sentence'</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span><span class="mi">2</span><span class="p">),</span> <span class="p">{</span><span class="s">'answer'</span><span class="p">:</span> <span class="mi">42</span><span class="p">}]</span> <span class="c"># here I construct a LIST containing different items</span>
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<div class=" highlight hl-ipython2"><pre><span class="n">listA</span><span class="o">.</span><span class="n">count</span><span class="o">?</span>
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<div class=" highlight hl-ipython2"><pre><span class="n">listA</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
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<h3 id="including-markdown-comments">including markdown comments<a class="anchor-link" href="#including-markdown-comments">¶</a></h3>
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<p><strong>see <a href="http://daringfireball.net/projects/markdown/">markdown</a></strong></p>
<p>Using markdown cells, you can insert formatted comments, observations ... directly in between executable code and outputs ...</p>
<p>To toggle from <em>code cell</em> (the default) to <em>markdown cell</em>, you can use the toolbar, or <code><ctrl>-<m> + <m></code> (<code><command>-<m> + <m></code> on Macs)</p>
<p>You can <em>italicize</em>, <strong>boldface</strong></p>
<ul>
<li><p>build</p>
</li>
<li><p>lists</p>
</li>
</ul>
<ol>
<li><p>enumerate</p>
</li>
<li><p>stuff</p>
</li>
</ol>
<p>and embed <font color='red'>syntax</font> highlighted code meant for illustration instead of execution in Python:</p>
<div class="highlight"><pre><span class="k">print</span><span class="p">(</span><span class="s">'hello'</span><span class="p">)</span>
</pre></div>
<div class="highlight"><pre><span class="k">def</span> <span class="nf">f</span><span class="p">(</span><span class="n">x</span><span class="p">):</span>
<span class="sd">"""a docstring"""</span>
<span class="k">return</span> <span class="n">x</span><span class="o">**</span><span class="mi">2</span>
</pre></div>
<p>or other languages:</p>
<div class="highlight"><pre><span class="cm">/* Fibonacci Series c language */</span>
<span class="cp">#include<stdio.h></span>
<span class="kt">int</span> <span class="nf">main</span><span class="p">()</span>
<span class="p">{</span>
<span class="kt">int</span> <span class="n">n</span><span class="p">,</span> <span class="n">first</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span> <span class="n">second</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span> <span class="n">next</span><span class="p">,</span> <span class="n">c</span><span class="p">;</span>
<span class="n">printf</span><span class="p">(</span><span class="s">"Enter the number of terms</span><span class="se">\n</span><span class="s">"</span><span class="p">);</span>
<span class="n">scanf</span><span class="p">(</span><span class="s">"%d"</span><span class="p">,</span><span class="o">&</span><span class="n">n</span><span class="p">);</span>
<span class="n">printf</span><span class="p">(</span><span class="s">"First %d terms of Fibonacci series are :-</span><span class="se">\n</span><span class="s">"</span><span class="p">,</span><span class="n">n</span><span class="p">);</span>
<span class="k">for</span> <span class="p">(</span> <span class="n">c</span> <span class="o">=</span> <span class="mi">0</span> <span class="p">;</span> <span class="n">c</span> <span class="o"><</span> <span class="n">n</span> <span class="p">;</span> <span class="n">c</span><span class="o">++</span> <span class="p">)</span>
<span class="p">{</span>
<span class="k">if</span> <span class="p">(</span> <span class="n">c</span> <span class="o"><=</span> <span class="mi">1</span> <span class="p">)</span>
<span class="n">next</span> <span class="o">=</span> <span class="n">c</span><span class="p">;</span>
<span class="k">else</span>
<span class="p">{</span>
<span class="n">next</span> <span class="o">=</span> <span class="n">first</span> <span class="o">+</span> <span class="n">second</span><span class="p">;</span>
<span class="n">first</span> <span class="o">=</span> <span class="n">second</span><span class="p">;</span>
<span class="n">second</span> <span class="o">=</span> <span class="n">next</span><span class="p">;</span>
<span class="p">}</span>
<span class="n">printf</span><span class="p">(</span><span class="s">"%d</span><span class="se">\n</span><span class="s">"</span><span class="p">,</span><span class="n">next</span><span class="p">);</span>
<span class="p">}</span>
<span class="k">return</span> <span class="mi">0</span><span class="p">;</span>
<span class="p">}</span>
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<p>You can insert images seemlessly into a Markdown cell, but if it is local instead of on the web, it needs to reside in an <strong>images</strong> folder in the <strong>same directory as your notebook</strong>.</p>
<p>The syntax is then</p>
<pre><code>
</code></pre>
<p>e.g.</p>
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<p>Thanks to <a href="www.wikipedia/mathjax">MathJax</a>, you can include mathematical expressions in a markdown cell using Latex syntax both inline and displayed:</p>
<ul>
<li><p>inline: <code>$ Latex expression here $</code></p>
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<li><p>displayed: <code>$$ Latex expression here $$</code></p>
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<p>For example <code>$e^{i\pi} + 1 = 0$</code> becomes $e^{i\pi} + 1 = 0$</p>
<p>and</p>
<p><code>$$e^x=\sum_{i=0}^\infty \frac{1}{i!}x^i$$</code></p>
<p>becomes:</p>
$$e^x=\sum_{i=0}^\infty \frac{1}{i!}x^i$$<p>Mathjax is a JavaScript library, and by default IPython uses the online version, from the <a href="http://cdn.mathjax.org/">Mathjax Content Distribution Network</a> (CDN), if you want to be able to use it <strong>offline</strong>, you need to install MathJax locally by running that (once and for all) in a code cell:</p>
<div class="highlight"><pre><span class="kn">from</span> <span class="nn">IPython.external.mathjax</span> <span class="kn">import</span> <span class="n">install_mathjax</span>
<span class="n">install_mathjax</span><span class="p">()</span>
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<h3 id="The-IPython-notebook-rich-display-system">The IPython notebook rich display system<a class="anchor-link" href="#The-IPython-notebook-rich-display-system">¶</a></h3>
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<div class=" highlight hl-ipython2"><pre><span class="kn">from</span> <span class="nn">IPython.display</span> <span class="kn">import</span> <span class="n">Image</span><span class="p">,</span> <span class="n">YouTubeVideo</span><span class="p">,</span> <span class="n">HTML</span>
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<div class=" highlight hl-ipython2"><pre><span class="c">### that will display a frame with specified width and height ... </span>
<span class="kn">from</span> <span class="nn">IPython.display</span> <span class="kn">import</span> <span class="n">HTML</span>
<span class="n">HTML</span><span class="p">(</span><span class="s">'<iframe src="http://numpy.org/" height=300 width=800>'</span>
<span class="s">'</iframe>'</span><span class="p">)</span>
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<div class=" highlight hl-ipython2"><pre><span class="c">### This inserts an image in the output cell</span>
<span class="n">Image</span><span class="p">(</span><span class="n">filename</span><span class="o">=</span><span class="s">'images/lost_wormhole.jpg'</span><span class="p">,</span><span class="n">width</span><span class="o">=</span><span class="mi">500</span><span class="p">)</span>
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<div class=" highlight hl-ipython2"><pre><span class="c">### This embeds a video from YouTube</span>
<span class="c">### You can embed Vimeo videos by calling from IPython.display import VimeoVideo</span>
<span class="c"># Fernando Pérez at PyConCA, here I start at 30 minutes </span>
<span class="n">YouTubeVideo</span><span class="p">(</span><span class="s">'F4rFuIb1Ie4'</span><span class="p">,</span> <span class="n">start</span> <span class="o">=</span> <span class="mi">30</span><span class="o">*</span><span class="mi">60</span><span class="p">)</span>
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<div class=" highlight hl-ipython2"><pre><span class="c">### You can also embed a LOCAL video in the notebook, but have to encode it: Not sure it will work </span>
<span class="c">### on Windows ...</span>
<span class="kn">import</span> <span class="nn">io</span>
<span class="kn">import</span> <span class="nn">base64</span>
<span class="n">filename</span> <span class="o">=</span> <span class="s">'../data/Monty_Python.mp4'</span>
<span class="n">video</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="s">'r+b'</span><span class="p">)</span><span class="o">.</span><span class="n">read</span><span class="p">()</span>
<span class="n">encoded</span> <span class="o">=</span> <span class="n">base64</span><span class="o">.</span><span class="n">b64encode</span><span class="p">(</span><span class="n">video</span><span class="p">)</span>
<span class="n">HTML</span><span class="p">(</span><span class="n">data</span><span class="o">=</span><span class="s">'''<video alt="A witch!" controls></span>
<span class="s"> <source src="data:video/mp4;base64,{0}" type="video/mp4" /></span>
<span class="s"> </video>'''</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">encoded</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s">'ascii'</span><span class="p">)))</span>
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<h3 id="Inline-plots-with-matplotlib">Inline plots with matplotlib<a class="anchor-link" href="#Inline-plots-with-matplotlib">¶</a></h3>
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<p>That is one of the most appealing aspect of the IPython notebook: the graphic outputs of some Python code can be displayed directly in the notebook, there is in particular great integration with the
Python plotting library <a href="http://www.matplotlib.org">Matplotlib</a> via the <code>%matplotlib inline</code> magic command</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>
<span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="kn">as</span> <span class="nn">plt</span>
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<div class=" highlight hl-ipython2"><pre><span class="n">t</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="o">*</span><span class="n">np</span><span class="o">.</span><span class="n">pi</span><span class="p">,</span> <span class="mi">100</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">sin</span><span class="p">(</span><span class="n">t</span><span class="p">))</span>
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<div class=" highlight hl-ipython2"><pre><span class="c"># you can also choose to display figure OUTSIDE the notebook</span>
<span class="c"># the available backends are [inline|qt|osx|gtx] ... For Windows try qt</span>
<span class="o">%</span><span class="k">matplotlib</span> osx
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<div class=" highlight hl-ipython2"><pre><span class="n">t</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="o">*</span><span class="n">np</span><span class="o">.</span><span class="n">pi</span><span class="p">,</span> <span class="mi">100</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">sin</span><span class="p">(</span><span class="n">t</span><span class="p">))</span>
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<p>from version 1.4 of Matplotlib, a special interactive backend for the IPython notebook is available</p>
<p>You need to restart the kernel and then run the following cell for it to work</p>
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<div class=" highlight hl-ipython2"><pre><span class="kn">import</span> <span class="nn">matplotlib</span>
<span class="n">matplotlib</span><span class="o">.</span><span class="n">use</span><span class="p">(</span><span class="s">'nbagg'</span><span class="p">)</span>
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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>
<span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="kn">as</span> <span class="nn">plt</span>
<span class="n">t</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="o">*</span><span class="n">np</span><span class="o">.</span><span class="n">pi</span><span class="p">,</span> <span class="mi">100</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">sin</span><span class="p">(</span><span class="n">t</span><span class="p">))</span>
<span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
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<p>restart the Kernel and go back to inline display</p>
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<div class=" highlight hl-ipython2"><pre><span class="o">%</span><span class="k">matplotlib</span> inline
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<h3 id="Some-useful-magic-commands-in-IPython">Some useful magic commands in IPython<a class="anchor-link" href="#Some-useful-magic-commands-in-IPython">¶</a></h3>
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<div class=" highlight hl-ipython2"><pre><span class="c"># for a list of available magic command </span>
<span class="o">%</span><span class="k">lsmagic</span>
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<p>For example</p>
<pre><code>%whos
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<p>list all variables (incl. classes, functions, etc) in the <strong>namespace</strong></p>
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<h3 id="Writing-the-content-of-a-cell-to-file">Writing the content of a cell to file<a class="anchor-link" href="#Writing-the-content-of-a-cell-to-file">¶</a></h3>
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<div class=" highlight hl-ipython2"><pre><span class="o">%%</span><span class="k">writefile</span> tmp.py
#!/Users/nicolasf/anaconda/bin/python
import numpy as np
print('Hello world')
a = np.arange(10) ### will be available in the namespace
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<h3 id="Running-some-external-python-script-(local-or-online)">Running some external python script (local or online)<a class="anchor-link" href="#Running-some-external-python-script-(local-or-online)">¶</a></h3>
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<div class=" highlight hl-ipython2"><pre><span class="o">%</span><span class="k">run</span> tmp.py
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<h3 id="Loading-the-content-of-some-local-python-script">Loading the content of some local python script<a class="anchor-link" href="#Loading-the-content-of-some-local-python-script">¶</a></h3>
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<p>you can load actually anything, e.g. a Markdown file</p>
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<div class=" highlight hl-ipython2"><pre><span class="c"># %load tmp.py</span>
<span class="c">#!/Users/nicolasf/anaconda/bin/python </span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="kn">as</span> <span class="nn">np</span>
<span class="k">print</span><span class="p">(</span><span class="s">'Hello world'</span><span class="p">)</span>
<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">10</span><span class="p">)</span> <span class="c">### will be available in the namespace </span>
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<p>works as well for scripts available online</p>
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<div class=" highlight hl-ipython2"><pre><span class="c"># %load http://matplotlib.org/mpl_examples/images_contours_and_fields/streamplot_demo_features.py</span>
<span class="sd">"""</span>
<span class="sd">Demo of the `streamplot` function.</span>
<span class="sd">A streamplot, or streamline plot, is used to display 2D vector fields. This</span>
<span class="sd">example shows a few features of the stream plot function:</span>
<span class="sd"> * Varying the color along a streamline.</span>
<span class="sd"> * Varying the density of streamlines.</span>
<span class="sd"> * Varying the line width along a stream line.</span>
<span class="sd">"""</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="kn">as</span> <span class="nn">np</span>
<span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="kn">as</span> <span class="nn">plt</span>
<span class="n">Y</span><span class="p">,</span> <span class="n">X</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">mgrid</span><span class="p">[</span><span class="o">-</span><span class="mi">3</span><span class="p">:</span><span class="mi">3</span><span class="p">:</span><span class="mi">100j</span><span class="p">,</span> <span class="o">-</span><span class="mi">3</span><span class="p">:</span><span class="mi">3</span><span class="p">:</span><span class="mi">100j</span><span class="p">]</span>
<span class="n">U</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span> <span class="o">-</span> <span class="n">X</span><span class="o">**</span><span class="mi">2</span> <span class="o">+</span> <span class="n">Y</span>
<span class="n">V</span> <span class="o">=</span> <span class="mi">1</span> <span class="o">+</span> <span class="n">X</span> <span class="o">-</span> <span class="n">Y</span><span class="o">**</span><span class="mi">2</span>
<span class="n">speed</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">U</span><span class="o">*</span><span class="n">U</span> <span class="o">+</span> <span class="n">V</span><span class="o">*</span><span class="n">V</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">streamplot</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">Y</span><span class="p">,</span> <span class="n">U</span><span class="p">,</span> <span class="n">V</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="n">U</span><span class="p">,</span> <span class="n">linewidth</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">cmap</span><span class="o">=</span><span class="n">plt</span><span class="o">.</span><span class="n">cm</span><span class="o">.</span><span class="n">autumn</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">colorbar</span><span class="p">()</span>
<span class="n">f</span><span class="p">,</span> <span class="p">(</span><span class="n">ax1</span><span class="p">,</span> <span class="n">ax2</span><span class="p">)</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">subplots</span><span class="p">(</span><span class="n">ncols</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span>
<span class="n">ax1</span><span class="o">.</span><span class="n">streamplot</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">Y</span><span class="p">,</span> <span class="n">U</span><span class="p">,</span> <span class="n">V</span><span class="p">,</span> <span class="n">density</span><span class="o">=</span><span class="p">[</span><span class="mf">0.5</span><span class="p">,</span> <span class="mi">1</span><span class="p">])</span>
<span class="n">lw</span> <span class="o">=</span> <span class="mi">5</span><span class="o">*</span><span class="n">speed</span><span class="o">/</span><span class="n">speed</span><span class="o">.</span><span class="n">max</span><span class="p">()</span>
<span class="n">ax2</span><span class="o">.</span><span class="n">streamplot</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">Y</span><span class="p">,</span> <span class="n">U</span><span class="p">,</span> <span class="n">V</span><span class="p">,</span> <span class="n">density</span><span class="o">=</span><span class="mf">0.6</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="s">'k'</span><span class="p">,</span> <span class="n">linewidth</span><span class="o">=</span><span class="n">lw</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
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<h3 id="Interacting-with-the-OS:-the-IPython-notebook-as-an-enhanced-shell">Interacting with the OS: the IPython notebook as an enhanced shell<a class="anchor-link" href="#Interacting-with-the-OS:-the-IPython-notebook-as-an-enhanced-shell">¶</a></h3>
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<div class=" highlight hl-ipython2"><pre><span class="o">!</span>rm tmp.py ### ! escapes to the OS <span class="o">(</span>!del tmp.py on windows<span class="o">)</span>
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<div class=" highlight hl-ipython2"><pre><span class="o">!</span>ls *.py
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<div class=" highlight hl-ipython2"><pre><span class="n">notebooks</span> <span class="o">=</span> <span class="o">!</span>ls *.ipynb ### notebooks is a python list ... not sure how to use wildcards on Windows
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<div class=" highlight hl-ipython2"><pre><span class="n">notebooks</span>
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<p>And if you need to actually quickly put together and run a bash script (linux / Mac), you don't need to escape the IPython notebook thanks to the</p>
<pre><code>%%bash
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<p>cell magic ...</p>
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<div class=" highlight hl-ipython2"><pre>%%bash
<span class="c"># Substitutes underscores for blanks in all the filenames in a directory.</span>
<span class="nv">ONE</span><span class="o">=</span><span class="m">1</span> <span class="c"># For getting singular/plural right (see below).</span>
<span class="nv">number</span><span class="o">=</span><span class="m">0</span> <span class="c"># Keeps track of how many files actually renamed.</span>
<span class="nv">FOUND</span><span class="o">=</span><span class="m">0</span> <span class="c"># Successful return value.</span>
<span class="k">for</span> filename in * <span class="c"># Traverses all files in directory.</span>
<span class="k">do</span>
<span class="nb">echo</span> <span class="s2">"</span><span class="nv">$filename</span><span class="s2">"</span> <span class="p">|</span> grep -q <span class="s2">" "</span> <span class="c"># Checks whether filename</span>
<span class="k">if</span> <span class="o">[</span> <span class="nv">$?</span> -eq <span class="nv">$FOUND</span> <span class="o">]</span> <span class="c"># contains space(s).</span>
<span class="k">then</span>
<span class="nv">fname</span><span class="o">=</span><span class="nv">$filename</span> <span class="c"># Strips off path.</span>
<span class="nv">n</span><span class="o">=</span><span class="sb">`</span><span class="nb">echo</span> <span class="nv">$fname</span> <span class="p">|</span> sed -e <span class="s2">"s/ /_/g"</span><span class="sb">`</span> <span class="c"># Substitutes underscore for blank.</span>
mv <span class="s2">"</span><span class="nv">$fname</span><span class="s2">"</span> <span class="s2">"</span><span class="nv">$n</span><span class="s2">"</span> <span class="c"># Do the actual renaming.</span>
<span class="nb">let</span> <span class="s2">"number += 1"</span>
<span class="k">fi</span>
<span class="k">done</span>
<span class="k">if</span> <span class="o">[</span> <span class="s2">"</span><span class="nv">$number</span><span class="s2">"</span> -eq <span class="s2">"</span><span class="nv">$ONE</span><span class="s2">"</span> <span class="o">]</span> <span class="c"># For correct grammar.</span>
<span class="k">then</span>
<span class="nb">echo</span> <span class="s2">"</span><span class="nv">$number</span><span class="s2"> file renamed."</span>
<span class="k">else</span>
<span class="nb">echo</span> <span class="s2">"</span><span class="nv">$number</span><span class="s2"> files renamed."</span>
<span class="k">fi</span>
<span class="nb">exit </span>0
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<h3 id="Exporting-your-notebook-in-other-formats">Exporting your notebook in other formats<a class="anchor-link" href="#Exporting-your-notebook-in-other-formats">¶</a></h3>
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<p>A notebook (extension .ipynb) is actually just a <a href="http://en.wikipedia.org/wiki/JSON">JSON</a> file, using built-in converters you can
convert a notebook into a variety of formats for sharing, illustration, publishing, etc.</p>
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<div class=" highlight hl-ipython2"><pre><span class="c">#!ipython nbconvert --help</span>
<span class="o">!</span>ipython nbconvert --help
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<div class=" highlight hl-ipython2"><pre><span class="n">name</span> <span class="o">=</span> <span class="s">'IPython_notebook'</span>
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<div class=" highlight hl-ipython2"><pre><span class="o">!</span>ipython nbconvert <span class="o">{</span>name<span class="o">}</span>.ipynb --to html
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<div class=" highlight hl-ipython2"><pre><span class="kn">from</span> <span class="nn">IPython.display</span> <span class="kn">import</span> <span class="n">HTML</span>
<span class="n">display</span><span class="p">(</span><span class="n">HTML</span><span class="p">(</span><span class="s">"<a href='{name}.html' target='_blank'> {name}.html </a>"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="n">name</span><span class="p">)))</span>
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<h2 id="Sharing-your-IPython-notebook">Sharing your IPython notebook<a class="anchor-link" href="#Sharing-your-IPython-notebook">¶</a></h2>
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<li>host your IPython notebook on the public internet (e.g. <a href="http://github.com">github</a> repo, github gist)</li>
<li>go to <a href="http://nbviewer.ipython.org/">http://nbviewer.ipython.org/</a> and copy the URL</li>
<li>Et voila !</li>
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<h2 id="Interacting-with-your-code-with-the-IPython-notebook-widgets">Interacting with your code with the IPython notebook widgets<a class="anchor-link" href="#Interacting-with-your-code-with-the-IPython-notebook-widgets">¶</a></h2>
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<p><a href="../../session_2/notebooks/IPython_widgets.ipynb">Follow this link</a></p>
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<h2 id="IPython-Parallel">IPython Parallel<a class="anchor-link" href="#IPython-Parallel">¶</a></h2>
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<li><a href="https://www.youtube.com/watch?v=y4hgalfhc1Y&list=PLYx7XA2nY5GfuhCvStxgbynFNrxr3VFog&index=49">Part 1</a></li>
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<div class=" highlight hl-ipython2"><pre><span class="n">YouTubeVideo</span><span class="p">(</span><span class="s">'y4hgalfhc1Y'</span><span class="p">)</span>
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<li><a href="https://www.youtube.com/watch?v=-9ijnHPCYhY&list=PLYx7XA2nY5GfuhCvStxgbynFNrxr3VFog&index=50">Part 2</a></li>
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<div class=" highlight hl-ipython2"><pre><span class="n">YouTubeVideo</span><span class="p">(</span><span class="s">'-9ijnHPCYhY'</span><span class="p">)</span>
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<li><a href="https://www.youtube.com/watch?v=U5mhpKkIx2Y&index=51&list=PLYx7XA2nY5GfuhCvStxgbynFNrxr3VFog">Part 3</a></li>
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<h2 id="IPython-on-a-HPC">IPython on a HPC<a class="anchor-link" href="#IPython-on-a-HPC">¶</a></h2>
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<p>Use IPython notebook interactively on a HPC system: <a href="https://github.com/pyHPC/ipynbhpc">https://github.com/pyHPC/ipynbhpc</a></p>
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