PythonTutorial.tex

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\begin{document}


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\begin{frame}[plain]
  \title{ {\fontsize{14}{1}\selectfont \bfseries Basic Python Tutorial} \\ \vspace{-3pt} {\fontsize{10}{1}\selectfont For Computational Neurodynamics Students} \\  }
\subtitle{ ~ }
\date{}
\vspace{5pt}
\titlepage
\vfill
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  ~ \\
  
  \vfill
  {\large Pedro Mediano \hspace{30pt} Marta Garnelo}\\ \vspace{-8pt}
  {\includegraphics[width=0.7\textwidth]{logo3.png}}\\ \vspace{-10pt}


  \ver{pmediano@ic.ac.uk} \hspace{20pt} \ver{garnelo@ic.ac.uk}
\end{center}
\end{frame}


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{ \scshape Introduction}
\subsection{Introduction}
\begin{frame}{}
\large

Completely legitimate question:

\vfill
\pause

\begin{itemize}
  \item \textbf{\Large Why are we using Python?}
\end{itemize}

\vfill

\end{frame}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\begin{frame}{Reasons to move to Python}

  (Or at least our reasons to do it)

  \begin{itemize}
    \Large
    \newcommand{\myitem}{\vfill \pause \item[{\color{darkgreen}\checkmark}]}
    \myitem It's free software.
    \myitem We know Python better than Matlab.
    \myitem We're making the code better.
  \end{itemize}

\end{frame}


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{\scshape Python basics}
\subsection{The import system}
\begin{frame}[fragile]{Python basics}

\textbf{The import system}

\begin{itemize}
	\item Often the definitions (e.g. functions) we want to use might be stored in a different script, i.e. another \textit{module}.
	\item In order to use definitions from other modules we need to import these modules at the beginning of our script.
	\item This is done via the \textit{import} command: 
  \mint{python}@    import numpy@
  \mint{python}@    import numpy as np@
  \begin{minted}{python}
    from scipy import *
    from matplotlib import pyplot
  \end{minted}
\end{itemize}

\end{frame}


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\subsection{\scshape Classes}
\begin{frame}[fragile]{Python basics}
\textbf{Classes}
\begin{itemize}
  \item Classes can contain \emph{members} and \emph{methods}.
  \item The constructor is the reserved method \verb@__init__@
\end{itemize}

\begin{minted}{python}
        class Shape:
            def __init__(self, x , y):
                self.x = x
                self.y = y

            def area(self):
                return self.x * self.y

        rectangle = Shape(100, 45)
        print rectangle.area()
\end{minted}

\end{frame}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\subsection{Indentation}
\begin{frame}[fragile]{Python basics}
\textbf{Indentations in python}
\begin{itemize}
\item Indentations mark the blocks of code within script 
\item Each line of a block must be indented by the same amount
\end{itemize}

\begin{minted}{python}
if some_condition:
    if the_number == 4:
        do_something(fancy)
else:
    do_something(different)
\end{minted}

\begin{itemize}
\item Mind that beginnings of blocks are indicated with a colon ":"
\end{itemize}

\pause

\textbf{0 - indexing}
\begin{itemize}
\item The index of the first element in python is 0
\item Tip: "-1" refers to the last element 
\end{itemize}
\end{frame}


  
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{ \scshape For Matlab Fans}
\begin{frame}{}
\large
\vspace{30pt}


First piece of advice:

\pause
\vspace{10pt}

\begin{itemize}
  \item \textbf{\Large Don't panic.}
\end{itemize}

\vspace{20pt}

\begin{figure}[b]
  \centering
  \includegraphics[width=\textwidth, clip, trim= 0 100 0 0]{HolyGrail072}
\end{figure}

\end{frame}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\begin{frame}[fragile]{General comments}
\textbf{Replacing Matlab with python}
\begin{itemize}
\item Overall Matlab and python are very similar in terms of syntax
\item \textbf{Similarities:} 
	\begin{enumerate}
	\item Both are \textit{dynamically typed} (every variable can contain data of any type)
	\item Both are \textit{interpreted}, they do not need to be compiled (almost)
	\end{enumerate}
\item \textbf{Differences}
	\begin{enumerate}
	\item Python files can contain unlimited functions that can all be accessed 
	\item Python does not have a matrix engine but there are useful packages with similar functionalities
		\begin{itemize}
		\item \textbf{Numpy}: enables basic matrix arithmetic on arrays
		\item \textbf{Scipy}: advanced mathematical routines
		\item \textbf{Matplotlib}: plotting
		\end{itemize}
	\end{enumerate}
\end{itemize}
\end{frame}


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\subsection{Basic commands}
\begin{frame}{Basic commands}

  \large

  Most Matlab has direct correspondence in Python:

  \vspace{5pt}

  \begin{itemize}
    \newcommand{\myitem}{\vspace{3pt} \pause \item}
    \myitem Variable declaration
    \myitem Loops
    \myitem Flow control
    \myitem Function handles
    \myitem That's it!
  \end{itemize}

\end{frame}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\subsection{Data structures}
\begin{frame}[fragile]{Common data structures}

  \large
  \vspace{-5pt}

  \begin{description}
    \item[Python] ~ \\ \hspace{-30pt} Lists, dictionaries, arrays, \ldots
    \vspace{8pt}
    \item[Matlab] ~ \\ \hspace{-30pt} Arrays, cells, structs, \ldots
  \end{description}

  \vspace{10pt}
  \pause

  \(
  \<{0.6\linewidth}

  \centering
  \textbf{Python}
  \begin{minted}{python}
    A = [1,3,2,4]
    B = {'a': 0.2,
         'b': 0.02}
    C = np.array([10,20])
  \end{minted}

  \> \<{0.6\linewidth}

  \centering
  \textbf{Matlab}
  \begin{minted}[frame=leftline]{octave}
    A = [1,3,2,4];
    B.a = 0.1;
    B.b = 0.02;
    C = [10,20];
  \end{minted}

  \>
  \)

  \vspace{25pt}
  \pause

  We recommend to use always \textbf{\texttt{np.array}}.

\end{frame}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\subsection{The Question}
\begin{frame}{The big question}

  \large

  \textbf{\Large Can I use Matlab?}

  \vspace{20pt}
  \pause

  Yes, but:

  \vspace{3pt}

  \begin{itemize}
    \newcommand{\myitem}{\vspace{3pt} \pause \item[{\color{darkgreen}\checkmark}]}
    \newcommand{\baditem}{\vspace{3pt} \pause \item[{\color{red}$\boldsymbol\times$}]}
    \baditem The Matlab code is not maintained.
    \baditem Matlab makes the markers sad.
    \baditem We provide limited support for Matlab questions.
    \myitem Come on, use Python.
  \end{itemize}

\end{frame}


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{ \scshape Tools}
\subsection{Development tools}
\begin{frame}{Development tools}

  \Large
  \begin{itemize}
    \newcommand{\myitem}{\vfill \pause \item}
    \myitem Editor + terminal
    \myitem Spyder
    \myitem iPython (notebook)
  \end{itemize}

  \vfill
  \pause

  Remember to use a debugger! \\
  ~ ~ $\rightarrow$ \textbf{pdb}

\end{frame}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\subsection{Virtual environments and packages}
\begin{frame}{Logistics and installation}

  \large

  \vfill

  \begin{itemize}
     
    \item If you still don't have access to the DoC machines, talk with me ASAP!

  \vfill
  \pause

    \item No mortal is allowed to install programs on the DoC machines, so we'll
  use Python's \textbf{virtualenv}.

  \begin{itemize}
    \item A \emph{virtual environment} is a small Python bubble.
    \vspace{3pt}
    \item You can~ \ver{pip install} packages inside without requiring permissions.
  \end{itemize}

  \end{itemize}

  \vfill
  ~
  \vfill

\end{frame}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\begin{frame}[fragile]{Virtual environment}

  \begin{itemize}
    \item Setting up your \ver{virtualenv}:
  \end{itemize}

  \begin{minted}[bgcolor=aliceblue]{bash}
    virtualenv venv
    cd venv
    source bin/activate
    pip install scipy
    pip install matplotlib
    pip install jpype1
  \end{minted}

\end{frame}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\begin{frame}[fragile]{Virtual environment}

  \begin{itemize}
    \item To install Spyder:
  \end{itemize}
  \begin{minted}[bgcolor=aliceblue]{bash}
    pip install PySide
    pip install spyder
  \end{minted}

  \vspace{10pt}

  \begin{itemize}
    \item Using the \ver{virtualenv}:
  \end{itemize}
  \begin{minted}[bgcolor=aliceblue]{bash}
    source /<PATHTOVENV>/bin/activate
    python EulerDemo.py
    spyder
  \end{minted}
  
\end{frame}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\subsection{Links}
\begin{frame}{Useful links}

  \large

  \begin{itemize}
    \item NumPy for Matlab users:

    \vspace{5pt}
    {\scriptsize \centering \url{http://mathesaurus.sourceforge.net/matlab-numpy.html}\\}

    \vspace{8pt}
    \item Using Vim as a Python IDE:

    \vspace{5pt}
    {\scriptsize \centering \url{https://www.youtube.com/watch?v=YhqsjUUHj6g} \\
    \url{http://blog.dispatched.ch/2009/05/24/vim-as-python-ide/}}

    \vspace{8pt}
    \item The Python tutorial:

    \vspace{5pt}
    {\scriptsize \centering \url{https://docs.python.org/2/tutorial/}\\}

  \end{itemize}


\end{frame}

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\section{}
\begin{frame}{Live example}

  \Large

  Let's go through \ver{IzNeuronDemo.py}

\end{frame}

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