day2/session6.tex
author Madhusudan.C.S <madhusudancs@gmail.com>
Fri, 06 Nov 2009 18:36:42 +0530
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% Tutorial slides on Python.
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%
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% Author: Prabhu Ramachandran <prabhu at aero.iitb.ac.in>
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% Copyright (c) 2005-2009, Prabhu Ramachandran
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\documentclass[compress,14pt]{beamer}
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% \documentclass[handout]{beamer}
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% \usepackage{pgfpages}
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% \pgfpagesuselayout{4 on 1}[a4paper,border, shrink=5mm,landscape]
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\usepackage{tikz}
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\newcommand{\hyperlinkmovie}{}
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%\usepackage{movie15}
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% Note that in presentation mode 
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% \paperwidth  364.19536pt
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% \paperheight 273.14662pt
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% h/w = 0.888
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\mode<presentation>
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{
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  \usetheme{Warsaw}
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  %\usetheme{Boadilla}
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  %\usetheme{default}
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  \useoutertheme{infolines}
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  \setbeamercovered{transparent}
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}
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% To remove navigation symbols
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\setbeamertemplate{navigation symbols}{}
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\usepackage{amsmath}
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\usepackage[english]{babel}
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\usepackage[latin1]{inputenc}
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\usepackage{times}
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\usepackage[T1]{fontenc}
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% Taken from Fernando's slides.
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\usepackage{ae,aecompl}
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\usepackage{mathpazo,courier,euler}
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\usepackage[scaled=.95]{helvet}
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\usepackage{pgf}
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\definecolor{darkgreen}{rgb}{0,0.5,0}
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\usepackage{listings}
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\lstset{language=Python,
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    basicstyle=\ttfamily\bfseries,
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    commentstyle=\color{red}\itshape,
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  stringstyle=\color{darkgreen},
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  showstringspaces=false,
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  keywordstyle=\color{blue}\bfseries}
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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% My Macros
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\setbeamercolor{postit}{bg=yellow,fg=black}
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\setbeamercolor{emphbar}{bg=blue!20, fg=black}
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\newcommand{\emphbar}[1]
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{\begin{beamercolorbox}[rounded=true]{emphbar} 
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      {#1}
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 \end{beamercolorbox}
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}
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%{\centerline{\fcolorbox{gray!50} {blue!10}{
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%\begin{minipage}{0.9\linewidth}
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%    {#1} 
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%\end{minipage}
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%    }}}
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\newcommand{\myemph}[1]{\structure{\emph{#1}}}
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\newcommand{\PythonCode}[1]{\lstinline{#1}}
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\newcommand{\tvtk}{\texttt{tvtk}}
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\newcommand{\mlab}{\texttt{mlab}}
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\newcounter{time}
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\setcounter{time}{0}
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\newcommand{\inctime}[1]{\addtocounter{time}{#1}{\vspace*{0.1in}\tiny \thetime\ m}}
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\newcommand\BackgroundPicture[1]{%
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  \setbeamertemplate{background}{%
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      \parbox[c][\paperheight]{\paperwidth}{%
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      \vfill \hfill
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 \hfill \vfill
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}}}
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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% Configuring the theme
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%\setbeamercolor{normal text}{fg=white}
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%\setbeamercolor{background canvas}{bg=black}
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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% Title page
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\title[3D Plotting]{3D data Visualization}
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\author[FOSSEE] {FOSSEE}
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\institute[IIT Bombay] {Department of Aerospace Engineering\\IIT Bombay}
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\date[] {8 November, 2009\\Day 2, Session 6}
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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%\pgfdeclareimage[height=0.75cm]{iitblogo}{iitblogo}
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%\logo{\pgfuseimage{iitblogo}}
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\AtBeginSection[]
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{
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  \begin{frame}<beamer>
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    \frametitle{Outline}      
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    \tableofcontents[currentsection,currentsubsection]
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  \end{frame}
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}
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%% Delete this, if you do not want the table of contents to pop up at
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%% the beginning of each subsection:
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\AtBeginSubsection[]
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{
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  \begin{frame}<beamer>
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    \frametitle{Outline}
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    \tableofcontents[currentsection,currentsubsection]
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  \end{frame}
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}
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\AtBeginSection[]
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{
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  \begin{frame}<beamer>
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    \frametitle{Outline}
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    \tableofcontents[currentsection,currentsubsection]
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  \end{frame}
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}
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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% DOCUMENT STARTS
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\begin{document}
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\begin{frame}
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  \maketitle
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\end{frame}
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\begin{frame}
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  \frametitle{Outline}
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  \tableofcontents
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  % You might wish to add the option [pausesections]
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\end{frame}
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\section{3D Data Visualization}
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\begin{frame}
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    \frametitle{What is visualization?}
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    \Large
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    \begin{center}
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    Visual representation of data
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    \end{center}
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\end{frame}
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%% \begin{frame}
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%%     \frametitle{Is this new?}    
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%%     \begin{center}
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%%     We have moved from:
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%%     \end{center}
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%%     \begin{columns}
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%%     \column{}
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%%     \hspace*{-1in}    
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%%     \includegraphics[width=1.75in,height=1.75in, interpolate=true]{data/3832}      
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%%     \column{}\hspace*{-0.25in}
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%%     To
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%%     \column{}
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%%     \hspace*{-1in}
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%%     \includegraphics[width=1.75in, height=1.75in, interpolate=true]{data/torus}  
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%%     \end{columns}
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%% \end{frame}
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\begin{frame}
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    \frametitle{3D visualization}
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    \Large
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    \begin{center}
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        Harder but important
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    \end{center}
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\end{frame}
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\begin{frame}
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    \frametitle{Is this Graphics?}
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    \Large
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    \begin{center}
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        Visualization is about data!
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    \end{center}
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\end{frame}
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\begin{frame}
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    \frametitle{Examples: trajectory in space}
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    \Large
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    \begin{center}
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        \pgfimage[width=2.5in]{MEDIA/m2/mlab/plot3d_ex}
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    \end{center}
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\end{frame}
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\begin{frame}
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    \frametitle{Examples: Fire in a room}
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    \Large
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    \begin{center}
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        Demo of data
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    \end{center}
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\inctime{10}
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\end{frame}
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\section{Tools available}
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\subsection{mlab}
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\begin{frame}
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    {Overview}
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    \Large
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    \begin{itemize}
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        \item Simple
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        \item Convenient
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        \item Full-featured
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    \end{itemize}
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\end{frame}
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\begin{frame}[fragile]
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    \frametitle{Getting started}
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    \myemph{\Large Vanilla:}
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    \begin{lstlisting}[language=bash]
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        $ ipython -wthread
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    \end{lstlisting}
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    \myemph{\Large with Pylab:}
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    \begin{lstlisting}[language=bash]
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        $ ipython -pylab -wthread
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    \end{lstlisting}
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\end{frame}
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\begin{frame}[fragile]
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    \frametitle{Using mlab}
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    \begin{lstlisting}
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In []:from enthought.mayavi import mlab
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    \end{lstlisting}
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    \vspace*{0.5in}
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    \myemph{\Large Try these}
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    \vspace*{0.25in}
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    \begin{lstlisting}
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In []: mlab.test_<TAB>
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In []: mlab.test_contour3d()
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In []: mlab.test_contour3d??
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    \end{lstlisting}
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\end{frame}
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\begin{frame}
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    {Exploring the view}
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    \begin{columns}
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        \column{0.6\textwidth}
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    \pgfimage[width=3in]{MEDIA/m2/contour3d}
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        \column{0.4\textwidth}
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        \begin{itemize}
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            \item Mouse
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            \item Keyboard
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            \item Toolbar
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            \item Mayavi icon\pgfimage[width=0.2in]{MEDIA/m2/m2_icon}
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        \end{itemize}
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    \end{columns}
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\end{frame}
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\begin{frame}[fragile]
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    \frametitle{\mlab\ plotting functions}
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    \begin{columns}
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        \column{0.25\textwidth}
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        \myemph{\Large 0D data}
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        \column{0.5\textwidth}
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    \pgfimage[width=2in]{MEDIA/m2/mlab/points3d_ex}
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    \end{columns}
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    \begin{lstlisting}
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In []: t = linspace(0, 2*pi, 50)
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In []: u = cos(t) * pi
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In []: x, y, z = sin(u), cos(u), sin(t)
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    \end{lstlisting}
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    \emphbar{\PythonCode{In []: mlab.points3d(x, y, z)}}
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\end{frame}
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\begin{frame}
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  \begin{columns}
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        \column{0.25\textwidth}
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        \myemph{\Large 1D data}
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        \column{0.5\textwidth}
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        \pgfimage[width=2.5in]{MEDIA/m2/mlab/plot3d_ex}
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  \end{columns}
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  \emphbar{\PythonCode{In []: mlab.plot3d(x, y, z, t)}}
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    Plots lines between the points
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\end{frame}
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\begin{frame}[fragile]
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    \begin{columns}
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        \column{0.25\textwidth}
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        \myemph{\Large 2D data}
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        \column{0.5\textwidth}
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        \pgfimage[width=2in]{MEDIA/m2/mlab/surf_ex}
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    \end{columns}            
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    \begin{lstlisting}
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In []: x, y = mgrid[-3:3:100j,-3:3:100j]
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In []: z = sin(x*x + y*y)
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    \end{lstlisting}
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    \emphbar{\PythonCode{In []: mlab.surf(x, y, z)}}
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    \alert{Assumes the points are rectilinear}
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\end{frame}
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\begin{frame}[fragile]
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  \frametitle{mgrid}
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  \begin{lstlisting}
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In []: mgrid[0:3,0:3]
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Out[]: 
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array([[[0, 0, 0],
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        [1, 1, 1],
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        [2, 2, 2]],
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       [[0, 1, 2],
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        [0, 1, 2],
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        [0, 1, 2]]])
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In []: mgrid[-1:1:5j]
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Out[]: array([-1., -0.5,  0.,  0.5,  1.])
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\end{lstlisting}
288
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\end{frame}
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\begin{frame}[fragile]
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  \frametitle{Example}
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  \begin{lstlisting}
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In []: x, y = mgrid[-1:1:5j, -1:1:5j]
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In []: z = x*x + y*y
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In []: z
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Out[]: 
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array([[ 2.  , 1.25, 1.  , 1.25, 2.  ],
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       [ 1.25, 0.5 , 0.25, 0.5 , 1.25],
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       [ 1.  , 0.25, 0.  , 0.25, 1.  ],
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       [ 1.25, 0.5 , 0.25, 0.5 , 1.25],
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       [ 2.  , 1.25, 1.  , 1.25, 2.  ]])
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\end{lstlisting}
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\end{frame}
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\begin{frame}[fragile]
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    \myemph{\Large 2D data: \texttt{mlab.mesh}}
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    \vspace*{0.25in}
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    \emphbar{\PythonCode{In []: mlab.mesh(x, y, z)}}
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    \alert{Points needn't be regular}
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    \vspace*{0.25in}
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\begin{lstlisting}
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In []: phi, theta = mgrid[0:pi:20j, 
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...                         0:2*pi:20j]
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In []: x = sin(phi)*cos(theta)
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In []: y = sin(phi)*sin(theta)
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In []: z = cos(phi)
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In []: mlab.mesh(x, y, z, 
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...           representation=
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...           'wireframe')
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\end{lstlisting}
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\end{frame}
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\begin{frame}[fragile]
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  \begin{columns}
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        \column{0.25\textwidth}
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        \myemph{\Large 3D data}
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        \column{0.5\textwidth}
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        \pgfimage[width=1.5in]{MEDIA/m2/mlab/contour3d}\\        
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    \end{columns}
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\begin{lstlisting}
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In []: x, y, z = mgrid[-5:5:64j, 
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...                -5:5:64j, 
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...                -5:5:64j]
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In []: mlab.contour3d(x*x*0.5 + y*y + 
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                   z*z*2)
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\end{lstlisting}
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\end{frame}
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\begin{frame}[fragile]
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    \myemph{\Large 3D vector data: \PythonCode{mlab.quiver3d}}
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   396
    \vspace*{0.25in}
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   397
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   398
    \pgfimage[width=2in]{MEDIA/m2/mlab/quiver3d_ex}\\
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diff changeset
   399
    
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   400
\begin{lstlisting}
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   401
In []: mlab.test_quiver3d()
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   402
\end{lstlisting}
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   403
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\emphbar{\PythonCode{obj = mlab.quiver3d(x, y, z, u, v, w)}}
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   405
\inctime{20}
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   406
\end{frame}
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   407
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   408
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   409
\subsection{Mayavi2}
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   410
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   411
\begin{frame}
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  \frametitle{Introduction to Mayavi}
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  \begin{itemize}
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   414
  \item Most scientists not interested in details of visualization
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   415
  \item Visualization of data files with a nice UI
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  \item Interactive visualization of data (think Matlab)
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  \item Embedding visualizations in applications
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   418
  \item Customization
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   419
  \end{itemize}
288
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   420
  \pause
289
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   421
  \begin{block}{The Goal}
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      Provide a \alert{flexible} library/app for all of these needs!
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   423
  \end{block}
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   424
\end{frame}
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   425
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   426
\begin{frame}
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   427
    {Overview of features}
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   428
      \vspace*{-0.3in}
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   429
  \begin{center}    
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    \hspace*{-0.2in}\pgfimage[width=5in]{MEDIA/m2/m2_app3_3}
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   431
  \end{center}    
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   432
\end{frame}
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   433
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   434
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   435
\begin{frame}
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    \frametitle{Mayavi in applications}
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   437
      \vspace*{-0.3in}
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   438
  \begin{center}    
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    \hspace*{-0.2in}\pgfimage[width=4.5in]{MEDIA/m2/m2_envisage}
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   440
  \end{center}
288
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\end{frame}
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\begin{frame}
289
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    \frametitle{Live in your dialogs}
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   445
      \vspace*{0.1in}
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   446
  \begin{center}    
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   447
    \hspace*{-0.2in}\pgfimage[width=2.5in]{MEDIA/m2/mlab_tui}
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   448
  \end{center}
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   449
\end{frame}
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   450
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   451
\begin{frame}
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   452
    {Exploring the documentation}
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   453
    \begin{center}
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    \pgfimage[width=4in]{MEDIA/m2/m2_ug_doc}
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   455
    \end{center}
288
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\end{frame}
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289
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   458
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   459
\begin{frame}
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   460
  \frametitle{Summary}
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   461
      \begin{itemize}
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   462
          \item \url{http://code.enthought.com/projects/mayavi}
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   463
          \item Uses VTK (\url{www.vtk.org})
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   464
          \item BSD license
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   465
          \item Linux, win32 and Mac OS X
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   466
          \item Highly scriptable
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   467
          \item Embed in Traits UIs (wxPython and PyQt4)
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   468
          \item Envisage Plugins
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   469
          \item Debian/Ubuntu/Fedora
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   470
          \item \alert{Pythonic}
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   471
      \end{itemize}
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diff changeset
   472
    
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   473
      \inctime{10}
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   474
288
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\end{frame}
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\begin{frame}
289
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   478
    {Getting hands dirty!}
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   479
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   480
        \begin{block}{Motivational problem}
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   481
        Atmospheric data of temperature over the surface of the earth.
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   482
        Let temperature ($T$) vary linearly with height ($z$):
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   483
        \begin{center}            
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   484
        $T = 288.15 - 6.5z$
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   485
        \end{center}
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   486
        \end{block}
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   487
\end{frame}
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   488
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   489
\begin{frame}[fragile]
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   490
    \frametitle{Simple solution}
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   491
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   492
    \begin{lstlisting}
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   493
lat = linspace(-89, 89, 37)
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   494
lon = linspace(0, 360, 37)
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   495
z = linspace(0, 100, 11)
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   496
    \end{lstlisting}
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   497
\pause
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   498
    \begin{lstlisting}
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   499
x, y, z = mgrid[0:360:37j,-89:89:37j,
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   500
                0:100:11j]
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   501
t = 288.15 - 6.5*z
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   502
mlab.contour3d(x, y, z, t)
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   503
mlab.outline()
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   504
mlab.colorbar()
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   505
    \end{lstlisting}
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   506
\end{frame}
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diff changeset
   507
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   508
\begin{frame}[fragile]
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   509
    \frametitle{Exercise: Lorenz equation}
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   510
    \begin{columns}
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   511
        \column{0.25\textwidth}
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   512
        \begin{eqnarray*}
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        \frac{d x}{dt} &=& s (y-x)\\
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        \frac{d y}{d t} &=& rx -y -xz\\
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   515
        \frac{d z}{d t} &=& xy - bz\\
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   516
        \end{eqnarray*}
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   517
        \column{0.25\textwidth}
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   518
        Let $s=10,$
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   519
        $r=28,$ 
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   520
        $b=8./3.$
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   521
    \end{columns}
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   522
    \structure{\Large Region of interest}
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   523
  \begin{lstlisting}
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   524
x, y, z = mgrid[-50:50:20j,-50:50:20j,
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                -10:60:20j]
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   526
  \end{lstlisting}
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\inctime{20}
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   528
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   529
\end{frame}
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   530
\begin{frame}[fragile]
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    \frametitle{Solution}
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   532
  \begin{lstlisting}
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def lorenz(x,y,z,s=10.,r=28.,b=8./3.):
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    u = s*(y-x)
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    v = r*x-y-x*z
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    w = x*y-b*z
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    return u,v,w
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x,y,z = mgrid [-50:50:20j,-50:50:20j,
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   539
                    -10:60:20j ]
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u,v,w = lorenz( x , y , z )
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   541
# Your plot here
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   542
#
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   543
mlab.show()
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   544
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   545
  \end{lstlisting}
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   546
\end{frame}
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   547
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   548
\begin{frame}
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  \frametitle{We have covered:}
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   550
  \begin{itemize}
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   551
  \item Need of visualization.
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   552
  \item Using mlab to create 3 D plots.
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   553
  \item Mayavi Toolkit.
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   554
  \end{itemize}
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\end{frame}
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\end{document}
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   558