\title[3D Plotting]{3D data Visualization}

\date[] {1 November, 2009\\Day 2, Session 5}

    \frametitle{Outline}      

\begin{frame}

  \frametitle{Outline}

  \tableofcontents

  % You might wish to add the option [pausesections]

\end{frame}

\section{3D Data Visualization}

\begin{frame}

    \frametitle{What is visualization?}

    \Large

    \begin{center}

    Visual representation of data

    \end{center}

\end{frame}

%% \begin{frame}

%%     \frametitle{Is this new?}    

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%%     \begin{columns}

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%%     \includegraphics[width=1.75in,height=1.75in, interpolate=true]{data/3832}      

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%%     \includegraphics[width=1.75in, height=1.75in, interpolate=true]{data/torus}  

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\begin{frame}

    \frametitle{3D visualization}

    \Large

    \begin{center}

        Harder but important

    \end{center}

\begin{frame}

    \frametitle{Is this Graphics?}

    \Large

    \begin{center}

        Visualization is about data!

    \end{center}

\end{frame}

\begin{frame}

    \frametitle{Examples: trajectory in space}

    \Large

    \begin{center}

        \pgfimage[width=2.5in]{MEDIA/m2/mlab/plot3d_ex}

    \end{center}

\end{frame}

\begin{frame}

    \frametitle{Examples: Fire in a room}

    \Large

    \begin{center}

        Demo of data

    \end{center}

\inctime{10}

\section{Tools available}

\subsection{mlab}

\begin{frame}

    {Overview}

    \Large

    \begin{itemize}

        \item Simple

        \item Convenient

        \item Full-featured

    \end{itemize}

\end{frame}

\begin{frame}[fragile]

    \frametitle{Getting started}

    \myemph{\Large Vanilla:}

    \begin{lstlisting}[language=bash]

        $ ipython -wthread

    \end{lstlisting}

    \myemph{\Large with Pylab:}

    \begin{lstlisting}[language=bash]

        $ ipython -pylab -wthread

    \end{lstlisting}

    \frametitle{Using mlab}

    \begin{lstlisting}

In []:from enthought.mayavi import mlab

    \end{lstlisting}

    \vspace*{0.5in}

    \myemph{\Large Try these}

    \vspace*{0.25in}

    \begin{lstlisting}

In []: mlab.test_<TAB>

In []: mlab.test_contour3d()

In []: mlab.test_contour3d??

    \end{lstlisting}

\begin{frame}

    {Exploring the view}

    \begin{columns}

        \column{0.6\textwidth}

    \pgfimage[width=3in]{MEDIA/m2/contour3d}

        \column{0.4\textwidth}

        \begin{itemize}

            \item Mouse

            \item Keyboard

            \item Toolbar

            \item Mayavi icon\pgfimage[width=0.2in]{MEDIA/m2/m2_icon}

        \end{itemize}

    \end{columns}

    \frametitle{\mlab\ plotting functions}

    \begin{columns}

        \column{0.25\textwidth}

        \myemph{\Large 0D data}

        \column{0.5\textwidth}

    \pgfimage[width=2in]{MEDIA/m2/mlab/points3d_ex}

    \end{columns}

    \begin{lstlisting}

In []: t = linspace(0, 2*pi, 50)

In []: u = cos(t) * pi

In []: x, y, z = sin(u), cos(u), sin(t)

    \end{lstlisting}

    \emphbar{\PythonCode{In []: mlab.points3d(x, y, z)}}

\begin{frame}

  \begin{columns}

        \column{0.25\textwidth}

        \myemph{\Large 1D data}

        \column{0.5\textwidth}

        \pgfimage[width=2.5in]{MEDIA/m2/mlab/plot3d_ex}

  \end{columns}

  \emphbar{\PythonCode{In []: mlab.plot3d(x, y, z, t)}}

    Plots lines between the points

    \begin{columns}

        \column{0.25\textwidth}

        \myemph{\Large 2D data}

        \column{0.5\textwidth}

        \pgfimage[width=2in]{MEDIA/m2/mlab/surf_ex}

    \end{columns}            

    \begin{lstlisting}

In []: x, y = mgrid[-3:3:100j,-3:3:100j]

In []: z = sin(x*x + y*y)

    \end{lstlisting}

    \emphbar{\PythonCode{In []: mlab.surf(x, y, z)}}

    \alert{Assumes the points are rectilinear}

  \frametitle{mgrid}

  \begin{lstlisting}

In []: mgrid[0:3,0:3]

Out[]: 

array([[[0, 0, 0],

        [1, 1, 1],

        [2, 2, 2]],

       [[0, 1, 2],

        [0, 1, 2],

        [0, 1, 2]]])

In []: mgrid[-1:1:5j]

Out[]: array([-1., -0.5,  0.,  0.5,  1.])

  \frametitle{Example}

In []: x, y = mgrid[-1:1:5j, -1:1:5j]

In []: z = x*x + y*y

In []: z

Out[]: 

array([[ 2.  , 1.25, 1.  , 1.25, 2.  ],

       [ 1.25, 0.5 , 0.25, 0.5 , 1.25],

       [ 1.  , 0.25, 0.  , 0.25, 1.  ],

       [ 1.25, 0.5 , 0.25, 0.5 , 1.25],

       [ 2.  , 1.25, 1.  , 1.25, 2.  ]])

\end{lstlisting}

    \myemph{\Large 2D data: \texttt{mlab.mesh}}

    \vspace*{0.25in}

    \emphbar{\PythonCode{In []: mlab.mesh(x, y, z)}}

    \alert{Points needn't be regular}

    \vspace*{0.25in}

\begin{lstlisting}

In []: phi, theta = mgrid[0:pi:20j, 

...                         0:2*pi:20j]

In []: x = sin(phi)*cos(theta)

In []: y = sin(phi)*sin(theta)

In []: z = cos(phi)

In []: mlab.mesh(x, y, z, 

...           representation=

...           'wireframe')

\end{lstlisting}

\end{frame}

\begin{frame}[fragile]

  \begin{columns}

        \column{0.25\textwidth}

        \myemph{\Large 3D data}

        \column{0.5\textwidth}

        \pgfimage[width=1.5in]{MEDIA/m2/mlab/contour3d}\\        

    \end{columns}

\begin{lstlisting}

In []: x, y, z = mgrid[-5:5:64j, 

...                -5:5:64j, 

...                -5:5:64j]

In []: mlab.contour3d(x*x*0.5 + y*y + 

                   z*z*2)

\end{lstlisting}

    \myemph{\Large 3D vector data: \PythonCode{mlab.quiver3d}}

    \vspace*{0.25in}

    \pgfimage[width=2in]{MEDIA/m2/mlab/quiver3d_ex}\\

In []: mlab.test_quiver3d()

\end{lstlisting}

\emphbar{\PythonCode{obj = mlab.quiver3d(x, y, z, u, v, w)}}

\inctime{20}

\end{frame}

\subsection{Mayavi2}

\begin{frame}

  \frametitle{Introduction to Mayavi}

  \begin{itemize}

  \item Most scientists not interested in details of visualization

  \item Visualization of data files with a nice UI

  \item Interactive visualization of data (think Matlab)

  \item Embedding visualizations in applications

  \item Customization

  \end{itemize}

  \pause

  \begin{block}{The Goal}

      Provide a \alert{flexible} library/app for all of these needs!

  \end{block}

\end{frame}

\begin{frame}

    {Overview of features}

      \vspace*{-0.3in}

  \begin{center}    

    \hspace*{-0.2in}\pgfimage[width=5in]{MEDIA/m2/m2_app3_3}

  \end{center}    

\begin{frame}

    \frametitle{Mayavi in applications}

      \vspace*{-0.3in}

  \begin{center}    

    \hspace*{-0.2in}\pgfimage[width=4.5in]{MEDIA/m2/m2_envisage}

  \end{center}

\end{frame}

\begin{frame}

    \frametitle{Live in your dialogs}

      \vspace*{0.1in}

  \begin{center}    

    \hspace*{-0.2in}\pgfimage[width=2.5in]{MEDIA/m2/mlab_tui}

  \end{center}

\end{frame}

\begin{frame}

    {Exploring the documentation}

    \begin{center}

    \pgfimage[width=4in]{MEDIA/m2/m2_ug_doc}

    \end{center}

  \frametitle{Summary}

      \begin{itemize}

          \item \url{http://code.enthought.com/projects/mayavi}

          \item Uses VTK (\url{www.vtk.org})

          \item BSD license

          \item Linux, win32 and Mac OS X

          \item Highly scriptable

          \item Embed in Traits UIs (wxPython and PyQt4)

          \item Envisage Plugins

          \item Debian/Ubuntu/Fedora

          \item \alert{Pythonic}

      \end{itemize}

      \inctime{10}

\begin{frame}

    {Getting hands dirty!}

        \begin{block}{Motivational problem}

        Atmospheric data of temperature over the surface of the earth.

        Let temperature ($T$) vary linearly with height ($z$):

        \begin{center}            

        $T = 288.15 - 6.5z$

        \end{center}

        \end{block}

    \frametitle{Simple solution}

    \begin{lstlisting}

lat = linspace(-89, 89, 37)

lon = linspace(0, 360, 37)

z = linspace(0, 100, 11)

    \end{lstlisting}

\pause

    \begin{lstlisting}

x, y, z = mgrid[0:360:37j,-89:89:37j,

                0:100:11j]

t = 288.15 - 6.5*z

mlab.contour3d(x, y, z, t)