--- a/day2/session4.tex Fri Nov 06 17:56:22 2009 +0530
+++ b/day2/session4.tex Fri Nov 06 18:33:08 2009 +0530
@@ -74,7 +74,7 @@
\newcommand{\tvtk}{\texttt{tvtk}}
\newcommand{\mlab}{\texttt{mlab}}
-\newcommand{\typ}[1]{\lstinline{#1}}
+
\newcounter{time}
\setcounter{time}{0}
\newcommand{\inctime}[1]{\addtocounter{time}{#1}{\vspace*{0.1in}\tiny \thetime\ m}}
@@ -95,12 +95,13 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Title page
-\title[Python Development]{Python Development}
+\title[3D Plotting]{3D data Visualization}
\author[FOSSEE] {FOSSEE}
\institute[IIT Bombay] {Department of Aerospace Engineering\\IIT Bombay}
-\date[] {1 November, 2009\\Day 2, Session 3}
+\date[] {1 November, 2009\\Day 2, Session 5}
+
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%\pgfdeclareimage[height=0.75cm]{iitblogo}{iitblogo}
@@ -109,8 +110,7 @@
\AtBeginSection[]
{
\begin{frame}<beamer>
- \frametitle{Outline}
- \Large
+ \frametitle{Outline}
\tableofcontents[currentsection,currentsubsection]
\end{frame}
}
@@ -140,423 +140,419 @@
\maketitle
\end{frame}
-\section{Tests: Getting started}
-\begin{frame}[fragile]
- \frametitle{gcd revisited!}
- \begin{itemize}
- \item Open gcd.py
- \end{itemize}
-\begin{lstlisting}
- def gcd(a, b):
- if a % b == 0:
- return b
- return gcd(b, a%b)
+\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}
+
- print gcd(15, 65)
- print gcd(16, 76)
-\end{lstlisting}
- \begin{itemize}
- \item python gcd.py
- \end{itemize}
+%% \begin{frame}
+%% \frametitle{Is this new?}
+%% \begin{center}
+%% We have moved from:
+%% \end{center}
+%% \begin{columns}
+%% \column{}
+%% \hspace*{-1in}
+%% \includegraphics[width=1.75in,height=1.75in, interpolate=true]{data/3832}
+%% \column{}\hspace*{-0.25in}
+%% To
+%% \column{}
+%% \hspace*{-1in}
+%% \includegraphics[width=1.75in, height=1.75in, interpolate=true]{data/torus}
+%% \end{columns}
+%% \end{frame}
+
+\begin{frame}
+ \frametitle{3D visualization}
+ \Large
+ \begin{center}
+ Harder but important
+ \end{center}
\end{frame}
-\begin{frame}[fragile]
- \frametitle{Find lcm using our gcd module}
- \begin{itemize}
- \item Open lcm.py
- \item $lcm = \frac{a*b}{gcd(a,b)}$
- \end{itemize}
-\begin{lstlisting}
- from gcd import gcd
- def lcm(a, b):
- return (a * b) / gcd(a, b)
-
- print lcm(14, 56)
-\end{lstlisting}
- \begin{itemize}
- \item python lcm.py
- \end{itemize}
- \begin{lstlisting}
-5
-4
-56
- \end{lstlisting}
+\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}
\end{frame}
-\begin{frame}[fragile]
- \frametitle{Writing stand-alone module}
-Edit gcd.py file to:
-\begin{lstlisting}
- def gcd(a, b):
- if a % b == 0:
- return b
- return gcd(b, a%b)
+\section{Tools available}
+
+\subsection{mlab}
- if __name__ == "__main__":
- print gcd(15, 65)
- print gcd(16, 76)
-\end{lstlisting}
- \begin{itemize}
- \item python gcd.py
- \item python lcm.py
- \end{itemize}
+\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}
\end{frame}
\begin{frame}[fragile]
- \frametitle{More use of main}
- For automating tests.
- \begin{lstlisting}
-if __name__ == '__main__':
- for line in open('numbers.txt'):
- numbers = line.split()
- x = int(numbers[0])
- y = int(numbers[1])
- result = (int(numbers[2]))
- assert gcd(x, y) == result
- \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}
\end{frame}
-\section{Coding Style}
-\begin{frame}{Readability and Consistency}
- \begin{itemize}
- \item Readability Counts!\\Code is read more often than its written.
- \item Consistency!
- \item Know when to be inconsistent.
- \end{itemize}
-\end{frame}
-
-\begin{frame}[fragile] \frametitle{A question of good style}
- \begin{lstlisting}
- amount = 12.68
- denom = 0.05
- nCoins = round(amount/denom)
- rAmount = nCoins * denom
- \end{lstlisting}
- \pause
- \begin{block}{Style Rule \#1}
- Naming is 80\% of programming
- \end{block}
+\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}
\end{frame}
\begin{frame}[fragile]
- \frametitle{Code Layout}
- \begin{itemize}
- \item Indentation
- \item Tabs or Spaces??
- \item Maximum Line Length
- \item Blank Lines
- \item Encodings
- \end{itemize}
-\end{frame}
+ \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{frame}{Whitespaces in Expressions}
- \begin{itemize}
- \item When to use extraneous whitespaces??
- \item When to avoid extra whitespaces??
- \item Use one statement per line
- \end{itemize}
+ \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)}}
\end{frame}
-\begin{frame}{Comments}
- \begin{itemize}
- \item No comments better than contradicting comments
- \item Block comments
- \item Inline comments
- \end{itemize}
-\end{frame}
+\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)}}
-\begin{frame}{Docstrings}
- \begin{itemize}
- \item When to write docstrings?
- \item Ending the docstrings
- \item One liner docstrings
- \end{itemize}
-More information at PEP8: http://www.python.org/dev/peps/pep-0008/
-\inctime{5}
-\end{frame}
-
-\section{Debugging}
-\subsection{Errors and Exceptions}
-\begin{frame}[fragile]
- \frametitle{Errors}
- \begin{lstlisting}
-In []: while True print 'Hello world'
- \end{lstlisting}
-\pause
- \begin{lstlisting}
- File "<stdin>", line 1, in ?
- while True print 'Hello world'
- ^
-SyntaxError: invalid syntax
-\end{lstlisting}
+ Plots lines between the points
+
\end{frame}
\begin{frame}[fragile]
- \frametitle{Exceptions}
- \begin{lstlisting}
-In []: print spam
-\end{lstlisting}
-\pause
-\begin{lstlisting}
-Traceback (most recent call last):
- File "<stdin>", line 1, in <module>
-NameError: name 'spam' is not defined
-\end{lstlisting}
+ \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}
+
\end{frame}
\begin{frame}[fragile]
- \frametitle{Exceptions}
- \begin{lstlisting}
-In []: 1 / 0
-\end{lstlisting}
-\pause
-\begin{lstlisting}
-Traceback (most recent call last):
- File "<stdin>", line 1, in <module>
-ZeroDivisionError: integer division
-or modulo by zero
+ \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.])
\end{lstlisting}
\end{frame}
\begin{frame}[fragile]
- \frametitle{Handling Exceptions}
- Python uses \typ{try} and \typ{except} clause.
- %%Revisiting the raw\_input
+ \frametitle{Example}
\begin{lstlisting}
-a = raw_input('Enter number(Q to quit):')
-try:
- num = int(a)
- print num
-except:
- if a == 'Q':
- print 'Exiting...'
- else:
- print 'Wrong input!'
- \end{lstlisting}
-
-
-\end{frame}
+In []: x, y = mgrid[-1:1:5j, -1:1:5j]
+In []: z = x*x + y*y
-%% \begin{frame}[fragile]
-%% \frametitle{Solving it with \typ{try} and \typ{except}}
-%% \vspace{-0.2in}
-%% \begin{lstlisting}
-%% highest = 0
-%% for record in open('sslc1.txt'):
-%% fields = record.split(';')
-%% try:
-%% total = 0
-%% for score_str in fields[3:8]:
-%% score = int(score_str)
-%% total += score
-%% if total > highest:
-%% highest = total
-%% except:
-%% pass
-%% print highest
-%% \end{lstlisting}
-%% \end{frame}
-\subsection{Strategy}
-\begin{frame}[fragile]
- \frametitle{Debugging effectively}
- \begin{itemize}
- \item \typ{print} based strategy
- \item Process:
- \end{itemize}
-\begin{center}
-\pgfimage[interpolate=true,width=5cm,height=5cm]{DebugginDiagram.png}
-\end{center}
+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}
\end{frame}
\begin{frame}[fragile]
- \frametitle{Debugging effectively}
- \begin{itemize}
- \item Using \typ{\%debug} in IPython
- \end{itemize}
+ \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}
\end{frame}
\begin{frame}[fragile]
-\frametitle{Debugging in IPython}
-\small
+
+ \myemph{\Large 3D vector data: \PythonCode{mlab.quiver3d}}
+ \vspace*{0.25in}
+
+ \pgfimage[width=2in]{MEDIA/m2/mlab/quiver3d_ex}\\
+
\begin{lstlisting}
-In []: import mymodule
-In []: mymodule.test()
----------------------------------------------
-NameError Traceback (most recent call last)
-<ipython console> in <module>()
-mymodule.py in test()
- 1 def test():
-----> 2 print spam
-NameError: global name 'spam' is not defined
+In []: mlab.test_quiver3d()
+\end{lstlisting}
+
+\emphbar{\PythonCode{obj = mlab.quiver3d(x, y, z, u, v, w)}}
+\inctime{20}
+\end{frame}
+
+
+\subsection{Mayavi2}
-In []: %debug
-> mymodule.py(2)test()
- 0 print spam
-ipdb>
-\end{lstlisting}
-\inctime{15}
+\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}
\end{frame}
-\subsection{Exercise}
-\begin{frame}[fragile]
-\frametitle{Debugging: Exercise}
-\small
-\begin{lstlisting}
-science = {}
-for record in open('sslc1.txt'):
- fields = record.split(';')
- region_code = fields[0].strip()
+\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}
- score_str = fields[6].strip()
- score = int(score_str) if score_str != 'AA'
- else 0
+\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}
- if score > 90:
- science[region_code] += 1
-
-pie(science.values(), labels=science.keys())
-savefig('science.png')
-\end{lstlisting}
-\inctime{10}
+\begin{frame}
+ {Exploring the documentation}
+ \begin{center}
+ \pgfimage[width=4in]{MEDIA/m2/m2_ug_doc}
+ \end{center}
\end{frame}
-%% \begin{frame}
-%% \frametitle{Testing}
-
-%% \begin{itemize}
-%% \item Writing tests is really simple!
-
-%% \item Using nose.
-
-%% \item Example!
-%% \end{itemize}
-%% \end{frame}
-\section{Test Driven Approach}
\begin{frame}
- \frametitle{Need for Testing!}
-
- \begin{itemize}
- \item Quality
- \item Regression
- \item Documentation
- \end{itemize}
- %% \vspace*{0.25in}
- %% \emphbar{It is to assure that section of code is working as it is supposed to work}
+ \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}
+
\end{frame}
-\begin{frame}[fragile]
- \frametitle{Example}
- \begin{block}{Problem Statement}
- Write a function to check whether a given input
- string is a palindrome.
- \end{block}
-\end{frame}
+\begin{frame}
+ {Getting hands dirty!}
-\begin{frame}[fragile]
- \frametitle{Function: palindrome.py}
-\begin{lstlisting}
-def is_palindrome(input_str):
- return input_str == input_str[::-1]
-\end{lstlisting}
+ \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}
\end{frame}
\begin{frame}[fragile]
- \frametitle{Test for the palindrome: palindrome.py}
-\begin{lstlisting}
-def test_function_normal_words():
- input = "noon"
- assert is_palindrome(input) == True
-
-if __name__ == "main'':
- test_function_normal_words()
-\end{lstlisting}
-\end{frame}
+ \frametitle{Simple solution}
-\begin{frame}[fragile]
- \frametitle{Running the tests.}
-\begin{lstlisting}
-$ nosetests palindrome.py
-.
-----------------------------------------------
-Ran 1 test in 0.001s
-
-OK
-\end{lstlisting}
+ \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)
+mlab.outline()
+mlab.colorbar()
+ \end{lstlisting}
\end{frame}
\begin{frame}[fragile]
- \frametitle{Exercise: Including new tests.}
-\begin{lstlisting}
-def test_function_ignore_cases_words():
- input = "Noon"
- assert is_palindrome(input) == True
-\end{lstlisting}
- \vspace*{0.25in}
- Check\\
- \PythonCode{$ nosetests palindrome.py} \\
- \begin{block}{Task}
- Tweak the code to pass this test.
- \end{block}
+ \frametitle{Exercise: Lorenz equation}
+ \begin{columns}
+ \column{0.25\textwidth}
+ \begin{eqnarray*}
+ \frac{d x}{dt} &=& s (y-x)\\
+ \frac{d y}{d t} &=& rx -y -xz\\
+ \frac{d z}{d t} &=& xy - bz\\
+ \end{eqnarray*}
+ \column{0.25\textwidth}
+ Let $s=10,$
+ $r=28,$
+ $b=8./3.$
+ \end{columns}
+ \structure{\Large Region of interest}
+ \begin{lstlisting}
+x, y, z = mgrid[-50:50:20j,-50:50:20j,
+ -10:60:20j]
+ \end{lstlisting}
+\inctime{20}
+
+\end{frame}
+\begin{frame}[fragile]
+ \frametitle{Solution}
+ \begin{lstlisting}
+def lorenz(x,y,z,s=10.,r=28.,b=8./3.):
+ u = s*(y-x)
+ v = r*x-y-x*z
+ w = x*y-b*z
+ return u,v,w
+x,y,z = mgrid [-50:50:20j,-50:50:20j,
+ -10:60:20j ]
+u,v,w = lorenz( x , y , z )
+# Your plot here
+#
+mlab.show()
+
+ \end{lstlisting}
\end{frame}
-%\begin{frame}[fragile]
-% \frametitle{Lets write some test!}
-%\begin{lstlisting}
-%#for form of equation y=mx+c
-%#given m and c for two equation,
-%#finding the intersection point.
-%def intersect(m1,c1,m2,c2):
-% x = (c2-c1)/(m1-m2)
-% y = m1*x+c1
-% return (x,y)
-%\end{lstlisting}
-%
-%Create a simple test for this
-%
-%function which will make it fail.
-%
-%\inctime{15}
-%\end{frame}
-%
-
-%% \begin{frame}[fragile]
-%% \frametitle{Exercise}
-%% Based on Euclid's algorithm:
-%% \begin{center}
-%% $gcd(a,b)=gcd(b,b\%a)$
-%% \end{center}
-%% gcd function can be written as:
-%% \begin{lstlisting}
-%% def gcd(a, b):
-%% if a%b == 0: return b
-%% return gcd(b, a%b)
-%% \end{lstlisting}
-%% \vspace*{-0.15in}
-%% \begin{block}{Task}
-%% \begin{itemize}
-%% \item Write at least
-%% two tests for above mentioned function.
-%% \item Write a non recursive implementation
-%% of gcd(), and test it using already
-%% written tests.
-%% \end{itemize}
-%% \end{block}
-
-%% \inctime{15}
-%% \end{frame}
-
\begin{frame}
- \frametitle{Summary}
-We have coverd:
+ \frametitle{We have covered:}
\begin{itemize}
- \item Following and Resolving Error Messages.
- \item Exceptions.
- \item Handling exceptions
- \item Approach for Debugging.
- \item Writting and running tests.
+ \item Need of visualization.
+ \item Using mlab to create 3 D plots.
+ \item Mayavi Toolkit.
\end{itemize}
\end{frame}
\end{document}
+