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Diffstat (limited to 'day2/session4.tex')
| -rw-r--r-- | day2/session4.tex | 692 |
1 files changed, 344 insertions, 348 deletions
diff --git a/day2/session4.tex b/day2/session4.tex index 577841f..bee8030 100644 --- a/day2/session4.tex +++ b/day2/session4.tex @@ -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} - print gcd(15, 65) - print gcd(16, 76) -\end{lstlisting} - \begin{itemize} - \item python gcd.py - \end{itemize} +\section{3D Data Visualization} + +\begin{frame} + \frametitle{What is visualization?} + \Large + \begin{center} + Visual representation of data + \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 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{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) - - 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} + \frametitle{Is this Graphics?} + \Large + \begin{center} + Visualization is about data! + \end{center} \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} +\begin{frame} + \frametitle{Examples: trajectory in space} + \Large + \begin{center} + \pgfimage[width=2.5in]{MEDIA/m2/mlab/plot3d_ex} + \end{center} \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} +\begin{frame} + \frametitle{Examples: Fire in a room} + \Large + \begin{center} + Demo of data + \end{center} +\inctime{10} \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} +\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{Code Layout} - \begin{itemize} - \item Indentation - \item Tabs or Spaces?? - \item Maximum Line Length - \item Blank Lines - \item Encodings - \end{itemize} -\end{frame} -\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} + \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}{Comments} - \begin{itemize} - \item No comments better than contradicting comments - \item Block comments - \item Inline comments - \end{itemize} +\begin{frame}[fragile] + \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} -\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} +\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} -\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} + \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)}} \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{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 + \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 -\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{Handling Exceptions} - Python uses \typ{try} and \typ{except} clause. - %%Revisiting the raw\_input + \frametitle{mgrid} \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} - - +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{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} + \frametitle{Example} + \begin{lstlisting} +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} \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] -\frametitle{Debugging in IPython} -\small + + \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 []: 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 []: %debug -> mymodule.py(2)test() - 0 print spam -ipdb> +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} -\inctime{15} \end{frame} -\subsection{Exercise} \begin{frame}[fragile] -\frametitle{Debugging: Exercise} -\small + + \myemph{\Large 3D vector data: \PythonCode{mlab.quiver3d}} + \vspace*{0.25in} + + \pgfimage[width=2in]{MEDIA/m2/mlab/quiver3d_ex}\\ + \begin{lstlisting} -science = {} +In []: mlab.test_quiver3d() +\end{lstlisting} -for record in open('sslc1.txt'): - fields = record.split(';') - region_code = fields[0].strip() +\emphbar{\PythonCode{obj = mlab.quiver3d(x, y, z, u, v, w)}} +\inctime{20} +\end{frame} - score_str = fields[6].strip() - score = int(score_str) if score_str != 'AA' - else 0 - if score > 90: - science[region_code] += 1 +\subsection{Mayavi2} -pie(science.values(), labels=science.keys()) -savefig('science.png') -\end{lstlisting} -\inctime{10} +\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} -%% \frametitle{Testing} - -%% \begin{itemize} -%% \item Writing tests is really simple! +\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} -%% \item Using nose. -%% \item Example! -%% \end{itemize} -%% \end{frame} +\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} -\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{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}[fragile] - \frametitle{Example} - \begin{block}{Problem Statement} - Write a function to check whether a given input - string is a palindrome. - \end{block} +\begin{frame} + {Exploring the documentation} + \begin{center} + \pgfimage[width=4in]{MEDIA/m2/m2_ug_doc} + \end{center} \end{frame} -\begin{frame}[fragile] - \frametitle{Function: palindrome.py} -\begin{lstlisting} -def is_palindrome(input_str): - return input_str == input_str[::-1] -\end{lstlisting} + +\begin{frame} + \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{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} +\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} \end{frame} \begin{frame}[fragile] - \frametitle{Running the tests.} -\begin{lstlisting} -$ nosetests palindrome.py -. ----------------------------------------------- -Ran 1 test in 0.001s - -OK -\end{lstlisting} + \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) +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} -\end{frame} + \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} -%\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} -% +\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() -%% \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} + \end{lstlisting} +\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} + |