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From: <fer...@us...> - 2008-10-25 07:06:55
|
Revision: 6335
http://matplotlib.svn.sourceforge.net/matplotlib/?rev=6335&view=rev
Author: fer_perez
Date: 2008-10-25 07:06:53 +0000 (Sat, 25 Oct 2008)
Log Message:
-----------
Updated numpy intro slides
Modified Paths:
--------------
trunk/py4science/talks/numpy_intro.lyx
Modified: trunk/py4science/talks/numpy_intro.lyx
===================================================================
--- trunk/py4science/talks/numpy_intro.lyx 2008-10-25 04:49:37 UTC (rev 6334)
+++ trunk/py4science/talks/numpy_intro.lyx 2008-10-25 07:06:53 UTC (rev 6335)
@@ -618,7 +618,7 @@
\end_deeper
\end_deeper
\begin_layout BeginPlainFrame
-Numerics
+Is it good enough for scientific computing?
\end_layout
\begin_layout AlertBlock
@@ -829,6 +829,52 @@
NumPy: flexible arrays
\end_layout
+\begin_layout Itemize
+Array is a container of objects
+\begin_inset Quotes eld
+\end_inset
+
+of the same kind
+\begin_inset Quotes erd
+\end_inset
+
+:
+\series bold
+\color blue
+homogeneous
+\series default
+\color inherit
+.
+\end_layout
+
+\begin_layout Itemize
+Concept of
+\begin_inset Quotes eld
+\end_inset
+
+kind
+\begin_inset Quotes erd
+\end_inset
+
+ embodied in the data type, or
+\series bold
+\color blue
+dtype
+\series default
+\color inherit
+.
+\end_layout
+
+\begin_layout Itemize
+Dtypes
+\series bold
+\color blue
+can be user-defined
+\series default
+\color inherit
+ to be arbitrarily complex.
+\end_layout
+
\begin_layout Standard
\align center
\begin_inset Graphics
@@ -842,7 +888,8 @@
\end_layout
\begin_layout Standard
-Foo
+Image credit: T.
+ Oliphant, Enthought Inc.
\end_layout
\begin_layout BeginPlainFrame
@@ -860,59 +907,214 @@
filename fig/numpy_indexing.pdf
lyxscale 50
height 85pheight%
- BoundingBox 0bp 300bp 900bp 768bp
+ BoundingBox 0bp 300bp 1000bp 768bp
\end_inset
\end_layout
-\begin_layout Standard
-Foo
-\end_layout
-
\begin_layout BeginPlainFrame
NumPy: fancy indexing
\end_layout
\begin_layout Standard
+Image credit: E.
+ Jones, Enthought Inc.
+\end_layout
+
+\begin_layout Standard
\align center
\begin_inset Graphics
filename fig/numpy_fancy_indexing.pdf
lyxscale 50
height 85pheight%
- BoundingBox -4bp -4bp 518bp 588bp
+ BoundingBox 0bp 300bp 1024bp 768bp
\end_inset
\end_layout
-\begin_layout Standard
-f
-\end_layout
-
\begin_layout BeginPlainFrame
NumPy: broadcasting
\end_layout
\begin_layout Standard
+Image credit: E.
+ Jones, Enthought Inc.
+\end_layout
+
+\begin_layout Standard
\align center
+\begin_inset ERT
+status open
+
+\begin_layout Standard
+
+
+\backslash
+vspace*{-5mm}
+\end_layout
+
+\end_inset
+
+
\begin_inset Graphics
filename fig/numpy_broadcasting.pdf
lyxscale 50
height 85pheight%
- BoundingBox -4bp -4bp 518bp 588bp
+ BoundingBox 0bp 140bp 1024bp 768bp
\end_inset
\end_layout
-\begin_layout Standard
-b
+\begin_layout BeginPlainFrame
+SciPy: numerical algorithms galore
\end_layout
+\begin_layout Itemize
+
+\series bold
+\color blue
+linalg
+\series default
+\color inherit
+ : Linear algebra routines (including BLAS/LAPACK)
+\end_layout
+
+\begin_layout Itemize
+
+\series bold
+\color blue
+sparse
+\series default
+\color inherit
+ : Sparse Matrices (including UMFPACK, ARPACK,...)
+\end_layout
+
+\begin_layout Itemize
+
+\series bold
+\color blue
+fftpack
+\series default
+\color inherit
+ : Discrete Fourier Transform algorithms
+\end_layout
+
+\begin_layout Itemize
+
+\series bold
+\color blue
+cluster
+\series default
+\color inherit
+ : Vector Quantization / Kmeans
+\end_layout
+
+\begin_layout Itemize
+
+\series bold
+\color blue
+odr
+\series default
+\color inherit
+ : Orthogonal Distance Regression
+\end_layout
+
+\begin_layout Itemize
+
+\series bold
+\color blue
+special
+\series default
+\color inherit
+ : Special Functions (Airy, Bessel, etc).
+\end_layout
+
+\begin_layout Itemize
+
+\series bold
+\color blue
+stats
+\series default
+\color inherit
+ : Statistical Functions
+\end_layout
+
+\begin_layout Itemize
+
+\series bold
+\color blue
+optimize
+\series default
+\color inherit
+ : Optimization Tools
+\end_layout
+
+\begin_layout Itemize
+
+\series bold
+\color blue
+maxentropy
+\series default
+\color inherit
+ : Routines for fitting maximum entropy models
+\end_layout
+
+\begin_layout Itemize
+
+\series bold
+\color blue
+integrate
+\series default
+\color inherit
+ : Numerical Integration routines
+\end_layout
+
+\begin_layout Itemize
+
+\series bold
+\color blue
+ndimage
+\series default
+\color inherit
+ : n-dimensional image package
+\end_layout
+
+\begin_layout Itemize
+
+\series bold
+\color blue
+interpolate
+\series default
+\color inherit
+ : Interpolation Tools
+\end_layout
+
+\begin_layout Itemize
+
+\series bold
+\color blue
+signal
+\series default
+\color inherit
+ : Signal Processing Tools
+\end_layout
+
+\begin_layout Itemize
+
+\series bold
+\color blue
+io
+\series default
+\color inherit
+ : Data input and output
+\end_layout
+
\begin_layout EndFrame
\end_layout
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <fer...@us...> - 2008-10-25 04:49:40
|
Revision: 6334
http://matplotlib.svn.sourceforge.net/matplotlib/?rev=6334&view=rev
Author: fer_perez
Date: 2008-10-25 04:49:37 +0000 (Sat, 25 Oct 2008)
Log Message:
-----------
Updates to intro talk
Modified Paths:
--------------
trunk/py4science/talks/0810_claremont.lyx
trunk/py4science/talks/fig/hello_world.png
Modified: trunk/py4science/talks/0810_claremont.lyx
===================================================================
--- trunk/py4science/talks/0810_claremont.lyx 2008-10-25 04:29:53 UTC (rev 6333)
+++ trunk/py4science/talks/0810_claremont.lyx 2008-10-25 04:49:37 UTC (rev 6334)
@@ -65,6 +65,8 @@
% call, which confuses xcolor. I'm defining 'none' to be black here.
\definecolor{none}{cmyk}{0,0,0,1}
%%%%% /HACK %%%%%
+
+\usepackage{url}
\end_preamble
\options compress
\language english
@@ -591,6 +593,32 @@
, not replace them!
\end_layout
+\begin_layout BeginPlainFrame
+Hello World
+\end_layout
+
+\begin_layout Standard
+Ref:
+\begin_inset LatexCommand htmlurl
+target "http://www.roesler-ac.de/wolfram/hello.htm"
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename fig/hello_world.png
+ lyxscale 50
+ width 95text%
+
+\end_inset
+
+
+\end_layout
+
\begin_layout BeginFrame
Complementary high level tools
\end_layout
Modified: trunk/py4science/talks/fig/hello_world.png
===================================================================
(Binary files differ)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <fer...@us...> - 2008-10-25 04:29:59
|
Revision: 6333
http://matplotlib.svn.sourceforge.net/matplotlib/?rev=6333&view=rev
Author: fer_perez
Date: 2008-10-25 04:29:53 +0000 (Sat, 25 Oct 2008)
Log Message:
-----------
retyring basemap commit
Added Paths:
-----------
trunk/py4science/talks/0810_claremont.lyx
trunk/py4science/talks/basemap_tutorial.ppt
trunk/py4science/talks/fig/basemap/
trunk/py4science/talks/fig/basemap/01.png
trunk/py4science/talks/fig/basemap/02.png
trunk/py4science/talks/fig/basemap/03.png
trunk/py4science/talks/fig/basemap/04.png
trunk/py4science/talks/fig/basemap/05.png
trunk/py4science/talks/fig/basemap/06.png
trunk/py4science/talks/fig/basemap/07.png
trunk/py4science/talks/fig/basemap/08.png
trunk/py4science/talks/fig/basemap/09.png
trunk/py4science/talks/fig/basemap/10.png
trunk/py4science/talks/fig/basemap/11.png
trunk/py4science/talks/fig/basemap/12.png
trunk/py4science/talks/fig/basemap/13.png
trunk/py4science/talks/fig/basemap/14.png
trunk/py4science/talks/fig/basemap/15.png
trunk/py4science/talks/fig/basemap/16.png
trunk/py4science/talks/fig/basemap/17.png
trunk/py4science/talks/fig/basemap/18.png
trunk/py4science/talks/fig/basemap/19.png
trunk/py4science/talks/fig/basemap/nplea_tissot.tiff
trunk/py4science/talks/fig/basemap/ortho.png
trunk/py4science/talks/fig/basemap/stere_tissot.tiff
trunk/py4science/talks/fig/dtype.png
trunk/py4science/talks/fig/numpy_broadcasting.pdf
trunk/py4science/talks/fig/numpy_broadcasting.svg
trunk/py4science/talks/fig/numpy_fancy_indexing.pdf
trunk/py4science/talks/fig/numpy_fancy_indexing.svg
trunk/py4science/talks/fig/numpy_indexing.pdf
trunk/py4science/talks/fig/numpy_indexing.svg
trunk/py4science/talks/numpy_intro.lyx
Added: trunk/py4science/talks/0810_claremont.lyx
===================================================================
--- trunk/py4science/talks/0810_claremont.lyx (rev 0)
+++ trunk/py4science/talks/0810_claremont.lyx 2008-10-25 04:29:53 UTC (rev 6333)
@@ -0,0 +1,2147 @@
+#LyX 1.5.5 created this file. For more info see http://www.lyx.org/
+\lyxformat 276
+\begin_document
+\begin_header
+\textclass beamer
+\begin_preamble
+% Include only certain frames - this speeds up compilation
+% The frames to be included need to be labeled, by using ERT
+% as [label=LABELNAME] (no backslashes or {})
+%\includeonlyframes{currentt}
+
+% To make a printable handout (one page per frame), pass
+% the handout option to the doc class (Layout menu)
+
+% For good fonts in PDFs, use pslatex fonts (Layout menu)
+
+% Colors and symbols
+\usepackage{latexsym}
+\usepackage{color}
+
+% Display covered items in transparent form (as opposed
+% to not showing them at all)
+\newcommand{\coveredinvisible}{
+ \setbeamercovered{invisible}
+}
+\newcommand{\coveredvisible}{
+ \setbeamercovered{highly dynamic}
+}
+
+% Choose default setting here:
+\coveredvisible
+
+\newcommand{\ps}{\vspace{-4mm} }
+
+% Theme configuration. I've basically built a custom theme out of
+% Warsaw, adding infoline and changing the nav. symbol bar
+
+% Warning: the commands below are order-sensitive!
+
+% load the infolines theme, b/c I want the headline Warsaw
+% uses (split), but the footline from infolines.
+% In the document body, these will be deactivated for the title and
+% turned on later
+\useoutertheme{infolines}
+% Main theme
+\usetheme{Warsaw}
+% Adjust the color for the center (title) box to be that of
+% infolines, which Warsaw changes
+\setbeamercolor*{title in head/foot}{parent=palette secondary}
+
+% Define a minimal set of navigation symbols
+\defbeamertemplate*{navigation symbols}{minmal}
+{%
+ \hbox{%
+ \hbox{\insertframenavigationsymbol}
+ \hbox{\insertdocnavigationsymbol}
+ \hbox{\insertbackfindforwardnavigationsymbol}%
+ }%
+}
+% activate the minimal navbar
+\setbeamertemplate{navigation symbols}[minimal]
+
+%%%%% HACK %%%%%
+% I started getting errors because LyX is emmitting a color 'none'
+% call, which confuses xcolor. I'm defining 'none' to be black here.
+\definecolor{none}{cmyk}{0,0,0,1}
+%%%%% /HACK %%%%%
+\end_preamble
+\options compress
+\language english
+\inputencoding auto
+\font_roman times
+\font_sans helvet
+\font_typewriter courier
+\font_default_family default
+\font_sc false
+\font_osf false
+\font_sf_scale 100
+\font_tt_scale 100
+\graphics default
+\paperfontsize default
+\spacing single
+\papersize default
+\use_geometry false
+\use_amsmath 2
+\use_esint 0
+\cite_engine basic
+\use_bibtopic false
+\paperorientation landscape
+\secnumdepth 2
+\tocdepth 2
+\paragraph_separation indent
+\defskip medskip
+\quotes_language english
+\papercolumns 1
+\papersides 1
+\paperpagestyle default
+\tracking_changes false
+\output_changes false
+\author ""
+\author ""
+\end_header
+
+\begin_body
+
+\begin_layout Standard
+\begin_inset Note Note
+status open
+
+\begin_layout Standard
+Some things to fix in a future version:
+\end_layout
+
+\begin_layout Standard
+- trim a bit of time
+\end_layout
+
+\begin_layout Standard
+- add more about ipython and my own python work, reduce that of others
+\end_layout
+
+\begin_layout Standard
+- add a final python pros/cons, esp.
+ the cons part.
+ It will make things more balanced.
+\end_layout
+
+\begin_layout Standard
+- the PDE part repeats a bit the 'python benefits' which were already pounded
+ on.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset ERT
+status open
+
+\begin_layout Standard
+
+% disable the bottom bar for the title and outline pages
+\end_layout
+
+\begin_layout Standard
+
+\end_layout
+
+\begin_layout Standard
+
+
+\backslash
+setbeamertemplate{footline}{}
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset ERT
+status open
+
+\begin_layout Standard
+
+
+\backslash
+vspace*{-5mm}
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Title
+Python in Scientific Computing
+\begin_inset OptArg
+status open
+
+\begin_layout Standard
+Python & Scientific Computing
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subtitle
+An Introduction
+\end_layout
+
+\begin_layout Author
+Fernando\InsetSpace ~
+Pérez
+\newline
+
+\family typewriter
+\size scriptsize
+<Fer...@be...>
+\family default
+\size default
+
+\newline
+John Hunter
+\newline
+
+\family typewriter
+\size scriptsize
+<jd...@gm...>
+\family default
+\size default
+
+\begin_inset OptArg
+status open
+
+\begin_layout Standard
+FP/JDH
+\begin_inset Note Note
+status collapsed
+
+\begin_layout Standard
+This is used by the 'split' footline theme on the left side of the page
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\begin_inset ERT
+status collapsed
+
+\begin_layout Standard
+
+
+\backslash
+vspace{5mm}
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Institute
+Neuroscience, UC Berkeley
+\newline
+Tradelink
+\begin_inset Note Note
+status open
+
+\begin_layout Standard
+- Use the
+\backslash
+inst command only if there are several affiliations.
+\end_layout
+
+\begin_layout Standard
+- Keep it simple, no one is interested in your street address.
+\end_layout
+
+\end_inset
+
+
+\begin_inset OptArg
+status open
+
+\begin_layout Standard
+UC Berkeley/Tradelink
+\begin_inset Note Note
+status open
+
+\begin_layout Standard
+optional, but mostly needed
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\begin_inset ERT
+status collapsed
+
+\begin_layout Standard
+
+
+\backslash
+vspace{5mm}
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Date
+Joint Sciences Division, Claremont, CA
+\newline
+Oct 25, 2008
+\begin_inset OptArg
+status open
+
+\begin_layout Standard
+Claremont, 10/25/08
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Note Note
+status open
+
+\begin_layout Standard
+If you have a file called "institution-logo-filename.xxx", where xxx is a
+ graphic format that can be processed by latex or pdflatex, resp., then you
+ can add a logo by uncommenting the following:
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset ERT
+status collapsed
+
+\begin_layout Standard
+
+%
+\backslash
+pgfdeclareimage[height=0.5cm]{institution-logo}{institution-logo-filename}
+\end_layout
+
+\begin_layout Standard
+
+\end_layout
+
+\begin_layout Standard
+
+%
+\backslash
+logo{
+\backslash
+pgfuseimage{institution-logo}}
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Note Note
+status open
+
+\begin_layout Standard
+The following causes the table of contents to be shown at the beginning
+ of every Section.
+ Delete this, if you do not want it.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset ERT
+status collapsed
+
+\begin_layout Standard
+
+
+\backslash
+AtBeginSection[]{
+\end_layout
+
+\begin_layout Standard
+
+\end_layout
+
+\begin_layout Standard
+
+
+\backslash
+frame<beamer>{
+\end_layout
+
+\begin_layout Standard
+
+\end_layout
+
+\begin_layout Standard
+
+
+\backslash
+frametitle{Outline}
+\end_layout
+
+\begin_layout Standard
+
+\end_layout
+
+\begin_layout Standard
+
+
+\backslash
+tableofcontents[currentsection]
+\end_layout
+
+\begin_layout Standard
+
+\end_layout
+
+\begin_layout Standard
+
+}
+\end_layout
+
+\begin_layout Standard
+
+\end_layout
+
+\begin_layout Standard
+
+}
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Note Note
+status open
+
+\begin_layout Standard
+If you wish to uncover everything in a step-wise fashion, uncomment the
+ following command:
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset ERT
+status collapsed
+
+\begin_layout Standard
+
+%
+\backslash
+beamerdefaultoverlayspecification{<+->}
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset ERT
+status open
+
+\begin_layout Standard
+
+% reactivate the footline
+\end_layout
+
+\begin_layout Standard
+
+\end_layout
+
+\begin_layout Standard
+
+
+\backslash
+setbeamertemplate{footline}[infolines theme]
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout BeginFrame
+Outline
+\end_layout
+
+\begin_layout Standard
+\begin_inset LatexCommand tableofcontents
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Section
+Scientific Computing
+\begin_inset OptArg
+status open
+
+\begin_layout Standard
+SciComp
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+Existing tools
+\end_layout
+
+\begin_layout BeginFrame
+Pure Fortran, C and C++
+\end_layout
+
+\begin_layout Itemize
+Tools optimized for the CPU, not the developer.
+\end_layout
+
+\begin_layout Itemize
+Low-level (data types and libraries).
+\end_layout
+
+\begin_layout Itemize
+Difficult access to visualization, quick profiling, text processing,
+\begin_inset ERT
+status collapsed
+
+\begin_layout Standard
+
+
+\backslash
+ldots
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Itemize
+No interactive facilities.
+\end_layout
+
+\begin_layout Standard
+
+\series bold
+\color blue
+However!
+\end_layout
+
+\begin_layout Itemize
+They deliver excellent performance.
+\end_layout
+
+\begin_layout Itemize
+Millions of LOC in proven scientific codes.
+
+\end_layout
+
+\begin_layout Itemize
+We need to
+\emph on
+\color blue
+work with these tools
+\emph default
+\color inherit
+, not replace them!
+\end_layout
+
+\begin_layout BeginFrame
+Complementary high level tools
+\end_layout
+
+\begin_layout Itemize
+Mathematica, Maple, Matlab, IDL: extremely popular, for good reasons.
+\end_layout
+
+\begin_deeper
+\begin_layout Itemize
+Interactivity, visualization, extensive libraries.
+\end_layout
+
+\begin_layout Itemize
+Unpleasant for large-scale programs and non-mathematical tasks.
+\end_layout
+
+\begin_layout Itemize
+Expensive, proprietary: lock-in.
+\end_layout
+
+\end_deeper
+\begin_layout Itemize
+Another common approach: the `command pipeline'
+\end_layout
+
+\begin_deeper
+\begin_layout Itemize
+FORTRAN, C, C++ programs ...
+\end_layout
+
+\begin_layout Itemize
+driven by Bash/awk/sed/Perl scripts ...
+\end_layout
+
+\begin_layout Itemize
+which feed them input and send the output ...
+\end_layout
+
+\begin_layout Itemize
+to visualization/analysis programs.
+\end_layout
+
+\end_deeper
+\begin_layout Subsection
+Python?
+\begin_inset OptArg
+status open
+
+\begin_layout Standard
+Python
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout BeginFrame
+Python in this context
+\end_layout
+
+\begin_layout Itemize
+
+\color blue
+Free
+\color none
+ (BSD license), highly portable (Linux, OSX, Windows, lots...).
+\end_layout
+
+\begin_layout Itemize
+
+\color blue
+Interactive
+\color none
+ interpreter provided.
+\end_layout
+
+\begin_layout Itemize
+Extremely readable syntax (
+\color blue
+
+\begin_inset Quotes eld
+\end_inset
+
+executable pseudo-code
+\begin_inset Quotes erd
+\end_inset
+
+
+\color none
+).
+\end_layout
+
+\begin_layout Itemize
+
+\color blue
+Simple
+\color none
+: non-professional programmers can use it effectively.
+\end_layout
+
+\begin_layout Itemize
+Clean object oriented model, but
+\color none
+
+\color blue
+not mandatory
+\color none
+.
+\end_layout
+
+\begin_layout Itemize
+Rich built-in types: lists, sets, dictionaries (hash tables), strings, ...
+\end_layout
+
+\begin_layout Itemize
+Very comprehensive standard library (
+\color blue
+batteries included
+\color none
+)
+\end_layout
+
+\begin_layout Itemize
+Standard libraries for IDL/Matlab-like arrays (NumPy)
+\end_layout
+
+\begin_layout Itemize
+Easy to wrap existing C, C++ and FORTRAN codes.
+\end_layout
+
+\begin_layout Section
+Interlude: Python in the real world
+\begin_inset OptArg
+status collapsed
+
+\begin_layout Standard
+Examples
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+EEG analysis for epilepsy
+\begin_inset OptArg
+status open
+
+\begin_layout Standard
+EEG
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout BeginPlainFrame
+Data analysis for epilepsy surgery
+\end_layout
+
+\begin_layout FrameSubtitle
+Isolating the origin of drug-resistant epileptic seizures which require
+ surgery.
+\end_layout
+
+\begin_layout Standard
+John Hunter, Department of Pediatric Neurology, University of Chicago.
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename fig/mpl_brain1.png
+ lyxscale 50
+ width 80text%
+ keepAspectRatio
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout BeginPlainFrame
+Electrode location in 3D, combined with MRI data
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename fig/mpl_brain3.png
+ lyxscale 50
+ width 90text%
+ keepAspectRatio
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout BeginPlainFrame
+Correlation analysis of seizure data
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename fig/mpl_brain4.png
+ lyxscale 50
+ width 90text%
+ keepAspectRatio
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout BeginPlainFrame
+Final location of epileptic foci for surgery
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename fig/mpl_brain5.png
+ lyxscale 50
+ width 90text%
+ keepAspectRatio
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+Multiwavelets for PDEs
+\begin_inset OptArg
+status open
+
+\begin_layout Standard
+PDEs
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout BeginFrame
+Adaptive, multiwavelet algorithms for integral operators
+\end_layout
+
+\begin_layout Standard
+Gregory Beylkin, Vani Cheruvu, Fernando Perez.
+ Applied Math, U.
+ of Colorado at Boulder.
+\end_layout
+
+\begin_layout Itemize
+Fast application of integral kernels.
+ (Partial Differential Equations)
+\end_layout
+
+\begin_layout Itemize
+Implementation went from 1 to 3 dimensions directly (
+\emph on
+extremely
+\emph default
+ unusual).
+\end_layout
+
+\begin_layout Itemize
+Very complex algorithm that goes beyond pure numerics.
+\end_layout
+
+\begin_layout Itemize
+Very good performance, thanks to NumPy, F2PY and weave.
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename fig/rho_2d_surf.png
+ lyxscale 80
+ width 35text%
+
+\end_inset
+
+
+\begin_inset ERT
+status collapsed
+
+\begin_layout Standard
+
+
+\backslash
+hspace{1cm}
+\end_layout
+
+\end_inset
+
+
+\begin_inset Graphics
+ filename fig/rho_2d_skel.eps
+ lyxscale 80
+ width 25text%
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+JPL: Mars mission data visualization
+\begin_inset OptArg
+status collapsed
+
+\begin_layout Standard
+JPL - Mars
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout BeginPlainFrame
+JPL: Mars mission trajectory design and nav data
+\end_layout
+
+\begin_layout FrameSubtitle
+Ted Drain and Lynn Craig, Jet Propulsion Laboratory (NASA/Caltech)
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+\size footnotesize
+From: Name Elided <nam...@jp...>
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+\size footnotesize
+Date: Oct 2, 2007 7:15 PM
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+\size footnotesize
+Subject: Fwd: matplotlib bug numbers
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+\size footnotesize
+To: John Hunter <jd...@gm...>
+\end_layout
+
+\begin_layout Standard
+\begin_inset ERT
+status open
+
+\begin_layout Standard
+
+
+\backslash
+vspace{5mm}
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+\size tiny
+One of my lead developers mentioned that they had sent a bug to you about
+ the annotations feature of MatPlotLib.
+ Would you be able to let me know what the timeline is to resolve that bug?
+ The reason is that
+\series bold
+\color red
+the feature is needed for the Phoenix project and their arrival at Mars
+ will be in March sometime
+\series default
+\color inherit
+, but they are doing their testing in the coming few months.
+ This annotation feature is used on reports that present the analysis of
+ the trajectory to the navigation team and it shows up on our schedule.
+
+\series bold
+\color red
+It would really help me to know approximately when it could be resolved.
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+\size tiny
+B-plane plots are used to show the trajectory of a spacecraft with respect
+ to the target body (specifically perpendicular to the incoming asymptote
+ of the spacecraft trajectory) and we plot them with the y-axis inverted.
+ The plot is used heavily in flight operations so it is important to our
+ customers.
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+\size tiny
+In addition, we have what is called a thundering heard plot where many different
+ trajectory solutions (determined from different measurement sources) are
+ plotted together.
+ The annotations are import there so we can see which plot corresponds to
+ each source of data.
+ I hope it helps to know how your code will be used in spacecraft navigation.
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+\size tiny
+Thanks for all your efforts.
+\end_layout
+
+\begin_layout BeginPlainFrame
+JPL: Mars mission data visualization
+\end_layout
+
+\begin_layout Standard
+Expected communication power levels between an orbiting spacecraft and a
+ lander as it goes through the atmosphere:
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename fig/jpl_lander_comm_power.png
+ lyxscale 25
+ width 90text%
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout BeginPlainFrame
+JPL: Mars mission data visualization (2)
+\end_layout
+
+\begin_layout Standard
+Summary of the current navigation team activities and modelling (data used,
+ event times etc):
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset ERT
+status open
+
+\begin_layout Standard
+
+
+\backslash
+vspace{-3mm}
+\end_layout
+
+\end_inset
+
+
+\begin_inset Graphics
+ filename fig/jpl_nav_summary.png
+ lyxscale 50
+ width 90text%
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+PMV: structural bioinformatics
+\begin_inset OptArg
+status collapsed
+
+\begin_layout Standard
+PMV
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout BeginPlainFrame
+PMV: the Python Molecule Viewer
+\end_layout
+
+\begin_layout FrameSubtitle
+Michel F.
+ Sanner, Molecular Biology Department, The Scripps Research Institute.
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename fig/pmv.png
+ lyxscale 50
+ width 100text%
+ keepAspectRatio
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+MayaVi: customizable data visualization
+\begin_inset OptArg
+status open
+
+\begin_layout Standard
+MayaVi
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout BeginFrame
+MayaVi: sophisticated data visualization
+\end_layout
+
+\begin_layout Itemize
+Free, easy to use scientific data visualizer.
+\end_layout
+
+\begin_layout Itemize
+Heavy lifting of OpenGL-based rendering: VTK (a C++ library).
+\end_layout
+
+\begin_layout Itemize
+A very good example of how to properly use Python:
+\end_layout
+
+\begin_deeper
+\begin_layout Itemize
+MayaVi is a standalone GUI program...
+\end_layout
+
+\begin_layout Itemize
+but also a Python library callable by any other Python program.
+\end_layout
+
+\begin_layout Itemize
+Python: very easy to modify, even by adding at runtime user-defined modules
+ which populate the GUI automatically.
+\end_layout
+
+\begin_layout Itemize
+C++: excellent rendering performance, fully hardware-accelerated OpenGL.
+\end_layout
+
+\end_deeper
+\begin_layout Standard
+
+\series bold
+\color blue
+The punchline:
+\series default
+\color none
+ fully programmable visualization, with builtin access to all kinds of numerical
+ (and other) libraries from within the viz tool.
+\end_layout
+
+\begin_layout BeginPlainFrame
+FluidLab: a MayaVi based CFD visualization tool
+\end_layout
+
+\begin_layout Standard
+K.
+ Julien, P.
+ Schmitt (now NCAR), B.
+ Barrow, F.
+ Pérez (App.
+ Math, CU).
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename fig/Fluidlab5.png
+ lyxscale 50
+ width 90text%
+ keepAspectRatio
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout BeginPlainFrame
+Volumetric rendering with FluidLab
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename fig/Fluidlab6.png
+ lyxscale 50
+ width 90text%
+ keepAspectRatio
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+SAGE: System for Algebra and Geometry Experimentation
+\begin_inset OptArg
+status collapsed
+
+\begin_layout Standard
+SAGE
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout BeginPlainFrame
+SAGE: open source mathematics
+\end_layout
+
+\begin_layout FrameSubtitle
+Winner of the 2007 Trophés du Libre, scientific software category
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename fig/sage_notebook-medium.jpg
+ lyxscale 50
+ width 90text%
+ keepAspectRatio
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+IPython
+\end_layout
+
+\begin_layout BeginFrame
+IPython
+\end_layout
+
+\begin_layout FrameSubtitle
+Extensible interactive environment with parallel computing support
+\end_layout
+
+\begin_layout Enumerate
+
+\color blue
+A better Python shell
+\color none
+: object introspection, system access, 'magic' command system for adding
+ functionality when working interactively,
+\begin_inset ERT
+status collapsed
+
+\begin_layout Standard
+
+
+\backslash
+ldots
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Enumerate
+
+\color blue
+An embeddable interpreter
+\color none
+: useful for debugging and for mixing batch-processing with interactive
+ work.
+\end_layout
+
+\begin_layout Enumerate
+
+\color blue
+A flexible component
+\color none
+: you can use it as the base environment for other systems with Python as
+ the underlying language.
+ It is very configurable in this direction.
+\end_layout
+
+\begin_layout Enumerate
+
+\color blue
+A system for interactive control of distributed/parallel computing systems.
+
+\color none
+
+\end_layout
+
+\begin_layout Enumerate
+
+\color blue
+An interactive component
+\color none
+ we can plug into GUIs, browser-based shells, etc.
+\end_layout
+
+\begin_layout BeginPlainFrame
+IPython: Matlab/IDL-like interactive use
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename fig/pylab-screen.png
+ lyxscale 30
+ width 90text%
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout BeginPlainFrame
+IPython: interactive control of VTK visualizations
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename fig/mlab-screen-black.png
+ lyxscale 50
+ width 90text%
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout BeginFrame
+Distributed/parallel computing
+\end_layout
+
+\begin_layout Standard
+Work with Brian Granger (Cal State San Luis Obispo) and Min Ragan-Kelley
+ (U.
+ C.
+ Berkeley).
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename fig/ipython_parallel.png
+ lyxscale 50
+ width 80text%
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout BeginPlainFrame
+High-level graphical control of parallel codes
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename fig/vision_beam_pattern.png
+ lyxscale 50
+ width 80text%
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+Others
+\end_layout
+
+\begin_layout BeginFrame
+Who else?
+\end_layout
+
+\begin_layout Standard
+
+\series bold
+Academia
+\end_layout
+
+\begin_layout Itemize
+
+\color blue
+PyRAF:
+\color none
+ Astronomical data analysis (Hubble Space Telescope).
+\end_layout
+
+\begin_layout Itemize
+
+\color blue
+PyTrilinos:
+\color none
+ Parallel solvers (Sandia National Lab's ).
+\end_layout
+
+\begin_layout Itemize
+
+\color blue
+DANSE:
+\color none
+ Spallation Neutron Source (ORNL/Caltech).
+\end_layout
+
+\begin_layout Itemize
+
+\color blue
+CDAT
+\color none
+: Climate Data Analysis Tools (Lawrence Livermore).
+\end_layout
+
+\begin_layout Itemize
+
+\color blue
+OOF2
+\color none
+: Finite Element Analysis of Microstructures (NIST).
+\end_layout
+
+\begin_layout Standard
+
+\series bold
+Industry
+\end_layout
+
+\begin_layout Itemize
+
+\color blue
+InteractiveSupercomputing.com:
+\color none
+ Python interface to their proprietary backend.
+\end_layout
+
+\begin_layout Itemize
+
+\color blue
+Numenta:
+\color none
+ pattern recognition algorithms (Jeff Hawkins-Palm)
+\end_layout
+
+\begin_layout Itemize
+
+\color blue
+Google/YouTube:
+\color none
+ Internally, new AppEngine web service platform.
+\end_layout
+
+\begin_layout Standard
+
+\series bold
+\color blue
+Lots
+\series default
+\color inherit
+ more
+\end_layout
+
+\begin_layout Itemize
+
+\color blue
+\begin_inset LatexCommand htmlurl
+target "http://www.scipy.org/Topical_Software"
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Section
+Development in Python
+\begin_inset OptArg
+status collapsed
+
+\begin_layout Standard
+Development\InsetSpace ~
+Model
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout BeginPlainFrame
+Python is a general programming language
+\end_layout
+
+\begin_layout ExampleBlock
+\begin_inset ERT
+status open
+
+\begin_layout Standard
+
+{
+\end_layout
+
+\end_inset
+
+
+\series bold
+It's not a bug, it's a feature
+\series default
+!
+\begin_inset ERT
+status open
+
+\begin_layout Standard
+
+}
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_deeper
+\begin_layout Itemize
+Get others to develop the non-scientific tools you may need.
+\end_layout
+
+\begin_layout Itemize
+Networking, text processing, XML parsing, databases, etc
+\begin_inset ERT
+status open
+
+\begin_layout Standard
+
+
+\backslash
+ldots
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Itemize
+Integrated support for automated testing.
+\end_layout
+
+\begin_layout Itemize
+Excellent documentation tools
+\end_layout
+
+\begin_layout Itemize
+Supports all major GUI toolkits.
+\end_layout
+
+\end_deeper
+\begin_layout Separator
+
+\end_layout
+
+\begin_layout AlertBlock
+\begin_inset ERT
+status open
+
+\begin_layout Standard
+
+{There are still rough edges - but we're working on these}
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_deeper
+\begin_layout Itemize
+Installation, deployment: harder than needed.
+\end_layout
+
+\begin_layout Itemize
+No good, single-point of entry environment (but see Sage)
+\end_layout
+
+\begin_layout Itemize
+Documentation too scattered.
+\end_layout
+
+\begin_layout Itemize
+Your favorite/critical tool may well not exist
+\series bold
+yet
+\series default
+.
+\end_layout
+
+\begin_layout Itemize
+Funding agency support for infrastructure work is difficult to get.
+\end_layout
+
+\end_deeper
+\begin_layout BeginFrame
+Using your codes from today with Python
+\end_layout
+
+\begin_layout Itemize
+Code too monolithic but with good core pieces?
+\end_layout
+
+\begin_deeper
+\begin_layout Itemize
+Break into a
+\color blue
+library core
+\color inherit
+ and control layers.
+\end_layout
+
+\begin_layout Itemize
+
+\color blue
+Wrap
+\color inherit
+ the libraries and expose them to Python.
+\end_layout
+
+\begin_layout Itemize
+Use Python for control or use
+\color blue
+interactively
+\color inherit
+.
+\end_layout
+
+\end_deeper
+\begin_layout Itemize
+For existing libraries in C/C++/Fortran
+\end_layout
+
+\begin_deeper
+\begin_layout Itemize
+Provide Python
+\color blue
+bindings
+\color inherit
+ for them.
+\end_layout
+
+\begin_layout Itemize
+It will make it much easier for others to test/use them.
+\end_layout
+
+\begin_layout Itemize
+The network economy benefits all.
+ In this case,
+\color blue
+
+\begin_inset Formula $O(n^{2})$
+\end_inset
+
+ is good!
+\end_layout
+
+\end_deeper
+\begin_layout BeginFrame
+Writing a new code?
+\end_layout
+
+\begin_layout Itemize
+Avoid whole programs in C/Fortran:
+\color none
+
+\color red
+you are optimizing globally!
+\end_layout
+
+\begin_deeper
+\begin_layout Itemize
+Prototype the problem in Python (get the algorithm right first)
+\end_layout
+
+\begin_deeper
+\begin_layout Itemize
+using fast libraries.
+\end_layout
+
+\end_deeper
+\begin_layout Itemize
+
+\color blue
+Profile
+\color none
+the hotspots.
+\end_layout
+
+\begin_layout Itemize
+Optimize
+\color none
+
+\color blue
+only those
+\color inherit
+, if needed.
+\end_layout
+
+\end_deeper
+\begin_layout Itemize
+The result may be production-ready:
+\color none
+
+\color blue
+less throw-away prototypes.
+\end_layout
+
+\begin_deeper
+\begin_layout Itemize
+Make your code available as a library for
+\color none
+
+\color blue
+interactive use
+\color none
+.
+\end_layout
+
+\begin_layout Itemize
+Integrate plotting, visualization, logging, ..., into your objects.
+\end_layout
+
+\end_deeper
+\begin_layout Section*
+Wrapup
+\end_layout
+
+\begin_layout BeginFrame
+Wrapup
+\end_layout
+
+\begin_layout Standard
+
+\series bold
+\color blue
+Python
+\end_layout
+
+\begin_layout Itemize
+Rapidly growing in scientific computing.
+\end_layout
+
+\begin_layout Itemize
+Collaborative effort:
+\color blue
+by scientists, for scientists.
+\end_layout
+
+\begin_layout Itemize
+An open stack supports truly
+\color blue
+reproducible computational research
+\color inherit
+.
+\end_layout
+
+\begin_layout Standard
+
+\series bold
+\color blue
+What's in it for you?
+\end_layout
+
+\begin_layout Itemize
+Hopefully a very useful tool.
+\end_layout
+
+\begin_layout Itemize
+Provide Python bindings to your own research codes.
+\end_layout
+
+\begin_deeper
+\begin_layout Itemize
+...
+ and we all benefit from the resulting network effect.
+\end_layout
+
+\end_deeper
+\begin_layout Standard
+\align center
+
+\series bold
+\size large
+Join in,
+\color blue
+there's plenty to do!
+\end_layout
+
+\begin_layout BeginPlainFrame
+Thank you! Questions?
+\end_layout
+
+\begin_layout FrameSubtitle
+Credit: http://xkcd.com/353
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset ERT
+status open
+
+\begin_layout Standard
+
+
+\backslash
+vspace{-5mm}
+\end_layout
+
+\end_inset
+
+
+\begin_inset Graphics
+ filename fig/xkcd_python.png
+ lyxscale 50
+ height 85pheight%
+ BoundingBox -4bp -4bp 518bp 588bp
+
+\end_inset
+
+
+\end_layout
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[truncated message content] |
|
From: <jd...@us...> - 2008-10-25 04:21:55
|
Revision: 6332
http://matplotlib.svn.sourceforge.net/matplotlib/?rev=6332&view=rev
Author: jdh2358
Date: 2008-10-25 04:21:52 +0000 (Sat, 25 Oct 2008)
Log Message:
-----------
added hello world
Added Paths:
-----------
trunk/py4science/talks/fig/hello_world.png
Added: trunk/py4science/talks/fig/hello_world.png
===================================================================
(Binary files differ)
Property changes on: trunk/py4science/talks/fig/hello_world.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <fer...@us...> - 2008-10-25 03:44:47
|
Revision: 6331
http://matplotlib.svn.sourceforge.net/matplotlib/?rev=6331&view=rev
Author: fer_perez
Date: 2008-10-25 03:44:44 +0000 (Sat, 25 Oct 2008)
Log Message:
-----------
Updated skeletons and mkprob to report number of lines missing.
Modified Paths:
--------------
trunk/py4science/examples/mkprob.py
trunk/py4science/examples/skel/fft_imdenoise_skel.py
trunk/py4science/examples/skel/qsort_skel.py
trunk/py4science/examples/skel/quad_newton_skel.py
trunk/py4science/examples/skel/trapezoid_skel.py
Modified: trunk/py4science/examples/mkprob.py
===================================================================
--- trunk/py4science/examples/mkprob.py 2008-10-25 03:37:12 UTC (rev 6330)
+++ trunk/py4science/examples/mkprob.py 2008-10-25 03:44:44 UTC (rev 6331)
@@ -91,9 +91,9 @@
# Add the summary of 'raise' lines
# flush counter of code (disabled, we report static summary)
- #msg = '1 line' if del_lines==1 else ('%s lines' % del_lines)
- #exc = exc_tpl % msg
- exc = exc_tpl
+ msg = '1 line' if del_lines==1 else ('%s lines' % del_lines)
+ exc = exc_tpl % msg
+ #exc = exc_tpl
# Use the last value of 'space'
line = '%s%s' % (spaces[0],exc)
@@ -104,8 +104,8 @@
return del_lines
# used to report actual # of lines removed - disabled
- #exc_tpl = "raise NotImplementedError('%s missing')\n"
- exc_tpl = "raise NotImplementedError('insert missing code here')\n"
+ exc_tpl = "raise NotImplementedError('Original solution has %s')\n"
+ #exc_tpl = "raise NotImplementedError('insert missing code here')\n"
# states for state machine and other initialization
normal,delete = 0,1
@@ -241,7 +241,7 @@
clean = """
first line
- raise NotImplementedError('insert missing code here')
+ raise NotImplementedError('Original solution has 1 line')
second line
"""
@@ -279,12 +279,12 @@
first line
# Hint: remember that
# idea we discussed before...
- raise NotImplementedError('insert missing code here')
+ raise NotImplementedError('Original solution has 3 lines')
second line:
- raise NotImplementedError('insert missing code here')
+ raise NotImplementedError('Original solution has 2 lines')
third line
- raise NotImplementedError('insert missing code here')
+ raise NotImplementedError('Original solution has 2 lines')
"""
cleaned = src2skel(srclines)
yield str_match,cleaned,clean
Modified: trunk/py4science/examples/skel/fft_imdenoise_skel.py
===================================================================
--- trunk/py4science/examples/skel/fft_imdenoise_skel.py 2008-10-25 03:37:12 UTC (rev 6330)
+++ trunk/py4science/examples/skel/fft_imdenoise_skel.py 2008-10-25 03:44:44 UTC (rev 6331)
@@ -17,12 +17,12 @@
# Compute the magnitude of the input F (call it mag). Then, rescale mag by
# amplify/maximum_of_mag. Numpy arrays can be scaled in-place with ARR *=
# number. For the max of an array, look for its max method.
- raise NotImplementedError('insert missing code here')
+ raise NotImplementedError('Original solution has 2 lines')
# Next, clip all values larger than one to one. You can set all elements
# of an array which satisfy a given condition with array indexing syntax:
# ARR[ARR<VALUE] = NEWVALUE, for example.
- raise NotImplementedError('insert missing code here')
+ raise NotImplementedError('Original solution has 1 line')
# Display: this one already works, if you did everything right with mag
plt.imshow(mag, plt.cm.Blues)
@@ -39,7 +39,7 @@
# - extract all rows, all columns, 0-th plane to get the first
# channel
# - the resulting array should have 2 dimensions only
- raise NotImplementedError('insert missing code here')
+ raise NotImplementedError('Original solution has 1 line')
print "Image shape:",im.shape
except:
print "Could not open image."
@@ -48,7 +48,7 @@
# Compute the 2d FFT of the input image
# Hint: Look for a 2-d FFT in np.fft.
# Note: call this variable 'F', which is the name we'll be using below.
- raise NotImplementedError('insert missing code here')
+ raise NotImplementedError('Original solution has 1 line')
# In the lines following, we'll make a copy of the original spectrum and
# truncate coefficients. NO immediate code is to be written right here.
@@ -58,25 +58,25 @@
# Call ff a copy of the original transform. Numpy arrays have a copy
# method for this purpose.
- raise NotImplementedError('insert missing code here')
+ raise NotImplementedError('Original solution has 1 line')
# Set r and c to be the number of rows and columns of the array.
# Hint: use the array's shape attribute.
- raise NotImplementedError('insert missing code here')
+ raise NotImplementedError('Original solution has 1 line')
# Set to zero all rows with indices between r*keep_fraction and
# r*(1-keep_fraction):
- raise NotImplementedError('insert missing code here')
+ raise NotImplementedError('Original solution has 1 line')
# Similarly with the columns:
- raise NotImplementedError('insert missing code here')
+ raise NotImplementedError('Original solution has 1 line')
# Reconstruct the denoised image from the filtered spectrum, keep only the
# real part for display.
# Hint: There's an inverse 2d fft in the np.fft module as well (don't
# forget that you only want the real part).
# Call the result im_new,
- raise NotImplementedError('insert missing code here')
+ raise NotImplementedError('Original solution has 1 line')
# Show the results
# The code below already works, if you did everything above right.
Modified: trunk/py4science/examples/skel/qsort_skel.py
===================================================================
--- trunk/py4science/examples/skel/qsort_skel.py 2008-10-25 03:37:12 UTC (rev 6330)
+++ trunk/py4science/examples/skel/qsort_skel.py 2008-10-25 03:44:44 UTC (rev 6331)
@@ -37,13 +37,13 @@
"""
# Hint: remember that all recursive functions need an exit condition
- raise NotImplementedError('insert missing code here')
+ raise NotImplementedError('Original solution has 2 lines')
# Select pivot and apply recursively
- raise NotImplementedError('insert missing code here')
+ raise NotImplementedError('Original solution has 3 lines')
# Upon return, make sure to properly concatenate the output lists
- raise NotImplementedError('insert missing code here')
+ raise NotImplementedError('Original solution has 1 line')
#-----------------------------------------------------------------------------
Modified: trunk/py4science/examples/skel/quad_newton_skel.py
===================================================================
--- trunk/py4science/examples/skel/quad_newton_skel.py 2008-10-25 03:37:12 UTC (rev 6330)
+++ trunk/py4science/examples/skel/quad_newton_skel.py 2008-10-25 03:44:44 UTC (rev 6331)
@@ -10,7 +10,7 @@
# test input function
def f(t):
# f(t): t * sin^2(t)
- raise NotImplementedError('insert missing code here')
+ raise NotImplementedError('Original solution has 1 line')
def g(t):
"Exact form for g by integrating f(t)"
@@ -21,18 +21,18 @@
"g(t) obtained by numerical integration"
u = 0.25
# Hint: use quad, see its return value carefully.
- raise NotImplementedError('insert missing code here')
+ raise NotImplementedError('Original solution has 1 line')
# main
tguess = 10.0
print '"Exact" solution (knowing the analytical form of the integral)'
-raise NotImplementedError('insert missing code here')
+raise NotImplementedError('Original solution has 1 line')
print "t0, g(t0) =",t0,g(t0)
print
print "Solution using the numerical integration technique"
-raise NotImplementedError('insert missing code here')
+raise NotImplementedError('Original solution has 1 line')
print "t1, g(t1) =",t1,g(t1)
print
Modified: trunk/py4science/examples/skel/trapezoid_skel.py
===================================================================
--- trunk/py4science/examples/skel/trapezoid_skel.py 2008-10-25 03:37:12 UTC (rev 6330)
+++ trunk/py4science/examples/skel/trapezoid_skel.py 2008-10-25 03:44:44 UTC (rev 6331)
@@ -20,13 +20,13 @@
#
# Hint: if the two inputs have mismatched lengths or less than 2
# elements, we raise ValueError with an explanatory message.
- raise NotImplementedError('insert missing code here')
+ raise NotImplementedError('Original solution has 4 lines')
# Efficient application of trapezoid rule via numpy
#
# Hint: think of using numpy slicing to compute the moving difference in
# the basic trapezoid formula.
- raise NotImplementedError('insert missing code here')
+ raise NotImplementedError('Original solution has 1 line')
def trapzf(f,a,b,npts=100):
"""Simple trapezoid-based integrator.
@@ -48,20 +48,20 @@
# what differences in timings result for long vectors x?
# Generate an equally spaced grid to sample the function.
- raise NotImplementedError('insert missing code here')
+ raise NotImplementedError('Original solution has 1 line')
# For an equispaced grid, the x spacing can just be read off from the first
# two points and factored out of the summation.
- raise NotImplementedError('insert missing code here')
+ raise NotImplementedError('Original solution has 1 line')
# Sample the input function at all values of x
#
# Hint: you need to make an array out of the evaluations, and the python
# builtin 'map' function can come in handy.
- raise NotImplementedError('insert missing code here')
+ raise NotImplementedError('Original solution has 1 line')
# Compute the trapezoid rule sum for the final result
- raise NotImplementedError('insert missing code here')
+ raise NotImplementedError('Original solution has 1 line')
#-----------------------------------------------------------------------------
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jd...@us...> - 2008-10-25 03:37:18
|
Revision: 6330
http://matplotlib.svn.sourceforge.net/matplotlib/?rev=6330&view=rev
Author: jdh2358
Date: 2008-10-25 03:37:12 +0000 (Sat, 25 Oct 2008)
Log Message:
-----------
reorg talk dir
Modified Paths:
--------------
trunk/py4science/examples/convolution_demo.py
trunk/py4science/examples/lotka_volterra.py
trunk/py4science/examples/mkprob.py
trunk/py4science/examples/skel/lotka_volterra_skel.py
trunk/py4science/workbook/README
trunk/py4science/workbook/add_problem
Added Paths:
-----------
trunk/py4science/talks/
trunk/py4science/talks/0712_ncar_intro.lyx
trunk/py4science/talks/0810_berkeley_intro.lyx
trunk/py4science/talks/fig/
trunk/py4science/talks/fig/Fluidlab5.png
trunk/py4science/talks/fig/Fluidlab6.png
trunk/py4science/talks/fig/ipython_parallel.eps
trunk/py4science/talks/fig/ipython_parallel.png
trunk/py4science/talks/fig/jpl_lander_comm_power.png
trunk/py4science/talks/fig/jpl_nav_summary.png
trunk/py4science/talks/fig/kernel2p.eps
trunk/py4science/talks/fig/kernel2p.png
trunk/py4science/talks/fig/mayavi_comb_vol.png
trunk/py4science/talks/fig/mlab-screen-black.png
trunk/py4science/talks/fig/mpl_brain1.png
trunk/py4science/talks/fig/mpl_brain2.png
trunk/py4science/talks/fig/mpl_brain3.png
trunk/py4science/talks/fig/mpl_brain4.png
trunk/py4science/talks/fig/mpl_brain5.png
trunk/py4science/talks/fig/ncar-world-seam.3.png
trunk/py4science/talks/fig/pmv.png
trunk/py4science/talks/fig/pylab-screen.png
trunk/py4science/talks/fig/rho_2d_skel.eps
trunk/py4science/talks/fig/rho_2d_surf.png
trunk/py4science/talks/fig/sage_notebook-medium.jpg
trunk/py4science/talks/fig/vision_beam_pattern.png
trunk/py4science/talks/fig/xkcd_python.png
trunk/py4science/talks/intro_python_scicomp.lyx
trunk/py4science/talks/matplotlib_intro.ppt
trunk/py4science/talks/pydap/
trunk/py4science/talks/pydap/pydap.lyx
trunk/py4science/talks/pydap/pydap.pdf
trunk/py4science/talks/pydap/pydap_arch.png
trunk/py4science/workbook/problems_skel/detect_action_potentials.py
trunk/py4science/workbook/problems_soln/detect_action_potentials.py
Removed Paths:
-------------
trunk/py4science/intro_talk/
trunk/py4science/slides/
trunk/py4science/talks/fig/Fluidlab5.png
trunk/py4science/talks/fig/Fluidlab6.png
trunk/py4science/talks/fig/ipython_parallel.eps
trunk/py4science/talks/fig/ipython_parallel.png
trunk/py4science/talks/fig/jpl_lander_comm_power.png
trunk/py4science/talks/fig/jpl_nav_summary.png
trunk/py4science/talks/fig/kernel2p.eps
trunk/py4science/talks/fig/kernel2p.png
trunk/py4science/talks/fig/mayavi_comb_vol.png
trunk/py4science/talks/fig/mlab-screen-black.png
trunk/py4science/talks/fig/mpl_brain1.png
trunk/py4science/talks/fig/mpl_brain2.png
trunk/py4science/talks/fig/mpl_brain3.png
trunk/py4science/talks/fig/mpl_brain4.png
trunk/py4science/talks/fig/mpl_brain5.png
trunk/py4science/talks/fig/ncar-world-seam.3.png
trunk/py4science/talks/fig/pmv.png
trunk/py4science/talks/fig/pylab-screen.png
trunk/py4science/talks/fig/rho_2d_skel.eps
trunk/py4science/talks/fig/rho_2d_surf.png
trunk/py4science/talks/fig/sage_notebook-medium.jpg
trunk/py4science/talks/fig/vision_beam_pattern.png
trunk/py4science/talks/fig/xkcd_python.png
trunk/py4science/talks/pydap/pydap.lyx
trunk/py4science/talks/pydap/pydap.pdf
trunk/py4science/talks/pydap/pydap_arch.png
Modified: trunk/py4science/examples/convolution_demo.py
===================================================================
--- trunk/py4science/examples/convolution_demo.py 2008-10-24 22:35:25 UTC (rev 6329)
+++ trunk/py4science/examples/convolution_demo.py 2008-10-25 03:37:12 UTC (rev 6330)
@@ -13,7 +13,7 @@
In this exercise, we will compute investigate the convolution of a
white noise process with a double exponential impulse response
-function, and compute the results
+function, and compute the results
* using numpy.convolve
@@ -21,40 +21,40 @@
temporal domain is a multiplication in the fourier domain
"""
-import numpy as npy
+import numpy as np
import matplotlib.mlab as mlab
-from pylab import figure, show
+import matplotlib.pyplot as plt
# build the time, input, output and response arrays
dt = 0.01
-t = npy.arange(0.0, 20.0, dt) # the time vector from 0..20
+t = np.arange(0.0, 20.0, dt) # the time vector from 0..20
Nt = len(t)
def impulse_response(t):
'double exponential response function'
- return (npy.exp(-t) - npy.exp(-5*t))*dt
+ return (np.exp(-t) - np.exp(-5*t))*dt
-x = npy.random.randn(Nt) # gaussian white noise
+x = np.random.randn(Nt) # gaussian white noise
# evaluate the impulse response function, and numerically convolve it
# with the input x
r = impulse_response(t) # evaluate the impulse function
-y = npy.convolve(x, r, mode='full') # convultion of x with r
+y = np.convolve(x, r, mode='full') # convultion of x with r
y = y[:Nt]
# compute y by applying F^-1[F(x) * F(r)]. The fft assumes the signal
# is periodic, so to avoid edge artificats, pad the fft with zeros up
# to the length of r + x do avoid circular convolution artifacts
-R = npy.fft.fft(r, len(r)+len(x)-1)
-X = npy.fft.fft(x, len(r)+len(x)-1)
+R = np.fft.fft(r, len(r)+len(x)-1)
+X = np.fft.fft(x, len(r)+len(x)-1)
Y = R*X
# now inverse fft and extract just the part up to len(x)
-yi = npy.fft.ifft(Y)[:len(x)].real
+yi = np.fft.ifft(Y)[:len(x)].real
# plot t vs x, t vs y and yi, and t vs r in three subplots
-fig = figure()
+fig = plt.figure()
ax1 = fig.add_subplot(311)
ax1.plot(t, x)
ax1.set_ylabel('input x')
@@ -73,4 +73,4 @@
fig.savefig('convolution_demo.png', dpi=150)
fig.savefig('convolution_demo.eps')
-show()
+plt.show()
Modified: trunk/py4science/examples/lotka_volterra.py
===================================================================
--- trunk/py4science/examples/lotka_volterra.py 2008-10-24 22:35:25 UTC (rev 6329)
+++ trunk/py4science/examples/lotka_volterra.py 2008-10-25 03:37:12 UTC (rev 6330)
@@ -1,24 +1,40 @@
-import numpy as n
-import pylab as p
+import numpy as np
+import matplotlib.pyplot as plt
import scipy.integrate as integrate
def dr(r, f):
- return alpha*r - beta*r*f
-
+ """
+ return the derivative of *r* (the rabbit population) evaulated as a
+ function of *r* and *f*. The function should work whether *r* and *f*
+ are scalars, 1D arrays or 2D arrays. The return value should have
+ the same dimensionality (shape) as the inputs *r* and *f*.
+ """
+ return alpha*r - beta*r*f #@
+
def df(r, f):
- return gamma*r*f - delta*f
+ """
+ return the derivative of *f* (the fox population) evaulated as a
+ function of *r* and *f*. The function should work whether *r* and *f*
+ are scalars, 1D arrays or 2D arrays. The return value should have
+ the same dimensionality (shape) as the inputs *r* and *f*.
+ """
+ return gamma*r*f - delta*f #@
def derivs(state, t):
"""
- Map the state variable [rabbits, foxes] to the derivitives
- [deltar, deltaf] at time t
+ Return the derivatives of r and f, stored in the *state* vector::
+
+ state = [r, f]
+
+ The return data should be [dr, df] which are the derivatives of r
+ and f at position state and time *t*
"""
- #print t, state
- r, f = state # rabbits and foxes
- deltar = dr(r, f) # change in rabbits
- deltaf = df(r, f) # change in foxes
- return deltar, deltaf
+ r, f = state # and foxes #@
+ deltar = dr(r, f) # in rabbits #@
+ deltaf = df(r, f) # in foxes #@
+ return deltar, deltaf #@
+# the parameters for rabbit and fox growth and interactions
alpha, delta = 1, .25
beta, gamma = .2, .05
@@ -26,53 +42,71 @@
r0 = 20
f0 = 10
-t = n.arange(0.0, 100, 0.1)
+# create a time array from 0..100 sampled at 0.1 second steps
+t = np.arange(0.0, 100, 0.1) #@
+
y0 = [r0, f0] # the initial [rabbits, foxes] state vector
-y = integrate.odeint(derivs, y0, t)
-r = y[:,0] # extract the rabbits vector
-f = y[:,1] # extract the foxes vector
-p.figure()
-p.plot(t, r, label='rabbits')
-p.plot(t, f, label='foxes')
-p.xlabel('time (years)')
-p.ylabel('population')
-p.title('population trajectories')
-p.grid()
-p.legend()
-p.savefig('lotka_volterra.png', dpi=150)
-p.savefig('lotka_volterra.eps')
+# integrate your ODE using scipy.integrate. Read the help to see what
+# is available
+#@ HINT: see scipy.integrate.odeint
+y = integrate.odeint(derivs, y0, t) #@
+# the return value from the integration is a Nx2 array. Extract it
+# into two 1D arrays caled r and f using numpy slice indexing
+r = y[:,0] # extract the rabbits vector #@
+f = y[:,1] # extract the foxes vector #@
-p.figure()
-p.plot(r, f, color='red')
-p.xlabel('rabbits')
-p.ylabel('foxes')
-p.title('phase plane')
+# time series plot: plot the population of rabbits and foxes as a
+# funciton of time
+plt.figure()
+plt.plot(t, r, label='rabbits')
+plt.plot(t, f, label='foxes')
+plt.xlabel('time (years)')
+plt.ylabel('population')
+plt.title('population trajectories')
+plt.grid()
+plt.legend()
+plt.savefig('lotka_volterra.png', dpi=150)
+plt.savefig('lotka_volterra.eps')
+# phase-plane plot: plot the population of foxes versus rabbits
+# make sure you include and xlabel, ylabel and title
+plt.figure() #@
+plt.plot(r, f, color='red') #@
+plt.xlabel('rabbits') #@
+plt.ylabel('foxes') #@
+plt.title('phase plane') #@
-# make a direction field plot with quiver
-rmax = 1.1 * r.max()
-fmax = 1.1 * f.max()
-R, F = n.meshgrid(n.arange(-1, rmax), n.arange(-1, fmax))
-dR = dr(R, F)
-dF = df(R, F)
-p.quiver(R, F, dR, dF)
+# Create 2D arrays for R and F to represent the entire phase plane --
+# the point (R[i,j], F[i,j]) is a single (rabbit, fox) combinations.
+# pass these arrays to the functions dr and df above to get 2D arrays
+# of dR and dF evaluated at every point in the phase plance.
+rmax = 1.1 * r.max() #@
+fmax = 1.1 * f.max() #@
+R, F = np.meshgrid(np.arange(-1, rmax), np.arange(-1, fmax)) #@
+dR = dr(R, F) #@
+dF = df(R, F) #@
+plt.quiver(R, F, dR, dF) #@
-R, F = n.meshgrid(n.arange(-1, rmax, .1), n.arange(-1, fmax, .1))
-dR = dr(R, F)
-dF = df(R, F)
-p.contour(R, F, dR, levels=[0], linewidths=3, colors='blue')
-p.contour(R, F, dF, levels=[0], linewidths=3, colors='green')
-p.ylabel('foxes')
-p.title('trajectory, direction field and null clines')
+# Now find the nul-clines, for dR and dF respectively. These are the
+# points where dR=0 and dF=0 in the (R, F) phase plane. You can use
+# matplotlib's countour routine to find the zero level. See the
+# levels keyword to contour. You will need a fine mesh of R and F,
+# reevaluate dr and df on the finer grid, and use contour to find the
+# level curves
+R, F = np.meshgrid(np.arange(-1, rmax, 0.1), np.arange(-1, fmax, 0.1)) #@
+dR = dr(R, F) #@
+dF = df(R, F) #@
+plt.contour(R, F, dR, levels=[0], linewidths=3, colors='blue') #@
+plt.contour(R, F, dF, levels=[0], linewidths=3, colors='green') #@
+plt.ylabel('foxes') #@
+plt.title('trajectory, direction field and null clines') #@
-p.savefig('lotka_volterra_pplane.png', dpi=150)
-p.savefig('lotka_volterra_pplane.eps')
+plt.savefig('lotka_volterra_pplane.png', dpi=150)
+plt.savefig('lotka_volterra_pplane.eps')
+plt.show()
-
-p.show()
-
Modified: trunk/py4science/examples/mkprob.py
===================================================================
--- trunk/py4science/examples/mkprob.py 2008-10-24 22:35:25 UTC (rev 6329)
+++ trunk/py4science/examples/mkprob.py 2008-10-25 03:37:12 UTC (rev 6330)
@@ -35,14 +35,14 @@
import sys
# Third-party imports
-import nose
+#import nose
# Constants
MARKER = '#@'
DEL_RE = re.compile(r'''^((\s*)(.*?))\s*%s\s*$''' % MARKER)
HINT_RE = re.compile(r'''^(?P<space>\s*)%s\s+(?P<hint>.*)$''' % MARKER)
-
+
#-----------------------------------------------------------------------------
# Main code begins
@@ -52,7 +52,7 @@
Inputs:
src : sequence of lines (file-like objects work out of the box)
"""
-
+
out = []
addline = out.append
for line in src:
@@ -66,7 +66,7 @@
# if marker is matched in code, strip it and leave the code
line = mdel.group(1)+'\n'
addline(line)
-
+
return ''.join(out)
@@ -94,19 +94,19 @@
#msg = '1 line' if del_lines==1 else ('%s lines' % del_lines)
#exc = exc_tpl % msg
exc = exc_tpl
-
+
# Use the last value of 'space'
line = '%s%s' % (spaces[0],exc)
out.append(line)
del_lines = 0
spaces[:] = []
-
+
return del_lines
-
+
# used to report actual # of lines removed - disabled
- #exc_tpl = "raise NotImplementedError('%s missing')\n"
+ #exc_tpl = "raise NotImplementedError('%s missing')\n"
exc_tpl = "raise NotImplementedError('insert missing code here')\n"
-
+
# states for state machine and other initialization
normal,delete = 0,1
state_cur = normal
@@ -114,7 +114,7 @@
spaces = []
normal_lines = []
out = []
-
+
# To remove multiple consecutive lines of input marked for deletion, we
# need a small state machine.
for line in src:
@@ -134,7 +134,7 @@
state_new = delete
del_lines += 1
spaces.append(mdel.group(2))
-
+
# Flush output only when there's a change of state
if state_new != state_cur:
del_lines = flush_buffers(normal_lines,del_lines)
@@ -144,7 +144,7 @@
# Final buffer flush is unconditional
flush_buffers(normal_lines)
-
+
return ''.join(out)
@@ -155,14 +155,14 @@
# get the mode of the input so that we can create the output files with the
# same mode
fmode = os.stat(fpath).st_mode
-
+
with open(fpath) as infile:
# Generate the skeleton
skel = src2skel(infile)
with open(fname_skel,'w') as fskel:
fskel.write(skel)
os.chmod(fname_skel,fmode)
-
+
# Reset the input file pointer and generate the solution
infile.seek(0)
soln = src2soln(infile)
@@ -193,7 +193,7 @@
def main(argv=None):
"""Main entry point as a command line script for normal execution"""
-
+
if argv is None:
argv = sys.argv
@@ -229,8 +229,8 @@
"""Check that two strings are equal ignoring trailing whitespace."""
#print '***S1\n',s1,'\n***S2\n',s2 # dbg
nose.tools.assert_equal(s1.rstrip(),s2.rstrip())
-
+
def test_simple():
src = """
first line
@@ -238,13 +238,13 @@
second line
"""
srclines = src.splitlines(True)
-
+
clean = """
first line
raise NotImplementedError('insert missing code here')
second line
"""
-
+
cleaned = src2skel(srclines)
yield str_match,cleaned,clean
@@ -255,8 +255,8 @@
"""
cleaned = src2soln(src.splitlines(True))
yield str_match,cleaned,clean
-
+
def test_multi():
src = """
first line
@@ -306,7 +306,7 @@
yield str_match,cleaned,clean
-...@no...ttest
+#@nose.tools.nottest
def test():
"""Simple self-contained test runner."""
nose.runmodule(__name__,exit=False,
Modified: trunk/py4science/examples/skel/lotka_volterra_skel.py
===================================================================
--- trunk/py4science/examples/skel/lotka_volterra_skel.py 2008-10-24 22:35:25 UTC (rev 6329)
+++ trunk/py4science/examples/skel/lotka_volterra_skel.py 2008-10-25 03:37:12 UTC (rev 6330)
@@ -1,24 +1,37 @@
-import numpy as n
-import pylab as p
+import numpy as np
+import matplotlib.pyplot as plt
import scipy.integrate as integrate
def dr(r, f):
- return alpha*r - beta*r*f
-
+ """
+ return the derivative of *r* (the rabbit population) evaulated as a
+ function of *r* and *f*. The function should work whether *r* and *f*
+ are scalars, 1D arrays or 2D arrays. The return value should have
+ the same dimensionality (shape) as the inputs *r* and *f*.
+ """
+ raise NotImplementedError('insert missing code here')
+
def df(r, f):
- return gamma*r*f - delta*f
+ """
+ return the derivative of *f* (the fox population) evaulated as a
+ function of *r* and *f*. The function should work whether *r* and *f*
+ are scalars, 1D arrays or 2D arrays. The return value should have
+ the same dimensionality (shape) as the inputs *r* and *f*.
+ """
+ raise NotImplementedError('insert missing code here')
def derivs(state, t):
"""
- Map the state variable [rabbits, foxes] to the derivitives
- [deltar, deltaf] at time t
+ Return the derivatives of r and f, stored in the *state* vector::
+
+ state = [r, f]
+
+ The return data should be [dr, df] which are the derivatives of r
+ and f at position state and time *t*
"""
- #print t, state
- r, f = state # rabbits and foxes
- deltar = dr(r, f) # change in rabbits
- deltaf = df(r, f) # change in foxes
- return deltar, deltaf
+ raise NotImplementedError('insert missing code here')
+
alpha, delta = 1, .25
beta, gamma = .2, .05
@@ -26,53 +39,53 @@
r0 = 20
f0 = 10
-t = n.arange(0.0, 100, 0.1)
+t = np.arange(0.0, 100, 0.1)
y0 = [r0, f0] # the initial [rabbits, foxes] state vector
y = integrate.odeint(derivs, y0, t)
r = y[:,0] # extract the rabbits vector
f = y[:,1] # extract the foxes vector
-p.figure()
-p.plot(t, r, label='rabbits')
-p.plot(t, f, label='foxes')
-p.xlabel('time (years)')
-p.ylabel('population')
-p.title('population trajectories')
-p.grid()
-p.legend()
-p.savefig('lotka_volterra.png', dpi=150)
-p.savefig('lotka_volterra.eps')
+plt.figure()
+plt.plot(t, r, label='rabbits')
+plt.plot(t, f, label='foxes')
+plt.xlabel('time (years)')
+plt.ylabel('population')
+plt.title('population trajectories')
+plt.grid()
+plt.legend()
+plt.savefig('lotka_volterra.png', dpi=150)
+plt.savefig('lotka_volterra.eps')
-p.figure()
-p.plot(r, f, color='red')
-p.xlabel('rabbits')
-p.ylabel('foxes')
-p.title('phase plane')
+plt.figure()
+plt.plot(r, f, color='red')
+plt.xlabel('rabbits')
+plt.ylabel('foxes')
+plt.title('phase plane')
# make a direction field plot with quiver
rmax = 1.1 * r.max()
fmax = 1.1 * f.max()
-R, F = n.meshgrid(n.arange(-1, rmax), n.arange(-1, fmax))
+R, F = np.meshgrid(np.arange(-1, rmax), np.arange(-1, fmax))
dR = dr(R, F)
dF = df(R, F)
-p.quiver(R, F, dR, dF)
+plt.quiver(R, F, dR, dF)
-R, F = n.meshgrid(n.arange(-1, rmax, .1), n.arange(-1, fmax, .1))
+R, F = np.meshgrid(np.arange(-1, rmax, .1), np.arange(-1, fmax, .1))
dR = dr(R, F)
dF = df(R, F)
-p.contour(R, F, dR, levels=[0], linewidths=3, colors='blue')
-p.contour(R, F, dF, levels=[0], linewidths=3, colors='green')
-p.ylabel('foxes')
-p.title('trajectory, direction field and null clines')
+plt.contour(R, F, dR, levels=[0], linewidths=3, colors='blue')
+plt.contour(R, F, dF, levels=[0], linewidths=3, colors='green')
+plt.ylabel('foxes')
+plt.title('trajectory, direction field and null clines')
-p.savefig('lotka_volterra_pplane.png', dpi=150)
-p.savefig('lotka_volterra_pplane.eps')
+plt.savefig('lotka_volterra_pplane.png', dpi=150)
+plt.savefig('lotka_volterra_pplane.eps')
-p.show()
+plt.show()
Copied: trunk/py4science/talks/0712_ncar_intro.lyx (from rev 6308, trunk/py4science/intro_talk/0712_ncar_intro.lyx)
===================================================================
--- trunk/py4science/talks/0712_ncar_intro.lyx (rev 0)
+++ trunk/py4science/talks/0712_ncar_intro.lyx 2008-10-25 03:37:12 UTC (rev 6330)
@@ -0,0 +1,2400 @@
+#LyX 1.5.1 created this file. For more info see http://www.lyx.org/
+\lyxformat 276
+\begin_document
+\begin_header
+\textclass beamer
+\begin_preamble
+% Include only certain frames - this speeds up compilation
+% The frames to be included need to be labeled, by using ERT
+% as [label=LABELNAME] (no backslashes or {})
+%\includeonlyframes{currentt}
+
+% To make a printable handout (one page per frame), pass
+% the handout option to the doc class (Layout menu)
+
+% For good fonts in PDFs, use pslatex fonts (Layout menu)
+
+% Colors and symbols
+\usepackage{latexsym}
+\usepackage{color}
+
+% Display covered items in transparent form (as opposed
+% to not showing them at all)
+\newcommand{\coveredinvisible}{
+ \setbeamercovered{invisible}
+}
+\newcommand{\coveredvisible}{
+ \setbeamercovered{highly dynamic}
+}
+
+% Choose default setting here:
+\coveredvisible
+
+\newcommand{\ps}{\vspace{-4mm} }
+
+% Theme configuration. I've basically built a custom theme out of
+% Warsaw, adding infoline and changing the nav. symbol bar
+
+% Warning: the commands below are order-sensitive!
+
+% load the infolines theme, b/c I want the headline Warsaw
+% uses (split), but the footline from infolines.
+% In the document body, these will be deactivated for the title and
+% turned on later
+\useoutertheme{infolines}
+% Main theme
+\usetheme{Warsaw}
+% Adjust the color for the center (title) box to be that of
+% infolines, which Warsaw changes
+\setbeamercolor*{title in head/foot}{parent=palette secondary}
+
+% Define a minimal set of navigation symbols
+\defbeamertemplate*{navigation symbols}{minmal}
+{%
+ \hbox{%
+ \hbox{\insertframenavigationsymbol}
+ \hbox{\insertdocnavigationsymbol}
+ \hbox{\insertbackfindforwardnavigationsymbol}%
+ }%
+}
+% activate the minimal navbar
+\setbeamertemplate{navigation symbols}[minimal]
+
+%%%%% HACK %%%%%
+% I started getting errors because LyX is emmitting a color 'none'
+% call, which confuses xcolor. I'm defining 'none' to be black here.
+\definecolor{none}{cmyk}{0,0,0,1}
+%%%%% /HACK %%%%%
+\end_preamble
+\options compress
+\language english
+\inputencoding auto
+\font_roman times
+\font_sans helvet
+\font_typewriter courier
+\font_default_family default
+\font_sc false
+\font_osf false
+\font_sf_scale 100
+\font_tt_scale 100
+\graphics default
+\paperfontsize default
+\spacing single
+\papersize default
+\use_geometry false
+\use_amsmath 2
+\use_esint 0
+\cite_engine basic
+\use_bibtopic false
+\paperorientation landscape
+\secnumdepth 2
+\tocdepth 2
+\paragraph_separation indent
+\defskip medskip
+\quotes_language english
+\papercolumns 1
+\papersides 1
+\paperpagestyle default
+\tracking_changes false
+\output_changes false
+\author ""
+\author ""
+\end_header
+
+\begin_body
+
+\begin_layout Standard
+\begin_inset Note Note
+status open
+
+\begin_layout Standard
+Some things to fix in a future version:
+\end_layout
+
+\begin_layout Standard
+- trim a bit of time
+\end_layout
+
+\begin_layout Standard
+- add more about ipython and my own python work, reduce that of others
+\end_layout
+
+\begin_layout Standard
+- add a final python pros/cons, esp.
+ the cons part.
+ It will make things more balanced.
+\end_layout
+
+\begin_layout Standard
+- the PDE part repeats a bit the 'python benefits' which were already pounded
+ on.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset ERT
+status open
+
+\begin_layout Standard
+
+% disable the bottom bar for the title and outline pages
+\end_layout
+
+\begin_layout Standard
+
+\end_layout
+
+\begin_layout Standard
+
+
+\backslash
+setbeamertemplate{footline}{}
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset ERT
+status open
+
+\begin_layout Standard
+
+
+\backslash
+vspace*{-5mm}
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Title
+Python in Scientific Computing
+\begin_inset OptArg
+status open
+
+\begin_layout Standard
+Python & Scientific Computing
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subtitle
+An Introduction
+\end_layout
+
+\begin_layout Author
+Fernando\InsetSpace ~
+Pérez
+\newline
+
+\family typewriter
+\size scriptsize
+<Fer...@co...>
+\family default
+\size default
+
+\newline
+John Hunter
+\newline
+
+\family typewriter
+\size scriptsize
+<jd...@gm...>
+\family default
+\size default
+
+\begin_inset OptArg
+status open
+
+\begin_layout Standard
+FP/JDH
+\begin_inset Note Note
+status collapsed
+
+\begin_layout Standard
+This is used by the 'split' footline theme on the left side of the page
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\begin_inset ERT
+status collapsed
+
+\begin_layout Standard
+
+
+\backslash
+vspace{5mm}
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Institute
+Applied Mathematics, U.
+ of Colorado at Boulder
+\newline
+Tradelink
+\begin_inset Note Note
+status open
+
+\begin_layout Standard
+- Use the
+\backslash
+inst command only if there are several affiliations.
+\end_layout
+
+\begin_layout Standard
+- Keep it simple, no one is interested in your street address.
+\end_layout
+
+\end_inset
+
+
+\begin_inset OptArg
+status open
+
+\begin_layout Standard
+CU\InsetSpace ~
+Boulder/Tradelink
+\begin_inset Note Note
+status open
+
+\begin_layout Standard
+optional, but mostly needed
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+
+
+\begin_inset ERT
+status collapsed
+
+\begin_layout Standard
+
+
+\backslash
+vspace{5mm}
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Date
+NCAR, Boulder
+\newline
+Dec 7, 2007
+\begin_inset OptArg
+status open
+
+\begin_layout Standard
+NCAR, 12/7/07
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Note Note
+status open
+
+\begin_layout Standard
+If you have a file called "institution-logo-filename.xxx", where xxx is a
+ graphic format that can be processed by latex or pdflatex, resp., then you
+ can add a logo by uncommenting the following:
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset ERT
+status collapsed
+
+\begin_layout Standard
+
+%
+\backslash
+pgfdeclareimage[height=0.5cm]{institution-logo}{institution-logo-filename}
+\end_layout
+
+\begin_layout Standard
+
+\end_layout
+
+\begin_layout Standard
+
+%
+\backslash
+logo{
+\backslash
+pgfuseimage{institution-logo}}
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Note Note
+status open
+
+\begin_layout Standard
+The following causes the table of contents to be shown at the beginning
+ of every Section.
+ Delete this, if you do not want it.
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset ERT
+status collapsed
+
+\begin_layout Standard
+
+
+\backslash
+AtBeginSection[]{
+\end_layout
+
+\begin_layout Standard
+
+\end_layout
+
+\begin_layout Standard
+
+
+\backslash
+frame<beamer>{
+\end_layout
+
+\begin_layout Standard
+
+\end_layout
+
+\begin_layout Standard
+
+
+\backslash
+frametitle{Outline}
+\end_layout
+
+\begin_layout Standard
+
+\end_layout
+
+\begin_layout Standard
+
+
+\backslash
+tableofcontents[currentsection]
+\end_layout
+
+\begin_layout Standard
+
+\end_layout
+
+\begin_layout Standard
+
+}
+\end_layout
+
+\begin_layout Standard
+
+\end_layout
+
+\begin_layout Standard
+
+}
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset Note Note
+status open
+
+\begin_layout Standard
+If you wish to uncover everything in a step-wise fashion, uncomment the
+ following command:
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset ERT
+status collapsed
+
+\begin_layout Standard
+
+%
+\backslash
+beamerdefaultoverlayspecification{<+->}
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+\begin_inset ERT
+status open
+
+\begin_layout Standard
+
+% reactivate the footline
+\end_layout
+
+\begin_layout Standard
+
+\end_layout
+
+\begin_layout Standard
+
+
+\backslash
+setbeamertemplate{footline}[infolines theme]
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout BeginFrame
+Outline
+\end_layout
+
+\begin_layout Standard
+\begin_inset LatexCommand tableofcontents
+
+\end_inset
+
+
+\begin_inset ERT
+status collapsed
+
+\begin_layout Standard
+
+[pausesections]
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Section
+Scientific Computing
+\begin_inset OptArg
+status open
+
+\begin_layout Standard
+SciComp
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+Traditional approaches
+\begin_inset OptArg
+status open
+
+\begin_layout Standard
+Status quo
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout BeginFrame
+FORTRAN, C and C++
+\end_layout
+
+\begin_layout Itemize
+Tools optimized for CPUs, not humans.
+\end_layout
+
+\begin_layout Itemize
+Low-level:
+\end_layout
+
+\begin_deeper
+\begin_layout Itemize
+Primitive data types (no good strings, sets, hash tables,
+\begin_inset ERT
+status collapsed
+
+\begin_layout Standard
+
+
+\backslash
+ldots
+\end_layout
+
+\end_inset
+
+).
+\end_layout
+
+\begin_layout Itemize
+Manual memory management: bugs, bugs, bugs.
+ Hard ones.
+\end_layout
+
+\begin_layout Itemize
+Slow edit/compile/test cycle.
+\end_layout
+
+\end_deeper
+\begin_layout Itemize
+Clumsy access to visualization, quick profiling, text processing,
+\begin_inset ERT
+status collapsed
+
+\begin_layout Standard
+
+
+\backslash
+ldots
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Itemize
+No interactive facilities - scientific work is inherently exploratory.
+\end_layout
+
+\begin_layout Pause
+
+\end_layout
+
+\begin_layout Standard
+
+\series bold
+\color blue
+However!
+\end_layout
+
+\begin_layout Itemize
+They deliver excellent performance.
+\end_layout
+
+\begin_layout Itemize
+Millions of LOC in proven scientific codes.
+
+\end_layout
+
+\begin_layout Itemize
+We need to
+\emph on
+\color blue
+work with these tools
+\emph default
+\color inherit
+, not replace them!
+\end_layout
+
+\begin_layout BeginFrame
+Higher level tools in the last decade
+\end_layout
+
+\begin_layout Itemize
+Mathematica and Maple: a unique niche we won't address today.
+\end_layout
+
+\begin_layout Itemize
+IDL and Matlab: extremely popular, for good reasons.
+\end_layout
+
+\begin_deeper
+\begin_layout Itemize
+Great interactivity, visualization, and extensive libraries.
+\end_layout
+
+\begin_layout Itemize
+Unpleasant languages for large-scale programs and non-numerical tasks.
+\end_layout
+
+\begin_layout Itemize
+Expensive/proprietary: lock-in.
+\end_layout
+
+\begin_layout Itemize
+Often considered `prototyping' tools: this leads to a lot of code rewriting.
+\end_layout
+
+\end_deeper
+\begin_layout Itemize
+A common approach (I've been there): mix and match multiple tools:
+\end_layout
+
+\begin_deeper
+\begin_layout Itemize
+FORTRAN, C, C++ programs ...
+\end_layout
+
+\begin_layout Itemize
+driven by Bash/awk/sed/Perl scripts ...
+\end_layout
+
+\begin_layout Itemize
+which feed them input and take their outputs ...
+\end_layout
+
+\begin_layout Itemize
+and pass them to Gnuplot, Grace, OpenDX, etc.
+\end_layout
+
+\end_deeper
+\begin_layout Itemize
+Many different syntaxes:
+\color none
+
+\color red
+huge context switching overhead!
+\end_layout
+
+\begin_layout Subsection
+Python?
+\begin_inset OptArg
+status open
+
+\begin_layout Standard
+Python
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout BeginFrame
+Python in this context
+\end_layout
+
+\begin_layout Itemize
+
+\color blue
+Free
+\color none
+ (BSD license), highly portable (Linux, OSX, Solaris, Windows, ...).
+\end_layout
+
+\begin_layout Itemize
+
+\color blue
+Interactive
+\color none
+ interpreter provided.
+\end_layout
+
+\begin_layout Itemize
+Extremely readable syntax (
+\color blue
+
+\begin_inset Quotes eld
+\end_inset
+
+executable pseudo-code
+\begin_inset Quotes erd
+\end_inset
+
+
+\color none
+).
+\end_layout
+
+\begin_layout Itemize
+
+\color blue
+Simple
+\color none
+: non-professional programmers can become (and remain) proficient with a
+ very small effort (c.f.
+ C++).
+\end_layout
+
+\begin_layout Itemize
+Clean object oriented model, but
+\color none
+
+\color blue
+not mandatory
+\color none
+.
+\end_layout
+
+\begin_layout Itemize
+Rich built-in types: lists, sets, dictionaries (hash tables), strings, ...
+\end_layout
+
+\begin_layout Itemize
+Very comprehensive standard library (
+\color blue
+batteries included
+\color none
+)
+\end_layout
+
+\begin_layout Itemize
+Standard libraries for IDL/Matlab-like arrays (NumPy)
+\end_layout
+
+\begin_layout Itemize
+Easy to wrap existing C, C++ and FORTRAN codes.
+\end_layout
+
+\begin_layout Section
+Interlude: Python in the real world
+\begin_inset OptArg
+status collapsed
+
+\begin_layout Standard
+Examples
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+EEG analysis for epilepsy
+\begin_inset OptArg
+status open
+
+\begin_layout Standard
+EEG
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout BeginPlainFrame
+Data analysis for epilepsy surgery
+\end_layout
+
+\begin_layout FrameSubtitle
+Isolating the origin of drug-resistant epileptic seizures which require
+ surgery.
+\end_layout
+
+\begin_layout Standard
+John Hunter, Department of Pediatric Neurology, University of Chicago.
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename fig/mpl_brain1.png
+ lyxscale 50
+ width 80text%
+ keepAspectRatio
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout BeginPlainFrame
+Electrode location in 3D, combined with MRI data
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename fig/mpl_brain3.png
+ lyxscale 50
+ width 90text%
+ keepAspectRatio
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout BeginPlainFrame
+Correlation analysis of seizure data
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename fig/mpl_brain4.png
+ lyxscale 50
+ width 90text%
+ keepAspectRatio
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout BeginPlainFrame
+Final location of epileptic foci for surgery
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename fig/mpl_brain5.png
+ lyxscale 50
+ width 90text%
+ keepAspectRatio
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+Multiwavelets for PDEs
+\begin_inset OptArg
+status open
+
+\begin_layout Standard
+PDEs
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout BeginFrame
+Adaptive, multiwavelet algorithms for integral operators
+\end_layout
+
+\begin_layout Standard
+Gregory Beylkin, Vani Cheruvu, Fernando Perez.
+ Applied Math, U.
+ of Colorado at Boulder.
+\end_layout
+
+\begin_layout Itemize
+Fast application of integral kernels.
+ (Partial Differential Equations)
+\end_layout
+
+\begin_layout Itemize
+Implementation went from 1 to 3 dimensions directly (
+\emph on
+extremely
+\emph default
+ unusual).
+\end_layout
+
+\begin_layout Itemize
+Very complex algorithm that goes beyond pure numerics.
+\end_layout
+
+\begin_layout Itemize
+Very good performance, thanks to NumPy, F2PY and weave.
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename fig/rho_2d_surf.png
+ lyxscale 80
+ width 35text%
+
+\end_inset
+
+
+\begin_inset ERT
+status collapsed
+
+\begin_layout Standard
+
+
+\backslash
+hspace{1cm}
+\end_layout
+
+\end_inset
+
+
+\begin_inset Graphics
+ filename fig/rho_2d_skel.eps
+ lyxscale 80
+ width 25text%
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+JPL: Mars mission data visualization
+\begin_inset OptArg
+status collapsed
+
+\begin_layout Standard
+JPL - Mars
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout BeginPlainFrame
+JPL: Mars mission trajectory design and nav data
+\end_layout
+
+\begin_layout FrameSubtitle
+Ted Drain and Lynn Craig, Jet Propulsion Laboratory (NASA/Caltech)
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+\size footnotesize
+From: Name Elided <nam...@jp...>
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+\size footnotesize
+Date: Oct 2, 2007 7:15 PM
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+\size footnotesize
+Subject: Fwd: matplotlib bug numbers
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+\size footnotesize
+To: John Hunter <jd...@gm...>
+\end_layout
+
+\begin_layout Standard
+\begin_inset ERT
+status open
+
+\begin_layout Standard
+
+
+\backslash
+vspace{5mm}
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+\size tiny
+One of my lead developers mentioned that they had sent a bug to you about
+ the annotations feature of MatPlotLib.
+ Would you be able to let me know what the timeline is to resolve that bug?
+ The reason is that the feature is needed for the Phoenix project and their
+ arrival at Mars will be in March sometime, but they are doing their testing
+ in the coming few months.
+ This annotation feature is used on reports that present the analysis of
+ the trajectory to the navigation team and it shows up on our schedule.
+ It would really help me to know approximately when it could be resolved.
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+\size tiny
+B-plane plots are used to show the trajectory of a spacecraft with respect
+ to the target body (specifically perpendicular to the incoming asymptote
+ of the spacecraft trajectory) and we plot them with the y-axis inverted.
+ The plot is used heavily in flight operations so it is important to our
+ customers.
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+\size tiny
+In addition, we have what is called a thundering heard plot where many different
+ trajectory solutions (determined from different measurement sources) are
+ plotted together.
+ The annotations are import there so we can see which plot corresponds to
+ each source of data.
+ I hope it helps to know how your code will be used in spacecraft navigation.
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+\size tiny
+Thanks for all your efforts.
+\end_layout
+
+\begin_layout BeginPlainFrame
+JPL: Mars mission data visualization
+\end_layout
+
+\begin_layout Standard
+Expected communication power levels between an orbiting spacecraft and a
+ lander as it goes through the atmosphere:
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename fig/jpl_lander_comm_power.png
+ lyxscale 25
+ width 90text%
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout BeginPlainFrame
+JPL: Mars mission data visualization (2)
+\end_layout
+
+\begin_layout Standard
+Summary of the current navigation team activities and modelling (data used,
+ event times etc):
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset ERT
+status open
+
+\begin_layout Standard
+
+
+\backslash
+vspace{-3mm}
+\end_layout
+
+\end_inset
+
+
+\begin_inset Graphics
+ filename fig/jpl_nav_summary.png
+ lyxscale 50
+ width 90text%
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+PMV: structural bioinformatics
+\begin_inset OptArg
+status collapsed
+
+\begin_layout Standard
+PMV
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout BeginPlainFrame
+PMV: the Python Molecule Viewer
+\end_layout
+
+\begin_layout FrameSubtitle
+Michel F.
+ Sanner, Molecular Biology Department, The Scripps Research Institute.
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename fig/pmv.png
+ lyxscale 50
+ width 100text%
+ keepAspectRatio
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+MayaVi: customizable data visualization
+\begin_inset OptArg
+status open
+
+\begin_layout Standard
+MayaVi
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout BeginFrame
+MayaVi: sophisticated data visualization
+\end_layout
+
+\begin_layout Itemize
+Free, easy to use scientific data visualizer.
+\end_layout
+
+\begin_layout Itemize
+Heavy lifting of OpenGL-based rendering: VTK (a C++ library).
+\end_layout
+
+\begin_layout Itemize
+A very good example of how to properly use Python:
+\end_layout
+
+\begin_deeper
+\begin_layout Itemize
+MayaVi is a standalone GUI program...
+\end_layout
+
+\begin_layout Itemize
+but also a Python library callable by any other Python program.
+\end_layout
+
+\begin_layout Itemize
+Python: very easy to modify, even by adding at runtime user-defined modules
+ which populate the GUI automatically.
+\end_layout
+
+\begin_layout Itemize
+C++: excellent rendering performance, fully hardware-accelerated OpenGL.
+\end_layout
+
+\end_deeper
+\begin_layout Pause
+
+\end_layout
+
+\begin_layout Standard
+
+\series bold
+\color blue
+The punchline:
+\series default
+\color none
+ fully programmable visualization, with builtin access to all kinds of numerical
+ (and other) libraries from within the viz tool.
+\end_layout
+
+\begin_layout BeginPlainFrame
+FluidLab: a MayaVi based CFD visualization tool
+\end_layout
+
+\begin_layout Standard
+K.
+ Julien, P.
+ Schmitt (now NCAR), B.
+ Barrow, F.
+ Pérez (App.
+ Math, CU).
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename fig/Fluidlab5.png
+ lyxscale 50
+ width 90text%
+ keepAspectRatio
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout BeginPlainFrame
+Volumetric rendering with FluidLab
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename fig/Fluidlab6.png
+ lyxscale 50
+ width 90text%
+ keepAspectRatio
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+SAGE: System for Algebra and Geometry Experimentation
+\begin_inset OptArg
+status collapsed
+
+\begin_layout Standard
+SAGE
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout BeginPlainFrame
+SAGE: open source mathematics
+\end_layout
+
+\begin_layout FrameSubtitle
+Winner of the 2007 Trophés du Libre, scientific software category
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename fig/sage_notebook-medium.jpg
+ lyxscale 50
+ width 90text%
+ keepAspectRatio
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+IPython
+\end_layout
+
+\begin_layout BeginFrame
+IPython
+\end_layout
+
+\begin_layout FrameSubtitle
+Extensible interactive environment with parallel computing support
+\end_layout
+
+\begin_layout Enumerate
+
+\color blue
+A better Python shell
+\color none
+: object introspection, system access, 'magic' command system for adding
+ functionality when working interactively,
+\begin_inset ERT
+status collapsed
+
+\begin_layout Standard
+
+
+\backslash
+ldots
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Enumerate
+
+\color blue
+An embeddable interpreter
+\color none
+: useful for debugging and for mixing batch-processing with interactive
+ work.
+\end_layout
+
+\begin_layout Enumerate
+
+\color blue
+A flexible component
+\color none
+: you can use it as the base environment for other systems with Python as
+ the underlying language.
+ It is very configurable in this direction.
+\end_layout
+
+\begin_layout Enumerate
+
+\color blue
+A system for interactive control of distributed/parallel computing systems.
+
+\color none
+
+\end_layout
+
+\begin_layout Enumerate
+
+\color blue
+An interactive component
+\color none
+ we can plug into GUIs, browser-based shells, etc.
+\end_layout
+
+\begin_layout BeginPlainFrame
+IPython: IDL-like interactive use
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename fig/pylab-screen.png
+ lyxscale 30
+ width 90text%
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout BeginPlainFrame
+IPython: interactive control of VTK visualizations
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename fig/mlab-screen-black.png
+ lyxscale 50
+ width 90text%
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout BeginFrame
+IPython's future
+\end_layout
+
+\begin_layout FrameSubtitle
+A 2-process kernel on the network
+\end_layout
+
+\begin_layout Standard
+Work with Brian Granger (Tech-X, Boulder) and Benjamin Ragan-Kelley (U.
+ C.
+ Berkeley physics).
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename fig/kernel2p.png
+ lyxscale 50
+ width 80text%
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout BeginFrame
+Distributed/parallel computing
+\end_layout
+
+\begin_layout Itemize
+Think of Python as 'the CPU'
+\end_layout
+
+\begin_layout Itemize
+But these souped-up kernels let you talk to it conveniently.
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename fig/ipython_parallel.png
+ lyxscale 50
+ width 80text%
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
+PyNGL
+\end_layout
+
+\begin_layout BeginPlainFrame
+PyNGL - Python interface to NCAR's NCL
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+import
+\family default
+\color none
+
+\family typewriter
+\color blue
+numpy
+\color none
+, Ngl, Nio
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+dirc = Ngl.pynglpath("data")
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+cfile = Nio.open_file(dirc + "/cdf/seam.nc")
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+lon =
+\family default
+\color none
+
+\family typewriter
+\color blue
+numpy
+\color none
+.ravel(cfile.variables["lon2d"][:,:])
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+lat =
+\family default
+\color none
+
+\family typewriter
+\color blue
+numpy
+\color none
+.ravel(cfile.variables["lat2d"][:,:])
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+ps =
+\family default
+\color none
+
+\family typewriter
+\color blue
+numpy
+\color none
+.ravel(cfile.variables["ps"][0,:,:])/100.
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+rlist = Ngl.Resources()
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+rlist.wkColorMap = "BlAqGrYeOrReVi200"
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+wks_type = "ps"
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+wks = Ngl.open_wks(wks_type,"seam",rlist)
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+resources = Ngl.Resources()
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+resources.sfXArray = lon
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+resources.sfYArray = lat
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+map = Ngl.contour_map(wks,ps,resources)
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+Ngl.end()
+\end_layout
+
+\begin_layout BeginFrame
+PyNGL
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset Graphics
+ filename fig/ncar-world-seam.3.png
+ lyxscale 50
+ width 90text%
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection*
+Others
+\end_layout
+
+\begin_layout BeginFrame
+A few other projects
+\end_layout
+
+\begin_layout FrameSubtitle
+Python is becoming very popular in many different scientific areas
+\end_layout
+
+\begin_layout Itemize
+
+\color blue
+PyDAP:
+\color none
+ Python implementation of the OpenDAP protocols (client
+\series bold
+and
+\series default
+ server).
+\end_layout
+
+\begin_layout Itemize
+
+\color blue
+PyTables:
+\color none
+ HDF-5 read-write support with excellent performance.
+\end_layout
+
+\begin_layout Itemize
+
+\color blue
+PyTrilinos:
+\color none
+ Python interface to Sandia's Trilinos parallel solvers.
+ Coupled with IPython, they can be used interactively.
+\end_layout
+
+\begin_layout Itemize
+
+\color blue
+PyRAF:
+\color none
+ Hubble Space Telescope interface to IRAF, a standard in astronomical image
+ processing.
+
+\end_layout
+
+\begin_layout Itemize
+
+\color blue
+VPython:
+\color none
+ easy, real-time 3D programming (Carnegie Mellon, used for an introductory
+ mechanics course).
+\end_layout
+
+\begin_layout Itemize
+
+\color blue
+Galaxy:
+\color none
+ integrated access to multiple tools in genomics research.
+
+\color blue
+Very impressive
+\color none
+.
+\end_layout
+
+\begin_layout Section
+Development in Python
+\begin_inset OptArg
+status collapsed
+
+\begin_layout Standard
+Development\InsetSpace ~
+Model
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout BeginPlainFrame
+Python compared to IDL, Matlab, etc.
+\end_layout
+
+\begin_layout ExampleBlock
+\begin_inset ERT
+status open
+
+\begin_layout Standard
+
+<+->{Pros}
+\end_layout
+
+\begin_layout Standard
+
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout ExampleBlock
+A general programming language:
+\series bold
+this is a feature
+\series default
+!
+\end_layout
+
+\begin_deeper
+\begin_layout Itemize
+Free, open source, extremely portable: from the OLPC or a cellphone (Nokia)
+ to a supercomputer.
+\end_layout
+
+\begin_layout Itemize
+Networking, text processing, XML parsing, databases, etc
+\begin_inset ERT
+status open
+
+\begin_layout Standard
+
+
+\backslash
+ldots
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Itemize
+Integrated support for testing (
+\family typewriter
+unittest
+\family default
+,
+\family typewriter
+doctest
+\family default
+)
+\end_layout
+
+\begin_layout Itemize
+Automatic API documentation tools (
+\family typewriter
+epydoc, doxygen
+\family default
+).
+\end_layout
+
+\begin_layout Itemize
+Supports all major GUI toolkits.
+\end_layout
+
+\begin_layout Itemize
+Extremely expressive for complex algorithms.
+\end_layout
+
+\end_deeper
+\begin_layout Separator
+
+\end_layout
+
+\begin_layout AlertBlock
+\begin_inset ERT
+status open
+
+\begin_layout Standard
+
+<+->{There are still rough edges!}
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_deeper
+\begin_layout Itemize
+Installation, deployment: harder than needed (but improving).
+\end_layout
+
+\begin_layout Itemize
+No good, single-point of entry integrated help system.
+\end_layout
+
+\begin_layout Itemize
+Lots of good documentation, but scattered all over.
+\end_layout
+
+\begin_layout Itemize
+Funding agency support for infrastructure work is difficult to get.
+\end_layout
+
+\end_deeper
+\begin_layout BeginFrame
+A different model of development
+\end_layout
+
+\begin_layout FrameSubtitle
+
+\emph on
+\color red
+Global optimization is the root of all evil
+\end_layout
+
+\begin_layout Itemize
+\begin_inset ERT
+status collapsed
+
+\begin_layout Standard
+
+<+->
+\end_layout
+
+\end_inset
+
+Never write `
+\family typewriter
+main()
+\family default
+' in C anymore:
+\color none
+
+\color red
+you are optimizing globally!
+\end_layout
+
+\begin_deeper
+\begin_layout Itemize
+Prototype the code in Python.
+\end_layout
+
+\begin_layout Itemize
+Wrap existing libraries for Python access and reuse them (Numeric, LAPACK,
+ VTK, ...)
+\end_layout
+
+\begin_layout Itemize
+Identify remaining hot spots via
+\color none
+
+\color blue
+profiling
+\color none
+.
+\end_layout
+
+\begin_layout Itemize
+Rewrite
+\color none
+
+\color blue
+only
+\color none
+ the code for those hot spots in C/C++/FORTRAN.
+\end_layout
+
+\end_deeper
+\begin_layout Itemize
+\begin_inset ERT
+status collapsed
+
+\begin_layout Standard
+
+<+->
+\end_layout
+
+\end_inset
+
+The resulting code will be production-ready:
+\color none
+
+\color blue
+no throw-away codes
+\color none
+.
+\end_layout
+
+\begin_deeper
+\begin_layout Itemize
+Make your code available as a library for
+\color none
+
+\color blue
+interactive use
+\color none
+.
+\end_layout
+
+\begin_layout Itemize
+Integrate plotting, visualization, logging, ..., into your objects.
+\end_layout
+
+\end_deeper
+\begin_layout Itemize
+\begin_inset ERT
+status collapsed
+
+\begin_layout Standard
+
+<+->
+\end_layout
+
+\end_inset
+
+
+\color blue
+Apply this to existing codes
+\color none
+
+\end_layout
+
+\begin_deeper
+\begin_layout Itemize
+Break them into a library core and control layers.
+\end_layout
+
+\begin_layout Itemize
+Wrap the libraries and expose them to Python.
+\end_layout
+
+\begin_layout Itemize
+Write all new control as quick, light Python scripts.
+\end_layout
+
+\end_deeper
+\begin_layout Section*
+Wrapup
+\end_layout
+
+\begin_layout BeginFrame
+Summary
+\end_layout
+
+\begin_layout Itemize
+\begin_inset ERT
+status collapsed
+
+\begin_layout Standard
+
+<+->
+\end_layout
+
+\end_inset
+
+
+\color blue
+Python
+\end_layout
+
+\begin_deeper
+\begin_layout Itemize
+An excellent language for scientific computing development.
+\end_layout
+
+\begin_layout Itemize
+Scales from interactive exploration to full-blown production codes.
+\end_layout
+
+\begin_layout Itemize
+Accessible to scientists who are not professional programmers.
+\end_layout
+
+\end_deeper
+\begin_layout Standard
+\begin_inset ERT
+status collapsed
+
+\begin_layout Standard
+
+
+\backslash
+vskip0pt plus.5fill
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Itemize
+\begin_inset ERT
+status collapsed
+
+\begin_layout Standard
+
+<+->
+\end_layout
+
+\end_inset
+
+
+\color red
+Outlook
+\end_layout
+
+\begin_deeper
+\begin_layout Itemize
+NumPy, SciPy, matplotlib, IPython, MayaVi, Sage, etc
+\begin_inset ERT
+status collapsed
+
+\begin_layout Standard
+
+
+\backslash
+ldots
+\end_layout
+
+\end_inset
+
+:
+\series bold
+all
+\series default
+are moving forward and improving.
+\end_layout
+
+\begin_layout Itemize
+Major DOE, NSF, NiH projects are adopting it as a core technology.
+\end_layout
+
+\begin_layout Itemize
+Yearly conference at Caltech (August) growing.
+\end_layout
+
+\begin_layout Itemize
+These projects are all Open Source: if you find a flaw, a bug, or a missing
+ feature,
+\color none
+
+\emph on
+\color blue
+jump on board!
+\end_layout
+
+\begin_layout Itemize
+There are still many rough edges to which various projects can contribute.
+\end_layout
+
+\end_deeper
+\begin_layout BeginPlainFrame
+Thank you! Questions?
+\end_layout
+
+\begin_layout FrameSubtitle
+Credit: http://xkcd.com/353
+\end_layout
+
+\begin_layout Standard
+\align center
+\begin_inset ERT
+status open
+
+\begin_layout Standard
+
+
+\backslash
+vspace{-5mm}
+\end_layout
+
+\end_inset
+
+
+\begin_inset Graphics
+ filename fig/xkcd_python.png
+ lyxscale 50
+ height 85pheight%
+ BoundingBox -4bp -4bp 518bp 588bp
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout BeginPlainFrame
+
+\end_layout
+
+\begin_layout Standard
+\align center
+
+\series bold
+\size largest
+\color blue
+We're done here!
+\end_layout
+
+\begin_layout EndFrame
+
+\end_layout
+
+\begin_layout Section*
+\start_of_appendix
+\begin_inset Note Note
+status collapsed
+
+\begin_layout Standard
+All of the following is optional and typically not needed.
+\end_layout
+
+\end_inset
+
+Appendix
+\end_layout
+
+\begin_layout Subsection*
+URLs
+\end_layout
+
+\begin_layout BeginFrame
+Some useful URLs
+\end_layout
+
+\begin_layout Itemize
+A collection of links on Python and Scientific Computing:
+\color blue
+
+\newline
+
+\begin_inset LatexCommand htmlurl
+target "http://amath.colorado.edu/faculty/fperez/python/scicomp"
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Itemize
+SciPy:
+\color none
+
+\color blue
+
+\begin_inset LatexCommand htmlurl
+target "http://www.scipy.org"
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Itemize
+IPython, an improved interactive shell
+\color blue
+:
+\newline
+
+\begin_inset LatexCommand htmlurl
+target "http://ipython.scipy.org"
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Itemize
+Matplotlib, 2d plotting with Matlab syntax
+\color blue
+:
+\newline
+
+\begin_inset LatexCommand htmlurl
+target "http://matplotlib.sourceforge.net"
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Itemize
+MayaVi, 3d data visualization:
+\color blue
+
+\newline
+
+\begin_inset LatexCommand htmlurl
+target "http://mayavi.sourceforge.net"
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Itemize
+PyX, programmatic PostScript generation (with
+\begin_inset ERT
+status collapsed
+
+\begin_layout Standard
+
+
+\backslash
+LaTeX
+\end_layout
+
+\end_inset
+
+ support)
+\color blue
+:
+\newline
+
+\begin_inset LatexCommand htmlurl
+target "http://pyx.sourceforge.net"
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Itemize
+F2Py (FORTRAN):
+\color none
+
+\color blue
+
+\begin_inset LatexCommand htmlurl
+target "http://cens.ioc.ee/projects/f2py2e"
+
+\end_inset
+
+
+\color none
+
+\end_layout
+
+\begin_layout Itemize
+SWIG (C/C++ for Python):
+\color none
+
+\color blue
+
+\begin_inset LatexCommand htmlurl
+target "http://swig.org"
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout BeginFrame
+URLs for projects mentioned earlier
+\end_layout
+
+\begin_layout Itemize
+VPython, real-time 3D:
+\color none
+
+\color blue
+
+\begin_inset LatexCommand htmlurl
+target "http://vpython.org"
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Itemize
+UCSF Chimera - interactive molecular graphics
+\color blue
+:
+\newline
+
+\begin_inset LatexCommand htmlurl
+target "http://www.cgl.ucsf.edu/chimera"
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Itemize
+PyRAF - Hubble Space Telescope interface to IRAF
+\color blue
+:
+\newline
+
+\begin_inset LatexCommand htmlurl
+target "http://www.stsci.edu/resources/software_hardware/pyraf"
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Itemize
+BioPython -
+\color none
+
+\color blue
+
+\begin_inset LatexCommand htmlurl
+target "http://biopython.org"
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Itemize
+VisionEgg - vision research experiments (OpenGL):
+\color blue
+
+\newline
+
+\begin_inset LatexCommand htmlurl
+target "http://www.visionegg.org"
+
+\end_inset
+
+
+\color none
+
+\end_layout
+
+\begin_layout Itemize
+Natural Language Toolkit:
+\newline
+
+\color blue
+
+\begin_inset LatexCommand htmlurl
+target "http://nltk.sourceforge.net"
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Itemize
+Neural Integrator - visual programming for neural networks:
+\newline
+
+\color blue
+
+\begin_inset LatexCommand htmlurl
+target "http://starship.python.net/crew/seehof/NeuralPython.html"
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Itemize
+Orange - component-based data mining:
+\newline
+
+\color blue
+
+\begin_inset LatexCommand htmlurl
+target "http://www.ailab.si/orange"
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout EndFrame
+
+\end_layout
+
+\end_body
+\end_document
Copied: trunk/py4science/talks/0810_berkeley_intro.lyx (from rev 6308, trunk/py4science/intro_talk/0810_berkeley_intro.lyx)
===================================================================
--- trunk/py4science/talks/0810_berkeley_intro.lyx (rev 0)
+++ trunk/py4science/talks/0810_berkeley_intro.lyx 2008-10-25 03:37:12 UTC (rev 6330)
@@ -0,0 +1,2274 @@
+#LyX 1.5.5 created this file. For more info see http://www.lyx.org/
+\lyxformat 276
+\begin_document
+\begin_header
+\textclass beamer
+\begin_preamble
+% Include only certain frames - this speeds up compilation
+% The frames to be included need to be labeled, by using ERT
+% as [label=LABELNAME] (no backslashes or {})
+%\includeonlyframes{currentt}
+
+% To make a printable handout (one page per frame), pass
+% the handout option to the doc class (Layout menu)
+
+% For good fonts in PDFs, use pslatex fonts (Layout menu)
+
+% Colors and symbols
+\usepackage{latexsym}
+\usepackage{color}
+
+% Display covered items in transparent form (as opposed
+% to not showing them at all)
+\newcommand{\coveredinvisible}{
+ \setbeamercovered{invisible}
+}
+\newcommand{\coveredvisible}{
+ \setbeamercovered{highly dynamic}
+}
+
+% Choose default setting here:
+\coveredvisible
+
+\newcommand{\ps}{\vspace{-4mm} }
+
+% Theme configuration. I've basically built a custom theme out of
+% Warsaw, adding infoline and changing the nav. symbol bar
+
+% Warning: the commands below are order-sensitive!
+
+% load the infolines theme, b/c I want the headline Warsaw
+% uses (split), but the footline from infolines.
+% In the document body, these will be deactivated for the title and
+% turned on later
+\useoutertheme{infolines}
+% Main theme
+\usetheme{Warsaw}
+% Adjust the color for the center (title) box to be that of
+% infolines, which Warsaw changes
+\setbeamercolor*{title in head/foot}{parent=palette secondary}
+
+% Define a minimal set of navigation symbols
+\defbeamertemplate*{navigat...
[truncated message content] |
|
From: <ef...@us...> - 2008-10-24 22:35:34
|
Revision: 6329
http://matplotlib.svn.sourceforge.net/matplotlib/?rev=6329&view=rev
Author: efiring
Date: 2008-10-24 22:35:25 +0000 (Fri, 24 Oct 2008)
Log Message:
-----------
Another typo bug in recent commit for shared axes support
Modified Paths:
--------------
trunk/matplotlib/lib/matplotlib/axes.py
Modified: trunk/matplotlib/lib/matplotlib/axes.py
===================================================================
--- trunk/matplotlib/lib/matplotlib/axes.py 2008-10-24 18:16:12 UTC (rev 6328)
+++ trunk/matplotlib/lib/matplotlib/axes.py 2008-10-24 22:35:25 UTC (rev 6329)
@@ -831,7 +831,7 @@
if self._sharey is not None:
self.yaxis.major = self._sharey.yaxis.major
self.yaxis.minor = self._sharey.yaxis.minor
- y0, y1 = self._sharex.get_ylim()
+ y0, y1 = self._sharey.get_ylim()
self.set_ylim(y0, y1, emit=False)
self.yaxis.set_scale(self._sharey.yaxis.get_scale())
else:
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <md...@us...> - 2008-10-24 18:22:09
|
Revision: 6325
http://matplotlib.svn.sourceforge.net/matplotlib/?rev=6325&view=rev
Author: mdboom
Date: 2008-10-24 17:35:50 +0000 (Fri, 24 Oct 2008)
Log Message:
-----------
Update some statuses.
Modified Paths:
--------------
trunk/matplotlib/doc/devel/outline.rst
Modified: trunk/matplotlib/doc/devel/outline.rst
===================================================================
--- trunk/matplotlib/doc/devel/outline.rst 2008-10-24 17:35:39 UTC (rev 6324)
+++ trunk/matplotlib/doc/devel/outline.rst 2008-10-24 17:35:50 UTC (rev 6325)
@@ -131,7 +131,7 @@
image needs conversion
legend needs conversion
lines needs conversion
-mathtext needs conversion
+mathtext Mike converted
mlab needs conversion
mpl needs conversion
patches Mike converted
@@ -144,7 +144,7 @@
table needs conversion
texmanager Darren needs conversion
text Mike converted
-ticker Mike needs conversion
+ticker John converted
transforms Mike converted
type1font needs conversion
units needs conversion
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <md...@us...> - 2008-10-24 18:16:22
|
Revision: 6328
http://matplotlib.svn.sourceforge.net/matplotlib/?rev=6328&view=rev
Author: mdboom
Date: 2008-10-24 18:16:12 +0000 (Fri, 24 Oct 2008)
Log Message:
-----------
Fix docstring.
Modified Paths:
--------------
trunk/matplotlib/lib/matplotlib/contour.py
Modified: trunk/matplotlib/lib/matplotlib/contour.py
===================================================================
--- trunk/matplotlib/lib/matplotlib/contour.py 2008-10-24 17:58:47 UTC (rev 6327)
+++ trunk/matplotlib/lib/matplotlib/contour.py 2008-10-24 18:16:12 UTC (rev 6328)
@@ -53,8 +53,6 @@
*fontsize*:
See http://matplotlib.sf.net/fonts.html
- .. TODO: Update this link to new fonts document
-
*colors*:
- if *None*, the color of each label matches the color of
the corresponding contour
@@ -1050,8 +1048,8 @@
Call signature::
- conmin,segmin,imin,xmin,ymin,dmin = find_nearest_contour(
- self, x, y, indices=None, pixel=True )
+ conmin,segmin,imin,xmin,ymin,dmin = find_nearest_contour(
+ self, x, y, indices=None, pixel=True )
Optional keyword arguments::
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <js...@us...> - 2008-10-24 17:58:54
|
Revision: 6327
http://matplotlib.svn.sourceforge.net/matplotlib/?rev=6327&view=rev
Author: jswhit
Date: 2008-10-24 17:58:47 +0000 (Fri, 24 Oct 2008)
Log Message:
-----------
defer import of netcdf module
Modified Paths:
--------------
trunk/toolkits/basemap/Changelog
Modified: trunk/toolkits/basemap/Changelog
===================================================================
--- trunk/toolkits/basemap/Changelog 2008-10-24 17:40:54 UTC (rev 6326)
+++ trunk/toolkits/basemap/Changelog 2008-10-24 17:58:47 UTC (rev 6327)
@@ -1,4 +1,6 @@
version 0.99.2 (not yet released)
+ * defer import of netcdf stuff till it is needed (in NetCDFFile
+ function).
* Added McBryde-Thomas Flat Polar Quartic (projection =
'mbtfpq'), Gall Stereographic Cylindrical (projection =
'gall') and van der Grinten (projection = 'vandg').
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ef...@us...> - 2008-10-24 17:40:59
|
Revision: 6326
http://matplotlib.svn.sourceforge.net/matplotlib/?rev=6326&view=rev
Author: efiring
Date: 2008-10-24 17:40:54 +0000 (Fri, 24 Oct 2008)
Log Message:
-----------
Fix error in recent shared axes changes; thanks to David Trem.
Modified Paths:
--------------
trunk/matplotlib/lib/matplotlib/axes.py
Modified: trunk/matplotlib/lib/matplotlib/axes.py
===================================================================
--- trunk/matplotlib/lib/matplotlib/axes.py 2008-10-24 17:35:50 UTC (rev 6325)
+++ trunk/matplotlib/lib/matplotlib/axes.py 2008-10-24 17:40:54 UTC (rev 6326)
@@ -512,8 +512,8 @@
self._adjustable = 'datalim'
if sharey is not None:
self._shared_y_axes.join(self, sharey)
- if sharex._adjustable == 'box':
- sharex._adjustable = 'datalim'
+ if sharey._adjustable == 'box':
+ sharey._adjustable = 'datalim'
#warnings.warn(
# 'shared axes: "adjustable" is being changed to "datalim"')
self._adjustable = 'datalim'
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <md...@us...> - 2008-10-24 17:35:42
|
Revision: 6324
http://matplotlib.svn.sourceforge.net/matplotlib/?rev=6324&view=rev
Author: mdboom
Date: 2008-10-24 17:35:39 +0000 (Fri, 24 Oct 2008)
Log Message:
-----------
Add mathtext api to toc
Modified Paths:
--------------
trunk/matplotlib/doc/api/index.rst
Modified: trunk/matplotlib/doc/api/index.rst
===================================================================
--- trunk/matplotlib/doc/api/index.rst 2008-10-24 17:35:23 UTC (rev 6323)
+++ trunk/matplotlib/doc/api/index.rst 2008-10-24 17:35:39 UTC (rev 6324)
@@ -23,6 +23,7 @@
colorbar_api.rst
colors_api.rst
nxutils_api.rst
+ mathtext_api.rst
mlab_api.rst
path_api.rst
pyplot_api.rst
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <md...@us...> - 2008-10-24 17:35:26
|
Revision: 6323
http://matplotlib.svn.sourceforge.net/matplotlib/?rev=6323&view=rev
Author: mdboom
Date: 2008-10-24 17:35:23 +0000 (Fri, 24 Oct 2008)
Log Message:
-----------
Minor docstring fix.
Modified Paths:
--------------
trunk/matplotlib/lib/matplotlib/figure.py
Modified: trunk/matplotlib/lib/matplotlib/figure.py
===================================================================
--- trunk/matplotlib/lib/matplotlib/figure.py 2008-10-24 17:12:24 UTC (rev 6322)
+++ trunk/matplotlib/lib/matplotlib/figure.py 2008-10-24 17:35:23 UTC (rev 6323)
@@ -280,15 +280,18 @@
Add a centered title to the figure.
kwargs are :class:`matplotlib.text.Text` properties. Using figure
- coordinates, the defaults are::
+ coordinates, the defaults are:
- *x* = 0.5
+ - *x* = 0.5
the x location of text in figure coords
- *y* = 0.98
+
+ - *y* = 0.98
the y location of the text in figure coords
- *horizontalalignment* = 'center'
+
+ - *horizontalalignment* = 'center'
the horizontal alignment of the text
- *verticalalignment* = 'top'
+
+ - *verticalalignment* = 'top'
the vertical alignment of the text
A :class:`matplotlib.text.Text` instance is returned.
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <md...@us...> - 2008-10-24 17:12:29
|
Revision: 6322
http://matplotlib.svn.sourceforge.net/matplotlib/?rev=6322&view=rev
Author: mdboom
Date: 2008-10-24 17:12:24 +0000 (Fri, 24 Oct 2008)
Log Message:
-----------
Add mathtext API docs.
Modified Paths:
--------------
trunk/matplotlib/lib/matplotlib/mathtext.py
Added Paths:
-----------
trunk/matplotlib/doc/api/mathtext_api.rst
Added: trunk/matplotlib/doc/api/mathtext_api.rst
===================================================================
--- trunk/matplotlib/doc/api/mathtext_api.rst (rev 0)
+++ trunk/matplotlib/doc/api/mathtext_api.rst 2008-10-24 17:12:24 UTC (rev 6322)
@@ -0,0 +1,14 @@
+*******************
+matplotlib mathtext
+*******************
+
+.. inheritance-diagram:: matplotlib.mathtext
+ :parts: 1
+
+:mod:`matplotlib.mathtext`
+=============================
+
+.. automodule:: matplotlib.mathtext
+ :members:
+ :undoc-members:
+ :show-inheritance:
Modified: trunk/matplotlib/lib/matplotlib/mathtext.py
===================================================================
--- trunk/matplotlib/lib/matplotlib/mathtext.py 2008-10-24 15:53:59 UTC (rev 6321)
+++ trunk/matplotlib/lib/matplotlib/mathtext.py 2008-10-24 17:12:24 UTC (rev 6322)
@@ -1,175 +1,21 @@
r"""
+:mod:`~matplotlib.mathtext` is a module for parsing a subset of the
+TeX math syntax and drawing them to a matplotlib backend.
-OVERVIEW
+For a tutorial of its usage see :ref:`mathtext-tutorial`. This
+document is primarily concerned with implementation details.
- mathtext is a module for parsing TeX expressions and drawing them
- into a matplotlib.ft2font image buffer. You can draw from this
- buffer into your backend.
+The module uses pyparsing_ to parse the TeX expression.
- A large set of the TeX symbols are provided (see below).
- Subscripting and superscripting are supported, as well as the
- over/under style of subscripting with \sum, \int, etc.
+.. _pyparsing: http://pyparsing.wikispaces.com/
- The module uses pyparsing to parse the TeX expression, an so can
- handle fairly complex TeX expressions Eg, the following renders
- correctly
+The Bakoma distribution of the TeX Computer Modern fonts, and STIX
+fonts are supported. There is experimental support for using
+arbitrary fonts, but results may vary without proper tweaking and
+metrics for those fonts.
- s = r'$\mathcal{R}\prod_{i=\alpha\mathcal{B}}^\infty a_i\sin(2 \pi f x_i)$'
-
- Different fonts may be selected:
- \mathcal Calligraphic fonts
- \mathrm Roman (upright) font
- \mathit Italic font
- \mathtt Typewriter (monospaced) font, similar to Courier
-
- Additionally, if using the STIX fonts:
- \mathbb Blackboard (double-struck) font
- \mathcircled Circled characters
- \mathfrak Fraktur (Gothic-style) font
- \mathscr Script (cursive) font
- \mathsf Sans-serif font
-
- The following accents are provided: \hat, \breve, \grave, \bar,
- \acute, \tilde, \vec, \dot, \ddot. All of them have the same
- syntax, eg to make an overbar you do \bar{o} or to make an o umlaut
- you do \ddot{o}. The shortcuts are also provided, eg: \"o \'e \`e
- \~n \.x \^y
-
- The spacing elements \ , \/ and \hspace{num} are provided. \/
- inserts a small space, and \hspace{num} inserts a fraction of the
- current fontsize. Eg, if num=0.5 and the fontsize is 12.0,
- hspace{0.5} inserts 6 points of space
-
-
-
- If you find TeX expressions that don't parse or render properly,
- please email me, but please check KNOWN ISSUES below first.
-
-REQUIREMENTS
-
- mathtext requires matplotlib.ft2font. Set BUILD_FT2FONT=True in
- setup.py. See BACKENDS below for a summary of availability by
- backend.
-
-LICENSING:
-
- The computer modern fonts this package uses are part of the BaKoMa
- fonts, which are (now) free for commercial and noncommercial use and
- redistribution; see license/LICENSE_BAKOMA in the matplotlib src
- distribution for redistribution requirements.
-
-USAGE:
-
- See http://matplotlib.sf.net/users/mathtext.html for a tutorial
- introduction.
-
- Any text element (xlabel, ylabel, title, text, etc) can use TeX
- markup, as in
-
- xlabel(r'$\Delta_i$')
- ^
- use raw strings
-
- Math and non-math can be interpresed in the same string. E.g.,
-
- r'My label $x_i$'.
-
- A large set of the TeX symbols are provided. Subscripting and
- superscripting are supported, as well as the over/under style of
- subscripting with \sum, \int, etc.
-
-
- Allowed TeX symbols:
-
- $ \% \AA \AE \BbbC \BbbN \BbbP \BbbQ \BbbR \BbbZ \Bumpeq \Cap \Colon
- \Cup \Delta \Doteq \Downarrow \Equiv \Finv \Gamma \H \Im \L \Lambda
- \Ldsh \Leftarrow \Leftrightarrow \Lleftarrow \Lsh \Nearrow \Nwarrow
- \O \OE \Omega \P \Phi \Pi \Psi \Rdsh \Re \Rightarrow \Rrightarrow
- \Rsh \S \Searrow \Sigma \Subset \Supset \Swarrow \Theta \Uparrow
- \Updownarrow \Upsilon \Vdash \Vert \Vvdash \Xi \_ \__sqrt__ \ac
- \acute \acwopencirclearrow \adots \ae \aleph \alpha \angle \approx
- \approxeq \approxident \arceq \ast \asymp \backcong \backprime
- \backsim \backsimeq \backslash \bar \barleftarrow \barwedge \because
- \beta \beth \between \bigcap \bigcirc \bigcup \bigodot \bigoplus
- \bigotimes \bigstar \bigtriangledown \bigtriangleup \biguplus
- \bigvee \bigwedge \blacksquare \blacktriangle \blacktriangledown
- \blacktriangleleft \blacktriangleright \bot \bowtie \boxbar \boxdot
- \boxminus \boxplus \boxtimes \breve \bullet \bumpeq \c \candra \cap
- \carriagereturn \cdot \cdotp \cdots \check \checkmark \chi \circ
- \circeq \circledR \circledS \circledast \circledcirc \circleddash
- \circumflexaccent \clubsuit \clubsuitopen \colon \coloneq
- \combiningacuteaccent \combiningbreve \combiningdiaeresis
- \combiningdotabove \combininggraveaccent \combiningoverline
- \combiningrightarrowabove \combiningtilde \complement \cong \coprod
- \copyright \cup \cupdot \curlyeqprec \curlyeqsucc \curlyvee
- \curlywedge \curvearrowleft \curvearrowright \cwopencirclearrow \d
- \dag \daleth \danger \dashv \ddag \ddddot \dddot \ddot \ddots
- \degree \delta \diamond \diamondsuit \digamma \div \divideontimes
- \dot \doteq \dotminus \dotplus \dots \doublebarwedge ? \downarrow
- \downdownarrows \downharpoonleft \downharpoonright \downzigzagarrow
- \ell \emdash \emptyset \endash \enspace \epsilon \eqcirc \eqcolon
- \eqdef \eqgtr \eqless \eqsim \equiv \eta \eth \exists \fallingdotseq
- \flat \forall \frakC \frakZ \frown \gamma \geq \geqq \gg \ggg \gimel
- \gneqq \gnsim \grave \greater \gtrdot \gtreqless \gtrless \gtrsim
- \hat \heartsuit \hookleftarrow \hookrightarrow \i \iiint \iint
- \imageof \imath \in \infty \int \intercal \invnot \iota \jmath \k
- \kappa \kernelcontraction \l \lambda \lambdabar \lasp \lbrace
- \lbrack \lceil \leftangle \leftarrow \leftarrowtail \leftbrace
- \leftharpoonaccent \leftharpoondown \leftharpoonup \leftleftarrows
- \leftparen \leftrightarrow \leftrightarrows \leftrightharpoons
- \leftthreetimes \leq \leqq \less \lessdot \lesseqgtr \lessgtr
- \lesssim \lfloor \ll \llcorner \lll \lneqq \lnsim \looparrowleft
- \looparrowright \lq \lrcorner \ltimes \maltese \mapsdown \mapsfrom
- \mapsto \mapsup \measeq \measuredangle \mho \mid \minus \models \mp
- \mu \multimap \nLeftarrow \nLeftrightarrow \nRightarrow \nVDash
- \nVdash \nabla \napprox \natural \ncong \ne \nearrow \neg \nequiv
- \nexists \ngeq \ngtr \ni \nleftarrow \nleftrightarrow \nleq \nless
- \nmid \not \notin \nparallel \nprec \nrightarrow \nsim \nsime
- \nsubset \nsubseteq \nsucc \nsupset \nsupseteq \ntriangleleft
- \ntrianglelefteq \ntriangleright \ntrianglerighteq \nu \nvDash
- \nvdash \nwarrow \o \obar \ocirc \odot \oe \oiiint \oiint \oint
- \omega \ominus \oplus \origof \oslash \otimes \overarc
- \overleftarrow \overleftrightarrow \parallel \partial \phi \pi
- \pitchfork \pm \prec \preccurlyeq \preceq \precnsim \precsim \prime
- \prod \propto \prurel \psi \quad \questeq \rasp \rbrace \rbrack
- \rceil \rfloor \rho \rightangle \rightarrow \rightarrowbar
- \rightarrowtail \rightbrace \rightharpoonaccent \rightharpoondown
- \rightharpoonup \rightleftarrows \rightleftharpoons \rightparen
- \rightrightarrows \rightthreetimes \rightzigzagarrow \risingdotseq
- \rq \rtimes \scrB \scrE \scrF \scrH \scrI \scrL \scrM \scrR \scre
- \scrg \scro \scurel \searrow \sharp \sigma \sim \simeq \slash
- \smallsetminus \smile \solbar \spadesuit \spadesuitopen
- \sphericalangle \sqcap \sqcup \sqsubset \sqsubseteq \sqsupset
- \sqsupseteq \ss \star \stareq \sterling \subset \subseteq \subsetneq
- \succ \succcurlyeq \succeq \succnsim \succsim \sum \supset \supseteq
- \supsetneq \swarrow \t \tau \textasciiacute \textasciicircum
- \textasciigrave \textasciitilde \textexclamdown \textquestiondown
- \textquotedblleft \textquotedblright \therefore \theta \thickspace
- \thinspace \tilde \times \to \top \triangledown \triangleleft
- \trianglelefteq \triangleq \triangleright \trianglerighteq
- \turnednot \twoheaddownarrow \twoheadleftarrow \twoheadrightarrow
- \twoheaduparrow \ulcorner \underbar \uparrow \updownarrow
- \updownarrowbar \updownarrows \upharpoonleft \upharpoonright \uplus
- \upsilon \upuparrows \urcorner \vDash \varepsilon \varkappa
- \varnothing \varphi \varpi \varrho \varsigma \vartheta \vartriangle
- \vartriangleleft \vartriangleright \vdash \vdots \vec \vee \veebar
- \veeeq \vert \wedge \wedgeq \widehat \widetilde \wp \wr \xi \yen
- \zeta \{ \| \}
-
-BACKENDS
-
- mathtext currently works with all backends.
-
-KNOWN ISSUES:
-
- - Certainly there are some...
-
-Author : John Hunter <jdh...@ac...>
- Michael Droettboom <md...@st...>
- (rewrite based on TeX box layout algorithms)
-Copyright : John Hunter (2004,2005)
-License : matplotlib license (PSF compatible)
-
+If you find TeX expressions that don't parse or render properly,
+please email md...@st..., but please check KNOWN ISSUES below first.
"""
from __future__ import division
import os
@@ -214,10 +60,9 @@
def get_unicode_index(symbol):
"""get_unicode_index(symbol) -> integer
-Return the integer index (from the Unicode table) of symbol.
-symbol can be a single unicode character, a TeX command (i.e. r'\pi'),
-or a Type1 symbol name (i.e. 'phi').
-
+Return the integer index (from the Unicode table) of symbol. *symbol*
+can be a single unicode character, a TeX command (i.e. r'\pi'), or a
+Type1 symbol name (i.e. 'phi').
"""
# From UTF #25: U+2212 minus sign is the preferred
# representation of the unary and binary minus sign rather than
@@ -239,32 +84,62 @@
class MathtextBackend(object):
+ """
+ The base class for the mathtext backend-specific code. The
+ purpose of :class:`MathtextBackend` subclasses is to interface
+ between mathtext and a specific matplotlib graphics backend.
+
+ Subclasses need to override the following:
+
+ - :meth:`render_glyph`
+ - :meth:`render_filled_rect`
+ - :meth:`get_results`
+
+ And optionally, if you need to use a Freetype hinting style:
+
+ - :meth:`get_hinting_type`
+ """
def __init__(self):
self.fonts_object = None
def set_canvas_size(self, w, h, d):
- 'Dimension the drawing canvas; may be a noop'
+ 'Dimension the drawing canvas'
self.width = w
self.height = h
self.depth = d
def render_glyph(self, ox, oy, info):
+ """
+ Draw a glyph described by *info* to the reference point (*ox*,
+ *oy*).
+ """
raise NotImplementedError()
def render_filled_rect(self, x1, y1, x2, y2):
+ """
+ Draw a filled black rectangle from (*x1*, *y1*) to (*x2*, *y2*).
+ """
raise NotImplementedError()
def get_results(self, box):
- """Return a backend specific tuple of things to return to the
- backend after all processing is done."""
+ """
+ Return a backend-specific tuple to return to the backend after
+ all processing is done.
+ """
raise NotImplementedError()
def get_hinting_type(self):
+ """
+ Get the Freetype hinting type to use with this particular
+ backend.
+ """
return LOAD_NO_HINTING
class MathtextBackendBbox(MathtextBackend):
- """A backend whose only purpose is to get a precise bounding box.
- Only required for the Agg backend."""
+ """
+ A backend whose only purpose is to get a precise bounding box.
+ Only required for the Agg backend.
+ """
def __init__(self, real_backend):
MathtextBackend.__init__(self)
@@ -310,6 +185,10 @@
self.real_backend.oy = self.bbox[1]
class MathtextBackendAggRender(MathtextBackend):
+ """
+ Render glyphs and rectangles to an FTImage buffer, which is later
+ transferred to the Agg image by the Agg backend.
+ """
def __init__(self):
self.ox = 0
self.oy = 0
@@ -353,9 +232,17 @@
return self.image, self.depth
def MathtextBackendBitmap():
+ """
+ A backend to generate standalone mathtext images. No additional
+ matplotlib backend is required.
+ """
return MathtextBackendBbox(MathtextBackendBitmapRender())
class MathtextBackendPs(MathtextBackend):
+ """
+ Store information to write a mathtext rendering to the PostScript
+ backend.
+ """
def __init__(self):
self.pswriter = StringIO()
self.lastfont = None
@@ -393,6 +280,10 @@
self.fonts_object.get_used_characters())
class MathtextBackendPdf(MathtextBackend):
+ """
+ Store information to write a mathtext rendering to the PDF
+ backend.
+ """
def __init__(self):
self.glyphs = []
self.rects = []
@@ -417,6 +308,10 @@
self.fonts_object.get_used_characters())
class MathtextBackendSvg(MathtextBackend):
+ """
+ Store information to write a mathtext rendering to the SVG
+ backend.
+ """
def __init__(self):
self.svg_glyphs = []
self.svg_rects = []
@@ -442,6 +337,11 @@
self.fonts_object.get_used_characters())
class MathtextBackendCairo(MathtextBackend):
+ """
+ Store information to write a mathtext rendering to the Cairo
+ backend.
+ """
+
def __init__(self):
self.glyphs = []
self.rects = []
@@ -466,7 +366,7 @@
class Fonts(object):
"""
- An abstract base class for fonts that want to render mathtext
+ An abstract base class for a system of fonts to use for mathtext.
The class must be able to take symbol keys and font file names and
return the character metrics. It also delegates to a backend class
@@ -474,11 +374,15 @@
"""
def __init__(self, default_font_prop, mathtext_backend):
- """default_font_prop: A FontProperties object to use for the
- default non-math font, or the base font for Unicode font
- rendering.
- mathtext_backend: A subclass of MathTextBackend used to
- delegate the actual rendering."""
+ """
+ *default_font_prop*: A
+ :class:`~matplotlib.font_manager.FontProperties` object to use
+ for the default non-math font, or the base font for Unicode
+ (generic) font rendering.
+
+ *mathtext_backend*: A subclass of :class:`MathTextBackend`
+ used to delegate the actual rendering.
+ """
self.default_font_prop = default_font_prop
self.mathtext_backend = mathtext_backend
# Make these classes doubly-linked
@@ -486,51 +390,86 @@
self.used_characters = {}
def destroy(self):
- """Fix any cyclical references before the object is about
- to be destroyed."""
+ """
+ Fix any cyclical references before the object is about
+ to be destroyed.
+ """
self.used_characters = None
def get_kern(self, font1, fontclass1, sym1, fontsize1,
font2, fontclass2, sym2, fontsize2, dpi):
"""
- Get the kerning distance for font between sym1 and sym2.
+ Get the kerning distance for font between *sym1* and *sym2*.
- fontX: one of the TeX font names, tt, it, rm, cal, sf, bf or
- default (non-math)
- symX: a symbol in raw TeX form. e.g. '1', 'x' or '\sigma'
- fontsizeX: the fontsize in points
- dpi: the current dots-per-inch
+ *fontX*: one of the TeX font names::
- sym is a single symbol(alphanum, punct) or a special symbol
- like \sigma.
+ tt, it, rm, cal, sf, bf or default (non-math)
+ *fontclassX*: TODO
+
+ *symX*: a symbol in raw TeX form. e.g. '1', 'x' or '\sigma'
+
+ *fontsizeX*: the fontsize in points
+
+ *dpi*: the current dots-per-inch
"""
return 0.
def get_metrics(self, font, font_class, sym, fontsize, dpi):
"""
- font: one of the TeX font names, tt, it, rm, cal, sf, bf or
- default (non-math)
- sym: a symbol in raw TeX form. e.g. '1', 'x' or '\sigma'
- fontsize: font size in points
- dpi: current dots-per-inch
+ *font*: one of the TeX font names::
- advance
- height
- width
- xmin, xmax, ymin, ymax - the ink rectangle of the glyph
- iceberg - the distance from the baseline to the top of the glyph.
- horiBearingY in Truetype parlance, height in TeX parlance
+ tt, it, rm, cal, sf, bf or default (non-math)
+
+ *font_class*: TODO
+
+ *sym*: a symbol in raw TeX form. e.g. '1', 'x' or '\sigma'
+
+ *fontsize*: font size in points
+
+ *dpi*: current dots-per-inch
+
+ Returns an object with the following attributes:
+
+ - *advance*: The advance distance (in points) of the glyph.
+
+ - *height*: The height of the glyph in points.
+
+ - *width*: The width of the glyph in points.
+
+ - *xmin*, *xmax*, *ymin*, *ymax* - the ink rectangle of the glyph
+
+ - *iceberg* - the distance from the baseline to the top of
+ the glyph. This corresponds to TeX's definition of
+ "height".
"""
info = self._get_info(font, font_class, sym, fontsize, dpi)
return info.metrics
def set_canvas_size(self, w, h, d):
- 'Dimension the drawing canvas; may be a noop'
+ """
+ Set the size of the buffer used to render the math expression.
+ Only really necessary for the bitmap backends.
+ """
self.width, self.height, self.depth = ceil(w), ceil(h), ceil(d)
self.mathtext_backend.set_canvas_size(self.width, self.height, self.depth)
def render_glyph(self, ox, oy, facename, font_class, sym, fontsize, dpi):
+ """
+ Draw a glyph at
+
+ - *ox*, *oy*: position
+
+ - *facename*: One of the TeX face names
+
+ - *font_class*:
+
+ - *sym*: TeX symbol name or single character
+
+ - *fontsize*: fontsize in points
+
+ - *dpi*: The dpi to draw at.
+ """
info = self._get_info(facename, font_class, sym, fontsize, dpi)
realpath, stat_key = get_realpath_and_stat(info.font.fname)
used_characters = self.used_characters.setdefault(
@@ -539,31 +478,52 @@
self.mathtext_backend.render_glyph(ox, oy, info)
def render_rect_filled(self, x1, y1, x2, y2):
+ """
+ Draw a filled rectangle from (*x1*, *y1*) to (*x2*, *y2*).
+ """
self.mathtext_backend.render_rect_filled(x1, y1, x2, y2)
def get_xheight(self, font, fontsize, dpi):
+ """
+ Get the xheight for the given *font* and *fontsize*.
+ """
raise NotImplementedError()
def get_underline_thickness(self, font, fontsize, dpi):
+ """
+ Get the line thickness that matches the given font. Used as a
+ base unit for drawing lines such as in a fraction or radical.
+ """
raise NotImplementedError()
def get_used_characters(self):
+ """
+ Get the set of characters that were used in the math
+ expression. Used by backends that need to subset fonts so
+ they know which glyphs to include.
+ """
return self.used_characters
def get_results(self, box):
+ """
+ Get the data needed by the backend to render the math
+ expression. The return value is backend-specific.
+ """
return self.mathtext_backend.get_results(box)
def get_sized_alternatives_for_symbol(self, fontname, sym):
"""
Override if your font provides multiple sizes of the same
- symbol.
+ symbol. Should return a list of symbols matching *sym* in
+ various sizes. The expression renderer will select the most
+ appropriate size for a given situation from this list.
"""
return [(fontname, sym)]
class TruetypeFonts(Fonts):
"""
A generic base class for all font setups that use Truetype fonts
- (through ft2font)
+ (through FT2Font).
"""
class CachedFont:
def __init__(self, font):
@@ -589,8 +549,6 @@
Fonts.destroy(self)
def _get_font(self, font):
- """Looks up a CachedFont with its charmap and inverse charmap.
- font may be a TeX font name (cal, rm, it etc.), or postscript name."""
if font in self.fontmap:
basename = self.fontmap[font]
else:
@@ -611,7 +569,6 @@
return 0.
def _get_info(self, fontname, font_class, sym, fontsize, dpi):
- 'load the cmfont, metrics and glyph with caching'
key = fontname, font_class, sym, fontsize, dpi
bunch = self.glyphd.get(key)
if bunch is not None:
@@ -665,8 +622,9 @@
return xHeight
def get_underline_thickness(self, font, fontsize, dpi):
- # This function used to grab underline thickness from the font,
- # but that information is just too un-reliable, so it is now hardcoded.
+ # This function used to grab underline thickness from the font
+ # metrics, but that information is just too un-reliable, so it
+ # is now hardcoded.
return ((0.75 / 12.0) * fontsize * dpi) / 72.0
def get_kern(self, font1, fontclass1, sym1, fontsize1,
@@ -681,7 +639,10 @@
class BakomaFonts(TruetypeFonts):
"""
- Use the Bakoma true type fonts for rendering
+ Use the Bakoma TrueType fonts for rendering.
+
+ Symbols are strewn about a number of font files, each of which has
+ its own proprietary 8-bit encoding.
"""
_fontmap = { 'cal' : 'cmsy10',
'rm' : 'cmr10',
@@ -788,15 +749,19 @@
_size_alternatives[alias] = _size_alternatives[target]
def get_sized_alternatives_for_symbol(self, fontname, sym):
- alternatives = self._size_alternatives.get(sym)
- if alternatives:
- return alternatives
- return [(fontname, sym)]
+ return self._size_alternatives.get(sym, [(fontname, sym)])
class UnicodeFonts(TruetypeFonts):
- """An abstract base class for handling Unicode fonts.
"""
+ An abstract base class for handling Unicode fonts.
+ While some reasonably complete Unicode fonts (such as DejaVu) may
+ work in some situations, the only Unicode font I'm aware of with a
+ complete set of math symbols is STIX.
+
+ This class will "fallback" on the Bakoma fonts when a required
+ symbol can not be found in the font.
+ """
fontmap = {}
use_cmex = True
@@ -900,7 +865,15 @@
class StixFonts(UnicodeFonts):
"""
- A font handling class for the STIX fonts
+ A font handling class for the STIX fonts.
+
+ In addition to what UnicodeFonts provides, this class:
+
+ - supports "virtual fonts" which are complete alpha numeric
+ character sets with different font styles at special Unicode
+ code points, such as "Blackboard".
+
+ - handles sized alternative characters for the STIXSizeX fonts.
"""
_fontmap = { 'rm' : 'STIXGeneral',
'it' : 'STIXGeneral:italic',
@@ -994,7 +967,7 @@
class StixSansFonts(StixFonts):
"""
- A font handling class for the STIX fonts (using sans-serif
+ A font handling class for the STIX fonts (that uses sans-serif
characters by default).
"""
_sans = True
@@ -1187,9 +1160,9 @@
pass
class Node(object):
- """A node in the TeX box model
- node133
"""
+ A node in the TeX box model
+ """
def __init__(self):
self.size = 0
@@ -1203,21 +1176,26 @@
return 0.0
def shrink(self):
- """Shrinks one level smaller. There are only three levels of sizes,
- after which things will no longer get smaller."""
+ """
+ Shrinks one level smaller. There are only three levels of
+ sizes, after which things will no longer get smaller.
+ """
self.size += 1
def grow(self):
- """Grows one level larger. There is no limit to how big something
- can get."""
+ """
+ Grows one level larger. There is no limit to how big
+ something can get.
+ """
self.size -= 1
def render(self, x, y):
pass
class Box(Node):
- """Represents any node with a physical location.
- node135"""
+ """
+ Represents any node with a physical location.
+ """
def __init__(self, width, height, depth):
Node.__init__(self)
self.width = width
@@ -1255,15 +1233,16 @@
Box.__init__(self, width, 0., 0.)
class Char(Node):
- """Represents a single character. Unlike TeX, the font
- information and metrics are stored with each Char to make it
- easier to lookup the font metrics when needed. Note that TeX
- boxes have a width, height, and depth, unlike Type1 and Truetype
- which use a full bounding box and an advance in the x-direction.
- The metrics must be converted to the TeX way, and the advance (if
- different from width) must be converted into a Kern node when the
- Char is added to its parent Hlist.
- node134"""
+ """
+ Represents a single character. Unlike TeX, the font information
+ and metrics are stored with each :class:`Char` to make it easier
+ to lookup the font metrics when needed. Note that TeX boxes have
+ a width, height, and depth, unlike Type1 and Truetype which use a
+ full bounding box and an advance in the x-direction. The metrics
+ must be converted to the TeX way, and the advance (if different
+ from width) must be converted into a :class:`Kern` node when the
+ :class:`Char` is added to its parent :class:`Hlist`.
+ """
def __init__(self, c, state):
Node.__init__(self)
self.c = c
@@ -1294,9 +1273,11 @@
return self._metrics.slanted
def get_kerning(self, next):
- """Return the amount of kerning between this and the given
+ """
+ Return the amount of kerning between this and the given
character. Called when characters are strung together into
- Hlists to create Kern nodes."""
+ :class:`Hlist` to create :class:`Kern` nodes.
+ """
advance = self._metrics.advance - self.width
kern = 0.
if isinstance(next, Char):
@@ -1307,7 +1288,9 @@
return advance + kern
def render(self, x, y):
- """Render the character to the canvas"""
+ """
+ Render the character to the canvas
+ """
self.font_output.render_glyph(
x, y,
self.font, self.font_class, self.c, self.fontsize, self.dpi)
@@ -1328,9 +1311,11 @@
self.depth *= GROW_FACTOR
class Accent(Char):
- """The font metrics need to be dealt with differently for accents,
+ """
+ The font metrics need to be dealt with differently for accents,
since they are already offset correctly from the baseline in
- TrueType fonts."""
+ TrueType fonts.
+ """
def _update_metrics(self):
metrics = self._metrics = self.font_output.get_metrics(
self.font, self.font_class, self.c, self.fontsize, self.dpi)
@@ -1347,14 +1332,17 @@
self._update_metrics()
def render(self, x, y):
- """Render the character to the canvas"""
+ """
+ Render the character to the canvas.
+ """
self.font_output.render_glyph(
x - self._metrics.xmin, y + self._metrics.ymin,
self.font, self.font_class, self.c, self.fontsize, self.dpi)
class List(Box):
- """A list of nodes (either horizontal or vertical).
- node135"""
+ """
+ A list of nodes (either horizontal or vertical).
+ """
def __init__(self, elements):
Box.__init__(self, 0., 0., 0.)
self.shift_amount = 0. # An arbitrary offset
@@ -1372,8 +1360,10 @@
' '.join([repr(x) for x in self.children]))
def _determine_order(self, totals):
- """A helper function to determine the highest order of glue
- used by the members of this list. Used by vpack and hpack."""
+ """
+ A helper function to determine the highest order of glue
+ used by the members of this list. Used by vpack and hpack.
+ """
o = 0
for i in range(len(totals) - 1, 0, -1):
if totals[i] != 0.0:
@@ -1411,8 +1401,9 @@
self.glue_set *= GROW_FACTOR
class Hlist(List):
- """A horizontal list of boxes.
- node135"""
+ """
+ A horizontal list of boxes.
+ """
def __init__(self, elements, w=0., m='additional', do_kern=True):
List.__init__(self, elements)
if do_kern:
@@ -1420,10 +1411,13 @@
self.hpack()
def kern(self):
- """Insert Kern nodes between Chars to set kerning. The
- Chars themselves determine the amount of kerning they need
- (in get_kerning), and this function just creates the linked
- list in the correct way."""
+ """
+ Insert :class:`Kern` nodes between :class:`Char` nodes to set
+ kerning. The :class:`Char` nodes themselves determine the
+ amount of kerning they need (in :meth:`~Char.get_kerning`),
+ and this function just creates the linked list in the correct
+ way.
+ """
new_children = []
num_children = len(self.children)
if num_children:
@@ -1455,20 +1449,24 @@
# return 0.0
def hpack(self, w=0., m='additional'):
- """The main duty of hpack is to compute the dimensions of the
- resulting boxes, and to adjust the glue if one of those dimensions is
- pre-specified. The computed sizes normally enclose all of the material
- inside the new box; but some items may stick out if negative glue is
- used, if the box is overfull, or if a \vbox includes other boxes that
- have been shifted left.
+ """
+ The main duty of :meth:`hpack` is to compute the dimensions of
+ the resulting boxes, and to adjust the glue if one of those
+ dimensions is pre-specified. The computed sizes normally
+ enclose all of the material inside the new box; but some items
+ may stick out if negative glue is used, if the box is
+ overfull, or if a ``\\vbox`` includes other boxes that have
+ been shifted left.
- w: specifies a width
- m: is either 'exactly' or 'additional'.
+ - *w*: specifies a width
- Thus, hpack(w, 'exactly') produces a box whose width is exactly w, while
- hpack (w, 'additional') yields a box whose width is the natural width
- plus w. The default values produce a box with the natural width.
- node644, node649"""
+ - *m*: is either 'exactly' or 'additional'.
+
+ Thus, ``hpack(w, 'exactly')`` produces a box whose width is
+ exactly *w*, while ``hpack(w, 'additional')`` yields a box
+ whose width is the natural width plus *w*. The default values
+ produce a box with the natural width.
+ """
# I don't know why these get reset in TeX. Shift_amount is pretty
# much useless if we do.
#self.shift_amount = 0.
@@ -1514,25 +1512,28 @@
self._set_glue(x, -1, total_shrink, "Underfull")
class Vlist(List):
- """A vertical list of boxes.
- node137"""
+ """
+ A vertical list of boxes.
+ """
def __init__(self, elements, h=0., m='additional'):
List.__init__(self, elements)
self.vpack()
def vpack(self, h=0., m='additional', l=float(inf)):
- """The main duty of vpack is to compute the dimensions of the
- resulting boxes, and to adjust the glue if one of those dimensions is
- pre-specified.
+ """
+ The main duty of :meth:`vpack` is to compute the dimensions of
+ the resulting boxes, and to adjust the glue if one of those
+ dimensions is pre-specified.
- h: specifies a height
- m: is either 'exactly' or 'additional'.
- l: a maximum height
+ - *h*: specifies a height
+ - *m*: is either 'exactly' or 'additional'.
+ - *l*: a maximum height
- Thus, vpack(h, 'exactly') produces a box whose width is exactly w, while
- vpack(w, 'additional') yields a box whose width is the natural width
- plus w. The default values produce a box with the natural width.
- node644, node668"""
+ Thus, ``vpack(h, 'exactly')`` produces a box whose height is
+ exactly *h*, while ``vpack(h, 'additional')`` yields a box
+ whose height is the natural height plus *h*. The default
+ values produce a box with the natural width.
+ """
# I don't know why these get reset in TeX. Shift_amount is pretty
# much useless if we do.
# self.shift_amount = 0.
@@ -1585,13 +1586,15 @@
self._set_glue(x, -1, total_shrink, "Underfull")
class Rule(Box):
- """A Rule node stands for a solid black rectangle; it has width,
- depth, and height fields just as in an Hlist. However, if any of these
- dimensions is inf, the actual value will be determined by running the
- rule up to the boundary of the innermost enclosing box. This is called
- a "running dimension." The width is never running in an Hlist; the
- height and depth are never running in a Vlist.
- node138"""
+ """
+ A :class:`Rule` node stands for a solid black rectangle; it has
+ *width*, *depth*, and *height* fields just as in an
+ :class:`Hlist`. However, if any of these dimensions is inf, the
+ actual value will be determined by running the rule up to the
+ boundary of the innermost enclosing box. This is called a "running
+ dimension." The width is never running in an :class:`Hlist`; the
+ height and depth are never running in a :class:`Vlist`.
+ """
def __init__(self, width, height, depth, state):
Box.__init__(self, width, height, depth)
self.font_output = state.font_output
@@ -1600,7 +1603,9 @@
self.font_output.render_rect_filled(x, y, x + w, y + h)
class Hrule(Rule):
- """Convenience class to create a horizontal rule."""
+ """
+ Convenience class to create a horizontal rule.
+ """
def __init__(self, state):
thickness = state.font_output.get_underline_thickness(
state.font, state.fontsize, state.dpi)
@@ -1608,18 +1613,21 @@
Rule.__init__(self, inf, height, depth, state)
class Vrule(Rule):
- """Convenience class to create a vertical rule."""
+ """
+ Convenience class to create a vertical rule.
+ """
def __init__(self, state):
thickness = state.font_output.get_underline_thickness(
state.font, state.fontsize, state.dpi)
Rule.__init__(self, thickness, inf, inf, state)
class Glue(Node):
- """Most of the information in this object is stored in the underlying
- GlueSpec class, which is shared between multiple glue objects. (This
+ """
+ Most of the information in this object is stored in the underlying
+ :class:`GlueSpec` class, which is shared between multiple glue objects. (This
is a memory optimization which probably doesn't matter anymore, but it's
easier to stick to what TeX does.)
- node149, node152"""
+ """
def __init__(self, glue_type, copy=False):
Node.__init__(self)
self.glue_subtype = 'normal'
@@ -1647,7 +1655,9 @@
self.glue_spec.width *= GROW_FACTOR
class GlueSpec(object):
- """node150, node151"""
+ """
+ See :class:`Glue`.
+ """
def __init__(self, width=0., stretch=0., stretch_order=0, shrink=0., shrink_order=0):
self.width = width
self.stretch = stretch
@@ -1709,26 +1719,32 @@
Glue.__init__(self, 'ss')
class HCentered(Hlist):
- """A convenience class to create an Hlist whose contents are centered
- within its enclosing box."""
+ """
+ A convenience class to create an :class:`Hlist` whose contents are
+ centered within its enclosing box.
+ """
def __init__(self, elements):
Hlist.__init__(self, [SsGlue()] + elements + [SsGlue()],
do_kern=False)
class VCentered(Hlist):
- """A convenience class to create an Vlist whose contents are centered
- within its enclosing box."""
+ """
+ A convenience class to create a :class:`Vlist` whose contents are
+ centered within its enclosing box.
+ """
def __init__(self, elements):
Vlist.__init__(self, [SsGlue()] + elements + [SsGlue()])
class Kern(Node):
- """A Kern node has a width field to specify a (normally negative)
- amount of spacing. This spacing correction appears in horizontal lists
- between letters like A and V when the font designer said that it looks
- better to move them closer together or further apart. A kern node can
- also appear in a vertical list, when its 'width' denotes additional
- spacing in the vertical direction.
- node155"""
+ """
+ A :class:`Kern` node has a width field to specify a (normally
+ negative) amount of spacing. This spacing correction appears in
+ horizontal lists between letters like A and V when the font
+ designer said that it looks better to move them closer together or
+ further apart. A kern node can also appear in a vertical list,
+ when its *width* denotes additional spacing in the vertical
+ direction.
+ """
def __init__(self, width):
Node.__init__(self)
self.width = width
@@ -1746,11 +1762,13 @@
self.width *= GROW_FACTOR
class SubSuperCluster(Hlist):
- """This class is a sort of hack to get around that fact that this
- code doesn't parse to an mlist and then an hlist, but goes directly
- to hlists. This lets us store enough information in the hlist itself,
- namely the nucleas, sub- and super-script, such that if another script
- follows that needs to be attached, it can be reconfigured on the fly."""
+ """
+ :class:`SubSuperCluster` is a sort of hack to get around that fact
+ that this code do a two-pass parse like TeX. This lets us store
+ enough information in the hlist itself, namely the nucleus, sub-
+ and super-script, such that if another script follows that needs
+ to be attached, it can be reconfigured on the fly.
+ """
def __init__(self):
self.nucleus = None
self.sub = None
@@ -1758,11 +1776,13 @@
Hlist.__init__(self, [])
class AutoHeightChar(Hlist):
- """A class that will create a character as close to the given height
- and depth as possible. When using a font with multiple height versions
- of some characters (such as the BaKoMa fonts), the correct glyph will
- be selected, otherwise this will always just return a scaled version
- of the glyph."""
+ """
+ :class:`AutoHeightChar` will create a character as close to the
+ given height and depth as possible. When using a font with
+ multiple height versions of some characters (such as the BaKoMa
+ fonts), the correct glyph will be selected, otherwise this will
+ always just return a scaled version of the glyph.
+ """
def __init__(self, c, height, depth, state, always=False):
alternatives = state.font_output.get_sized_alternatives_for_symbol(
state.font, c)
@@ -1784,11 +1804,13 @@
self.shift_amount = shift
class AutoWidthChar(Hlist):
- """A class that will create a character as close to the given width
- as possible. When using a font with multiple width versions
- of some characters (such as the BaKoMa fonts), the correct glyph will
- be selected, otherwise this will always just return a scaled version
- of the glyph."""
+ """
+ :class:`AutoWidthChar` will create a character as close to the
+ given width as possible. When using a font with multiple width
+ versions of some characters (such as the BaKoMa fonts), the
+ correct glyph will be selected, otherwise this will always just
+ return a scaled version of the glyph.
+ """
def __init__(self, c, width, state, always=False, char_class=Char):
alternatives = state.font_output.get_sized_alternatives_for_symbol(
state.font, c)
@@ -1808,13 +1830,15 @@
self.width = char.width
class Ship(object):
- """Once the boxes have been set up, this sends them to output.
- Since boxes can be inside of boxes inside of boxes, the main
- work of Ship is done by two mutually recursive routines, hlist_out
- and vlist_out , which traverse the Hlists and Vlists inside of
- horizontal and vertical boxes. The global variables used in TeX to
- store state as it processes have become member variables here.
- node592."""
+ """
+ Once the boxes have been set up, this sends them to output. Since
+ boxes can be inside of boxes inside of boxes, the main work of
+ :class:`Ship` is done by two mutually recursive routines,
+ :meth:`hlist_out` and :meth:`vlist_out`, which traverse the
+ :class:`Hlist` nodes and :class:`Vlist` nodes inside of horizontal
+ and vertical boxes. The global variables used in TeX to store
+ state as it processes have become member variables here.
+ """
def __call__(self, ox, oy, box):
self.max_push = 0 # Deepest nesting of push commands so far
self.cur_s = 0
@@ -1959,6 +1983,9 @@
# PARSER
def Error(msg):
+ """
+ Helper class to raise parser errors.
+ """
def raise_error(s, loc, toks):
raise ParseFatalException(msg + "\n" + s)
@@ -1967,6 +1994,14 @@
return empty
class Parser(object):
+ """
+ This is the pyparsing-based parser for math expressions. It
+ actually parses full strings *containing* math expressions, in
+ that raw text may also appear outside of pairs of ``$``.
+
+ The grammar is based directly on that in TeX, though it cuts a few
+ corners.
+ """
_binary_operators = set(r'''
+ *
\pm \sqcap \rhd
@@ -2198,11 +2233,20 @@
self.clear()
def clear(self):
+ """
+ Clear any state before parsing.
+ """
self._expr = None
self._state_stack = None
self._em_width_cache = {}
def parse(self, s, fonts_object, fontsize, dpi):
+ """
+ Parse expression *s* using the given *fonts_object* for
+ output, at the given *fontsize* and *dpi*.
+
+ Returns the parse tree of :class:`Node` instances.
+ """
self._state_stack = [self.State(fonts_object, 'default', 'rm', fontsize, dpi)]
try:
self._expression.parseString(s)
@@ -2219,6 +2263,12 @@
# is pushed and popped accordingly. The current state always
# exists in the top element of the stack.
class State(object):
+ """
+ Stores the state of the parser.
+
+ States are pushed and popped from a stack as necessary, and
+ the "current" state is always at the top of the stack.
+ """
def __init__(self, font_output, font, font_class, fontsize, dpi):
self.font_output = font_output
self._font = font
@@ -2243,12 +2293,22 @@
font = property(_get_font, _set_font)
def get_state(self):
+ """
+ Get the current :class:`State` of the parser.
+ """
return self._state_stack[-1]
def pop_state(self):
+ """
+ Pop a :class:`State` off of the stack.
+ """
self._state_stack.pop()
def push_state(self):
+ """
+ Push a new :class:`State` onto the stack which is just a copy
+ of the current state.
+ """
self._state_stack.append(self.get_state().copy())
def finish(self, s, loc, toks):
@@ -2674,14 +2734,6 @@
# MAIN
class MathTextParser(object):
- """
- Parse the math expression s, return the (bbox, fonts) tuple needed
- to render it.
-
- fontsize must be in points
-
- return is width, height, fonts
- """
_parser = None
_backend_mapping = {
@@ -2701,10 +2753,23 @@
}
def __init__(self, output):
+ """
+ Create a MathTextParser for the given backend *output*.
+ """
self._output = output.lower()
self._cache = maxdict(50)
def parse(self, s, dpi = 72, prop = None):
+ """
+ Parse the given math expression *s* at the given *dpi*. If
+ *prop* is provided, it is a
+ :class:`~matplotlib.font_manager.FontProperties` object
+ specifying the "default" font to use in the math expression,
+ used for all non-math text.
+
+ The results are cached, so multiple calls to :meth:`parse`
+ with the same expression should be fast.
+ """
if prop is None:
prop = FontProperties()
cacheKey = (s, dpi, hash(prop))
@@ -2712,7 +2777,7 @@
if result is not None:
return result
- if self._output == 'PS' and rcParams['ps.useafm']:
+ if self._output == 'ps' and rcParams['ps.useafm']:
font_output = StandardPsFonts(prop)
else:
backend = self._backend_mapping[self._output]()
@@ -2748,6 +2813,15 @@
def to_mask(self, texstr, dpi=120, fontsize=14):
"""
+ *texstr*
+ A valid mathtext string, eg r'IQ: $\sigma_i=15$'
+
+ *dpi*
+ The dots-per-inch to render the text
+
+ *fontsize*
+ The font size in points
+
Returns a tuple (*array*, *depth*)
- *array* is an NxM uint8 alpha ubyte mask array of
@@ -2755,15 +2829,6 @@
- depth is the offset of the baseline from the bottom of the
image in pixels.
-
- ''texstr''
- A valid mathtext string, eg r'IQ: $\sigma_i=15$'
-
- ''dpi''
- The dots-per-inch to render the text
-
- ''fontsize''
- The font size in points
"""
assert(self._output=="bitmap")
prop = FontProperties(size=fontsize)
@@ -2774,27 +2839,25 @@
def to_rgba(self, texstr, color='black', dpi=120, fontsize=14):
"""
- Returns a tuple (*array*, *depth*)
+ *texstr*
+ A valid mathtext string, eg r'IQ: $\sigma_i=15$'
- - *array* is an NxMx4 RGBA array of ubyte rasterized tex.
+ *color*
+ Any matplotlib color argument
- - depth is the offset of the baseline from the bottom of the
- image in pixels.
+ *dpi*
+ The dots-per-inch to render the text
- Returns a tuple (array, depth), where depth is the offset of
- the baseline from the bottom of the image.
+ *fontsize*
+ The font size in points
- ''texstr''
- A valid mathtext string, eg r'IQ: $\sigma_i=15$'
+ Returns a tuple (*array*, *depth*)
- ''color''
- A valid matplotlib color argument
+ - *array* is an NxM uint8 alpha ubyte mask array of
+ rasterized tex.
- ''dpi''
- The dots-per-inch to render the text
-
- ''fontsize''
- The font size in points
+ - depth is the offset of the baseline from the bottom of the
+ image in pixels.
"""
x, depth = self.to_mask(texstr, dpi=dpi, fontsize=fontsize)
@@ -2813,22 +2876,24 @@
Returns the offset of the baseline from the bottom of the
image in pixels.
- ''filename''
+ *filename*
A writable filename or fileobject
- ''texstr''
+ *texstr*
A valid mathtext string, eg r'IQ: $\sigma_i=15$'
- ''color''
+ *color*
A valid matplotlib color argument
- ''dpi''
+ *dpi*
The dots-per-inch to render the text
- ''fontsize''
+ *fontsize*
The font size in points
- """
+ Returns the offset of the baseline from the bottom of the
+ image in pixels.
+ """
rgba, depth = self.to_rgba(texstr, color=color, dpi=dpi, fontsize=fontsize)
numrows, numcols, tmp = rgba.shape
@@ -2840,16 +2905,15 @@
Returns the offset of the baseline from the bottom of the
image in pixels.
- ''texstr''
+ *texstr*
A valid mathtext string, eg r'IQ: $\sigma_i=15$'
- ''dpi''
+ *dpi*
The dots-per-inch to render the text
- ''fontsize''
+ *fontsize*
The font size in points
-
- """
+ """
assert(self._output=="bitmap")
prop = FontProperties(size=fontsize)
ftimage, depth = self.parse(texstr, dpi=dpi, prop=prop)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jd...@us...> - 2008-10-24 15:54:02
|
Revision: 6321
http://matplotlib.svn.sourceforge.net/matplotlib/?rev=6321&view=rev
Author: jdh2358
Date: 2008-10-24 15:53:59 +0000 (Fri, 24 Oct 2008)
Log Message:
-----------
added action potential example
Added Paths:
-----------
trunk/py4science/examples/data/membrane.dat
trunk/py4science/examples/detect_action_potentials.py
Added: trunk/py4science/examples/data/membrane.dat
===================================================================
--- trunk/py4science/examples/data/membrane.dat (rev 0)
+++ trunk/py4science/examples/data/membrane.dat 2008-10-24 15:53:59 UTC (rev 6321)
@@ -0,0 +1,64 @@
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\xF7i\x9F\xBE\xCF霾\xCF霾闾Wi\x95\xBEWi\x95\xBEgh\x86\xBE\xD5M]\xBE\xD5M]\xBE9\x8E\xE3\xBDi\x8B\xB6\xBDi\x8B\xB6\xBD\x9D\xC9\xBE]\xCDU\xBE]\xCDU\xBE\xD3*\xAD\xBEc,ƾ\xA3-ھk\xAE\xE6\xBE3/\xF3\xBE\xD3/\xFD\xBE \xB8\xBF \xB8\xBFb\xBFvX\xBFvX\xBF\x8A\x98\xBF\x948 \xBF\x948 \xBF\xB2 \xBF\xA8x
+\xBF\xA8x
+\xBF\xA8x
+\xBF\x8A\x98\xBF\xA8x
+\xBF\x9E\xD8 \xBF\x948 \xBF\x8A\x98\xBF\xA8x
+\xBF\xA8x
+\xBF\x80\xF8\xBF\x8A\x98\xBF\x8A\x98\xBF\x80\xF8\xBFl\xB8\xBFl\xB8\xBFvX\xBFl\xB8\xBFl\xB8\xBFN\xD8\xBFb\xBFb\xBFXx\xBFXx\xBFN\xD8\xBF:\x98\xBF:\x98\xBF:\x98\xBF&X\xBF&X\xBF \xB8\xBF&X\xBF&X\xBF\xFB\xAF\xFF\xBEx |
|
From: <md...@us...> - 2008-10-24 14:57:40
|
Revision: 6320
http://matplotlib.svn.sourceforge.net/matplotlib/?rev=6320&view=rev
Author: mdboom
Date: 2008-10-24 14:57:38 +0000 (Fri, 24 Oct 2008)
Log Message:
-----------
Remove empty "else" clause.
Modified Paths:
--------------
trunk/matplotlib/src/_png.cpp
Modified: trunk/matplotlib/src/_png.cpp
===================================================================
--- trunk/matplotlib/src/_png.cpp 2008-10-24 14:55:14 UTC (rev 6319)
+++ trunk/matplotlib/src/_png.cpp 2008-10-24 14:57:38 UTC (rev 6320)
@@ -221,7 +221,6 @@
png_set_strip_16(png_ptr);
} else if (bit_depth < 8) {
png_set_packing(png_ptr);
- } else {
}
// convert misc color types to rgb for simplicity
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <md...@us...> - 2008-10-24 14:55:19
|
Revision: 6319
http://matplotlib.svn.sourceforge.net/matplotlib/?rev=6319&view=rev
Author: mdboom
Date: 2008-10-24 14:55:14 +0000 (Fri, 24 Oct 2008)
Log Message:
-----------
Remove unnecessary declaration.
Modified Paths:
--------------
trunk/matplotlib/src/_backend_agg.cpp
Modified: trunk/matplotlib/src/_backend_agg.cpp
===================================================================
--- trunk/matplotlib/src/_backend_agg.cpp 2008-10-24 14:05:07 UTC (rev 6318)
+++ trunk/matplotlib/src/_backend_agg.cpp 2008-10-24 14:55:14 UTC (rev 6319)
@@ -823,7 +823,6 @@
typedef agg::image_accessor_clip<agg::pixfmt_rgba32> image_accessor_type;
typedef agg::span_interpolator_linear<> interpolator_type;
typedef agg::span_image_filter_rgba_nn<image_accessor_type, interpolator_type> image_span_gen_type;
- typedef agg::renderer_scanline_aa_solid<amask_ren_type> amask_aa_renderer_type;
typedef agg::renderer_scanline_aa<amask_ren_type, color_span_alloc_type, image_span_gen_type> renderer_type;
color_span_alloc_type sa;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <md...@us...> - 2008-10-24 14:05:13
|
Revision: 6318
http://matplotlib.svn.sourceforge.net/matplotlib/?rev=6318&view=rev
Author: mdboom
Date: 2008-10-24 14:05:07 +0000 (Fri, 24 Oct 2008)
Log Message:
-----------
Support reading low-bit depth (< 8) PNG images. Add PNG test suite to make sure we're supporting the basic kinds of PNG files available.
Modified Paths:
--------------
trunk/matplotlib/src/_png.cpp
Added Paths:
-----------
trunk/matplotlib/examples/tests/pngsuite/
trunk/matplotlib/examples/tests/pngsuite/basn0g01.png
trunk/matplotlib/examples/tests/pngsuite/basn0g02.png
trunk/matplotlib/examples/tests/pngsuite/basn0g04.png
trunk/matplotlib/examples/tests/pngsuite/basn0g08.png
trunk/matplotlib/examples/tests/pngsuite/basn0g16.png
trunk/matplotlib/examples/tests/pngsuite/basn2c08.png
trunk/matplotlib/examples/tests/pngsuite/basn2c16.png
trunk/matplotlib/examples/tests/pngsuite/basn3p01.png
trunk/matplotlib/examples/tests/pngsuite/basn3p02.png
trunk/matplotlib/examples/tests/pngsuite/basn3p04.png
trunk/matplotlib/examples/tests/pngsuite/basn3p08.png
trunk/matplotlib/examples/tests/pngsuite/basn4a08.png
trunk/matplotlib/examples/tests/pngsuite/basn4a16.png
trunk/matplotlib/examples/tests/pngsuite/basn6a08.png
trunk/matplotlib/examples/tests/pngsuite/basn6a16.png
trunk/matplotlib/examples/tests/pngsuite/pngsuite.py
trunk/matplotlib/examples/tests/pngsuite/truth.png
Added: trunk/matplotlib/examples/tests/pngsuite/basn0g01.png
===================================================================
(Binary files differ)
Property changes on: trunk/matplotlib/examples/tests/pngsuite/basn0g01.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/matplotlib/examples/tests/pngsuite/basn0g02.png
===================================================================
(Binary files differ)
Property changes on: trunk/matplotlib/examples/tests/pngsuite/basn0g02.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/matplotlib/examples/tests/pngsuite/basn0g04.png
===================================================================
(Binary files differ)
Property changes on: trunk/matplotlib/examples/tests/pngsuite/basn0g04.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/matplotlib/examples/tests/pngsuite/basn0g08.png
===================================================================
(Binary files differ)
Property changes on: trunk/matplotlib/examples/tests/pngsuite/basn0g08.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/matplotlib/examples/tests/pngsuite/basn0g16.png
===================================================================
(Binary files differ)
Property changes on: trunk/matplotlib/examples/tests/pngsuite/basn0g16.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/matplotlib/examples/tests/pngsuite/basn2c08.png
===================================================================
(Binary files differ)
Property changes on: trunk/matplotlib/examples/tests/pngsuite/basn2c08.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/matplotlib/examples/tests/pngsuite/basn2c16.png
===================================================================
(Binary files differ)
Property changes on: trunk/matplotlib/examples/tests/pngsuite/basn2c16.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/matplotlib/examples/tests/pngsuite/basn3p01.png
===================================================================
(Binary files differ)
Property changes on: trunk/matplotlib/examples/tests/pngsuite/basn3p01.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/matplotlib/examples/tests/pngsuite/basn3p02.png
===================================================================
(Binary files differ)
Property changes on: trunk/matplotlib/examples/tests/pngsuite/basn3p02.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/matplotlib/examples/tests/pngsuite/basn3p04.png
===================================================================
(Binary files differ)
Property changes on: trunk/matplotlib/examples/tests/pngsuite/basn3p04.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/matplotlib/examples/tests/pngsuite/basn3p08.png
===================================================================
(Binary files differ)
Property changes on: trunk/matplotlib/examples/tests/pngsuite/basn3p08.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/matplotlib/examples/tests/pngsuite/basn4a08.png
===================================================================
(Binary files differ)
Property changes on: trunk/matplotlib/examples/tests/pngsuite/basn4a08.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/matplotlib/examples/tests/pngsuite/basn4a16.png
===================================================================
(Binary files differ)
Property changes on: trunk/matplotlib/examples/tests/pngsuite/basn4a16.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/matplotlib/examples/tests/pngsuite/basn6a08.png
===================================================================
(Binary files differ)
Property changes on: trunk/matplotlib/examples/tests/pngsuite/basn6a08.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/matplotlib/examples/tests/pngsuite/basn6a16.png
===================================================================
(Binary files differ)
Property changes on: trunk/matplotlib/examples/tests/pngsuite/basn6a16.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/matplotlib/examples/tests/pngsuite/pngsuite.py
===================================================================
--- trunk/matplotlib/examples/tests/pngsuite/pngsuite.py (rev 0)
+++ trunk/matplotlib/examples/tests/pngsuite/pngsuite.py 2008-10-24 14:05:07 UTC (rev 6318)
@@ -0,0 +1,24 @@
+"""
+This test loads a subset of the files in Willem van Schaik's PNG test
+suite available here:
+
+ http://libpng.org/pub/png/pngsuite.html
+
+The result should look like truth.png.
+"""
+
+from matplotlib import pyplot as plt
+import glob
+
+files = glob.glob("basn*.png")
+files.sort()
+
+plt.figure(figsize=(len(files), 2))
+
+for i, fname in enumerate(files):
+ data = plt.imread(fname)
+ plt.imshow(data, extent=[i,i+1,0,1])
+
+plt.gca().get_frame().set_facecolor("#ddffff")
+plt.gca().set_xlim(0, len(files))
+plt.show()
Added: trunk/matplotlib/examples/tests/pngsuite/truth.png
===================================================================
(Binary files differ)
Property changes on: trunk/matplotlib/examples/tests/pngsuite/truth.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Modified: trunk/matplotlib/src/_png.cpp
===================================================================
--- trunk/matplotlib/src/_png.cpp 2008-10-24 11:43:31 UTC (rev 6317)
+++ trunk/matplotlib/src/_png.cpp 2008-10-24 14:05:07 UTC (rev 6318)
@@ -213,19 +213,25 @@
png_uint_32 width = info_ptr->width;
png_uint_32 height = info_ptr->height;
+ bool do_gray_conversion = (info_ptr->bit_depth < 8 &&
+ info_ptr->color_type == PNG_COLOR_TYPE_GRAY);
+ int bit_depth = info_ptr->bit_depth;
+ if (bit_depth == 16) {
+ png_set_strip_16(png_ptr);
+ } else if (bit_depth < 8) {
+ png_set_packing(png_ptr);
+ } else {
+ }
+
// convert misc color types to rgb for simplicity
if (info_ptr->color_type == PNG_COLOR_TYPE_GRAY ||
- info_ptr->color_type == PNG_COLOR_TYPE_GRAY_ALPHA)
+ info_ptr->color_type == PNG_COLOR_TYPE_GRAY_ALPHA) {
png_set_gray_to_rgb(png_ptr);
- else if (info_ptr->color_type == PNG_COLOR_TYPE_PALETTE)
+ } else if (info_ptr->color_type == PNG_COLOR_TYPE_PALETTE) {
png_set_palette_to_rgb(png_ptr);
+ }
-
- int bit_depth = info_ptr->bit_depth;
- if (bit_depth == 16) png_set_strip_16(png_ptr);
-
-
png_set_interlace_handling(png_ptr);
png_read_update_info(png_ptr, info_ptr);
@@ -247,8 +253,6 @@
png_read_image(png_ptr, row_pointers);
-
-
npy_intp dimensions[3];
dimensions[0] = height; //numrows
dimensions[1] = width; //numcols
@@ -256,19 +260,31 @@
PyArrayObject *A = (PyArrayObject *) PyArray_SimpleNew(3, dimensions, PyArray_FLOAT);
-
- for (png_uint_32 y = 0; y < height; y++) {
- png_byte* row = row_pointers[y];
- for (png_uint_32 x = 0; x < width; x++) {
-
- png_byte* ptr = (rgba) ? &(row[x*4]) : &(row[x*3]);
- size_t offset = y*A->strides[0] + x*A->strides[1];
- //if ((y<10)&&(x==10)) std::cout << "r = " << ptr[0] << " " << ptr[0]/255.0 << std::endl;
- *(float*)(A->data + offset + 0*A->strides[2]) = (float)(ptr[0]/255.0f);
- *(float*)(A->data + offset + 1*A->strides[2]) = (float)(ptr[1]/255.0f);
- *(float*)(A->data + offset + 2*A->strides[2]) = (float)(ptr[2]/255.0f);
- *(float*)(A->data + offset + 3*A->strides[2]) = rgba ? (float)(ptr[3]/255.0f) : 1.0f;
+ if (do_gray_conversion) {
+ float max_value = (float)((1L << bit_depth) - 1);
+ for (png_uint_32 y = 0; y < height; y++) {
+ png_byte* row = row_pointers[y];
+ for (png_uint_32 x = 0; x < width; x++) {
+ float value = row[x] / max_value;
+ size_t offset = y*A->strides[0] + x*A->strides[1];
+ *(float*)(A->data + offset + 0*A->strides[2]) = value;
+ *(float*)(A->data + offset + 1*A->strides[2]) = value;
+ *(float*)(A->data + offset + 2*A->strides[2]) = value;
+ *(float*)(A->data + offset + 3*A->strides[2]) = 1.0f;
+ }
}
+ } else {
+ for (png_uint_32 y = 0; y < height; y++) {
+ png_byte* row = row_pointers[y];
+ for (png_uint_32 x = 0; x < width; x++) {
+ png_byte* ptr = (rgba) ? &(row[x*4]) : &(row[x*3]);
+ size_t offset = y*A->strides[0] + x*A->strides[1];
+ *(float*)(A->data + offset + 0*A->strides[2]) = (float)(ptr[0]/255.0);
+ *(float*)(A->data + offset + 1*A->strides[2]) = (float)(ptr[1]/255.0);
+ *(float*)(A->data + offset + 2*A->strides[2]) = (float)(ptr[2]/255.0);
+ *(float*)(A->data + offset + 3*A->strides[2]) = rgba ? (float)(ptr[3]/255.0) : 1.0f;
+ }
+ }
}
//free the png memory
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <js...@us...> - 2008-10-24 12:14:38
|
Revision: 6317
http://matplotlib.svn.sourceforge.net/matplotlib/?rev=6317&view=rev
Author: jswhit
Date: 2008-10-24 11:43:31 +0000 (Fri, 24 Oct 2008)
Log Message:
-----------
defer import of netcdf module
Modified Paths:
--------------
trunk/toolkits/basemap/lib/mpl_toolkits/basemap/__init__.py
Modified: trunk/toolkits/basemap/lib/mpl_toolkits/basemap/__init__.py
===================================================================
--- trunk/toolkits/basemap/lib/mpl_toolkits/basemap/__init__.py 2008-10-24 06:51:29 UTC (rev 6316)
+++ trunk/toolkits/basemap/lib/mpl_toolkits/basemap/__init__.py 2008-10-24 11:43:31 UTC (rev 6317)
@@ -36,7 +36,7 @@
import numpy as np
import numpy.ma as ma
from shapelib import ShapeFile
-import _geoslib, netcdf, netcdftime
+import _geoslib, netcdftime
# basemap data files now installed in lib/matplotlib/toolkits/basemap/data
basemap_datadir = os.sep.join([os.path.dirname(__file__), 'data'])
@@ -3758,6 +3758,7 @@
accesses to the same URL avoid the network.
"""
+ import netcdf
if file.startswith('http'):
return netcdf._RemoteFile(file,maskandscale=maskandscale,\
cache=cache,username=username,password=password,verbose=verbose)
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|
From: <ef...@us...> - 2008-10-24 06:51:38
|
Revision: 6316
http://matplotlib.svn.sourceforge.net/matplotlib/?rev=6316&view=rev
Author: efiring
Date: 2008-10-24 06:51:29 +0000 (Fri, 24 Oct 2008)
Log Message:
-----------
Make shared axes work better with constrained aspect ratio.
This is restricted to the case of adjustable=datalim, and is
experimental.
Modified Paths:
--------------
trunk/matplotlib/lib/matplotlib/axes.py
Modified: trunk/matplotlib/lib/matplotlib/axes.py
===================================================================
--- trunk/matplotlib/lib/matplotlib/axes.py 2008-10-24 00:08:58 UTC (rev 6315)
+++ trunk/matplotlib/lib/matplotlib/axes.py 2008-10-24 06:51:29 UTC (rev 6316)
@@ -499,15 +499,24 @@
self._originalPosition = self._position.frozen()
self.set_axes(self)
self.set_aspect('auto')
- self.set_adjustable('box')
+ self._adjustable = 'box'
self.set_anchor('C')
self._sharex = sharex
self._sharey = sharey
if sharex is not None:
self._shared_x_axes.join(self, sharex)
+ if sharex._adjustable == 'box':
+ sharex._adjustable = 'datalim'
+ #warnings.warn(
+ # 'shared axes: "adjustable" is being changed to "datalim"')
+ self._adjustable = 'datalim'
if sharey is not None:
self._shared_y_axes.join(self, sharey)
-
+ if sharex._adjustable == 'box':
+ sharex._adjustable = 'datalim'
+ #warnings.warn(
+ # 'shared axes: "adjustable" is being changed to "datalim"')
+ self._adjustable = 'datalim'
self.set_label(label)
self.set_figure(fig)
@@ -772,6 +781,11 @@
if which in ('both', 'original'):
self._originalPosition.set(pos)
+ def reset_position(self):
+ 'Make the original position the active position'
+ pos = self.get_position(original=True)
+ self.set_position(pos, which='active')
+
def _set_artist_props(self, a):
'set the boilerplate props for artists added to axes'
a.set_figure(self.figure)
@@ -992,6 +1006,10 @@
ACCEPTS: [ 'box' | 'datalim' ]
"""
if adjustable in ('box', 'datalim'):
+ if self in self._shared_x_axes or self in self._shared_y_axes:
+ if adjustable == 'box':
+ raise ValueError(
+ 'adjustable must be "datalim" for shared axes')
self._adjustable = adjustable
else:
raise ValueError('argument must be "box", or "datalim"')
@@ -1043,11 +1061,11 @@
axes box or the view limits.
'''
if position is None:
- position = self.get_position(True)
+ position = self.get_position(original=True)
aspect = self.get_aspect()
if aspect == 'auto':
- self.set_position( position , 'active')
+ self.set_position( position , which='active')
return
if aspect == 'equal':
@@ -1058,7 +1076,10 @@
#Ensure at drawing time that any Axes involved in axis-sharing
# does not have its position changed.
if self in self._shared_x_axes or self in self._shared_y_axes:
- self._adjustable = 'datalim'
+ if self._adjustable == 'box':
+ self._adjustable = 'datalim'
+ warnings.warn(
+ 'shared axes: "adjustable" is being changed to "datalim"')
figW,figH = self.get_figure().get_size_inches()
fig_aspect = figH/figW
@@ -1069,6 +1090,10 @@
self.set_position(pb1.anchored(self.get_anchor(), pb), 'active')
return
+ # reset active to original in case it had been changed
+ # by prior use of 'box'
+ self.set_position(position, which='active')
+
xmin,xmax = self.get_xbound()
xsize = max(math.fabs(xmax-xmin), 1e-30)
ymin,ymax = self.get_ybound()
@@ -1489,7 +1514,7 @@
if not self.get_visible(): return
renderer.open_group('axes')
- self.apply_aspect(self.get_position(True))
+ self.apply_aspect()
# the patch draws the background rectangle -- the frame below
# will draw the edges
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|
|
From: <ef...@us...> - 2008-10-24 00:09:02
|
Revision: 6315
http://matplotlib.svn.sourceforge.net/matplotlib/?rev=6315&view=rev
Author: efiring
Date: 2008-10-24 00:08:58 +0000 (Fri, 24 Oct 2008)
Log Message:
-----------
Support autoscaling with shared axes
Modified Paths:
--------------
trunk/matplotlib/CHANGELOG
trunk/matplotlib/lib/matplotlib/axes.py
trunk/matplotlib/lib/matplotlib/ticker.py
Modified: trunk/matplotlib/CHANGELOG
===================================================================
--- trunk/matplotlib/CHANGELOG 2008-10-23 19:56:04 UTC (rev 6314)
+++ trunk/matplotlib/CHANGELOG 2008-10-24 00:08:58 UTC (rev 6315)
@@ -1,3 +1,5 @@
+2008-10-23 Autoscaling is now supported with shared axes - EF
+
2008-10-23 Fixed exception in dviread that happened with Minion - JKS
2008-10-21 set_xlim, ylim now return a copy of the viewlim array to
Modified: trunk/matplotlib/lib/matplotlib/axes.py
===================================================================
--- trunk/matplotlib/lib/matplotlib/axes.py 2008-10-23 19:56:04 UTC (rev 6314)
+++ trunk/matplotlib/lib/matplotlib/axes.py 2008-10-24 00:08:58 UTC (rev 6315)
@@ -1451,20 +1451,30 @@
"""
# if image data only just use the datalim
if not self._autoscaleon: return
+ if scalex:
+ xshared = self._shared_x_axes.get_siblings(self)
+ dl = [ax.dataLim for ax in xshared]
+ bb = mtransforms.BboxBase.union(dl)
+ x0, x1 = bb.intervalx
+ if scaley:
+ yshared = self._shared_y_axes.get_siblings(self)
+ dl = [ax.dataLim for ax in yshared]
+ bb = mtransforms.BboxBase.union(dl)
+ y0, y1 = bb.intervaly
if (tight or (len(self.images)>0 and
len(self.lines)==0 and
len(self.patches)==0)):
-
- if scalex: self.set_xbound(self.dataLim.intervalx)
-
- if scaley: self.set_ybound(self.dataLim.intervaly)
+ if scalex:
+ self.set_xbound(x0, x1)
+ if scaley:
+ self.set_ybound(y0, 11)
return
if scalex:
- XL = self.xaxis.get_major_locator().autoscale()
+ XL = self.xaxis.get_major_locator().view_limits(x0, x1)
self.set_xbound(XL)
if scaley:
- YL = self.yaxis.get_major_locator().autoscale()
+ YL = self.yaxis.get_major_locator().view_limits(y0, y1)
self.set_ybound(YL)
#### Drawing
Modified: trunk/matplotlib/lib/matplotlib/ticker.py
===================================================================
--- trunk/matplotlib/lib/matplotlib/ticker.py 2008-10-23 19:56:04 UTC (rev 6314)
+++ trunk/matplotlib/lib/matplotlib/ticker.py 2008-10-24 00:08:58 UTC (rev 6315)
@@ -641,9 +641,17 @@
'Return the locations of the ticks'
raise NotImplementedError('Derived must override')
+ def view_limits(self, vmin, vmax):
+ """
+ select a scale for the range from vmin to vmax
+
+ Normally This will be overridden.
+ """
+ return mtransforms.nonsingular(vmin, vmax)
+
def autoscale(self):
'autoscale the view limits'
- return mtransforms.nonsingular(*self.axis.get_view_interval())
+ return self.view_limits(*self.axis.get_view_interval())
def pan(self, numsteps):
'Pan numticks (can be positive or negative)'
@@ -773,11 +781,9 @@
def _set_numticks(self):
self.numticks = 11 # todo; be smart here; this is just for dev
- def autoscale(self):
+ def view_limits(self, vmin, vmax):
'Try to choose the view limits intelligently'
- vmin, vmax = self.axis.get_data_interval()
-
if vmax<vmin:
vmin, vmax = vmax, vmin
@@ -859,13 +865,11 @@
locs = vmin + np.arange(n+1) * base
return locs
- def autoscale(self):
+ def view_limits(self, dmin, dmax):
"""
Set the view limits to the nearest multiples of base that
contain the data
"""
- dmin, dmax = self.axis.get_data_interval()
-
vmin = self._base.le(dmin)
vmax = self._base.ge(dmax)
if vmin==vmax:
@@ -946,8 +950,7 @@
vmin, vmax = mtransforms.nonsingular(vmin, vmax, expander = 0.05)
return self.bin_boundaries(vmin, vmax)
- def autoscale(self):
- dmin, dmax = self.axis.get_data_interval()
+ def view_limits(self, dmin, dmax):
if self._symmetric:
maxabs = max(abs(dmin), abs(dmax))
dmin = -maxabs
@@ -1043,9 +1046,9 @@
return np.array(ticklocs)
- def autoscale(self):
+ def view_limits(self, vmin, vmax):
'Try to choose the view limits intelligently'
- vmin, vmax = self.axis.get_data_interval()
+
if vmax<vmin:
vmin, vmax = vmax, vmin
@@ -1114,10 +1117,9 @@
ticklocs = np.sign(decades) * b ** np.abs(decades)
return np.array(ticklocs)
- def autoscale(self):
+ def view_limits(self, vmin, vmax):
'Try to choose the view limits intelligently'
b = self._transform.base
- vmin, vmax = self.axis.get_data_interval()
if vmax<vmin:
vmin, vmax = vmax, vmin
@@ -1167,13 +1169,12 @@
d = abs(vmax-vmin)
self._locator = self.get_locator(d)
- def autoscale(self):
+ def view_limits(self, vmin, vmax):
'Try to choose the view limits intelligently'
- vmin, vmax = self.axis.get_data_interval()
d = abs(vmax-vmin)
self._locator = self.get_locator(d)
- return self._locator.autoscale()
+ return self._locator.view_limits(vmin, vmax)
def get_locator(self, d):
'pick the best locator based on a distance'
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|
|
From: <ef...@us...> - 2008-10-23 19:56:11
|
Revision: 6314
http://matplotlib.svn.sourceforge.net/matplotlib/?rev=6314&view=rev
Author: efiring
Date: 2008-10-23 19:56:04 +0000 (Thu, 23 Oct 2008)
Log Message:
-----------
Update movie_demo.py to work with current mpl.
Modified Paths:
--------------
trunk/matplotlib/examples/animation/movie_demo.py
Modified: trunk/matplotlib/examples/animation/movie_demo.py
===================================================================
--- trunk/matplotlib/examples/animation/movie_demo.py 2008-10-23 17:35:50 UTC (rev 6313)
+++ trunk/matplotlib/examples/animation/movie_demo.py 2008-10-23 19:56:04 UTC (rev 6314)
@@ -15,9 +15,12 @@
# the script to suit your own needs.
#
-
-from matplotlib.matlab import * # For plotting graphs.
-import os # For issuing commands to the OS.
+import matplotlib
+matplotlib.use('Agg')
+import matplotlib.pyplot as plt # For plotting graphs.
+import numpy as np
+import subprocess # For issuing commands to the OS.
+import os
import sys # For determining the Python version.
#
@@ -25,24 +28,29 @@
# Python interpreter, and matplotlib. The version of
# Mencoder is printed when it is called.
#
-# This script is known to have worked for:
-#
-# OS version: ('Linux', 'flux-capacitor', '2.4.26', '#1 SMP Sa Apr 17 19:33:42 CEST 2004', 'i686')
-# Python version: 2.3.4 (#2, May 29 2004, 03:31:27) [GCC 3.3.3 (Debian 20040417)]
-# matplotlib version: 0.61.0
-# MEncoder version:
-# MEncoder 1.0pre4-3.3.3 (C) 2000-2004 MPlayer Team
-# CPU: Intel Celeron 2/Pentium III Coppermine,Geyserville 996.1 MHz (Family: 6, Stepping: 10)
-# Detected cache-line size is 32 bytes
-# CPUflags: Type: 6 MMX: 1 MMX2: 1 3DNow: 0 3DNow2: 0 SSE: 1 SSE2: 0
-# Compiled for x86 CPU with extensions: MMX MMX2 SSE
-#
print 'Executing on', os.uname()
print 'Python version', sys.version
print 'matplotlib version', matplotlib.__version__
+not_found_msg = """
+The mencoder command was not found;
+mencoder is used by this script to make an avi file from a set of pngs.
+It is typically not installed by default on linux distros because of
+legal restrictions, but it is widely available.
+"""
+try:
+ subprocess.check_call(['mencoder'])
+except subprocess.CalledProcessError:
+ print "mencoder command was found"
+ pass # mencoder is found, but returns non-zero exit as expected
+ # This is a quick and dirty check; it leaves some spurious output
+ # for the user to puzzle over.
+except OSError:
+ print not_found_msg
+ sys.exit("quitting\n")
+
#
# First, let's create some data to work with. In this example
# we'll use a normalized Gaussian waveform whose mean and
@@ -57,16 +65,16 @@
# Initialize variables needed to create and store the example data set.
numberOfTimeSteps = 100 # Number of frames we want in the movie.
-x = arange(-10,10,0.01) # Values to be plotted on the x-axis.
+x = np.arange(-10,10,0.01) # Values to be plotted on the x-axis.
mean = -6 # Initial mean of the Gaussian.
stddev = 0.2 # Initial standard deviation.
meaninc = 0.1 # Mean increment.
stddevinc = 0.1 # Standard deviation increment.
# Create an array of zeros and fill it with the example data.
-y = zeros((numberOfTimeSteps,len(x)), Float64)
+y = np.zeros((numberOfTimeSteps,len(x)), float)
for i in range(numberOfTimeSteps) :
- y[i] = (1/sqrt(2*pi*stddev))*exp(-((x-mean)**2)/(2*stddev))
+ y[i] = (1/np.sqrt(2*np.pi*stddev))*np.exp(-((x-mean)**2)/(2*stddev))
mean = mean + meaninc
stddev = stddev + stddevinc
@@ -81,15 +89,15 @@
#
# The next four lines are just like Matlab.
#
- plot(x,y[i],'b.')
- axis((x[0],x[-1],-0.25,1))
- xlabel('time (ms)')
- ylabel('probability density function')
-
+ plt.plot(x,y[i],'b.')
+ plt.axis((x[0],x[-1],-0.25,1))
+ plt.xlabel('time (ms)')
+ plt.ylabel('probability density function')
+
#
# Notice the use of LaTeX-like markup.
#
- title(r'$\cal{N}(\mu, \sigma^2)$', fontsize=20)
+ plt.title(r'$\cal{N}(\mu, \sigma^2)$', fontsize=20)
#
# The file name indicates how the image will be saved and the
@@ -100,7 +108,7 @@
# images directly to a file without displaying them.
#
filename = str('%03d' % i) + '.png'
- savefig(filename, dpi=100)
+ plt.savefig(filename, dpi=100)
#
# Let the user know what's happening.
@@ -110,7 +118,7 @@
#
# Clear the figure to make way for the next image.
#
- clf()
+ plt.clf()
#
# Now that we have graphed images of the dataset, we will stitch them
@@ -137,4 +145,12 @@
'-o',
'output.avi')
-os.spawnvp(os.P_WAIT, 'mencoder', command)
+#os.spawnvp(os.P_WAIT, 'mencoder', command)
+
+print "\n\nabout to execute:\n%s\n\n" % ' '.join(command)
+subprocess.check_call(command)
+
+print "\n\n The movie was written to 'output.avi'"
+
+print "\n\n You may want to delete *.png now.\n\n"
+
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|
|
From: <md...@us...> - 2008-10-23 17:36:03
|
Revision: 6313
http://matplotlib.svn.sourceforge.net/matplotlib/?rev=6313&view=rev
Author: mdboom
Date: 2008-10-23 17:35:50 +0000 (Thu, 23 Oct 2008)
Log Message:
-----------
Fix math expression.
Modified Paths:
--------------
trunk/matplotlib/lib/matplotlib/axes.py
Modified: trunk/matplotlib/lib/matplotlib/axes.py
===================================================================
--- trunk/matplotlib/lib/matplotlib/axes.py 2008-10-23 17:35:14 UTC (rev 6312)
+++ trunk/matplotlib/lib/matplotlib/axes.py 2008-10-23 17:35:50 UTC (rev 6313)
@@ -6623,7 +6623,7 @@
.. math::
- C_{xy} = \\frac{|P_{xy}|^2}{P_{xx}*P_{yy}}
+ C_{xy} = \\frac{|P_{xy}|^2}{P_{xx}P_{yy}}
The return value is a tuple (*Cxy*, *f*), where *f* are the
frequencies of the coherence vector.
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|
|
From: <md...@us...> - 2008-10-23 17:35:24
|
Revision: 6312
http://matplotlib.svn.sourceforge.net/matplotlib/?rev=6312&view=rev
Author: mdboom
Date: 2008-10-23 17:35:14 +0000 (Thu, 23 Oct 2008)
Log Message:
-----------
Fix duplicate aliases.
Modified Paths:
--------------
trunk/matplotlib/lib/matplotlib/artist.py
Modified: trunk/matplotlib/lib/matplotlib/artist.py
===================================================================
--- trunk/matplotlib/lib/matplotlib/artist.py 2008-10-23 17:21:49 UTC (rev 6311)
+++ trunk/matplotlib/lib/matplotlib/artist.py 2008-10-23 17:35:14 UTC (rev 6312)
@@ -651,7 +651,7 @@
if not self.is_alias(func): continue
docstring = func.__doc__
fullname = docstring[10:]
- aliases.setdefault(fullname[4:], []).append(name[4:])
+ aliases.setdefault(fullname[4:], {})[name[4:]] = None
return aliases
_get_valid_values_regex = re.compile(r"\n\s*ACCEPTS:\s*((?:.|\n)*?)(?:$|(?:\n\n))")
@@ -731,7 +731,7 @@
"""
if s in self.aliasd:
- aliases = ''.join([' or %s' % x for x in self.aliasd[s]])
+ aliases = ''.join([' or %s' % x for x in self.aliasd[s].keys()])
else:
aliases = ''
return ':meth:`%s <%s>`%s' % (s, target, aliases)
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|
|
From: <md...@us...> - 2008-10-23 17:21:53
|
Revision: 6311
http://matplotlib.svn.sourceforge.net/matplotlib/?rev=6311&view=rev
Author: mdboom
Date: 2008-10-23 17:21:49 +0000 (Thu, 23 Oct 2008)
Log Message:
-----------
Fix collections property list.
Modified Paths:
--------------
trunk/matplotlib/lib/matplotlib/artist.py
trunk/matplotlib/lib/matplotlib/collections.py
Modified: trunk/matplotlib/lib/matplotlib/artist.py
===================================================================
--- trunk/matplotlib/lib/matplotlib/artist.py 2008-10-23 16:38:04 UTC (rev 6310)
+++ trunk/matplotlib/lib/matplotlib/artist.py 2008-10-23 17:21:49 UTC (rev 6311)
@@ -651,7 +651,7 @@
if not self.is_alias(func): continue
docstring = func.__doc__
fullname = docstring[10:]
- aliases[fullname[4:]] = name[4:]
+ aliases.setdefault(fullname[4:], []).append(name[4:])
return aliases
_get_valid_values_regex = re.compile(r"\n\s*ACCEPTS:\s*((?:.|\n)*?)(?:$|(?:\n\n))")
@@ -731,8 +731,10 @@
"""
if s in self.aliasd:
- return ':meth:`%s <%s>` or %s' % (s, target, self.aliasd[s])
- else: return ':meth:`%s <%s>`' % (s, target)
+ aliases = ''.join([' or %s' % x for x in self.aliasd[s]])
+ else:
+ aliases = ''
+ return ':meth:`%s <%s>`%s' % (s, target, aliases)
def pprint_setters(self, prop=None, leadingspace=2):
"""
Modified: trunk/matplotlib/lib/matplotlib/collections.py
===================================================================
--- trunk/matplotlib/lib/matplotlib/collections.py 2008-10-23 16:38:04 UTC (rev 6310)
+++ trunk/matplotlib/lib/matplotlib/collections.py 2008-10-23 17:21:49 UTC (rev 6311)
@@ -253,7 +253,7 @@
else:
return self._uniform_offsets
- def set_linewidths(self, lw):
+ def set_linewidth(self, lw):
"""
Set the linewidth(s) for the collection. *lw* can be a scalar
or a sequence; if it is a sequence the patches will cycle
@@ -263,11 +263,18 @@
"""
if lw is None: lw = mpl.rcParams['patch.linewidth']
self._linewidths = self._get_value(lw)
- set_lw = set_linewidth = set_linewidths
- def set_linestyles(self, ls):
+ def set_linewidths(self, lw):
+ """alias for set_linewidth"""
+ return self.set_linewidth(lw)
+
+ def set_lw(self, lw):
+ """alias for set_linewidth"""
+ return self.set_linewidth(lw)
+
+ def set_linestyle(self, ls):
"""
- Set the linestyles(s) for the collection.
+ Set the linestyle(s) for the collection.
ACCEPTS: ['solid' | 'dashed', 'dashdot', 'dotted' |
(offset, on-off-dash-seq) ]
@@ -306,8 +313,15 @@
except ValueError:
raise ValueError('Do not know how to convert %s to dashes'%ls)
self._linestyles = dashes
- set_dashes = set_linestyle = set_linestyles
+ def set_linestyles(self, ls):
+ """alias for set_linestyle"""
+ return self.set_linestyle(ls)
+
+ def set_dashes(self, ls):
+ """alias for set_linestyle"""
+ return self.set_linestyle(ls)
+
def set_antialiased(self, aa):
"""
Set the antialiasing state for rendering.
@@ -317,8 +331,11 @@
if aa is None:
aa = mpl.rcParams['patch.antialiased']
self._antialiaseds = self._get_bool(aa)
- set_antialiaseds = set_antialiased
+ def set_antialiaseds(self, aa):
+ """alias for set_antialiased"""
+ return self.set_antialiased(aa)
+
def set_color(self, c):
"""
Set both the edgecolor and the facecolor.
@@ -344,7 +361,9 @@
self._facecolors_original = c
self._facecolors = _colors.colorConverter.to_rgba_array(c, self._alpha)
- set_facecolors = set_facecolor
+ def set_facecolors(self, c):
+ """alias for set_facecolor"""
+ return self.set_facecolor(c)
def get_facecolor(self):
return self._facecolors
@@ -377,7 +396,9 @@
self._edgecolors_original = c
self._edgecolors = _colors.colorConverter.to_rgba_array(c, self._alpha)
- set_edgecolors = set_edgecolor
+ def set_edgecolors(self, c):
+ """alias for set_edgecolor"""
+ return self.set_edgecolor(c)
def set_alpha(self, alpha):
"""
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