Speeding up code using Cython
December 18, 2007 | Filed Under Uncategorized | Leave a Comment
The graph below compares a brute-force depth first search in Sage/Python (red line) to an implementation of the same algorithm in Cython (blue line). Vertical axis is run time in seconds, horizontal axis is number of latin square completions generated:
Cython does pretty well, and the code is far more readable than the earlier C++ version that I wrote.
For more about writing Cython code in Sage, see Chapter 5 of the documentation.
Using ‘yield’ to simulate a Markov chain
December 16, 2007 | Filed Under sage | Leave a Comment
One thing that I really like about Sage is that it uses Python as its underlying language. This means that we get “for free” many nice features of Python. One of these features that I particularly like is the yield keyword. Here is a small example:
def foo():
i = 0
while True:
yield i
i = i + 1
We can use the foo function as a generator:
sage: g = foo() sage: print g.next() 0 sage: print g.next() 1 sage: print g.next() 2
In other words, the yield keyword acts as a way to a Python function into a generator. The execution of foo is paused until the next call to g.next(). If we reach the end of the function, the StopIteration exception is raised.
The yield keyword makes it pretty easy to write the skeleton for a Markov chain simulator, using the following basic form:
def markov_chain():
state = initial_state()
while True:
yield state
state = new_state(state)
if some_condition: return
For a real example, see the latin_square_generator function in
latin.sage which is part of a small library for
latin square manipulations in Sage. The Markov chain itself was given by Jacobson and Matthews in “Generating uniformly distributed random Latin squares,” Journal of Combinatorial Designs, vol 4, 1996, no 6, pp 405–437.
MetaPost Examples
December 11, 2007 | Filed Under LaTeX | Leave a Comment
2008-10-19: I use PyX instead of Metapost. It’s based on Python so the syntax is clear and straightforward, and is easily used from Sage (install with “sage -python setup.py install” from the PyX source directory).
Introduction
My favourite package for drawing diagrams is
MetaPost. Here’s an
example, taken from my PhD thesis:
The best page for examples is the one by
Navigator.
Compiling with LaTeX fonts
Normally MetaPost uses TeX to compile but it is nicer to have access to
LaTeX fonts/symbols/etc. To do this put the following at the top of your
MetaPost file:
verbatimtex
\documentclass[12pt]{article}
\usepackage{amsmath}
\usepackage{amssymb}
\usepackage{amsthm}
\begin{document}
etex
Then set the TEX environment variable and compile. For example, in
Bash, you could do:
$ export TEX=latex && mpost case1.mp
My examples
Here are all the MetaPost diagrams from my PhD thesis. There are a
few duplicates and some dodgy code, I make no claim of being an expert
in MetaPost.
All files in a compressed
tar archive
Metapost to PDF
A few of my Metapost files use the following TEX function
(copied from here):
vardef TEX primary s =
write "verbatimtex" to "mptextmp.mp";
write "\documentclass[12pt]{article}" to "mptextmp.mp";
write "\usepackage[T1]{fontenc}" to "mptextmp.mp";
write "\usepackage{amsmath,amssymb}" to "mptextmp.mp";
write "\begin{document}" to "mptextmp.mp";
write "etex" to "mptextmp.mp";
write "btex "&s&" etex" to "mptextmp.mp";
write EOF to "mptextmp.mp";
scantokens "input mptextmp"
enddef;
The command mptopdf seems to have trouble with the temporary
file mptextmp.mp. In particular I got this error when doing
mptopdf bug.mp:
This is MetaPost, Version 0.901 (Web2C 7.5.5)
(/usr/share/texmf-texlive/web2c/natural.tcx)
(bug.mp (mptextmp.mp
>> mptextmp.mp
>> mptextmp.mpx
! Unable to make mpx file.
l.5 btex
1 etex
Transcript written on bug.log.
error in metapost run : bug.mp:5
total run time : 0 seconds
MPtoPDF 1.3 : error while processing mp file
On the other hand, this seems to work:
mpost bug.mp mptopdf bug.1
I’m not sure why this is the case – is this a bug or just
undocumented behaviour?
Other stuff
MetaFun looks
good. It’s also worth checking out what other peope have
as metapost on del.icio.us.
Installing Minion Pro fonts
December 11, 2007 | Filed Under LaTeX | 9 Comments
Introduction
This post describes how to install Minion Pro fonts on Ubuntu 7.04/7.10. It should work for any modern Linux distribution with TexLive.
Update: these instructions seem to work on later versions of Ubuntu and even OSX (see the comments for details). And someone’s done a translation into Japanese. Cool 
Someone adapted my notes for installing on a Mac: http://jklukas.blogspot.com/2010/02/installing-minionpro-tex-package.html
We will install to /usr/local/share/texmf. Check that this matches the
definition of TEXMFLOCAL in your installation:
$ kpsexpand '$TEXMFLOCAL' /usr/local/share/texmf
It is vital that you install to the right path in
/usr/local.
Install mnsymbol
Click on mnsymbol and
download the entire directory as mnsymbol.zip.
unzip mnsymbol.zip cd mnsymbol/tex latex MnSymbol.ins mkdir -p /usr/local/share/texmf/tex/latex/MnSymbol/ mkdir -p /usr/local/share/texmf/fonts/source/public/MnSymbol/ mkdir -p /usr/local/share/texmf/doc/latex/MnSymbol/ cp MnSymbol.sty /usr/local/share/texmf/tex/latex/MnSymbol/MnSymbol.sty cd .. cp source/* /usr/local/share/texmf/fonts/source/public/MnSymbol/ cp MnSymbol.pdf README /usr/local/share/texmf/doc/latex/MnSymbol/ mkdir -p /usr/local/share/texmf/fonts/map/dvips/MnSymbol mkdir -p /usr/local/share/texmf/fonts/enc/dvips/MnSymbol mkdir -p /usr/local/share/texmf/fonts/type1/public/MnSymbol mkdir -p /usr/local/share/texmf/fonts/tfm/public/MnSymbol cp enc/MnSymbol.map /usr/local/share/texmf/fonts/map/dvips/MnSymbol/ cp enc/*.enc /usr/local/share/texmf/fonts/enc/dvips/MnSymbol/ cp pfb/*.pfb /usr/local/share/texmf/fonts/type1/public/MnSymbol/ cp tfm/* /usr/local/share/texmf/fonts/tfm/public/MnSymbol/
Regenerate the indexes and enable MnSymbol:
mktexlsr updmap-sys --enable MixedMap MnSymbol.map
You should be able to compile
mnsymbol-test.tex with no errors.
Install the MinionPro package
We will need a few files from here:
http://www.ctan.org/tex-archive/fonts/minionpro/.
Download scripts.zip and unpack it:
mkdir minionpro-scripts cd minionpro-scripts unzip ../scripts.zip
Copy your OTF fonts into the local directory.
find /youradobefonts/ -iname '*minion*pro*otf' -exec cp -v '{}' otf/ ';'
Hint: Adobe Reader ships with some Minion Pro fonts.
Make sure you have the latest version of lcdf-typetools and then
convert the fonts:
sudo apt-get install lcdf-typetools ./convert.sh
Install the fonts:
mkdir -p /usr/local/share/texmf/fonts/type1/adobe/MinionPro/ cp pfb/*.pfb /usr/local/share/texmf/fonts/type1/adobe/MinionPro/
Determine which version of the Adobe fonts you have. For example,
I have the “002.000″ family:
$ otfinfo -v ~/Desktop/minionpro-scripts/otf/MinionPro-Regular.otf Version 2.015;PS 002.000;Core 1.0.38;makeotf.lib1.7.9032
You need to download one of the following encoding files:
Version | Encoding file ------------------------ 001.000 | enc-v1.000.zip 001.001 | enc-v1.001.zip 002.000 | env-v2.000.zip
The last few steps:
cd /usr/local/share/texmf unzip ~/Desktop/metrics-base.zip unzip ~/Desktop/metrics-full.zip unzip ~/Desktop/enc-X.XXX.zip (pick your version)
Edit /etc/texmf/updmap.d/10local.cfg and add the following
line:
Map MinionPro.map
Regenerate all indexes:
mktexlsr update-updmap updmap-sys
You should see a line like this:
updmap-sys: using map file `/usr/local/share/texmf/fonts/map/dvips/MnSymbol/MnSymbol.map'
You should now be able to compile
minionpro-test.tex with no errors.
You might see this error on large documents:
Font OMS/MnSymbolS/m/n/17.28=MnSymbolS12 at 17.28pt not loaded: Not enough room left.
Edit /etc/texmf/texmf.d/95NonPath.cnf and change
font_mem_size = 500000
to
font_mem_size = 5000000
or some other large value. Then run
update-texmf
1st Istanbul design theory and combinatorics conference
December 11, 2007 | Filed Under mathematics | Leave a Comment
In June 2008 there will be a design theory and combinatorics conference in Istanbul:
This is the second announcement for The 1st Istanbul
Design Theory and Combinatorics Conference in honor of 70th birthday of Curt Lindner that will be held from 16th to 20th of June 2008 at Koç
University, Turkey.Please feel free to FORWARD THIS ANNOUNCEMENT to OTHER COLLEAGUES and STUDENTS that may be interested in attending to the conference.
The web page of the conference was updated recently. You can find more information about the registration, accommodation options and the cost of the conference.
We will be delighted to see all of you in Istanbul. Please fill in
the pre-registration form in the webpage of the conference as soon as possible if you haven’t done so.
There is no obligations attached to filling the Pre-Registration form. This information is very important for us to have an estimate on the number of participants.For more information please refer to the conference webpage.
For all other questions please e-mail to: design@ku.edu.tr
Yours Sincerely
SULE YAZICI and SELDA KUCUKCIFCI