sudo or do not

R and Rserve on Windows

2012-02-06T07:17:00.000-08:00

This is easy if your system is 32-bit. If it is 64 bit you need to make sure you are using 32-bit R because the R serve binary is 32 bit!

Install the windows R binary package (accepting the defaults)
Put the R bin directory on your path (right click computer → Advanced Properties → Environment Variables).

For a 32-bit Windows install you should use a path like this: C:\Program Files\R\R-2.14.1\bin
For a 64-bit Windows install you need to link to the i386 folder: C:\Program Files\R\R-2.14.1\bin\i386

Fire up R from the cmd line (make sure that it is the 32 bit R, even if you are on a 64-bit computer) and execute the command: install.packages("Rserve") -- note to where it installs Rserve.
Copy the binaries Rserve.exe and Rserve_d.exe to your R bin directory referenced aboved.
Fire up a new cmd line and run the command: "R CMD Rserve' and configure the firewall popup to allow rserve to work.
You know if everything is working if you can execute this code inside of irb (depends on rserve/simpler [gem install rserve-simpler]):

require 'rserve/simpler/R'

Listen to Youtube on linux (legally)

2011-08-08T10:18:00.000-07:00

Per the terms of service, you are not supposed to download YouTube videos. However, it does NOT say that you cannot view them in something other than a web browser. The main problem with youtube is how much garbage/dodginess there is. Also, most of the time I just want to listen to the music anyway.... what to do?

The answer: use youtube-dl to provide the correct download link, then stream to mplayer and null the video.

Steps:

Download youtube-dl and put somewhere in your path (such as ~/bin/) and make executable. If your player breaks, just download the latest version (up within 24 hrs of a youtube site modification) and it should work again. They have a youtube-dl .deb package in the ubuntu repos, but it is obsoleted pretty fast (for instance 10.04 doesn't work).
make sure mplayer and python are installed: (sudo apt-get install mplayer python)
Use this command:

mplayer -vo null -cookies -cookies-file /tmp/cookie.txt $(youtube-dl -g -f 34 --cookies /tmp/cookie.txt "http://www.youtube.com/watch?v=pGruu89cCw8")

Of course, you will change the video link to be the one you like. Here is some explanation of what is going on:

Youtube requires cookies to be enabled. We get the video link via youtube-dl and put it into the cookie file. mplayer is using cookies and reads the url to play from the cookie file.
The -g means get the url, and -f changes which file format you are getting the link to (look up youtube codes... current options are 5, 34, 35, 18, 22, 37, 38, 43, 44, 45, 17). 34 is the lowest resolution flv format at 128 kbits/s sound (and I think is standard "360"). 18 would give you 96 kbits/s sound.
-vo null means no video output. Use -fs instead if you want full screen, or nothing for that option if you want regular.

There you have it. Robust, legal, streaming audio player for youtube.

This also seems to work on short playlists, but not always:

mplayer -vo null -cookies -cookies-file /tmp/cookie.txt $(youtube-dl -g -f 34 --cookies /tmp/cookie.txt "http://www.youtube.com/view_play_list?p=460F66B8E8E56FB6")

Navigate through the tracks with ">" and "<".

rvm with Ubuntu 10.04 and 10.10

2011-04-11T08:22:00.000-07:00

If you plan on doing a lot of development in ruby, then rvm (ruby version manager) is the way to use lots of different ruby versions and gems. If you just want to run ruby, you should use your system's package manager.

This is a condensed version of Chistopher Irish's excellent write-up

(leading $ is the bash prompt)


$ sudo apt-get install curl git-core ruby
$ bash < <(curl -s https://rvm.beginrescueend.com/install/rvm)

If you haven't already replaced your .bashrc, you probably have a line in there like this:

[ -z "$PS1" ] && return

Replace that line with:


if [[ -n "$PS1" ]]; then

Then, add this to the last line of the .bashrc file (however, you can leave off that very final, dangling 'fi' if you did NOT have a return statement that you replaced earlier).


if [[ -s $HOME/.rvm/scripts/rvm ]] ; then source $HOME/.rvm/scripts/rvm ; fi

fi

There are going to be prerequisites to installing most ruby's. Use the command rvm notes to discover those dependencies for your system.

Okay, we'll grab some prerequisites for compiling 1.9.2:


$ sudo aptitude install build-essential bison openssl libreadline5 libreadline-dev curl git-core zlib1g zlib1g-dev libssl-dev vim libsqlite3-0 libsqlite3-dev sqlite3 libreadline-dev libxml2-dev git-core subversion autoconf

Now, we can list the ruby versions we can install, install 1.9.2, and set it as default.


rvm list known  # see which ruby versions we could install
rvm install 1.9.2-head
rvm --default 1.9.2-head  # make ruby 1.9.2 our default

bacon and autotest

2011-03-15T15:32:00.000-07:00

Took a little to figure this out, so thought I would share. You need an empty file in your spec folder called .bacon in your spec folder. This appears to load up a lot of the proper bacon environment things into autotest. However, if you want to override specific behaviors, you do that in a .autotest file in the top directory.


touch spec/.bacon

Inside .autotest:


require 'rubygems'
require 'bacon'
require 'autotest/bacon'

# see inside /lib/autotest/bacon.rb for template

class Autotest::Bacon < Autotest
  undef make_test_cmd
  def make_test_cmd(files_to_test)
    # I modified this to only include _spec.rb files:
    args = files_to_test.keys.flatten.select {|v| v =~ /_spec.rb$/ }.join(' ')
    args = '-a' if args.empty?
    # TODO : make regex to pass to -n using values
    # use bacon -h to see all your possible options!
    "#{ruby} -S bacon -I#{libs} -o TestUnit #{args}"
  end
end

image landscapes for ebooks (and other digital-based reading)

2011-03-07T10:05:00.000-08:00

The problem with electronic text is that it lacks the spatial character of a book. You don't really know where you are at in a giant, monolithic column of perfect text, especially when resizing it changes where text is located. However, in a book, you have several spatial cues that are constant: which page, which part of the page, how deep into the book (depth) and any imperfections on the page itself or with the text. So, with ebooks, how can you duplicate this effect?

One could write a program that lays books out so that the book is more like a book (there are cues that indicate depth, etc.). With svg you could easily add certain permanent imperfections to the text to give it more character.

There are two other ways to add a spatial dimension to reading text:

1. Layer text, or pages, into a 3D landscape. If the pages of your book traversed an interesting cityscape, room, landscape, or mountain path, etc., you would have spatial anchors upon which to peg the text.

2. The page itself could link out into either auto-generated or user defined images (or text). In this way, each page is given visual character that links it to other ideas and images.

IMO, both the ideas and the implementation of these ideas (i.e., embedding pages of text, with textual imperfections into a 3D landscape, or adding pictures and text to the pages of the book itself, etc.) are obvious and trivial. Any college student taking a web or 3D design class could do it. It merely remains for someone to do it.

ruby list comprehension

2011-02-21T23:08:00.000-08:00

I have seen list comprehension cited as a feature of python that ruby lacks. I want to play around with the idea to see where it goes...

A nice write up on list comprehensions in python has an example where you can use list comprehension to find prime numbers. They divide it into two steps because it gets a little hairy on one line. Here's finding primes on one line using list comprehension:


>>> [x for x in range(2, 50) if x not in [j for i in range(2, 8) for j in range(i*2, 50, i)]]
[2, 3, 5, 7, 11, 13, 17, 19, 23, 29, 31, 37, 41, 43, 47]

It's not bad, but it's easy to get lost in there (my ruby eyes are not highly trained in python, of course).

Now, one of the things list comprehensions do is it does selection and modification in the same phrase. This part of list comprehensions is easy to implement.

[ add the equivalent python here ]


(2..10).select(&:even?).map {|v| v**2 }
(2..10).map {|v| v**2 if v.even? }.compact

Implementing this aspect of list comprehensions in ruby is less than trivial:


module Enumerable
  def lc(&block)
    block.nil? ? self : self.map(&block).compact
  end
end

The other part of list comprehensions is the fact that the evaluation happens from right to left (in the python code) so that the execution of the code is efficient.

This gets the job done, but the right-most block is executed multiple times to make it work:


(2..50).reject {|j| (2..8).map {|i| (i*2).step(50,i).to_a}.flatten.include?(j) 

# also other ways to think about this (need to finish this post)
Set.new(2..50) - (2..8).reduce(Set.new) {|np,i| np.merge((i*2).step(50,i)) }

Using Dropbox and git

2011-02-09T11:32:00.000-08:00

Dropbox is really fantastic, but its version control abilities are limited. Git is a fantastic tool for versioning things. Here's how I use both to keep detailed version history of the projects that matter to me:

Solo Repo (use a Normal git repo)

For most projects, I do not need to merge changes with multiple people, but I want a version history. For these, I set up a normal git repository. This repo has no "origin", so I never push to anything, just stage and checkin.


cd ~/Dropbox/myproject
git init
git add .
git commit -m 'first commit'
# after a while
git status
git commit -a -m 'another commit'

Easy to do, and all my changes (even when I don't happen to check them in) follow me on all the computers I use dropbox on.

Shared Repo (use a Bare git repo)

In this case, I'll make a bare git repo and then share the folder with others. I'll assume I'm starting with an existing project directory, but it is not a git repo yet. (there are other ways to do this).


# my project is sitting on my local machine somewhere.
# I will make it a normal git repository
cd someproject
git init
git add .
git commit -m 'first commit'
# now make a bare git repository on my dopbox folder
# by convention, bare repos end in '.git'
mkdir -p ~/Dropbox/git/someproject.git  
pushd ~/Dropbox/git/someproject.git 
git init --bare
popd  # back where I was
git remote add origin ~/Dropbox/git/someproject.git
# now we can push and pull to our origin (see below if you get errors)
git pull
git push

If you get trouble when pushing or pulling to your remote, add these lines to your ~/.gitconfig file:


[push]
 default = matching
[branch "master"]
 remote = origin
 merge = refs/heads/master

Shell escaped file names in ruby

2010-12-17T14:52:00.000-08:00

When files have crazy characters in their filename (like ' or ""), it can make creating a robust script challenging. After all, if you write the script with either a single quotation mark or a double quotation mark, the other one will trip you up:


file1 = "my'crazy'file.txt"
file2 = 'my"crazy"file.txt'
system "mv \"#{file2}\" bettername.txt"  # fails on file2
system "mv '#{file2}' bettername.txt"    # fails on file1

The answer is to use the multiple arguments invocation, which will properly escape your filename to be fully shell compatible:


system "mv", file1, "bettername.txt"  # works on file1 or file2

Playing with (compiling) the redesigned NArray

2010-12-09T21:40:00.000-08:00

Masahiro Tanaka has been redesigning NArray. Word is that it may be pulled into mainline ruby.

So, what is it like? Amazing from what I can tell. How do you play with it? At least on Ubuntu 10.10, this is what I did (there may be other dependencies I've neglected here):


sudo apt-get install libatlas-dev libatlas-base-dev
# modify extconf.rb:
have_header("atlas/cblas.h")   ===>   have_header("cblas.h")
# modify linalg.c
#include <atlas/cblas.h>   ===>   #include <cblas.h>
# for ruby 1.9, you also need to change a few normal array things:

diff -r ../narray-new-1.8/narray.c ./narray.c
211,212c211,212
<     n = RARRAY(idxargs)->len;
<     ptr = RARRAY(idxargs)->ptr;
---
>     n = RARRAY_LEN(idxargs);
>     ptr = RARRAY_PTR(idxargs);
232c232,233
< const static size_t zero=0;
---
> //const static size_t zero=0;
> static const size_t zero=0;
463c464
<      ndim = RARRAY(v)->len;
---
>      ndim = RARRAY_LEN(v);
761a763
>     VALUE *ptr;
774,775c776,778
<  RARRAY(v)->ptr[i] = SIZE2NUM(na->shape[c]);
<  RARRAY(v)->len++;
---
>  RARRAY_PTR(v)[i] = SIZE2NUM(na->shape[c]);
>  ptr = RARRAY_LEN(v);
>     ptr++;
diff -r ../narray-new-1.8/nstruct.c ./nstruct.c
301c301
<      ndim = RARRAY(argv[i])->len;
---
>      ndim = RARRAY_LEN(argv[i]);

now, you should be able to "ruby extconf.rb", "make", and then require 'narray' or require './narray.so'

Compile ruby 1.9.2 on Ubuntu

2010-09-28T09:22:00.000-07:00

assumes you have build-essential package installed


wget http://ftp.ruby-lang.org/pub/ruby/1.9/ruby-1.9.2-p0.tar.bz2
tar -xjvf ruby-1.9.2-p0.tar.bz2
cd ruby-1.9.2-p0
./configure --enable-shared --program-suffix=1.9.2
make
make check # optional
sudo checkinstall make install
# [follow the defaults until here:
# NOTE that you want the extra files inside your directory.
# those extra files contain things like the openssl libraries!!

    Some of the files created by the installation are inside the build
    directory: /home/jtprince/src/ruby-1.9.2-p0

    You probably don't want them to be included in the package,
    especially if they are inside your home directory.
    Do you want me to list them?  [n]: n
    Should I exclude them from the package? (Saying yes is a good idea)  [y]: n

# At this point, you can install the package on machines of the same
# architecture with "sudo dpkg -i ruby-1.9.2_p0-1_amd64.deb" [depending on your arch]

sudo rm /usr/bin/ruby
sudo ln -s /usr/local/bin/ruby1.9.2 /usr/bin/ruby

Okay, now you need to get rubygems working properly. Remember, rubygems comes with ruby 1.9.X, so you don't need to download it separately.

At this point, we have to ensure our soft links point where we want and to tell gems to point to ruby 1.9.2


sudo cp /usr/bin/gem1.9.{1,2}
# then edit /usr/bin/gem1.9.2
# change #!/usr/bin/ruby1.9.1 ==> #!/usr/local/bin/ruby1.9.2

# now set up the soft link so that "gem" calls our gem1.9.2
sudo rm /etc/alternatives/gem
sudo ln -s /usr/bin/gem1.9.2 /etc/alternatives/gem

Maybe it is unnecessary, but I moved my local gem folder so that all my gems are compiled from scratch again to ensure they have been built against 1.9.2. how to set up a local gem environment


mv ~/.gem/ruby/{,not_using_}1.9.1
mkdir ~/.gem/ruby/1.9.2

Installing graphviz on Ubuntu Lucid Lynx 10.04

2010-09-21T13:17:00.000-07:00

If you want sfdp (a great layout for large graphs), then you need the .debs from the graphviz site (not through the ubuntu repos).

Download the develpment snapshots here
note, if you don't use the language specific bindings listed, you don't need to download those.


sudo aptitude install libdevil1c2 libgtkglext1
sudo dpkg -i graphviz_*.deb graphviz-dev*_all.deb 
graphviz-doc*_all.deb libgraphviz4_*.deb libgraphviz-dev_*.deb libgv-ruby_*.deb

Now, you can run sfdp!

Biostatistics vs Lab Research

2010-09-14T18:57:00.001-07:00

for anything complicated, ruby eats bash for breakfast

2010-09-05T22:42:00.000-07:00

http://www.sklav.com/node/4 shows a bash solution to the issue debated here. Regardless of how good a bash script is, it inevitably is not very DRY, I think because it is hard to be DRY in bash scripting.

Here is a ruby solution. Of course, all I did was factor, which is easy in ruby:


#!/usr/bin/env ruby

lame_opts = "--preset standard -q0"

if ARGV.size == 0
  puts "usage: #{File.basename(__FILE__)} .flac ..."
  puts "output: .mp3"
  puts ""
  puts "uses lame opts: #{lame_opts}"
  puts "retains tag info"
  exit
end

tag_convert = {
  :tt => "TITLE",
  :tl => "ALBUM",
  :ta => "ARTIST",
  :tn => "TRACKNUMBER",
  :tg => "GENRE",
  :ty => "DATE",
}

ARGV.each do |file|
  tag_opts = tag_convert.map do |key,val|
    # comes out as TITLE=
    data = `metaflac --show-tag=#{val} #{file}`.split("=",2).last
    "--#{key} #{data}"
  end
  mp3name = file.chomp(File.extname(file)) + ".mp3"
  `flac -dc #{file} | lame #{lame_opts} #{tag_opts.join(" ")} --add-id3v2 - #{mp3name}`
end

Fairly easy to follow, especially since we don't repeat ourselves. Most of the code is in creating a useful help message.

For Perl hackers, here is the entire script on a few lines of less than 105 chars per line:


tag_convert = {:tt=>"TITLE",:tl=>"ALBUM",:ta=>"ARTIST",:tn=>"TRACKNUMBER",:tg=>"GENRE",:ty=>"DATE"}
ARGV.each do |f| 
  tgs = tag_convert.map {|k,v| "--#{k} "+`metaflac --show-tag=#{v} #{f}`.split("=",2).last}.join(" ")
  `flac -dc #{f} | lame --preset standard -q0 #{tgs} --add-id3v2 - #{f.sub(/.flac$/i,".mp3")}`
end

There are still ways to compress this further, but it is very concise and surprisingly easy to follow (if you know ruby).

For sets of integers, lookup speed goes: Array > Hash > Set

2010-09-01T15:46:00.000-07:00

You have some set of integers and you need to query it repeatedly to determine if a member is in it or not.


require 'benchmark'
require 'set'

ar = (0...1000).to_a

ar_index = []
hash_index = {}
ar.each do |v|
  ar_index[v] = true
  hash_index[v] = true
end

set_index = Set.new(ar)
access = (0...1000).to_a

TIMES = 10000

Benchmark.bmbm do |r|
  r.report("array index") { TIMES.times { access.each {|v| ar_index[v] } } }
  r.report("hash index") { TIMES.times { access.each {|v| hash_index[v] } } }
  r.report("hash include") { TIMES.times { access.each {|v| hash_index.include?(v) } } }
  r.report("set include") { TIMES.times { access.each {|v| set_index.include?(v) } } }
end

The output (ruby 1.9.1p378 (2010-01-10 revision 26273) [x86_64-linux]):


                   user     system      total        real
array index    0.730000   0.000000   0.730000 (  0.745341)
hash index     0.990000   0.000000   0.990000 (  1.003517)
hash include   1.310000   0.000000   1.310000 (  1.332846)
set include    1.970000   0.000000   1.970000 (  2.024808)

It's faster to numerically round than to sprintf in ruby

2010-09-01T13:17:00.000-07:00

require 'benchmark'

class Float
  def round_to(x)
    (self * 10**x).round.to_f / 10**x
  end

  def ceil_to(x)
    (self * 10**x).ceil.to_f / 10**x
  end

  def floor_to(x)
    (self * 10**x).floor.to_f / 10**x
  end

  def round_to_sprintf_f(x)
    ("%.#{x}f" % x).to_f
  end

  def round_to_sprintf_sprintf(x)
    sprintf("%.#{x}f", x)
  end

  def round_to_sprintf_modulus(x)
    "%.#{x}f" % x
  end

end

num = 34.2342134
place = 3

TIMES = 1000000
Benchmark.bmbm do |r|
  r.report("numeric round_to (float)") { TIMES.times { num.round_to(place) } }
  r.report("numeric round_to (to string)") { TIMES.times { num.round_to(place).to_s } }
  r.report("sprintf (float)") { TIMES.times { num.round_to_sprintf_f(place) } }
  r.report("sprintf (string)") { TIMES.times { num.round_to_sprintf_sprintf(place) } }
  r.report("sprintf modulus (string)") { TIMES.times { num.round_to_sprintf_modulus(place) } }
end

The output:


% ruby -v
ruby 1.9.1p378 (2010-01-10 revision 26273) [x86_64-linux]
...
                                   user     system      total        real
numeric round_to (float)       0.820000   0.000000   0.820000 (  0.819920)
numeric round_to (to string)   1.990000   0.000000   1.990000 (  1.989912)
sprintf (float)                3.620000   0.000000   3.620000 (  3.614758)
sprintf (string)               2.650000   0.000000   2.650000 (  2.654812)
sprintf modulus (string)       3.190000   0.000000   3.190000 (  3.191807)

The conclusion: Regardless of whether you are going to a string or numeric after rounding, it is faster to round numerically than with sprintf. Also, using the sprintf function is faster than '%'. Usually speed doesn't matter, but when it does...

apply & sweep : Column-wise & Row-wise operations in R

2010-08-19T11:05:00.000-07:00

How do you do operations on rows and columns in R? apply and sweep are the main tools. Here is an example of "autoscaling" (mean center and divide by standard deviation) on each column:

[I verified that this is correct on oocalc]


# 1 -> across the rows
# 2 -> across the columns 
m <- matrix(data=c(1,2,3,4,4.5,6,7,8,9,10,11,13), nrow=4, ncol=3)
m
#      [,1] [,2] [,3]
# [1,]    1  4.5    9
# [2,]    2  6.0   10
# [3,]    3  7.0   11
# [4,]    4  8.0   13

colmeans <- apply(mymatrix, 2, mean)  # the column-wise means
# mc = the column-wise mean centered data
mc <- sweep(m, 2, colmeans, "-")   # subtract is the default

col_stdev <- apply(m, 2, sd)  # column-wise standard deviations

mcstd <- sweep(mc, 2, col_stdev, "/")  # divide by standard deviations

mcstd
#            [,1]       [,2]      [,3]
# [1,] -1.1618950 -1.2558275 -1.024695
# [2,] -0.3872983 -0.2511655 -0.439155
# [3,]  0.3872983  0.4186092  0.146385
# [4,]  1.1618950  1.0883839  1.317465

Regression line, R^2 (Pearson's correlation coefficient), slope, and y intercept in R

2010-08-05T16:56:00.000-07:00

A basic feature in Excel and OpenOffice Calc is to find and plot the regression line. Here is an example of doing this in R. This is more work in R, but you are sacrificing for more power.

Here is how we get the data out:

x = c(1,2,3,4,5)
y = c(3,4,5,5.1,6.2)
pearsons_r = cor(x,y)
r_squared = pearsons_r^2
fit = lm(y~x) # notice the order of variables
y_intercept = as.numeric(fit$coeff[1])
slope = as.numeric(fit$coeff[2])

Here is how we plot it:

plot(x,y)
abline(lm(y~x)) # again, notice the order
function_string = paste("f(x) = ", slope, "x + ", y_intercept,  sep="")
r_sq_string = paste("R^2 =", r_squared)
display_string = paste(function_string, r_sq_string, sep="\n")
mtext(display_string, side=3, adj=1)  # top right outside of the margin

clone a VDI Virtual Box image for using elsewhere

2010-06-17T14:01:00.000-07:00

How robust is this procedure (found here)?

Shut down the virtual machine you would like to copy
In File > Virtualdiskmanager, select the virtual machine disk image you would like to copy, and press the Release button
In a terminal window, issue following command (see virtualbox user manual):
vboxmanage clonevdi /directory/image1.vdi /directory/image2.vdi
In File > Virtualdiskmanager, add the new disk image you've created in step 3
In the main virtualbox window, press the New button to create a new virtual machine, and link it to the new disk image you've created.

Cartoons in biology?? How about: diagram, figure, illustration or schematic

2010-06-09T16:40:00.000-07:00

Molecular biologists often refer to depictions of cellular processes or structure as cartoons. (here is an example). I think it is a poor word choice. Cartoon is generally used to indicate a humorous depiction or an unfinished product (i.e., a sketch on a carton), so it is somewhat insulting to the creator of the illustration (unless it is, in fact, unfinished or humorous). What I think they are trying to say by calling their diagram a cartoon is something like: "do not forget that this diagram is a vast oversimplification of reality! Proteins are not really boxes and lines are really not protein associations! Proteins aren't made of ribbons!" At times, one also gets the feeling they are trying to convey something more, "Our field is so complex, our diagrams are ludicrously simple compared to reality!" or even, "Aren't I cute for calling this a cartoon even though this is a science talk!"

Fortunately, there are several other words suggesting that a depiction is not a precise representation of reality but rather a simplification that serves to emphasize certain facts or relationships, and they don't carry any of cartoon's demeaning connotations: diagram, figure, illustration, schematic. IMHO, these are vastly preferable for referring to depictions of biological phenomenon. This seems to be well supported by definitions, synonyms, and word associations:

Merriam-Webster (online)

diagram

Etymology: Greek diagramma, from diagraphein to mark out by lines, from dia- + graphein to write — more at carve

Date: 1619

1 : a graphic design that explains rather than represents; especially : a drawing that shows arrangement and relations (as of parts)
2 : a line drawing made for mathematical or scientific purposes

schema

Inflected Form(s): plural sche·ma·ta \-mə-tə\ also schemas

Etymology: Greek schēmat-, schēma

Date: circa 1890

1 : a diagrammatic presentation; broadly : a structured framework or plan : outline

figure

Etymology: Middle English, from Anglo-French, from Latin figura, from fingere

Date: 13th century

2 a : a geometric form (as a line, triangle, or sphere) especially when considered as a set of geometric elements (as points) in space of a given number of dimensions b : bodily shape or form especially of a person c : an object noticeable only as a shape or form

s moving in the dusk>
3 a : the graphic representation of a form especially of a person or geometric entity b : a diagram or pictorial illustration of textual matter

illustration

Date: 14th century

2 : something that serves to illustrate: as a : an example or instance that helps make something clear b : a picture or diagram that helps make something clear or attractive

cartoon

Etymology: Italian cartone pasteboard, cartoon, augmentative of carta leaf of paper — more at card

Date: 1671

1 : a preparatory design, drawing, or painting (as for a fresco)
2 a : a drawing intended as satire, caricature, or humor b : comic strip
3 : animated cartoon
4 : a ludicrously simplistic, unrealistic, or one-dimensional portrayal or version ;

Thesaurus.com

diagram
Part of Speech:     noun
Definition:     drawing, sketch of form or plan
Synonyms:     big picture, blueprint, chart, description, design, draft, figure, floor plan, game, game plan, ground plan, layout, outline, perspective, representation, rough draft

schema
Part of Speech:     noun
Definition:     design
Synonyms:     architecture, arrangement, blueprint, chart, comp, composition, conception, constitution, construction, delineation, depiction, diagram, doodle, drawing, dummy, form, formation, game plan, idea, layout, makeup, map, method, model, outline, paste-up, pattern, perspective, picture, plan, project, scheme, strategy, study, tracery, tracing, treatment

figure
Part of Speech:     noun
Definition:     object with design; depiction
Synonyms:     cast, composition, decoration, device, diagram, drawing, effigy, embellishment, emblem, illustration, image, model, mold, motif, motive, ornamentation, pattern, piece, portrait, representation, sketch, statue

illustration
Part of Speech:     noun
Definition:     drawing, artwork that assists explanation
Synonyms:     adornment, cartoon, decoration, depiction, design, engraving, etching, figure, frontispiece, halftone, image, line drawing, painting, photo, photograph, picture, plate, sketch, snapshot, tailpiece, vignette

cartoon
Part of Speech:     noun
Definition:     funny drawing, often with dialogue or caption
Synonyms:     animation, caricature, comic strip, drawing, lampoon, parody, representation, satire, sketch, takeoff

www.wordassociation.org

associated to diagram
1.    chart    weak
2.    graph    weak
3.    draw    v. weak
4.    plan    v. weak
5.    block    v. weak

associated from diagram
1.    chart    medium
2.    picture    medium
3.    diaphragm    weak
4.    drawing    v. weak
5.    graph    v. weak

associated to schema
1.    scheme    strong
2.    axiom    weak
3.    concept    weak
4.    fema    weak
5.    pooh    weak

associated from schema
1.    scheme    strong
2.    database    weak
3.    diagram    weak
4.    paradigm    weak
5.    seem    weak

associated to figure
1.    stick    medium
2.    action    weak
3.    father    weak
4.    shape    weak
5.    authority    v. weak

associated from figure
1.    shape    medium
2.    eight    medium
3.    skate    weak
4.    skating    v. weak
5.    out    v. weak

associated to schematic
1.    plan    strong
2.    scheme    medium
3.    architecture    weak
4.    blueprint    weak
5.    diagram    weak

associated from schematic
1.    blueprint    strong
2.    system    strong
3.    design    medium
4.    drawing    medium
5.    love    medium

associated to illustration
1.    example    medium
2.    drawing    medium
3.    graphic    weak
4.    book    v. weak
5.    capella    v. weak

associated from illustration
1.    picture    strong
2.    drawing    medium
3.    book    weak
4.    cartoon    weak
5.    draw    weak

associated to cartoon
1.    animation    v. weak
2.    simpsons    v. weak
3.    anime    v. weak
4.    disney    v. weak
5.    character    v. weak

associated from cartoon
1.    character    medium
2.    network    weak
3.    animation    weak
4.    comic    v. weak
5.    tv    v. weak

Download all the mp3 links in a page given the url with ruby and nokogiri

2010-05-26T22:09:00.000-07:00

You'll need ruby and the gem nokogiri installed. Then run this


#!/usr/bin/env ruby

require 'nokogiri'
require 'open-uri'

if ARGV.size == 0
  puts "usage: #{File.basename(__FILE__)} 'url' ..."
  exit
end

ARGV.each do |url|
  doc = open(url) {|io| Nokogiri.HTML(io.read) }

  mp3_links = doc.xpath("//a").select {|link| link['href'] =~ /\.mp3$/ }
  mp3_links.each do |link|
    href = link['href']
    outname = File.basename(href)
    puts "Downloading: #{outname}"
    open(href) do |io|
      File.open(outname,'w') {|out| out.print(io.read) }
    end
  end
end

A debian/ubuntu gem environment of your very own

2010-05-12T08:36:00.000-07:00

There are some differences with the way apt-get rubygems and downloaded and 'sudo ruby setup.rb' gems behave. Here is how to bring the directory structure in conformity with the apt-get version and have your gem's bin folder in your path. This is for using gems on a per-user basis.

Add these two lines to your ~/.bashrc file:

# this will export the path to whatever version of ruby you are using:
export GEM_HOME="$HOME/.gem/ruby/`ruby -e 'x=RUBY_VERSION;print(x=~/^1.8/ ? "1.8" : x)'`"
export PATH="$PATH:$GEM_HOME/bin"

Then 'source ~/.bashrc' if needed and you can use either version of rubygems indistinguishably.

Now, you can install gems with either rubygems, you don't need sudo privileges, and your gem executables will be active. Wallah!

gem install rake

Yet another reason to love Ubuntu, multiple folder extraction

2010-05-07T13:06:00.000-07:00

Today I needed to extract 20+ folders and I thought, I don't want to right-click over 20 times, wouldn't it be cool if I could just select all the folders, right-click and extract? Well, it worked like a charm and made my day. Now if only Ubuntu could solve the problem of all of my folders being over 2.5 Gb and taking forever to extract.

Your own legal ssh personal server on comcast with Ubuntu 10.04

2010-05-04T22:42:00.000-07:00

Legal Matters

It appears to me that a personal ssh server is legal and acceptable to use [at least if you are with Comcast].

The Comcast Terms of Service:

The relevant bullets under Technical restrictions are:

* use or run dedicated, stand-alone equipment or servers from the Premises that provide network content or any other services to anyone outside of your Premises local area network (“Premises LAN”), also commonly referred to as public services or servers. Examples of prohibited equipment and servers include, but are not limited to, e-mail, Web hosting, file sharing, and proxy services and servers;
* use or run programs from the Premises that provide network content or any other services to anyone outside of your Premises LAN, except for personal and non-commercial residential use; (my emphasis)

Also, note that the ssh port (22) is not blocked by comcast.

How to setup a personal ssh server

This should work in many different distros and versions with only minor modification.

```
sudo aptitude install openssh-server
```
Since I have kids with weak passwords using my computer, I only want a couple accounts to be accessible. Edit /etc/ssh/sshd_config and add something like this:
```
AllowUsers user1 user2 user3
```
This will prevent other user accounts from being accessible.
It is generally a good idea to use a static IP address so your router knows where to send the ssh traffic. Right click your wireless icon on the panel and edit your connection. Shown to the right is a setup that is compatible with a linksys router (i.e., the router IP address is 192.168.1.1).
Forward port 22 traffic to your statically assigned PC (see image below for router specs).
Use a service like dyndns.com to associate a static IP address with your dynamically assigned address.

Run ddclient to update dyndns.com.

sudo aptitude install ddclient

Here is a configuration file (/etc/ddclient.conf) that works for me:

daemon=600
use=web, web=checkip.dyndns.com/, web-skip='IP Address'
login=
password=protocol=dyndns2
server=members.dyndns.org
wildcard=YES
jtprince.dyndns.org, bwv549.homeip.net

Now, you should be able to ssh into your home computer from anywhere in the world. Also, please note that you can do just about anything with ssh access.

Asus Eee PC 1201N Wireless WPA2 Ubuntu Lucid Lynx 10.04 Fix

2010-04-30T16:27:00.000-07:00

I was able to use wireless on 9.10 by compiling the one talked about on newegg and elsewhere. However, I couldn't connect to the school's network. On 10.04, it appears that they are using the same driver and it has the same problems (appears to work but won't connect to my school's WPA2 network). I used Matt Price's package and it works now!

Here are the steps:
sudo add-apt-repository ppa:matt-price/mattprice

Then add these lines to /etc/apt/sources.list:

deb http://ppa.launchpad.net/matt-price/mattprice/ubuntu lucid main 
deb-src http://ppa.launchpad.net/matt-price/mattprice/ubuntu lucid main

ssh tunneling (port forwarding)

2010-03-06T23:02:00.001-08:00

The past two places I've worked at have had a single computer that would accept outside ssh communication. However, other computers in the network also had useful things on them but could only be reached from inside the network. How to connect to these other computers directly?

ssh port forwarding allows you to open up an ssh session between you and your gateway computer. Then, you can use that port to interact with the other computers in the network. Here is an example of how to do this:

Open a terminal and type in something like this:

ssh -L<unused_port#>:<final_destination>:22 <gateway_computer>
ssh -L22000:internalserver.super.duper.com:22 gateway.super.duper.com    # e.g.
# you might want to add the -N and -C flags:
ssh -N -C ...
# -N   Do not execute a remote command (useful for forwarding ports)
# -C   compress (for slow network connections only)

Then, open another terminal and you can interact with the internal server as you normally would, just by interacting with your localhost through the specified port:

# log in to the internal server
ssh -p 22000 localhost
# scp stuff from the internal server
scp -P 22000 localhost:~/somefile.txt ./     # copy files from the internal server to local
# mount a folder from the internal server locally using sshfs
sshfs -p 22000 localhost:/home/<user>/<internal_dir> /home/<user>/mnt -o follow_symlinks

Yes that is localhost. You are connecting to port 22000 on the localhost and that is being tunneled via the gateway computer to the internal server!

This works but isn't the absolute slickest setup. Anyone know the equivalent commands for .ssh/config files?

This site has some alternative methods for mounting across ssh.

Fonts in rumai (wmii)

2010-03-04T10:55:00.000-08:00

How do you know what fonts you can use in rumai or wmii?
xlsfonts will list all the fonts in the format that wmii expects:

xlsfonts > available_fonts.txt

You can use the '*' symbol to generalize. Here are some that work ok. Some are quite ugly, others OK:

-*-fixed-medium-r-*-*-18-*-*-*-*-*-*-*
-*-fixed-bold-r-*-*-12-*-*-*-*-*-*-*
-*-fixed-medium-r-*-*-12-*-*-*-*-*-*-*
lucidasans-bold-12
-adobe-helvetica-medium-r-*-*-12
-adobe-helvetica-bold-r-*-*-12
-adobe-palatino-bold-r-*-*-14
-*-lucida-bold-r-*-*-12
-*-dejavu sans mono-medium-r-*-*-14
-*-dejavu sans mono-medium-r-*-*-14

wmii (rumai) with gnome in Ubuntu 9.10 & 10.04

2010-03-02T22:01:00.000-08:00

NOTE: modified from here

This is a step by step to install rumai as the windows manager in gnome.

install necessary packages


sudo apt-get install dwm-tools # for menus
sudo apt-get install libixp libx11-dev  # for the install itself (necessary??)

sudo apt-get install 9base libxft2-dev   # plan 9 file system (need on 10.04)

Install a good build

here

src

sudo make install

modify some gnome settings


gconftool-2 -s /apps/nautilus/preferences/show_desktop --type bool false
gconftool-2 -s /desktop/gnome/background/draw_background --type bool false
## Tell gnome to use wmii as the window manager
gconftool-2 -s /desktop/gnome/session/required_components/windowmanager wmii --type string

have wmii fire up at login

/usr/bin/wmii

get rumai

gem install rumai

export PATH="$PATH:$HOME/.gem/ruby/`ruby -e 'print RUBY_VERSION'`/bin"

grab a rumai config wmiirc

git clone git://github.com/jtprince/wmiirc.git ~/.wmii

sunaku's

git clone git://github.com/sunaku/wmiirc.git ~/.wmii

ln -s ~/.wmii ~/.wmii-hg

multifactorial plotting in R: lattice

2010-01-08T16:59:00.000-08:00

I've mentioned before in personal communications that if you have lots of factors in a data set you can just flatten out the data set and then use openoffice data pilot to pivot around different factors (also can be done in ruby with Ruport and 'pivot'). This is a good method.

There is a much better method I recently came across: "trellis plots". The package in R is called lattice.

This is clearly the way to quickly and neatly plot multifactorial data in lots of meaningful ways.

Some resources:

In R (as sudo if you want system wide installation):

install.packages("lattice", dependencies=TRUE)  # I don't think there are any dependencies
library("lattice")

pymix compilation errors on Ubuntu

2010-01-04T23:04:00.000-08:00

pymix was a little tricky to compile. Here's what I did to get it working.

I downloaded and installed numpy [but that is probably not necessary].

Then I finally had to go into pymix's setup.py and change the location for where it was looking for arrayobject.h:
From:
numpypath = prefix + '/lib/python' +pyvs + '/site-packages/numpy/core/include/numpy' # path to arrayobject.h
To:
numpypath = '/usr/share/pyshared/numpy/core/include/numpy' # path to arrayobject.h

At this point, 'python setup.py build' worked, but the install failed with this error:

byte-compiling /usr/local/lib/python2.6/dist-packages/AminoAcidPropertyPrior.py to AminoAcidPropertyPrior.pyc
SyntaxError: ('invalid syntax', ('/usr/local/lib/python2.6/dist-packages/AminoAcidPropertyPrior.py', 170, 14, ' as = alpha.pop(0)\n'))

turns out that 'as' is a reserved keyword in python 2.6, so you need to go in to that file and change it to something else, like: nada = alpha.pop(0)

Bayesian Optimal Discovery Procedure (BODP) R code

2009-12-15T07:40:00.000-08:00

The r code given as an additional file to the paper Bayesian optimal discovery procedure for simultaneous significance testing requires your data to be in matrix form. I spent a day trying to troubleshoot the code when all you need to do is the following:

Open R

Copy and paste the R code from Cao et al.

x<-read.table("x.txt") #your control state

y<-read.table("y.txt") #your test state

x<-as.matrix(x)

y<-as.matrix(y)

BODP(x,y,1000,10) #feel free to change 1000 and 10 to whatever you'd like

2009-11-29T23:03:00.000-08:00

A thread I started a while ago suggests a solution to getting hibernation and suspend working properly with nvidia cards on Inspiron 5160 in Ubuntu. At least as of Karmic Koala (9.10), the solution one-line easier:

In the device section of /etc/X11/xorg.conf add the line:

Option "NvAGP" "1"

To /etc/modprobe.d/blacklist.conf add the following:

blacklist intel_agp

then reboot

slow browsing in firefox in Ubuntu 9.10 Karmic Koala

2009-11-29T22:50:00.000-08:00

type in about:config into the browser bar

change the value of the key "network.dns.disableIPv6" from 'false' to 'true'

drastically increased browsing speed for me.

a little Perl spice for ruby

2009-11-14T23:11:00.000-08:00

An insightful blog post got me envying some of the brevity of Perl, so I implemented a couple useful idioms from Test::More in Ruby (which is pretty trivial since it allows opening up a class).

We'd like to have a really terse vocabulary when describing the most common test cases:


## equality
num = 8
num.should.equal 8  # bacon
num.must_equal 8    # minitest::spec
num.should == 8     # rspec
num.is 8            # clearly superior,  similar to Test::More "is a, b"

## true/false
(num == 8).should.be.true # bacon
(num == 8).ok             # superior, like Test::more "ok (something)"

So, for Bacon at least, this is all that needs to be done (put in your spec_helper.rb file)


class Object
  def is(arg)
    should.equal(arg)
  end
  def ok
    should.equal true
  end
end

The argument against this would go, "well, it's better to be more verbose and understood". The counter-argument something like, "this still makes sense and is way easier to write, so I can write more spec's which == better code".

wxruby: wxWidgets for ruby on Ubuntu

2009-10-12T21:11:00.001-07:00

A nice link on how to get the basic wxruby (wxWidgets for ruby) going on Ubuntu/debian.

Some examples in the examples folder require some more libraries. For instance, the opengl example requires libopengl-ruby (and maybe freeglut3 libglut [??]) and one of the drawing examples requires librmagick-ruby.

So this should be enough to get you going with most of the examples:

sudo apt-get install libwxbase2.8-{0,dev} libwxgtk2.8-{0,dev} librmagick-ruby libopengl-ruby
sudo gem install wxruby

how to safely delete things in Ubuntu/Linux

2009-10-10T11:45:00.000-07:00

I accidentally performed a `rm -rf` on a very big and important directory. I was able to recover close to half of the files using extundelete, but it still left me with a sour taste in my mouth. Now that there is a solid freedesktop specification for how to Trash things, it seems high time to remedy this situation.

In my ~/.bashrc file:

if [ ! `which gvfs-trash 2>/dev/null` ]
then
 alias dl='mv -t ~/.Trash/' # for older systems
else
 alias dl='gvfs-trash'
fi

So, now we can simply dl files and they go to a safe place. Still, I find myself using rm, so this little alias will help cure my addiction, by reminding me that I should be using dl instead of rm. I can still use the rm command by putting it in single quotes (that's how to get past any alias) as in: 'rm' -rf some_directory.

alias rm="echo \"use dl or 'rm'\""

How to share a VirtualBox virtual machine with multiple users on Linux/Ubuntu

2009-10-07T22:41:00.000-07:00

Have you ever wanted to share your virtual machine with other users? Doing so will save a lot of space (since you only need one virtual machine) and keep you more in line with the EULA of the distribution you are running virtual (assuming that's Windows or Mac).

There are many tutorials online (for example) that will help you to install VirtualBox on your linux machine. A couple things to note:

You probably want to use the package from the VirtualBox download site (and not the open source one that you can get with apt-get) since it has many of the features that are important for a good virtual machine (like USB support and OpenGL acceleration etc).

Make sure a vboxusers group was created and that everyone who would want to use the virtual machine is part of that group.

Prerequisite: right now the only way I can get this to work is if everyone wanting to share the virtual machine has sudo privileges. I'd be interested if anyone can suggest a way to do this without them. OK, we're ready to start:

Make a shared directory for your virtual machines:
```
sudo mkdir /var/local/VirtualBox
```
Create a soft link from the home directory of each user sharing:
```
ln -s /var/local/VirtualBox $HOME/.VirtualBox
```
Now create a custom application launcher for your panel:
```
sh -c "gksudo 'chown -R $USER:$USER /var/local/VirtualBox'; VirtualBox"
```
(that command [or similar] could be wrapped up in a .bashrc function, a script placed in your $HOME/bin directory or whatever).

Also, remember when you buy your next computer to think about getting one with virtualization capabilities (for instance, an intel chart of core 2 duo desktop processors which support virtualization)

Make coloring pages from any picture for free

2009-09-20T12:48:00.000-07:00

Download and install GIMP.
windows download or ubuntu (sudo apt-get install gimp).

In GIMP,

Filters -> Artistic -> Photocopy

A dialog box will allow you to adjust the sharpness and amount of black and white you want to see with a preview.

That's it!

starting with timidity and soundfonts on Ubuntu Linux

2009-08-03T20:26:00.000-07:00

On the command line:

sudo aptitude install timidity

I like to have a folder with my timidity configuration files and soundfonts in my home directory:

/home/<user>/timidity

Inside that folder I'll have my "master" configuration called "timidity.cfg" and a layout something like this (I'm actually omitting a lot here):


timidity
|-- Piano.cfg
|-- ensemble.cfg
|-- harpsichord.cfg
|-- organ.cfg
|-- patches
|   |-- eawpats12_full
|   |   |-- acbass.pat
|   |   |-- [...]
|-- soundfonts
|   |-- Ensemble
|   |   |-- Zemljak_Overture.sf2
|   |   |-- choir
|   |   |   |-- 052_Florestan_Ahh_Choir.sf2
|   |   |   |-- Boychoir.sf2
|   |   |   `-- boychoir.txt
|   |-- Organ
|   |   |-- GothicOrgan.sf2
|   |   |-- jeux14.sf2
|   |   `-- jeux2.sf2
|   |-- Piano
|   |   |-- ClavinovaGrandPiano2.sf2
|   |   |-- RolandPowerGrand.sf2
|   |   |-- harpsichord
|   |   |   |-- Blanchet-440_ver.1.0.sf2
|   |   |   |-- Campbells_Harpischord_tuned_1.sf2
|   |   |   `-- Petit_Italien.sf2

Now, we can edit the "global" configuration file to point to our timidity configuration file:


sudo gedit /etc/timidity/timidity.cfg
---
# Instrument configuration file for timidity
# $Id: timidity.cfg,v 1.7 2005/09/03 19:26:03 hmh Exp $

# [... omitting some for brevity ...]
# [ NOTE: With a recent CPU you can leave everything commented in this file no problem ]

# Include a configuration for the selected patchset or soundfont
# By default, try to use the instrument patches from freepats:

source /etc/timidity/freepats.cfg

## added by JTP ##
source /home/john/timidity/timidity.cfg

That file basically turns on freepats and then points to your home configuration. Timidity lets you "cascade" sounds, so activating freepats will ensure that you have some kind of sound for most of the banks accessed by your midi files. Any patches/soundfonts you later specify will override those previously specified.

Here's my timidity.cfg file:


dir /home/john/timidity
# (NOTE: I just comment out the config files I'm not using)
#source jeux14.cfg
#source organ.cfg
#source merlin.cfg
#source Piano.cfg

source harpsichord.cfg

The dir command just "activates" a given directory so that I can then call the configuration files in it by their basename as shown. With this configuration, I can set up lots of preconfigured sounds that I can easily turn on and off in my "master" configuration file.

OK, so now, lets get a soundfont and use it to play some music:

The Blanchet is my favorite harpsichord soundfont at the moment (Download the sf2 file Download the sf2 file). Turns out most sf2 files are compressed with sfark, so you need to download software to decompress it. After you decompress the soundfont, you'll want to look at the soundfont. Linux has a soundfont editor called "swami" that lets you see what's in a soundfont:


# only in Ubuntu 9.04 or earlier !!
sudo aptitude install swami
# you can fire it up with the soundfont on the command line if you want (or without)
swami timidity/soundfonts/Piano/harpsichord/Blanchet-440_ver.1.0.sf2

At least for Karmic and Lucid (9.10) you will need to follow instructions here to install swami. Some guy is working to get GTK2.0 integration at which point we'll probably see the package surface again.

We are interested in the little numbers in the Melodic section: (001-001 ... 001-004). The code is this: <bank>-<instrument>. That means that for this soundfont the 4 "sounds" are in bank 1 and are deposited as instrument 1-4. OK, so now we know the layout of the sound font. Now, when we play a midi file, we can map these to the appropriate instruments to get the sounds we want. So, how do we do that? We do it in timidity configuration files. My "harpsichord.cfg" file that is referenced by my timidity.cfg file looks like this:


dir /home/john/timidity/soundfonts/Piano/harpsichord

bank 0

6 %font Blanchet-440_ver.1.0.sf2 1 1
7 %font Blanchet-440_ver.1.0.sf2 1 2
8 %font Blanchet-440_ver.1.0.sf2 1 3
9 %font Blanchet-440_ver.1.0.sf2 1 4

Again, the "dir" command "activates" the directory that contains my Blanchet-400_ver.1.0.sf2 soundfont file so I can access it in my file by its base filename. The bank 0 is now specifying which instrument sounds we are going to provide for midi files that access bank 0 (which is most of them since bank 0 is the main bank).

<midi_instrument> %font <soundfont.sf2> <soundfont_bank> <soundfont_instrument>

midi_instrument: the program change found in the midi file. The General Midi (GM) typical mapping (note: timidity starts numbering at '0', so you need to subtract '1' from each of these to specify them in timidity).

%font: means this is a soundfont (patches don't require it), then .

soundfont_bank: the bank the instrument is found in your soundfont
soundfont_instrument: the instrument as found in your soundfont

So, here I've mapped the first harpsichord manual (bank 1, instrument 1) to instrument 6 ("harpsichord" in GM), the second harpsichord manual (bank 1, instrument 2) to instrument 7 ("clavinet"), the lute harpsichord sound (bank 1, instrument 3) to instrument 9 ("Celesta") and the sound with both harpsichords (bank 1, instrument 4) to instrument 10 ("Glockenspiel"). Now, a midi file that has a "program change" (instrument) specifying a harpsichord will access my first harpsichord manual and so on.

If a midi file is just one instrument, just match up the soundfont sound with the instrument specified in the midi file. If you have different midi tracks, you can go in and change the midi track to match up with those in your timidity file. This can be done in rosegarden (sudo aptitude install rosegarden) or many other midi editors (I write my own ruby programs based on midilib to modify instruments, volumes, pan, in my midi files but these (pan and volume) can also be specified in your timidity file (as long as each midi track accesses a different instrument). For example:


19 %font FluidR3GM.SF2 0 19 amp=140 pan=0

Now we can fire up timidity on our midi file (here are some good ones). These each have different numbers of tracks, but each track is for "harpsichord" (which we've pointed to the first soundfont of the Blanchet file in harpsichord.cfg file):


timidity <your_midi>.mid
# or what I often will use:
timidity --verbose  <your_midi>.mid -EFreverb=3,40 -A150
# once you have it sounding like you want, you can record to a .wav file:
timidity <your_midi>.mid -Ow
# then you can convert to an mp3 with lame (install with: 'sudo aptitude install lame')
lame --preset medium <your_midi>.wav <your_midi>.mp3

Let me know if you have any questions/troubles and I'll try to update this post to answer them.

How to version control your projects with bazaar

2009-07-17T13:38:00.000-07:00

So you have a project named 'supercool' that happens to sit in a directory named (what else) 'supercool'. Assuming you have bazaar installed on your client computer and the server, this is how you start a project under a centralized "lock-step" model. IMHO, this model works best for solo projects if you have a server available to you:


cd supercool # make sure you are at the top level directory of your project
bzr init  # starts up version control in this directory (an independent branch right now)
bzr add   # will recursively add files in your project
bzr ci -m 'initial commit'  # makes a commit to your branch
# the next step assumes you have already made the directory /home//bzr on your server
# this step will create a centralized repository on your remote
bzr push sftp://<user>@myserver.domain.org/home/<user>/bzr/supercool
# now, we need to 'bind' our independent branch to the remote branch
# which transforms it into "centralized mode"
bzr bind sftp://<user>@myserver.domain.org/home/<user>/bzr/supercool

# to check out a fresh copy on a different computer
bzr co sftp://<user>@myserver.domain.org/home/<user>/bzr/supercool

So, now you can work on files in your project and have them versioned. Your daily work-flow will look like this:


# assuming you are in your project directory...
bzr up  # update your repo with any changes in the centralized repo
## do some work...
bzr add <file1> <file2>  # add any new files, etc.
bzr ci -m 'adding new files, changed some other ones'

That's it! The bazaar documentation is great, particularly the user guide.

Adding Music to a Blogger Blog using Playlist.com

2009-06-26T10:40:00.000-07:00

There are basically two ways you can add a playlist.com music player to your blog on blogger blogs. The first that I tried was to use one of blogger's prepared gadgets. I found that these did not look very good. Instead, there is a better way.

1) Visit playlist.com and go to "Post My Playlist." Choose "Get the code for any other social network, blog or your own personal website >>". It is currently the last choice, choice "E". Follow their directions to get the code. Select and copy it.

2) Go to your blog and sign in. Go to "Customize", "Layout", "Page Elements", "Add a Gadget", "HTML/Javascript". Paste the code into the main field and you're set.

3) Sizing the player: View the blog and see how it looks. If you don't like the dimensions, you can change the element dimensions by going back and editing the html of the element. The height and width show up in several places in the code, so you'll want to change them all. For my blog, I currently have it set to 300px wide and 208px tall. I have copied the code from my blog, removing the "<" and ">" characters so that it wouldn't actually insert the player into this post. You can see that the easiest approach is really to do a ctrl+f to find all the numbers. Just be careful that they are really dimensions and not part of another number or for something else (for an example of a number you shouldn't change, see the blue 208).

div style="text-align: left; margin-left: auto; visibility:visible; margin-right: auto; width:300px;" object width="300" height="208" param value="http://www.profileplaylist.net/mc/mp3player_new.swf" name="movie"/ param value="never" name="allowscriptaccess"/ param value="transparent" name="wmode"/ param value="config=http%3A%2F%2Fwww.indimusic.us%2Fext%2Fpc%2Fconfig_black_shuffle.xml&mywidth=290&myheight=208&playlist_url=http%3A%2F%2Fwww.indimusic.us%2Floadplaylist.php%3Fplaylist%3D42390100%26t%3D1245208454&wid=os" name="flashvars"/ embed border="0" allowscriptaccess="never" flashvars="config=http%3A%2F%2Fwww.indimusic.us%2Fext%2Fpc%2Fconfig_black_shuffle.xml&mywidth=300&myheight=208&playlist_url=http://www.indimusic.us/loadplaylist.php?playlist=42390100&t=1245208454&wid=os" type="application/x-shockwave-flash" height="208" src="http://www.profileplaylist.net/mc/mp3player_new.swf" style="width:300px; visibility:visible; height:208px;" width="300" wmode="transparent" name="mp3player"/ /embed/object br/ a /a /div

To know what will look best in your blog, you might take some time to read through the html for your blog to find your sidebar width. If it is a percentage then you may just have to guess at the width until you get it how you want it. If it is set to a number of pixels (like 250px) then you can just change the width to 250px. That should usually give a good fit. If not, try a different width.

Weather-util alias for linux

2009-06-24T14:03:00.000-07:00

With administrator rights open weatherrc (should be in etc/)

The file should have a bunch of entries that look similar to this. I am showing how I created an alias for DFW.

[DFW] #Alias name
City = Dallas Ft Worth #http://tinyurl.com/28pxfg (Find your city)
ID = KDFW #ID code, see note below on how to find it
St = TX #Enter your state's abbreviation

It is easiest to find your ID code by going to http://weather.noaa.gov/ and finding your Current Weather Conditions location. When you have found it look for the four letter identification, that is your ID.

Create your own aliases by adding to the weatherrc file.

Save the file and go to the terminal and type: weather DFW
If you want more information, tell it to be verbose: weather DFW -v
If you want the forecast: weather DFW -f

Multiple ANOVA tests in R by a grouping factor

2009-05-21T18:45:00.000-07:00

If you have ever needed to run multiple ANOVA's according to or by a certain grouping factor here is your guide:

To do Type III sums of squares you'll need the car package. To split up your data by a grouping factor you'll need the doBy package.

install.packages("car")
install.packages("doBy")
library(car)
library(doBy)

Begin with a dataframe that has your factors, response, and grouping factor as columns (Y = response, A = factor A, B = factor B, Group = grouping factor)

If you have never read in data before into R, try something like this:

data<- read.table("/home/user/Desktop/data.txt")

I prefer to simply use text files that are delimited by space or tab.

Next name your columns:

names(data)<-c("Y","A","B","Group")

Now you need to split your data up according to your grouping factor.

data_split<-splitBy(~Group,data=data)

Lastly, run this loop:

i <-1 while(i <=length(data_split)){    
 print (Anova(lm(Y~A+B+A*B, data_split[[i]]),type="III")[4,4])   
 i<- i +1
}

R output can be accessed in row and column fashion [r,c]. I have this particular code give me only the p-value from the interaction of factors A and B. By changing [4,4] to other numbers you can access whatever part of the ANOVA table you want. Hope this helps.

two-column default for wmii-ruby (sort of like xmonad)

2009-05-08T23:02:00.001-07:00

How to default to 2 columns in wmii-ruby?

Add this to your wmiirc-config.rb file:

on_createclient do |cid|
  tag = read("/client/#{cid}/tags")
  # does the last line start with a "1", then only one column
  if read("/tag/#{tag}/index").split("\n").last.match(/^1\s+/)
    write("/tag/sel/ctl", "send sel right")
  end
end

Basically, if you have one column of applications and you open another client, this will shove your client to the right, making a 2nd column. This should work on the wmii 3.5-3.6 series.

This (not going automatically into 2 columns) has bothered me a lot in the past and when I was trying out xmonad I found that they do this in the default layout. [It would be fun to implement the rest of the basic xmonad layouts in wmii-ruby...]

What is wmii-ruby? (in case you're asking)

I've been playing around again with wmii-ruby. wmii is a minimalist window manager for X11 (i.e., graphics on *nix-ish OS's) that is very scriptable and wmii-ruby is (you guessed it) wmii scripted in ruby. Best features:

tiling window manager (use all your screen space)
uses very flexible tagging system to keep things organized.
very scriptable (see above example)
can use a mouse but don't really need to

It really is aimed more at hacker-types than the general public, but it is quite educational figuring out how to do many of the things you take for granted with a more feature rich desktop like gnome or KDE.

Battle for Wesnoth: Kid-Friendly

2009-04-30T22:00:00.000-07:00

artwork from Battle for Wesnoth, modified by JTP

Introduction

Skip intro

The Battle for Wesnoth--consistently ranked at the top of open-source games--is a really extraordinary strategy game that also happens to be free. On the surface it doesn't seem that special: it doesn't feature any stunning graphics and it is turn-based, so it is much more contemplative than action-packed. Why is it so great? Well, you really need to play it a while to understand, but the main things are:

Very interesting strategy component - sort of feels like playing a higher-level Risk game or a slower turn-based Rise of Nations. To win you have to deal effectively with day/night, terrain, attack/defense, recruitment, character development, health etc. There are enough components to keep things interesting but not so many to be overwhelming.
Engaging storylines - compelling single (and even some multi-user) campaigns.
Character development - Characters can be developed somewhat (i.e, raise levels) which provides some familiarity (and hence attachment) to them but this is limited to only a few levels which prevents this aspect from overshadowing the game's strategy component.
Good AI - the computer doesn't really make dumb moves, you either have to outsmart or overpower the enemy to win.
Visually beautiful - I mentioned that the graphics are 2D, but even though they are simple, they are quite engaging. Much of the artwork is really great.
Good music - in a classical-esque tradition.
Free.
Extendable - it isn't very difficult to create your own game or campaign.

Kid-friendly graphics

I have a lot of young boys who happen to really like this game. For a game set in a fantasy world completely realized with community contributed artwork, Wesnoth is remarkably kid-friendly. While there is nothing approaching pornography in it, there are a handful of portraits and units that are not attired as modestly as could be hoped. Most of the ones I've tidied up really didn't need it much, but since I was at it...

The beauty of open-source is that the software (in this case the images) can be modified to suit one's own tastes. I took liberty to touch up a few pictures, trimmed some others and wrote a script that will replace them in one click. The replacement artwork is rough around the edges, but it gets the job done (see my conglomerate image above).

How to run wesnoth-kid-friendly

This assumes you are on Windows (instructions are included in the zip file for other OS's):

Install Battle for Wesnoth - ideally in the default location so my script can find it.
Install the one-click ruby installer. (go the section "Ruby on Windows" and click on the "Ruby One-Click Installer link")
Download my zip file. (this contains kid-friendly up artwork and a script to copy them into place).
Unzip it.
Click on wesnoth-kid-friendly.rb (NOTE: this writes over the old images. Of course, you can always reinstall it if you don't like what I've done)

By default, I scan typical linux and windows directories for a Battle for Wesnoth directory. If the script isn't finding your installation, you can run the program on the commandline with the path to the Wesnoth directory given as the only argument. Or email me with the path of your directory and I'll add it to the script.

Keyboard Shortcuts in Gnome, KDE, wmii, or whatever

2009-04-28T14:13:00.001-07:00

Ubuntu Jaunty Jackelope put keyboard shortcuts in their proper place (disabling those in metacity and putting them in 'Keyboard Shortcuts'). However, when opening a gnome terminal from this shortcut, you have to explicitly tell it to start in your home directory or it will start in '/'

System->Preferences->KeyboardShortcuts  then [+Add]

gnome-terminal --geometry 80x52 --working-directory $HOME

I like to set up my keyboard shortcuts with a script since I like to use them on whatever computer I'm on. I did this before with gconftool2 and that worked fine, but now a person has to set them in a different location in a different way... which got me thinking that it would be nice to set keyboard shortcuts in a cross-desktop (KDE, Gnome, wmii, whatever) kind of way.

Solution: xbindkeys

sudo apt-get install xbindkeys

Make a file called '.xbindkeysrc' in your home directory with something like this in it:

"gvim"
  control+alt + g
"nautilus"
  control+alt + n
"firefox -new-window http://gmail.com"
  control+alt + e
"nautilus"
  control+alt + h
"firefox"
  control+alt + f
"gnome-terminal --geometry 80x40"
  control+alt + t
"rhythmbox"
  control+alt + m

now you can turn on the shortcuts with the simple command 'xbindkeys', but we'd really like for them to be turned on once when we login. Turns out cross-desktop startup is not very uniform but I think the proper way to do this (cross-desktop) is to do this:

Make sure you have a directory called '.config/autostart'. Then add a file to it called 'xbindkeys.desktop' with content along these lines:

[Desktop Entry]
Type=Application
Name=XBindKeys
Exec=xbindkeys
Icon=system-run
Comment=
Name[en_US]=XBindKeys
Comment[en_US]=
X-GNOME-Autostart-enabled=true

This is what happens in Gnome when you add an entry in System->Preferences->StartupApplications.

Installing Storey's edge microarray software on Ubuntu

2009-04-14T23:26:00.000-07:00

It takes a few steps to install this (Intrepid Ibex, Ubuntu 8.10), but here's how I got it working (we'll see if there are any bugs):

edge website

Install R

sudo aptitude install r-base

Download and unpack the source file:

linux src page

Install impute

sudo R CMD INSTALL packages/impute_1.0-5.tar.gz

prepare the compiling environment

sudo aptitude install g++-4.2 gfortran-4.2 tetex-base
# (also might need tetex-extras ...)
sudo rm /usr/bin/g++  # just removes the soft link
sudo ln -s /usr/bin/g++4.2 /usr/bin/g++
sudo rm /bin/sh  # just a link to /bin/dash
sudo ln -s /bin/bash /bin/sh

Compile the sucker

cd src ; make ; make install

Run the software

source("edge.r")
edge()

Restore the original environment

sudo rm /usr/bin/g++
sudo ln -s /usr/bin/g++4.3 /usr/bin/g++
sudo rm /bin/sh
sudo ln -s /bin/dash /bin/sh

Parametric and non-parametric t-testing

2009-04-14T20:12:00.000-07:00

If your data are distributed normally, the t-test can help you determine if the means of your two samples are greater than or less than each other (one-tailed) or just plain different from each other (two-tailed). These examples are for paired samples, to make them not paired just delete the "paired=TRUE" statement altogether, default is unpaired.

We'll use the same data throughout:
x <- c(1.83, 0.50, 1.62, 2.48, 1.68, 1.88, 1.55, 3.06, 1.30)
y <- c(0.878, 0.647, 0.598, 2.05, 1.06, 1.29, 1.06, 3.14, 1.29)

When using your own data you just need them in vectors (as shown).

One-tailed
t.test(x,y,paired=TRUE,alternative="greater")
t.test(x,y,paired=TRUE,alternative="less")

Two-tailed
t.test(x,y,paired=TRUE)

What if your data are not normal? The non-parametric Wilcoxon test will do the trick. The Wilcoxon rank-sum test is for independent samples (unpaired). The Wilcoxon signed rank test is for paired samples.

wilcox.test(x, y, paired = TRUE)

Who is R?

2009-04-14T20:04:00.001-07:00

After several years of using R to do various tasks from simple t-tests to much larger data sets I think I finally understand who R is.

R is like the computers of yesteryear, it does what you tell it, and only what you tell it, period. If you want more than the minimal amount of output, you have to ask for it. But it also has a bit of an attitude, for example, instead of outputting the type 3 sums of squares in ANOVA like virtually every other statistical package, it outputs the type 1 sums of squares by default. Why you might ask? The reason is because they want you to first think about what type of sums of squares you want, so by default they give you the one that isn't the most commonly used one. Hence R has a steep learning curve, which after several years I am still trying to surmount.

Enough talk, time for some code in the next post.

Instant switching: compiz (gtk), emerald, metacity

2009-04-11T00:13:00.000-07:00

In various places these are incorrectly listed. At least as of Intrepid Ibex, here's how to switch between window managers... still trying to figure this out...

metacity --replace
emerald --replace
compiz-decorator --replace
compiz  # to start things up for compiz

Oh, but when I try it out I'm getting some problems. In theory ... Just put each of these lines in a custom application launcher on your panel (and maybe put those in a single drawer)

ocaml batteries on Ubuntu

2009-03-26T20:31:00.000-07:00

OCaml is a functional programming language. I'm trying to learn it right now, but it clearly has a steep learning curve, especially if you aren't familiar with functional programming languages. It does seem impressive in many ways, but we'll see, eh?

Anyway, the standard library seems a little sparse, so I am trying to install 'batteries'. Turns out it wants some dependencies to build and they aren't entirely straightforward. Here's how to get it building:

sudo aptitude install libcamomile-ocaml-dev libzip-ocaml-dev libtype-conv-camlp4-dev
libsexplib-ocaml-dev libbin-prot-camlp4-dev libocamlnet-ocaml-dev

(do we need libmagic-ocaml-dev ??)
This is super weird, you have to configure the program as super user because it wants to make a directory for batteries in /usr/local. Anyway, here's the install

sudo ./configure
sudo make all opt install install-doc

And it does take forever to make the documentation (maybe 5 minutes to install on my computer).

how to set up your own git repository with only a server, ssh, and git

2009-03-06T22:55:00.000-08:00

This assumes you have ssh access to a server somewhere which you want to use as a sort of centralized repository and that server and your local machine have git on them. Don't tell anyone I used centralized and git in the same sentence, but centralized makes a lot of sense to me for lots of things, especially my own projects.

I'll do it the long way first and then with a tiny bit of bash scripting:

# ssh into your server
ssh jtprince@yourserver.domain.edu
# on remote machine:
mkdir git
mkdir git/project1.git && cd git/project1.git
git --bare init
exit

# on local machine
mkdir project1 && cd project1  # if you don't already have a project
# make a commit (you need at least one commit)
git init
echo "some text" > file.txt
git add .
git commit -m 'init commit'

# now we will push it to the server
git push ssh://jtprince@yourserver.domain.edu/home/jtprince/git/project1.git master

# we still need to link our git folder with the server
git remote add origin ssh://jtprince@yourserver.domain.edu/home/jtprince/git/project1.git
git config branch.master.remote origin
git config branch.master.merge refs/heads/master

Now for the BASH scripting I promised. This is basically the same thing but maybe a little easier to copy and paste once you set up your variables:

SERVER='jtprince@yourserver.domain.edu'
PROJ="project2"
PROJ_URL="ssh://$SERVER/home/jtprince/git/${PROJ}.git"

# set up the remote git repo in one command:
ssh $SERVER "mkdir git/${PROJ}.git; cd git/${PROJ}.git; git --bare init"

# (inside your project directory... with files/dirs already present):
git init ; git add . ; git commit -m 'init commit'; git push $PROJ_URL master ; git remote add origin $PROJ_URL ; git config branch.master.remote origin ; git config branch.master.merge refs/heads/master

And my rant...

At least in the ruby and linux developer community, Git seems to be quite hip right now. I personally think bazaar wipes git all over the floor, but due to server circumstances beyond my control I need to version control my files with git.

While the above operation is CLEARLY and SUCCINCTLY documented in the main bazaar docs, I've had to piece this together myself for git. Now, I suppose if I had actually read and digested the volumes of arcane documentation, switches, and nuances of git, I wouldn't be griping right now. That said, projects like 'eg' can make it easier and I'm sure the things people want to do with a vcs will become documented soon enough in git... the beauties of open source.

Gnome Do Dominates

2009-02-17T13:12:00.001-08:00

I am always trying to do things faster, and as we all know, using the keyboard is often faster than the mouse. Gnome Do, which you can install from synaptic is intuitive and lets you really fly. Try it out.

Can't mount external hard drive

2009-02-13T23:22:00.000-08:00

Some people have suggested "forcing" your external hard drive to mount. This is a bad idea as you can lose your data. Simply plug your external hard drive into a Windows system and then safely remove the external hard drive; if you just unplug it without safely removing it, Ubuntu won't let you mount it without forcing it to.

Aggregate in R

2009-01-13T14:16:00.000-08:00

For data that needs to be collapsed, the aggregate() function works great. For example:

If you need to collapse these so you only have one row per GLEAN, and have the Female and Male columns be the average of the collapsed rows, aggregate() can do this in one line:

collapsed_data<-aggregate(x=original_data, by=file_with_GLEAN_names_only, FUN=mean)

I used this to find the average expression levels of genes from a table that had the expression levels of each exon. Since some genes had one exon while others had many exons, aggregate was perfect for this situation. It did take a few minutes to compute, but I had over 57,000 rows and 8 columns, so that's understandable.

Virtualization with Virtual Box in Ubuntu

2009-01-13T08:34:00.000-08:00

I copied some material from these links in doing this (there are one or two errors in them that I correct here):
http://www.ubuntu-unleashed.com/2008/04/howto-install-virtualbox-in-hardy-heron.html
http://www.linuxhaxor.net/2008/05/05/creating-seamless-virtual-machine-with-virtualbox-16/

make sure you have the 'build-essential' package installed:
sudo apt-get install build-essential
Download your version of virtual box (probably i386 unless you have a 64 bit processor) and install it

After download, right click the package and install with the GDeb package manager

Add your user to the vboxusers group:
sudo adduser $USER vboxusers

Follow the Setup VirtualBox USB Support section here for USB support
I did both of the things recommended. Note that the last step should read:
sudo /etc/init.d/mountkernfs.sh start

Install Guest Addons and turn on seamless mode
after firing up the virtual OS, go to the 'Devices' window on the top and 'Install Guest Additions'
Set up shared directories following this.

autotest with specs in a normal ruby library

2009-01-07T13:21:00.000-08:00

Put this in a '.autotest' file in your project's base directory:

# -*- ruby -*-

# in .autotest file:

Autotest.add_hook :initialize do |at|
  at.clear_mappings
end

Autotest.add_hook :initialize do |at|
  at.add_mapping(%r%^lib/(.*)\.rb$%) { |_, m|
    ["spec/#{m[1]}_spec.rb"]
    ## for both specs and tests:
    #["spec/#{m[1]}_spec.rb","test/#{m[1]}_test.rb"]
  }
end

Smaller playlist.com music player for blog

2008-12-26T11:04:00.000-08:00

Playlist.com is a popular source for getting free music on your blog. My problem was I didn't want it to be at the bottom of the blog, but on the sidebar. The code they give you makes a music player that is much too wide for a sidebar. Here is how you can edit the code to fit whatever width you want.

Your code should resemble the code below. Simply change the bold numbers from your code to smaller, or larger numbers, depending on the size you want (I only included the beginning of the code, where you need to make changes). For my sidebar I used 285 to replace 450 and then 275 to replace all the 435's.

div style="text-align: center; margin-left: auto; visibility:visible; margin-right: auto; width:450px;"embed style="width: 435px; visibility: visible; height: 270px;" allowscriptaccess="never" src="http://www.greatprofilemusic.com/mc/mp3player-othersite.swf?config=http://www.greatprofilemusic.com/mc/config/config_black.xml&mywidth=435&myheight=270&playlist_url=http://www.greatprofilemusic.com/loadplaylist.php?playlist=55939558" menu="false" quality="high" name="mp3player" width="435" height="270">

Set Timex 1440 Sports watch

2008-11-30T19:56:00.001-08:00

Couldn't find this anywhere on the web (the instruction manual for this watch does not match the watch). After many, many attempts I finally figured it out:

Press and hold the mode button for a few seconds, then, press the mode button again!

The 'set' button then changes the value while the 'start/stop' button will advance to the next thing to set.

Set the Timex 1440 Sports Watch (wr50m) Magnetism watch

hold down the "mode" button for 2 seconds. When the digits on the watch face start to blink, then press the "mode" button again. To change the hours, press the "adjust button". [instructions thanks to a comment below]

To turn the alarm off:

Press and hold "set."
At the same time press (and hold?) "start/stop."
You will see the alarm bell icon go away.

Also, see wiki.answers post for more details.

Clean surfing on YouTube

2008-10-23T17:04:00.000-07:00

YouTube is a great service. Unfortunately, it seems like dodgy promo videos (at least dodgy thumbnail images) are the norm for the site. Here's how to disable them (I'm assuming you are using Firefox):

install the addon GreaseMonkey
install the YouTube customization script
on a video page, customize:

Now, all videos will have blocked Promotional Videos! Hooray! (Note: you can click on the little monkey in the bottom right hand of your browser to disable GreaseMonkey at any time)

Installing emerald with Ubuntu 8.04

2008-07-31T17:24:00.000-07:00

http://hacktivision.com/index.php/2008/06/07/how-to-enhance-ubuntu-8-04-hardy-heron-e?blog=2

Export plots in R

2008-05-17T13:13:00.000-07:00

In R exporting plots is easy:

jpeg("/home/Desktop/nameplot_here.jpg") #name the file and where to export it

hist(data) #this makes a histogram of your data

dev.off() #actually do the exporting

To do png or pdf just substitute it for jpeg.

2008-04-10T17:58:00.000-07:00

Cool applications for Linux

2008-03-24T22:22:00.000-07:00

http://linuxondesktop.blogspot.com/2007/07/35-cool-applications-to-install-on.html

Great website, I highly recommend it.

HP scanjet 4370 on Gutsy Gibbon (Ubuntu 7.10)

2008-02-22T18:34:00.000-08:00

Here's how I got our scanner working on Gutsy.

Install sane:

sudo aptitude install sane sane-utils

Then find out where your scanner resides:

sane-find-scanner

You're interested in the series of usb ports that your usb is connected to:

found USB scanner (vendor=0x03f0 [hewlett packard],
product=0x4105 [hp scanjet], chip=rts8822L-01H?) at libusb:007:006

In my case, the scanner is plugged into usb port 007 and subport 006 (I have no idea if that's the proper way to talk about it, but you'll see that it will work to think like that)
Then, you need the driver for your scanner, so go to the sane supported devices page and find your scanner. You access the driver by clicking under the 'Backend' link.
At least in theory, this driver is supposed to be in the sane-backends distribution. I'm not sure where to get it (already come with sane?). Anyway, my device wasn't really recognized when firing up 'xsane' until I downloaded and installed the driver.
Now, we have to set the permissions such that we can access our scanner. Notice that we use the the usb port information gleaned about to accomplish this:

sudo chmod a+rw /proc/bus/usb/007/006

A person is supposed to be able to automate that process, but I haven't figured it out yet. In any case, we can now fire up sane with the command 'xsane' or install 'gimp2.0-quiteinsane' to access from within gimp.

Using LCD Projectors or monitors with Ubuntu Gutsy Gibbon and Nvidia

2008-02-16T12:45:00.000-08:00

Under Edgy and Feisty, you could just restart your machine, hit your [CRT/LCD] (Fn+F8 on my machine) while it was loading and it would automatically do this for you.

Under Gutsy, this will work (may be easier/better ways to do this):

run command 'nvidia-settings' and go to 'X Server Display Configuration'
If you are all plugged in, there should be two grey boxes displayed, one labeled 'LGP' (your LCD screen) and another (mine's labeled 'LG').
Change the resolution of your current display to match what you will be using (most projectors are 1024x768)
Now, click on the LG box. (The way to control which display you are dealing with are clicking and moving those boxes)
You should see a box with a Configuration: Disabled and button [Configure]; click the Configure button.
How Should this display device be configured? Click 'TwinView'
Resolution 'Auto'
Position 'Clones'
Then hit 'Apply'

That's it!

If you want to run this configuration with no setup, then click on the 'Save to X Configuration File' and copy it over your /etc/X11/xorg.conf file whenever you need it (make sure you backup your original xorg.conf file!)

To undo it, click on the Configure button for LG, and click 'Disabled'. Then, change the resolution for your current screen and hit the 'Apply' button.

NOTE: this does not want to work under wmii-ruby because it does not want to respond to the change in resolution from gnome-display-properties.

Gutsy Gibbon broken matplotlib, pylab

2008-02-15T10:46:00.000-08:00

Usually, Ubuntu's package management system gets everything right. However, on Gutsy Gibbon when you install the very handy matplotlib it gives you a broken installation. Basically, you'll get some error messages like this:

>>> import pylab
Traceback (most recent call last):
  File "", line 1, in ?
  File "/usr/lib/python2.4/site-packages/pylab.py", line 1, in ?
    from matplotlib.pylab import *
  File "/usr/lib/python2.4/site-packages/matplotlib/pylab.py", line 199, in ?
    import cm
  File "/usr/lib/python2.4/site-packages/matplotlib/cm.py", line 5, in ?
    import colors
  File "/usr/lib/python2.4/site-packages/matplotlib/colors.py", line 38, in ?
    from numerix import array, arange, take, put, Float, Int, putmask, \
  File "/usr/lib/python2.4/site-packages/matplotlib/numerix/__init__.py", line 82, in ?
    import numpy
  File "/usr/lib/python2.4/site-packages/numpy/__init__.py", line 43, in ?
    import linalg
  File "/usr/lib/python2.4/site-packages/numpy/linalg/__init__.py", line 4, in ?
    from linalg import *
  File "/usr/lib/python2.4/site-packages/numpy/linalg/linalg.py", line 25, in ?
    from numpy.linalg import lapack_lite
ImportError: /usr/lib/atlas/liblapack.so.3: undefined symbol: ATL_chemv

So, I think they are trying to allow you to use whatever linear algebra backend you want. A fix (maybe there are better ones) is to install lapack3:

 sudo aptitude install lapack3

CSS for ruby syntax highlighting

2008-02-14T09:41:00.000-08:00

Add this to your css to get ruby code colored nicely.

from http://redcorundum.blogspot.com/2006/07/syntax-coloring.html


pre.code {
  padding: 1ex 1ex 1ex 1ex;
  border: 4px groove #CC0000;
  overflow-x: auto;
}

pre.code span.attribute { color: #009900; }
pre.code span.char { color: #F00; }
pre.code span.class { color: #A020F0; font-weight: bold; }
pre.code span.comment { color: #0000FF; }
pre.code span.constant { color: #008B8B; }
pre.code span.escape { color: #6A5ACD; }
pre.code span.expr { color: #2222CC; }
pre.code span.global { color: #11AA44; }
pre.code span.ident { color: #000000; }
pre.code span.keyword { color: #A52A2A; font-weight: bold; }
pre.code span.method { color: #008B8B; }
pre.code span.module { color: #A020F0; font-weight: bold; }
pre.code span.number { color: #DD00DD; }
pre.code span.punct { color: #6A5ACD; }
pre.code span.regex { color: #DD00DD; }
pre.code span.string { color: #DD00DD; }
pre.code span.symbol { color: #008B8B; }

Install Ubuntu as a file in windows with one-click

2008-01-31T14:23:00.000-08:00

If you want to try out linux (Ubuntu), this is BY FAR the easiest method. Just download this installer. The next time you reboot you can choose Windows or Linux:

http://wubi-installer.org/index.php

Basically, a file (6GB by default) is allocated inside of windows and a boot loader is installed. On reboot, you can choose windows or linux. When you are done, you can uninstall it and it goes away. Or, there are ways to migrate that file into a fresh partition if you want.

Very smooth.

R help in a browser

2008-01-28T13:05:00.001-08:00

Really annoying to try to look up docs in a window you are using. Instead, try this:


help.start()  # this will start up documentation in a browser
help(plot)    # shows documentation in browswer window now!

data.frame in R (the key object)

2008-01-28T07:45:00.000-08:00

I've been wading through R trying to figure out how it all works. It looks like the most important data structure is the data frame, and here I demo how to make a dataframe that a person can then play with. Yes, you can import data from a spreadsheet, but a person should understand the underlying data structure.

A data.frame is just a list of vectors or matrices where each has the same number of rows (think of the vectors as columns). It really is just the same as data in a spreadsheet:

var1	var2	var3	fac1	fac2
1	3	4	hot	TX
0	2	3	cold	WI
3	8	2	cold	UT

In fact, when one reads in this type of info, one gets a data.frame back:


df = read.csv(".csv", quote="")  # <-reads an unquoted csv file with headers

So, assuming we have some data like the above, now lets make it in R:


> var1 <- c(1,0,3)    #  '<-' is the assignment operator (like a directional '=')
                      #  'c()' is the concatenate operator (makes lists of things)
> var2 <- c(3,2,8)
> var3 <- array( c(4,3,2), c(3) )  # here's how you make a more mathematical vector

> fac1 <- c("hot", "cold", "cold")
> fac2 <- c("TX","WI","UT")

# alright, lets add all this stuff together into a dataframe:

> df <- data.frame(var1,var2,var3,fac1,fac2, row.names=NULL, check.rows=TRUE)

# creates this:
  var1 var2 var3 fac1 fac2
1    1    3    4  hot   TX
2    0    2    3 cold   WI
3    3    8    2 cold   UT

# want to see the names of the columns in the dataset:
> names(df)
[1] "var1" "var2" "var3" "fac1" "fac2"

# change the names:
> names(df) <- c("height", "weight", "nose.length", "temp", "state")
> df
  height weight nose.length temp state
1      1      3           4  hot    TX
2      0      2           3 cold    WI
3      3      8           2 cold    UT

# so, now we have a data.frame, the preferred data structure in R.  Let the magic begin:

> plot(df)

Installing and basic plotting in R

2008-01-25T09:28:00.000-08:00

Windows users:
http://cran.r-project.org/bin/windows/base/
Download R-2.6.1-win32.exe and install it like any program.
Start it like any other program from the start menu

Linux users:
sudo apt-get install r-base
Just type R in the terminal

Read in a file
Go into excel or even a text editor and create a simple data set like this:
1,3
2,5
2,6
3,8
4,4
6,3
7,9
Where the second column is after the comma.
Save your file as a .csv
Look up where you saved it and insert that as the location in the following code:
data<-read.table("/home/eldon/Desktop/data.csv",sep=",") #this reads in your data and assigns it to the data frame "data"
plot(data) #this gives you a simple plot of your data
If you want to learn more about simple plotting just enter:
help(plot)

Scientists for Better PCR

2008-01-24T13:22:00.000-08:00

http://bio-rad.cnpg.com/lsca/videos/ScientistsForBetterPCR/

Good for a laugh

What about R?

2008-01-23T22:47:00.000-08:00

Isn't R important enough to put into the subtitle?

R from ruby

2008-01-23T21:55:00.000-08:00

rsruby lets you run supposedly any function in R from ruby.

Elaborating on the sci-ruby page

sudo apt-get install r-base ruby1.9.1-full ruby1.9.1-dev
sudo ln -s /usr/lib/R/lib/libR.so /usr/lib/libR.so
sudo ln -s /usr/share/R/include/R.h /usr/include/R.h
gem install rsruby -- --with-R-dir=/usr/share/R

I thought this was necessary, but don't so much any more:

# add a line to your .bashrc file to point to R:
echo "export R_HOME=/usr/lib/R" >> ~/.bashrc
source ~/.bashrc   # read the bashrc file to get the variable

the lightsaber: our weapon of choice

2008-01-23T21:46:00.001-08:00

http://www.tecnosquad.com/wp-content/uploads/2007/09/lightsaber.jpg

sudo make me a sandwich

2008-01-23T20:20:00.001-08:00

http://imgs.xkcd.com/comics/sandwich.png

If you don't know what this is about, stick around and you might. eventually. after an explanation.