Trix & Graphix

Two tips to create comments in programs edited thorough VIM

2011-02-11T14:07:00.000+01:00

Here are a couple of simple tips to help you in the hard task of programming in VIM (the hard task is to write the code, not to do it in VIM, of course :) )

Inserting 50 symbols to create a header
Normaly it is a good idea to remark something within a program using comments. It's just something like

#########################################
# HERE GO IMPORTANT VARIABLES!
#########################################

In general, writing a large numbers of symbols is not a hard task, but it can be even easier using VIM. You only have to type a character, and repeat the order many times. To do this, use the command

100i#

and press ESC, and you will get a hundred symbols "#" all together. Later just push "." to repeat the last command. You will have exactly 2 lines of 100 symbols having pressed only 7 keys. Oh yeah.

Commenting several lines of code with few commands
This tip is less silly than the former one, and it may save you a lot of time. Unfortunately I don't know illustrate it, so I'll try to explain in my own words. Imagine you want to comment 20 lines, inserting some character (for example "#", but it may be other depending on the language of your choice) in the first column of these lines. To do it in VIM, use the block selection tool by pressing "ctrl+v" in command mode (remember that "v" is to use the standard selection, whereas "V" is the line selection). Then, select the first character, and only the first one!, in every line you want to comment. In this moment, press "I" (capital "i", the lowercase does not work) and type the character that you want to insert in every selected line. At the moment you will only see the change in the first line, but after pressing ESC, all selected lines will be commented automatically.

I don't even know how I could live without this! :)

Converting eps to pdf

2011-02-11T13:41:00.000+01:00

In most Unix-like systems there is a tool called epstopdf. It is very simple, but incredibly useful for preparing figures for a LaTeX document. Nevertheless there are some cases in which this tool is not present in your system by default. For example Snow Leopard, the SO of Mac, does not provide it. If I remember correctly, this tool is also missing in Ubuntu, and I guess that this can be the case in many other Linux distributions. There are other cases in which although the tool is present, it does not work properly, and you get unexpected results with the warning message:

==> Warning: BoundingBox not found!

In this case, the problem is because you are using a too old version of this program.

I have had problems in the past looking for a newer version, since you get a lot of garbage when searching epstopdf in google. Hence, this post is a simple hint to help you getting the program. Hopefully someone in the future will reach this post through google and will save a lot of time :)

The solution is simple: just go to the CTAN page of this software. Actually it is just a perl script. Place it somewhere and add the location of the script to your PATH. That's all folks.

Improving the search in VIM

2011-02-08T11:22:00.001+01:00

Here are a couple of tips to improve the searching engine in VIM.

First of all, searching patterns in VIM is quite simple. In command mode, use the

/

command. You can use regular expressions too. For example

/^foo

searches for the text "foo" in the beginning of a line. You can use very complex regular expresions, whose explanation if far away from the scope of this blog.

The searching commands in VIM takes the focus of the cursor to the next match going downward within the text. If you want to go to the next match, use the command

n

Similarly,

N

takes you to the former match. The command

?

makes the same than "/" but in the opposite direction, this is from the end of the file to the beginning.

Besides these commands, you can configure some of the behaviour of VIM when searchig patterns by adding some lines to the .vimrc file. For example

set incsearch

search in the text meanwhile you are typing, without waiting you to press enter. Another interesting feature is

set hlsearch

which highlight the found text. This is very usefull when debuggingg scripts, since you have a very convenient way to taking a look at the patters you want in a given moment.

Changing the colours in the output of "ls" command

2011-02-02T17:19:00.000+01:00

During the last weeks I'm working quite often with Mac OSX. However I normally use a lot the terminal, but the default terminal in this OS is quite lame. Thus, I recommend to use the program iTerm. This terminal has some interesting features, which I don't want to discuss in detail. Take a look and decide yourself!

However there is an interesting feature which is not activated by default in this OS (and has nothing to do with the terminal program you use). It is the use of fancy colours according to the type of file when listing the content of a directory through the command ls. This is a very important feature, very useful to easily identify the kind of files you have into a directory. In fact, it has few to do with the fancy aspect, but with how comfortable you feel yourself working in a terminal.

To allow the use of colours you have to use the -G option. Nevertheless having to write this every time is a pain (you would type it a thousand times every day!). It's much easier to use an alias in the .bass_profile in your home

alias ls="ls -G"

Finally, in order to customize these coulours, you have to use the environment variable LSCOLOR. To do so, you only have to add also this line to the .bash_profile in your home:

export LSCOLORS="exfxcxdxcxegedabagacad"

But what in the hell means that line? Well, I could explain it in detail but... finally I would only sumarize the content of the man page of ls. So here I copy the explanations you may need, directly taken from this man page:

LSCOLORS The value of this variable describes what color to use for which attribute
when colors are enabled with CLICOLOR. This string is a concatenation of
pairs of the format fb, where f is the foreground color and b is the back-
ground color.

The color designators are as follows:

a black
b red
c green
d brown
e blue
f magenta
g cyan
h light grey
A bold black, usually shows up as dark grey
B bold red
C bold green
D bold brown, usually shows up as yellow
E bold blue
F bold magenta
G bold cyan
H bold light grey; looks like bright white
x default foreground or background

Note that the above are standard ANSI colors. The actual display may differ
depending on the color capabilities of the terminal in use.

The order of the attributes are as follows:

1. directory
2. symbolic link
3. socket
4. pipe
5. executable
6. block special
7. character special
8. executable with setuid bit set
9. executable with setgid bit set
10. directory writable to others, with sticky bit
11. directory writable to others, without sticky bit

The default is "exfxcxdxbxegedabagacad", i.e. blue foreground and default
background for regular directories, black foreground and red background for
setuid executables, etc.

Forcing vim to remember the cursor position

2011-01-31T10:46:00.003+01:00

In some VIM installations this awesome editor does not remember the last cursor position in the former edition of a file. Of course, this can be a pain. Here is a small tip to solve this problem. You only need to copy this code into your .vimrc file

" Uncomment the following to have Vim jump to the last position when
" reopening a file
if has("autocmd")
au BufReadPost * if line("'\"") > 0 && line("'\"") <= line("$")

\| exe "normal g'\"" | endif
endif

Customizing the Unix prompt

2011-01-28T14:04:00.006+01:00

This is a very fast post about the prompt (basically this is an auto-remainder for myself xD).

The appearance of the prompt in an Unix terminal is determined by the environment variable PS1. You can (you have to) modify it if you want to change the prompt. It is easy to take a look at the current value of variable: just type in an open terminal

echo $PS1

and here is it. The prompt that I'm currently using is this one:

PS1='$(tput setaf 1)\u@\h $(tput setaf 2)\w> $(tput setaf 0)'

There are a number of commands very useful to depict important information. In my example \h shows the name of the host, whereas \u is the user and \w is the current working path. The commands tput setaf change the color. Take a look to the man pages of tput and terminfo to learn more.

Of course there are many more options. Here there is a more complete reference in this respect. By the way, it is a good idea to modify this variable in the .bash_profile file in your home directory :)

Reading a file until it ends

2010-06-12T17:52:00.004+02:00

It is a commont task that you have to read some information from a file to perform some calculations. This uses to be done inside a loop. The problem is that many times you don't know how many lines the file has, so you can't use a counter as the condition to stop reading. Or maybe you know, but you don't want to pass that information to the program every time you run it. In this post I'm showing how to "teach" a Fortran and Bash program to read until it reach the end of the file.

Fortran version
In fortran, you have to use the option iostat when you use the read function. By doing so, there is an integer variable (ierr in the example below) that contains the output code of the last read action. If it is different to 0, it means that the end of the files has been reached (or something even worse). I think the example is self explanatory

program readtotheend
implicit none
integer :: i, ierr, number
open(unit=10,file='filein.asc',status='old',action='read')
ierr=0
i=0
do while(ierr.eq.0)
i=i+1
read(10,*,iostat=ierr),number
print*, 'Element', i, number
enddo
close(unit=10)
print*, 'Reading finished', i-1, 'lines'
end program

Bash version
The Bash version of this idea is to use a while loop and feed it with the input file

set -ex
while read number; do
# Here you can do whatever you want to do with the variable, which is stored in the variable number
done < filein.asc

This is a really elegant solution to perform some operation to all the lines of a file.

Generating random numbers within a Bash script

2010-06-12T16:50:00.005+02:00

Unix systems has their own random numgers generator. It can be employed, for instance, to generate a sequence of random numbers inside a Bash script. The only thing that has to be done is to use the internal function $RANDOM

The next example illustrates the idea:

set -ex

for i in $(jot 100 1 1); do
echo $RANDOM >> file
done

Switch in Fortran 90

2009-12-01T09:32:00.004+01:00

A very quick post... I have just found out the Fortran 90 syntax for the equivalent of the switch command in C or case in Bash.

selectcase(var)
case(a)
print*, 'var=', a
case(b)
print*, 'var=', b
end select

Columns to rows and vice versa in ASCII files

2009-10-26T15:30:00.005+01:00

Imagine you have a table with data within an ASCII file. Let's asume your table is homogenious (otherwise you can take a look at this post. You may want to turn it into just one row, or just one column. I'm going to explain how to do it in two different ways using two different Unix tools: awk and tr.

- tr version:

This is the easiest way. In order to turn the file into just one row, the "\n" characters have to be removed. This can be done with the command:

tr "\n" " " < filein.asc > fileout.asc

Similarly, in order to turn the file into a column you can change the "\n" characters as field separator:

tr " " "\n" < filein.asc > fileout.asc

- awk version

Focusing now in the awk version, you can use

awk '{for(i=1;i<=NF;i++) print $i}' filein.asc > fileout.asc

in order to turn the file into a column, or

awk '{for(i=1;i<=NF;i++) printf "%s ", $i}' filein.asc > fileout.asc

to turn the file into just one row.

Easy, isn't?

Tips for cleaning up an ascii file

2009-10-26T12:28:00.011+01:00

Suposse you have a table in ASCII file such as this one:

element1x1 element1x2 element1x3

element2x2 element2x2 element2x3

element3x1, element3x2, element3x3

It's full of undesirable heterogeneities: tabs, comma instead of just spaces as columns delimiters, undesired spaces, empty lines... How can you homogenize this file using simple command-line Unix tools?

Well, the first thing is to remove the tabs. This is easy using the tr tool, which substitutes some character by others. To remove the tabs just type

tr "\t" " " < file.asc

and this will return a copy of the file but without tabs through the standard output. Similarly, to remove the "," symbols you can pipe the last command:

tr "\t" " " < file.asc | tr "," " "

Next thing is to remove the emply lines and some undesired spaces. This may be done using awk:

tr "\t" " " < file.asc | tr "," " " | awk '{ if(NF>0) {for(i=1;i<=NF;i++) printf "%s ", $i; printf "\n"}}'

Finally, last command adds an undesired space at the end of each line. It can be removed using sed:

tr "\t" " " < file | tr "," " " | awk '{ if(NF>0) {for(i=1;i<=NF;i++) printf "%s ", $i; printf "\n"}}' | sed 's/ $//'

Well, this is all. The final output you get through the standard output after running this command is

element1x1 element1x2 element1x3
element2x2 element2x2 element2x3
element3x1 element3x2 element3x3

Yes, I know, I have used a lot of tools with few explanations. Maybe in some post in the future I will explain some these tools in more detail...

Strings in BASH

2009-10-23T21:29:00.004+02:00

This post is to show some really nice features I have just found regarding the management of strings in Bash scripts. How have I been abled to live without this? :-)

Strings index

An array may be splitted using indexes. The sitanxis is something like ${variable:indx1:elemensts}, where inx1 is the first element on the substring you want to get (the first element is numbered 0, as in C), and elements in the number of elements you want to remain. Maybe it's easier to understand with some few examples:

var="asdf1234"

echo ${var:0}
asdf1234

echo ${var:4}
1234

echo ${var:4:1}
1

echo ${var:4:2}
12

Note that ${var:0} is equivalent to ${var}. A really interesting feature is that you may index from the right

var="asdf1234"
echo ${var: -2:2}
34

Note the blank space before the minus sign!!!

Replacing elements (regular expresions-like)

Another interesting feature is that you can use Bash to replace some elements of the string. This is a thing that people use to do with sed or awk. Nevertheless for easy tasks the direct form using Bask I'm going to explain may be useful. The sytanxis is ${variable/substringToBeReplaced/stringReplacing/}. Let's see some exmamples:

var=123ASDF123

echo ${var/123/XY}
XYASDF123

echo ${var//123/XY}
XYASDFXY

echo ${var/23}
1ASDF123

As you can see the sintaxis is similar to awk. By default, only the first time that the substring is found from the left it is replaced. Using "//" you can force to replace all the instances of the substring in the main string. Finally, if only one string is specified, it's simply removed (replaced by a null string).

Finally, if you want to replace, but beginning from the right, "%" has to be appended:

var=123ASDF123

echo ${var/#123/XY}
XYASDF123

echo ${var/%123/XY}
123ASDFXY

Note that the simbol "#" means "reading from the left". In general it is not necesary as this is the default behaviour.

Just two more examples. In order to get the name and the extension of a file:

var=name.ext

echo "The filename is ${var/%.*}"
The filename is name

echo "The extension is ${var/#*.}"
The extension is ext

Here you can see that "*" can mean the beginning as well as the end of the string.

I hope it may be useful for you :-).

Removing the transparent background when converting formats in Imagemagick

2009-10-21T12:20:00.006+02:00

By some reason, the version of Imagemagick I have in my workstation (6.4.3) sets the background to transparent when I convert EPS files to PNG format (for example the EPS files from GMT or gnuplot).

Although it's in general a desirable feature, sometimes you just want a plain white background. In order to get it, I have found a solution (there must be many others, but this one just works for me), which consists in adding this options:

convert -layers flatten figure.eps figure.png

Boundary annotations in GMT

2009-10-18T23:04:00.014+02:00

In the last post, I tried to give a general description of GMT. In the next few post I'm going to try to explain, by means of several examples, some details of the use of these tools.

In this first example, I'm going to use pscoast to create a simple map of Europe. Mostly I'm going to focus in how to customise annotation boundaries. In the next post I'll explain in more detail some flags of pscoast.

This is the output we want to get:

And this is the simple bash script which generates it

#!/bin/sh
# Bash script for using GMT

# Some environment variables
gmtset PAPER_MEDIA a5+
gmtset PAGE_ORIENTATION portrait
gmtset HEADER_FONT_SIZE 18
gmtset PLOT_DEGREE_FORMAT ddd:mm:ssF
gmtset DEGREE_SYMBOL none

# The only command of this plot
pscoast -Jl15/35/30/60/1:20000000 -R-15/45/35/70 -A0/0/1 -Ba5g5/a5g5nSEW:."Europe": -Ggrey > map.eps

# To convert the EPS file into png
convert -density 100 map.eps map.png

The main task is developed by pscoast, which uses 5 flags (-J, -R, -A, -B and -G). By the way, the order of these flags is not relevant. Before that, there are some options which controls the general behaviour of GMT and the aspect of the final result, like fonts styles, colors, formats and so on. Finally Imagemagick converts the EPS file to a more friendly png image.

The explanation of the flags is as follows:

J defines the projection, meanwhile R defines the region you want to plot. Of course, depending on the region you want to plot, you have to chose the adequate projection. I have chosen the Lambert Conic Conformal projection, in which you have to set the central coordinates, two true latitudes and the scale. It's beyond the scope of this blog to explain the exact meaning of these parameters, sorry. I have chosen -Jl15/35/30/60/1:20000000 because 15 degrees East is the central latitude of the region I have chosen (-R-15/45/35/70), and 30 and 60 as the two true latitude just because they are inside the domain I want to plot.

A is to select whether you want or not to show small water regions, like lakes. It's a bit confusing and in fact I don't understand it very well. I just use it with those options as far as I have found out it removes the lakes...

G is to say GMT to plot the land areas. The option grey is just to set the colour you want. You can also use the RGB model, for example G255/0/0 is red.

Finally, B is to specify the boundaries of the plot. It's quite important to get nice maps. I have used -Ba5g5/a5g5nSEW:."Europe":, which may appear to be really complex, but don't worry, isn't so hard ;-). a5 says GMT to set the degree label every 5 degrees. g5 says it to draw the white-black rectangles every 5 degrees, and also to plot the inner grid lines along the map. If you use f instead of g, you removes the inner grid. I use it twice, a5g5/a5g5, because first one is for horizontal and second for vertical boundaries (if you only set it once, both horizontal and vertical share same options). Later I add nSEW. This is to say in which axis you want to set degree annotations, lower case means no annotations, and upper case means annotations. Then, for example, NsWe sets annotations only in West and North. Finally, :."Europe": adds a title to the map.

A last comment regarding the general options of the map. By default, these are the options. gmtset allows you to modify these options. DEGREE_SYMBOL none disables the degree symbol, and PLOT_DEGREE_FORMAT ddd:mm:ssF sets the degree interval to -180/180 and adds a W instead of the minus symbol for west coordinates. HEADER_FONT_SIZE 18 sets to this size the title font and so on.

This is all. I hope this post is not too confusing. In the next one I'll try to add some more options to pscoast in order to get a more complex map.

GMT: a very brief introduction

2009-10-18T22:15:00.004+02:00

GMT is a set of tools (command line programs) to manipulating geographic data sets, and in particular to create maps. This set of tools are a great example of the philosofy that should follow all the Unix programs: very light, fast and each tools does just one thing, but does it well. Here there are some examples of the kind of things that you can get with these tools. Maybe the bigger problem with GMT is the complexity when using it, the thousand of options and its dark syntax. In this blog I'll try to post some tips & tricks I have found out up to now... I still learn new things every day.

The general way of plotting a map with GMT is to use several tools sequentially. Each tool adds a new detail in the final result. For example, the coastlines are added with pscoast, shadings are added with grdimage, some symbols are included later with psxy and so on. When a command is called, the output of GMT is EPS code through the standard output of the terminal. Thus, you have to redirect the output after each call to GMT to the same EPF file (which is, by the way, an ASCII file). As you can understand, in order to work sucessfully with GMT, bash scripting is mandatory. Otherwise, you will become mad after just 10 minutes using it.

The syntax is nevertheless quite complex. In the next posts I'll explain some details about it. Anyway, the best place to learn about GMT is, as could be expected in a Unix program, the man pages. Just as a general comment, the syntax is something like:

command -Flag1Options -Flag2Options > file.eps

where command is one of the many GMT tools. Flag1 and Flag2 can be -D, -O, -B,... there are tens of flags which deppend on the exact tool. Finally, Options are the many options you can use for each flag. It's important to note that there is no space between the flag and the option. For example you have to use -Aa0tf10 instead of -A a0 t f10.

Well, I know, it's very complicated. I'll put some examples in the next posts...

La Ciencia en España no necesita tijeras

2009-10-07T14:01:00.003+02:00

Ésta es mi modestia aportación a la iniciativa "La Ciencia en España no necesita tijeras" propuesta por La aldea irreductible.

Mi argumento será del tipo del que les interesan a los políticos: ECONÓMICO. Vamos a ver, ¿de qué cojones sirve que el estado se gaste un montón de dinero en formar a doctorandos, si luego no hay un proyecto científico serio en España para dar plaza a esta gente? ¿Qué pasa si recortan el presupuesto para nuevos proyectos? que cuando termine el doctorado (y como yo otros cuantos miles de estudiantes de doctorado) me quedan dos opciones:

- me voy al extranjero a seguir con mi carrera científica, en cuyo caso el estado se ha gastado mucho dinero en formarme para mandarme a que se beneficio otro país de mi formación

- me voy a la paro. En este caso, de todas formas tendré que seguir cobrando del estado, con la diferencia de que ahora me tocaré los cojones.

En cualquier caso, la Ciencia en España no necesita tijeras, sino una inversión continuada y a más largo plazo que el que marcan los putos 4 años electorales. La ciencia no se hace al ritmo que marcan los ciclos políticos ni económicos, e intentar forzar eso es estrangularla.

Plots inside other plots with Gnuplot

2009-10-05T19:37:00.005+02:00

This is another post when I'm going to try to explain how to use the multiplot environment. In this case, I'm going to use the multiplot environment, but setting the position of the plots "by hand" in order to get the effect of one plot inside other. This may be useful if you want to show some detail of a small part of the general plot. This is the final result:

Well, the overall idea is the same than in this other post, but in this case I won't use the automatic layout. In order to set the size and position of the plot manually, you have to use the parameters size and origin, respectively. You have to know that the units of these commands are the size of the whole figure, and first number refers to x axis. Then for example, set size 1,1 means use the whole figure as the size of the plot. Analogously, set origin 0.5,0.5 sets the bottom left corner of the plot in the centre of the figure.

Other example: if you want to insert two plots, one over the other, you could set size 1,0.5 in order to reduce the vertical size to half the total, and then use set origin 0,0.5 before plotting the second graph.

This is the code to generate the figure above. I have plotted also a rectangle and an arrow. You can skip that, it's not really important, but I just wanted to show some more capabilities of Gnuplot.

gnuplot << TOEND
set terminal postscript eps color enhanced
set output 'multiplot2.eps'

#set ytics 0.25
#set format y "%.2f"

set multiplot

# Bigger plot options
set yrange [-4:5]
set size 1,1
set origin 0,0
set title 'Whole plot'
set xlabel 'time/s'
set ylabel 'variable/m'

### This is to plot the square. You can skip this ###
set arrow from 1.1,-0.9 to 1.0,0.3 lw 1 back filled
set arrow from 0.9,-3 to 1.5,-3 lw 1 front nohead
set arrow from 0.9,-1 to 1.5,-1 lw 1 front nohead
set arrow from 0.9,-1 to 0.9,-3 lw 1 front nohead
set arrow from 1.5,-1 to 1.5,-3 lw 1 front nohead
###################################

# This plots the big plot
plot 'datos.dat' w l lt 1 lc 3 lw 3 t ''

# Now we set the options for the smaller plot
set size 0.6,0.4
set origin 0.2,0.5
set title 'Zoom'
set xrange [0.9:1.5]
set yrange [-3:-1]
set xlabel ""
set ylabel ""
unset arrow
set grid

# And finally let's plot the same set of data, but in the smaller plot
plot 'datos.dat' w l lt 1 lc 3 lw 3 t ''

# It's important to close the multiplot environment!!!
unset multiplot

TOEND

Array of plots in Gnuplot

2009-10-05T19:24:00.005+02:00

In this post I will explain how to create an array of plots. This may be useful for example if you need to merge several plots in the same figure in a paper. Within this post, by figure I will mean a file which in general may contain several independent plots. The aim of this post is to explain how to get the next figure:

For this purpose, gnuplot has the multiplot environment. To use it, you just have to type multiplot once you are already in gnuplot. From that moment on, each time you type the command plot, you will get a new plot added to the same figure. You have to take into account that every new plot is independent of the former ones. This means that you can (or you have to) reset again all parameters you want to change for the next plot. If you don't reset them, they will remain as in the previous call to plot command. For example, if you set xlabel to "variable x", all plots will have in common this label for their x axis. Of course you can change this by just typing sex xlabel "whatever" always before to use the next plot command. For this reason, it's a good idea to set all common parameters to every plots in the figure before initiating the multiplot environment.

I think the next example is quite self-explanatory, so just one thing has to be remarked. In the multiplot environment you can use an automatic layout for the plots or a manual one. If you want to create a regular array of plots, it makes more sense to use the first option. In the next post I will put an example of how to use the manual approach for a more complex result.

gnuplot << TOEND
set terminal postscript eps color enhanced
set output 'multiplot.eps'

# Some common options
set xrange [-pi:pi]
set mxtics 2
set ytics 0.25
set xtics ("-{/Symbol p}" -pi, "-{/Symbol p}/2" -pi/2, "0" 0,"{/Symbol p}/2" pi/
2, "{/Symbol p}" pi)
set format y "%.2f"

set grid

# This begins the multiplot environment. This example uses a 2x2 regular layout
set multiplot layout 2,2 title 'Using layout 2x2

# Now, every time I use the plot command, I will get a new plot
# in the correct position acording to the selected layout

set title 'Plot 1'
plot sin(1*x) w l lt 1 lc 1 lw 3 t ''

set title 'Plot 2'
plot sin(2*x) w l lt 1 lc 2 lw 3 t ''

set title 'Plot 3'
plot sin(3*x) w l lt 1 lc 3 lw 3 t ''

set title 'Plot 4'
plot sin(4*x) w l lt 1 lc 4 lw 3 t ''

# It is important to close the multiplot environment before leave!!!
unset multiplot

TOEND

Complex axis in Gnuplot

2009-09-22T22:39:00.010+02:00

This post is to show the great flexibility of gnuplot regarding axis format. I'm going to explain some commands to get the next graph:

Yeah, I know, may be it's the most ugly and pointless plot ever. Nevertheless, it's a complex one, and it's not easy to get. That's the point ;-)

First of all, it's important to note that every plot has 4 different and independent axis called x, y, x2 and y2, respectively for bottom, left, top and right. Furthermore, each axis if the combination of three elements: the border (a straight line), the tics (short lines perpendicular to the border) and the tic labels (normally a number seting a value for the tic). The idea is that you can change every one of these elements separately.

Let's begin with the border. The border of the graph is just a square containing the plot. You can set or unset separately each one of the 4 borders, so it's easy to understand that you have 2x2x2x2=16 possibilities. To select what borders you want, gnuplot uses something like binary numaration. Each border has associated a power of two: 1, 2, 4 and 8 for bottom, left, top and right, respectively, like in the figure.

So for example if you want to set only the top border, you have to type:

set border 4

Other examples: if you want to set top and bottom borders, you have to sum both numbers, 4+1=5 and type set border 5. For the same reason, 0 sets no border, and 15 sets the four borders. Easy, isn't?

Now we are ready to go to tics. Tics and borders may be set or unset independently. So for example if you unset the top border, the y2 tics will still remain, so you can get unexpected results. To unset a tic set, you have to use the unset command, like for example

unset xtics

The same for ytics, x2tics and y2tics. By default, the 4 sets of tics are enabled.

Once you know in which axis you want to have tics, it's the moment to set how many you want. There are several ways of setting tics, and of course you can set the number of tics in each axis separately.

You can specify only the spacing between them, leaving the initial and final one to be set automatically by gnuplot by typing

set xtics 20

On the other hand, you can also specify the initial, final and the spacing by:

set xtics 20,1,30

Finally you can set the tics "by hand" following this syntax

set xtics ("one" 1, "two" 2, "3" 3, "{/Symbol p}" pi)

Where the string between quotes is the tic label to be set, and the number is the position of the label in the axis. This last options is really useful if you are dealing with a really complex and custimized plot.

A last note about tics and borders is that they all share the same line style. You can specify it like any other line options, like for example

set border 12 ls 2 lw 3 lc 3

This command will unset bottom and left boders. The rest will be, as well as the tics, dashed blue lines, 3 pixels width.

Let's now focus in the format of the tic labels. One important point to have into account is that if you want to unset only the labels, but keeping the tics, you can do it by changing the axis format to empty:

set format x ""

And of course analogously for the others 3 axis. By default x2 and y2 axis have this format. Regarding the formatting, you may set how numbers are displayed following C conventions, like for example

set x2tics "%02g"

and so on. There are plenty of places in internet where this convention is explained.

Other interesting options are offset and rotate. With these options you can shift the label of the tics and to rotate them, which is not an easy effect to get in other programs. A example of these is shown in the final example.

Finally, you can also change the color of the labels of the tics using the textcolor option, like

set x2tics textcolor lt 2

Well, I know, I have explained a lot of options, and not very much in detail. But rebember that all these options, and much more, are explained in the gnuplot interactive help. The idea of this post was to demonstrate to those who think gnuplot is lame that they are wrong.

Now I'll sumarize some of these concepts with the code to get of the initial example.

#!/bin/bash

gnuplot << TOEND
# Setting the output file
set terminal postscript eps color enhanced "Helvetica" 20
set output 'borders.eps'

# Setting the top an right border (4+8=12).
#We change also the color and line style
set border 12 ls 2 lw 3 lc 3

# Setting the margins (distance between borders
#of the graph and the borders of the image)
set tmargin 5
set bmargin 5
set lmargin 5
set rmargin 15

# Setting the xtics
unset xtics
set x2tics ("-{/Symbol p}"-pi, -1, 0, "one" 1, 2, "three" 3, 4, 5, 6) textcolor
lt 2
set x2label "x2 axis"

# Setting the ytics
unset ytics
set y2tics -1,.2,1 textcolor lt -1 offset 2 rotate by 30
set format y2 "%.2f"

# The rest is just for a boring normal plot
set xrange [-5:5]
set yrange [-1:1]

set title "Pointless but rather complex graph"
plot sin(x) w l lt 1 lc rgb "#FF00FF" lw 6 t ''
TOEND

convert -density 100 borders.eps borders.png

Uper to lowecase and vice versa

2009-09-20T00:21:00.004+02:00

I'm going to tell three ways of doing the same task: changing the capitalization. This is a pretty comon task, and there are many ways of doing it.

The first way is to use my favourite text editor: Vim. The idea is to open the file to be modified. Then, select the whole content of the file and push u to change it to lowercase. Analogously push U to change it to upercase. To select the whole file, you just have to type ggVG. The explanation is as follows: the first gg is to go to the begining of the file, V is for changing to select lines mode, and G to go to the end of the file.

This last way is useful (and fast) if you have to change the content of just one file. It is nevertheless less useful if you have to change many files. In these cases, is better to use awk or sed.

To use awk (my favourite option) you only have to use the function tolower, like in this example:

echo TEXT TO BE CHANGED TO LOWECASE | awk '{print tolower($0)}'

and similary the function toupper changes the string to upercase.

This task may also be achieved with sed. To do it, the command line should be now

echo text to capitals | sed 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'

Well, this is all for today. It looks like the sed way is less elegant. The fact is that I'm pretty sure there must be a better way, althought I don't know it yet ;-).

Simple animations with Imagemagick

2009-09-19T21:09:00.006+02:00

Imagemagick allows to generate simple animations (this is, a gif file) by using several input images as frames in a movie. Here I'm going to show the main idea, which it's actually very simple.

In order to have several images to be mounted in the movie, I have used a bash script together with gnuplot. This will generate 20 slightly different images of a sinusoidal fuction, little bit shifted between them. This is the code:

#!/bin/bash

N=20

# Note the -w option in seq
for i in $(seq -w 1 $N); do
gnuplot << TOEND
# Setting the output
set terminal postscript eps color "Helvetica" 20
set output 'sin$i.eps'

# This removes the numbers in the graph and sets the grid
set format x ""
set format y ""
set grid

# The plot itself
plot sin(x+2*pi/$N*$i) w l lt 1 lc 3 lw 4 t ''

TOEND

# Now transform the postscript file into a png one, and remove the eps
convert -density 50 -layers flatten sin$i.eps sin$i.png
rm sin$i.eps
done

It's important to note the "-w" option in the seq command. This will generate numbers with the correct padding. This is, it will generate the list "01 02 ... 09 10 11 ..." instead of "1 2 ... 9 10 11 ..." which may be a problem when you want to list the resulting files in the correct order to create the movie.

So now we have 20 png files. To merge them, the convert command may be invoked with just an option to set the delay (in miliseconds) between images.

convert -delay 10 sin*png animation.gif

That's all, it's pretty easi, isn't?

Ant this is the result:

EDIT: By some unknown reason, gif animations doesn't seem to work when I upload them to Picasa. Well, you have to trust me, it evolves with time, and it's even pretty funny ;-).

ACTUALIZATION: Using other (my own) web server, I have been abled to upload a real gif animation. With minor changes in the script, this is what I get:

Greek letters in gnuplot

2009-09-12T09:52:00.005+02:00

Gnuplot is a powerful scientific plotting program. In fact is more powerful than people usually think first time time they use it. May be this is because it has no GUI. Instead of that, you have to type commands in a plain boring terminal.

Well, in this post I'm going to put an example of how to perform a relatively complex graph, using greek letters and legend. Of course, everything I use here is explained perfectly in the help.

Gnuplot has several output formats (called terminals). Depending on what you are going to do later with the output you get from the program, you can use one or another (from raster formats like png of jpeg, up to vectorial ones such as eps or svg). In general I advice to use the terminal postscript, and later on to export the file to a raster format like png using a images manipulation program like Imagemagick. I also advice to use the options: eps (to get encapsulated postscript code), color (to have colors enabled) and enhanced (to be able to use advanced postscript options such as greek letters).

To get a greek letter, you have to use the postscript terminal, with the option enhanced. Then, to add the alpha greek letter, you have to type {/Symbol a}. Analogously for other letters, changing the "a" by other, like "D" for Delta and so on...

Finally, the thing I like most about Gnuplot is that it's easily scriptable. Here there is a simple script which shows all these ideas in practice (comments are added to make code more readable):

#!/bin/bash

gnuplot << TOEND
# Setting the terminal postscript with the options
set terminal postscript eps color enhanced "Helvetica" 20

# Setting the output file name
set output 'plot.eps'

#Setting up the grid and labels
set grid
set title "A simple graphic without LaTeX"
set xrange [-pi:pi]
set xlabel "Angle {/Symbol a}"
set ylabel "{/Symbol Dw}"
set ytics 0.5
set xtics ("{/Symbol p}" -pi, "{/Symbol p}/2" -pi/2, "0" 0, "{/Symbol p}/2" pi/2, "{/Symbol p}" pi)

# Setting the legend
set key horizontal below height 2
set key box lt 2 lc -1 lw 3

# The plot itself (\ is to broke lines)
set size 1,1
plot sin(x)**2 w l lt 1 lc 1 lw 3 t "sin^2({/Symbol a})", \
sin(2*x)/x w l lt 2 lc 3 lw 3 t "sin(2{/Symbol a})/{/Symbol a}", \
sin(x) w l lt 3 lc 2 lw 3 t "sin{/Symbol a})"
TOEND

convert -density 150 plot.eps plot.png
rm plot.eps

And this is the result (click to enlarge).

Well, is not bad, but it's not still wonderful. In a future post I will explain how to use the terminal epslatex to get impressive book-quality results ;-).

My own (botch) version of LaTeX in blogger

2009-09-08T17:45:00.012+02:00

There are, as far as I know, at least two different ways of using within blogger. In both cases the idea is the same, and it's similar as in some forums or in the TeXIM plugin for AMSN: somewhere there is a third part server which uses a LaTeX distribution to generate a dvi file, together with some other tools to convert this file into an image, which can be included in the html code of your blog.

Well, the problem with such solutions is that they parasite a server developed for this purpose, but this server has few (or not at all) options. In particular, the image you get is only useful with light backgrounds, so you lose freedom for choosing the design of your blog. Just to put an example, this is what I get:

\int_{0}^{1}\frac{x^{4}\left(1-x\right)^{4}}{1+x^{2}}dx
=\frac{22}{7}-\pi

Lame.

I have to say, first of all, that I have not found the perfect solution to this problem. Instead of that, my aproach consists in adding the image by hand, using Picasa. Yeah, I know, I know,... it isn't very satisfactory, but if you don't need thousands of equations, it could be good enought. Again, just for example, this is my result:

Is not bad, isn't it? But the main problem remains unsolved: how to get the image with the equation. Well, here is my solution, a bash script:

#!/bin/bash

COLOR="0.8,0.8,0.8"
DENSITY=150

cat > equation.tex << PART1
\documentclass[12pt]{article}
\usepackage{amsfonts}
\usepackage[usenames]{color}
\definecolor{my_color}{rgb}{$COLOR}

\begin{document}
\pagestyle{empty}
%\pagecolor{black}
{\color{my_color}

\begin{eqnarray}
PART1

cat equation.asc >> equation.tex

cat >> equation.tex << PART2
\end{eqnarray}
}
\end{document}
PART2

latex equation.tex
dvips -f -E -o equation.ps equation.dvi
convert -density $DENSITY equation.ps equation.png

rm equation.log equation.aux equation.tex equation.dvi equation.ps

The idea is pretty simple. To use it, you have to type your formula in the file equation.asc, in standard latex (rebembering that you are inside a eqnarray environment). Then, by running the script in your computer you get a png file with the equation, which you can upload by hand. The good thing of this aproach is that you can choose the colour of the equation playing around the variable COLOR (setting the colour you want in rbg), as well as with the size of the image changing DENSITY.

A last thing is that in order to run successfully the script, a distribution and Imagemagick have to be installed and working in the system you want to run the script.

cat and tac

2009-09-07T15:33:00.011+02:00

Unix-like system are based on a very simple set of ideas, one of them is: every program has to solve just one task, and do it right. Well, this is exactly what does one of the most common tools in Linux: cat.

Many people use cat just for getting the output from an ascii file, in commands like

$ cat file.asc

Well, open a file, decode the ascii format and print out a human-readable version in screen is a great thing, but it is not the only thing cat can do.

cat may be used to concatenate files, independently of their format. For example

$ cat file1.asc file2.asc > files1-2.asc

joins both files in another ascii format file.

Not only ascii files, but it also work with binary ones, for example with metheorological EXTRA format

$ cat file1.ext file2.ext > files1-2.ext

But the most powerful feature of cat is that it is a text editor. To use it, you have to type:

$ cat > file.txt << EDIT
some text
you want to add
into your file
EDIT

which means something like "take the input of the keyboard and insert it in file.txt. Wait until I type again EDIT, which will mean I want you to stop listening".

This feature is extremely useful for scripting purposes, as you can make scripts which create other scripts and so on. May be I will put some example of this in a (I hope) near future.

Finally, there exists another command, which I found out few time ago, tac. This programs do exactly the same as cat, but from bottom to up. This is, tac may be used for printing a file reversing the order of rows. It may be very useful when you know that the interesting part is at the end of a file.

BTW. Many people use the command:

$ cat file.txt | grep something

trying to look for "something" in the file. There is no point to do that. grep is another tool which does not need at all cat to work. The correct form would be:

$ grep something file.txt

A new project: justification

2009-09-07T14:26:00.005+02:00

Two years ago I started this blog. Well, actually I began it and later on I forgot it because I thought I had nothing interesting to say. Now the situation has not changed too much, but I have had a brand new idea*: I could convert this in something like a list of technical recipes about Unix commands and related issues, like computing, advanced scientific plotting and so on.

The thing is that sometimes I need to know how to do a technical task, like filtering some lines within an ascii file, or plot complex graphs with gnuplot, or I get an unknown error when compiling fortran programs,... in these cases I spend up to a whole day looking for in Internet how to solve the problem. From now on, every time I solve a problem, I will publish the solution here, so it may be helpful for something else, as well as for myself in future (I'm very chaotic).

One thing I should explain is why I write so poorly. And the answer is simple: I don't know English enough. You could ask me then why do you write in English? Well, I want to learn, and keep practising is a great opportunity to improve my grammar and increase my vocabulary. That's the only reason.

* I had the idea when I saw this great blog.