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Document Preparation. LaTeX and other vital tools for computing scientists. CMPUT 603: Teaching and Research Methods Paul Berube Sept. 19, 2005. Anatomy of a Thesis. 6 Chapters, 2 Appendixes 14 Section 18 Subsections 196 Charts 11 Figures 48 Tables 35 cited works. Data for a Thesis.

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document preparation

Document Preparation

LaTeX and other vital tools for computing scientists.

CMPUT 603: Teaching and Research Methods

Paul Berube

Sept. 19, 2005

anatomy of a thesis
Anatomy of a Thesis
  • 6 Chapters, 2 Appendixes
  • 14 Section
  • 18 Subsections
  • 196 Charts
  • 11 Figures
  • 48 Tables
  • 35 cited works

CMPUT 603, Paul Berube

data for a thesis
Data for a Thesis
  • ~ 40,000 raw data files
  • ~ 8,000 processed data files
  • 865 charts
  • 41 tables
  • Charts and tables change when data changes!

CMPUT 603, Paul Berube

managing the complexity
Managing the Complexity
  • Scripts to process data
    • Shell scripts, awk, bc, grep, sed, wc, etc…
  • Non-interactive programs to create charts
    • Matlab, gnuplot
  • A document preparation system that:
    • Decomposes and compartmentalizes writing
    • Integrates with other tools
    • Automates formatting and numbering

CMPUT 603, Paul Berube

the basics
The Basics
  • Commands start with a ‘\’
    • \chapter, \section, \subsection, \subsubsection
    • {\tt <monospaced text>}, {\bf <bold text>}, {\it <italicized text>}
    • \input{<filename}
  • Some special characters: ‘#’, ‘&’, ‘\’, ‘{‘, ‘}’
    • ‘~’ : non-breaking space
    • ‘$’ : math mode, ‘^’ superscript, ‘_’ subscript
    • ‘%’ : comments

CMPUT 603, Paul Berube

document structure
Document Structure

Root

File

Local.bib

Intro.tex

Results.tex

Conc.tex

Fig1.eps

Sec1.tex

Sec2.tex

Tab.tex

Fig2.eps

CMPUT 603, Paul Berube

document structure1
Document Structure

Root

File

Local.bib

Intro.tex

Results.tex

Conc.tex

Fig1.eps

Sec1.tex

Sec2.tex

xfig

gnuplot

Tab.tex

Fig2.eps

script

CMPUT 603, Paul Berube

the figure environment
The figure environment
  • Used for inserting images, graphs, charts, etc…
  • A “float” environment
    • Latex will put the figure where it thinks is best

Figure 2, top of page 4:

\begin{figure}

\centering

\includegraphics{motiv2.eps}

\caption{Motivating Example.}

\label{fig:motiv-exmp}

\end{figure}

CMPUT 603, Paul Berube

captions
Captions

\begin{figure}

\centering

\includegraphics{motiv2.eps}

\caption{Motivating Example.}

\label{fig:motiv-exmp}

\end{figure}

Caption

CMPUT 603, Paul Berube

labels references
Labels & References

\begin{figure}

\centering

\includegraphics{motiv2.eps}

\caption{Motivating Example.}

\label{fig:motiv-exmp}

\end{figure}

Label

CMPUT 603, Paul Berube

labels references1
Labels & References

Reference

Figure~\ref{fig:motiv-exmp} shows…

\begin{figure}

\centering

\includegraphics{motiv2.eps}

\caption{Motivating Example.}

\label{fig:motiv-exmp}

\end{figure}

Label

CMPUT 603, Paul Berube

labels references2
Labels & References

Reference

Figure~\ref{fig:motiv-exmp} shows…

Figure 2 shows…

\begin{figure}

\centering

\includegraphics{motiv2.eps}

\caption{Motivating Example.}

\label{fig:motiv-exmp}

\end{figure}

Label

CMPUT 603, Paul Berube

conclusion tex motiv2 eps overfull hbox 196 49pt too wide
(conclusion.tex <motiv2.eps>Overfull \hbox (196.49pt too wide)

\begin{figure}

\centering

\includegraphics{motiv2.eps}

\caption{Motivating Example.}

\label{fig:motiv-exmp}

\end{figure}

CMPUT 603, Paul Berube

figure
figure*
  • Adding a ‘*’ lets a figure or table span the whole page in multi-column documents

\begin{figure*}

\centering

\includegraphics{motiv2.eps}

\caption{Motivating Example.}

\label{fig:motiv-exmp}

\end{figure*}

CMPUT 603, Paul Berube

tables
Tables
  • Also a “float” environment

\begin{table}

\centering

\begin{tabular}{|l|c|} \hline

{\bf Evaluation Category} & {\bf Score} \\

How confident are [snip] & \\ \hline

{\bf Reviewer Confidence} & \\

Are you convinced [snip] & \\ \hline

\end{tabular}

\caption{Peer-based referee report for \paper.}

\label{tab:eval1}

\end{table}

Table 1, Page 3

CMPUT 603, Paul Berube

tables1
Tables
  • Also a “float” environment

\begin{table}

\centering

\begin{tabular}{|l|c|} \hline

{\bf Evaluation Category} & {\bf Score} \\

How confident are [snip] & \\ \hline

{\bf Reviewer Confidence} & \\

Are you convinced [snip] & \\ \hline

\end{tabular}

\caption{Peer-based referee report for \paper.}

\label{tab:eval1}

\end{table}

Table 1, Page 3

  • Table Format Specifier:
  • ‘r’ : right-justified column
  • ‘l’ : left-justified column
  • ‘c’: center-justified column
  • ‘|’ : vertical line

CMPUT 603, Paul Berube

tables2
Tables
  • Also a “float” environment

\begin{table}

\centering

\begin{tabular}{|l|c|} \hline

{\bf Evaluation Category} & {\bf Score} \\

How confident are [snip] & \\ \hline

{\bf Reviewer Confidence} & \\

Are you convinced [snip] & \\ \hline

\end{tabular}

\caption{Peer-based referee report for \paper.}

\label{tab:eval1}

\end{table}

Table 1, Page 3

& = column separator

CMPUT 603, Paul Berube

tables3
Tables
  • Also a “float” environment

\begin{table}

\centering

\begin{tabular}{|l|c|} \hline

{\bf Evaluation Category} & {\bf Score} \\

How confident are [snip] & \\ \hline

{\bf Reviewer Confidence} & \\

Are you convinced [snip] & \\ \hline

\end{tabular}

\caption{Peer-based referee report for \paper.}

\label{tab:eval1}

\end{table}

Table 1, Page 3

\\ = newline

CMPUT 603, Paul Berube

tables4
Tables
  • Also a “float” environment

\begin{table}

\centering

\begin{tabular}{|l|c|} \hline

{\bf Evaluation Category} & {\bf Score} \\

How confident are [snip] & \\ \hline

{\bf Reviewer Confidence} & \\

Are you convinced [snip] & \\ \hline

\end{tabular}

\caption{Peer-based referee report for \paper.}

\label{tab:eval1}

\end{table}

Table 1, Page 3

\hline

CMPUT 603, Paul Berube

text figures
Text-figures
  • To create a figure containing text, use a tabular inside a figure
  • Works great for code segments, etc

\begin{figure}

\centering

\begin{tabular}{|l|}

\hline

Title\\

1. Introduction\\

Acknowlegments\\ \hline

\end{tabular}

\caption{Organization for \paper.}

\label{fig:organization}

\end{figure}

CMPUT 603, Paul Berube

other table tricks
Other Table Tricks
  • Multicolumn
    • \multicolumn{<span>}{<text>}
  • Multirow
    • \multirow{<span>}*{<common text>}

CMPUT 603, Paul Berube

enumeration environments
Enumeration Environments
  • Not a float
  • Enumerate : ordered list
  • Itemize : unordered list
  • Description : unordered list with item labels

Canadian bands include:

\begin{itemize}

\item Chilliwack

\item Harlequin

\item The Guess Who

\end{itemize}

CMPUT 603, Paul Berube

math mode
Math Mode
  • LaTeX is the tool to typeset mathematics and symbols
  • $ <math> $ : inline math
  • $$ <math> $$ : not-inline math

CMPUT 603, Paul Berube

make your own commands
Make your own commands
  • Customized commands
    • Shorthand
    • Help ensure consistency
  • \def
    • \def\course{{\tt CMPUT}~603}
      • This course is \course.
  • \let, \newcommand, \newenvironment

This course is CMPUT 603.

CMPUT 603, Paul Berube

citations bibliographies
Citations & Bibliographies
  • Bibtex makes it easy
    • Create a .bib file with your references
    • Cite references with \cite{<name>} in text
    • \cite{<name>}  [<num>] in text, eg, [3]
    • Bibliography automatically generated with proper formatting
    • Bibliography only includes references you actually cite

CMPUT 603, Paul Berube

citations bibliographies1
Citations & Bibliographies

.bib file

CMPUT 603, Paul Berube

citations bibliographies2
Citations & Bibliographies
  • Color-coded items

Required

Optional

CMPUT 603, Paul Berube

citations bibliographies3
Citations & Bibliographies
  • Fill in everything you can find out.

CMPUT 603, Paul Berube

citations bibliographies4
Citations & Bibliographies
  • CTRL-C, CTRL-C to clean up bib entry

CMPUT 603, Paul Berube

things to read about
Things to read about
  • Math mode
  • Subfigures
  • Tabularx environment
  • Tabbing environment
  • Minipages
  • Algorithmics packages

CMPUT 603, Paul Berube

bash scripting

Bash scripting

See: Advanced Bash-Scripting Guide

scripts
Scripts
  • Automate tedious tasks
  • Tests and checks  more robust than manual execution
  • “Glue” to bind a collection of tasks
  • High-level programming
    • Scripts like a “meta-program”?
  • Rely on common utilities to do the “real work”

CMPUT 603, Paul Berube

slide34

sed

See: Advanced Bash-Scripting Guide

slide35
Sed
  • String manipluation utility
  • Substitution
    • $> sed –e “s/hate/love/” file
    • $> find ./data/ -name “*.data” | sed –e “s/\.\/data\///” < file
  • Selection
    • $> sed –n –e “10p” file

CMPUT 603, Paul Berube

slide36

awk

See: Google

slide37
Awk
  • Used to process data in plain-text formats
  • C-like syntax
  • Can address file data by column
    • $> awk ‘{print $3}’ file

CMPUT 603, Paul Berube

slide38
Awk
  • Use to process data in plain-text formats
  • C-like syntax
  • Can address file data by column
  • Can perform math, has variables

awk ‘BEGIN \

{max = 0; min = 9999; cnt = 0; sum = 0} \

{ cnt++; sum += $1; \

if($1 > max) max = $1; \

if($1 < min) min = $1; } \

END \

{printf "%f %f %f\n", min, max, sum/cnt}’

CMPUT 603, Paul Berube

slide39
Awk
  • Use to process data in plain-text formats
  • C-like syntax
  • Can address file data by column
  • Can perform math, has variables

awk ‘BEGIN \

{max = 0; min = 9999; cnt = 0; sum = 0} \

{cnt++; sum += $1; \

if($1 > max) max = $1; \

if($1 < min) min = $1; } \

END \

{printf "%f %f %f\n", min, max, sum/cnt}’

CMPUT 603, Paul Berube

slide40
Awk
  • Use to process data in plain-text formats
  • C-like syntax
  • Can address file data by column
  • Can perform math, has variables

awk ‘BEGIN \

{max = 0; min = 9999; cnt = 0; sum = 0} \

{cnt++; sum += $1; \

if($1 > max) max = $1; \

if($1 < min) min = $1; } \

END \

{printf "%f %f %f\n", min, max, sum/cnt}’

CMPUT 603, Paul Berube

slide41
Awk
  • Use to process data in plain-text formats
  • C-like syntax
  • Can address file data by column
  • Can perform math, has variables

awk ‘BEGIN \

{max = 0; min = 9999; cnt = 0; sum = 0} \

{cnt++; sum += $1; \

if($1 > max) max = $1; \

if($1 < min) min = $1; } \

END \

{printf "%f %f %f\n", min, max, sum/cnt}’

CMPUT 603, Paul Berube

gnuplot

gnuplot

See: gnuplot webpage, Google

gnuplot1
gnuplot
  • Script-based 2D and 3D plotting
  • Many output formats, including eps
  • Graph functions and/or data from files
  • Apply functions to data in files before graphing

CMPUT 603, Paul Berube

gnuplot2
gnuplot

set term postscript eps

set output ‘sincos.eps’

set title “sin(x), cos(x)”

set xrange [-2*pi:2*pi]

plot sin(x) with lines, cos(x) with points

CMPUT 603, Paul Berube

putting it all together
Putting It All Together
  • A Script:
    • Build the program if needed
    • Run the program to simulate M experiments, each run N times
    • Calulate the min, max, and average of the N runs for each experiment
    • Graph the results
      • Max and min lines
      • Smooth average line
      • Each data point

CMPUT 603, Paul Berube

putting it all together1
Putting It All Together

Demo…

CMPUT 603, Paul Berube

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