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MastodonManual.tex
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\documentclass[numbers=endperiod]{scrartcl}
% Tickz.
\usepackage{tikz}
\usetikzlibrary{shapes}
\usetikzlibrary{arrows}
\usetikzlibrary{decorations.pathreplacing}
\usetikzlibrary{fit}
\usetikzlibrary{positioning}
\usetikzlibrary{shadows}
\usetikzlibrary{calc}
\usetikzlibrary{backgrounds}
\usetikzlibrary{matrix}
% Algorithms.
\usepackage[vlined,ruled]{algorithm2e}
% Fonts.
\usepackage{libertine}
\usepackage[libertine]{newtxmath}
\renewcommand{\familydefault}{\sfdefault}
\usepackage[T1]{fontenc}
\usepackage[utf8]{inputenc}
\usepackage{courier}
\usepackage[scaled=.75]{beramono}
% Decorate key bindings and menu paths.
\usepackage{menukeys}
% Several figures in a figure.
\usepackage{subfig}
% Tables.
\usepackage{tabulary}
\usepackage{booktabs}
% Links.
\usepackage{hyperref}
\PassOptionsToPackage{hyphens}{url}
\usepackage[htt]{hyphenat}
% Colored links.
\newcommand\coloredlink[1]{\textcolor{blue!75!black}{\underline{\smash{#1}}}}
\newcommand\wikilink[2]{\href{http://imagej.net/#1}{\coloredlink{#2}}}
% Epigraph.
\usepackage{epigraph}
% Test math symbols.
\usepackage{textcomp}
% Small images in text (for e.g. small icon).
\newcommand*{\smallimg}[1]{%
\raisebox{-.1\baselineskip}{%
\includegraphics[
height=0.7\baselineskip,
width=\baselineskip,
keepaspectratio,
]{figures/#1}%
}%
}
% Properly hyphen TrackMate & TrackScheme & friends
\newcommand\TrackScheme[0]{Track\-Scheme\ }
\newcommand\TrackMate[0]{Track\-Mate\ }
\newcommand{\bdv}{BigDataViewer\ }
\newcommand{\Bdv}{BigDataViewer\ }
\newcommand{\Ie}{\textit{I.e.{}}\ }
\newcommand{\Eg}{\textit{E.g.{}}\ }
\newcommand{\Cf}{\textit{Cf.{}}\ }
\newcommand{\ie}{\textit{i.e.{}}\ }
\newcommand{\eg}{\textit{e.g.{}}\ }
\newcommand{\cf}{\textit{cf.{}}\ }
\newcommand{\etc}{\textit{etc}\ }
\newcommand{\etal}{\emph{et~al.}}
% Making 1.5 spaced lines
\usepackage{setspace}
\onehalfspacing
% More space between paragraphs and indent.
\setlength{\parskip}{6pt}
\setlength\parindent{24pt}
% Syntax highlighting
\usepackage{listings}
\usepackage{lstautogobble} % Fix relative indenting
\usepackage{color} % Code coloring
\usepackage{zi4} % Nice font
\definecolor{bluekeywords}{rgb}{0.13, 0.13, 1}
\definecolor{greencomments}{rgb}{0, 0.5, 0}
\definecolor{redstrings}{rgb}{0.9, 0, 0}
\definecolor{graynumbers}{rgb}{0.5, 0.5, 0.5}
\lstset{
autogobble,
columns=fullflexible,
showspaces=false,
showtabs=false,
breaklines=true,
showstringspaces=false,
breakatwhitespace=true,
escapeinside={(*@}{@*)},
commentstyle=\color{greencomments},
keywordstyle=\color{bluekeywords},
stringstyle=\color{redstrings},
numberstyle=\color{graynumbers},
basicstyle=\ttfamily\footnotesize,
frame=l,
framesep=12pt,
xleftmargin=12pt,
tabsize=4,
captionpos=b
}
% Figure caption with special fonts.
\usepackage[font=small,labelfont=bf,format=plain]{caption}
% Smaller margins. Paper is expensive and we write in big characters.
\usepackage[margin=1in]{geometry}
%---------------------------------------------------------------------------------
% Contents
%---------------------------------------------------------------------------------
\begin{document}
\input{src/TitlePage.tex}
% Introduction and generalities about Mastodon.
\newpage
\input{src/Preamble.tex}
\newpage
\tableofcontents
\newpage
\part{Using Mastodon.}
% Automated tracking.
\newpage
\input{src/Chapter_A1.tex}
% Manual tracking. TrackScheme.
\newpage
\input{src/Chapter_A2.tex}
% Orienting in Mastodon.
\newpage
\input{src/Chapter_A3.tex}
% Feature, tags and tables.
\newpage
\input{src/Chapter_A4.tex}
% Semi automated-tracking.
\newpage
\input{src/Chapter_A5.tex}
% Selection editor.
\newpage
\input{src/Chapter_A6.tex}
\newpage
\part{Mastodon interoperability.}
\vfill
\setlength{\epigraphwidth}{0.45\textwidth}
\epigraph{
\textit{My mistress' eyes are nothing like the sun; \\
Coral is far more red than her lips' red;\\
If snow be white, why then her breasts are dun;\\
If hairs be wires, black wires grow on her head;\\
I have seen roses damasked, red and white,\\
But no such roses see I in her cheeks;\\
And in some pérfumes is there more delight\\
Than in the breath that from my mistress reeks.\\
I love to hear her speak, yet well I know\\
That music hath a far more pleasing sound.\\
I grant I never saw a goddess go;\\
My mistress, when she walks, treads on the ground.\\
\quad And yet, by heaven, I think my love as rare\\
\quad As any she belied with false compare.}}
{William Shakespeare}
\newpage
\part{Extending Mastodon.}
\vfill
\setlength{\epigraphwidth}{0.35\textwidth}
\epigraph{
\textit{As palavras, senhor, estão por aí, no ar, qualquer as pode aprender.}
}{José Saramago}
\newpage
\part{Technical information.}
\vfill
\epigraph{
\textit{Frères humains qui après nous vivez \\
N'ayez les cœurs contre nous endurcis, \\
Car, se pitié de nous pauvres avez, \\
Dieu en aura plus tost de vous merciz.}
}{Francois Villon}
% Technical description of features.
\newpage
\input{src/Chapter_D1.tex}
% The graph of Mastodon.
\newpage
\input{src/Chapter_D2.tex}
% KD-tree searched on Convex polytopes.
\newpage
\input{src/Chapter_D3.tex}
\newpage
\bibliographystyle{ieeetr}
\clearpage
\bibliography{References}
\end{document}
% vim::set expandtab tabstop=4 softtabstop=2 shiftwidth=2 ft=tex: