doc: Add preliminary project documentation

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diff --git a/doc/.gitignore b/doc/.gitignore
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+*.aux
+*.log
+*.synctex.gz
+*.toc
diff --git a/doc/abstract.tex b/doc/abstract.tex
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+\chapter{Abstract}
+
+\TODO{Even needed?}
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diff --git a/doc/bibliography.bib b/doc/bibliography.bib
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+/Users/tklauser/Documents/BibTeX/UZH-Master Projektarbeit.bib
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diff --git a/doc/bibliography_additional.bib b/doc/bibliography_additional.bib
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+@book{Bernstein1967,
+author = {Bernstein, Nikolai A},
+title = {The co-ordination and regulation of movements},
+publisher = {Pergamon Press},
+year = {1967}
+}
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diff --git a/doc/conclusion.tex b/doc/conclusion.tex
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+\chapter{Conclusion}
+
+\TODO{Conclusion about work done}
+
+Thus OpenSim with the provided and used muscle-skeleton models is in its current state 
+not feasible for the simulation of tasks such as those that were subject of this project.
+
+\begin{itemize}
+	\item Precise EMG data from an actual subject (no averaged an processed patterns) would be needed in order to achieve realistic behavior in simulation with OpenSim.
+	\item Focus of OpenSim more on clinical applications where such data is available.
+	\item A more abstract muscoloskeletal model of a human would need to be developed in OpenSim, for such simulations, but is outside of the focus of this project. The OpenSim API would provide a decent foundation for developing such a model from scratch.
+	\item Ground contact forces would need to be incorporated (and provided by the study the project is based on).
+\end{itemize}
+
+More abstract models such as the ones used by Geyer and Herr \cite{Geyer2010}, Marques et al \cite{Marques2012a, Marques2012} might be more suitable.
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diff --git a/doc/discussion.tex b/doc/discussion.tex
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+\chapter{Discussion}
+
+Problems with data (missing ground contact forces), OpenSim more suited for analysis of precise data acquired in subject studies. Ground contact forces key to investigate walking.
+
+\section{Evaluation of OpenSim}
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diff --git a/doc/images/uzh_ifi_logo_e_pos.pdf b/doc/images/uzh_ifi_logo_e_pos.pdf
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diff --git a/doc/introduction.tex b/doc/introduction.tex
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+\chapter{Introduction}
+
+Controlling and learning to control movements of a many degree of freedom system such as the human body is a non-trivial task. This problem is famously known as Bernstein's problem \cite{Bernstein1967}.
+
+Complex movements of humans (and other animals) are thought to develop based on a simple, rudimentary set of building blocks -- commonly called motor primitives -- during ontogenetic development \cite{Flash2005, Hart2010}. Contrary to the hitherto belief that these innate simple reflexes get completely replaced by more complex ones with age, a recent publication by Dominici et al. \cite{Dominici2011} shows that certain basic patterns of muscle activation are instead retained and are being built upon during development in order to achieve a variety of walking movement behaviours.
+
+This project thesis attempts to investigate the role such locomotor primitives play in the development of human biped walking by building a muscoloskeletal simulation model in the OpenSim software \cite{Delp2007} and then applying the basic activation patterns at different stages of human development (neonate, toddlers, preschooler and adults) identified by Dominici et al. \cite{Dominici2011} to it.
+
+\TODO{Describe steps taken and goals of the individual steps.}
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diff --git a/doc/masterproject_klauser.tex b/doc/masterproject_klauser.tex
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+\documentclass[
+  a4paper,
+  11pt,
+  liststotoc,
+  bibtotoc,
+  appendixprefix,
+  final]{scrreprt}
+  
+\usepackage[latin1]{inputenc}
+\usepackage[english]{babel}
+
+\usepackage{geometry}
+\geometry{top=40mm,bottom=50mm,textwidth=142mm}
+
+\usepackage{hyperref}
+\usepackage[pdftex]{graphicx}
+
+\usepackage[citestyle=numeric-comp,doi=false,url=false,isbn=false]{biblatex}
+\addbibresource{bibliography.bib}
+\addbibresource{bibliography_additional.bib}
+
+\setlength{\parindent}{0cm}
+\setlength{\parskip}{0.3cm plus0.5mm minus0.5mm}
+
+\newcommand{\HRule}{\rule{\linewidth}{0.25mm}}
+\newcommand{\TODO}[1]{\textbf{TODO:} #1}
+
+\begin{document}
+
+%%%
+
+%\frontmatter
+\include{title}
+% One page completely empty: back side of title page
+\newpage
+\thispagestyle{empty}
+\mbox{}
+\pagebreak
+
+\include{abstract}
+% One page completely empty: back side of abstract
+\newpage
+\thispagestyle{empty}
+\mbox{}
+\pagebreak
+\tableofcontents
+
+%%%
+
+%\mainmatter
+\include{introduction}
+
+% Methods
+\include{methods}
+% Results
+\include{results}
+% Discussion
+\include{discussion}
+
+\include{conclusion}
+
+%%%
+
+\appendix
+\listoffigures
+\listoftables
+%\bibliographystyle{numeric-comp}
+%\bibliography{bibliography}
+\printbibliography
+
+\end{document}
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diff --git a/doc/methods.tex b/doc/methods.tex
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+\chapter{Methods}
+
+\section{Simulation Software}
+
+Simulation is performed using the OpenSim software platform \cite{Delp2007}. OpenSim is an open-source platform for modeling and analyzing neuromusculoskeletal structures and simulating their dynamic movement behavior. It's developed and maintained as part of the Simtk.org repository.
+
+The software provides an extensive application programming interface (API) in order to develop custom simulation controllers. Additionally it contains a graphical user interface (GUI) used to visualize simulations, edit models and muscle excitation data, as well as to access predefined simulation controllers.
+
+The provided controllers turned out to require a very specific data collection as input, which is typically generated during experiments using motion capturing systems and force plates.
+
+In the context of this project, no such data is generated or used, but we rather solely rely on relatively sparse muscle activation data and have no ground force measurements available. Also we are interested in general principles of movement rather than the detailed analysis of the walking behaviour of an individual subject.
+
+Thus a custom controller making use of the provided OpenSIM API was developed. This allows to specifically tune the simulation behavior to the requirements of this project and the data available.
+
+For all tasks performed as part of this project, version 3.0 of OpenSim was used as provided on \url{http://www.simtk.org}.
+
+\section{Muscoloskeletal Model}
+
+The muscoloskeletal model used in the project was developed based on the Gait2354 model provided with OpenSim 3.0. This is a 23-degree-of-freedom model of the human muscoloskeletal system. By default it contains 54 musclotendon actuators and represents a subject with a height of 1.8 m and a mass of 75.16 kg\footnote{More information on the Gait2354 model and its kinematic and dynamic properties as well as references to the studies the model is based on can be found on \url{http://simtk-confluence.stanford.edu:8080/display/OpenSim/Gait+2392+and+2354+Models}}.
+
+Gait model provided with OpenSim (\TODO{Add reference to paper describing model}), muscles removes where no data was available from the paper. Muscles which were measured in combination in the study (hamstring, \dots) needed to be properly accounted for.
+
+\TODO{Add Screenshot}
+
+In order to verify the principal working of the OpenSim model, random data was generated and applied to it.
+
+\section{Muscle Model}
+
+For all muscles in the model, the Thelen muscle model \cite{Thelen2003} was used. This model is the default muscle model used OpenSim 3.0\footnote{\TODO{Add note about deprecated model of same name from previous versions of OpenSim}} and is employed in all muscloloskeletal models provided with OpenSim. The Thelen muscle model is based on the well-known and widely used Hill muscle-tendon model (\TODO{add reference}), but incorporates adjustments in order to better account for age-related changes in the muscle properties.
+
+The behavior of the Thelen muscles can be tuned using various parameters, see table \ref{table:thelen2003_parameters}. These were left in their 
+
+\begin{table}[htb!]
+\label{table:thelen2003_parameters}
+\centering
+\begin{tabular}{|c|c|c|c|}
+\hline
+\textbf{Parameter} & \textbf{Description} & \textbf{Value range} & \textbf{Chosen Value} \\
+\hline
+\end{tabular}
+\caption{Parameters of the Thelen muscle model \cite{Thelen2003}}
+\end{table}%
+
+\section{Simulation Controller}
+
+\section{Data Preparation}
+
+Since the original data from the publication by Dominici et al. \cite{Dominici2011} could not be used, the respective pattern curves had to be extracted from the paper. In order to gather the data from there, a graph digitizer software (GraphClick by Arizona Software) was used. The data was then preprocessed by applying a curve interpolation in order to allow arbitrary, linearly spaced sampling of data points later on in the OpenSim model controller.
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diff --git a/doc/results.tex b/doc/results.tex
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+\chapter{Results}
+
+\section{Random Data}
+
+In order to validate the model and the developed controller, random data resembling muscle activation patterns was generated for all the 53 muscles of the model.
+
+\TODO{Add example plot}
+
+\section{Locomotor Primitives Study Data}
+
+\TODO{Add example plot}
+
+\TODO{Add example image sequence of simulation}
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diff --git a/doc/title.tex b/doc/title.tex
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+%
+% Title page
+%
+% Based on http://en.wikibooks.org/wiki/LaTeX/Title_Creation
+%
+
+\begin{titlepage}
+
+	\begin{center}
+
+	\includegraphics[width=0.6\textwidth]{images/uzh_ifi_logo_e_pos.pdf}\\
+	\vspace*{1.5ex}
+	\ \\
+	Artificial Intelligence Laboratory
+	\ \\
+	\ \\
+	\vspace*{1.5ex}	
+	\HRule
+
+	\vspace*{10ex}
+
+	% textsc is small caps
+	\textsc{\Large
+	%
+	Master Project Report\\
+	\ \\}
+	%
+	% the title
+	%
+	{\huge \bfseries
+	Simulation of the Ontogenetic Development of Human Biped Walking
+	\\}
+	\vspace*{2ex}
+	\ \\
+	\ \\
+	\ \\
+	
+	\HRule
+
+	\vspace*{2ex}
+	\ \\
+	\ \\
+	\ \\
+
+	% split the page into two columns
+	% left column
+	\begin{minipage}[t]{0.48\textwidth}
+	\begin{flushleft} \large
+	\emph{Author:}\\
+	Tobias Klauser\\
+	%Winterthur, Switzerland\\
+	Registration Number: 05-535-927
+	\end{flushleft}
+	\end{minipage}
+	%
+	% right column
+	\begin{minipage}[t]{0.48\textwidth}
+	\begin{flushright} \large
+	\emph{Supervised by:} \\
+	Prof. Dr. Rolf Pfeifer\\
+	Dr. Hugo Gravato Marques\\
+	% ensure vertical alignment with LHS
+	\footnotesize{\ }
+	\end{flushright}
+	\end{minipage}
+
+	\vspace*{15ex}
+	%
+	\vfill % fill vertical space
+	%
+	% Bottom of the page
+	% \today is the compilation date
+	{\large \today}
+	%
+	\end{center}
+\end{titlepage}
+