Commit a7875e1b authored by matecellab's avatar matecellab
Browse files

update documentation

parent 47e44ae7
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% document specific conventions
\newcommand\gibbon{GIBB\textsl{On}}
\newcommand\warning{\marginpar{\center\includegraphics[width=1cm]{Exclamation.png}\\}}
% \renewcommand{\thesubsection}{\thesection.\alph{subsection}}
% the books notation conventions
%\renewcommand{\ten}[2][]{%
......@@ -130,11 +131,47 @@ Author: Kevin Mattheus Moerman <Kevin-Mattheus-Moerman@users.noreply.github.com>
Date: Tue Jul 7 15:09:39 2015 +0200
\end{lstlisting}
Both Matlab and Abaqus suffer from (in)compatibility issues between software versions. The \gibbon{} toolbox does not work well with Matlab R2012b or lower. Abaqus recently changed the formulation of some python commands that we use and the current scripts e.g.\ do not work with Abaqus version 6.11. See table \eqref{tab:software} and listing \eqref{Gibbonversion} for the software versions that were used to develop and test BasilLab.
Both Matlab and Abaqus suffer from (in)compatibility issues between software versions. The \gibbon{} toolbox does not work well with Matlab R2012b or lower; and the Matlab command \texttt{DelaunayTri} will be removed from a future release. Abaqus recently changed the formulation of some python commands that we use and the current scripts e.g.\ do not work with Abaqus version 6.11. See table \eqref{tab:software} and listing \eqref{Gibbonversion} for the software versions that were used to develop and test BasilLab.
\section{License and availability}
BasilLab is released under a \href{https://creativecommons.org/licenses/by-nc/2.5/}{Creative Commons Attribution-NonCommercial 2.5 License}. This means you're free to copy and share this software (but not to sell them).
Note that there is ABSOLUTELY NO WARRANTY; not even for FITNESS FOR A PARTICULAR PURPOSE, and certainly not for MERCHANTABILITY.\warning\\
\noindent BasilLab is available from the \href{mailto:m.c.v.turnhout@tue.nl}{author}. BasilLab is maintained in a Git repository that is hosted at \href{https://bitbucket.org/matecellab/mylab}{BitBucket}. If you wish to have access to that Git repository, again: contact the \href{mailto:m.c.v.turnhout@tue.nl}{author}.
\chapter{Conventions}
\section{Spatial dimensions}
All spatial dimensions of the FE model are in mm, both for input and output. Thus, if you supply e.g.\ a stiffness parameter, you should convert it from N/m\ap{2} to N/mm\ap{2}:
\begin{equation}
E = 15.6\,\text{kPa} = 15600\,{\text{N}}/{\text{m}^2} = 0.0156\,{\text{N}}/{\text{mm}^2}
\end{equation}
And if you read the element volume from the Abaqus output, this volume is in mm\ap{3}.
\section{Directory structure}
BasilLab requires knowledge on two directories: one \texttt{<MRI-root>} where the (raw) MRI-data can be found, and one \texttt{<basilhome>} where the processed MRI-data and model data can be found. Raw MRI-data for each individual experiment/animal should be stored in a unique folder \textsl{inside} \texttt{<MRI-root>}. Processed MRI-data and model data is stored \textsl{inside} a unique folder in \texttt{<basilhome>}.
The link between the unique raw MRI-data folder inside \texttt{<MRI-root>} and the unique folder for model data inside \texttt{<basilhome>} is \textsl{hard-coded} in \texttt{bas\_getMeta.m}. When you add animals/experiments or rename certain directories, you will have to adopt this file.
Each animal/experiment should have unique \textsl{numerical} identifier \texttt{<basilid>}. BasilLab calls \texttt{bas\_getMeta.m} to find out where the raw MRI-data is stored for \texttt{<basilid>}, and it will look for \texttt{<basilhome>/<basilid>/} to store and read modelling data. Currently, the unique \texttt{<basilid>} is the date of the experiment in \texttt{yymmdd}-format.\\
Thus, for the experiment performed on June 11\ap{th} 2015
\begin{description}
\item[experiment identifier] \texttt{<basilid> = 140611}
\item[model data] is stored and sought in \texttt{<basilhome>/140611/}
\item[raw MRI-data] is stored in \texttt{<MRI-root>/140611.qd1/}
\item[the link] between \texttt{<basilid> = 140611} and raw MRI-data is stored in \texttt{<MRI-root>/140611.qd1/} is hard-coded in \texttt{bas\_getMeta.m}
\end{description}
\noindent BasilLab provides \texttt{bas\_setMRIroot.m} to set \texttt{<MRI-root>} and \texttt{bas\_setDataRoot.m} to set \texttt{<basilhome>}.
\def\bibname{References}
%\begin{savequote}
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