Commit 14f7fbee authored by Mark van Turnhout's avatar Mark van Turnhout
Browse files

split into main file and chapter files. added quotes (could not resist...)

parent b6e36d2e
......@@ -6,6 +6,14 @@
\href{https://www.ncbi.nlm.nih.gov/pubmed/#1}{#1}}
\addcontentsline{toc}{chapter}{\protect\numberline{\color{white}}{\refname}}
\bibitem{Armstrong1995}
Sarah~J. Armstrong, Richard~A. Read and Roger Price.
\newblock {T}opographical variation within the articular cartilage and
subchondral bone of the normal ovine knee joint: a histological approach.
\newblock \emph{Osteoarthritis \& Cartilage}, \textbf{3}(1):25--33, March 1995.
\newblock \pmid{7719953}.
\newblock \doi{10.1016/S1063-4584(05)80035-4}.
\bibitem{Ceelen2008}
K.K. Ceelen, A.~Stekelenburg, S.~Loerakker, G.J. Strijkers, D.L. Bader,
K.~Nicolay, F.P.T. Baaijens and C.W.J. Oomens.
......@@ -15,6 +23,16 @@ K.K. Ceelen, A.~Stekelenburg, S.~Loerakker, G.J. Strijkers, D.L. Bader,
\newblock \pmid{19010470}.
\newblock \doi{10.1016/j.jbiomech.2008.09.016}.
\bibitem{Dawkins2009}
Richard Dawkins.
\newblock \emph{{T}he greatest show on earth -- the evidence for evolution}.
\newblock Bantam publishers, p. 230, 1$^\text{st}$ edition, 2009.
\bibitem{Feynman2006}
Richard~P. Feynman.
\newblock \emph{{QED} -- the strange theory of light and matter}.
\newblock Princeton University Press, Princeton, New Jersey, 2006.
\bibitem{Loerakker2011a}
S.~Loerakker, E.~Manders, G.J. Strijkers, K.~Nicolay, F.P.T. Baaijens, D.L.
Bader and C.W.J. Oomens.
......
......@@ -97,92 +97,9 @@
\mainmatter
\chapter{Introduction}
Pressure ulcers are localised injuries to the skin and/or underlying tissue due to mechanical loading. Deep Tissue Injury is a severe type of pressure ulcer originating subcutaneously. To better understand the aetiology of Deep Tissue Injury, \href{https://www.tue.nl/stbe}{our group} studies physiological changes due to mechanical loading in a rat model \cite{Loerakker2010,Loerakker2011,Loerakker2011a,Oomens2010,Nierop2010,Ceelen2008, Stekelenburg2006, Stekelenburg2006a, Stekelenburg2007}. In this rat model, the animal's tibialis anterior muscle is deformed with an indenter inside a magnetic resonance (MR) imaging scanner. MR imaging allows for assessment of physiological changes, e.g. (re)perfusion and tissue damage, due to the deformation of the muscle. Animal specific finite element (FE) models are used to assess the relationship between the mechanical internal tissue state and tissue damage in the rat model.
Until recently, (animal specific) FE analysis of the experiments was restricted to cross sectional (2D) FE models. In the current project \textsl{Non-invasive monitoring of deep tissue injury} \cite{Traa2015} the aim is to extend a previously developed cross sectional (2D) FE models \cite{Loerakker2010} to a FE model of the complete leg (i.e.\ 3D) \cite{Traa2014}. The first objective of these animal specific full leg 3D models is to assess the shortcomings of cross sectional 2D modelling (or: to assess what extra information can be obtained by switching to full leg 3D modelling).\\
\noindent BasilLab is a collection of scripts to facilitate the animal specific full leg 3D modelling of these experiments.
% \nocite{Loerakker2013,Loerakker2012,Loerakker2011,Loerakker2011a,Loerakker2010,Oomens2010,Nagel2009,Nierop2010,Ceelen2008,Ceelen2008a,Stekelenburg2006,Stekelenburg2006a,Stekelenburg2007}
\section{Software}\label{sec:software}
BasilLab consists of a number of (pre-processing) Matlab-scripts that extract information from the MR images of the experiments and subsequently write a python script that can be fed to Abaqus: the FE software that runs the analysis. Parts of the pre-processing, in particular the segmentation of the MR images, rely on the \gibbon{} toolbox\footnote{``The Geometry and Image-Based Bioengineering add-On''. Source available from \href{https://github.com/Kevin-Mattheus-Moerman/GIBBON}{https://github.com/Kevin-Mattheus-Moerman/GIBBON}} developed by Kevin Moerman \cite[\href{http://kevinmoerman.org/portfolio/gibbon/}{http://kevinmoerman.org/ portfolio/gibbon/}]{Moerman2013}.
Next to the pre-processing Matlab scripts, a number of python scripts is provided to extract model results from the Abaqus output file. These results can be easily fed back to Matlab for post-processing puposes\footnote{Other than these python scripts to write the Abaqus results to a Matlab- and human-readable text file, no post-processing is provided in BasilLab.}.
\begin{table}[h!]
\center
\caption{Software used for development and testing of BasilLab.}\label{tab:software}
\begin{tabulary}{\linewidth}{l l R}
\hline\noalign{\smallskip}
Name & author & tested with version\\
\noalign{\smallskip}\hline\noalign{\bigskip}
Abaqus/Simulia & \href{http://www.3ds.com/products-services/simulia/products/abaqus/}{Dassault Syst{\`e}mes} & Abaqus 6.14-1 \\
Matlab & \href{http://www.mathworks.com/products/matlab/}{MathWorks} & MATLAB Version: 8.2.0.701 (R2013b)\\
\gibbon & \href{https://github.com/Kevin-Mattheus-Moerman/GIBBON}{Kevin Mattheus Moerman} &See listing \ref{Gibbonversion} \\
\noalign{\smallskip}\hline
\end{tabulary}
\end{table}
\begin{lstlisting}[numbers=none, language=bash, float, caption={First three lines of the Git log for \gibbon, showing the version ('commit') that was used to develop and test BasilLab.}, label=Gibbonversion]
mark@telab11:~/git/gibbon$ git log | head -n 3
commit c060143843d1d6f30ee39ddab1d65c6731a0c83e
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; 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 when you read the element volume from the Abaqus output, this volume is in mm\ap{3}.\\
\noindent See also section `1.2.2 Conventions' in the Abaqus Analysis User's Guide of the \adoc{} and the \href{http://furnace.wfw.wtb.tue.nl:2080/v6.14/books/popups/usb-tbl.html}{Conversion Tables, Constants, and Material Properties} provided by Abaqus.
\section{Large displacements and logarithmic strain}
The FE models are analysed with Abaqus' `Large Displacement' option for geometrically non-linear problems. As a result, Abaqus will output \textsl{logarithmic} strains `LE':
\begin{equation}
\text{LE} = \epsilon^\text{L} = \ln V = \sum_{i=1}^3 \ln \lambda_i \ten{n}_i {\ten{n}_i}^\text{T}
\end{equation}
When you use a hyperelastic material law (such as the Ogden material model that is used in BasilLab), Abaqus will also output the logarithmic strains `LE'. See section `1.2.2 Conventions' in the Abaqus Analysis User's Guide of the \adoc{}.
\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 adapt 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>}.
\include{introduction}
\include{conventions}
\include{workflow}
\def\bibname{References}
%\begin{savequote}
......
% !TeX root = BasilLab.tex
\begin{savequote}
I have pointed out these things because the more you see how strangely Nature behaves, the harder it is to make a model that explains how even the simplest phenomena actually work. So theoretical physics has given up on that. \qauthor{Richard P.\ Feynman \cite{Feynman2006} }
\end{savequote}
\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 when you read the element volume from the Abaqus output, this volume is in mm\ap{3}.\\
\noindent See also section `1.2.2 Conventions' in the Abaqus Analysis User's Guide of the \adoc{} and the \href{http://furnace.wfw.wtb.tue.nl:2080/v6.14/books/popups/usb-tbl.html}{Conversion Tables, Constants, and Material Properties} provided by Abaqus.
\section{Large displacements and logarithmic strain}
The FE models are analysed with Abaqus' `Large Displacement' option for geometrically non-linear problems. As a result, Abaqus will output \textsl{logarithmic} strains `LE':
\begin{equation}
\text{LE} = \epsilon^\text{L} = \ln V = \sum_{i=1}^3 \ln \lambda_i \ten{n}_i {\ten{n}_i}^\text{T}
\end{equation}
When you use a hyperelastic material law (such as the Ogden material model that is used in BasilLab), Abaqus will also output the logarithmic strains `LE'. See section `1.2.2 Conventions' in the Abaqus Analysis User's Guide of the \adoc{}.
\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 adapt 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>}.
\ No newline at end of file
% !TeX root = BasilLab.tex
\begin{savequote}
The use of an ovine model circumvents the ethical and financial problems associated with the use of bipedal animal models. \qauthor{Armstrong, Read \& Price \cite{Armstrong1995} }
\end{savequote}
\chapter{Introduction}
Pressure ulcers are localised injuries to the skin and/or underlying tissue due to mechanical loading. Deep Tissue Injury is a severe type of pressure ulcer originating subcutaneously. To better understand the aetiology of Deep Tissue Injury, \href{https://www.tue.nl/stbe}{our group} studies physiological changes due to mechanical loading in a rat model \cite{Loerakker2010,Loerakker2011,Loerakker2011a,Oomens2010,Nierop2010,Ceelen2008, Stekelenburg2006, Stekelenburg2006a, Stekelenburg2007}. In this rat model, the animal's tibialis anterior muscle is deformed with an indenter inside a magnetic resonance (MR) imaging scanner. MR imaging allows for assessment of physiological changes, e.g. (re)perfusion and tissue damage, due to the deformation of the muscle. Animal specific finite element (FE) models are used to assess the relationship between the mechanical internal tissue state and tissue damage in the rat model.
Until recently, (animal specific) FE analysis of the experiments was restricted to cross sectional (2D) FE models. In the current project \textsl{Non-invasive monitoring of deep tissue injury} \cite{Traa2015} the aim is to extend a previously developed cross sectional (2D) FE models \cite{Loerakker2010} to a FE model of the complete leg (i.e.\ 3D) \cite{Traa2014}. The first objective of these animal specific full leg 3D models is to assess the shortcomings of cross sectional 2D modelling (or: to assess what extra information can be obtained by switching to full leg 3D modelling).\\
\noindent BasilLab is a collection of scripts to facilitate the animal specific full leg 3D modelling of these experiments.
% \nocite{Loerakker2013,Loerakker2012,Loerakker2011,Loerakker2011a,Loerakker2010,Oomens2010,Nagel2009,Nierop2010,Ceelen2008,Ceelen2008a,Stekelenburg2006,Stekelenburg2006a,Stekelenburg2007}
\section{Software}\label{sec:software}
BasilLab consists of a number of (pre-processing) Matlab-scripts that extract information from the MR images of the experiments and subsequently write a python script that can be fed to Abaqus: the FE software that runs the analysis. Parts of the pre-processing, in particular the segmentation of the MR images, rely on the \gibbon{} toolbox\footnote{``The Geometry and Image-Based Bioengineering add-On''. Source available from \href{https://github.com/Kevin-Mattheus-Moerman/GIBBON}{https://github.com/Kevin-Mattheus-Moerman/GIBBON}} developed by Kevin Moerman \cite[\href{http://kevinmoerman.org/portfolio/gibbon/}{http://kevinmoerman.org/ portfolio/gibbon/}]{Moerman2013}.
Next to the pre-processing Matlab scripts, a number of python scripts is provided to extract model results from the Abaqus output file. These results can be easily fed back to Matlab for post-processing puposes\footnote{Other than these python scripts to write the Abaqus results to a Matlab- and human-readable text file, no post-processing is provided in BasilLab.}.
\begin{table}[h!]
\center
\caption{Software used for development and testing of BasilLab.}\label{tab:software}
\begin{tabulary}{\linewidth}{l l R}
\hline\noalign{\smallskip}
Name & author & tested with version\\
\noalign{\smallskip}\hline\noalign{\bigskip}
Abaqus/Simulia & \href{http://www.3ds.com/products-services/simulia/products/abaqus/}{Dassault Syst{\`e}mes} & Abaqus 6.14-1 \\
Matlab & \href{http://www.mathworks.com/products/matlab/}{MathWorks} & MATLAB Version: 8.2.0.701 (R2013b)\\
\gibbon & \href{https://github.com/Kevin-Mattheus-Moerman/GIBBON}{Kevin Mattheus Moerman} &See listing \ref{Gibbonversion} \\
\noalign{\smallskip}\hline
\end{tabulary}
\end{table}
\begin{lstlisting}[numbers=none, language=bash, float, caption={First three lines of the Git log for \gibbon, showing the version ('commit') that was used to develop and test BasilLab.}, label=Gibbonversion]
mark@telab11:~/git/gibbon$ git log | head -n 3
commit c060143843d1d6f30ee39ddab1d65c6731a0c83e
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; 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}. Feel free to copy and share this software.
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}.
% !TeX root = BasilLab.tex
\begin{savequote}
In the computer model, all the microfilaments were given certain quantitative properties with names that mean something to physicists: a `viscous damping coefficient' and an `elastic spring constant'. Never mind exactly what these mean: they are the kind of things physicists like to measure in a spring. \qauthor{Richard Dawkins \cite{Dawkins2009}}
\end{savequote}
\chapter{Workflow}
\ No newline at end of file
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