Commit faea2f28 authored by Mark van Turnhout's avatar Mark van Turnhout
Browse files

added extract-documentation

parent a2fa0b36
\newcommand{\noopsort}[1]{}
\begin{thebibliography}{10}
\begin{thebibliography}{1}
\providecommand{\noopsort}[1]{}
\providecommand{\doi}[1]{doi: \href{https://dx.doi.org/#1}{#1}}
\providecommand{\doi}[1]{doi: \href{http://dx.doi.org/#1}{#1}}
\providecommand{\pmid}[1]{pmid:
\href{https://www.ncbi.nlm.nih.gov/pubmed/#1}{#1}}
\href{http://www.ncbi.nlm.nih.gov/pubmed/#1}{#1}}
\addcontentsline{toc}{chapter}{\protect\numberline{\color{white}}{\refname}}
\bibitem{Armstrong1995}
......@@ -14,24 +14,6 @@ Sarah~J. Armstrong, Richard~A. Read and Roger Price.
\newblock \pmid{7719953}.
\newblock \doi{10.1016/S1063-4584(05)80035-4}.
\bibitem{Bosboom2003}
E.M.H. Bosboom, C.V.C. Bouten, C.W.J. Oomens, F.P.T. Baaijens and K.~Nicolay.
\newblock {Q}uantifying pressure sore-related muscle damage using
high-resolution {MRI}.
\newblock \emph{Journal of Applied Physiology}, \textbf{95}(6):2235--2240,
December 2003.
\newblock \pmid{12819217}.
\newblock \doi{10.1152/japplphysiol.01023.2001}.
\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.
\newblock {C}ompression-induced damage and internal tissue strains are related.
\newblock \emph{Journal of Biomechanics}, \textbf{41}(16):3399--3404, December
2008.
\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}.
......@@ -42,106 +24,4 @@ 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.
\newblock {T}he effects of deformation, ischemia, and reperfusion on the
development of muscle damage during prolonged loading.
\newblock \emph{Journal of Applied Physiology}, \textbf{111}(4):1168--1177,
October 2011.
\newblock \pmid{21757578}.
\newblock \doi{10.1152/japplphysiol.00389.2011}.
\bibitem{Loerakker2011}
S.~Loerakker, C.W.J. Oomens, E.~Manders, T.~Schakel, D.L. Bader, F.P.T.
Baaijens, K.~Nicolay and G.J. Strijkers.
\newblock {I}schemia-reperfusion injury in rat skeletal muscle assessed with
{T}2-weighted and dynamic contrast-enhanced {MRI}.
\newblock \emph{Magnetic Resonance In Medicine}, \textbf{66}(2):528--537,
August 2011.
\newblock \pmid{21360588}.
\newblock \doi{10.1002/mrm.22801}.
\bibitem{Loerakker2010}
S.~Loerakker, A.~Stekelenburg, G.J. Strijkers, J.J.M. Rijpkema, F.P.T.
Baaijens, D.L. Bader, K.~Nicolay and C.W.J. Oomens.
\newblock {T}emporal effects of mechanical loading on deformation-induced
damage in skeletal muscle tissue.
\newblock \emph{Annals of Biomedical Engineering}, \textbf{38}(8):2577--2587,
August 2010.
\newblock \pmid{20232152}.
\newblock \doi{10.1007/s10439-010-0002-x}.
\bibitem{Moerman2013}
Kevin~M. Moerman, Aart~J. Nederveen and Ciaran~K. Simms.
\newblock {I}mage based model construction, boundary condition specification
and inverse {FEA} control: a basic {M}atlab toolkit for {FEB}io.
\newblock In: \emph{Proceedings of the 11th International Symposium on Computer
Methods in Biomechanics and Biomedical Engineering}. Salt Lake City, Utah,
USA, April 2013.
\bibitem{Nierop2010}
Bastiaan~J. \noopsort{Nierop}van Nierop, Anke Stekelenburg, Sandra Loerakker,
Cees~W. Oomens, Dan Bader, Gustav~J. Strijkers and Klaas Nicolay.
\newblock {D}iffusion of water in skeletal muscle tissue is not influenced by
compression in a rat model of deep tissue injury.
\newblock \emph{Journal of Biomechanics}, \textbf{43}(3):570--575, February
2010.
\newblock \pmid{19897200}.
\newblock \doi{10.1016/j.jbiomech.2009.07.043}.
\bibitem{Oomens2010}
C.W.J. Oomens, Sandra Loerakker and D.L. Bader.
\newblock {T}he importance of internal strain as opposed to interface pressure
in the prevention of pressure related deep tissue injury.
\newblock \emph{Journal of tissue viability}, \textbf{19}(2):35--42, May 2010.
\newblock \pmid{20005716}.
\newblock \doi{10.1016/j.jtv.2009.11.002}.
\bibitem{Stekelenburg2006}
A.~Stekelenburg, C.W.J. Oomens, G.J. Strijkers, L.~\noopsort{Graaf}de Graaf,
D.L. Bader and K.~Nicolay.
\newblock {A} new {MR}-compatible loading device to study in vivo muscle damage
development in rats due to compressive loading.
\newblock \emph{Medical Engineering and Physics}, \textbf{28}(4):331--338, May
2006.
\newblock \pmid{16118060}.
\newblock \doi{10.1016/j.medengphy.2005.07.005}.
\bibitem{Stekelenburg2006a}
A.~Stekelenburg, C.W.J. Oomens, G.J. Strijkers, K.~Nicolay and D.L. Bader.
\newblock {C}ompression-induced deep tissue injury examined with magnetic
resonance imaging and histology.
\newblock \emph{Journal of Applied Physiology}, \textbf{100}(6):1946--1954,
June 2006.
\newblock \pmid{16484364}.
\newblock \doi{10.1152/japplphysiol.00889.2005}.
\bibitem{Stekelenburg2007}
Anke Stekelenburg, Gustav~J. Strijkers, Henry Parusel, Dan~L. Bader, Klaas
Nicolay and Cees~W. Oomens.
\newblock {R}ole of ischemia and deformation in the onset of
compression-induced deep tissue injury: {MRI}-based studies in a rat model.
\newblock \emph{Journal of Applied Physiology}, \textbf{102}(5):2002--2011, May
2007.
\newblock \pmid{17255369}.
\newblock \doi{10.1152/japplphysiol.01115.2006}.
\bibitem{Traa2015}
W.A. Traa, D.L. Bader and C.W.J. Oomens.
\newblock \href{http://repository.tue.nl/posters/801419.pdf}{Non-invasive
monitoring of pressure ulcer formation.}
\newblock Annual MaTe Poster Award of the Materials Technology (MaTe) group
(Eindhoven University of Technology, Eindhoven, The Netherlands), December
2015.
\bibitem{Traa2014}
W.A. Traa, J.L. Nelissen, K.M. Moerman, F.P.T. Baaijens, D.L. Bader and C.W.J.
Oomens.
\newblock \href{http://repository.tue.nl/posters/783267.pdf}{Investigating deep
tissue injury with MRI based 3D FEA.}
\newblock Annual MaTe Poster Award of the Materials Technology (MaTe) group
(Eindhoven University of Technology, Eindhoven, The Netherlands), December
2014.
\end{thebibliography}
......@@ -271,10 +271,48 @@ As with building and running the FE model, post-processing works in the current
Since \texttt{basil<basilid>.odb\index{basil<basilid>.odb@\texttt{basil<basilid>.odb}}} is only readable for Abaqus, BasilLab provides some Abaqus python scripts to extract simulation data from this file. The data that is read from the \texttt{odb}-file is written to a text-file that can easily be fed to your favorite post-processing software (Matlab).
Note that only results for the soft tissue in the model are extracted, results for the indenter or the cast are not processed.\\
\noindent The python script \texttt{extract\_topology.py\index{extract\_topology.py@\texttt{extract\_topology.py}}} writes the mesh toplogy for \texttt{basil\-<basilid>.odb\index{basil<basilid>.odb@\texttt{basil<basilid>.odb}}} to the file \texttt{basil<basilid>.top\index{basil<basilid>.top@\texttt{basil<basilid>.top}}}. This file contains a row for each element in the soft tissue set with the format:
\begin{framed}
\texttt{element number}, \texttt{node number 1}, \texttt{node number 2}, \texttt{node number 3}, \dots, \texttt{node number n}
\end{framed}
The length of each row depends on the number of nodes \texttt{n} for the specific element. \\
\noindent The python script \texttt{extract\_COORD.py\index{extract\_COORD.py@\texttt{extract\_COORD.py}}} writes the node coordinates for \texttt{basil\-<basilid>.odb\index{basil<basilid>.odb@\texttt{basil<basilid>.odb}}} to the file \texttt{basil<basilid>.xyz\index{basil<basilid>.xyz@\texttt{basil<basilid>.xyz}}}. This file contains a row for each node at the start of the simulation and at the end of the simulation with the format
\begin{framed}
\texttt{time}, \texttt{node number}, \texttt{x-coordinate}, \texttt{y-coordinate}, \texttt{z-coordinate}
\end{framed}
The \texttt{time} at the start of the simulation is \texttt{0}, the \texttt{time} at the end of the simulation is the \textsl{step} time of the last (indentation) step in the FEM\footnote{With the default settings (see chapter \ref{buildfem}) this step lasts 100\,s. If you find any other \texttt{time} than that step duration, the simulation did not converge.}. Coordinates are in mm.\\
\noindent The python script \texttt{extract\_EVOL.py\index{extract\_EVOL.py@\texttt{extract\_EVOL.py}}} writes the element volumes for \texttt{basil\-<basilid>.odb\index{basil<basilid>.odb@\texttt{basil<basilid>.odb}}} to the file \texttt{basil<basilid>.evol\index{basil<basilid>.evol@\texttt{basil<basilid>.evol}}}. This file contains a row for each element at the start of the simulation and at the end of the simulation with the format
\begin{framed}
\texttt{time}, \texttt{element number}, \texttt{element volume}
\end{framed}
The \texttt{time} at the start of the simulation is \texttt{0}, the \texttt{time} at the end of the simulation is the \textsl{step} time of the last (indentation) step in the FEM. Volumes are in mm$^3$.\\
\noindent The python script \texttt{extract\_ELSE.py\index{extract\_ELSE.py@\texttt{extract\_ELSE.py}}} writes the strain energy per element for \texttt{basil\-<basilid>.odb\index{basil<basilid>.odb@\texttt{basil<basilid>.odb}}} to the file \texttt{basil<basilid>.sen\index{basil<basilid>.sen@\texttt{basil<basilid>.sen}}}. This file contains a row for each element at the end of the simulation with the format
\begin{framed}
\texttt{time}, \texttt{element number}, \texttt{strain energy}
\end{framed}
The \texttt{time} at the end of the simulation is the \textsl{step} time of the last (indentation) step in the FEM. Strain energies are in J.\\
\noindent The python script \texttt{extract\_ESEDEN.py\index{extract\_ESEDEN.py@\texttt{extract\_ESEDEN.py}}} writes the strain energy density per element for \texttt{basil\-<basilid>.odb\index{basil<basilid>.odb@\texttt{basil<basilid>.odb}}} to the file \texttt{basil<basilid>.sed\index{basil<basilid>.sed@\texttt{basil<basilid>.sed}}}. This file contains a row for each element at the end of the simulation with the format
\begin{framed}
\texttt{time}, \texttt{element number}, \texttt{strain energy density}
\end{framed}
The \texttt{time} at the end of the simulation is the \textsl{step} time of the last (indentation) step in the FEM. Strain energies are in J/mm$^3$.\\
\noindent The python script \texttt{extract\_LE.py\index{extract\_LE.py@\texttt{extract\_LE.py}}} writes the (unique) logarithmic strain tensor components per node for \texttt{basil\-<basilid>.odb\index{basil<basilid>.odb@\texttt{basil<basilid>.odb}}} to the file \texttt{basil<basilid>.le\index{basil<basilid>.le@\texttt{basil<basilid>.le}}}. This file contains a row for each node at the end of the simulation with the format
\begin{framed}
\texttt{time}, \texttt{node number}, \texttt{LE11}, \texttt{LE22}, \texttt{LE33}, \texttt{LE12}, \texttt{LE13}, \texttt{LE23}
\end{framed}
The \texttt{time} at the end of the simulation is the \textsl{step} time of the last (indentation) step in the FEM. Strains are dimensionless.\\
\noindent To extract data from \texttt{basil\-<basilid>.odb\index{basil<basilid>.odb@\texttt{basil<basilid>.odb}}} with these Abaqus python scripts, use
\begin{lstlisting}[numbers=none, language=bash]
mark@telab11:~$ abaqus python extract_<var>.py -odb basil<basilid>.odb
mark@telab11:~$ abaqus python extract_<var>.py -odb basil<basilid>
\end{lstlisting}
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment