Commit cafa53d5 authored by Turnhout, M.C. van's avatar Turnhout, M.C. van
Browse files

contributing & readme

parents f5ac9225 796d855a
...@@ -11,7 +11,6 @@ ...@@ -11,7 +11,6 @@
############ ############
# it's better to unpack these files and commit the raw source # it's better to unpack these files and commit the raw source
# git has its own built in compression methods # git has its own built in compression methods
*.rpy*
*.7z *.7z
*.dmg *.dmg
*.gz *.gz
...@@ -59,16 +58,20 @@ Thumbs.db ...@@ -59,16 +58,20 @@ Thumbs.db
# Simulink Code Generation # Simulink Code Generation
slprj/ slprj/
matlab/Gibbon/
# Abaqus gitignore
*.rpy*
# LaTeX git ignore # LaTeX git ignore
*.acn *.acn
*.acr *.acr
*.alg *.alg
*.aux *.aux
*.bak
*.bbl *.bbl
*.blg *.blg
*.dvi *.dvi
*.dep
*.fls *.fls
*.fdb_latexmk *.fdb_latexmk
*.glg *.glg
...@@ -89,6 +92,7 @@ matlab/Gibbon/ ...@@ -89,6 +92,7 @@ matlab/Gibbon/
*.out *.out
*.pdfsync *.pdfsync
*.ps *.ps
*.sav
*.snm *.snm
*.synctex.gz *.synctex.gz
*.toc *.toc
...@@ -96,3 +100,4 @@ matlab/Gibbon/ ...@@ -96,3 +100,4 @@ matlab/Gibbon/
*.xdy *.xdy
*.tdo *.tdo
# repo specific ignores
...@@ -2,18 +2,18 @@ Contributing ...@@ -2,18 +2,18 @@ Contributing
============ ============
Your contributions and thoughts are highly valued. Your contributions and thoughts are highly valued.
In order to conribute to the repo, you need to make a GitLab account (http://stbe-nas.wfw.wtb.tue.nl:3000/). In order to conribute to the repo, you need to make a BitBucket account (http://bitbucket.org).
Permissions for the repos can then be requested with the GitLab-admin: m.c.v.turnhout@tue.nl Permissions for the repos can then be requested with the BasilLab-admin: m.c.v.turnhout@tue.nl
Note Note
==== ====
that when you commit code to the STEM repos that when you commit code to this repo
- everybody from within the university domain can access the STEM repos and see your commits - everybody can access the repo and see your commits
- your code will be released with a GNU Public License, for all eternity ever - your code will be released with a GNU Public License, for all eternity ever
For working on/with a repo For working on/with a repo
- when in doubt, work in your own branch - when in doubt, work in your own branch
- when in doubt, discuss with the FibLab-admin: m.c.v.turnhout@tue.nl - when in doubt, discuss with the BasiLab-admin: m.c.v.turnhout@tue.nl
Of course: Of course:
========== ==========
......
basillab BasilLab
======== ========
http://stbe-nas.wfw.wtb.tue.nl:3000/STEM/basillab https://bitbucket.org/matecellab/basillab
FYI (for your inspiration): a toolbox to get from raw MRI data to a FYI (for your inspiration): a toolbox to get from raw MRI data to a
3D Abaqus FE model with as little user interaction as possible. 3D Abaqus FE model with as little user interaction as possible.
...@@ -10,7 +10,7 @@ using & downloading ...@@ -10,7 +10,7 @@ using & downloading
=================== ===================
You do not need (to run or use) Git to able to use basillab. You can You do not need (to run or use) Git to able to use basillab. You can
download your favourite version from http://stbe-nas.wfw.wtb.tue.nl:3000/STEM/basillab download your favourite version from https://bitbucket.org/matecellab/basillab
Once downloaded, the code is yours to (ab)use to your liking (as Once downloaded, the code is yours to (ab)use to your liking (as
long as you do not violate the GPL license). long as you do not violate the GPL license).
...@@ -25,7 +25,7 @@ compiling documentation from source ...@@ -25,7 +25,7 @@ compiling documentation from source
The main file to be compiled is BasilLab.tex The main file to be compiled is BasilLab.tex
In order to compile from source, you may need some custom LaTeX-files In order to compile from source, you may need some custom LaTeX-files
from stexmf: http://stbe-nas.wfw.wtb.tue.nl:3000/STEM/stexmf from stexmf: http://mategit.wfw.wtb.tue.nl/STEM/stexmf
copyright copyright
========= =========
...@@ -36,7 +36,7 @@ Technology. ...@@ -36,7 +36,7 @@ Technology.
Copyright (C) 2017 Soft Tissue Engineering and Mechanobiology (STEM) Copyright (C) 2017 Soft Tissue Engineering and Mechanobiology (STEM)
group, Department of Biomedical Engineering, Eindhoven University of group, Department of Biomedical Engineering, Eindhoven University of
Technology: http://www.stem-research.nl https://www.tue.nl/stem Technology: https://www.tue.nl/stem
This program is free software; you can redistribute it and/or modify This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by it under the terms of the GNU General Public License as published by
......
...@@ -177,7 +177,7 @@ The \texttt{cae}-file can be opened with the Abaqus GUI. When this model is subm ...@@ -177,7 +177,7 @@ The \texttt{cae}-file can be opened with the Abaqus GUI. When this model is subm
\subsection{Processing \texttt{param} options} \subsection{Processing \texttt{param} options}
The function \bas{buildFEM} starts with some book-keeping. First the options in the parameter structure \texttt{param} are processed, and defaults substitued for missing values. When all necessary fields of \texttt{param} have been read or set, the first action of \bas{buildFEM} is to write the file \texttt{basil<basilid>\_model\-param.m\index{basil<basilid>\_modelparam.m@\texttt{basil<basilid>\_modelparam.m}}}. The function \bas{buildFEM} starts with some book-keeping. First the options in the parameter structure \texttt{param} are processed, and defaults substituted for missing values. When all necessary fields of \texttt{param} have been read or set, the first action of \bas{buildFEM} is to write the file \texttt{basil<basilid>\_model\-param.m\index{basil<basilid>\_modelparam.m@\texttt{basil<basilid>\_modelparam.m}}}.
All \texttt{<basilid}$i$\texttt{>} are processed with the same \texttt{param}-options, so this file is equal for each \texttt{<basilid}$i$\texttt{>} (except for the small differences in the \texttt{buildon}-time). All \texttt{<basilid}$i$\texttt{>} are processed with the same \texttt{param}-options, so this file is equal for each \texttt{<basilid}$i$\texttt{>} (except for the small differences in the \texttt{buildon}-time).
......
...@@ -169,7 +169,7 @@ These Euler angles follow the \gibbon-convention (see \gib{euler2DCM.m}): $\alph ...@@ -169,7 +169,7 @@ These Euler angles follow the \gibbon-convention (see \gib{euler2DCM.m}): $\alph
\begin{equation} \begin{equation}
\mat{R}_{\alpha\beta\gamma} = \mat{R}_\alpha\cdot\mat{R}_\beta \cdot \mat{R}_\gamma \mat{R}_{\alpha\beta\gamma} = \mat{R}_\alpha\cdot\mat{R}_\beta \cdot \mat{R}_\gamma
\end{equation} \end{equation}
This kind of angle multiplication is not commutative. Abaqus uses a different definition for Euler angles. These three Euler angles from \gibbon{} can not be directly used in Abaqus. It will wreak havoc. This kind of angle multiplication is not commutative. Abaqus uses a different definition for Euler angles. These three Euler angles from \warning\gibbon{} can not be directly used in Abaqus. It will wreak havoc.
The $3\times 3$ matrix (centres of mass, Euler angles) is written to \texttt{Bone\_preload\_loading.txt\index{Bone\_preload\_loading.txt@\texttt{Bone\_preload\_loading.txt}}} or \texttt{Bone\_preload\_postload.txt\index{Bone\_preload\_postload.txt@\texttt{Bone\_preload\_postload.txt}}}, depending on the case, in \basilhome\texttt{/<basilid>/}. To map the tibia movements for \texttt{<basilid> = 140611} and \texttt{<basilid> = 140613} call: The $3\times 3$ matrix (centres of mass, Euler angles) is written to \texttt{Bone\_preload\_loading.txt\index{Bone\_preload\_loading.txt@\texttt{Bone\_preload\_loading.txt}}} or \texttt{Bone\_preload\_postload.txt\index{Bone\_preload\_postload.txt@\texttt{Bone\_preload\_postload.txt}}}, depending on the case, in \basilhome\texttt{/<basilid>/}. To map the tibia movements for \texttt{<basilid> = 140611} and \texttt{<basilid> = 140613} call:
\begin{lstlisting}[numbers=none,language=basillab] \begin{lstlisting}[numbers=none,language=basillab]
......
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