Commit 90b8c20e authored by Turnhout, M.C. van's avatar Turnhout, M.C. van
Browse files

update version

parents 9cbb7d21 16c3d737
......@@ -187,7 +187,7 @@ file & description & source \\ \noalign{\smallskip}\hline\noalign{\smallskip}
\texttt{<expname>\_film$i$\_frame$j$.odb} & The Abaqus Output DataBase, contains the results of the simulation in binary (Abaqus) format for frame $j$ of film $i$. Can be opened and read with Abaqus cae or Abaqus viewer. & Abaqus \\
\texttt{<expname>\_film$i$\_frame$j$.dat} & text file that contains the results of Abaqus' parsing of the input file for frame $j$ of film $i$. When something is wrong with your input file, the \texttt{dat}-file tells you what it is. & Abaqus \\
\texttt{<expname>\_film$i$\_frame$j$.msg} & text file that contains Abaqus messages during the simulation for frame $j$ of film $i$. When your simulation fails, the \texttt{msg}-file may tell you what the reason is. & Abaqus \\
\texttt{<expname>\_film$i$\_frame$j$.sta} & text file that contains the progress of the simulation for frame $j$ of film $i$. You can monitor this file to see how well your simulations runs, converges.\\\noalign{\smallskip}\hline
\texttt{<expname>\_film$i$\_frame$j$.sta} & text file that contains the progress of the simulation for frame $j$ of film $i$. You can monitor this file to see how well your simulations runs, converges.& Abaqus\\\noalign{\smallskip}\hline
\end{tabularx}
\end{table}
......@@ -207,7 +207,7 @@ file & description & deleted? \\ \noalign{\smallskip}\hline\noalign{\smallskip}
\texttt{<expname>\_film$i$\_frame$j$.1.SMAFocus} & binary file & yes\\
\texttt{<expname>\_film$i$\_frame$j$.023} & binary file & yes\\
\texttt{<expname>\_film$i$\_frame$j$.cid} & text file, contains the name of your computer and some numbers & yes\\
\texttt{<expname>\_film$i$\_frame$j$.lck} & 'lock'-file that tells Abaqus that that job is already running. & yes\\
\texttt{<expname>\_film$i$\_frame$j$.lck} & `lock'-file that tells Abaqus that that job is already running. & yes\\
\texttt{<expname>\_film$i$\_frame$j$.mdl} & binary file& yes\\
\texttt{<expname>\_film$i$\_frame$j$.prt} & a text file with plenty numbers & no\\
\texttt{<expname>\_film$i$\_frame$j$.sst} & binary file & yes\\
......
......@@ -60,6 +60,15 @@
url = {https://fivethirtyeight.com/features/science-isnt-broken/#part2},
}
@Misc{Regier2016,
author = {Regier, Ryan},
title = {{C}ounting {E}lsevier {P}ublications {I}ndexed in {S}copus},
month = {April},
year = {2016},
note = {\href{https://awayofhappening.wordpress.com/2016/04/28/counting-elsevier-publications-indexed-in-scopus/}{https://awayofhappening.wordpress.com/2016/04/28/counting-elsevier-publications-indexed-in-scopus/}},
url = {https://awayofhappening.wordpress.com/2016/04/28/counting-elsevier-publications-indexed-in-scopus/},
}
@InCollection{Wonder1973,
author = {Wonder, Stevie},
title = {Don't You Worry 'bout a Thing},
......@@ -174,7 +183,7 @@
}
@Article{Haaften2019,
author = {\noopsort{Haaften}van Haaften, Eline E. and \noopsort{Turnhout}van Turnhout, Mark C. and Kurnianwan, Nicholas A.},
author = {\noopsort{Haaften}van Haaften, Eline E. and \noopsort{Turnhout}van Turnhout, Mark C. and Kurniawan, Nicholas A.},
title = {{I}mage-based analysis of uniaxial ring test for mechanical characterization of soft materials and biological tissues},
journal = {Soft Matter},
year = {2019},
......
......@@ -91,7 +91,7 @@
%\cofeAm{0.5}{1.0}{125}{10cm}{-1cm}
%%\cofeBm{alpha}{scale}{angle}{xoff}{yoff}
\begin{center}
\Huge{\textbf{\href{https://gitlab.tue.nl/STEM/TFlab}{TFlab}}}, \href{https://gitlab.tue.nl/STEM/TFlab/tree/v0.2.1}{v0.2}\\
\Huge{\textbf{\href{https://gitlab.tue.nl/STEM/TFlab}{TFlab}}}, \href{https://gitlab.tue.nl/STEM/TFlab/tree/v0.2.1}{v0.2.1}\\
\Huge{\textbf{User manual}}\\
\mbox{}\\
\vfill
......@@ -121,8 +121,11 @@
\def\bibname{References}
\begin{savequote}\vspace*{-0.5cm}
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} }
%\begin{savequote}\vspace*{-0.5cm}
%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}
\begin{savequote}\vspace*{-1cm}
I see that you have hitherto been one of that herd who, in order to learn how matters such as this take place, and in order to acquire a knowledge of natural effects, do not betake themselves to ships or crossbows or cannons, but retire into their studies and glance through an index and a table of contents to see whether Aristotle has said anything about them; and, being assured of the true sense of his text, consider that nothing else can be known. \qauthor{Galileo Galilei \cite{Galilei1632}}
\end{savequote}
\bibliographystyle{myplainhp}
......@@ -130,8 +133,11 @@ I have pointed out these things because the more you see how strangely Nature be
\clearpage
\begin{savequote}\vspace*{-1cm}
I see that you have hitherto been one of that herd who, in order to learn how matters such as this take place, and in order to acquire a knowledge of natural effects, do not betake themselves to ships or crossbows or cannons, but retire into their studies and glance through an index and a table of contents to see whether Aristotle has said anything about them; and, being assured of the true sense of his text, consider that nothing else can be known. \qauthor{Galileo Galilei \cite{Galilei1632}}
%\begin{savequote}\vspace*{-1cm}
%I see that you have hitherto been one of that herd who, in order to learn how matters such as this take place, and in order to acquire a knowledge of natural effects, do not betake themselves to ships or crossbows or cannons, but retire into their studies and glance through an index and a table of contents to see whether Aristotle has said anything about them; and, being assured of the true sense of his text, consider that nothing else can be known. \qauthor{Galileo Galilei \cite{Galilei1632}}
%\end{savequote}\addcontentsline{toc}{chapter}{\protect\numberline{\color{white}}Index}
\begin{savequote}\vspace*{-0.5cm}
Elsevier prides itself on only indexing high quality publications in Scopus, and if doesn't index all of the journals it publishes, isn't that admitting that not all of the journals Elsevier publishes are not high quality? \dots{} So, it is a good question to ask. And ask it I did. \qauthor{Ryan Regier \cite{Regier2016}}
\end{savequote}\addcontentsline{toc}{chapter}{\protect\numberline{\color{white}}Index}
\printindex
......
......@@ -142,9 +142,7 @@ For $\varphi \geq \frac{\piup}{2}$, the simple (and obvious, figure \ref{figcurl
\end{figure}
Now, it is easy to check whether $\frac{L}{l} \geq \frac{\piup}{2}$ (equation \ref{lfR2}) in which case it is equally easy to calculate $R = l$. Our attempts to write equation \ref{lfR1} in the form $R = f(l, L)$, however, have failed. Still, we can work this relationship out numerically (figure \ref{lfRfl}).
The combination of the projected length of a film that only curves in the $\vec{y}\vec{z}$-plane (i.e.\ not `sideways') and its radius of curvature is unique (figure \ref{lfRfl}). This allows us to calculate the radius of curvature from the \textsl{projected} film length $l$. This is not the case for the actual film \textsl{tip} position: different radii of curvature may result in the same film tip position (figure \ref{figcurllnR}, green)
The combination of the projected length of a film that only curves in the $\vec{y}\vec{z}$-plane (i.e.\ not `sideways') and its radius of curvature is unique (figure \ref{lfRfl}). This allows us to calculate the radius of curvature from the \textsl{projected} film length $l$. This is not the case for the actual film \textsl{tip} position: different radii of curvature may result in the same film tip position (figure \ref{figcurllnR}, green).
\section{Actin fibre orientations}\label{conv:actin}
......@@ -160,7 +158,7 @@ The combination of the projected length of a film that only curves in the $\vec{
\caption{Conventions for actin fibre orientations. With \textbf{(a)} actin fibre orientations $\phi$ are defined positive in the counter-clockwise direction, and zero for the positive $\vec{x}$-direction; \textbf{(b)} example with a 180-bin histogram of a simulated example (inset) and a main fibre orientation of about 30\,\degree{} (compared to about 20\,\degree{} in (a)); and \textbf{(c)} data from (b) converted for the FEM: 30 (histogram) bin counts from the raw data in (b) (grey), or 30 bin counts generated from the \fiblab-parameters that were estimated from the raw data in (b) (blue). \label{fibdef}}
\end{figure}
Please be aware that these (angle) definitions are different from what Inge \cite{Loosdregt2018} used, and that might you do well to check your preprocessing methods for compatibility with \tflab. \warning\\
Please be aware that these (angle) definitions are different from what Inge \cite{Loosdregt2018} used, and that you might do well to check your preprocessing methods for compatibility with \tflab. \warning\\
\noindent Actin fibre orientations $\phi$ are defined positive in the counter clock-wise direction with $\phi = 0$ for the positive $\vec{x}$-axis (figures \ref{fibdefdef}-\ref{fibdefhist}).
......
......@@ -61,7 +61,7 @@ figure(1)
hold on
% dummy for legend
plot(-1,-1,'r.',-1,-1,'ro',-1,-1,'b.',-1,-1,'bo',-1,-1,'g.',-1,-1,'go')
h = legend('linear, frame 1', 'linear, frame 1', 'quasi-fancy, frame 1', ...
h = legend('linear, frame 1', 'linear, frame 2', 'quasi-fancy, frame 1', ...
'quasi-fancy, frame 2', 'fancy, frame 1', 'fancy, frame 2');
set(h, 'box', 'off')
......@@ -91,7 +91,7 @@ figure(2)
hold on
% dummy for legend
plot(-1,-1,'r.-',-1,-1,'ro-',-1,-1,'b.-',-1,-1,'bo-',-1,-1,'g.-',-1,-1,'go-')
h = legend('linear, frame 1', 'linear, frame 1', 'quasi-fancy, frame 1', ...
h = legend('linear, frame 1', 'linear, frame 2', 'quasi-fancy, frame 1', ...
'quasi-fancy, frame 2', 'fancy, frame 1', 'fancy, frame 2');
set(h, 'box', 'off')
......
......@@ -152,7 +152,7 @@ fancy & 7 & 2 & 9 & 31\,m\\ \noalign{\smallskip}\hline
\noindent In the example that we choose to show you, fancy estimation \textsl{rocks}, big time. Of course.
But in all honesty, we had to actively look for this impressive example. If we had for instance chosen to fit frame 2 \textsl{before} frame 1, the benefit of fancy estimation had been much less impressive. Likewise if the target length for frame 2 had been (much) closer to that of frame 1. Furthermore, the old adage that 'life is like a sewer -- what you get out of it depends on what you put into it.'\footnote{bagger in = bagger uit} \cite{Lehrer1960}, also holds for the estimation of the parameters of our analytical function. The quality of the fit, and therefore of the new estimate for $\sigma_x$ depends on the quality of the input values (estimates so far).
But in all honesty, we had to actively look for this impressive example. If we had for instance chosen to fit frame 2 \textsl{before} frame 1, the benefit of fancy estimation had been much less impressive. Likewise if the target length for frame 2 had been (much) closer to that of frame 1. Furthermore, the old adage that `life is like a sewer -- what you get out of it depends on what you put into it.'\footnote{bagger in = bagger uit} \cite{Lehrer1960}, also holds for the estimation of the parameters of our analytical function. The quality of the fit, and therefore of the new estimate for $\sigma_x$ depends on the quality of the input values (estimates so far).
In general, the quality of the fit will improve with more input estimates, and for input estimates that are equally spaced (no clustering of points). But it is impossible to predict beforehand how the fits are going to behave during the estimation process. And when the analytical fit is off, linear interpolation may actually be better than the `fancy' estimation.
......
......@@ -753,11 +753,11 @@ Isotropic constructs curl well and the parameter space might have been evaluated
We are fitting a linear model to parameters that may not respond linearly, if only because of the geometrical effects of film curling. Furthermore, the response of the model as function of $\sigma_x$ shows unexpected non-linear effects around $\sigma_x = 0.007$\,MPa for the main read-out $\frac{l}{L}$ (figure \ref{fig:pspaceiso_lL_as}). We hypothesised that some geometrical effect in film curling may predominantly occur around $\sigma_x = 0.007$\,MPa, and a more in-depth analysis of the non-linear (geometrical) effects on film curling in this isotropic parameter space is certainly warranted.\\
\noindent The analysis of film curvature from projected edge does not account for asymmetric boundary conditions and curling edge effects (figure \ref{isospace_dk_fig}), but it is a good estimation for the actual mean local curvature over the length of the constructs (figure \ref{isospace_dR_fig}). Furthermore, constructs hardly change length during curling (figure \ref{isospace_dL_fig}), and these small changes in length only affect the analysis for $l > \frac{2L_d}{\piup}$, by a fraction $\abs{\frac{L_d}{L}} \ll 1$.
\noindent The analysis of film curvature from projected edge does not account for asymmetric boundary conditions and curling edge effects (figure \ref{isospace_dk_fig}), but it is a good estimation for the actual mean local curvature over the length of the constructs (figure \ref{isospace_dR_fig}). Furthermore, constructs hardly change length during curling (figure \ref{isospace_dL_fig}), and these small changes in length only affect the analysis for $l > \frac{2L_d}{\piup}$, by a factor of $\left|\frac{L_d}{L}\right| \simeq 1$.
Grossberg \textsl{et al.} remark that \cite{Grosberg2011}: ``For $x$-projections approaching the length of the film, the radius of curvature increases rapidly; however, that does not negatively impact the accuracy of the stress calculations because the stress at large radius of curvature is very small compared to peak systole.'' We already argued that projected edge $\frac{l}{L}$ is a better metric for $\sigma_x$ than curvature $R$, but we note that $l$ too, is more accurately estimated for constructs that `curl more'.
Grossberg \textsl{et al.} remark that \cite{Grosberg2011}: ``For $x$-projections approaching the length of the film, the radius of curvature increases rapidly; however, that does not negatively impact the accuracy of the stress calculations because the stress at large radius of curvature is very small compared to peak systole.'' We already argued that projected edge length $\frac{l}{L}$ is a better metric for $\sigma_x$ than curvature $R$, but we note that $l$ too, is more accurately estimated for constructs that `curl more'.
Al in all, we can conclude that the analysis of film curvature $R$ from projected edge $\frac{l}{L}$ is valid assessment of cell traction stresses $\sigma_x$ in isotropic constructs. \\
Al in all, we can conclude that the analysis of film curvature $R$ from projected edge length $\frac{l}{L}$ is valid assessment of cell traction stresses $\sigma_x$ in isotropic constructs. \\
\noindent Alford \textsl{et al.} performed an analytical parameter space analysis of free curling constructs with $\nu_\text{film} = \nu_\text{cells} = 0.5$ \cite[figure 5]{Alford2010}. The results of our analysis qualitatively agree with theirs: film thickness and cell layer thickness have an opposite effect, cell layer stiffness has no effect. Alford \textsl{et al.} did not investigate film stiffness $E_\text{film}$. Our analysis suggests that this parameter may be the most important one (based on its coefficient), and that construct length $L$, also not investigated in \cite{Alford2010}, may be as important as cell layer thickness $t_\text{cells}$.
......@@ -775,7 +775,7 @@ For starters, the analysis is hampered by convergence issues for larger values o
Projected edge length only assesses curvature in 2D. For anisotropic constructs it therefore becomes a non-linear proxy for the actual cell traction stresses that deforms the construct in 3D. And because the predominant fibre orientation affects the amount of out-of-plane deformation, comparison of projected edge lengths between constructs can only be valid for (near) equal values of $\mu$.\\
But it gets worse.\\
\noindent Even for a given predominant fibre orientation $\mu$, projected edge length $\frac{l}{L}$ may not be unique for a given value of cell traction stress $\sigma_x$ (figure \ref{lfmu_sigma}). We found a minimum in the $\frac{l}{L}\left(\sigma_x\right)$ relationship \textsl{for more than half of our random models} (figure \ref{anispace_md_fig}). The measurement of $\frac{l}{L}$ is ambiguous around these minima.\warning
\noindent Even for a given predominant fibre orientation $\mu$, projected edge length $\frac{l}{L}$ may not be unique for a given value of cell traction stress $\sigma_x$ (figure \ref{lfmu_sigma}). We found a minimum in the $\frac{l}{L}\left(\sigma_x\right)$ relationship \textsl{for more than half of our random models} (figure \ref{anispace_md_fig}). The estimation of $\sigma_x$ from $\frac{l}{L}$ is ambiguous around these minima.\warning
Our current analysis does not suffice to predict the occurrence or severity of these minima in terms of the \fiblab{} parameters $\mu$, $\sigma$, and $P$. Figure \ref{lfmu_sigma} suggests that the occurrence this minimum is most prevalent around a predominant orientation $\mu$ that is about 30\,\degree{} off-axis $\left(90\,\degree \pm 30\,\degree\right)$, but $\sigma$ and $P$ will also have their influence.\\
......
......@@ -80,7 +80,7 @@
\put(0.0633877,0.68491143){\color[rgb]{0,0,0}\makebox(0,0)[rb]{\smash{3.5}}}%
\put(0.0633877,0.77292216){\color[rgb]{0,0,0}\makebox(0,0)[rb]{\smash{4}}}%
\put(0.71642126,0.73741386){\color[rgb]{0,0,0}\makebox(0,0)[lb]{\smash{linear, frame 1}}}%
\put(0.71642126,0.69623468){\color[rgb]{0,0,0}\makebox(0,0)[lb]{\smash{linear, frame 1}}}%
\put(0.71642126,0.69623468){\color[rgb]{0,0,0}\makebox(0,0)[lb]{\smash{linear, frame 2}}}%
\put(0.71642126,0.65299859){\color[rgb]{0,0,0}\makebox(0,0)[lb]{\smash{quasi-fancy, frame 1}}}%
\put(0.71642126,0.60976045){\color[rgb]{0,0,0}\makebox(0,0)[lb]{\smash{quasi-fancy, frame 2}}}%
\put(0.71642126,0.56652436){\color[rgb]{0,0,0}\makebox(0,0)[lb]{\smash{fancy, frame 1}}}%
......
......@@ -74,7 +74,7 @@
\put(0.09138167,0.66383471){\color[rgb]{0,0,0}\makebox(0,0)[rb]{\smash{0.013}}}%
\put(0.09138167,0.76354144){\color[rgb]{0,0,0}\makebox(0,0)[rb]{\smash{0.014}}}%
\put(0.73872919,0.72834231){\color[rgb]{0,0,0}\makebox(0,0)[lb]{\smash{linear, frame 1}}}%
\put(0.73872919,0.68752168){\color[rgb]{0,0,0}\makebox(0,0)[lb]{\smash{linear, frame 1}}}%
\put(0.73872919,0.68752168){\color[rgb]{0,0,0}\makebox(0,0)[lb]{\smash{linear, frame 2}}}%
\put(0.73872919,0.64466206){\color[rgb]{0,0,0}\makebox(0,0)[lb]{\smash{quasi-fancy, frame 1}}}%
\put(0.73872919,0.6018004){\color[rgb]{0,0,0}\makebox(0,0)[lb]{\smash{quasi-fancy, frame 2}}}%
\put(0.73872919,0.55894077){\color[rgb]{0,0,0}\makebox(0,0)[lb]{\smash{fancy, frame 1}}}%
......
This diff is collapsed.
......@@ -33,6 +33,9 @@ iFEM & \TF{estsigmax} &\\
~~~~~~~~\texttt{getstress\_stressfibers.f}&&\\
~~***~~\paraminc{} & \TF{writeFEMinc} & \\
~~~~~~~~\texttt{Ep}: substrate (film) Youngs Modulus [MPa] & \TF{prepexp} & \param{Efilm}\\
~~~~~~~~\texttt{vp}: substrate (film) Poisson ratio [-] & \TF{prepexp} & \param{vfilm}\\
~~~~~~~~\texttt{Ec}: cell layer Youngs Modulus [MPa] & \TF{prepexp} & \param{Ecells}\\
~~~~~~~~\texttt{vc}: cell layer Poisson ratio [-] & \TF{prepexp} & \param{vcells}\\
~~~~~~~~\texttt{sigmax}: cell traction stress [MPa] & \TF{prepexp} & \param{sigmax}\\
~~~~~~~~\texttt{phi\_sf(i)}: actin orientations [rad] & \TF{FOA2paraminc} & \param{phisf}\\
~~~~~~~~~~(optional) path to orientation csv-files & \TF{FOA2paraminc} & \param{fibpath}\\
......@@ -56,8 +59,7 @@ iFEM & \TF{estsigmax} &\\
When all necessary information has been added to the \texttt{param}-structure, it can be fed to \TF{estsigmax} which will estimate the experimental cell stress with iFEM (section \ref{sectfestsigmax}).
\begin{table}[p!]
\begin{table}[b!]
\caption{A brief look under the hood of \TF{prepexp} and \TF{estsigmax}. \href{https://en.wikipedia.org/wiki/Unix_philosophy}{Yes}, there is a \textsl{very} good reason for all those tiny separate scripts.\label{hoodtable}}
\begin{tabularx}{\linewidth}{l X}
\hline\noalign{\smallskip}
......@@ -125,7 +127,7 @@ Note that the `default configuration' that \TF{prepexp} uses (and indeed all scr
First, the user selects the image(s) of the (un)curled films (figure \ref{guiselectimages}). A single TIF-file in case all images are collected in a single image stack, or multiple images when all images are stored in separate (TIF-) files.
Note that multiple image files have be stored in the same directory, and note that \tflab{} only handles \warning TIF-images.
Note that multiple image files have be stored in the same directory, and note that \tflab{} only handles TIF-images.
The GUI will start in the current working directory. \\
\begin{shaded}
......
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