fought LaTeX and won.

arbeit/Makefile

@@ -1,13 +1,16 @@
 all: ma.md bibma.bib template.tex settings/abkuerzungen.tex settings/commands.tex settings/environments.tex settings/hyphenation.tex settings/packages.tex files/titlepage.tex files/erklaerung.tex
 	pandoc -s -N --template=template.tex ma.md -o ma.tex
-	rm -f ma.pdf ma.aux ma.idx ma.lof ma.log ma.lot ma.out ma.tdo ma.toc
+	rm -f ma.pdf ma.aux ma.idx ma.lof ma.log ma.lot ma.out ma.tdo ma.toc ma.bbl ma.blg ma.loa
 	pdflatex -interaction batchmode ma.tex || true
-	while test `cat ma.log | grep -e "rerunfilecheck \(Warning\|Info\).*has changed" | wc -l` -gt 0 ; do \
+	bibtexu ma
+	pdflatex -interaction batchmode ma.tex || true
+	while test `cat ma.log | grep -e "\(Rerun to get citations correct\)" | wc -l` -gt 0 ; do \
 		rm ma.log && (pdflatex -interaction batchmode ma.tex || true) \
 	done
-	rm -f ma.aux ma.idx ma.lof ma.log ma.lot ma.out ma.tdo ma.toc
+	rm -f ma.aux ma.idx ma.lof ma.lot ma.out ma.tdo ma.toc ma.bbl ma.blg ma.loa
+	# rm -f ma.log
 
 
 clean:
-	rm -f ma.pdf ma.aux ma.idx ma.lof ma.log ma.lot ma.out ma.tdo ma.toc
+	rm -f ma.pdf ma.aux ma.idx ma.lof ma.log ma.lot ma.out ma.tdo ma.toc ma.bbl ma.blg ma.loa
 	rm -f ma.tex

arbeit/bibma.bib

@@ -1,122 +1,8 @@
-@article{ohm2003mpeg,
-  title={The MPEG-7 Color Descriptors},
-  author={Ohm, Jens-Rainer and Cieplinski, Leszek and Kim, Heon Jun and Krishnamachari, Santhana and Manjunath, BS and Messing, Dean S and Yamada, Akio},
-  year={2003}
+@inproceedings{anrichterEvol,
+  author       = "Richter, Andreas and Achenbach, Jascha and Menzel, Stefan and Botsch, Mario",
+  booktitle    = "IEEE Congress on Evolutionary Computation",
+  location     = "Vancouver, Canada",
+  publisher    = "IEEE",
+  title        = "Evolvability as a Quality Criterion for Linear Deformation Representations in Evolutionary Optimization",
+  year         = "2016",
 }
-@article{schoening2012,
-
-  abstract     = {Megafauna play an important role in benthic ecosystem function and are sensitive indicators of environmental change. Non-invasive monitoring of benthic communities can be accomplished by seafloor imaging. However, manual quantification of megafauna in images is labor-intensive and therefore, this organism size class is often neglected in ecosystem studies. Automated image analysis has been proposed as a possible approach to such analysis, but the heterogeneity of megafaunal communities poses a non-trivial challenge for such automated techniques. Here, the potential of a generalized object detection architecture, referred to as iSIS (intelligent Screening of underwater Image Sequences), for the quantification of a heterogenous group of megafauna taxa is investigated. The iSIS system is tuned for a particular image sequence (i.e. a transect) using a small subset of the images, in which megafauna taxa positions were previously marked by an expert. To investigate the potential of iSIS and 
-compare its results with those obtained from human experts, a group of eight different taxa from one camera transect of seafloor images taken at the Arctic deep-sea observatory HAUSGARTEN is used. The results show that inter- and intra-observer agreements of human experts exhibit considerable variation between the species, with a similar degree of variation apparent in the automatically derived results obtained by iSIS. Whilst some taxa (e. g. Bathycrinus stalks, Kolga hyalina, small white sea anemone) were well detected by iSIS (i. e. overall Sensitivity: 87\%, overall Positive Predictive Value: 67\%), some taxa such as the small sea cucumber Elpidia heckeri remain challenging, for both human observers and iSIS.},
-  author       = {Schoening, Timm and Bergmann, Melanie  and Purser, Autun and Dannheim, Jennifer and Gutt, Julian and Nattkemper, Tim Wilhelm},
-  issn         = {1932-6203},
-  journal      = {PLoS ONE},
-  language     = {English},
-  number       = {6},
-  title        = {Semi-automated image analysis for the assessment of megafaunal densities at the Arctic deep-sea observatory HAUSGARTEN},
-  doi          = {10.1371/journal.pone.0038179},
-  volume       = {7},
-  year         = {2012},
-}
-
-@article{rubinstein2010double,
-  title={Double sparsity: Learning sparse dictionaries for sparse signal approximation},
-  author={Rubinstein, Ron and Zibulevsky, Michael and Elad, Michael},
-  journal={Signal Processing, IEEE Transactions on},
-  volume={58},
-  number={3},
-  pages={1553--1564},
-  year={2010},
-  publisher={IEEE}
-}
-
-@ARTICLE{NNS_Scholarpedia,
-AUTHOR = {Peterson, L. E.},
-TITLE   = {K-nearest neighbor},
-YEAR	= {2009},
-JOURNAL	= {Scholarpedia},
-VOLUME  = {4},
-NUMBER  = {2},
-PAGES   = {1883},
-URL = {http://www.scholarpedia.org/article/K-nearest_neighbor}
-}
-@article{natarajan1995sparse,
-  title={Sparse approximate solutions to linear systems},
-  author={Natarajan, Balas Kausik},
-  journal={SIAM journal on computing},
-  volume={24},
-  number={2},
-  pages={227--234},
-  year={1995},
-  publisher={SIAM},
-  URL={http://dx.doi.org/10.1137/S0097539792240406}
-}
-@article{tropp2007signal,
-  title={Signal recovery from random measurements via orthogonal matching pursuit},
-  author={Tropp, Joel A and Gilbert, Anna C},
-  journal={Information Theory, IEEE Transactions on},
-  volume={53},
-  number={12},
-  pages={4655--4666},
-  year={2007},
-  publisher={IEEE}
-}
-@ARTICLE{SIFT_Scholarpedia,
-AUTHOR = {Lindeberg, T. },
-TITLE   = {Scale Invariant Feature Transform},
-YEAR	= {2012},
-JOURNAL	= {Scholarpedia},
-VOLUME  = {7},
-NUMBER  = {5},
-PAGES   = {10491},
-URL= {http://www.scholarpedia.org/article/Scale_Invariant_Feature_Transform#Scale_and_orientation_normalization}
-}
-
-@article{foldiak1995sparse,
-  title={Sparse coding in the primate cortex},
-  author={F{\"o}ldi{\'a}k, Peter and Young, Malcom P},
-  journal={The handbook of brain theory and neural networks},
-  volume={1},
-  pages={1064--1068},
-  year={1995},
-  publisher={Citeseer}
-}
-
-
-@article{lewicki2000,
-    author = {Michael S. Lewicki and Terrence J. Sejnowski},
-    title = { Learning Overcomplete Representations},
-    year = {2000}
-}
-
-@misc{2dtree,
-author = {Eiseleda},
-title = {\url{http://upload.wikimedia.org/wikipedia/commons/9/90/2dbaum.svg}},
-year = {2013}
-}
-
-@misc{Muj11FLANN,
- author={Marius Muja},
- title={FLANN,  Fast Library for Approximate Nearest Neighbors},
- year={2011},
- note={\url{http://mloss.org/software/view/143/}}
-}
-
-@ARTICLE{entropy2007,
-AUTHOR = {Downarowicz, T. },
-TITLE   = {Entropy},
-YEAR	= 2007,
-JOURNAL	= Scholarpedia,
-VOLUME  = 2,
-NUMBER  = 11,
-PAGES   = 3901
-}
-
-@article{weber1998,
-  title={A quantitative analysis and performance study for similarity-search methods in high-dimensional spaces},
-  author={Weber, Roger and Schek, Hans-J{\"o}rg and Blott, Stephen},
-  booktitle={VLDB},
-  volume={98},
-  pages={194--205},
-  year={1998}
-}
-

arbeit/files/erklaerung.aux

@@ -1,7 +1,7 @@
 \relax 
 \providecommand\hyper@newdestlabel[2]{}
 \@setckpt{files/erklaerung}{
-\setcounter{page}{11}
+\setcounter{page}{15}
 \setcounter{equation}{0}
 \setcounter{enumi}{0}
 \setcounter{enumii}{0}
@@ -10,8 +10,8 @@
 \setcounter{footnote}{0}
 \setcounter{mpfootnote}{0}
 \setcounter{part}{0}
-\setcounter{chapter}{0}
-\setcounter{section}{0}
+\setcounter{chapter}{5}
+\setcounter{section}{5}
 \setcounter{subsection}{0}
 \setcounter{subsubsection}{0}
 \setcounter{paragraph}{0}
@@ -22,7 +22,7 @@
 \setcounter{ContinuedFloat}{0}
 \setcounter{float@type}{16}
 \setcounter{lstnumber}{1}
-\setcounter{NAT@ctr}{0}
+\setcounter{NAT@ctr}{1}
 \setcounter{AM@survey}{0}
 \setcounter{r@tfl@t}{0}
 \setcounter{subfigure}{0}
@@ -30,7 +30,7 @@
 \setcounter{@todonotes@numberoftodonotes}{0}
 \setcounter{Item}{0}
 \setcounter{Hfootnote}{0}
-\setcounter{bookmark@seq@number}{20}
+\setcounter{bookmark@seq@number}{17}
 \setcounter{algorithm}{0}
 \setcounter{ALC@unique}{0}
 \setcounter{ALC@line}{0}

arbeit/files/titlepage.tex

@@ -47,7 +47,6 @@
 	\hspace{0.99cm}	{\huge\bfseries Evaluation of the Performance\\[4mm] 
 	\hspace{0.99cm}	of Randomized FFD Control Grids}\\[28mm]
 	\hspace{0.99cm}	{\LARGE Master Thesis}\\[3mm]
-    \hspace{0.99cm}	{\fontsize{60pt}{} \selectfont\Huge\bfseries DRAFT}\\[3mm]
 	\hspace{0.99cm}	{\Large {\normalsize at the}\\[4mm]
 	\hspace{0.99cm}	AG Computer Graphics}\\[2mm]
 	\hspace{0.99cm}	at the Faculty of Technology\\

arbeit/ma.md

@@ -2,9 +2,40 @@
 fontsize: 11pt
 ---
 
-# Einleitung
+# How to read this Thesis
 
-## Wieso ist FFD cool?
+As a guide through the nomenclature used in the formulas we prepend this chapter.
+
+Unless otherwise noted the following holds:
+
+- lowercase letters $x,y,z$  
+  refer to real variables and represent a point in 3D-Space.
+- lowercase letters $u,v,w$  
+  refer to real variables between $0$ and $1$ used as coefficients in a 3D B-Spline grid.
+- other lowercase letters  
+  refer to other scalar (real) variables.
+- lowercase **bold** letters (e.g. $\vec{x},\vec{y}$)  
+  refer to 3D coordinates
+- uppercase **BOLD** letters (e.g. $D, M$)  
+  refer to Matrices
+
+# Introduction
+
+In this Master Thesis we try to extend a previously proposed concept of predicting
+the evolvability of \acf{FFD} given a Deformation-Matrix\cite{anrichterEvol}.
+In the original publication the author used random sampled points weighted with
+\acf{RBF} to deform the mesh and defined three different criteria that can be
+calculated prior to using an evolutional optimisation algorithm to asses the
+quality and potential of such optimisation.
+
+We will replicate the same setup on the same meshes but use \acf{FFD} instead of
+\acf{RBF} to create a deformation and evaluate if the evolution-criteria still
+work as a predictor given the different deformation.
+
+## What is \acf{FFD}?
+
+First of all we have to establish how a \ac{FFD} works and why this is a good
+tool for deforming meshes in the first place.
 
 ## Was ist evolutionäre Optimierung?
 

arbeit/ma.tex

@@ -67,6 +67,19 @@ titlepage,
 % % 	files/7_0_evaluation%
 % % 	,files/8_0_conclusion%
 % }
+
+%%%%%%%%%%%%%%% PANDOC-nedded defs %%%%%%%%%%
+\providecommand{\tightlist}{%
+  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
+
+%disable "Redefining ngerman shorthand"-Message
+% \makeatletter
+% \patchcmd{\pdfstringdef}
+%   {\csname HyPsd@babel@}
+%   {\let\bbl@info\@gobble\csname HyPsd@babel@}
+%   {}{}
+% \makeatother
+
 %%%%%%%%%%%%%%% Hauptdokument %%%%%%%%%%%%%%%
 \begin{document}
 
@@ -97,18 +110,59 @@ titlepage,
 %%%%%%%%%%%%%%% Verzeichnisse %%%%%%%%%%%%%%%
 \frontmatter % Abstrakte Gliederungsebene: Anfang des Buches
 	\tableofcontents		% Rueckseite leer
-	\listoffigures
-	\listoftables
 %\lstlistoflistings % fuer listingsverzeichnis mit package listings
 
 %%%%%%%%%%%%%%% Hauptteil %%%%%%%%%%%%%%%
 % Insgesamt ca. 60-100 Seiten Davon mindesten 50% Eigene Arbeit
 \mainmatter %Abstrakte Gliederungsebene: Hauptteil des Buches
 \pagestyle{fancy}
-	%\pagenumbering{arabic}
-\chapter{Einleitung}\label{einleitung}
+\pagenumbering{arabic}
+\chapter{How to read this Thesis}\label{how-to-read-this-thesis}
 
-\section{Wieso ist FFD cool?}\label{wieso-ist-ffd-cool}
+As a guide through the nomenclature used in the formulas we prepend this
+chapter.
+
+Unless otherwise noted the following holds:
+
+\begin{itemize}
+\tightlist
+\item
+  lowercase letters \(x,y,z\)\\
+   refer to real variables and represent a point in 3D-Space.
+\item
+  lowercase letters \(u,v,w\)\\
+   refer to real variables between \(0\) and \(1\) used as coefficients
+  in a 3D B-Spline grid.
+\item
+  other lowercase letters\\
+   refer to other scalar (real) variables.
+\item
+  lowercase \textbf{bold} letters (e.g. \(\vec{x},\vec{y}\))\\
+   refer to 3D coordinates
+\item
+  uppercase \textbf{BOLD} letters (e.g. \(D, M\))\\
+   refer to Matrices
+\end{itemize}
+
+\chapter{Introduction}\label{introduction}
+
+In this Master Thesis we try to extend a previously proposed concept of
+predicting the evolvability of \acf{FFD} given a
+Deformation-Matrix\cite{anrichterEvol}. In the original publication the
+author used random sampled points weighted with \acf{RBF} to deform the
+mesh and defined three different criteria that can be calculated prior
+to using an evolutional optimisation algorithm to asses the quality and
+potential of such optimisation.
+
+We will replicate the same setup on the same meshes but use \acf{FFD}
+instead of \acf{RBF} to create a deformation and evaluate if the
+evolution-criteria still work as a predictor given the different
+deformation.
+
+\section{\texorpdfstring{What is \acf{FFD}?}{What is ?}}\label{what-is}
+
+First of all we have to establish how a \ac{FFD} works and why this is a
+good tool for deforming meshes in the first place.
 
 \section{Was ist evolutionäre
 Optimierung?}\label{was-ist-evolutionuxe4re-optimierung}
@@ -227,27 +281,41 @@ Optimierung}\label{besonderheiten-der-optimierung}
 
 HAHA .. als ob -.-
 
-%%%%%%%%%%%%%%% Literaturverzeichnis %%%%%%%%%%%%%%%
 \backmatter
- 	%\pagenumbering{roman}
-	\cleardoublepage
-	\bibliographystyle{natdin} % 	\bibliographystyle{abbrv}
-	\bibliography{bibma}
-	\addcontentsline{toc}{chapter}{\numberline{}\bibname} % Literaturverzeichnis in das Inhaltsverzeichnis aufnehmen
-% 	\nocite{*}
+\cleardoublepage
+
+\renewcommand\thesection{\Roman{section}}
+\addtocontents{toc}{\protect\setcounter{tocdepth}{1}}
+\setcounter{section}{1} % reset section to 1 so its stars I, II, III,...
+\chapter*{Appendix}
+\addcontentsline{toc}{chapter}{\protect\numberline{}Appendix}
+\pagenumbering{roman}
+%%%%%%%%%%%%%%% Literaturverzeichnis %%%%%%%%%%%%%%%
+    \bibliographystyle{natdin} % 	\bibliographystyle{natdin}
+    \bibliography{bibma}
+    \addcontentsline{toc}{section}{\protect\numberline{\thesection}Bibliography} % Literaturverzeichnis in das Inhaltsverzeichnis aufnehmen
+    \addtocounter{section}{1}
+    \newpage
 
 %%%%%%%%%%%%%%% Anhang %%%%%%%%%%%%%%%
-% 	\clearpage					%spaeter alles wieder rein
- 	\begin{appendix} % Anhang, technische Details
+%    \clearpage					%spaeter alles wieder rein
 % % 		\input{files/appendix}
-%	\listofalgorithms
-%	\listoftheorems
-%	\listof{theorem}{List of Theorems}
+    \input{settings/abkuerzungen}
+    \addcontentsline{toc}{section}{\protect\numberline{\thesection}Abbreviations}
+    \addtocounter{section}{1}
+    \newpage
 
-%	\addcontentsline{toc}{chapter}{\numberline{}Abkürzungen}
-%	\input{settings/abkuerzungen}
+    \listofalgorithms
+    \addcontentsline{toc}{section}{\protect\numberline{\thesection}List of Algorithms}
+    \addtocounter{section}{1}
+    \newpage
+	
+	\listoffigures
+	\listoftables
 	\listoftodos
- 	\end{appendix}
+    \addcontentsline{toc}{section}{\protect\numberline{\thesection}TODOs}
+    \addtocounter{section}{1}
+    \newpage
 % 	\printindex
 
 %%%%%%%%%%%%%%% Erklaerung %%%%%%%%%%%%%%%

arbeit/settings/abkuerzungen.tex

@@ -1,4 +1,4 @@
-\chapter*{Abkürzungen}
+\chapter*{Abbreviations}
 \label{cha:abbrev}
 \begin{acronym}
 % Zugriff ueber \ac{BWT} 1te mal Vollreferenz, danach Abk.
@@ -10,14 +10,9 @@
 %
 %\acro{GPL}{GNU General Public License} --
 % License for free software, see \url{http://www.gnu.org/copyleft/gpl.html}.
-\acro{KNN}{K-Nearest-Neighbor}
-\acro{ODCT}{Overcomplete Discrete Cosine Transform}
-\acro{OMP}{Orthogonal Matching Pursuit}
-\acro{PCA}{Principle Component Analysis} 
-\acro{POI}{Points of Interest}
-\acro{RMSE}{Rooted Mean Square Error}
-\acro{SAS}{Sparse Approximate Solution} - Abschätzungsproblem einer spärlichen Repräsentation.
-\acro{SAT}{Summed Area Table}
+\acro{FFD}{Freeform-Deformation}
+\acro{DM-FFD}{Direct Manipulation Freeform-Deformation}
+\acro{RBF}{Radial Basis Function}
 
 %
 %

arbeit/settings/packages.tex

@@ -6,14 +6,16 @@
 \usepackage{amsthm}						%Theorems
 %% algorithm needs to be after hyperref
 %\usepackage{ae} 							% Umbruch von Woertern mit Umlauten
-%\usepackage[english]{babel}
-\usepackage[ngerman]{babel} 					% benutzt globales ngerman
+\usepackage[english]{babel}
+%\usepackage[ngerman]{babel} 					% benutzt globales ngerman
 \usepackage{bbold}
 \usepackage{booktabs}
 \usepackage{cancel}
 \usepackage{caption}
 \usepackage{color}						%\colorbox
 \usepackage{dsfont}						%\mathds
+\usepackage{draftwatermark}
+\SetWatermarkLightness{0.9} % default: 0.8
 \usepackage{epigraph}
 % \usepackage{euler}  					% euler: uni, eucal: baake, ohne: standard
 \usepackage{eucal}						% euler calligraphy
@@ -35,7 +37,9 @@
 \usepackage{multirow}
 \usepackage{nicefrac}
 \usepackage[numbers,square]{natbib}
-% \usepackage[draft]{pdfpages}
+\newcommand*{\refname}{References}
+\usepackage{patchcmd}
+%\usepackage[draft]{pdfpages}
 \usepackage{pdfpages}
 %\usepackage{pst-all}					% PSTricks-Grafikerstellung
 %\usepackage{pstricks}

arbeit/template.tex

@@ -67,6 +67,19 @@ titlepage,
 % % 	files/7_0_evaluation%
 % % 	,files/8_0_conclusion%
 % }
+
+%%%%%%%%%%%%%%% PANDOC-nedded defs %%%%%%%%%%
+\providecommand{\tightlist}{%
+  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
+
+%disable "Redefining ngerman shorthand"-Message
+% \makeatletter
+% \patchcmd{\pdfstringdef}
+%   {\csname HyPsd@babel@}
+%   {\let\bbl@info\@gobble\csname HyPsd@babel@}
+%   {}{}
+% \makeatother
+
 %%%%%%%%%%%%%%% Hauptdokument %%%%%%%%%%%%%%%
 \begin{document}
 
@@ -97,38 +110,50 @@ titlepage,
 %%%%%%%%%%%%%%% Verzeichnisse %%%%%%%%%%%%%%%
 \frontmatter % Abstrakte Gliederungsebene: Anfang des Buches
 	\tableofcontents		% Rueckseite leer
-	\listoffigures
-	\listoftables
 %\lstlistoflistings % fuer listingsverzeichnis mit package listings
 
 %%%%%%%%%%%%%%% Hauptteil %%%%%%%%%%%%%%%
 % Insgesamt ca. 60-100 Seiten Davon mindesten 50% Eigene Arbeit
 \mainmatter %Abstrakte Gliederungsebene: Hauptteil des Buches
 \pagestyle{fancy}
-	%\pagenumbering{arabic}
+\pagenumbering{arabic}
 $body$
 
-%%%%%%%%%%%%%%% Literaturverzeichnis %%%%%%%%%%%%%%%
 \backmatter
- 	%\pagenumbering{roman}
-	\cleardoublepage
-	\bibliographystyle{natdin} % 	\bibliographystyle{abbrv}
-	\bibliography{bibma}
-	\addcontentsline{toc}{chapter}{\numberline{}\bibname} % Literaturverzeichnis in das Inhaltsverzeichnis aufnehmen
-% 	\nocite{*}
+\cleardoublepage
+
+\renewcommand\thesection{\Roman{section}}
+\addtocontents{toc}{\protect\setcounter{tocdepth}{1}}
+\setcounter{section}{1} % reset section to 1 so its stars I, II, III,...
+\chapter*{Appendix}
+\addcontentsline{toc}{chapter}{\protect\numberline{}Appendix}
+\pagenumbering{roman}
+%%%%%%%%%%%%%%% Literaturverzeichnis %%%%%%%%%%%%%%%
+    \bibliographystyle{natdin} % 	\bibliographystyle{natdin}
+    \bibliography{bibma}
+    \addcontentsline{toc}{section}{\protect\numberline{\thesection}Bibliography} % Literaturverzeichnis in das Inhaltsverzeichnis aufnehmen
+    \addtocounter{section}{1}
+    \newpage
 
 %%%%%%%%%%%%%%% Anhang %%%%%%%%%%%%%%%
-% 	\clearpage					%spaeter alles wieder rein
- 	\begin{appendix} % Anhang, technische Details
+%    \clearpage					%spaeter alles wieder rein
 % % 		\input{files/appendix}
-%	\listofalgorithms
-%	\listoftheorems
-%	\listof{theorem}{List of Theorems}
+    \input{settings/abkuerzungen}
+    \addcontentsline{toc}{section}{\protect\numberline{\thesection}Abbreviations}
+    \addtocounter{section}{1}
+    \newpage
 
-%	\addcontentsline{toc}{chapter}{\numberline{}Abkürzungen}
-%	\input{settings/abkuerzungen}
+    \listofalgorithms
+    \addcontentsline{toc}{section}{\protect\numberline{\thesection}List of Algorithms}
+    \addtocounter{section}{1}
+    \newpage
+	
+	\listoffigures
+	\listoftables
 	\listoftodos
- 	\end{appendix}
+    \addcontentsline{toc}{section}{\protect\numberline{\thesection}TODOs}
+    \addtocounter{section}{1}
+    \newpage
 % 	\printindex
 
 %%%%%%%%%%%%%%% Erklaerung %%%%%%%%%%%%%%%