fixed plots

thesis/base/declaration_en.tex

@@ -24,15 +24,12 @@
 not used other than the declared sources/resources, and that I have
 explicitly indicated all material which has been quoted either
 literally or by content from the sources used.
-\ifthenelse{\equal{\ThesisTitle}{master's thesis} \or
+The text document uploaded to TUGRAZonline is identical to the present \ThesisTitle.
-	\equal{\ThesisTitle}{diploma thesis} \or
-	\equal{\ThesisTitle}{doctoral thesis}}
-{The text document uploaded to TUGRAZonline is identical to the present \ThesisTitle.}{\reminder{TODO: fix \textbackslash ThesisTitle}}
 
 
 \par\vspace*{4cm}
 \centerline{
-\begin{tabular}{m{1.5cm}cm{1.5cm}m{3cm}m{1.5cm}cm{1.5cm}}
+	\begin{tabular}{m{1.5cm}cm{1.5cm}m{3cm}m{1.5cm}cm{1.5cm}}
-\cline{1-3} \cline{5-7}
+		\cline{1-3} \cline{5-7}
- & date & & & & (signature) &\\
+		 & date &  &  &  & (signature) & \\
-\end{tabular}}
+	\end{tabular}}

thesis/base/layout_thesis.tex

@@ -55,7 +55,7 @@
 \makeatother
 
 % header and footer texts
-\clearscrheadfoot % clear everything
+\clearpairofpagestyles % clear everything
 \KOMAoptions{headlines=1} % header needs two lines here
 % [plain]{actual (scrheadings)}
 \ihead[]{}%
@@ -141,46 +141,46 @@
 \ifthenelse{\equal{\DocumentLanguage}{en}}{\renewcaptionname{USenglish}{\figurename}{Figure}}{}%
 \ifthenelse{\equal{\DocumentLanguage}{de}}{\renewcaptionname{ngerman}{\figurename}{Abbildung}}{}%
 \captionsetup{%
-format=hang,% hanging captions
+	format=hang,% hanging captions
-labelformat=simple,% just name and number
+	labelformat=simple,% just name and number
-labelsep=colon,% colon and space
+	labelsep=colon,% colon and space
-justification=justified,%
+	justification=justified,%
-singlelinecheck=true,% center single line captions
+	singlelinecheck=true,% center single line captions
-font={footnotesize,it},% font style of label and text
+	font={footnotesize,it},% font style of label and text
-margin=0.025\textwidth,% margin left/right of the caption (to textwidth)
+	margin=0.025\textwidth,% margin left/right of the caption (to textwidth)
-indention=0pt,% no further indention (just hanging)
+	indention=0pt,% no further indention (just hanging)
-hangindent=0pt,% no further indention (just hanging)}
+	hangindent=0pt,% no further indention (just hanging)}
-aboveskip=8pt,% same spacing above and...
+	aboveskip=8pt,% same spacing above and...
-belowskip=8pt}% ...below the float (this way tables shouln't be a problem, either)
+	belowskip=8pt}% ...below the float (this way tables shouln't be a problem, either)
 
 % code listings
 \lstloadlanguages{VHDL,Matlab,[ANSI]C,Java,[LaTeX]TeX}
 \lstset{%
-%   general
+	%   general
-breaklines=true,% automatically break long lines
+	breaklines=true,% automatically break long lines
-breakatwhitespace=true,% break only at white spaces
+	breakatwhitespace=true,% break only at white spaces
-breakindent=1cm,% additional indentation for broken lines
+	breakindent=1cm,% additional indentation for broken lines
-%   positioning
+	%   positioning
-linewidth=\linewidth,% set width of whole thing to \linewidth
+	linewidth=\linewidth,% set width of whole thing to \linewidth
-xleftmargin=0.1\linewidth,%
+	xleftmargin=0.1\linewidth,%
-%   frame and caption
+	%   frame and caption
-frame=tlrb,% frame the entire thing
+	frame=tlrb,% frame the entire thing
-framexleftmargin=1cm,% to include linenumbering into frame
+	framexleftmargin=1cm,% to include linenumbering into frame
-captionpos=b,% caption at bottom
+	captionpos=b,% caption at bottom
-%   format parameters
+	%   format parameters
-basicstyle=\ttfamily\tiny,% small true type font
+	basicstyle=\ttfamily\tiny,% small true type font
-keywordstyle=\color{black},%
+	keywordstyle=\color{black},%
-identifierstyle=\color{black},%
+	identifierstyle=\color{black},%
-commentstyle=\color[rgb]{0.45,0.45,0.45},% gray
+	commentstyle=\color[rgb]{0.45,0.45,0.45},% gray
-stringstyle=\color{black},%
+	stringstyle=\color{black},%
-showstringspaces=false,%
+	showstringspaces=false,%
-showtabs=false,%
+	showtabs=false,%
-tabsize=2,%
+	tabsize=2,%
-%   linenumbers
+	%   linenumbers
-numberstyle=\tiny,%
+	numberstyle=\tiny,%
-numbers=left,%
+	numbers=left,%
-numbersep=3mm,%
+	numbersep=3mm,%
-firstnumber=1,%
+	firstnumber=1,%
-stepnumber=1,% number every line (0: off)
+	stepnumber=1,% number every line (0: off)
-numberblanklines=true%
+	numberblanklines=true%
 }

thesis/base/macros.tex

@@ -147,22 +147,22 @@
 %   standard
 \newcommand{\fig}[3]{\begin{figure}\centering\includegraphics[width=\textwidth]{#2}\caption{#3}\label{fig:#1}\end{figure}}%
 %   with controllable parameters
-\newcommand{\figc}[4]{\begin{figure}\centering\includegraphics[#1]{#2}\caption{#3}\label{fig:#4}\end{figure}}%
+\newcommand{\figc}[4]{\begin{figure}\centering\includegraphics[#4]{#2}\caption{#3}\label{fig:#1}\end{figure}}%
 %   two subfigures
 \newcommand{\twofig}[6]{\begin{figure}\centering%
-\subfigure[#2]{\includegraphics[width=0.495\textwidth]{#1}}%
+		\subfigure[#2]{\includegraphics[width=0.495\textwidth]{#1}}%
-\subfigure[#4]{\includegraphics[width=0.495\textwidth]{#3}}%
+		\subfigure[#4]{\includegraphics[width=0.495\textwidth]{#3}}%
-\caption{#5}\label{fig:#6}\end{figure}}%
+		\caption{#5}\label{fig:#6}\end{figure}}%
 %   two subfigures with labels for each subplot
 \newcommand{\twofigs}[8]{\begin{figure}\centering%
-\subfigure[#2]{\includegraphics[width=0.495\textwidth]{#1}\label{fig:#8#3}}%
+		\subfigure[#2]{\includegraphics[width=0.495\textwidth]{#1}\label{fig:#8#3}}%
-\subfigure[#5]{\includegraphics[width=0.495\textwidth]{#4}\label{fig:#8#6}}%
+		\subfigure[#5]{\includegraphics[width=0.495\textwidth]{#4}\label{fig:#8#6}}%
-\caption{#7}\label{fig:#8}\end{figure}}%
+		\caption{#7}\label{fig:#8}\end{figure}}%
 %   two subfigures and controllable parameters
 \newcommand{\twofigc}[8]{\begin{figure}\centering%
-\subfigure[#3]{\includegraphics[#1]{#2}}%
+		\subfigure[#3]{\includegraphics[#1]{#2}}%
-\subfigure[#6]{\includegraphics[#4]{#5}}%
+		\subfigure[#6]{\includegraphics[#4]{#5}}%
-\caption{#7}\label{fig:#8}\end{figure}}%
+		\caption{#7}\label{fig:#8}\end{figure}}%
 
 % framed figures
 %   standard
@@ -171,19 +171,19 @@
 \newcommand{\figcf}[4]{\begin{figure}\centering\fbox{\includegraphics[#1]{#2}}\caption{#3}\label{fig:#4}\end{figure}}%
 %   two subfigures
 \newcommand{\twofigf}[6]{\begin{figure}\centering%
-\fbox{\subfigure[#2]{\includegraphics[width=0.495\textwidth]{#1}}}%
+		\fbox{\subfigure[#2]{\includegraphics[width=0.495\textwidth]{#1}}}%
-\fbox{\subfigure[#4]{\includegraphics[width=0.495\textwidth]{#3}}}%
+		\fbox{\subfigure[#4]{\includegraphics[width=0.495\textwidth]{#3}}}%
-\caption{#5}\label{fig:#6}\end{figure}}%
+		\caption{#5}\label{fig:#6}\end{figure}}%
 %   two subfigures with labels for each subplot
 \newcommand{\twofigsf}[8]{\begin{figure}\centering%
-\fbox{\subfigure[#2]{\includegraphics[width=0.495\textwidth]{#1}\label{fig:#8#3}}}%
+		\fbox{\subfigure[#2]{\includegraphics[width=0.495\textwidth]{#1}\label{fig:#8#3}}}%
-\fbox{\subfigure[#5]{\includegraphics[width=0.495\textwidth]{#4}\label{fig:#8#6}}}%
+		\fbox{\subfigure[#5]{\includegraphics[width=0.495\textwidth]{#4}\label{fig:#8#6}}}%
-\caption{#7}\label{fig:#8}\end{figure}}%
+		\caption{#7}\label{fig:#8}\end{figure}}%
 %   two subfigures and controllable parameters
 \newcommand{\twofigcf}[8]{\begin{figure}\centering%
-\fbox{\subfigure[#3]{\includegraphics[#1]{#2}}}%
+		\fbox{\subfigure[#3]{\includegraphics[#1]{#2}}}%
-\fbox{\subfigure[#6]{\includegraphics[#4]{#5}}}%
+		\fbox{\subfigure[#6]{\includegraphics[#4]{#5}}}%
-\caption{#7}\label{fig:#8}\end{figure}}%
+		\caption{#7}\label{fig:#8}\end{figure}}%
 
 % listings
 \newcommand{\filelisting}[5][]{\lstinputlisting[style=#2,caption={#4},label={lst:#5},#1]{#3}}

thesis/base/packages.tex

@@ -47,33 +47,33 @@
 \usepackage{fixltx2e}% LaTeX 2e bugfixes
 \usepackage{ifthen}% for optional parts
 \ifthenelse{\equal{\PaperSize}{a4paper}}{
-\usepackage[paper=\PaperSize,twoside=\Twosided,%
+	\usepackage[paper=\PaperSize,twoside=\Twosided,%
-textheight=246mm,%
+		textheight=246mm,%
-textwidth=160mm,%
+		textwidth=160mm,%
-heightrounded=true,% round textheight to multiple of lines (avoids overfull vboxes)
+		heightrounded=true,% round textheight to multiple of lines (avoids overfull vboxes)
-ignoreall=true,% do not include header, footer, and margins in calculations
+		ignoreall=true,% do not include header, footer, and margins in calculations
-marginparsep=5pt,% marginpar only used for signs (centered), thus only small sep. needed
+		marginparsep=5pt,% marginpar only used for signs (centered), thus only small sep. needed
-marginparwidth=10mm,% prevent margin notes to be out of page
+		marginparwidth=10mm,% prevent margin notes to be out of page
-hmarginratio=2:1,% set margin ration (inner:outer for twoside) - (2:3 is default)
+		hmarginratio=2:1,% set margin ration (inner:outer for twoside) - (2:3 is default)
-]{geometry}}{}%
+	]{geometry}}{}%
 \ifthenelse{\equal{\PaperSize}{letterpaper}}{
-\usepackage[paper=\PaperSize,twoside=\Twosided,%
+	\usepackage[paper=\PaperSize,twoside=\Twosided,%
-textheight=9in,%
+		textheight=9in,%
-textwidth=6.5in,%
+		textwidth=6.5in,%
-heightrounded=true,% round textheight to multiple of lines (avoids overfull vboxes)
+		heightrounded=true,% round textheight to multiple of lines (avoids overfull vboxes)
-ignoreheadfoot=false,% do not include header and footer in calculations
+		ignoreheadfoot=false,% do not include header and footer in calculations
-marginparsep=5pt,% marginpar only used for signs (centered), thus only small sep. needed
+		marginparsep=5pt,% marginpar only used for signs (centered), thus only small sep. needed
-marginparwidth=10mm,% prevent margin notes to be out of page
+		marginparwidth=10mm,% prevent margin notes to be out of page
-hmarginratio=3:2,% set margin ration (inner:outer for twoside) - (2:3 is default)
+		hmarginratio=3:2,% set margin ration (inner:outer for twoside) - (2:3 is default)
-]{geometry}}{}%
+	]{geometry}}{}%
 \ifthenelse{\equal{\DocumentLanguage}{en}}{\usepackage[T1]{fontenc}\usepackage[utf8]{inputenc}\usepackage[USenglish]{babel}}{}%
 \ifthenelse{\equal{\DocumentLanguage}{de}}{\usepackage[T1]{fontenc}\usepackage[utf8]{inputenc}\usepackage[ngerman]{babel}}{}%
 \usepackage[%
-headtopline,plainheadtopline,% activate all lines (header and footer)
+	headtopline,plainheadtopline,% activate all lines (header and footer)
-headsepline,plainheadsepline,%
+	headsepline,plainheadsepline,%
-footsepline,plainfootsepline,%
+	footsepline,plainfootsepline,%
-footbotline,plainfootbotline,%
+	footbotline,plainfootbotline,%
-automark% auto update \..mark
+	automark% auto update \..mark
 ]{scrlayer-scrpage}% (KOMA)
 \usepackage{imakeidx}
 \usepackage[]{caption}% customize captions
@@ -91,7 +91,7 @@ automark% auto update \..mark
 \usepackage[normalem]{ulem}% cross-out, strike-out, underlines (normalem: keep \emph italic)
 %\usepackage[safe]{textcomp}% loading in safe mode to avoid problems (see LaTeX companion)
 %\usepackage[geometry,misc]{ifsym}% technical symbols
-\usepackage{remreset}%\@removefromreset commands (e.g., for continuous footnote numbering)
+%\usepackage{remreset}%\@removefromreset commands (e.g., for continuous footnote numbering)
 \usepackage{paralist}% extended list environments
 % \usepackage[Sonny]{fncychap}
 \usepackage[avantgarde]{quotchap}
@@ -140,35 +140,35 @@ automark% auto update \..mark
 \usepackage{mdwlist}              %list extensions
 \ifthenelse{\equal{\DocumentLanguage}{de}}
 {
-  \usepackage[german]{fancyref}   %Bessere Querverweise
+	\usepackage[german]{fancyref}   %Bessere Querverweise
-  \usepackage[locale=DE]{siunitx}     %Zahlen und SI Einheiten => Binary units aktivieren...
+	\usepackage[locale=DE]{siunitx}     %Zahlen und SI Einheiten => Binary units aktivieren...
-  \usepackage[autostyle=true,     %Anführungszeichen und Übersetzung der Literaturverweise
+	\usepackage[autostyle=true,     %Anführungszeichen und Übersetzung der Literaturverweise
-  german=quotes]{csquotes}        %Anführungszeichen und Übersetzung der Literaturverweise
+		german=quotes]{csquotes}        %Anführungszeichen und Übersetzung der Literaturverweise
 }
 {
-  \usepackage[english]{fancyref}  %Bessere Querverweise
+	\usepackage[english]{fancyref}  %Bessere Querverweise
-  \usepackage[locale=US]{siunitx}     %Zahlen und SI Einheiten => Binary units aktivieren...
+	\usepackage[locale=US]{siunitx}     %Zahlen und SI Einheiten => Binary units aktivieren...
-  \usepackage[autostyle=true]     %Anführungszeichen und Übersetzung der Literaturverweise
+	\usepackage[autostyle=true]     %Anführungszeichen und Übersetzung der Literaturverweise
-  {csquotes}
+	{csquotes}
 }
 \sisetup{detect-weight=true, detect-family=true} %format like surrounding environment
 %extending fancyref for listings in both languages:
 \newcommand*{\fancyreflstlabelprefix}{lst}
 \fancyrefaddcaptions{english}{%
-  \providecommand*{\freflstname}{listing}%
+	\providecommand*{\freflstname}{listing}%
-  \providecommand*{\Freflstname}{Listing}%
+	\providecommand*{\Freflstname}{Listing}%
 }
 \fancyrefaddcaptions{german}{%
-  \providecommand*{\freflstname}{Listing}%
+	\providecommand*{\freflstname}{Listing}%
-  \providecommand*{\Freflstname}{Listing}%
+	\providecommand*{\Freflstname}{Listing}%
 }
 \frefformat{plain}{\fancyreflstlabelprefix}{\freflstname\fancyrefdefaultspacing#1}
 \Frefformat{plain}{\fancyreflstlabelprefix}{\Freflstname\fancyrefdefaultspacing#1}
 \frefformat{vario}{\fancyreflstlabelprefix}{%
-  \freflstname\fancyrefdefaultspacing#1#3%
+	\freflstname\fancyrefdefaultspacing#1#3%
 }
 \Frefformat{vario}{\fancyreflstlabelprefix}{%
-  \Freflstname\fancyrefdefaultspacing#1#3%
+	\Freflstname\fancyrefdefaultspacing#1#3%
 }
 
 \sisetup{separate-uncertainty}    %enable uncertainity for siunitx
@@ -176,30 +176,30 @@ automark% auto update \..mark
 \DeclareSIUnit\permille{\text{\textperthousand}} %add \permille to siunitx
 \usepackage{xfrac}                %Schönere brüche für SI Einheiten
 \sisetup{per-mode=fraction,       %Bruchstriche bei SI Einheiten aktivieren
-fraction-function=\sfrac}         %xfrac als Bruchstrichfunktion verwenden
+	fraction-function=\sfrac}         %xfrac als Bruchstrichfunktion verwenden
 \usepackage[scaled=0.78]{inconsolata}%Schreibmaschinenschrift für Quellcode
 
 \usepackage[backend=biber,        %Literaturverweiserweiterung Backend auswählen
-bibencoding=utf8,                 %.bib-File ist utf8-codiert...
+	bibencoding=utf8,                 %.bib-File ist utf8-codiert...
-maxbibnames=99,                   %Immer alle Authoren in der Bibliographie darstellen...
+	maxbibnames=99,                   %Immer alle Authoren in der Bibliographie darstellen...
-style=ieee
+	style=ieee
 ]{biblatex}
 \bibliography{bib/bibliography}      %literatur.bib wird geladen und als Literaturverweis Datei verwendet
 
 \ifthenelse{\equal{\FramedLinks}{true}}
 {
-  \usepackage[%
+	\usepackage[%
-  breaklinks=true,% allow line break in links
+		breaklinks=true,% allow line break in links
-  colorlinks=false,% if false: framed link
+		colorlinks=false,% if false: framed link
-  linkcolor=black,anchorcolor=black,citecolor=black,filecolor=black,%
+		linkcolor=black,anchorcolor=black,citecolor=black,filecolor=black,%
-  menucolor=black,urlcolor=black,bookmarksnumbered=true]{hyperref}% hyperlinks for references
+		menucolor=black,urlcolor=black,bookmarksnumbered=true]{hyperref}% hyperlinks for references
 }
 {
-  \usepackage[%
+	\usepackage[%
-  breaklinks=true,% allow line break in links
+		breaklinks=true,% allow line break in links
-  colorlinks=true,% if false: framed link
+		colorlinks=true,% if false: framed link
-  linkcolor=black,anchorcolor=black,citecolor=black,filecolor=black,%
+		linkcolor=black,anchorcolor=black,citecolor=black,filecolor=black,%
-  menucolor=black,urlcolor=black,bookmarksnumbered=true]{hyperref}% hyperlinks for references
+		menucolor=black,urlcolor=black,bookmarksnumbered=true]{hyperref}% hyperlinks for references
 }
 
 \setcounter{biburlnumpenalty}{100}%Urls in Bibliographie Zeilenbrechbar machen
@@ -213,8 +213,8 @@ style=ieee
 
 \ifthenelse{\equal{\DocumentLanguage}{de}}
 {
-  \deftranslation[to=ngerman]       %Dem Paket babel den deutschen Abkürzungsverzeichnis-Kapitelnamen
+	\deftranslation[to=ngerman]       %Dem Paket babel den deutschen Abkürzungsverzeichnis-Kapitelnamen
-  {Acronyms}{Abkürzungsverzeichnis} %beibringen
+	{Acronyms}{Abkürzungsverzeichnis} %beibringen
 }{}
 
 % misc

thesis/bib/bibliography.bib

@@ -41,7 +41,7 @@
 	numpages = {58},
 	keywords = {outlier detection, Anomaly detection},
 },
-@dataset{alexander_kyuroson_2023_7913307,
+dataset{alexander_kyuroson_2023_7913307,
 	author = {Alexander Kyuroson and Niklas Dahlquist and Nikolaos Stathoulopoulos
 	          and Vignesh Kottayam Viswanathan and Anton Koval and George
 	          Nikolakopoulos},
@@ -85,37 +85,6 @@
 	pages = {716–721},
 }
 ,
-@inproceedings{deepsvdd,
-	title = {Deep One-Class Classification},
-	author = {Ruff, Lukas and Vandermeulen, Robert and Goernitz, Nico and Deecke,
-	          Lucas and Siddiqui, Shoaib Ahmed and Binder, Alexander and M{\"u}ller
-	          , Emmanuel and Kloft, Marius},
-	booktitle = {Proceedings of the 35th International Conference on Machine
-	             Learning},
-	pages = {4393--4402},
-	year = {2018},
-	editor = {Dy, Jennifer and Krause, Andreas},
-	volume = {80},
-	series = {Proceedings of Machine Learning Research},
-	month = {10--15 Jul},
-	publisher = {PMLR},
-	pdf = {http://proceedings.mlr.press/v80/ruff18a/ruff18a.pdf},
-	url = {https://proceedings.mlr.press/v80/ruff18a.html},
-	abstract = {Despite the great advances made by deep learning in many machine
-	            learning problems, there is a relative dearth of deep learning
-	            approaches for anomaly detection. Those approaches which do exist
-	            involve networks trained to perform a task other than anomaly
-	            detection, namely generative models or compression, which are in
-	            turn adapted for use in anomaly detection; they are not trained on
-	            an anomaly detection based objective. In this paper we introduce a
-	            new anomaly detection method—Deep Support Vector Data Description—,
-	            which is trained on an anomaly detection based objective. The
-	            adaptation to the deep regime necessitates that our neural network
-	            and training procedure satisfy certain properties, which we
-	            demonstrate theoretically. We show the effectiveness of our method
-	            on MNIST and CIFAR-10 image benchmark datasets as well as on the
-	            detection of adversarial examples of GTSRB stop signs.},
-},
 @inproceedings{deep_svdd,
 	title = {Deep One-Class Classification},
 	author = {Ruff, Lukas and Vandermeulen, Robert and Goernitz, Nico and Deecke,
@@ -235,7 +204,7 @@
 	            performance;Current measurement},
 	doi = {10.1109/IROS51168.2021.9636694},
 },
-  @article{deep_learning_overview,
+article{deep_learning_overview,
 	title = {Deep learning in neural networks: An overview},
 	journal = {Neural Networks},
 	volume = {61},
@@ -289,7 +258,7 @@
 	            autoencoder algorithm are summarized, and prospected for its future
 	            development directions are addressed.},
 }, 
-@article{semi_overview,
+article{semi_overview,
 	author = {Yang, Xiangli and Song, Zixing and King, Irwin and Xu, Zenglin},
 	journal = {IEEE Transactions on Knowledge and Data Engineering},
 	title = {A Survey on Deep Semi-Supervised Learning},
@@ -302,7 +271,7 @@
 	            learning;semi-supervised learning;deep learning},
 	doi = {10.1109/TKDE.2022.3220219},
 }, 
-@book{ai_fundamentals_book,
+book{ai_fundamentals_book,
 	title = {Fundamentals of Artificial Intelligence},
 	url = {http://dx.doi.org/10.1007/978-81-322-3972-7},
 	DOI = {10.1007/978-81-322-3972-7},
@@ -312,7 +281,7 @@
 	language = {en},
 },
 
-@article{machine_learning_overview,
+article{machine_learning_overview,
 	title = {Machine Learning from Theory to Algorithms: An Overview},
 	volume = {1142},
 	ISSN = {1742-6596},
@@ -550,7 +519,7 @@
 	year = {1998},
 	pages = {2278–2324},
 },
-@article{ef_concept_source,
+article{ef_concept_source,
 	title = {Multi-Year ENSO Forecasts Using Parallel Convolutional Neural
 	         Networks With Heterogeneous Architecture},
 	volume = {8},
@@ -563,8 +532,226 @@
 	          and Tian, Hao and Song, Dehai and Wei, Zhiqiang},
 	year = {2021},
 	month = aug,
+}, 
+@article{ml_supervised_unsupervised_figure_source,
+	title = {Virtual reality in biology: could we become virtual naturalists?},
+	volume = {14},
+	ISSN = {1936-6434},
+	url = {http://dx.doi.org/10.1186/s12052-021-00147-x},
+	DOI = {10.1186/s12052-021-00147-x},
+	number = {1},
+	journal = {Evolution: Education and Outreach},
+	publisher = {Springer Science and Business Media LLC},
+	author = {Morimoto, Juliano and Ponton, Fleur},
+	year = {2021},
+	month = may,
+},
+@article{ml_autoencoder_figure_source,
+	title = "From Autoencoder to Beta-VAE",
+	author = "Weng, Lilian",
+	journal = "lilianweng.github.io",
+	year = "2018",
+	url = "https://lilianweng.github.io/posts/2018-08-12-vae/",
+},
+
+@conference{bg_lidar_figure_source,
+	title = "1D MEMS Micro-Scanning LiDAR",
+	author = "Norbert Druml and Ievgeniia Maksymova and Thomas Thurner and Lierop,
+	          {D. van} and Hennecke, {Marcus E.} and Andreas Foroutan",
+	year = "2018",
+	month = sep,
+	day = "16",
+	language = "English",
+},
+@book{deep_learning_book,
+	title = {Deep Learning},
+	author = {Ian Goodfellow and Yoshua Bengio and Aaron Courville},
+	publisher = {MIT Press},
+	note = {\url{http://www.deeplearningbook.org}},
+	year = {2016},
+},
+@misc{mobilenet,
+	doi = {10.48550/ARXIV.1704.04861},
+	url = {https://arxiv.org/abs/1704.04861},
+	author = {Howard, Andrew G. and Zhu, Menglong and Chen, Bo and Kalenichenko,
+	          Dmitry and Wang, Weijun and Weyand, Tobias and Andreetto, Marco and
+	          Adam, Hartwig},
+	keywords = {Computer Vision and Pattern Recognition (cs.CV), FOS: Computer and
+	            information sciences, FOS: Computer and information sciences},
+	title = {MobileNets: Efficient Convolutional Neural Networks for Mobile Vision
+	         Applications},
+	publisher = {arXiv},
+	year = {2017},
+	copyright = {arXiv.org perpetual, non-exclusive license},
+},
+@inproceedings{shufflenet,
+	title = {ShuffleNet: An Extremely Efficient Convolutional Neural Network for
+	         Mobile Devices},
+	url = {http://dx.doi.org/10.1109/CVPR.2018.00716},
+	DOI = {10.1109/cvpr.2018.00716},
+	booktitle = {2018 IEEE/CVF Conference on Computer Vision and Pattern
+	             Recognition},
+	publisher = {IEEE},
+	author = {Zhang, Xiangyu and Zhou, Xinyu and Lin, Mengxiao and Sun, Jian},
+	year = {2018},
+	month = jun,
+},
+@article{bg_svm,
+	title = {Support-vector networks},
+	author = {Cortes, Corinna and Vapnik, Vladimir},
+	journal = {Machine learning},
+	volume = {20},
+	number = {3},
+	pages = {273--297},
+	year = {1995},
+	publisher = {Springer},
+},
+
+@article{bg_kmeans,
+	author = {Lloyd, S.},
+	journal = {IEEE Transactions on Information Theory},
+	title = {Least squares quantization in PCM},
+	year = {1982},
+	volume = {28},
+	number = {2},
+	pages = {129-137},
+	keywords = {Noise;Quantization (signal);Voltage;Receivers;Pulse
+	            modulation;Sufficient conditions;Stochastic processes;Probabilistic
+	            logic;Urban areas;Q measurement},
+	doi = {10.1109/TIT.1982.1056489},
+},
+
+@inproceedings{bg_dbscan,
+	added-at = {2023-12-13T07:32:13.000+0100},
+	author = {Ester, Martin and Kriegel, Hans-Peter and Sander, Jörg and Xu,
+	          Xiaowei},
+	biburl = {
+	          https://www.bibsonomy.org/bibtex/279a9f3560daefa3775bd35543b4482e1/admin
+	          },
+	booktitle = {KDD},
+	crossref = {conf/kdd/1996},
+	editor = {Simoudis, Evangelos and Han, Jiawei and Fayyad, Usama M.},
+	ee = {http://www.aaai.org/Library/KDD/1996/kdd96-037.php},
+	interhash = {ba33e4d6b4e5b26bd9f543f26b7d250a},
+	intrahash = {79a9f3560daefa3775bd35543b4482e1},
+	isbn = {1-57735-004-9},
+	keywords = {},
+	pages = {226-231},
+	publisher = {AAAI Press},
+	timestamp = {2023-12-13T07:32:13.000+0100},
+	title = {A Density-Based Algorithm for Discovering Clusters in Large Spatial
+	         Databases with Noise.},
+	url = {http://dblp.uni-trier.de/db/conf/kdd/kdd96.html#EsterKSX96},
+	year = 1996,
+},
+ @article{bg_pca,
+	author = { Karl Pearson F.R.S. },
+	title = {LIII. On lines and planes of closest fit to systems of points in
+	         space},
+	journal = {The London, Edinburgh, and Dublin Philosophical Magazine and
+	           Journal of Science},
+	volume = {2},
+	number = {11},
+	pages = {559-572},
+	year = {1901},
+	publisher = {Taylor & Francis},
+	doi = {10.1080/14786440109462720},
+},
+@article{bg_infomax,
+	author = {Linsker, R.},
+	journal = {Computer},
+	title = {Self-organization in a perceptual network},
+	year = {1988},
+	volume = {21},
+	number = {3},
+	pages = {105-117},
+	keywords = {Intelligent networks;Biological information
+	            theory;Circuits;Biology computing;Animal
+	            structures;Neuroscience;Genetics;System testing;Neural
+	            networks;Constraint theory},
+	doi = {10.1109/2.36},
+},
+@article{bg_slam,
+	title = {On the Representation and Estimation of Spatial Uncertainty},
+	volume = {5},
+	ISSN = {1741-3176},
+	url = {http://dx.doi.org/10.1177/027836498600500404},
+	DOI = {10.1177/027836498600500404},
+	number = {4},
+	journal = {The International Journal of Robotics Research},
+	publisher = {SAGE Publications},
+	author = {Smith, Randall C. and Cheeseman, Peter},
+	year = {1986},
+	month = dec,
+	pages = {56–68},
+},
+@article{roc_vs_prc2,
+	title = {Context discovery for anomaly detection},
+	volume = {19},
+	ISSN = {2364-4168},
+	url = {http://dx.doi.org/10.1007/s41060-024-00586-x},
+	DOI = {10.1007/s41060-024-00586-x},
+	number = {1},
+	journal = {International Journal of Data Science and Analytics},
+	publisher = {Springer Science and Business Media LLC},
+	author = {Calikus, Ece and Nowaczyk, Slawomir and Dikmen, Onur},
+	year = {2024},
+	month = jun,
+	pages = {99–113},
+},
+@article{roc_vs_prc,
+	title = {On the evaluation of unsupervised outlier detection: measures,
+	         datasets, and an empirical study},
+	volume = {30},
+	ISSN = {1573-756X},
+	url = {http://dx.doi.org/10.1007/s10618-015-0444-8},
+	DOI = {10.1007/s10618-015-0444-8},
+	number = {4},
+	journal = {Data Mining and Knowledge Discovery},
+	publisher = {Springer Science and Business Media LLC},
+	author = {Campos, Guilherme O. and Zimek, Arthur and Sander, J\"{o}rg and
+	          Campello, Ricardo J. G. B. and Micenková, Barbora and Schubert, Erich
+	          and Assent, Ira and Houle, Michael E.},
+	year = {2016},
+	month = jan,
+	pages = {891–927},
+},
+@inproceedings{roc,
+	title = {Basic principles of ROC analysis},
+	author = {Metz, Charles E},
+	booktitle = {Seminars in nuclear medicine},
+	volume = {8},
+	number = {4},
+	pages = {283--298},
+	year = {1978},
+	organization = {Elsevier},
+},
+@article{prc,
+	title = {A critical investigation of recall and precision as measures of
+	         retrieval system performance},
+	volume = {7},
+	ISSN = {1558-2868},
+	url = {http://dx.doi.org/10.1145/65943.65945},
+	DOI = {10.1145/65943.65945},
+	number = {3},
+	journal = {ACM Transactions on Information Systems},
+	publisher = {Association for Computing Machinery (ACM)},
+	author = {Raghavan, Vijay and Bollmann, Peter and Jung, Gwang S.},
+	year = {1989},
+	month = jul,
+	pages = {205–229},
+},
+@article{zscore,
+	title = {Advanced engineering mathematics},
+	author = {Kreyszig, Erwin and Stroud, K and Stephenson, G},
+	journal = {Integration},
+	volume = {9},
+	number = {4},
+	pages = {1014},
+	year = {2008},
+	publisher = {John Wiley \& Sons, Inc. 9 th edition, 2006 Page 2 of 6 Teaching
+	             methods~…},
 }
 
 
 
-

thesis/diagrams/deepsad_procedure/deepsad_procedure.tex

@@ -1,5 +1,6 @@
 \documentclass[tikz,border=10pt]{standalone}
 \usepackage{tikz}
+\usepackage{amsfonts}
 \usetikzlibrary{positioning, shapes.geometric, fit, arrows, arrows.meta, backgrounds}
 
 % Define box styles
@@ -7,9 +8,9 @@
   databox/.style={rectangle, align=center, draw=black, fill=blue!50, thick, rounded corners},%, inner sep=4},
   procbox/.style={rectangle, align=center, draw=black, fill=orange!30, thick, rounded corners},
   hyperbox/.style={rectangle, align=center, draw=black, fill=green!30, thick, rounded corners},
-  stepsbox/.style={rectangle, align=left, draw=black,fill=white, rounded corners, minimum width=6cm, minimum height=1.5cm, font=\small},
+  stepsbox/.style={rectangle, align=left, draw=black,fill=white, rounded corners, minimum width=5.2cm, minimum height=1.5cm, font=\small},
-  outputbox/.style={rectangle, align=center, draw=red!80, fill=red!20, rounded corners, minimum width=6cm, minimum height=1.5cm, font=\small},
+  outputbox/.style={rectangle, align=center, draw=red!80, fill=red!20, rounded corners, minimum width=5.2cm, minimum height=1.5cm, font=\small},
-  hlabelbox/.style={rectangle, align=center, draw=black,fill=white, rounded corners, minimum width=6cm, minimum height=1.5cm, font=\small},
+  hlabelbox/.style={rectangle, align=center, draw=black,fill=white, rounded corners, minimum width=5.2cm, minimum height=1.5cm, font=\small},
   vlabelbox/.style={rectangle, align=center, draw=black,fill=white, rounded corners, minimum width=3cm, minimum height=1.8cm, font=\small},
   arrow/.style={-{Latex[length=3mm]}},
   arrowlabel/.style={fill=white,inner sep=2pt,midway}
@@ -25,11 +26,11 @@
 \begin{tikzpicture}[node distance=1cm and 2cm]
 
 	\node (data) {Data};
-	\node[right=7 of data] (process) {Procedure};
+	\node[right=4.9 of data] (process) {Procedure};
-	\node[right=7 of process] (hyper) {Hyperparameters};
+	\node[right=4.1 of process] (hyper) {Hyperparameters};
 
 	\begin{pgfonlayer}{foreground}
-		\node[hlabelbox, below=of data] (unlabeled) {\boxtitle{Unlabeled Data} More normal than \\ anomalous samples required};
+		\node[hlabelbox, below=1.29 of data] (unlabeled) {\boxtitle{Unlabeled Data} Significantly more normal than \\ anomalous samples required};
 		\node[hlabelbox, below=.1 of unlabeled] (labeled) {\boxtitle{Labeled Data} No requirement regarding ratio \\ +1 = normal, -1 = anomalous};
 	\end{pgfonlayer}
 	\begin{pgfonlayer}{background}
@@ -39,16 +40,16 @@
 	%\draw[arrow] (latent.east) -- node{} (autoenc.west);
 
 	\begin{pgfonlayer}{foreground}
-		\node[stepsbox, below=of process] (pretrainproc) {Train Autoencoder for $E_A$ Epochs \\ with $L_A$ Learning Rate \\ No Labels Used};
+		\node[stepsbox, below=of process] (pretrainproc) {Train Autoencoder $\mathcal{\phi}_{AE}$ \\ optimize Autoencoding Objective \\ for $E_A$ Epochs \\ with $L_A$ Learning Rate \\ No Labels Used / Required};
-		\node[outputbox, below=.1 of pretrainproc] (pretrainout) {\boxtitle{Outputs} Encoder Network \\ $\mathbf{w}$: Network Weights};
+		\node[outputbox, below=.1 of pretrainproc] (pretrainout) {\boxtitle{Outputs} $\mathcal{\phi}$: Encoder / DeepSAD Network \\ $\mathcal{W}_E$: Encoder Network Weights};
 	\end{pgfonlayer}
 	\begin{pgfonlayer}{background}
 		\node[procbox, fit=(pretrainproc) (pretrainout), label={[label distance = 1, name=pretrainlab]above:{\textbf{Pre-Training of Autoencoder}}}] (pretrain) {};
 	\end{pgfonlayer}
 
 	\begin{pgfonlayer}{foreground}
-    \node[hlabelbox, below=of hyper] (autoencarch) {\boxtitle{Autoencoder Architecture} Choose based on data type \\ Latent Space Size (based on complexity)};
+		\node[hlabelbox, below=1.26 of hyper] (autoencarch) {\boxtitle{Autoencoder Architecture} $\mathcal{\phi}_{AE}$: Autoencoder Network \\ $\mathbb{R}^d$: Latent Space Size };
-		\node[hlabelbox, below=.1 of autoencarch] (pretrainhyper) {\boxtitle{Hyperparameters} $E_A$: Number of Epochs  \\ $L_A$: Learning Rate};
+		\node[hlabelbox, below=.1 of autoencarch] (pretrainhyper) {\boxtitle{Hyperparameters} $E_A$: Number of Epochs  \\ $L_A$: Learning Rate AE};
 	\end{pgfonlayer}
 	\begin{pgfonlayer}{background}
 		\node[hyperbox, fit=(autoencarch) (pretrainhyper), label={[label distance = 1, name=autoenclabel]above:{\textbf{Pre-Training Hyperparameters}}}] (pretrainhyp) {};
@@ -61,7 +62,7 @@
 	%	\draw[arrow] (node cs:name=autoenc,angle=196) |- (node cs:name=pretrain,angle=5);
 
 	\begin{pgfonlayer}{foreground}
-		\node[stepsbox, below=1.4 of pretrain] (calccproc) {1. Init Encoder with $\mathbf{w}$ \\ 2. Forward Pass on all data \\ 3. $\mathbf{c}$ = Mean Latent Representation};
+		\node[stepsbox, below=1.4 of pretrain] (calccproc) {Init Network $\mathcal{\phi}$ with $\mathcal{W}_E$ \\ Forward Pass on all data \\  Hypersphere center $\mathbf{c}$ is mean \\ of all Latent Representation};
 		\node[outputbox, below=.1 of calccproc] (calccout) {\boxtitle{Outputs} $\mathbf{c}$: Hypersphere Center};
 	\end{pgfonlayer}
 	\begin{pgfonlayer}{background}
@@ -76,21 +77,21 @@
 	%\draw[arrow] (node cs:name=traindata,angle=-45) |- node[arrowlabel]{all training data, labels removed} (node cs:name=calcc,angle=200);
 
 	\begin{pgfonlayer}{foreground}
-		\node[stepsbox, below=1.4 of calcc] (maintrainproc) {Train Network for $E_M$ Epochs \\ with $L_M$ Learning Rate \\ Considers Labels with $\eta$ strength};
+		\node[stepsbox, below=1.4 of calcc] (maintrainproc) {Init Network $\mathcal{\phi}$ with $\mathcal{W}_E$ \\ Train Network $\mathcal{\phi}$  \\ optimize DeepSAD Objective\\ for $E_M$ Epochs \\ with $L_M$ Learning Rate \\ Considers Labels with $\eta$ strength};
-		\node[outputbox, below=.1 of maintrainproc] (maintrainout) {\boxtitle{Outputs} Encoder Network \\ $\mathbf{w}$: Network Weights  \\ $\mathbf{c}$: Hypersphere Center};
+		\node[outputbox, below=.1 of maintrainproc] (maintrainout) {\boxtitle{Outputs} $\mathcal{\phi}$: DeepSAD Network \\ $\mathcal{W}$: DeepSAD Network Weights  \\ $\mathbf{c}$: Hypersphere Center};
 	\end{pgfonlayer}
 	\begin{pgfonlayer}{background}
 		\node[procbox, fit=(maintrainproc) (maintrainout), label={[label distance = 1, name=maintrainlab]above:{\textbf{Main Training}}}] (maintrain) {};
 	\end{pgfonlayer}
 
 	\begin{pgfonlayer}{foreground}
-		\node[hlabelbox, below=11.25 of hyper] (maintrainhyper) {$E_M$: Number of Epochs  \\ $L_M$: Learning Rate  \\ $\eta$: Strength Labeled/Unlabeled};
+		\node[hlabelbox, below=12.48 of hyper] (maintrainhyper) {$E_M$: Number of Epochs  \\ $L_M$: Learning Rate  \\ $\eta$: Weight Labeled/Unlabeled};
 	\end{pgfonlayer}
 	\begin{pgfonlayer}{background}
 		\node[hyperbox, fit=(maintrainhyper), label={[label distance = 1, name=autoenclabel]above:{\textbf{Main-Training Hyperparameters}}}] (maintrainhyp) {};
 	\end{pgfonlayer}
 
-  \draw[arrow] (node cs:name=pretrain,angle=-20) -- +(1, 0) |- (node cs:name=maintrain,angle=20);
+	\draw[arrow] (node cs:name=pretrain,angle=-50) |- +(1.5, -0.55) -- +(1.5,-5.4) -| (node cs:name=maintrain,angle=50);
 
 
 	%\draw[arrow] (pretrainoutput.south) -- (node cs:name=maintrain,angle=22);
@@ -101,7 +102,7 @@
 
 
 	\begin{pgfonlayer}{foreground}
-		\node[stepsbox, below=1.4 of maintrain] (inferenceproc) {Forward Pass through Network = $\mathbf{p}$ \\ Calculate Geometric Distance $\mathbf{p} \rightarrow \mathbf{c}$ \\ Anomaly Score = Geometric Distance};
+		\node[stepsbox, below=1.4 of maintrain] (inferenceproc) {Init Network $\mathcal{\phi}$ with $\mathcal{W}$ \\Forward Pass on sample = $\mathbf{p}$ \\ Calculate Distance $\mathbf{p} \rightarrow \mathbf{c}$ \\ Distance = Anomaly Score};
 		\node[outputbox, below=.1 of inferenceproc] (inferenceout) {\boxtitle{Outputs} Anomaly Score (Analog Value) \\ Higher for Anomalies};
 	\end{pgfonlayer}
 	\begin{pgfonlayer}{background}
@@ -109,7 +110,7 @@
 	\end{pgfonlayer}
 
 	\begin{pgfonlayer}{foreground}
-		\node[hlabelbox, below=11.8 of traindata] (newdatasample) {\boxtitle{New Data Sample} Same data type as training data};
+		\node[hlabelbox, below=13.32 of traindata] (newdatasample) {\boxtitle{New Data Sample} Same data type as training data};
 	\end{pgfonlayer}
 	\begin{pgfonlayer}{background}
 		\node[databox, fit=(newdatasample),  label={[label distance = 1] above:{\textbf{Unseen Data}}}] (newdata) {};

thesis/filters/drop-images.lua

@@ -0,0 +1,11 @@
+-- drop-images.lua
+-- Replaces all images (figures, graphics) with a short placeholder.
+function Image(el) return pandoc.Str("[image omitted]") end
+
+-- For LaTeX figures that are still raw
+function RawBlock(el)
+    if el.format == "tex" and el.text:match("\\begin%s*{%s*figure%s*}") then
+        return pandoc.Plain({pandoc.Str("[figure omitted]")})
+    end
+end
+

thesis/filters/drop-tables.lua

@@ -0,0 +1,11 @@
+-- drop-tables.lua
+-- Removes LaTeX tabular and tabularx environments (and their contents).
+function RawBlock(el)
+    if el.format == "tex" then
+        -- Check for tabular or tabularx environment
+        if el.text:match("\\begin%s*{%s*tabularx?%s*}") then
+            return pandoc.Plain({pandoc.Str("[table omitted]")})
+        end
+    end
+end
+

thesis/filters/keep-citations.lua

@@ -0,0 +1,43 @@
+-- keep-citations.lua
+-- Replace citations with a placeholder and eat any preceding space.
+local PH = "[citation]"
+
+-- Pandoc-native citations (if the reader produced Cite nodes)
+function Cite(el) return pandoc.Str(PH) end
+
+-- Raw LaTeX \cite-like macros (when not parsed as Cite)
+function RawInline(el)
+    if el.format and el.format:match("tex") and el.text:match("\\%a-*cite%*?") then
+        return pandoc.Str(PH)
+    end
+end
+
+-- Remove a single leading Space before our placeholder
+local function squash_spaces(inlines)
+    local out = {}
+    local i = 1
+    while i <= #inlines do
+        local cur = inlines[i]
+        local nxt = inlines[i + 1]
+        if cur and cur.t == "Space" and nxt and nxt.t == "Str" and nxt.text ==
+            PH then
+            table.insert(out, nxt)
+            i = i + 2
+        else
+            table.insert(out, cur)
+            i = i + 1
+        end
+    end
+    return out
+end
+
+function Para(el)
+    el.content = squash_spaces(el.content)
+    return el
+end
+
+function Plain(el)
+    el.content = squash_spaces(el.content)
+    return el
+end
+

thesis/filters/math-omit.lua

@@ -0,0 +1,48 @@
+-- math-omit.lua
+-- Replace any math with a placeholder and ensure a space before it when appropriate.
+local PH = "[math omitted]"
+
+function Math(el)
+    -- Emit the placeholder as a Str; spacing is fixed in Para/Plain below.
+    return pandoc.Str(PH)
+end
+
+local function ensure_space_before_ph(inlines)
+    local out = {}
+    for i = 1, #inlines do
+        local cur = inlines[i]
+        if cur.t == "Str" and cur.text == PH then
+            local prev = out[#out]
+            local need_space = true
+
+            -- No space if it's the first token in the block
+            if not prev then
+                need_space = false
+            elseif prev.t == "Space" then
+                need_space = false
+            elseif prev.t == "Str" then
+                -- If previous char is an opening bracket/paren/slash/hyphen or whitespace, skip
+                local last = prev.text:sub(-1)
+                if last:match("[%(%[%{%/%-]") or last:match("%s") then
+                    need_space = false
+                end
+            end
+
+            if need_space then table.insert(out, pandoc.Space()) end
+            table.insert(out, cur)
+        else
+            table.insert(out, cur)
+        end
+    end
+    return out
+end
+
+function Para(el)
+    el.content = ensure_space_before_ph(el.content)
+    return el
+end
+
+function Plain(el)
+    el.content = ensure_space_before_ph(el.content)
+    return el
+end

thesis/flake.nix

@@ -15,6 +15,8 @@
       let
         pkgs = import nixpkgs { inherit system; };
 
+        aspellWithDicts = pkgs.aspellWithDicts (d: [ d.en ]);
+
         latex-packages = with pkgs; [
           texlive.combined.scheme-full
           which
@@ -26,16 +28,42 @@
           zathura
           wmctrl
           python312
+          pandoc
+          pandoc-lua-filters
         ];
+        filtersPath = "${pkgs.pandoc-lua-filters}/share/pandoc/filters";
       in
       {
         devShell = pkgs.mkShell {
           buildInputs = [
             latex-packages
             dev-packages
+            aspellWithDicts
           ];
         };
 
+        shellHook = ''
+          set -eu
+          # local folder in your repo to reference in commands
+          link_target="pandoc-filters"
+          # refresh symlink each time you enter the shell
+          ln -sfn ${filtersPath} "$link_target"
+          echo "Linked $link_target -> ${filtersPath}"
+
+          # (optional) write a defaults file that uses the relative symlink
+          if [ ! -f pandoc.defaults.yaml ]; then
+            cat > pandoc.defaults.yaml <<'YAML'
+            from: latex
+            to: plain
+            wrap: none
+            lua-filter:
+              - pandoc-filters/latex-hyphen.lua
+              - pandoc-filters/pandoc-quotes.lua
+            YAML
+            echo "Wrote pandoc.defaults.yaml"
+          fi
+        '';
+
       }
     );
 }

thesis/tex2plaintext.sh

@@ -0,0 +1,61 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# Usage:
+#   ./tex2plaintext.sh [INPUT_TEX] [OUT_BASENAME]
+#
+# Defaults:
+#   INPUT_TEX     = Main.txt     (your original file name)
+#   OUT_BASENAME  = thesis       (produces thesis.txt, thesis_part1.txt, thesis_part2.txt)
+
+INPUT_TEX="${1:-Main.tex}"
+OUT_BASE="${2:-thesis}"
+
+FLAT_TEX="flat.tex"
+NO_TABLES_TEX="flat_notables.tex"
+PLAIN_TXT="${OUT_BASE}.txt"
+PART1_TXT="${OUT_BASE}_part1.txt"
+PART2_TXT="${OUT_BASE}_part2.txt"
+MARKER="Data and Preprocessing"
+
+echo "[1/5] Flattening with latexpand -> ${FLAT_TEX}"
+latexpand "${INPUT_TEX}" > "${FLAT_TEX}"
+
+echo "[2/5] Removing tabular/tabularx environments -> ${NO_TABLES_TEX}"
+# Replace entire tabular / tabularx environments with a placeholder
+perl -0777 -pe 's/\\begin\{(tabularx?)\}.*?\\end\{\1\}/[table omitted]/gs' \
+  "${FLAT_TEX}" > "${NO_TABLES_TEX}"
+
+echo "[3/5] Converting to plain text with pandoc -> ${PLAIN_TXT}"
+pandoc -f latex -t plain --wrap=none \
+  --lua-filter=filters/keep-citations.lua \
+  --lua-filter=filters/math-omit.lua \
+  "${NO_TABLES_TEX}" -o "${PLAIN_TXT}"
+
+echo "[4/5] Replacing [] placeholders with [figure]"
+sed -i 's/\[\]/[figure]/g' "${PLAIN_TXT}"
+
+echo "[5/5] Splitting ${PLAIN_TXT} before the marker line: \"${MARKER}\""
+
+# Ensure the marker exists exactly on its own line
+if ! grep -xq "${MARKER}" "${PLAIN_TXT}"; then
+  echo "ERROR: Marker line not found exactly as \"${MARKER}\" in ${PLAIN_TXT}."
+  echo "       (It must be the only content on that line.)"
+  exit 1
+fi
+
+# Clean previous outputs if present
+rm -f -- "${PART1_TXT}" "${PART2_TXT}"
+
+# Split so the marker line becomes the FIRST line of part 2
+awk -v marker="${MARKER}" -v out1="${PART1_TXT}" -v out2="${PART2_TXT}" '
+BEGIN { current = out1 }
+$0 == marker { current = out2; print $0 > current; next }
+{ print $0 > current }
+' "${PLAIN_TXT}"
+
+echo "Done."
+echo "  - ${PLAIN_TXT}"
+echo "  - ${PART1_TXT}"
+echo "  - ${PART2_TXT}"
+

thesis/thesis_preamble/abstract.tex

@@ -1,3 +1,9 @@
-\addcontentsline{toc}{chapter}{Abstract (English)}
+\addcontentsline{toc}{chapter}{Abstract}
-\begin{center}\Large\bfseries Abstract (English)\end{center}\vspace*{1cm}\noindent 
+\begin{center}\Large\bfseries Abstract\end{center}\vspace*{1cm}\noindent
-Write some fancy abstract here!
+Autonomous robots are increasingly used in search and rescue (SAR) missions. In these missions, LiDAR sensors are often the most important source of environmental data. However, LiDAR data can degrade under hazardous conditions, especially when airborne particles such as smoke or dust are present. This degradation can lead to errors in mapping and navigation and may endanger both the robot and humans. Therefore, robots need a way to estimate the reliability of their LiDAR data, so that they can make better-informed decisions.
+\bigskip
+
+This thesis investigates whether anomaly detection methods can be used to quantify LiDAR data degradation caused by airborne particles such as smoke and dust. We apply a semi-supervised deep learning approach called DeepSAD, which produces an anomaly score for each LiDAR scan, serving as a measure of data reliability.
+\bigskip
+
+We evaluate this method against baseline methods on a subterranean dataset that includes LiDAR scans degraded by artificial smoke. Our results show that DeepSAD consistently outperforms the baselines and can clearly distinguish degraded from normal scans. At the same time, we find that the limited availability of labeled data and the lack of robust ground truth remain major challenges. Despite these limitations, our work demonstrates that anomaly detection methods are a promising tool for LiDAR degradation quantification in SAR scenarios.

thesis/thesis_preamble/acknowledgements.tex

@@ -1,3 +1,3 @@
-\addcontentsline{toc}{chapter}{Acknowledgements}
+\addcontentsline{toc}{chapter}{Artificial Intelligence Usage Disclaimer}
-\begin{center}\Large\bfseries Acknowledgements\end{center}\vspace*{1cm}\noindent 
+\begin{center}\Large\bfseries Artificial Intelligence Usage Disclaimer\end{center}\vspace*{1cm}\noindent
-Here you can tell us, how thankful you are for this amazing template ;)
+During the creation of this thesis, an LLM-based Artificial Intelligence tool was used for stylistic and grammatical revision of the author's own work.

thesis/third_party/PlotNeuralNet/deepsad/arch_ef_decoder.py

@@ -30,7 +30,8 @@ arch = [
         height=H8 * 1.6,
         depth=D1,
         width=W1,
-        caption=f"Latent Space",
+        caption="Latent Space",
+        captionshift=0,
     ),
     # to_connection("fc1", "latent"),
     # --------------------------- DECODER ---------------------------
@@ -39,19 +40,20 @@ arch = [
         "fc3",
         n_filer="{{8×128×8}}",
         zlabeloffset=0.5,
-        offset="(2,0,0)",
+        offset="(2,-.5,0)",
         to="(latent-east)",
         height=H1,
         depth=D512,
         width=W1,
         caption=f"FC",
+        captionshift=20,
     ),
     to_Conv(
         "unsqueeze",
         s_filer="{{128×8}}",
         zlabeloffset=0.4,
         n_filer=32,
-        offset="(2,0,0)",
+        offset="(1.4,0,0)",
         to="(fc3-east)",
         height=H8,
         depth=D128,
@@ -62,7 +64,7 @@ arch = [
     # Reshape to 4×8×512
     to_UnPool(
         "up1",
-        offset="(2,0,0)",
+        offset="(1.2,0,0)",
         n_filer=32,
         to="(unsqueeze-east)",
         height=H16,
@@ -101,7 +103,8 @@ arch = [
         height=H16,
         depth=D1024,
         width=W32,
-        caption="",
+        caption="Deconv2",
+        captionshift=20,
     ),
     to_Conv(
         "dwdeconv3",
@@ -112,7 +115,7 @@ arch = [
         height=H16,
         depth=D1024,
         width=W1,
-        caption="Deconv2",
+        caption="",
     ),
     to_Conv(
         "dwdeconv4",
@@ -134,7 +137,8 @@ arch = [
         height=H32,
         depth=D2048,
         width=W16,
-        caption="",
+        caption="Deconv3",
+        captionshift=10,
     ),
     to_Conv(
         "dwdeconv5",
@@ -145,7 +149,7 @@ arch = [
         height=H32,
         depth=D2048,
         width=W1,
-        caption="Deconv3",
+        caption="",
     ),
     to_Conv(
         "dwdeconv6",
@@ -164,7 +168,7 @@ arch = [
         s_filer="{{2048×32}}",
         zlabeloffset=0.15,
         n_filer=1,
-        offset="(2,0,0)",
+        offset="(1.5,0,0)",
         to="(dwdeconv6-east)",
         height=H32,
         depth=D2048,
@@ -178,12 +182,13 @@ arch = [
         s_filer="{{2048×32}}",
         zlabeloffset=0.15,
         n_filer=1,
-        offset="(2,0,0)",
+        offset="(1.5,0,0)",
         to="(outconv-east)",
         height=H32,
         depth=D2048,
         width=W1,
         caption="Output",
+        captionshift=5,
     ),
     # to_connection("deconv2", "out"),
     to_end(),

thesis/third_party/PlotNeuralNet/deepsad/arch_ef_decoder.tex

@@ -28,6 +28,7 @@
     {Box={
         name=latent,
         caption=Latent Space,
+        captionshift=0,
         xlabel={{, }},
         zlabeloffset=0.3,
         zlabel=latent dim,
@@ -39,10 +40,11 @@
     };
 
 
-\pic[shift={(2,0,0)}] at (latent-east)
+\pic[shift={(2,-.5,0)}] at (latent-east)
     {Box={
         name=fc3,
         caption=FC,
+        captionshift=20,
         xlabel={{" ","dummy"}},
         zlabeloffset=0.5,
         zlabel={{8×128×8}},
@@ -55,10 +57,11 @@
     };
 
 
-\pic[shift={(2,0,0)}] at (fc3-east) 
+\pic[shift={(1.4,0,0)}] at (fc3-east) 
     {Box={
         name=unsqueeze,
         caption=Unsqueeze,
+        captionshift=0,
         xlabel={{32, }},
         zlabeloffset=0.4,
         zlabel={{128×8}},
@@ -70,10 +73,11 @@
     };
 
 
-\pic[shift={ (2,0,0) }] at (unsqueeze-east) 
+\pic[shift={ (1.2,0,0) }] at (unsqueeze-east) 
     {Box={
         name=up1,
         caption=,
+        captionshift=0,
         fill=\UnpoolColor,
         opacity=0.5,
         xlabel={{32, }},
@@ -88,6 +92,7 @@
     {Box={
         name=dwdeconv1,
         caption=Deconv1,
+        captionshift=0,
         xlabel={{1, }},
         zlabeloffset=0.3,
         zlabel=,
@@ -103,6 +108,7 @@
     {Box={
         name=dwdeconv2,
         caption=,
+        captionshift=0,
         xlabel={{32, }},
         zlabeloffset=0.4,
         zlabel={{256×16}},
@@ -117,7 +123,8 @@
 \pic[shift={ (2,0,0) }] at (dwdeconv2-east) 
     {Box={
         name=up2,
-        caption=,
+        caption=Deconv2,
+        captionshift=20,
         fill=\UnpoolColor,
         opacity=0.5,
         xlabel={{32, }},
@@ -131,7 +138,8 @@
 \pic[shift={(0,0,0)}] at (up2-east) 
     {Box={
         name=dwdeconv3,
-        caption=Deconv2,
+        caption=,
+        captionshift=0,
         xlabel={{1, }},
         zlabeloffset=0.3,
         zlabel=,
@@ -147,6 +155,7 @@
     {Box={
         name=dwdeconv4,
         caption=,
+        captionshift=0,
         xlabel={{16, }},
         zlabeloffset=0.17,
         zlabel={{1024×16}},
@@ -161,7 +170,8 @@
 \pic[shift={ (2,0,0) }] at (dwdeconv4-east) 
     {Box={
         name=up3,
-        caption=,
+        caption=Deconv3,
+        captionshift=10,
         fill=\UnpoolColor,
         opacity=0.5,
         xlabel={{16, }},
@@ -175,7 +185,8 @@
 \pic[shift={(0,0,0)}] at (up3-east) 
     {Box={
         name=dwdeconv5,
-        caption=Deconv3,
+        caption=,
+        captionshift=0,
         xlabel={{1, }},
         zlabeloffset=0.3,
         zlabel=,
@@ -191,6 +202,7 @@
     {Box={
         name=dwdeconv6,
         caption=,
+        captionshift=0,
         xlabel={{8, }},
         zlabeloffset=0.15,
         zlabel={{2048×32}},
@@ -202,10 +214,11 @@
     };
 
 
-\pic[shift={(2,0,0)}] at (dwdeconv6-east) 
+\pic[shift={(1.5,0,0)}] at (dwdeconv6-east) 
     {Box={
         name=outconv,
         caption=Deconv4,
+        captionshift=0,
         xlabel={{1, }},
         zlabeloffset=0.15,
         zlabel={{2048×32}},
@@ -217,10 +230,11 @@
     };
 
 
-\pic[shift={(2,0,0)}] at (outconv-east) 
+\pic[shift={(1.5,0,0)}] at (outconv-east) 
     {Box={
         name=out,
         caption=Output,
+        captionshift=5,
         xlabel={{1, }},
         zlabeloffset=0.15,
         zlabel={{2048×32}},

thesis/third_party/PlotNeuralNet/deepsad/arch_ef_encoder.py

@@ -125,7 +125,7 @@ arch = [
         n_filer=8,
         zlabeloffset=0.45,
         s_filer="{{128×8}}",
-        offset="(2,0,0)",
+        offset="(1,0,0)",
         to="(pool3-east)",
         height=H8,
         depth=D128,
@@ -137,12 +137,13 @@ arch = [
         "fc1",
         n_filer="{{8×128×8}}",
         zlabeloffset=0.5,
-        offset="(2,0,0)",
+        offset="(2,-.5,0)",
         to="(squeeze-east)",
         height=H1,
         depth=D512,
         width=W1,
-        caption=f"FC",
+        caption="FC",
+        captionshift=0,
     ),
     # to_connection("pool2", "fc1"),
     # --------------------------- LATENT  ---------------------------
@@ -150,7 +151,7 @@ arch = [
         "latent",
         n_filer="",
         s_filer="latent dim",
-        offset="(2,0,0)",
+        offset="(1.3,0.5,0)",
         to="(fc1-east)",
         height=H8 * 1.6,
         depth=D1,

thesis/third_party/PlotNeuralNet/deepsad/arch_ef_encoder.tex

@@ -28,6 +28,7 @@
     {Box={
         name=input,
         caption=Input,
+        captionshift=0,
         xlabel={{1, }},
         zlabeloffset=0.2,
         zlabel={{2048×32}},
@@ -43,6 +44,7 @@
     {Box={
         name=dwconv1,
         caption=,
+        captionshift=0,
         xlabel={{1, }},
         zlabeloffset=0.3,
         zlabel=,
@@ -58,6 +60,7 @@
     {Box={
         name=dwconv2,
         caption=Conv1,
+        captionshift=0,
         xlabel={{16, }},
         zlabeloffset=0.15,
         zlabel={{2048×32}},
@@ -76,6 +79,7 @@
         zlabeloffset=0.3,
         zlabel={{512×32}},
         caption=,
+        captionshift=0,
         fill=\PoolColor,
         opacity=0.5,
         height=26,
@@ -89,6 +93,7 @@
     {Box={
         name=dwconv3,
         caption=,
+        captionshift=0,
         xlabel={{1, }},
         zlabeloffset=0.3,
         zlabel=,
@@ -104,6 +109,7 @@
     {Box={
         name=dwconv4,
         caption=Conv2,
+        captionshift=0,
         xlabel={{32, }},
         zlabeloffset=0.3,
         zlabel={{512×32}},
@@ -122,6 +128,7 @@
         zlabeloffset=0.45,
         zlabel={{256×16}},
         caption=,
+        captionshift=0,
         fill=\PoolColor,
         opacity=0.5,
         height=18,
@@ -138,6 +145,7 @@
         zlabeloffset=0.45,
         zlabel={{128×8}},
         caption=,
+        captionshift=0,
         fill=\PoolColor,
         opacity=0.5,
         height=12,
@@ -147,10 +155,11 @@
     };
 
 
-\pic[shift={(2,0,0)}] at (pool3-east) 
+\pic[shift={(1,0,0)}] at (pool3-east) 
     {Box={
         name=squeeze,
         caption=Squeeze,
+        captionshift=0,
         xlabel={{8, }},
         zlabeloffset=0.45,
         zlabel={{128×8}},
@@ -162,10 +171,11 @@
     };
 
 
-\pic[shift={(2,0,0)}] at (squeeze-east)
+\pic[shift={(2,-.5,0)}] at (squeeze-east)
     {Box={
         name=fc1,
         caption=FC,
+        captionshift=0,
         xlabel={{" ","dummy"}},
         zlabeloffset=0.5,
         zlabel={{8×128×8}},
@@ -178,10 +188,11 @@
     };
 
 
-\pic[shift={(2,0,0)}] at (fc1-east) 
+\pic[shift={(1.3,0.5,0)}] at (fc1-east) 
     {Box={
         name=latent,
         caption=Latent Space,
+        captionshift=0,
         xlabel={{, }},
         zlabeloffset=0.3,
         zlabel=latent dim,

thesis/third_party/PlotNeuralNet/deepsad/arch_lenet_decoder.py

@@ -39,19 +39,20 @@ arch = [
         "fc3",
         n_filer="{{4×512×8}}",
         zlabeloffset=0.35,
-        offset="(2,0,0)",
+        offset="(2,-.5,0)",
         to="(latent-east)",
         height=1.3,
         depth=D512,
         width=W1,
         caption=f"FC",
+        captionshift=20,
     ),
     # to_connection("latent", "fc3"),
     # Reshape to 4×8×512
     to_UnPool(
         "up1",
         n_filer=4,
-        offset="(2,0,0)",
+        offset="(2.5,0,0)",
         to="(fc3-east)",
         height=H16,
         depth=D1024,
@@ -82,7 +83,8 @@ arch = [
         height=H32,
         depth=D2048,
         width=W8,
-        caption="",
+        caption="Deconv2",
+        captionshift=10,
     ),
     # to_connection("deconv1", "up2"),
     # DeConv2 (5×5, same): 8->1, 32×2048
@@ -96,7 +98,7 @@ arch = [
         height=H32,
         depth=D2048,
         width=W1,
-        caption="Deconv2",
+        caption="",
     ),
     # to_connection("up2", "deconv2"),
     # Output
@@ -111,6 +113,7 @@ arch = [
         depth=D2048,
         width=1.0,
         caption="Output",
+        captionshift=5,
     ),
     # to_connection("deconv2", "out"),
     to_end(),

thesis/third_party/PlotNeuralNet/deepsad/arch_lenet_decoder.tex

@@ -28,6 +28,7 @@
     {Box={
         name=latent,
         caption=Latent Space,
+        captionshift=0,
         xlabel={{, }},
         zlabeloffset=0.3,
         zlabel=latent dim,
@@ -39,10 +40,11 @@
     };
 
 
-\pic[shift={(2,0,0)}] at (latent-east)
+\pic[shift={(2,-.5,0)}] at (latent-east)
     {Box={
         name=fc3,
         caption=FC,
+        captionshift=20,
         xlabel={{" ","dummy"}},
         zlabeloffset=0.35,
         zlabel={{4×512×8}},
@@ -55,10 +57,11 @@
     };
 
 
-\pic[shift={ (2,0,0) }] at (fc3-east) 
+\pic[shift={ (2.5,0,0) }] at (fc3-east) 
     {Box={
         name=up1,
         caption=,
+        captionshift=0,
         fill=\UnpoolColor,
         opacity=0.5,
         xlabel={{4, }},
@@ -73,6 +76,7 @@
     {Box={
         name=deconv1,
         caption=Deconv1,
+        captionshift=0,
         xlabel={{8, }},
         zlabeloffset=0.2,
         zlabel={{1024×16}},
@@ -87,7 +91,8 @@
 \pic[shift={ (2,0,0) }] at (deconv1-east) 
     {Box={
         name=up2,
-        caption=,
+        caption=Deconv2,
+        captionshift=10,
         fill=\UnpoolColor,
         opacity=0.5,
         xlabel={{8, }},
@@ -101,7 +106,8 @@
 \pic[shift={(0,0,0)}] at (up2-east) 
     {Box={
         name=deconv2,
-        caption=Deconv2,
+        caption=,
+        captionshift=0,
         xlabel={{1, }},
         zlabeloffset=0.15,
         zlabel={{2048×32}},
@@ -117,6 +123,7 @@
     {Box={
         name=out,
         caption=Output,
+        captionshift=5,
         xlabel={{1, }},
         zlabeloffset=0.15,
         zlabel={{2048×32}},

thesis/third_party/PlotNeuralNet/deepsad/arch_lenet_encoder.py

@@ -91,13 +91,14 @@ arch = [
     to_fc(
         "fc1",
         n_filer="{{4×512×8}}",
-        offset="(2,0,0)",
+        offset="(2,-.5,0)",
         zlabeloffset=0.5,
         to="(pool2-east)",
         height=1.3,
         depth=D512,
         width=W1,
         caption=f"FC",
+        captionshift=20,
     ),
     # to_connection("pool2", "fc1"),
     # --------------------------- LATENT  ---------------------------

thesis/third_party/PlotNeuralNet/deepsad/arch_lenet_encoder.tex

@@ -28,6 +28,7 @@
     {Box={
         name=input,
         caption=Input,
+        captionshift=0,
         xlabel={{1, }},
         zlabeloffset=0.15,
         zlabel={{2048×32}},
@@ -43,6 +44,7 @@
     {Box={
         name=conv1,
         caption=Conv1,
+        captionshift=0,
         xlabel={{8, }},
         zlabeloffset=0.15,
         zlabel={{2048×32}},
@@ -61,6 +63,7 @@
         zlabeloffset=0.3,
         zlabel={{1024×16}},
         caption=,
+        captionshift=0,
         fill=\PoolColor,
         opacity=0.5,
         height=18,
@@ -74,6 +77,7 @@
     {Box={
         name=conv2,
         caption=Conv2,
+        captionshift=0,
         xlabel={{4, }},
         zlabeloffset=0.4,
         zlabel={{1024×16\hspace{2.5em}512×8}},
@@ -92,6 +96,7 @@
         zlabeloffset=0.3,
         zlabel={{}},
         caption=,
+        captionshift=0,
         fill=\PoolColor,
         opacity=0.5,
         height=12,
@@ -101,10 +106,11 @@
     };
 
 
-\pic[shift={(2,0,0)}] at (pool2-east)
+\pic[shift={(2,-.5,0)}] at (pool2-east)
     {Box={
         name=fc1,
         caption=FC,
+        captionshift=20,
         xlabel={{" ","dummy"}},
         zlabeloffset=0.5,
         zlabel={{4×512×8}},
@@ -121,6 +127,7 @@
     {Box={
         name=latent,
         caption=Latent Space,
+        captionshift=0,
         xlabel={{, }},
         zlabeloffset=0.3,
         zlabel=latent dim,

thesis/third_party/PlotNeuralNet/layers/Box.sty

@@ -57,8 +57,12 @@
 \path (b1) edge ["\ylabel",midway] (a1);  %height label
 
 
-\tikzstyle{captionlabel}=[text width=15*\LastEastx/\scale,text centered]       
+% \tikzstyle{captionlabel}=[text width=15*\LastEastx/\scale,text centered,xshift=\captionshift pt]       
-\path (\LastEastx/2,-\y/2,+\z/2) + (0,-25pt) coordinate (cap) 
+% \path (\LastEastx/2,-\y/2,+\z/2) + (0,-25pt) coordinate (cap) 
+% edge ["\textcolor{black}{ \bf \caption}"',captionlabel](cap) ; %Block caption/pic object label
+
+% Place caption: shift the coordinate by captionshift (NEW)
+\path (\LastEastx/2,-\y/2,+\z/2) + (\captionshift pt,-25pt) coordinate (cap)
 edge ["\textcolor{black}{ \bf \caption}"',captionlabel](cap) ; %Block caption/pic object label
 
 %Define nodes to be used outside on the pic object
@@ -103,6 +107,7 @@ ylabel/.store       in=\ylabel,
 zlabel/.store       in=\zlabel,
 zlabeloffset/.store in=\zlabeloffset,
 caption/.store      in=\caption,
+captionshift/.store in=\captionshift,
 name/.store         in=\name,
 fill/.store         in=\fill,
 opacity/.store      in=\opacity,
@@ -117,5 +122,6 @@ ylabel=,
 zlabel=,
 zlabeloffset=0.3,
 caption=,
+captionshift=0,
 name=,
 }

thesis/third_party/PlotNeuralNet/pycore/tikzeng.py

@@ -75,6 +75,7 @@ def to_Conv(
     height=40,
     depth=40,
     caption=" ",
+    captionshift=0,
 ):
     return (
         r"""
@@ -90,6 +91,9 @@ def to_Conv(
         caption="""
         + caption
         + r""",
+        captionshift="""
+        + str(captionshift)
+        + """,
         xlabel={{"""
         + str(n_filer)
         + """, }},
@@ -182,6 +186,7 @@ def to_Pool(
     depth=32,
     opacity=0.5,
     caption=" ",
+    captionshift=0,
 ):
     return (
         r"""
@@ -206,6 +211,9 @@ def to_Pool(
         caption="""
         + caption
         + r""",
+        captionshift="""
+        + str(captionshift)
+        + """,
         fill=\PoolColor,
         opacity="""
         + str(opacity)
@@ -236,6 +244,7 @@ def to_UnPool(
     depth=32,
     opacity=0.5,
     caption=" ",
+    captionshift=0,
 ):
     return (
         r"""
@@ -251,6 +260,9 @@ def to_UnPool(
         caption="""
         + caption
         + r""",
+        captionshift="""
+        + str(captionshift)
+        + r""",
         fill=\UnpoolColor,
         opacity="""
         + str(opacity)
@@ -335,6 +347,7 @@ def to_ConvSoftMax(
     height=40,
     depth=40,
     caption=" ",
+    captionshift=0,
 ):
     return (
         r"""
@@ -350,6 +363,9 @@ def to_ConvSoftMax(
         caption="""
         + caption
         + """,
+        captionshift="""
+        + str(captionshift)
+        + """,
         zlabel="""
         + str(s_filer)
         + """,
@@ -380,6 +396,7 @@ def to_SoftMax(
     depth=25,
     opacity=0.8,
     caption=" ",
+    captionshift=0,
     z_label_offset=0,
 ):
     return (
@@ -396,6 +413,9 @@ def to_SoftMax(
         caption="""
         + caption
         + """,
+        captionshift="""
+        + str(captionshift)
+        + """,
         xlabel={{" ","dummy"}},
         zlabel="""
         + str(s_filer)
@@ -455,6 +475,7 @@ def to_fc(
     height=2,
     depth=10,
     caption=" ",
+    captionshift=0,
     # titlepos=0,
 ):
     return (
@@ -471,6 +492,9 @@ def to_fc(
         caption="""
         + caption
         + """,
+        captionshift="""
+        + str(captionshift)
+        + """,
         xlabel={{" ","dummy"}},
         zlabeloffset="""
         + str(zlabeloffset)

tools/devenv.nix

@@ -1,6 +1,6 @@
 { pkgs, ... }:
 let
-  native_dependencies = with pkgs.python312Packages; [
+  native_dependencies = with pkgs.python311Packages; [
     torch-bin
     torchvision-bin
     aggdraw # for visualtorch
@@ -16,7 +16,7 @@ in
   packages = native_dependencies ++ tools;
   languages.python = {
     enable = true;
-    package = pkgs.python312;
+    package = pkgs.python311;
     uv = {
       enable = true;
       sync.enable = true;

tools/plot_scripts/ae_elbow_lenet.py

@@ -12,7 +12,7 @@ import numpy as np
 import polars as pl
 
 # CHANGE THIS IMPORT IF YOUR LOADER MODULE IS NAMED DIFFERENTLY
-from plot_scripts.load_results import load_pretraining_results_dataframe
+from load_results import load_pretraining_results_dataframe
 
 # ----------------------------
 # Config
@@ -78,8 +78,8 @@ def build_arch_curves_from_df(
             "overall": (dims, means, stds),
         } }
     """
-    if "split" not in df.columns:
+    # if "split" not in df.columns:
-        raise ValueError("Expected 'split' column in AE dataframe.")
+    #     raise ValueError("Expected 'split' column in AE dataframe.")
     if "scores" not in df.columns:
         raise ValueError("Expected 'scores' column in AE dataframe.")
     if "network" not in df.columns or "latent_dim" not in df.columns:
@@ -88,7 +88,7 @@ def build_arch_curves_from_df(
         raise ValueError(f"Expected '{label_field}' column in AE dataframe.")
 
     # Keep only test split
-    df = df.filter(pl.col("split") == "test")
+    # df = df.filter(pl.col("split") == "test")
 
     groups: dict[tuple[str, int], dict[str, list[float]]] = {}
 
@@ -201,7 +201,7 @@ def plot_multi_loss_curve(arch_results, title, output_path, colors=None):
 
     plt.xlabel("Latent Dimensionality")
     plt.ylabel("Test Loss")
-    plt.title(title)
+    # plt.title(title)
     plt.legend()
     plt.grid(True, alpha=0.3)
     plt.xticks(all_dims)

tools/plot_scripts/data_anomalies_timeline.py

@@ -171,28 +171,28 @@ def plot_combined_timeline(
             range(num_bins), near_sensor_binned, color=color, linestyle="--", alpha=0.6
         )
 
-        # Add vertical lines for manually labeled frames if available
+        # # Add vertical lines for manually labeled frames if available
-        if all_paths[i].with_suffix(".npy").name in manually_labeled_anomaly_frames:
+        # if all_paths[i].with_suffix(".npy").name in manually_labeled_anomaly_frames:
-            begin_frame, end_frame = manually_labeled_anomaly_frames[
+        #     begin_frame, end_frame = manually_labeled_anomaly_frames[
-                all_paths[i].with_suffix(".npy").name
+        #         all_paths[i].with_suffix(".npy").name
-            ]
+        #     ]
-            # Convert frame numbers to normalized timeline positions
+        #     # Convert frame numbers to normalized timeline positions
-            begin_pos = (begin_frame / exp_len) * (num_bins - 1)
+        #     begin_pos = (begin_frame / exp_len) * (num_bins - 1)
-            end_pos = (end_frame / exp_len) * (num_bins - 1)
+        #     end_pos = (end_frame / exp_len) * (num_bins - 1)
 
-            # Add vertical lines with matching color and loose dotting
+        #     # Add vertical lines with matching color and loose dotting
-            ax1.axvline(
+        #     ax1.axvline(
-                x=begin_pos,
+        #         x=begin_pos,
-                color=color,
+        #         color=color,
-                linestyle=":",
+        #         linestyle=":",
-                alpha=0.6,
+        #         alpha=0.6,
-            )
+        #     )
-            ax1.axvline(
+        #     ax1.axvline(
-                x=end_pos,
+        #         x=end_pos,
-                color=color,
+        #         color=color,
-                linestyle=":",
+        #         linestyle=":",
-                alpha=0.6,
+        #         alpha=0.6,
-            )
+        #     )
 
     # Customize axes
     ax1.set_xlabel("Normalized Timeline")
@@ -202,7 +202,7 @@ def plot_combined_timeline(
     ax1.set_ylabel("Missing Points (%)")
     ax2.set_ylabel("Points with <0.5m Range (%)")
 
-    plt.title(title)
+    # plt.title(title)
 
     # Create legends without fixed positions
     # First get all lines and labels for experiments
@@ -221,7 +221,8 @@ def plot_combined_timeline(
     )
 
     # Create single legend in top right corner with consistent margins
-    fig.legend(all_handles, all_labels, loc="upper right", borderaxespad=4.8)
+    # fig.legend(all_handles, all_labels, loc="upper right", borderaxespad=2.8)
+    fig.legend(all_handles, all_labels, bbox_to_anchor=(0.95, 0.99))
 
     plt.grid(True, alpha=0.3)
 

tools/plot_scripts/data_count_lidar_frames.py

@@ -122,8 +122,8 @@ def plot_data_points_pie(normal_experiment_frames, anomaly_experiment_frames):
 
     # prepare data for pie chart
     labels = [
-        "Normal Lidar Frames\nNon-Degraded Pointclouds",
+        "Normal Lidar Frames\nNon-Degraded Point Clouds",
-        "Anomalous Lidar Frames\nDegraded Pointclouds",
+        "Anomalous Lidar Frames\nDegraded Point Clouds",
     ]
     sizes = [total_normal_frames, total_anomaly_frames]
     explode = (0.1, 0)  # explode the normal slice
@@ -150,9 +150,9 @@ def plot_data_points_pie(normal_experiment_frames, anomaly_experiment_frames):
         va="center",
         color="black",
     )
-    plt.title(
+    # plt.title(
-        "Distribution of Normal and Anomalous\nPointclouds in all Experiments (Lidar Frames)"
+    #     "Distribution of Normal and Anomalous\nPointclouds in all Experiments (Lidar Frames)"
-    )
+    # )
     plt.tight_layout()
 
     # save the plot

tools/plot_scripts/data_missing_points.py

@@ -5,7 +5,6 @@ from pathlib import Path
 
 import matplotlib.pyplot as plt
 import numpy as np
-from pointcloudset import Dataset
 
 # define data path containing the bag files
 all_data_path = Path("/home/fedex/mt/data/subter")
@@ -82,7 +81,7 @@ def plot_data_points(normal_experiment_paths, anomaly_experiment_paths, title):
     plt.figure(figsize=(10, 5))
     plt.hist(missing_points_normal, bins=100, alpha=0.5, label="Normal Experiments")
     plt.hist(missing_points_anomaly, bins=100, alpha=0.5, label="Anomaly Experiments")
-    plt.title(title)
+    # plt.title(title)
     plt.xlabel("Number of Missing Points")
     plt.ylabel("Number of Pointclouds")
     plt.legend()
@@ -109,7 +108,7 @@ def plot_data_points(normal_experiment_paths, anomaly_experiment_paths, title):
         label="Anomaly Experiments",
         orientation="horizontal",
     )
-    plt.title(title)
+    # plt.title(title)
     plt.xlabel("Number of Pointclouds")
     plt.ylabel("Number of Missing Points")
     plt.legend()
@@ -142,7 +141,7 @@ def plot_data_points(normal_experiment_paths, anomaly_experiment_paths, title):
         label="Anomaly Experiments",
         density=True,
     )
-    plt.title(title)
+    # plt.title(title)
     plt.xlabel("Number of Missing Points")
     plt.ylabel("Density")
     plt.legend()
@@ -169,7 +168,7 @@ def plot_data_points(normal_experiment_paths, anomaly_experiment_paths, title):
         label="Anomaly Experiments (With Artifical Smoke)",
         density=True,
     )
-    plt.title(title)
+    # plt.title(title)
     plt.xlabel("Percentage of Missing Lidar Measurements")
     plt.ylabel("Density")
     # display the x axis as percentages
@@ -210,7 +209,7 @@ def plot_data_points(normal_experiment_paths, anomaly_experiment_paths, title):
         alpha=0.5,
         label="Anomaly Experiments",
     )
-    plt.title(title)
+    # plt.title(title)
     plt.xlabel("Number of Missing Points")
     plt.ylabel("Normalized Density")
     plt.legend()

tools/plot_scripts/data_particles_near_sensor.py

@@ -5,7 +5,6 @@ from pathlib import Path
 
 import matplotlib.pyplot as plt
 import numpy as np
-from pointcloudset import Dataset
 
 # define data path containing the bag files
 all_data_path = Path("/home/fedex/mt/data/subter")
@@ -164,7 +163,7 @@ def plot_data_points(normal_experiment_paths, anomaly_experiment_paths, title):
         plt.gca().set_yticklabels(
             ["{:.0f}%".format(y * 100) for y in plt.gca().get_yticks()]
         )
-        plt.title("Particles Closer than 0.5m to the Sensor")
+        # plt.title("Particles Closer than 0.5m to the Sensor")
         plt.ylabel("Percentage of measurements closer than 0.5m")
         plt.tight_layout()
         plt.savefig(output_datetime_path / f"particles_near_sensor_boxplot_{rt}.png")
@@ -186,7 +185,7 @@ def plot_data_points(normal_experiment_paths, anomaly_experiment_paths, title):
         plt.gca().set_yticklabels(
             ["{:.0f}%".format(y * 100) for y in plt.gca().get_yticks()]
         )
-        plt.title("Particles Closer than 0.5m to the Sensor")
+        # plt.title("Particles Closer than 0.5m to the Sensor")
         plt.ylabel("Percentage of measurements closer than 0.5m")
         plt.ylim(0, 0.05)
         plt.tight_layout()

tools/plot_scripts/data_spherical_projection.py

@@ -112,18 +112,27 @@ cmap = get_colormap_with_special_missing_color(
     args.colormap, args.missing_data_color, args.reverse_colormap
 )
 
-# --- Create a figure with 2 vertical subplots ---
+# --- Create a figure with 2 vertical subplots and move titles to the left ---
 fig, (ax1, ax2) = plt.subplots(nrows=2, ncols=1, figsize=(10, 5))
-for ax, frame, title in zip(
+# leave extra left margin for the left-side labels
+fig.subplots_adjust(left=0.14, hspace=0.05)
+
+for ax, frame, label in zip(
     (ax1, ax2),
     (frame1, frame2),
-    (
+    ("(a)", "(b)"),
-        "Projection of Lidar Frame without Degradation",
-        "Projection of Lidar Frame with Degradation (Artifical Smoke)",
-    ),
 ):
     im = ax.imshow(frame, cmap=cmap, aspect="auto", vmin=global_vmin, vmax=global_vmax)
-    ax.set_title(title)
+    # place the "title" to the left, vertically centered relative to the axes
+    ax.text(
+        -0.02,  # negative x places text left of the axes (in axes coordinates)
+        0.5,
+        label,
+        transform=ax.transAxes,
+        va="center",
+        ha="right",
+        fontsize=12,
+    )
     ax.axis("off")
 
 # Adjust layout to fit margins for a paper

tools/plot_scripts/results_ap_over_latent.py

@@ -0,0 +1,273 @@
+#!/usr/bin/env python3
+from __future__ import annotations
+
+import shutil
+from dataclasses import dataclass
+from datetime import datetime
+from pathlib import Path
+from typing import Dict, List, Tuple
+
+import matplotlib.pyplot as plt
+import numpy as np
+import polars as pl
+from matplotlib.ticker import MaxNLocator
+
+# =========================
+# Config
+# =========================
+ROOT = Path("/home/fedex/mt/results/copy")
+OUTPUT_DIR = Path("/home/fedex/mt/plots/results_ap_over_latent")
+
+# Labeling regimes (shown as separate subplots)
+SEMI_LABELING_REGIMES: list[tuple[int, int]] = [(0, 0), (50, 10), (500, 100)]
+
+# Evaluations: separate figure per eval
+EVALS: list[str] = ["exp_based", "manual_based"]
+
+# X-axis (latent dims)
+LATENT_DIMS: list[int] = [32, 64, 128, 256, 512, 768, 1024]
+
+# Visual style
+FIGSIZE = (8, 8)  # one tall figure with 3 compact subplots
+MARKERSIZE = 7
+SCATTER_ALPHA = 0.95
+LINEWIDTH = 2.0
+TREND_LINEWIDTH = 2.2
+BAND_ALPHA = 0.18
+
+# Toggle: show ±1 std bands (k-fold variability)
+SHOW_STD_BANDS = True  # <<< set to False to hide the bands
+
+# Colors for the two DeepSAD backbones
+COLOR_LENET = "#1f77b4"  # blue
+COLOR_EFFICIENT = "#ff7f0e"  # orange
+
+# =========================
+# Loader
+# =========================
+from load_results import load_results_dataframe
+
+
+# =========================
+# Helpers
+# =========================
+def _with_net_label(df: pl.DataFrame) -> pl.DataFrame:
+    return df.with_columns(
+        pl.when(
+            pl.col("network").cast(pl.Utf8).str.to_lowercase().str.contains("lenet")
+        )
+        .then(pl.lit("LeNet"))
+        .when(
+            pl.col("network").cast(pl.Utf8).str.to_lowercase().str.contains("efficient")
+        )
+        .then(pl.lit("Efficient"))
+        .otherwise(pl.col("network").cast(pl.Utf8))
+        .alias("net_label")
+    )
+
+
+def _filter_deepsad(df: pl.DataFrame) -> pl.DataFrame:
+    return df.filter(
+        (pl.col("model") == "deepsad")
+        & (pl.col("eval").is_in(EVALS))
+        & (pl.col("latent_dim").is_in(LATENT_DIMS))
+        & (pl.col("net_label").is_in(["LeNet", "Efficient"]))
+    ).select(
+        "eval",
+        "net_label",
+        "latent_dim",
+        "semi_normals",
+        "semi_anomalous",
+        "fold",
+        "ap",
+    )
+
+
+@dataclass(frozen=True)
+class Agg:
+    mean: float
+    std: float
+
+
+def aggregate_ap(df: pl.DataFrame) -> Dict[Tuple[str, str, int, int, int], Agg]:
+    out: Dict[Tuple[str, str, int, int, int], Agg] = {}
+    gb = (
+        df.group_by(
+            ["eval", "net_label", "latent_dim", "semi_normals", "semi_anomalous"]
+        )
+        .agg(pl.col("ap").mean().alias("mean"), pl.col("ap").std().alias("std"))
+        .to_dicts()
+    )
+    for row in gb:
+        key = (
+            str(row["eval"]),
+            str(row["net_label"]),
+            int(row["latent_dim"]),
+            int(row["semi_normals"]),
+            int(row["semi_anomalous"]),
+        )
+        m = float(row["mean"]) if row["mean"] == row["mean"] else np.nan
+        s = float(row["std"]) if row["std"] == row["std"] else np.nan
+        out[key] = Agg(mean=m, std=s)
+    return out
+
+
+def _lin_trend(xs: List[int], ys: List[float]) -> Tuple[np.ndarray, np.ndarray]:
+    if len(xs) < 2:
+        return np.array(xs, dtype=float), np.array(ys, dtype=float)
+    x = np.array(xs, dtype=float)
+    y = np.array(ys, dtype=float)
+    a, b = np.polyfit(x, y, 1)
+    x_fit = np.linspace(x.min(), x.max(), 200)
+    y_fit = a * x_fit + b
+    return x_fit, y_fit
+
+
+def _dynamic_ylim(all_vals: List[float], all_errs: List[float]) -> Tuple[float, float]:
+    vals = np.array(all_vals, dtype=float)
+    errs = np.array(all_errs, dtype=float) if SHOW_STD_BANDS else np.zeros_like(vals)
+    valid = np.isfinite(vals)
+    if not np.any(valid):
+        return (0.0, 1.0)
+    v, e = vals[valid], errs[valid]
+    lo = np.min(v - e)
+    hi = np.max(v + e)
+    span = max(1e-3, hi - lo)
+    pad = 0.08 * span
+    y0 = max(0.0, lo - pad)
+    y1 = min(1.0, hi + pad)
+    if (y1 - y0) < 0.08:
+        mid = 0.5 * (y0 + y1)
+        y0 = max(0.0, mid - 0.04)
+        y1 = min(1.0, mid + 0.04)
+    return (float(y0), float(y1))
+
+
+def _get_dim_mapping(dims: list[int]) -> dict[int, int]:
+    """Map actual dimensions to evenly spaced positions (0, 1, 2, ...)"""
+    return {dim: i for i, dim in enumerate(dims)}
+
+
+def plot_eval(ev: str, agg: Dict[Tuple[str, str, int, int, int], Agg], outdir: Path):
+    fig, axes = plt.subplots(
+        len(SEMI_LABELING_REGIMES),
+        1,
+        figsize=FIGSIZE,
+        constrained_layout=True,
+        sharex=True,
+    )
+
+    if len(SEMI_LABELING_REGIMES) == 1:
+        axes = [axes]
+
+    # Create dimension mapping
+    dim_mapping = _get_dim_mapping(LATENT_DIMS)
+
+    for ax, regime in zip(axes, SEMI_LABELING_REGIMES):
+        semi_n, semi_a = regime
+        data = {}
+        for net in ["LeNet", "Efficient"]:
+            xs, ys, es = [], [], []
+            for dim in LATENT_DIMS:
+                key = (ev, net, dim, semi_n, semi_a)
+                if key in agg:
+                    xs.append(
+                        dim_mapping[dim]
+                    )  # Use mapped position instead of actual dim
+                    ys.append(agg[key].mean)
+                    es.append(agg[key].std)
+            data[net] = (xs, ys, es)
+
+        for net, color in [("LeNet", COLOR_LENET), ("Efficient", COLOR_EFFICIENT)]:
+            xs, ys, es = data[net]
+            if not xs:
+                continue
+
+            # Set evenly spaced ticks with actual dimension labels
+            ax.set_xticks(list(dim_mapping.values()))
+            ax.set_xticklabels(LATENT_DIMS)
+
+            ax.yaxis.set_major_locator(MaxNLocator(nbins=5))
+            ax.scatter(
+                xs, ys, s=35, color=color, alpha=SCATTER_ALPHA, label=f"{net} (points)"
+            )
+            x_fit, y_fit = _lin_trend(xs, ys)  # Now using mapped positions
+            ax.plot(
+                x_fit,
+                y_fit,
+                color=color,
+                linewidth=TREND_LINEWIDTH,
+                label=f"{net} (trend)",
+            )
+            if SHOW_STD_BANDS and es and np.any(np.isfinite(es)):
+                ylo = np.clip(np.array(ys) - np.array(es), 0.0, 1.0)
+                yhi = np.clip(np.array(ys) + np.array(es), 0.0, 1.0)
+                ax.fill_between(
+                    xs, ylo, yhi, color=color, alpha=BAND_ALPHA, linewidth=0
+                )
+
+        all_vals, all_errs = [], []
+        for net in ["LeNet", "Efficient"]:
+            _, ys, es = data[net]
+            all_vals.extend(ys)
+            all_errs.extend(es)
+        y0, y1 = _dynamic_ylim(all_vals, all_errs)
+        ax.set_ylim(y0, y1)
+
+        ax.set_title(f"Labeling regime {semi_n}/{semi_a}", fontsize=11)
+        ax.grid(True, alpha=0.35)
+
+    axes[-1].set_xlabel("Latent dimension")
+    for ax in axes:
+        ax.set_ylabel("AP")
+
+    handles, labels = axes[0].get_legend_handles_labels()
+    fig.legend(handles, labels, ncol=2, loc="upper center", bbox_to_anchor=(0.75, 0.97))
+    fig.suptitle(f"AP vs. Latent Dimensionality — {ev.replace('_', ' ')}", y=1.05)
+
+    fname = f"ap_trends_{ev}.png"
+    fig.savefig(outdir / fname, dpi=150)
+    plt.close(fig)
+
+
+def plot_all(agg: Dict[Tuple[str, str, int, int, int], Agg], outdir: Path):
+    outdir.mkdir(parents=True, exist_ok=True)
+    for ev in EVALS:
+        plot_eval(ev, agg, outdir)
+
+
+def main():
+    df = load_results_dataframe(ROOT, allow_cache=True)
+    df = _with_net_label(df)
+    df = _filter_deepsad(df)
+    agg = aggregate_ap(df)
+
+    OUTPUT_DIR.mkdir(parents=True, exist_ok=True)
+    archive_dir = OUTPUT_DIR / "archive"
+    archive_dir.mkdir(parents=True, exist_ok=True)
+    ts_dir = archive_dir / datetime.now().strftime("%Y-%m-%d_%H-%M-%S")
+    ts_dir.mkdir(parents=True, exist_ok=True)
+
+    plot_all(agg, ts_dir)
+
+    try:
+        script_path = Path(__file__)
+        shutil.copy2(script_path, ts_dir / script_path.name)
+    except Exception:
+        pass
+
+    latest = OUTPUT_DIR / "latest"
+    latest.mkdir(parents=True, exist_ok=True)
+    for f in latest.iterdir():
+        if f.is_file():
+            f.unlink()
+    for f in ts_dir.iterdir():
+        if f.is_file():
+            shutil.copy2(f, latest / f.name)
+
+    print(f"Saved plots to: {ts_dir}")
+    print(f"Also updated: {latest}")
+
+
+if __name__ == "__main__":
+    main()

tools/plot_scripts/results_ap_over_semi.py

@@ -0,0 +1,260 @@
+#!/usr/bin/env python3
+from __future__ import annotations
+
+import shutil
+from dataclasses import dataclass
+from datetime import datetime
+from pathlib import Path
+from typing import Dict, List, Tuple
+
+import matplotlib.pyplot as plt
+import numpy as np
+import polars as pl
+from matplotlib.ticker import MaxNLocator
+
+# =========================
+# Config
+# =========================
+ROOT = Path("/home/fedex/mt/results/copy")
+OUTPUT_DIR = Path("/home/fedex/mt/plots/results_ap_over_semi")
+
+# Labeling regimes (shown as separate subplots)
+SEMI_LABELING_REGIMES: list[tuple[int, int]] = [(0, 0), (50, 10), (500, 100)]
+
+# Evaluations: separate figure per eval
+EVALS: list[str] = ["exp_based", "manual_based"]
+
+# X-axis (latent dims)
+LATENT_DIMS: list[int] = [32, 64, 128, 256, 512, 768, 1024]
+LATENT_DIM: int = [32, 64, 128, 256, 512, 768, 1024]
+
+# Visual style
+FIGSIZE = (8, 8)  # one tall figure with 3 compact subplots
+MARKERSIZE = 7
+SCATTER_ALPHA = 0.95
+LINEWIDTH = 2.0
+TREND_LINEWIDTH = 2.2
+BAND_ALPHA = 0.18
+
+# Toggle: show ±1 std bands (k-fold variability)
+SHOW_STD_BANDS = True  # <<< set to False to hide the bands
+
+# Colors for the two DeepSAD backbones
+COLOR_LENET = "#1f77b4"  # blue
+COLOR_EFFICIENT = "#ff7f0e"  # orange
+
+# =========================
+# Loader
+# =========================
+from load_results import load_results_dataframe
+
+
+# =========================
+# Helpers
+# =========================
+def _with_net_label(df: pl.DataFrame) -> pl.DataFrame:
+    return df.with_columns(
+        pl.when(
+            pl.col("network").cast(pl.Utf8).str.to_lowercase().str.contains("lenet")
+        )
+        .then(pl.lit("LeNet"))
+        .when(
+            pl.col("network").cast(pl.Utf8).str.to_lowercase().str.contains("efficient")
+        )
+        .then(pl.lit("Efficient"))
+        .otherwise(pl.col("network").cast(pl.Utf8))
+        .alias("net_label")
+    )
+
+
+def _filter_deepsad(df: pl.DataFrame) -> pl.DataFrame:
+    return df.filter(
+        (pl.col("model") == "deepsad")
+        & (pl.col("eval").is_in(EVALS))
+        & (pl.col("latent_dim").is_in(LATENT_DIMS))
+        & (pl.col("net_label").is_in(["LeNet", "Efficient"]))
+    ).select(
+        "eval",
+        "net_label",
+        "latent_dim",
+        "semi_normals",
+        "semi_anomalous",
+        "fold",
+        "ap",
+    )
+
+
+@dataclass(frozen=True)
+class Agg:
+    mean: float
+    std: float
+
+
+def aggregate_ap(df: pl.DataFrame) -> Dict[Tuple[str, str, int, int, int], Agg]:
+    out: Dict[Tuple[str, str, int, int, int], Agg] = {}
+    gb = (
+        df.group_by(
+            ["eval", "net_label", "latent_dim", "semi_normals", "semi_anomalous"]
+        )
+        .agg(pl.col("ap").mean().alias("mean"), pl.col("ap").std().alias("std"))
+        .to_dicts()
+    )
+    for row in gb:
+        key = (
+            str(row["eval"]),
+            str(row["net_label"]),
+            int(row["latent_dim"]),
+            int(row["semi_normals"]),
+            int(row["semi_anomalous"]),
+        )
+        m = float(row["mean"]) if row["mean"] == row["mean"] else np.nan
+        s = float(row["std"]) if row["std"] == row["std"] else np.nan
+        out[key] = Agg(mean=m, std=s)
+    return out
+
+
+def _lin_trend(xs: List[int], ys: List[float]) -> Tuple[np.ndarray, np.ndarray]:
+    if len(xs) < 2:
+        return np.array(xs, dtype=float), np.array(ys, dtype=float)
+    x = np.array(xs, dtype=float)
+    y = np.array(ys, dtype=float)
+    a, b = np.polyfit(x, y, 1)
+    x_fit = np.linspace(x.min(), x.max(), 200)
+    y_fit = a * x_fit + b
+    return x_fit, y_fit
+
+
+def _dynamic_ylim(all_vals: List[float], all_errs: List[float]) -> Tuple[float, float]:
+    vals = np.array(all_vals, dtype=float)
+    errs = np.array(all_errs, dtype=float) if SHOW_STD_BANDS else np.zeros_like(vals)
+    valid = np.isfinite(vals)
+    if not np.any(valid):
+        return (0.0, 1.0)
+    v, e = vals[valid], errs[valid]
+    lo = np.min(v - e)
+    hi = np.max(v + e)
+    span = max(1e-3, hi - lo)
+    pad = 0.08 * span
+    y0 = max(0.0, lo - pad)
+    y1 = min(1.0, hi + pad)
+    if (y1 - y0) < 0.08:
+        mid = 0.5 * (y0 + y1)
+        y0 = max(0.0, mid - 0.04)
+        y1 = min(1.0, mid + 0.04)
+    return (float(y0), float(y1))
+
+
+def plot_eval(ev: str, agg: Dict[Tuple[str, str, int, int, int], Agg], outdir: Path):
+    fig, axes = plt.subplots(
+        len(SEMI_LABELING_REGIMES),
+        1,
+        figsize=FIGSIZE,
+        constrained_layout=True,
+        sharex=True,
+    )
+
+    if len(SEMI_LABELING_REGIMES) == 1:
+        axes = [axes]
+
+    for ax, regime in zip(axes, SEMI_LABELING_REGIMES):
+        semi_n, semi_a = regime
+        data = {}
+        for net in ["LeNet", "Efficient"]:
+            xs, ys, es = [], [], []
+            for dim in LATENT_DIMS:
+                key = (ev, net, dim, semi_n, semi_a)
+                if key in agg:
+                    xs.append(dim)
+                    ys.append(agg[key].mean)
+                    es.append(agg[key].std)
+            data[net] = (xs, ys, es)
+
+        for net, color in [("LeNet", COLOR_LENET), ("Efficient", COLOR_EFFICIENT)]:
+            xs, ys, es = data[net]
+            if not xs:
+                continue
+            ax.set_xticks(LATENT_DIMS)
+            ax.yaxis.set_major_locator(MaxNLocator(nbins=5))  # e.g., always 5 ticks
+            ax.scatter(
+                xs, ys, s=35, color=color, alpha=SCATTER_ALPHA, label=f"{net} (points)"
+            )
+            x_fit, y_fit = _lin_trend(xs, ys)
+            ax.plot(
+                x_fit,
+                y_fit,
+                color=color,
+                linewidth=TREND_LINEWIDTH,
+                label=f"{net} (trend)",
+            )
+            if SHOW_STD_BANDS and es and np.any(np.isfinite(es)):
+                ylo = np.clip(np.array(ys) - np.array(es), 0.0, 1.0)
+                yhi = np.clip(np.array(ys) + np.array(es), 0.0, 1.0)
+                ax.fill_between(
+                    xs, ylo, yhi, color=color, alpha=BAND_ALPHA, linewidth=0
+                )
+
+        all_vals, all_errs = [], []
+        for net in ["LeNet", "Efficient"]:
+            _, ys, es = data[net]
+            all_vals.extend(ys)
+            all_errs.extend(es)
+        y0, y1 = _dynamic_ylim(all_vals, all_errs)
+        ax.set_ylim(y0, y1)
+
+        ax.set_title(f"Labeling regime {semi_n}/{semi_a}", fontsize=11)
+        ax.grid(True, alpha=0.35)
+
+    axes[-1].set_xlabel("Latent dimension")
+    for ax in axes:
+        ax.set_ylabel("AP")
+
+    handles, labels = axes[0].get_legend_handles_labels()
+    fig.legend(handles, labels, ncol=2, loc="upper center", bbox_to_anchor=(0.75, 0.97))
+    fig.suptitle(f"AP vs. Latent Dimensionality — {ev.replace('_', ' ')}", y=1.05)
+
+    fname = f"ap_trends_{ev}.png"
+    fig.savefig(outdir / fname, dpi=150)
+    plt.close(fig)
+
+
+def plot_all(agg: Dict[Tuple[str, str, int, int, int], Agg], outdir: Path):
+    outdir.mkdir(parents=True, exist_ok=True)
+    for ev in EVALS:
+        plot_eval(ev, agg, outdir)
+
+
+def main():
+    df = load_results_dataframe(ROOT, allow_cache=True)
+    df = _with_net_label(df)
+    df = _filter_deepsad(df)
+    agg = aggregate_ap(df)
+
+    OUTPUT_DIR.mkdir(parents=True, exist_ok=True)
+    archive_dir = OUTPUT_DIR / "archive"
+    archive_dir.mkdir(parents=True, exist_ok=True)
+    ts_dir = archive_dir / datetime.now().strftime("%Y-%m-%d_%H-%M-%S")
+    ts_dir.mkdir(parents=True, exist_ok=True)
+
+    plot_all(agg, ts_dir)
+
+    try:
+        script_path = Path(__file__)
+        shutil.copy2(script_path, ts_dir / script_path.name)
+    except Exception:
+        pass
+
+    latest = OUTPUT_DIR / "latest"
+    latest.mkdir(parents=True, exist_ok=True)
+    for f in latest.iterdir():
+        if f.is_file():
+            f.unlink()
+    for f in ts_dir.iterdir():
+        if f.is_file():
+            shutil.copy2(f, latest / f.name)
+
+    print(f"Saved plots to: {ts_dir}")
+    print(f"Also updated: {latest}")
+
+
+if __name__ == "__main__":
+    main()

tools/plot_scripts/results_inference_timelines_exp_compare.py

@@ -260,11 +260,11 @@ def baseline_transform(clean: np.ndarray, other: np.ndarray, mode: str):
 
 
 def pick_method_series(gdf: pl.DataFrame, label: str) -> Optional[np.ndarray]:
-    if label == "DeepSAD (LeNet)":
+    if label == "DeepSAD LeNet":
         sel = gdf.filter(
             (pl.col("network") == "subter_LeNet") & (pl.col("model") == "deepsad")
         )
-    elif label == "DeepSAD (efficient)":
+    elif label == "DeepSAD Efficient":
         sel = gdf.filter(
             (pl.col("network") == "subter_efficient") & (pl.col("model") == "deepsad")
         )
@@ -311,8 +311,8 @@ def compare_two_experiments_progress(
     include_stats: bool = True,
 ):
     methods = [
-        "DeepSAD (LeNet)",
+        "DeepSAD LeNet",
-        "DeepSAD (efficient)",
+        "DeepSAD Efficient",
         "OCSVM",
         "Isolation Forest",
     ]
@@ -392,8 +392,8 @@ def compare_two_experiments_progress(
     axes = axes.ravel()
 
     method_to_axidx = {
-        "DeepSAD (LeNet)": 0,
+        "DeepSAD LeNet": 0,
-        "DeepSAD (efficient)": 1,
+        "DeepSAD Efficient": 1,
         "OCSVM": 2,
         "Isolation Forest": 3,
     }
@@ -404,6 +404,8 @@ def compare_two_experiments_progress(
     if not stats_available:
         print("[WARN] One or both stats missing. Subplots will include methods only.")
 
+    letters = ["a", "b", "c", "d"]
+
     for label, axidx in method_to_axidx.items():
         ax = axes[axidx]
         yc = curves_clean.get(label)
@@ -412,7 +414,7 @@ def compare_two_experiments_progress(
             ax.text(
                 0.5, 0.5, "No data", ha="center", va="center", transform=ax.transAxes
             )
-            ax.set_title(label)
+            ax.set_title(f"({letters[axidx]}) {label}")
             ax.grid(True, alpha=0.3)
             continue
 
@@ -435,6 +437,7 @@ def compare_two_experiments_progress(
         )
         ax.set_ylabel(y_label)
         ax.set_title(label)
+        ax.set_title(f"({letters[axidx]}) {label}")
         ax.grid(True, alpha=0.3)
 
         # Right axis #1 (closest to plot): Missing points (%)
@@ -550,11 +553,11 @@ def compare_two_experiments_progress(
     for ax in axes:
         ax.set_xlabel("Progress through experiment (%)")
 
-    fig.suptitle(
+    # fig.suptitle(
-        f"AD Method vs Stats Inference — progress-normalized\n"
+    #     f"AD Method vs Stats Inference — progress-normalized\n"
-        f"Transform: z-score normalized to non-degraded experiment | EMA(α={EMA_ALPHA_METHODS})",
+    #     f"Transform: z-score normalized to non-degraded experiment | EMA(α={EMA_ALPHA_METHODS})",
-        fontsize=14,
+    #     fontsize=14,
-    )
+    # )
     fig.tight_layout(rect=[0, 0, 1, 0.99])
 
     out_name = (

tools/plot_scripts/results_latent_space_comparisons.py

@@ -161,7 +161,7 @@ def _ensure_dim_axes(fig_title: str):
     fig, axes = plt.subplots(
         nrows=4, ncols=2, figsize=(12, 16), constrained_layout=True
     )
-    fig.suptitle(fig_title, fontsize=14)
+    # fig.suptitle(fig_title, fontsize=14)
     axes = axes.ravel()
     return fig, axes
 
@@ -213,11 +213,13 @@ def plot_grid_from_df(
     legend_labels = []
     have_legend = False
 
+    letters = ["a", "b", "c", "d", "e", "f", "g", "h"]
+
     for i, dim in enumerate(LATENT_DIMS):
         if i >= 7:
             break  # last slot reserved for legend
         ax = axes[i]
-        ax.set_title(f"Latent Dim. = {dim}")
+        ax.set_title(f"({letters[i]}) Latent Dim. = {dim}")
         ax.grid(True, alpha=0.3)
 
         if kind == "roc":

tools/plot_scripts/results_semi_labels_comparison.py

@@ -8,11 +8,11 @@ from pathlib import Path
 import matplotlib.pyplot as plt
 import numpy as np
 import polars as pl
-from matplotlib.lines import Line2D
-from scipy.stats import sem, t
 
 # CHANGE THIS IMPORT IF YOUR LOADER MODULE NAME IS DIFFERENT
-from plot_scripts.load_results import load_results_dataframe
+from load_results import load_results_dataframe
+from matplotlib.lines import Line2D
+from scipy.stats import sem, t
 
 # ---------------------------------
 # Config
@@ -23,6 +23,10 @@ OUTPUT_DIR = Path("/home/fedex/mt/plots/results_semi_labels_comparison")
 LATENT_DIMS = [32, 64, 128, 256, 512, 768, 1024]
 SEMI_REGIMES = [(0, 0), (50, 10), (500, 100)]
 EVALS = ["exp_based", "manual_based"]
+EVALS_LABELS = {
+    "exp_based": "Experiment-Based Labels",
+    "manual_based": "Manually-Labeled",
+}
 
 # Interp grids
 ROC_GRID = np.linspace(0.0, 1.0, 200)
@@ -30,6 +34,10 @@ PRC_GRID = np.linspace(0.0, 1.0, 200)
 
 # Baselines are duplicated across nets; use Efficient-only to avoid repetition
 BASELINE_NET = "Efficient"
+BASELINE_LABELS = {
+    "isoforest": "Isolation Forest",
+    "ocsvm": "One-Class SVM",
+}
 
 # Colors/styles
 COLOR_BASELINES = {
@@ -147,12 +155,8 @@ def _select_rows(
     return df.filter(pl.all_horizontal(exprs))
 
 
-def _auc_list(sub: pl.DataFrame) -> list[float]:
+def _auc_list(sub: pl.DataFrame, kind: str) -> list[float]:
-    return [x for x in sub.select("auc").to_series().to_list() if x is not None]
+    return [x for x in sub.select(f"{kind}_auc").to_series().to_list() if x is not None]
-
-
-def _ap_list(sub: pl.DataFrame) -> list[float]:
-    return [x for x in sub.select("ap").to_series().to_list() if x is not None]
 
 
 def _plot_panel(
@@ -165,7 +169,7 @@ def _plot_panel(
     kind: str,
 ):
     """
-    Plot one panel: DeepSAD (net_for_deepsad) with 3 regimes + baselines (from Efficient).
+    Plot one panel: DeepSAD (net_for_deepsad) with 3 regimes + Baselines (from Efficient).
     Legend entries include mean±CI of AUC/AP.
     """
     ax.grid(True, alpha=0.3)
@@ -200,9 +204,9 @@ def _plot_panel(
             continue
 
         # Metric for legend
-        metric_vals = _auc_list(sub_b) if kind == "roc" else _ap_list(sub_b)
+        metric_vals = _auc_list(sub_b, kind)
         m, ci = mean_ci(metric_vals)
-        lab = f"{model} ({'AUC' if kind == 'roc' else 'AP'}={m:.3f}±{ci:.3f})"
+        lab = f"{BASELINE_LABELS[model]}\n(AUC={m:.3f}±{ci:.3f})"
 
         color = COLOR_BASELINES[model]
         h = ax.plot(grid, mean_y, lw=2, color=color, label=lab)[0]
@@ -230,9 +234,9 @@ def _plot_panel(
         if np.all(np.isnan(mean_y)):
             continue
 
-        metric_vals = _auc_list(sub_d) if kind == "roc" else _ap_list(sub_d)
+        metric_vals = _auc_list(sub_d, kind)
         m, ci = mean_ci(metric_vals)
-        lab = f"DeepSAD {net_for_deepsad} — semi {sn}/{sa} ({'AUC' if kind == 'roc' else 'AP'}={m:.3f}±{ci:.3f})"
+        lab = f"DeepSAD {net_for_deepsad} — {sn}/{sa}\n(AUC={m:.3f}±{ci:.3f})"
 
         color = COLOR_REGIMES[regime]
         ls = LINESTYLES[regime]
@@ -246,7 +250,7 @@ def _plot_panel(
         ax.plot([0, 1], [0, 1], "k--", alpha=0.6, label="Chance")
 
     # Legend
-    ax.legend(loc="lower right", fontsize=9, frameon=True)
+    ax.legend(loc="upper right", fontsize=9, frameon=True)
 
 
 def make_figures_for_dim(
@@ -254,9 +258,11 @@ def make_figures_for_dim(
 ):
     # ROC: 2×1
     fig_roc, axes = plt.subplots(
-        nrows=1, ncols=2, figsize=(14, 5), constrained_layout=True
+        nrows=2, ncols=1, figsize=(7, 10), constrained_layout=True
     )
-    fig_roc.suptitle(f"ROC — {eval_type} — latent_dim={latent_dim}", fontsize=14)
+    # fig_roc.suptitle(
+    #     f"ROC — {EVALS_LABELS[eval_type]} — Latent Dim.={latent_dim}", fontsize=14
+    # )
 
     _plot_panel(
         axes[0],
@@ -266,7 +272,7 @@ def make_figures_for_dim(
         latent_dim=latent_dim,
         kind="roc",
     )
-    axes[0].set_title("DeepSAD (LeNet) + baselines")
+    axes[0].set_title("(a) DeepSAD (LeNet) + Baselines")
 
     _plot_panel(
         axes[1],
@@ -276,7 +282,7 @@ def make_figures_for_dim(
         latent_dim=latent_dim,
         kind="roc",
     )
-    axes[1].set_title("DeepSAD (Efficient) + baselines")
+    axes[1].set_title("(b) DeepSAD (Efficient) + Baselines")
 
     out_roc = out_dir / f"roc_{latent_dim}_{eval_type}.png"
     fig_roc.savefig(out_roc, dpi=150, bbox_inches="tight")
@@ -284,9 +290,11 @@ def make_figures_for_dim(
 
     # PRC: 2×1
     fig_prc, axes = plt.subplots(
-        nrows=1, ncols=2, figsize=(14, 5), constrained_layout=True
+        nrows=2, ncols=1, figsize=(7, 10), constrained_layout=True
     )
-    fig_prc.suptitle(f"PRC — {eval_type} — latent_dim={latent_dim}", fontsize=14)
+    # fig_prc.suptitle(
+    #     f"PRC — {EVALS_LABELS[eval_type]} — Latent Dim.={latent_dim}", fontsize=14
+    # )
 
     _plot_panel(
         axes[0],
@@ -296,7 +304,7 @@ def make_figures_for_dim(
         latent_dim=latent_dim,
         kind="prc",
     )
-    axes[0].set_title("DeepSAD (LeNet) + baselines")
+    axes[0].set_title("(a)")
 
     _plot_panel(
         axes[1],
@@ -306,7 +314,7 @@ def make_figures_for_dim(
         latent_dim=latent_dim,
         kind="prc",
     )
-    axes[1].set_title("DeepSAD (Efficient) + baselines")
+    axes[1].set_title("(b)")
 
     out_prc = out_dir / f"prc_{latent_dim}_{eval_type}.png"
     fig_prc.savefig(out_prc, dpi=150, bbox_inches="tight")

tools/pyproject.toml

@@ -6,6 +6,8 @@ readme = "README.md"
 requires-python = ">=3.11.9"
 dependencies = [
     "pandas>=2.3.2",
+    "pointcloudset>=0.11.0",
     "polars>=1.33.0",
     "pyarrow>=21.0.0",
+    "tabulate>=0.9.0",
 ]