intermediate clean up.

thesis/review_version/macros.tex

@@ -2,85 +2,95 @@
 % Load Packages
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-\usepackage[latin1]{inputenc}
-\usepackage{pdfpages}
-% This package sets the margin width 
-% (change "right" if you want them wider, but then change the 34.8pt in \note bigger too)
-\usepackage[top=1.2in, bottom=1.5in, left=1in, right=1.6cm]{geometry}
-\usepackage{latexsym}
-\usepackage{graphicx}
-
-\usepackage[lined, boxed, ruled, commentsnumbered, noend]{algorithm2e}
-\usepackage{algpseudocode}
-\usepackage{bbding}
+% fonts
+\usepackage{showframe}
 \usepackage{bm}
+\usepackage{bbding}
 \usepackage{cancel}
-\usepackage{colortbl}
-\usepackage{enumerate}
-\usepackage{mathtools}
-\usepackage{multirow}
 \usepackage{pifont}
 \usepackage{savesym}
-\usepackage{subcaption}
-\usepackage{thmtools,thm-restate}
+\usepackage{latexsym}
+\usepackage[latin1]{inputenc}
+\usepackage[square,numbers]{natbib}
+
+% figures
 \usepackage{tikz}
+\usepackage{graphicx}
+\usepackage[top=1.2in, bottom=1.5in, left=1in, right=1.6cm]{geometry}
+
+% math and algorithms
+\usepackage{mathtools}
+\usepackage{enumerate}
+\usepackage{algpseudocode}
+\usepackage{thmtools,thm-restate}
+\usepackage[lined, boxed, ruled, commentsnumbered, noend]{algorithm2e}
+
+% tables
 \usepackage{float}
 \usepackage{caption}
+\usepackage{subcaption}
 \usepackage{booktabs}
+\usepackage{colortbl}
+\usepackage{multirow}
+
+% inserts
 \usepackage{lipsum}
-\usepackage[square,numbers]{natbib}
+\usepackage{pdfpages}
+\usepackage{emptypage}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % Package Setup
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-\usetikzlibrary{arrows,shapes,shadows,decorations.text,positioning,automata,shapes.geometric}
-
 \savesymbol{u}
 \savesymbol{v}
 
+\usetikzlibrary{arrows,shapes,shadows,decorations.text,positioning,automata,shapes.geometric}
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Standard Commands
+% Standard Environments and Macros
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-\DeclareMathOperator*{\argmin}{arg\,min}
-\DeclareMathOperator*{\argmax}{arg\,max}
 \newtheorem{defn}{Definition}
 \newtheorem{problem}{Problem}
 \newtheorem{remark}{Remark}
-
 \newtheorem{theorem}{Theorem}[chapter]
 \newenvironment{proof}{\noindent\textbf{Proof.} }{$\Box$}
 
+\newcommand{\cmark}{\textcolor{green!80!black}{\ding{51}}}
+\newcommand{\xmark}{\textcolor{red}{\ding{55}}}
+\newcommand{\revision}[1]{\textcolor{blue}{{#1}}}
+\newcommand{\attention}[1]{\textcolor{red}{{#1}}}
+\newcommand{\spara}[1]{\subsubsection*{\textnormal{\textbf{#1}}}}
+
+\definecolor{forestgreen}{rgb}{0.13, 0.55, 0.13}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Standard Math Commands
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\DeclareMathOperator*{\argmin}{arg\,min}
+\DeclareMathOperator*{\argmax}{arg\,max}
+
 \newcommand{\R}{\mathbb{R}}
 \newcommand{\E}{\mathbb{E}}
 \newcommand{\identitymat}{\mathbb{I}}
 \newcommand{\np}{\ensuremath{\mathbf{NP}}\xspace}
 
-\newcommand{\bigObound}{\ensuremath{\mathcal{O}}\xspace}
 \newcommand{\smallObound}{\ensuremath{o}\xspace}
 \newcommand{\Thetabound}{\ensuremath{\Theta}\xspace}
 \newcommand{\Omegabound}{\ensuremath{\Omega}\xspace}
+\newcommand{\bigObound}{\ensuremath{\mathcal{O}}\xspace}
 
 \newcommand{\norm}[1]{\|#1\|}
-\newcommand{\inner}[2]{\langle #1, #2 \rangle}
 \newcommand{\round}[1]{\left(#1\right)}
-\newcommand{\braces}[1]{\left\{#1\right\}}
 \newcommand{\squares}[1]{\left[#1\right]}
+\newcommand{\braces}[1]{\left\{#1\right\}}
+\newcommand{\inner}[2]{\langle #1, #2 \rangle}
 \newcommand{\product}[1]{\left\langle#1\right\rangle}
 
-\newcommand{\cmark}{\textcolor{green!80!black}{\ding{51}}}
-\newcommand{\xmark}{\textcolor{red}{\ding{55}}}
-
-\newcommand{\spara}[1]{\subsubsection*{\textnormal{\textbf{#1}}}}
-
-\newcommand{\revision}[1]{\textcolor{blue}{{#1}}}
-\newcommand{\attention}[1]{\textcolor{red}{{#1}}}
-
-\definecolor{forestgreen}{rgb}{0.13, 0.55, 0.13}
-
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Thesis Specific Commands
+% Thesis-Specific Commands
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 % algorithms

thesis/review_version/sample_article_1.tex

@@ -2,10 +2,22 @@
 % Original Paper 1 
 % ******************************************************************************
 
+
 % insert title of paper here
-\chapter*{Paper I}\thispagestyle{empty}
-\note{I}{-222pt}{black}
+\chapter*{Paper 1}\thispagestyle{empty}
+% \note{IOI}{-237.1063pt}{black}
+% \note{I}{0pt}{black}
+% \note{IO}{-5pt}{black}
+% \note{II}{-237.1063pt}{black}
+% \note{I}{-468.32pt}{black}
 %\notee{-222pt}{\dvWHITE}
+\the\paperheight \the\textheight \the\voffset \the\topmargin
+
+% \marginpar{\vspace{0pt}\colorbox{red}{\parbox[c][\textheight][t]{\textwidth}{\the\paperheight \\ \the\textheight \\ \the\voffset \\ \the\topmargin}}}
+
+\marginpar{\vspace{-220pt}\colorbox{white}{\parbox[c][\dvheight][t]{34.8pt}{\vspace{0.3cm}\color{white}\centering\Huge{\textbf{O}}}}}
+\marginpar{\vspace{-4.5pt}\colorbox{black}{\parbox[c][\dvheight][t]{34.8pt}{\vspace{0.3cm}\color{white}\centering\Huge{\textbf{I}}}}}
+\marginpar{\vspace{-50.5pt}\colorbox{black}{\parbox[c][\dvheight][t]{34.8pt}{\vspace{0.3cm}\color{white}\centering\Huge{\textbf{II}}}}}
 
 % Here it's not necessary to draw the following boxes to position right,
 % and drawing them occasionally creates unwanted gray lines

thesis/review_version/thesis.tex

@@ -6,10 +6,8 @@
 
 \input{macros}
 
-% modify section on Interleaf pages based on number of articles in the thesis
 \input{frontmatter}
 
-\pagestyle{empty}
 \begin{document}
 
 \frontmatter
@@ -22,27 +20,26 @@
 
 \tableofcontents
 
-% ******************************************************************************
-% Preamble
-% ******************************************************************************
-
 \input{list_of_publications}
 
-% chapters in the introductory section of an article based thesis
 \mainmatter
 
-% introduction to the thesis
+% aligns page numbers correctly by flushing them to the left/right
+\fancyheadoffset[LE,RO]{0cm}
+\fancyhead[RO,LE]{\thepage}
+
+% ******************************************************************************
+% Preamble
+% ******************************************************************************
+
 \input{introduction}
 
-% one chapter per article (probably)
 \input{summary_article_1}
 
 \input{summary_article_2}
 
-% conclusion to the thesis
 \input{conclusion}
 
-% references in the preamble of the thesis
 \bibliographystyle{abbrvnat}
 \bibliography{references}
 
@@ -50,7 +47,6 @@
 % Articles 
 % ******************************************************************************
 
-% include original articles
 \input{sample_article_1}
 
 \input{sample_article_2}
@@ -59,8 +55,6 @@
 
 \input{sample_article_4}
 
-% \input{sample_article_5}
-
 % ******************************************************************************
 % Backmatter
 % ******************************************************************************