Thesis - Seperate file for SEM analysis

Having everything in one massive thesis.tex file is starting to confuse me
I will start to break up into several .tex files and recombine later.

This section needs a *lot* of work. But then, so does everything.

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+\documentclass[10pt]{article}
+\usepackage{graphicx}
+\usepackage{caption}
+\usepackage{amsmath} % needed for math align
+\usepackage{bm} % needed for maths bold face
+ \usepackage{graphicx}    % needed for including graphics e.g. EPS, PS
+\usepackage{fancyhdr}  % needed for header
+%\usepackage{epstopdf} % Needed for eps graphics
+\usepackage{hyperref}
+\usepackage{lscape}  % Needed for landscaping stuff 
+ \topmargin -1.5cm        % read Lamport p.163
+ \oddsidemargin -0.04cm   % read Lamport p.163
+ \evensidemargin -0.04cm  % same as oddsidemargin but for left-hand pages
+ \textwidth 16.59cm
+ \textheight 21.94cm 
+ %\pagestyle{empty}       % Uncomment if don't want page numbers
+ \parskip 7.2pt           % sets spacing between paragraphs
+ %\renewcommand{\baselinestretch}{1.5}         % Uncomment for 1.5 spacing between lines
+ \parindent 0pt                  % sets leading space for paragraphs
+
+
+\newcommand{\vect}[1]{\boldsymbol{#1}} % Draw a vector
+\newcommand{\divg}[1]{\nabla \cdot #1} % divergence
+\newcommand{\curl}[1]{\nabla \times #1} % curl
+\newcommand{\grad}[1]{\nabla #1} %gradient
+\newcommand{\pd}[3][ ]{\frac{\partial^{#1} #2}{\partial #3^{#1}}} %partial derivative
+\newcommand{\der}[3][ ]{\frac{d^{#1} #2}{d #3^{#1}}} %full derivative
+\newcommand{\phasor}[1]{\tilde{#1}} % make a phasor
+\newcommand{\laplacian}[1]{\nabla^2 {#1}} % The laplacian operator
+
+\usepackage{color}
+\usepackage{listings}
+
+\definecolor{darkgray}{rgb}{0.95,0.95,0.95}
+\definecolor{darkred}{rgb}{0.75,0,0}
+\definecolor{darkblue}{rgb}{0,0,0.75}
+\definecolor{pink}{rgb}{1,0.5,0.5}
+\lstset{language=Java}
+\lstset{backgroundcolor=\color{darkgray}}
+\lstset{numbers=left, numberstyle=\tiny, stepnumber=1, numbersep=5pt}
+\lstset{keywordstyle=\color{darkred}\bfseries}
+\lstset{commentstyle=\color{darkblue}}
+%\lstset{stringsyle=\color{red}}
+\lstset{showstringspaces=false}
+\lstset{basicstyle=\small}
+
+
+\begin{document}
+
+\pagestyle{fancy}
+\fancyhead{}
+\fancyfoot{}
+
+\fancyhead[LO, L]{}
+\fancyfoot[CO, C]{\thepage}
+
+%\title{\bf Characterisation of nanostructured thin films}
+%\author{Sam Moore\\ School of Physics, University of Western Australia}
+%\date{April 2012}
+%\maketitle
+
+\section{Scanning Electron Microscopy Results}
+
+A number of samples of metallic-black and metallic-bright films were sent to the Centre for Microscopy Characterisation and Analysis (CMCA) at UWA for study. In this section we will present and discuss some of the images produced by CMCA. These images provide an invaluable aid to understanding the structural differences between metallic-black and metallic-bright films.
+
+
+Figure \ref{SEM_images} shows a comparison of an Au-Black and Au-Bright film imaged using a scanning electron microscope (SEM). The intensity of each pixel is proportional to the total current of secondary electrons scattered from the surface at that point.
+\begin{center}
+
+
+\begin{tabular}{cc}
+       \includegraphics[scale=0.20]{figures/Au_BLACK_200nm.png} & %\captionof{figure}{Au-Black SEM Image} \label{Au_BLACK_200nm.png} &
+       \includegraphics[scale=0.20]{figures/Au_semi-shiny_1_SEM.png} %\captionof{figure}{Au SEM Image} \label{Au_semi-shiny_1_SEM.png}         
+       
+       \label{SEM_images}
+\end{tabular}
+
+       \captionof{figure}{{\bf 2500 x 1900nm SEM images of Au-Black (left) and Au-Bright (right) deposited on Si} \\ Preparation pressures were $2\times10^{-2}$mbar and $1\times10^{-6}$mbar respectively. \\ The films are sufficiently thick to be able to observe the colour with the naked eye.}
+
+\end{center}
+
+From these images, the structural difference between the two films is striking. The surface of the Au-bright film appears to consist of a layer of well defined metallic nanoparticles with sizes ranging from $20$ to $100$nm. In contrast, the Au-black film shows a highly irregular pattern, of interconnected strands of material. This pattern has lead some researchers to refer to metallic-black films as ``smokes'' \cite{}.
+
+\pagebreak
+
+\subsection*{Fourier Analysis of SEM Images}
+
+
+ 
+\pagebreak
+\begin{center}
+       \includegraphics[scale=0.35]{fourier/Au_BLACK_82pix_200nm_fft_abs.png} 
+       \captionof{figure}{Amplitude density plot of DFT for Au-Black SEM image}
+       %\captionof[figure]{Amplitude density plot of DFT for Au-Black}
+\end{center}
+\begin{center}
+       \includegraphics[scale=0.35]{fourier/Au_BRIGHT_42pix_100nm_fft_abs.png} 
+       \captionof{figure}{Amplitude density plot of DFT for Au-Bright SEM image}
+\end{center}
+\pagebreak
+\begin{center}
+       \includegraphics[scale=0.35]{fourier/Au_BLACK_82pix_200nm_fft_phase.png} 
+       \captionof{figure}{Phase density plot of DFT for Au-Black}
+\end{center}
+\begin{center}
+       \includegraphics[scale=0.35]{fourier/Au_BRIGHT_42pix_100nm_fft_phase.png}       
+       \captionof{figure}{Phase density plot of DFT for Au-Bright}
+\end{center}
+\pagebreak
+
+
+
+Higher magnification images confirm 
+ 
+\end{document}
+