\documentclass[letterpaper,12pt]{report}%
\usepackage{graphicx}
\usepackage{texhelp}
\usepackage{fancyhea}
\usepackage{mysober}
\usepackage{mytitle}
\usepackage{verbatim}
\usepackage{makeidx}
%\usepackage{times}
\usepackage{hyperref}
\input{psbox.tex}

\latexonly{\includeonly{ctsim-concepts,ctsim-install,ctsim-gui,ctsim-textui,ctsim-web,ctsim-appendix}}
\hyphenation{poly-gon-al}

\newcommand{\ctsim}{\texttt{CTSim}}
\newcommand{\ctsimtext}{\texttt{CTSimText}}
\newcommand{\usage}{\textbf{Usage}\par}

\newcommand{\commandref}[2]{\helpref{{\tt $\backslash$#1}}{#2}}%
\newcommand{\commandrefn}[2]{\helprefn{{\tt $\backslash$#1}}{#2}\index{#1}}%
\newcommand{\commandpageref}[2]{\latexignore{\helprefn{{\tt $\backslash$#1}}{#2}}\latexonly{{\tt $\backslash$#1} {\it page \pageref{#2}}}\index{#1}}
\newcommand{\indexit}[1]{#1\index{#1}}%
\newcommand{\inioption}[1]{{\bf {\tt #1}}\index{#1}}%

\newcommand{\manvernum}[0]{0.3}
\newcommand{\manver}[0]{v\manvernum}
\newcommand{\mandate}[0]{February 12, 2001}
\newcommand{\ctsimfooter}{\setfooter{\thepage}{}{}{\small Manual \manver}{\small \mandate}{\thepage}}
\newcommand{\doublehyphen}[1]{-\,-\texttt{#1}}
\newcommand{\ctsimvernum}[0]{3.0.0beta1}
\newcommand{\ctsimver}[0]{CTSim \ctsimvernum}
\newcommand{\ctsimheadtitle}{\ctsimver Manual}

\latexignore{\newcommand{\sqrt}[2]{sqrt(#2)}}

\parskip=10pt%
\parindent=0pt%
%\backgroundcolour{255;255;255}\textcolour{0;0;0}% Has an effect in HTML only
\title{CTSim 3.0 User Manual}%
\author{Kevin Rosenberg, M.D.}%
\date{February 9, 2001}%
\makeindex%

\begin{document}%
\maketitle%
\pagestyle{fancyplain}%
\pagenumbering{roman}%

\setheader{{\it CONTENTS}}{}{}{\ctsimheadtitle}{}{{\it CONTENTS}}%
\ctsimfooter
\parskip=2pt
\tableofcontents%

\parskip=10pt
\chapter*{Copyright notice}%
\setheader{{\it COPYRIGHT}}{}{}{\ctsimheadtitle}{}{{\it COPYRIGHT}}%
\setfooter{\thepage}{}{}{}{\manver}{\thepage}%

Copyright (c) 1983-2001 Kevin Rosenberg, M.D.

Permission to use, copy, modify, and distribute this software and its
documentation for any purpose is hereby granted without fee, provided that the
above copyright notice, author statement and this permission notice appear in
all copies of this software and related documentation.

THE SOFTWARE IS PROVIDED ``AS-IS'' AND WITHOUT WARRANTY OF ANY KIND, EXPRESS,
IMPLIED OR OTHERWISE, INCLUDING WITHOUT LIMITATION, ANY WARRANTY OF
MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.

IN NO EVENT SHALL KEVIN ROSENBERG BE LIABLE FOR ANY
SPECIAL, INCIDENTAL, INDIRECT OR CONSEQUENTIAL DAMAGES OF ANY KIND, OR
ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS,
WHETHER OR NOT ADVISED OF THE POSSIBILITY OF DAMAGE, AND ON ANY THEORY
OF LIABILITY, ARISING OUT OF OR IN CONNECTION WITH THE USE OR
PERFORMANCE OF THIS SOFTWARE.

\chapter{Introduction}\label{introduction}
\pagenumbering{arabic}
\setheader{{\it CHAPTER \thechapter}}{}{}{\ctsimheadtitle}{}{{\it CHAPTER \thechapter}}%
\ctsimfooter


\centerline{\image{3cm;3cm}{logo-huge.eps}}
Computed Tomography is a technique for estimating the interior of an
object from
measurement of radiation collected around the object. This
radiation can be either projected through or emitted from the
object. \ctsim\ simulates the process of projecting X-rays
through a phantom object. \ctsim\ can then reconstruct the
interior of the object from the projections collected around the
phantom object.

This manual begins with an introduction into the concepts of
\ctsim. The graphical, \helprefn{ctsim}{ctsim}, and
command-line, \helprefn{ctsimtext}{ctsimtext}, shells are then
presented. Finally, the web-based
\helprefn{interface}{webinterface} and
\helprefn{installation}{installation} are discussed.

I hope that you enjoy \ctsim!

\include{ctsim-concepts}

\include{ctsim-gui}

\include{ctsim-textui}

\include{ctsim-web}

\include{ctsim-install}

\include{ctsim-appendix}

\newpage

\bibliographystyle{plain}
\bibliography{ctsim}
\addcontentsline{toc}{chapter}{Bibliography}
\setheader{{\it REFERENCES}}{}{}{\ctsimheadtitle}{}{{\it REFERENCES}}
\ctsimfooter

\addcontentsline{toc}{chapter}{Index}
\setheader{{\it INDEX}}{}{}{\ctsimheadtitle}{}{{\it INDEX}} %
\ctsimfooter
\printindex

\end{document}
