X-Git-Url: http://git.kpe.io/?p=ctsim.git;a=blobdiff_plain;f=doc%2Ftex2rtf%2Fctsim.tex;h=05ddbf77c5e10914bc2ec6a801e06973a2f9eadd;hp=f6e893bca3709a3dce7d89f16b4e6a1585b4eebf;hb=3195acb0c7c6e7a660fe27eb653a0aca56e91024;hpb=90ce7e809b3a9b06102cb94ba3f127cfe5aeab27

diff --git a/doc/tex2rtf/ctsim.tex b/doc/tex2rtf/ctsim.tex
index f6e893b..05ddbf7 100644
--- a/doc/tex2rtf/ctsim.tex
+++ b/doc/tex2rtf/ctsim.tex
@@ -3,8 +3,9 @@
 \usepackage{times}
 \usepackage{hyperref}
 
-\newcommand{\ctsim}{{\it CTSim}}
-\newcommand{\ctsimtext}{{\it CTSimText}}
+\newcommand{\ctsim}{{\tt CTSim}}
+\newcommand{\ctsimtext}{{\tt CTSimText}}
+\newcommand{\usage}{{\bf Usage}{\par}}
 
 \newcommand{\commandref}[2]{\helpref{{\tt $\backslash$#1}}{#2}}%
 \newcommand{\commandrefn}[2]{\helprefn{{\tt $\backslash$#1}}{#2}\index{#1}}%
@@ -19,7 +20,7 @@
 \date{January 2001}%
 }%
 \winhelponly{\title{Manual for CTSim 3.0}%
-\author{by Julian Smart\\$$\image{1cm;0cm}{tex2rtf.wmf}$$}%
+\author{by Kevin Rosenberg, M.D.\\$$\image{3cm;3cm}{logo-huge.bmp}$$}%
 }%
 \makeindex%
 \begin{document}%
@@ -27,6 +28,7 @@
 \pagestyle{fancyplain}%
 \bibliographystyle{plain}%
 \pagenumbering{roman}%
+
 \setheader{{\it CONTENTS}}{}{}{}{}{{\it CONTENTS}}%
 \setfooter{\thepage}{}{}{}{}{\thepage}%
 \tableofcontents%
@@ -53,23 +55,27 @@ 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}%
+\chapter{Introduction}\label{introduction}%
 \pagenumbering{arabic}%
 \setheader{{\it CHAPTER \thechapter}}{}{}{}{}{{\it CHAPTER \thechapter}}%
 \setfooter{\thepage}{}{}{}{}{\thepage}%
 
+\winhelponly{$$\image{3cm;3cm}{logo-huge}$$}%
+
 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
+\rtfsp\ctsim\ simulates the process of projecting X-rays through a phantom object.
+\rtfsp\ctsim\ can then reconstruct the interior of the object from the projections
 collected around the phantom object.
 
+The \ctsim\ package has two executable files: the graphical \helprefn{ctsim}{ctsim} and text \helprefn{ctsimtext}{ctsimtext} programs.
+
 \chapter{Installation}\index{Installation}%
 \setheader{{\it CHAPTER \thechapter}}{}{}{}{}{{\it CHAPTER \thechapter}}%
 \setfooter{\thepage}{}{}{}{}{\thepage}%
 
-\section{Download}%\index{Installation,Download}%
+\section{Download}\label{download}\index{Installation,Download}%
 
 The latest version of CTSim, plus source code, can be accessed from:
 
@@ -84,12 +90,11 @@ It is available in Windows 95/NT/2000 and Linux GUI versions and non-GUI version
 
 \section{Installing Windows Binary}\index{Installation,Windows}%
 
-\section{Build From Sources}%\index{Installation,Build}%
+\section{Build From Sources}\label{build}\index{Installation,Build}%
 
 See the INSTALL file included in the source distribution for instructions.
 
-\section{Requirements}\index{Installation,Build,Requirements}%
-  \item Building CTSim
+\section{Requirements}\label{installreq}\index{Installation,Requirements}%
   \begin{itemize}\itemsep=0pt
   \item zlib Library (optional)
         \par Used for PNG file export.
@@ -109,14 +114,14 @@ See the INSTALL file included in the source distribution for instructions.
 	\par Used for debugging memory allocation
 	\par www.dmalloc.com
 
-  \item wxWindows library (optional) \par Used for
-  platform-independent graphical interface. The graphical-shell
-  program \ctsim requires this library.  \par www.wxwindows.org
+  \item wxWindows library (optional) 
+  \par Used for platform-independent graphical interface. The graphical-shell
+  program \ctsim\ requires this library.  
+  \par www.wxwindows.org
 
-  \end{itemize}
 \end{itemize}
 
-\chapter{ctsim - the Graphical User Interface}%\index{ctsim}% 
+\chapter{ctsim - the Graphical User Interface}\label{ctsim}\index{ctsim}% 
 \setheader{{\it CHAPTER \thechapter}}{}{}{}{}{{\it CHAPTER \thechapter}}%
 \setfooter{\thepage}{}{}{}{}{\thepage}%
 
@@ -125,29 +130,39 @@ written using the wxLibrary for cross-platform compatibility with GTK,
 Motif, and Microsoft Windows. It includes all of the functionality of
 the command-line tool {\tt ctsimtext} as well as image processing and visualization features.
 
-\section{Usage}
-ctsim [OPTIONS] [files to open...]
+\ctsim\ can open projection files, image files, phantom definition files, and plotfiles.
 
-\ctsim can open projection files, image files, phantom definition files, and plotfiles.
+\usage
+ctsim [OPTIONS] [files to open...]
 
-\chapter{ctsimtext - The Command Line Interface}\index{ctsimtext}%
-\ctsimtext is a master shell for all of the command-line utilities. 
+\chapter{ctsimtext}\label{ctsimtext}\index{ctsimtext}%
 \setheader{{\it CHAPTER \thechapter}}{}{}{}{}{{\it CHAPTER \thechapter}}%
 \setfooter{\thepage}{}{}{}{}{\thepage}%
 
-\section{Usage}%
+\ctsimtext\ is a master shell for all of the command-line utilities. 
 
-\ctsimtext can be executed without any parameters. In that case, \ctsimtext
+\usage
+\ctsimtext\ can be executed without any parameters. In that case, \ctsimtext
 offers a command-line to enter the function-names and their parameters. The output of the command is displayed. Further commands may be given to \ctsimtext. The shell is exited by the {\tt quit} command.
 
-\ctsimtext can also be called to execute a single command. This is especially useful for batch files containing multiple \ctsimtext commands. This is invoked by calling {\tt ctsimtext function-name parameters...}.
+\ctsimtext\ can also be called to execute a single command. This is especially useful for batch files containing multiple \ctsimtext\ commands. This is invoked by calling {\tt ctsimtext function-name parameters...}.
 
 The following function names are available:
 
-\subsection{if1}\index{Programs,ctsimtext,if1}%
+\helprefn{if1}{if1}\par
+\helprefn{if2}{if2}\par
+\helprefn{ifexport}{ifexport}\par
+\helprefn{ifinfo}{ifinfo}\par
+\helprefn{phm2if}{phm2if}\par
+\helprefn{phm2pj}{phm2pj}\par
+\helprefn{pj2if}{pj2if}\par
+\helprefn{pjinfo}{pjinfo}\par
+\helprefn{pjrej}{pjrec}\par
+
+\subsection{if1}\label{if1}\index{ctsimtext,if1}%
 Perfoms math functions on a single image.
 
-\subsubsection{Usage}%
+\usage
 \begin{itemize}\itemsep=0pt
   \item --invert
   \item --log
@@ -156,10 +171,10 @@ Perfoms math functions on a single image.
   \item --sqrt
 \end{itemize}
 
-\subsection{if2}\index{Programs,ctsimtext,if2}%
+\subsection{if2}\label{if2}\index{ctsimtext,if2}%
 Perfoms math functions on a two images.
 
-\subsubsection{Usage}%
+\usage
 \begin{itemize}\itemsep=0pt
   \item --add
   \item --sub
@@ -169,22 +184,10 @@ Perfoms math functions on a two images.
   \item --row-plot
 \end{itemize}
 
-\subsection{ifinfo}\index{Programs,ctsimtext,ifinfo}%
-
-Displays information about an imagefile.
-\subsubsection{Usage}%
-\begin{itemize}\itemsep=0pt
-  \item --labels
-  \item --no-labels
-  \item --stats
-  \item --no-stats
-  \item --help
-\end{itemize}
-
-\subsection{ifexport}\index{Programs,ctsimtext,ifexport}%
+\subsection{ifexport}\label{ifexport}\index{ctsimtext,ifexport}%
 Export an imagefile to a standard graphics file.
 
-\subsubsection{Usage}%
+\usage
 \begin{itemize}\itemsep=0pt
   \item --format
   \begin{itemize}\itemsep=0pt
@@ -213,10 +216,23 @@ Export an imagefile to a standard graphics file.
   \item --max
 \end{itemize}
 
-\subsection{phm2pj}\index{Programs,ctsimtext,phm2pj}%
+\subsection{ifinfo}\label{ifinfo}\index{ctsimtext,ifinfo}%
+
+Displays information about an imagefile.
+
+\usage
+\begin{itemize}\itemsep=0pt
+  \item --labels
+  \item --no-labels
+  \item --stats
+  \item --no-stats
+  \item --help
+\end{itemize}
+
+\subsection{phm2pj}\label{phm2pj}\index{ctsimtext,phm2pj}%
 Simulates collection of X-rays data (projections) around a phantom object.
 
-\subsubsection{Usage}%
+\usage
 phm2pj projection-file-name number-of-detectors number-of-views [options...]
 \begin{itemize}\itemsep=0pt
   \item --phantom
@@ -252,27 +268,29 @@ a rotation angle of 1 and for equilinear and equiangular geometries use a rotati
     Sets the distance of the radiation source and detectors from the center of the object as a ratio of the radius of the object. For parallel geometries, a value of 1.0 is fine. For other geometries, this should be at least 2.0 to avoid artifacts.
 \end{itemize}
 
-\subsection{phm2if}\index{Programs,ctsimtext,phm2if}%
+The Herman phantom is taken with permission from Gabor Hermans 1980 book\cite{HERMAN80}. The Shepp-Logan phantom was published in 1974\cite{SHEPP74}.
+
+\subsection{phm2if}\label{phm2if}\index{ctsimtext,phm2if}%
 Converts a geometric phantom object into an imagefile. The size of the
 imagefile in pixels must be specified as well as the number of samples
 to average per pixel.
 
-\subsubsection{Usage}%
+\usage
 \begin{itemize}\itemsep=0pt
   \item --nsamples
 \end{itemize}
 
-\subsection{pj2if}\index{Programs,ctsimtext,pj2if}%
+\subsection{pj2if}\label{pj2if}\index{ctsimtext,pj2if}%
 Convert a projection file into an imagefile.
 
-\subsubsection{Usage}%
+\usage
 \begin{itemize}\itemsep=0pt
 \end{itemize}
 
-\subsection{pjinfo}\index{Programs,ctsimtext,pjinfo}%
+\subsection{pjinfo}\label{pjinfo}\index{ctsimtext,pjinfo}%
 Displays information about a projection file.
 
-\subsubsection{Usage}%
+\usage
 \begin{itemize}\itemsep=0pt
   \item --binaryheader
   \item --binaryview
@@ -281,14 +299,12 @@ Displays information about a projection file.
   \item --dump
 \end{itemize}
 
-\subsection{pjrec}\index{Programs,ctsimtext,pjrec}%
+\subsection{pjrec}\label{pjrec}\index{ctsimtext,pjrec}%
 Reconstructs the interior of an object from a projection file.
 
-\subsubsection{Usage}%
-
-\subsubsection{Parameters}%
+\usage
 \begin{itemize}\itemsep=0pt
-  \item Filter 
+  \item Filter \par
   Selects which filter to apply to each projection. To
   properly reconstruct an image, this filter should be multiplied 
   by the absolute value of distance from zero frequency.
@@ -296,11 +312,10 @@ Reconstructs the interior of an object from a projection file.
     \item abs_bandlimit
     \item abs_cosine
     \item abs_hamming
-    \item abs_sinc
   \end{itemize}
 
-  \item Filter Parameter 
-  \par Sets the alpha level for Hamming
+  \item Filter Parameter \par
+  Sets the alpha level for Hamming
   window. At setting of 0.54, this equals the Hanning window.
 
   \item Filter Method
@@ -338,7 +353,7 @@ Reconstructs the interior of an object from a projection file.
   \item Preinterpolation Factor
 \end{itemize}
 
-\chapter{The Web Browser CGI Interface}\index{Web Interface}%
+\chapter{The Web Browser CGI Interface}\label{webinterface}\index{Web Interface}%
 \setheader{{\it CHAPTER \thechapter}}{}{}{}{}{{\it CHAPTER \thechapter}}%
 \setfooter{\thepage}{}{}{}{}{\thepage}%
 
@@ -351,24 +366,27 @@ statistics as described by Herman\cite{HERMAN80}.
 
 \section{Requirements}\index{Web Interface,Requirements}%
 \begin{itemize}\itemsep=0pt
-   \item For Web Interface
    \begin{itemize}\itemsep=0pt
       \item Apache or other CGI compatible web server
 
       \item Perl (version 4.0 or higher)
 
       \item A client web browser than can display PNG files. Most
-      current web browswer do support PNG.
-    \end{itemize}
-
+      current web browsers support PNG.
   \end{itemize}
 
-\bibliographystyle{abbrv}
-\bibliography{yes}
+\newpage
+
+\bibliographystyle{plain}
+\bibliography{ctsim}
+\addcontentsline{toc}{chapter}{Bibliography}
+\setheader{{\it REFERENCES}}{}{}{}{}{{\it REFERENCES}}%
+\setfooter{\thepage}{}{}{}{}{\thepage}%
 
 \addcontentsline{toc}{chapter}{Index}
 \setheader{{\it INDEX}}{}{}{}{}{{\it INDEX}}%
 \setfooter{\thepage}{}{}{}{}{\thepage}%
 \printindex%
 
-\end{document} 
+\end{document}%
+