From 751de723fd6e8a258a7a4730893efe937b7db971 Mon Sep 17 00:00:00 2001 From: "Kevin M. Rosenberg" Date: Tue, 13 Feb 2001 23:04:44 +0000 Subject: [PATCH] r537: no message --- doc/ctsim-appendix.tex | 4 ++-- doc/ctsim-concepts.tex | 32 +++++++++++++-------------- doc/ctsim-gui.tex | 49 ++++++++++++++++++++++++++++++------------ doc/ctsim-install.tex | 8 +++---- doc/ctsim-textui.tex | 18 ++++++++-------- doc/ctsim-web.tex | 4 ++-- doc/ctsim.tex | 9 +++++++- 7 files changed, 76 insertions(+), 48 deletions(-) diff --git a/doc/ctsim-appendix.tex b/doc/ctsim-appendix.tex index 8be0087..a8e90ef 100644 --- a/doc/ctsim-appendix.tex +++ b/doc/ctsim-appendix.tex @@ -1,6 +1,6 @@ \appendix -\chapter{Simple Graphics Package}\label{appendix}\index{Appendix}% +\chapter{Simple Graphics Package}\label{appendix}\index{Simple Graphics Package} \setheader{{\it Appendix \thechapter}}{}{}{\ctsimheadtitle}{}{{\it Appendix \thechapter}}% \ctsimfooter% @@ -41,7 +41,7 @@ Convert to Physical device coordinates (PDC) \\ \subsection{Master coordinate functions} \begin{twocollist} -\twocolitem{setWindow(xmin, ymin, xmax, ymax)}{Set window for world +\twocolitem{\texttt{setWindow(xmin, ymin, xmax, ymax)}}{Set window for world coordinates} \twocolitem{\texttt{moveAbs(x, y)}}{Move graphics cursor to absolute position} \twocolitem{\texttt{moveRel(dx, dy)}}{Move graphics cursor relative to current position} diff --git a/doc/ctsim-concepts.tex b/doc/ctsim-concepts.tex index 3a01615..c7c3ffd 100644 --- a/doc/ctsim-concepts.tex +++ b/doc/ctsim-concepts.tex @@ -2,7 +2,7 @@ \setheader{{\it CHAPTER \thechapter}}{}{}{\ctsimheadtitle}{}{{\it CHAPTER \thechapter}}% \ctsimfooter% -\section{Overview}\label{conceptoverview}\index{Concepts,Overview}% +\section{Overview}\label{conceptoverview}\index{Conceptual Overview}% The operation of \ctsim\ begins with the phantom object. A phantom object consists of geometric elements. A scanner is specified and the collection of x-ray data, or projections, is @@ -16,8 +16,8 @@ and the approach taken is required. \ctsim\ deals with a variety of object, but the two objects we need to be concerned with are the \emph{phantom} and the \emph{scanner}. -\section{Phantoms}\label{conceptphantom}\index{Concepts,Phantoms}% -\subsection{Overview}\label{phantomoverview}\index{Concepts,Phantoms,Overview}% +\section{Phantoms}\label{conceptphantom} +\subsection{Overview}\label{phantomoverview}\index{Phantom Overview}% \ctsim\ uses geometrical objects to describe the object being scanned. A phantom is composed a one or more phantom elements. @@ -32,7 +32,7 @@ user-defined phantoms. The types of phantom elements and their definitions are taken with permission from G.T. Herman's 1980 book\cite{HERMAN80}. -\subsection{Phantom File}\label{phantomfile}\index{Concepts,Phantoms,File} +\subsection{Phantom File}\label{phantomfile}\index{Phantom file syntax} Each line in the text file describes an element of the phantom. Each line contains seven entries, in the following form: \begin{verbatim} @@ -50,7 +50,7 @@ coefficient of the object. Where objects overlap, the attenuations of the overlapped objects are summed. -\subsection{Phantom Elements}\label{phantomelements}\index{Concepts,Phantoms,Elements} +\subsection{Phantom Elements}\label{phantomelements}\index{Phantom elements} \subsubsection{ellipse} Ellipses use \texttt{dx} and \texttt{dy} to define the semi-major and @@ -88,14 +88,14 @@ The perimeter of the circle is then draw between those two points below the x-axis. The sector is then rotated and translated the same as a segment. -\subsection{Phantom Size} +\subsection{Phantom Size}\index{Phantom size} The overall dimensions of the phantom are increased by 1\% above the specified sizes to avoid clipping due to round-off errors from sampling the polygons of the phantom elements. So, if the phantom is defined as a rectangle of size 0.1 by 0.1, the actual phantom has extent 0.101 in each direction. -\section{Scanner}\label{conceptscanner}\index{Concepts,Scanner}% +\section{Scanner}\label{conceptscanner}\index{Scanner concepts}% \subsection{Dimensions} Understanding the scanning geometry is the most complicated aspect of using \ctsim. For real-world CT simulators, this is actually quite @@ -119,7 +119,7 @@ the \emph{view diameter}, \emph{scan diameter}, and \emph{focal length}. These variables are all input into \ctsim\ in terms of ratios rather than absolute values. -\subsubsection{Phantom Diameter} +\subsubsection{Phantom Diameter}\index{Phantom diameter} \begin{figure} $$\image{5cm;0cm}{scangeometry.eps}$$ \caption{\label{phantomgeomfig} Phantom Geometry} @@ -138,7 +138,7 @@ the diameter of the boundary square relationships are diagrammed in figure~\ref{phantomgeomfig}.} \latexignore{emph{Pd}.} -\subsubsection{View Diameter} +\subsubsection{View Diameter}\index{View diameter} The \emph{view diameter} is the area that is being processed during scanning of phantoms as well as during rasterization of phantoms. By default, the \emph{view diameter} \rtfsp is set equal @@ -159,7 +159,7 @@ This will lead to significant artifacts. Physically, this would be impossible and is analagous to inserting an object into the CT scanner that is larger than the scanner itself! -\subsubsection{Scan Diameter} +\subsubsection{Scan Diameter}\index{Scan diameter} By default, the entire \emph{view diameter} is scanned. For experimental purposes, it may be desirable to scan an area either larger or smaller than the \emph{view diameter}. Thus, the concept @@ -172,7 +172,7 @@ for all ordinary scanning, the \emph{scan ratio} is to \texttt{1}. If the \emph{scan ratio} is less than \texttt{1}, you can expect significant artifacts. -\subsubsection{Focal Length} +\subsubsection{Focal Length}\index{Focal length} The \emph{focal length}, \latexonly{$f$,}\latexignore{\emph{F},} is the distance of the X-ray source to the center of @@ -190,7 +190,7 @@ physically impossible and it analagous to have having the x-ray source inside of the \emph{view diameter}. -\subsection{Parallel Geometry}\label{geometryparallel}\index{Concepts,Scanner,Geometries,Parallel} +\subsection{Parallel Geometry}\label{geometryparallel}\index{Parallel Geometry} As mentioned above, the focal length is not used in this simple geometry. The detector array is set to be the same size as the @@ -202,7 +202,7 @@ values of less than \texttt{1} are used for these two variables, significant distortions will occur. -\subsection{Divergent Geometries}\label{geometrydivergent}\index{Concepts,Scanner,Geometries,Divergent} +\subsection{Divergent Geometries}\label{geometrydivergent}\index{Divergent geometry} \subsubsection{Overview} Next consider the case of equilinear (second generation) and equiangular (third, fourth, and fifth generation) geometries. In these cases, @@ -297,7 +297,7 @@ length}. It is calculated as \latexonly{$4\,f \tan (\alpha / 2)$} \subsubsection{Examples of Geometry Settings} -\section{Reconstruction}\label{conceptreconstruction}\index{Concepts,Reconstruction}% +\section{Reconstruction}\label{conceptreconstruction}\index{Reconstruction Overview}% \subsection{Overview} \subsection{Direct Inverse Fourier} This method is not currently implemented in \ctsim, however it is @@ -306,7 +306,7 @@ accurate as filtered backprojection. The difference is due primarily because interpolation occurs in the frequency domain rather than the spatial domain. -\subsection{Filtered Backprojection} +\subsection{Filtered Backprojection}\index{Filtered backprojection} The technique is comprised of two sequential steps: filtering projections and then backprojecting the filtered projections. Though these two steps are sequential, each view position can be processed individually. @@ -338,7 +338,7 @@ Backprojection is the process of ``smearing'' the filtered projections over the reconstructing image. Various levels of interpolation can be specified. -\section{Image Comparison} +\section{Image Comparison}\index{Image comparison} Images can be compared statistically. Three measurements can be calculated by \ctsim. They are taken from the standard measurements used by Herman\cite{HERMAN80}. diff --git a/doc/ctsim-gui.tex b/doc/ctsim-gui.tex index 4bc989c..9436faf 100644 --- a/doc/ctsim-gui.tex +++ b/doc/ctsim-gui.tex @@ -3,7 +3,7 @@ \ctsimfooter% -\section{Overview} +\section{Overview}\index{Graphical shell} \ctsim\ is the graphical shell for the CTSim project. It utilizes using the \urlref{wxWindows}{http://www.wxwindows.org} library for cross-platform compatibility. The graphical shell is compatible @@ -18,7 +18,7 @@ automatically open. \ctsim\ can open projection files, image files, phantom files, and plot files. -\section{File Types Support} +\section{File Types Support}\index{File types} Phantom and plot files are stored as ASCII text. In contrast, image and projection files are stored in binary format. @@ -62,7 +62,27 @@ files for easy cross-platform support. These commands are present on the menus for all of the windows of \ctsim. -\subsection{Preferences...} +\subsection{Create Phantom...}\index{Create phantom dialog} +This command brings up a dialog box showing the phantoms that are pre-programmed +into \ctsim. After selecting one of these phantoms, the new window with that +phantom will be generated. The pre-programmed phantoms are: + +\begin{description}\itemsep=0pt +\item[Herman] The Herman head phantom\cite{HERMAN80} + \item[Shepp-Logan] The head phantom of Shepp \& Logan\cite{SHEPP74} +\item[Unit pulse] A phantom that has a value of \texttt{1} for the +center of the phantom and \texttt{0} everywhere else. +\end{description} + +\subsection{Create Filter...}\index{Create filter dialog} +This command brings up a dialog box showing the pre-programmed filters +of \ctsim. This command will create a 2-dimensional image of the selected filter. +The center of the filter is at the center of the image. + +These filters can be created in their natural frequency domain or in their spatial domain. + + +\subsection{Preferences...}\index{Preferences} This command displays a dialog box that allows users to control the behavior of \ctsim. These options are saved across \ctsim sessions. Under Microsoft Windows environments, they are stored in the registry. @@ -112,7 +132,7 @@ Displays the properties of a phantom which includes: \item A list of all component phantom elements \end{itemize} -\subsection{Rasterize Dialog} +\subsection{Rasterize Dialog}\index{Rasterize} This creates an image file from a phantom. Technically, it converts the phantom from a vector (infinite resolution) object into a 2-dimension array of floating-point pixels. The parameters @@ -128,7 +148,7 @@ per pixel in both the x and y directions. For example, if the pixel in the image file 9 samples (3 x 3) are averaged.} \end{twocollist} -\subsection{Projection Dialog} +\subsection{Projection Dialog}\index{Projection collection} This creates a projection file from a phantom. The options available when collecting projections are: @@ -182,7 +202,7 @@ Properties of image files include \item Image file labels \end{itemize} -\subsection{File - Export} +\subsection{File - Export}\index{Image export} This command allows for exporting image files to a standard graphics file format. This is helpful when you want to take an image and import it into another application. The current @@ -260,7 +280,7 @@ include: \item Color scale \end{itemize} -\subsection{Filter} +\subsection{Filter}\index{Image filter} These commands filter and modify the image. \subsubsection{Arithmetic} @@ -304,12 +324,13 @@ The displayed properties include: \item The variables used when generating the projections from the phantom \end{itemize} -\subsection{Process - Convert Polar Dialog}\label{convertpolardialog} -The parameters are \texttt{xsize}, \texttt{ysize}, and \texttt{interpolation}. -The \texttt{xsize} and \texttt{ysize} parameters set the size of the -resulting image file. The \texttt{interpolation} parameter selects the -interpolation method. Currently, the \texttt{bilinear} option provides -the highest quality interpolation. +\subsection{Process - Convert Polar Dialog}\label{convertpolardialog}\index{Polar conversion} +The parameters are \texttt{xsize}, \texttt{ysize}, and +\texttt{interpolation}. The \texttt{xsize} and \texttt{ysize} +parameters set the size of the resulting image file. The +\texttt{interpolation} parameter selects the interpolation method. +Currently, the \texttt{bilinear} option provides the highest +quality interpolation. \subsection{Process - Convert FFT Polar Dialog} The parameters for this option are the same as \helprefn{Convert @@ -317,7 +338,7 @@ Polar Dialog}{convertpolardialog}. For this command, though, the projections are Fourier transformed prior to conversion to polar image. -\subsection{Reconstruct - Filtered Backprojection Dialog} +\subsection{Reconstruct - Filtered Backprojection Dialog}\index{Reconstruction dialog} This dialog sets the parameters for reconstructing an image from projections using the Filtered Backprojection technique. diff --git a/doc/ctsim-install.tex b/doc/ctsim-install.tex index eb32f91..26035ed 100644 --- a/doc/ctsim-install.tex +++ b/doc/ctsim-install.tex @@ -2,7 +2,7 @@ \setheader{{\it CHAPTER \thechapter}}{}{}{\ctsimheadtitle}{}{{\it CHAPTER \thechapter}}% \ctsimfooter% -\section{Download}\label{download}\index{Installation,Download}% +\section{Download}\label{download}\index{Download}% The latest version of \ctsim, both executable programs and source code, can be downloaded from the official @@ -10,7 +10,7 @@ The latest version of \ctsim, both executable programs and source code, files are also available from the \urlref{FTP site}{ftp://ftp.ctsim.org}. -\section{Installing Windows Binary}\index{Installation,Windows}% +\section{Installing Windows Binary} Download the Windows executable file. Simply execute this program to unpack \ctsim\ and begin the @@ -21,7 +21,7 @@ installation program. \ctsim\ will then be accessible from the and Windows 2000. Due to use of the OpenGL and htmlhelp libraries, \ctsim\ is not compatible with the stock Windows 95 system. -\section{Installing Linux RPM}\index{Installation,Linux}% +\section{Installing Linux RPM} Download the RPM file, then use the \texttt{rpm} manager program:\\ \hspace{1cm}\texttt{rpm -Uvh} \emph{ctsim-*.rpm}\\ @@ -30,7 +30,7 @@ the \texttt{rpm} manager program:\\ directory. The online help file, \texttt{ctsim.hhp}, will be installed in directory \texttt{/usr/local/man}. -\section{Build From Sources}\label{build}\index{Installation,Build}% +\section{Build From Sources}\label{build}\index{Build} Refer to the INSTALL file included in the source distribution for instructions. diff --git a/doc/ctsim-textui.tex b/doc/ctsim-textui.tex index 166a0dc..6a72fda 100644 --- a/doc/ctsim-textui.tex +++ b/doc/ctsim-textui.tex @@ -47,7 +47,7 @@ This parallel processing version has been tested with excellent results on a 16-CPU \urlref{Beowulf}{http://www.beowulf.org} cluster. -\section{if1}\label{if1}\index{ctsimtext,if1}% +\section{if1}\label{if1}\index{if1}% Performs math functions on a single image. \usage @@ -59,7 +59,7 @@ Performs math functions on a single image. \item \doublehyphen{sqrt} \end{itemize} -\section{if2}\label{if2}\index{ctsimtext,if2}% +\section{if2}\label{if2}\index{if2}% Performs math functions on a two images. \usage @@ -72,7 +72,7 @@ Performs math functions on a two images. \item \doublehyphen{row-plot} \end{itemize} -\section{ifexport}\label{ifexport}\index{ctsimtext,ifexport}% +\section{ifexport}\label{ifexport}\index{ifexport}% Export an image file to a standard graphics file. \usage @@ -104,7 +104,7 @@ Export an image file to a standard graphics file. \item \doublehyphen{max} \end{itemize} -\section{ifinfo}\label{ifinfo}\index{ctsimtext,ifinfo}% +\section{ifinfo}\label{ifinfo}\index{ifinfo}% Displays information about an imagefile. @@ -117,7 +117,7 @@ Displays information about an imagefile. \item \doublehyphen{help} \end{itemize} -\section{phm2pj}\label{phm2pj}\index{ctsimtext,phm2pj}% +\section{phm2pj}\label{phm2pj}\index{phm2pj}% Simulates collection of X-rays data (projections) around a phantom object. \usage @@ -160,7 +160,7 @@ appropriate rotation angle based on the geometry.} \end{twocollist} -\section{phm2if}\label{phm2if}\index{ctsimtext,phm2if}% +\section{phm2if}\label{phm2if}\index{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. @@ -172,7 +172,7 @@ to average per pixel. the default value of \texttt{1.0} is optimal.} \end{twocollist} -\section{pj2if}\label{pj2if}\index{ctsimtext,pj2if}% +\section{pj2if}\label{pj2if}\index{pj2if}% Convert a projection file into an imagefile. \usage @@ -182,7 +182,7 @@ Convert a projection file into an imagefile. \twocolitem{\doublehyphen{help}}{Print brief online help} \end{twocollist} -\section{pjinfo}\label{pjinfo}\index{ctsimtext,pjinfo}% +\section{pjinfo}\label{pjinfo}\index{pjinfo}% Displays information about a projection file. \usage @@ -194,7 +194,7 @@ Displays information about a projection file. \item \doublehyphen{dump} \end{itemize} -\section{pjrec}\label{pjrec}\index{ctsimtext,pjrec}% +\section{pjrec}\label{pjrec}\index{pjrec}% Reconstructs the interior of an object from a projection file. \begin{twocollist} diff --git a/doc/ctsim-web.tex b/doc/ctsim-web.tex index e2a933d..4646bbc 100644 --- a/doc/ctsim-web.tex +++ b/doc/ctsim-web.tex @@ -2,7 +2,7 @@ \setheader{{\it CHAPTER \thechapter}}{}{}{\ctsimheadtitle}{}{{\it CHAPTER \thechapter}}% \ctsimfooter% -\section{Overview}\index{Web Interface,Overview}% +\section{Overview} \ctsim\ can also be executed via a web browser. The CGI program \texttt{ctsim.cgi} takes projections of a standard phantom object, performs reconstruction, and then compares the rasterized phantom @@ -10,7 +10,7 @@ object with the reconstruction. The comparison is performed both visually by an image subtraction as well as by statistical analysis. -\section{Requirements}\index{Web Interface,Requirements}% +\section{Requirements} \begin{itemize}\itemsep=0pt \item Apache or other CGI compatible web server diff --git a/doc/ctsim.tex b/doc/ctsim.tex index 2eda7d7..ab99e20 100644 --- a/doc/ctsim.tex +++ b/doc/ctsim.tex @@ -10,6 +10,13 @@ \usepackage{hyperref} \input{psbox.tex} +\setlength{\textheight}{9in} +\setlength{\textwidth}{6.5in} +\setlength{\topmargin}{-0.25in} +\setlength{\evensidemargin}{0in} +\setlength{\oddsidemargin}{0in} + + \latexonly{\includeonly{ctsim-concepts,ctsim-install,ctsim-gui,ctsim-textui,ctsim-web,ctsim-appendix}} \hyphenation{poly-gon-al} @@ -23,7 +30,7 @@ \newcommand{\indexit}[1]{#1\index{#1}}% \newcommand{\inioption}[1]{{\bf {\tt #1}}\index{#1}}% -\newcommand{\manvernum}[0]{0.3} +\newcommand{\manvernum}[0]{0.31} \newcommand{\manver}[0]{v\manvernum} \newcommand{\mandate}[0]{February 12, 2001} \newcommand{\ctsimfooter}{\setfooter{\thepage}{}{}{\small Manual \manver}{\small \mandate}{\thepage}} -- 2.34.1