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[ctsim.git] / doc / ctsim-concepts.tex

diff --git a/doc/ctsim-concepts.tex b/doc/ctsim-concepts.tex
index 3a01615190f08910ee6a0a81ae9201ac403d35c4..c7c3ffd39350bd3a66b965e2c8aa25e2b5dcc8c9 100644 (file)
--- a/doc/ctsim-concepts.tex
+++ b/doc/ctsim-concepts.tex
@@ -2,7 +2,7 @@
 \setheader{{\it CHAPTER \thechapter}}{}{}{\ctsimheadtitle}{}{{\it CHAPTER \thechapter}}%
 \ctsimfooter%
 
 \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
 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}.
 
 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.
 
 \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}.
 
 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}
 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.
 
 
 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
 
 \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.
 
 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.
 
 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
 \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.
 
 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}
 \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}.}
 
 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
 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!
 
 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
 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.
 
 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
 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}.
 
 
 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
 
 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.
 
 
 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,
 \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}
 
 
 \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
 \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.
 
 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.
 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.
 
 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}.
 Images can be compared statistically. Three measurements can be calculated
 by \ctsim. They are taken from the standard measurements used by
 Herman\cite{HERMAN80}.