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

diff --git a/doc/ctsim-textui.tex b/doc/ctsim-textui.tex
index 409f580877c6ac2f6afaf26526a11a296fca8beb..07e73c394ad31e8b9edfd439de9e16d9530011fb 100644 (file)
--- a/doc/ctsim-textui.tex
+++ b/doc/ctsim-textui.tex
@@ -1,15 +1,15 @@
-\chapter{The Command Line Interface}\label{ctsimtext}\index{ctsimtext}
+\chapter{The Command Line Interface}\label{ctsimtext}\index{ctsimtext}\index{Command line interface}

 \setheader{{\it CHAPTER \thechapter}}{}{}{\ctsimheadtitle}{}{{\it CHAPTER \thechapter}}%
 \ctsimfooter%
 
 \setheader{{\it CHAPTER \thechapter}}{}{}{\ctsimheadtitle}{}{{\it CHAPTER \thechapter}}%
 \ctsimfooter%
 

-\section{Overview}\index{Command line interface}
-\ctsimtext\ is a master shell for all of the command-line tools. The
+\ctsimtext\ is the master shell for all of the command-line tools. The

 command-line tools can perform most of the functions of the graphical
 command-line tools can perform most of the functions of the graphical

-shell. These command-line utilities are especially appropriate for use on
+shell. These command-line tools are especially appropriate for use on

 systems without graphical capability or for batch processing, shell scripting,
 and parallel processing.
 
 systems without graphical capability or for batch processing, shell scripting,
 and parallel processing.
 

-\usage \ctsimtext\ can be invoked via three different
+\section{Starting ctsimtext}
+\ctsimtext\ can be invoked via three different

 methods.
 \begin{enumerate}\itemsep=3pt
 \item \ctsimtext\ can executed without any parameters. In that case,
 methods.
 \begin{enumerate}\itemsep=3pt
 \item \ctsimtext\ can executed without any parameters. In that case,


@@ -31,7 +31,7 @@ be linked to the function names. This is automatically done by
 the installation program and the \texttt{rpm} manager. Thus, to use \ctsimtext\ with the
 function name \texttt{pjrec}, the below command can be executed:\\
 \hspace*{1.5cm}\texttt{pjrec parameters...} \\
 the installation program and the \texttt{rpm} manager. Thus, to use \ctsimtext\ with the
 function name \texttt{pjrec}, the below command can be executed:\\
 \hspace*{1.5cm}\texttt{pjrec parameters...} \\

-as a shortcut rather to the equivalent command \\
+as a shortcut to the equivalent command \\

 \hspace*{1.5cm}\texttt{ctsimtext pjrec parameters...}
 
 \end{enumerate}
 \hspace*{1.5cm}\texttt{ctsimtext pjrec parameters...}
 
 \end{enumerate}


@@ -86,8 +86,8 @@ real and complex-valued images.
   \twocolitem{\doublehyphen{divide}}{Divide the two images.}
   \twocolitem{\doublehyphen{comp}}{Statistically compare the two images. The standard
   \helpref{three distance measurements}{conceptimagecompare} are reported.}
   \twocolitem{\doublehyphen{divide}}{Divide the two images.}
   \twocolitem{\doublehyphen{comp}}{Statistically compare the two images. The standard
   \helpref{three distance measurements}{conceptimagecompare} are reported.}

-  \twocolitem{\doublehyphen{column-plot n}}{Plot the values of a particular column.}
-  \twocolitem{\doublehyphen{row-plot n}}{Plot the values of a particular row.}
+  \twocolitem{\doublehyphen{column-plot n}}{Plot the values of a particular column. The plot file is saved to disk.}
+  \twocolitem{\doublehyphen{row-plot n}}{Plot the values of a particular row. The plot file is saved to disk.}

 \end{twocollist}
 
 \section{ifexport}\label{ifexport}\index{ifexport}%
 \end{twocollist}
 
 \section{ifexport}\label{ifexport}\index{ifexport}%


@@ -170,10 +170,9 @@ Simulates collection of X-rays data (projections) around a phantom object.
 
 \twocolitem{\doublehyphen{nray}}{ Number of samples per each detector}
 
 
 \twocolitem{\doublehyphen{nray}}{ Number of samples per each detector}
 

-\twocolitem{\doublehyphen{rotangle}}{The rotation angle as a multiple of \latexonly{$\pi$.}
-\latexignore{pi.}
-For parallel geometries use a rotation angle of \texttt{1} and for equilinear and equiangular
-geometries use a rotation angle of \texttt{2}. The default is to use to
+\twocolitem{\doublehyphen{rotangle}}{The rotation angle as a fraction of a circle.
+For parallel geometries use a rotation angle of \texttt{0.5} and for equilinear and equiangular
+geometries use a rotation angle of \texttt{1}. The default is to use to

 appropriate rotation angle based on the geometry.}
 
 \twocolitem{\doublehyphen{view-ratio}}{Sets the field of view as a ratio of the diameter of the phantom.
 appropriate rotation angle based on the geometry.}
 
 \twocolitem{\doublehyphen{view-ratio}}{Sets the field of view as a ratio of the diameter of the phantom.


@@ -204,10 +203,11 @@ Generates a raster image file based on a phantom.
 \end{twocollist}
 
 \section{pj2if}\label{pj2if}\index{pj2if}%
 \end{twocollist}
 
 \section{pj2if}\label{pj2if}\index{pj2if}%

-Convert a projection file into an imagefile.
+Convert a projection file into an image file where each row of the
+image file contains the projection data from a single view.

 
 \usage
 
 \usage

-\texttt{pj2if projection-filename image-filename x-size y-size [options...]}
+\texttt{pj2if projection-filename image-filename [options...]}

 
 \textbf{Options}
 
 
 \textbf{Options}
 


@@ -247,8 +247,9 @@ Reconstructs the interior of an object from a projection file.
 \twocolitemruled{\textbf{Parameter}}{\textbf{Options}}
 \twocolitem{\doublehyphen{filter}}{Selects which filter to apply to
 each projection. To properly reconstruct an image, this filter should
 \twocolitemruled{\textbf{Parameter}}{\textbf{Options}}
 \twocolitem{\doublehyphen{filter}}{Selects which filter to apply to
 each projection. To properly reconstruct an image, this filter should

-be consist of the the absolute value of distance from zero
-frequency optionally multiplied by a smoothing filter.
+consist of the the absolute value of distance from zero
+frequency optionally multiplied by a smoothing filter. The optimal
+filters to use are:

 \begin{itemize}\itemsep=0pt
 \item \texttt{abs\_bandlimit}
 \item \texttt{abs\_cosine}
 \begin{itemize}\itemsep=0pt
 \item \texttt{abs\_bandlimit}
 \item \texttt{abs\_cosine}


@@ -294,9 +295,9 @@ using a smoothing filter. In the absence of smooth data, \texttt{linear} gives b
 is many times faster than cubic interpolation.
 
 \begin{itemize}\itemsep=0pt
 is many times faster than cubic interpolation.
 
 \begin{itemize}\itemsep=0pt

-\item \texttt{nearest}
-\item \texttt{linear}
-\item \texttt{cubic}
+\item \texttt{nearest} - No interpolation, selects nearest point.
+\item \texttt{linear} - Uses fast straight line interpolation.
+\item \texttt{cubic} - Uses cubic interpolating polynomial.

 \end{itemize}
 }
 
 \end{itemize}
 }