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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%
 
-\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
-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.
 
-\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,
@@ -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...} \\
-as a shortcut rather to the equivalent command \\
+as a shortcut to the equivalent command \\
 \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{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}%
@@ -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{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.
@@ -204,10 +203,11 @@ Generates a raster image file based on a phantom.
 \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
-\texttt{pj2if projection-filename image-filename x-size y-size [options...]}
+\texttt{pj2if projection-filename image-filename [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
-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}
@@ -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
-\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}
 }