-\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 utilities. The
-command-line utilities can perform most of the functions of the graphical
-shell. These command-line utilities are especially appropriate for use on
-systems without graphical capability, batch processing, shell scripting,
-and parallel processing with a Beowulf-type computer cluster.
+\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 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,
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 than the equivalent command \\
+as a shortcut to the equivalent command \\
\hspace*{1.5cm}\texttt{ctsimtext pjrec parameters...}
\end{enumerate}
-\section{Parallel Processing}\index{Parallel processing}
-\ctsimtext\ can be used to spread it's processing over a cluster. Specifically,
+\section{Parallel Processing}\label{ctsimtextlam}\index{Parallel processing}\index{MPI}\index{LAM}
+\ctsimtext\ can distribute it's processing over a cluster. Specifically,
\ctsimtext\ supports the \urlref{LAM}{http://www.mpi.nd.edu/lam} version of
the MPI environment. On platforms with LAM installed, a parallel version of
\ctsimtext\ is created. The name of this program is \texttt{ctsimtext-lam}.
\section{if1}\label{if1}\index{if1}%
Performs math functions on a single image. The commands works with
-both real and complex valued images.
+both real and complex-valued images.
\usage
\texttt{if1 input-filename output-filename [options...]}
\section{if2}\label{if2}\index{if2}%
Performs math functions on a two images. The command works with both
-real and complex valued images.
+real and complex-valued images.
\usage
\texttt{if2 input-filename1 input-filename2 output-filename [options...]}
\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}%
Export an image file to a standard graphics file.
\usage
-\texttt{ifexport input-filename output-filename -\,-format }\emph{graphic-format} \texttt{ [options...]}
+\texttt{ifexport input-filename output-filename [options...]}
\textbf{Options}
\twocolitem{\doublehyphen{nray}}{ Number of samples per each detector}
-\twocolitem{\doublehyphen{rotangle}}{The rotation angle as a multiple of 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.
\section{phm2if}\label{phm2if}\index{phm2if}%
-Generates rasterized image file based on a phantom.
+Generates a raster image file based on a phantom.
\usage
-\texttt{phm2if phantom-filename image-filename [options...]}
+\texttt{phm2if phantom-filename image-filename x-image-size y-image-size [options...]}
\textbf{Options}
\begin{twocollist}
- \twocolitem{\doublehyphen{nsamples}}{Number of samples in x \& y directions per pixel}
- \twocolitem{\doublehyphen{view-ratio}}{Sets the view ration. For normal scanning,
+ \twocolitem{\doublehyphen{nsamples}}{Number of samples in x and y directions per pixel}
+ \twocolitem{\doublehyphen{view-ratio}}{Sets the view ratio. For normal scanning,
the default value of \texttt{1.0} is optimal.}
\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}
\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}
\end{itemize}
}
-\twocolitem{\doublehyphen{interpolation}}{Interpolation technique.
-\texttt{cubic} is optimal when the
+\twocolitem{\doublehyphen{interpolation}}{Interpolation technique during backprojection.
+\texttt{cubic} has optimal quality when the
data is smooth. Smooth data is obtained by taking many projections and/or
using a smoothing filter. In the absence of smooth data, \texttt{linear} gives better results and
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}
}
projects / ctsim.git / blobdiff