\chapter{The Command Line Interface}\label{ctsimtext}\index{ctsimtext}%
\setheader{{\it CHAPTER \thechapter}}{}{}{\ctsimheadtitle}{}{{\it CHAPTER \thechapter}}%
\ctsimfooter%

\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 graphics, batch files, and parallel processing in a Beowulf
computer cluster.

\usage \ctsimtext\ can be invoked via three different
methods.
\begin{enumerate}\itemsep=3pt
\item \ctsimtext\ can executed without any parameters. In that case,
\ctsimtext\ offers a command-line to enter the function-names and
their parameters. The output of the command is displayed. Further
commands may be given to \ctsimtext. The shell is exited by the
\texttt{quit} command. \ctsimtext\ uses the
\urlref{readline}{http://www.gnu.org} library on UNIX and Linux platforms
to provide for command history processing.

\item \ctsimtext\ can also be called to
execute a single command. This is especially useful for batch
files containing multiple \ctsimtext\ commands. This is invoked by
calling\\ \texttt{ctsimtext function-name parameters...}.

\item Using operating systems that support soft or hard linking of
files (such as UNIX and Linux), the executable file \ctsimtext\ can
be linked to the function names. This is automatically done by
the installation file for Linux. Thus, to use \ctsimtext\ with the
function name \texttt{pjrec}, the below command can be executed:\\
\texttt{pjrec parameters...} \\
as a shortcut rather than the equivalent command \\
\texttt{ctsimtext pjrec parameters...}

\end{enumerate}

\section{Parallel Processing}
\ctsimtext\ can be used to spread 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}.
The functions that take advantage of the parallel processing are
\texttt{phm2if}, \texttt{phm2pj}, \texttt{pjrec}.

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}%
Performs math functions on a single image.

\usage
\begin{itemize}\itemsep=0pt
  \item \doublehyphen{invert}
  \item \doublehyphen{log}
  \item \doublehyphen{exp}
  \item \doublehyphen{sqr}
  \item \doublehyphen{sqrt}
\end{itemize}

\section{if2}\label{if2}\index{ctsimtext,if2}%
Performs math functions on a two images.

\usage
\begin{itemize}\itemsep=0pt
  \item \doublehyphen{add}
  \item \doublehyphen{sub}
  \item \doublehyphen{mul}
  \item \doublehyphen{comp}
  \item \doublehyphen{column-plot}
  \item \doublehyphen{row-plot}
\end{itemize}

\section{ifexport}\label{ifexport}\index{ctsimtext,ifexport}%
Export an image file to a standard graphics file.

\usage
\begin{itemize}\itemsep=0pt
  \item \doublehyphen{format}
  \begin{itemize}\itemsep=0pt
    \item \texttt{gm}
    \item \texttt{pgmasc}
    \item \texttt{png}
    \item \texttt{png16}
  \end{itemize}
  \item \doublehyphen{center}
  \begin{itemize}\itemsep=0pt
    \item \texttt{median}
    \item \texttt{mode}
    \item \texttt{mean}
  \end{itemize}
  \item \doublehyphen{auto}
  \begin{itemize}\itemsep=0pt
     \item \texttt{full}
     \item \texttt{std0.1}
     \item \texttt{std0.5}
     \item \texttt{std1}
     \item \texttt{std2}
     \item \texttt{std3}
  \end{itemize}
  \item \doublehyphen{scale}
  \item \doublehyphen{min}
  \item \doublehyphen{max}
\end{itemize}

\section{ifinfo}\label{ifinfo}\index{ctsimtext,ifinfo}%

Displays information about an imagefile.

\usage
\begin{itemize}\itemsep=0pt
  \item \doublehyphen{labels}
  \item \doublehyphen{no-labels}
  \item \doublehyphen{stats}
  \item \doublehyphen{no-stats}
  \item \doublehyphen{help}
\end{itemize}

\section{phm2pj}\label{phm2pj}\index{ctsimtext,phm2pj}%
Simulates collection of X-rays data (projections) around a phantom object.

\usage
\texttt{phm2pj projection-file-name number-of-detectors number-of-views [options...]}

\begin{twocollist}
\twocolitem{\doublehyphen{phantom}}{Select a standard phantom.
\begin{itemize}\itemsep=0pt
\item \texttt{herman}
\item \texttt{shepp-logan}
\item \texttt{unit-pulse}
\end{itemize}
}
\twocolitem{\doublehyphen{phmfile}}{Load a phantom definition definition}

\twocolitem{\doublehyphen{geometry}}{
  \begin{itemize}\itemsep=0pt
    \item \texttt{parallel}
    \item \texttt{equiangular}
    \item \texttt{equilinear}
  \end{itemize}
}

\twocolitem{\doublehyphen{nray}}{ Number of samples per each detector}

\twocolitem{\doublehyphen{rotangle}}{Sets the rotation amount 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
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.
    For normal scanning, a default value of \texttt{1.0} is optimal.}

\twocolitem{\doublehyphen{scan-ratio}}{Sets the length of scanning as a ratio of the view diameter.
    For normal scanning, a value of \texttt{1.0} is optimal.}

\twocolitem{\doublehyphen{focal-length}}{Sets the distance of the radiation source and detectors from the center of the object as a ratio of the radius of the object.
    For parallel geometries, a value of \texttt{1.0} is optimal. For other
    geometries, this should be at least \texttt{2.0} to avoid artifacts.}
\end{twocollist}


\section{phm2if}\label{phm2if}\index{ctsimtext,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.

\usage
\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,
  the default value of \texttt{1.0} is optimal.}
\end{twocollist}

\section{pj2if}\label{pj2if}\index{ctsimtext,pj2if}%
Convert a projection file into an imagefile.

\usage
\texttt{pj2if projection-file-name image-file-name x-size ysize [options...]}

\begin{twocollist}
\twocolitem{\doublehyphen{help}}{Print brief online help}
\end{twocollist}

\section{pjinfo}\label{pjinfo}\index{ctsimtext,pjinfo}%
Displays information about a projection file.

\usage
\begin{itemize}\itemsep=0pt
  \item \doublehyphen{binaryheader}
  \item \doublehyphen{binaryview}
  \item \doublehyphen{startview}
  \item \doublehyphen{endview}
  \item \doublehyphen{dump}
\end{itemize}

\section{pjrec}\label{pjrec}\index{ctsimtext,pjrec}%
Reconstructs the interior of an object from a projection file.

\begin{twocollist}
\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 multiplied by the absolute value of distance from zero
frequency.
\begin{itemize}\itemsep=0pt
\item \texttt{abs\_bandlimit}
\item \texttt{abs\_cosine}
\item \texttt{abs\_hamming}
\end{itemize}
} \twocolitem{\doublehyphen{filter-parameter}}{Sets the alpha level
for Hamming window. At setting of \texttt{0.54}, this equals
the Hanning window.}

\twocolitem{\doublehyphen{filter-method}}{Selects the filtering
method. For large numbers of detectors, \texttt{rfftw} is optimal.
For smaller numbers of detectors, \texttt{convolution} might be a
bit faster.
\begin{itemize}\itemsep=0pt
\item \texttt{convolution}
\item \texttt{fourier}
\item \texttt{fourier-table}
\item \texttt{fftw}
\item \texttt{rfftw}
\item fftw
\item rfftw
\end{itemize}
}

\twocolitem{\doublehyphen{filter-generation}}{Selects the filter
generation. With convolution, \texttt{direct} is the proper method
to select. With any of the frequency methods,
\texttt{inverse-fourier} is the best method.
\begin{itemize}\itemsep=0pt
\item direct
\item inverse-fourier
\end{itemize}
}

\twocolitem{\doublehyphen{interpolation}}{Interpolation technique.
\texttt{linear} is optimal.
\begin{itemize}\itemsep=0pt
\item nearest
\item linear
\item cubic
\end{itemize}
}

\twocolitem{\doublehyphen{backprojection}}{Selects the
backprojection technique. A setting of \texttt{idiff} is optimal.
\begin{itemize}\itemsep=0pt
\item trig
\item table
\item diff
\item idiff
\end{itemize}
}

\twocolitem{\doublehyphen{zeropad}}{Zeropad factor. A setting of
\texttt{1} is optimal.}

\end{twocollist}
