\chapter{ctsimtext}\label{ctsimtext}\index{ctsimtext}%
\setheader{{\it CHAPTER \thechapter}}{}{}{}{}{{\it CHAPTER \thechapter}}%
\setfooter{\thepage}{}{}{}{}{\thepage}%

\ctsimtext\ is a master shell for all of the command-line utilities. 

\usage
\ctsimtext\ can be 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\ 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 \par
\texttt{ctsimtext function-name parameters...}.

The available functions are:

\section{if1}\label{if1}\index{ctsimtext,if1}%
Perfoms math functions on a single image.

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

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

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

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

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

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

Displays information about an imagefile.

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

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

\usage
phm2pj projection-file-name number-of-detectors number-of-views [options...]
\begin{itemize}\itemsep=0pt
  \item --phantom
  Select a standard phantom 
  \begin{itemize}\itemsep=0pt
    \item herman
    \item herman-b
    \item shepp-logan
    \item shepp-logan-b
  \end{itemize}

  \item --phmfile
  Load a phantom definition definition

  \item --geometry
  \begin{itemize}\itemsep=0pt
    \item parallel
    \item equiangular
    \item equilinear
  \end{itemize}

  \item --nray
    Number of samples per each detector

  \item --rotangle
    Sets the rotation amount as a multiple of pi. For parallel geometries use
a rotation angle of 1 and for equilinear and equiangular geometries use a rotation angle of 2.

  \item --field-of-view
    Sets the field of view as a ratio of the diameter of the phantom. For parallel geometries, using a value of 1.0 is fine. For other geometies, this should be at least 1.3 to avoid artifacts.

  \item --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 1.0 is fine. For other geometries, this should be at least 2.0 to avoid artifacts.
\end{itemize}

The Herman phantom is taken with permission from Gabor Hermans 1980 book\cite{HERMAN80}. The Shepp-Logan phantom was published in 1974\cite{SHEPP74}.

\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{itemize}\itemsep=0pt
  \item --nsamples
\end{itemize}

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

\usage
\begin{itemize}\itemsep=0pt
\item --help    Print brief online help
\end{itemize}

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

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

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

\usage
\begin{twocollist}
\twocolitemruled{\textbf{Parameter}}{\textbf{Options}}
\twocolitem{\textbf{--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 abs\_bandlimit
\item abs\_cosine
\item abs\_hamming
\end{itemize}
}
\twocolitem{\textbf{\-\-filter-parameter}}{Sets the alpha level for Hamming
  window. At setting of 0.54, this equals the Hanning window.}

\twocolitem{\textbf{\-\-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 convolution
\item fourier
\item fourier\_table
\item fftw
\item rfftw
\end{itemize}
}
\twocolitem{\textbf{\-\-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{\textbf{--interpolation}}{Interpolation technique. \texttt{linear} is optimal.
\begin{itemize}\itemsep=0pt
\item nearest
\item linear
\end{itemize}
}
\twocolitem{\textbf{-backprojection}}{Selects the backprojection technique. A setting of \texttt{idiff3} is optimal.
\begin{itemize}\itemsep=0pt
\item trig
\item table
\item diff
\item diff2
\item idiff2
\item idiff3
\end{itemize}
}
\twocolitem{\textbf{--zeropad}}{Zeropad factor. A setting of \texttt{1} is optimal.}

\twocolitem{\textbf{--preinterpolate}}{Selects preinterpolation interpolation technique and sets the preinterpolation factor. Currently, this is experimental and does not work well.}
\end{twocollist}

