\chapter{The Command Line Interface}\label{ctsimtext}\index{ctsimtext}%
\setheader{{\it CHAPTER \thechapter}}{}{}{}{}{{\it CHAPTER \thechapter}}%
-\setfooter{\thepage}{}{}{}{}{\thepage}%
+\ctsimfooter%
\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...}.
+\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.
+
+\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 With a Computer Cluster}
+\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.
-The available functions are:
\section{if1}\label{if1}\index{ctsimtext,if1}%
-Perfoms math functions on a single image.
+Performs math functions on a single image.
\usage
\begin{itemize}\itemsep=0pt
- \item -\,-invert
- \item -\,-log
- \item -\,-exp
- \item -\,-sqr
- \item -\,-sqrt
+ \item \doublehyphen{invert}
+ \item \doublehyphen{log}
+ \item \doublehyphen{exp}
+ \item \doublehyphen{sqr}
+ \item \doublehyphen{sqrt}
\end{itemize}
\section{if2}\label{if2}\index{ctsimtext,if2}%
-Perfoms math functions on a two images.
+Performs 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
+ \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 imagefile to a standard graphics file.
+Export an image file to a standard graphics file.
\usage
\begin{itemize}\itemsep=0pt
- \item --format
+ \item \doublehyphen{format}
\begin{itemize}\itemsep=0pt
- \item -\,-pgm
- \item -\,-pgmasc
- \item -\,-png
- \item -\,-png16
+ \item \texttt{gm}
+ \item \texttt{pgmasc}
+ \item \texttt{png}
+ \item \texttt{png16}
\end{itemize}
- \item -\,-center
+ \item \doublehyphen{center}
\begin{itemize}\itemsep=0pt
- \item median
- \item mode
- \item mean
+ \item \texttt{median}
+ \item \texttt{mode}
+ \item \texttt{mean}
\end{itemize}
- \item -\,-auto
+ \item \doublehyphen{auto}
\begin{itemize}\itemsep=0pt
- \item -\,-full
- \item -\,-std0.1
- \item -\,-std0.5
- \item -\,-std1
- \item -\,-std2
- \item -\,-std3
+ \item \texttt{full}
+ \item \texttt{std0.1}
+ \item \texttt{std0.5}
+ \item \texttt{std1}
+ \item \texttt{std2}
+ \item \texttt{std3}
\end{itemize}
- \item -\,-scale
- \item -\,-min
- \item -\,-max
+ \item \doublehyphen{scale}
+ \item \doublehyphen{min}
+ \item \doublehyphen{max}
\end{itemize}
\section{ifinfo}\label{ifinfo}\index{ctsimtext,ifinfo}%
\usage
\begin{itemize}\itemsep=0pt
- \item -\,-labels
- \item -\,-no-labels
- \item -\,-stats
- \item -\,-no-stats
- \item -\,-help
+ \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
-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 shepp-logan
- \item unit-pulse
- \end{itemize}
+\texttt{phm2pj projection-file-name number-of-detectors number-of-views [options...]}
- \item -\,-phmfile
- Load a phantom definition definition
+\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}
- \item -\,-geometry
+\twocolitem{\doublehyphen{geometry}}{
\begin{itemize}\itemsep=0pt
- \item parallel
- \item equiangular
- \item equilinear
+ \item \texttt{parallel}
+ \item \texttt{equiangular}
+ \item \texttt{equilinear}
\end{itemize}
+}
- \item -\,-nray
- Number of samples per each detector
+\twocolitem{\doublehyphen{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.
+\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.}
- \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.
+\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.}
- \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}
+\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}
-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
to average per pixel.
\usage
-\begin{itemize}\itemsep=0pt
- \item -\,-nsamples
-\end{itemize}
+\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
-\begin{itemize}\itemsep=0pt
-\item -\,-help Print brief online help
-\end{itemize}
+\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 -\,-binaryheader
- \item -\,-binaryview
- \item -\,-startview
- \item -\,-endview
- \item -\,-dump
+ \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.
-\usage
\begin{twocollist}
\twocolitemruled{\textbf{Parameter}}{\textbf{Options}}
-\twocolitem{\textbf{-\,-filter}}{Selects which filter to apply to
+\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 abs\_bandlimit
-\item abs\_cosine
-\item abs\_hamming
+\item \texttt{abs\_bandlimit}
+\item \texttt{abs\_cosine}
+\item \texttt{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{\doublehyphen{filter-parameter}}{Sets the alpha level
+for Hamming window. At setting of \texttt{0.54}, this equals
+the Hanning window.}
-\twocolitem{\textbf{-\,-filter-method}}{Selects the filtering
+\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 convolution
-\item fourier
-\item fourier\_table
+\item \texttt{convolution}
+\item \texttt{fourier}
+\item \texttt{fourier-table}
+\item \texttt{fftw}
+\item \texttt{rfftw}
\item fftw
\item rfftw
\end{itemize}
-} \twocolitem{\textbf{-\,-interpolation}}{Interpolation technique.
+}
+
+\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 cubic
\end{itemize}
}
-\end{twocollist}
-
-\subsection{Advanced Options}
-These options are only visible if \emph{Advanced Options} has been
-selected in the \texttt{File/Preferences} dialog.
-
-\begin{twocollist}
-\twocolitem{\textbf{-\,-backprojection}}{Selects the
+\twocolitem{\doublehyphen{backprojection}}{Selects the
backprojection technique. A setting of \texttt{idiff} is optimal.
\begin{itemize}\itemsep=0pt
\item trig
\end{itemize}
}
-\twocolitem{\textbf{-\,-zeropad}}{Zeropad factor. A setting of
+\twocolitem{\doublehyphen{zeropad}}{Zeropad factor. A setting of
\texttt{1} is optimal.}
-\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}
-
\end{twocollist}
-}
projects / ctsim.git / blobdiff