\chapter{The Command Line Interface}\label{ctsimtext}\index{ctsimtext}%
-\setheader{{\it CHAPTER \thechapter}}{}{}{}{}{{\it CHAPTER \thechapter}}%
-\setfooter{\thepage}{}{}{}{}{\thepage}%
+\setheader{{\it CHAPTER \thechapter}}{}{}{\ctsimheadtitle}{}{{\it CHAPTER \thechapter}}%
+\ctsimfooter%
-\ctsimtext\ is a master shell for all of the command-line utilities.
+\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{itemize}\itemsep=0pt
+\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.
+\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
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...}
+\texttt{pjrec parameters...} \\
+as a shortcut rather than the equivalent command \\
+\texttt{ctsimtext pjrec parameters...}
-\end{itemize}
+\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}.
-\section{if1}\label{if1}\index{ctsimtext,if1}%
-Perfoms math functions on a single image.
+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{if1}%
+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.
+\section{if2}\label{if2}\index{if2}%
+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.
+\section{ifexport}\label{ifexport}\index{ifexport}%
+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}%
+\section{ifinfo}\label{ifinfo}\index{ifinfo}%
Displays information about an imagefile.
\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}%
+\section{phm2pj}\label{phm2pj}\index{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. The default is to use to
-appropriate rotation angle based on the geometry.
+\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 -\,-view-ratio
- Sets the field of view as a ratio of the diameter of the phantom.
- For normal scanning, a value of 1.0 is fine.
+\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 -\,-scan-ratio
- Sets the length of scanning as a ratio of the view diameter.
- For normal scanning, a value of 1.0 is fine.
+\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.}
- \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{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}%
+\section{phm2if}\label{phm2if}\index{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
- \item -\,-view-ratio
-\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}%
+\section{pj2if}\label{pj2if}\index{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}%
+\section{pjinfo}\label{pjinfo}\index{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}%
+\section{pjrec}\label{pjrec}\index{pjrec}%
Reconstructs the interior of an object from a projection file.
\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