\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
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{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.
-\end{itemize}
\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. 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}%
Converts a geometric phantom object into an imagefile. The size of the
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}%
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}%
\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{-\,-filter-generation}}{Selects the filter
+\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.
\end{itemize}
}
-\twocolitem{\textbf{-\,-interpolation}}{Interpolation technique.
+\twocolitem{\doublehyphen{interpolation}}{Interpolation technique.
\texttt{linear} is optimal.
\begin{itemize}\itemsep=0pt
\item nearest
\end{itemize}
}
-\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.}
\end{twocollist}
projects / ctsim.git / blobdiff