-\chapter{The Command Line Interface}\label{ctsimtext}\index{ctsimtext}%
+\chapter{The Command Line Interface}\label{ctsimtext}\index{ctsimtext}\index{Command line interface}
\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 graphical capability, batch files, and parallel processing
-with a Beowulf-type computer cluster.
+\ctsimtext\ is the master shell for all of the command-line tools. The
+command-line tools can perform most of the functions of the graphical
+shell. These command-line tools are especially appropriate for use on
+systems without graphical capability or for batch processing, shell scripting,
+and parallel processing.
-\usage \ctsimtext\ can be invoked via three different
+\section{Starting ctsimtext}
+\ctsimtext\ can be invoked via three different
methods.
\begin{enumerate}\itemsep=3pt
\item \ctsimtext\ can executed without any parameters. In that case,
\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
+the installation program and the \texttt{rpm} manager. 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...}
+\hspace*{1.5cm}\texttt{pjrec parameters...} \\
+as a shortcut to the equivalent command \\
+\hspace*{1.5cm}\texttt{ctsimtext pjrec parameters...}
\end{enumerate}
-\section{Parallel Processing}
-\ctsimtext\ can be used to spread it's processing over a cluster. Specifically,
+\section{Parallel Processing}\label{ctsimtextlam}\index{Parallel processing}\index{MPI}\index{LAM}
+\ctsimtext\ can distribute 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}.
+The functions that take advantage of the parallel processing are:
+
+\begin{itemize}\itemsep=0pt
+\item \texttt{phm2if}
+\item \texttt{phm2pj}
+\item \texttt{pjrec}
+\end{itemize}
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. The commands works with
-both real and complex valued images.
+both real and complex-valued images.
\usage
\texttt{if1 input-filename output-filename [options...]}
\textbf{Options}
-\begin{itemize}\itemsep=0pt
- \item \doublehyphen{invert} - Negate pixel values
- \item \doublehyphen{log} - Take natural logrithm of pixel values
- \item \doublehyphen{exp} - Take natural exponent of pixel values
- \item \doublehyphen{sqr} - Take square of pixel values
- \item \doublehyphen{sqrt} - Take square root of pixel values
-\end{itemize}
+
+\begin{twocollist}
+ \twocolitem{\doublehyphen{invert}}{Negate pixel values.}
+ \twocolitem{\doublehyphen{log}}{Take natural logrithm of pixel values.}
+ \twocolitem{\doublehyphen{exp}}{Take natural exponent of pixel values.}
+ \twocolitem{\doublehyphen{sqr}}{Take square of pixel values.}
+ \twocolitem{\doublehyphen{sqrt}}{Take square root of pixel values.}
+\end{twocollist}
\section{if2}\label{if2}\index{if2}%
Performs math functions on a two images. The command works with both
-real and complex valued images.
+real and complex-valued images.
\usage
\texttt{if2 input-filename1 input-filename2 output-filename [options...]}
\textbf{Options}
-\begin{itemize}\itemsep=0pt
- \item \doublehyphen{add} - Add the two images
- \item \doublehyphen{sub} - Subtract the two images
- \item \doublehyphen{multiply} - Multiply the two images
- \item \doublehyphen{divide} - Divide the two images
- \item \doublehyphen{comp} - Statistically compare the two images
- \item \doublehyphen{column-plot n} - Plot the values of a particular col
- \item \doublehyphen{row-plot n} - Plot the values of a particular row
-\end{itemize}
+
+\begin{twocollist}
+ \twocolitem{\doublehyphen{add}}{Add the two images.}
+ \twocolitem{\doublehyphen{sub}}{Subtract the two images.}
+ \twocolitem{\doublehyphen{multiply}}{Multiply the two images.}
+ \twocolitem{\doublehyphen{divide}}{Divide the two images.}
+ \twocolitem{\doublehyphen{comp}}{Statistically compare the two images. The standard
+ \helpref{three distance measurements}{conceptimagecompare} are reported.}
+ \twocolitem{\doublehyphen{column-plot n}}{Plot the values of a particular column. The plot file is saved to disk.}
+ \twocolitem{\doublehyphen{row-plot n}}{Plot the values of a particular row. The plot file is saved to disk.}
+\end{twocollist}
\section{ifexport}\label{ifexport}\index{ifexport}%
Export an image file to a standard graphics file.
\usage
-\texttt{ifexport input-filename output-filename -\,-format }\emph{graphic-format} \texttt{ [options...]}
+\texttt{ifexport input-filename output-filename [options...]}
\textbf{Options}
-\begin{itemize}\itemsep=0pt
- \item \doublehyphen{format}
+
+\begin{twocollist}
+ \twocolitem{\doublehyphen{format}}{
\begin{itemize}\itemsep=0pt
- \item \texttt{pgm} - Portable graymap format.
- \item \texttt{pgmasc} - ASCII PGM format.
- \item \texttt{png} - Portable network graphics format.
+ \item \texttt{png} - Portable network graphics format. This is the default output format.
\item \texttt{png16} - 16-bit PNG format.
- \end{itemize}
- \item \doublehyphen{center} - Set center of intensity window.
+ \item \texttt{pgm} - Portable graymap format, binary format.
+ \item \texttt{pgmasc} - ASCII PGM format.
+ \end{itemize}}
+ \twocolitem{\doublehyphen{center}}{Set center of intensity window.
\begin{itemize}\itemsep=0pt
\item \texttt{median}
\item \texttt{mode}
\item \texttt{mean}
- \end{itemize}
- \item \doublehyphen{auto} - Set half-width of intensity window.
+ \end{itemize}}
+ \twocolitem{\doublehyphen{auto}}{Set half-width of intensity window as a multiple of the standard deviation.
\begin{itemize}\itemsep=0pt
\item \texttt{full}
\item \texttt{std0.1}
\item \texttt{std1}
\item \texttt{std2}
\item \texttt{std3}
- \end{itemize}
- \item \doublehyphen{scale} - Set size of output image. A value of
- \texttt{1} is default and creates an output image the same size as the input image.
- \item \doublehyphen{min} - Set the minimum intensity value.
- \item \doublehyphen{max} - Set the maximum intensity value.
-\end{itemize}
+ \end{itemize}}
+ \twocolitem{\doublehyphen{scale}}{Set size of output image. A value of
+ \texttt{1} is default and creates an output image the same size as the input image. A value of \texttt{2} will double the
+ size of the output image.}
+ \twocolitem{\doublehyphen{min}}{Set the minimum intensity value.}
+ \twocolitem{\doublehyphen{max}}{Set the maximum intensity value.}
+\end{twocollist}
\section{ifinfo}\label{ifinfo}\index{ifinfo}%
-Displays information about an imagefile.
+Displays information about an image file. By default, history labels and image statistics are displayed.
\usage
\texttt{ifinfo input-filename [options...]}
\textbf{Options}
-\begin{itemize}\itemsep=0pt
- \item \doublehyphen{labels} - Display history labels.
- \item \doublehyphen{no-labels} - Suppress history labels.
- \item \doublehyphen{stats} - Display image statistics.
- \item \doublehyphen{no-stats} - Suppress image statistics.
-\end{itemize}
+
+\begin{twocollist}
+ \twocolitem{\doublehyphen{no-labels}}{Suppress history labels.}
+ \twocolitem{\doublehyphen{no-stats}}{Suppress image statistics.}
+\end{twocollist}
\section{phm2pj}\label{phm2pj}\index{phm2pj}%
Simulates collection of X-rays data (projections) around a phantom object.
\usage
\texttt{phm2pj projection-filename number-detectors number-views [options...]}
+\textbf{Options}
+
\begin{twocollist}
\twocolitem{\doublehyphen{phantom}}{Select a standard phantom.
\begin{itemize}\itemsep=0pt
\twocolitem{\doublehyphen{nray}}{ Number of samples per each detector}
-\twocolitem{\doublehyphen{rotangle}}{The rotation angle 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
+\twocolitem{\doublehyphen{rotangle}}{The rotation angle as a fraction of a circle.
+For parallel geometries use a rotation angle of \texttt{0.5} and for equilinear and equiangular
+geometries use a rotation angle of \texttt{1}. 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.
\twocolitem{\doublehyphen{focal-length}}{Sets the distance between the radiation source
and 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.}
+ geometries, this should be at least \texttt{2.0} to avoid artifacts. The default value is \texttt{2}.}
\end{twocollist}
\section{phm2if}\label{phm2if}\index{phm2if}%
-Converts a geometric phantom object into an imagefile.
+Generates a raster image file based on a phantom.
\usage
-\texttt{phm2if phantom-filename image-filename [options...]}
+\texttt{phm2if phantom-filename image-filename x-image-size y-image-size [options...]}
\textbf{Options}
+
\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,
+ \twocolitem{\doublehyphen{nsamples}}{Number of samples in x and y directions per pixel}
+ \twocolitem{\doublehyphen{view-ratio}}{Sets the view ratio. For normal scanning,
the default value of \texttt{1.0} is optimal.}
\end{twocollist}
\section{pj2if}\label{pj2if}\index{pj2if}%
-Convert a projection file into an imagefile.
+Convert a projection file into an image file where each row of the
+image file contains the projection data from a single view.
\usage
-\texttt{pj2if projection-filename image-filename x-size y-size [options...]}
+\texttt{pj2if projection-filename image-filename [options...]}
\textbf{Options}
+
\begin{twocollist}
\twocolitem{\doublehyphen{dump}}{Print all projection data to the console.}
\end{twocollist}
\texttt{pjinfo projection-filename [options...]}
\textbf{Options}
-\begin{itemize}\itemsep=0pt
- \item \doublehyphen{binaryheader} - Dump the binary header to the standard output.
+
+\begin{twocollist}
+ \twocolitem{\doublehyphen{binaryheader}}{Dump the binary header to the standard output.
This option is only used when manually creating a composite projection file from
- several different projection files.
- \item \doublehyphen{binaryview} - Dump binary view data to the standard output.
+ several different projection files.}
+ \twocolitem{\doublehyphen{binaryview}}{Dump binary view data to the standard output.
This option is only used when manually creating a composite projection file from
- several different projection files.
- \item \doublehyphen{startview} - Sets starting view to display. Default is \texttt{0}.
- \item \doublehyphen{endview} - Sets ending view to display. Default is the last view.
- \item \doublehyphen{dump} - Print all projection data to the console.
-\end{itemize}
+ several different projection files.}
+ \twocolitem{\doublehyphen{startview}}{Sets starting view to display. Default is \texttt{0}.}
+ \twocolitem{\doublehyphen{endview}}{Sets ending view to display. Default is the last view.}
+ \twocolitem{\doublehyphen{dump}}{Print all projection data to the console.}
+\end{twocollist}
\section{pjrec}\label{pjrec}\index{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.
+each projection. To properly reconstruct an image, this filter should
+consist of the the absolute value of distance from zero
+frequency optionally multiplied by a smoothing filter. The optimal
+filters to use are:
\begin{itemize}\itemsep=0pt
\item \texttt{abs\_bandlimit}
\item \texttt{abs\_cosine}
\item \texttt{abs\_hamming}
+\item \texttt{abs\_hanning}
\end{itemize}
} \twocolitem{\doublehyphen{filter-parameter}}{Sets the alpha level
-for Hamming window. At setting of \texttt{0.54}, this equals
-the Hanning window.}
+for Hamming window. This parameter adjusts the smoothing of the Hamming
+filter and can range from \texttt{0} to \texttt{1}.
+At a setting of \texttt{1}, the Hamming filter is the same as the bandlimit filter.
+At a setting of \texttt{0.54}, the Hamming filter is the same as the Hanning
+window.}
\twocolitem{\doublehyphen{filter-method}}{Selects the filtering
method. For large numbers of detectors, \texttt{rfftw} is optimal.
\end{itemize}
}
-\twocolitem{\doublehyphen{interpolation}}{Interpolation technique.
-\texttt{cubic} is optimal when the
+\twocolitem{\doublehyphen{interpolation}}{Interpolation technique during backprojection.
+\texttt{cubic} has optimal quality when the
data is smooth. Smooth data is obtained by taking many projections and/or
using a smoothing filter. In the absence of smooth data, \texttt{linear} gives better results and
is many times faster than cubic interpolation.
\begin{itemize}\itemsep=0pt
-\item \texttt{nearest}
-\item \texttt{linear}
-\item \texttt{cubic}
+\item \texttt{nearest} - No interpolation, selects nearest point.
+\item \texttt{linear} - Uses fast straight line interpolation.
+\item \texttt{cubic} - Uses cubic interpolating polynomial.
\end{itemize}
}
\item \texttt{trig} - Use trigometric functions at each image point.
\item \texttt{table} - Use precalculated trigometric tables.
\item \texttt{diff} - Use difference method to iterate within image.
-\item \texttt{idiff} - Use integer iteration math.
+\item \texttt{idiff} - Use integer iteration technique.
\end{itemize}
}
\twocolitem{\doublehyphen{zeropad}}{Zeropad factor. A setting of
-\texttt{1} is optimal whereas a zeropad of \texttt{0} performs no zeropadding.}
+\texttt{1} is optimal whereas a zeropad of \texttt{0} performs no zero padding.
+Settings greater than \texttt{1} perform additional zero padding, but without
+any significant output difference.}
\end{twocollist}
projects / ctsim.git / blobdiff