X-Git-Url: http://git.kpe.io/?a=blobdiff_plain;f=doc%2Fctsim-textui.tex;h=f926e0211976d02959dbb055512230b8cb85861d;hb=b7519560db07975f7a16cd24d12fe61ba0b4d84c;hp=cfcea75191616614ced5d821e317c9f7b6c1101d;hpb=17f20398d8bb0e4b97b5884b999bbe8d58c5254f;p=ctsim.git diff --git a/doc/ctsim-textui.tex b/doc/ctsim-textui.tex index cfcea75..f926e02 100644 --- a/doc/ctsim-textui.tex +++ b/doc/ctsim-textui.tex @@ -1,15 +1,15 @@ -\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% -\section{Overview}\index{Command line interface} -\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 processing, shell scripting, -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, @@ -31,13 +31,13 @@ be linked to the function names. This is automatically done by the installation program and the \texttt{rpm} manager. Thus, to use \ctsimtext\ with the function name \texttt{pjrec}, the below command can be executed:\\ \hspace*{1.5cm}\texttt{pjrec parameters...} \\ -as a shortcut rather than the equivalent command \\ +as a shortcut to the equivalent command \\ \hspace*{1.5cm}\texttt{ctsimtext pjrec parameters...} \end{enumerate} -\section{Parallel Processing}\index{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}. @@ -55,7 +55,7 @@ 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...]} @@ -72,7 +72,7 @@ both real and complex valued images. \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...]} @@ -86,15 +86,15 @@ real and complex valued 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.} - \twocolitem{\doublehyphen{row-plot n}}{Plot the values of a particular row.} + \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} @@ -170,9 +170,9 @@ Simulates collection of X-rays data (projections) around a phantom object. \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. @@ -189,24 +189,25 @@ appropriate rotation angle based on the geometry.} \section{phm2if}\label{phm2if}\index{phm2if}% -Generates rasterized image file based on a phantom. +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} @@ -246,8 +247,9 @@ Reconstructs the interior of an object from a projection file. \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 consist of the the absolute value of distance from zero -frequency optionally multiplied by a smoothing filter. +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} @@ -286,16 +288,16 @@ to select. With any of the frequency methods, \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} }