doc/ctsim-textui.tex

   1 \chapter{The Command Line Interface}\label{ctsimtext}\index{ctsimtext}%
   2 \setheader{{\it CHAPTER \thechapter}}{}{}{}{}{{\it CHAPTER \thechapter}}%
   3 \ctsimfooter%
   4
   5 \ctsimtext\ is a master shell for all of the command-line utilities.
   6
   7 \usage \ctsimtext\ can be invoked via three different
   8 methods.
   9 \begin{enumerate}\itemsep=3pt
  10 \item \ctsimtext\ can executed without any parameters. In that case,
  11 \ctsimtext\ offers a command-line to enter the function-names and
  12 their parameters. The output of the command is displayed. Further
  13 commands may be given to \ctsimtext. The shell is exited by the
  14 \texttt{quit} command.
  15
  16 \item \ctsimtext\ can also be called to
  17 execute a single command. This is especially useful for batch
  18 files containing multiple \ctsimtext\ commands. This is invoked by
  19 calling\\ \texttt{ctsimtext function-name parameters...}.
  20
  21 \item Using operating systems that support soft or hard linking of
  22 files (such as UNIX and Linux), the executable file \ctsimtext\ can
  23 be linked to the function names. This is automatically done by
  24 the installation file for Linux. Thus, to use \ctsimtext\ with the
  25 function name \texttt{pjrec}, the below command can be executed:\\
  26 \texttt{pjrec parameters...} \\
  27 as a shortcut rather than the equivalent command \\
  28 \texttt{ctsimtext pjrec parameters...}
  29
  30 \end{enumerate}
  31
  32 \section{Parallel Processing With a Computer Cluster}
  33 \ctsimtext\ can be used to spread it's processing over a cluster. Specifically,
  34 \ctsimtext\ supports the \urlref{LAM}{http://www.mpi.nd.edu/lam} version of
  35 the MPI environment. On platforms with LAM installed, a parallel version of
  36 \ctsimtext\ is created. The name of this program is \texttt{ctsimtext-lam}.
  37 The functions that take advantage of the parallel processing are
  38 \texttt{phm2if}, \texttt{phm2pj}, \texttt{pjrec}.
  39
  40 This parallel processing version has been tested with excellent results on
  41 a 16-CPU \urlref{Beowulf}{http://www.beowulf.org} cluster.
  42
  43
  44 \section{if1}\label{if1}\index{ctsimtext,if1}%
  45 Performs math functions on a single image.
  46
  47 \usage
  48 \begin{itemize}\itemsep=0pt
  49   \item \doublehyphen{invert}
  50   \item \doublehyphen{log}
  51   \item \doublehyphen{exp}
  52   \item \doublehyphen{sqr}
  53   \item \doublehyphen{sqrt}
  54 \end{itemize}
  55
  56 \section{if2}\label{if2}\index{ctsimtext,if2}%
  57 Performs math functions on a two images.
  58
  59 \usage
  60 \begin{itemize}\itemsep=0pt
  61   \item \doublehyphen{add}
  62   \item \doublehyphen{sub}
  63   \item \doublehyphen{mul}
  64   \item \doublehyphen{comp}
  65   \item \doublehyphen{column-plot}
  66   \item \doublehyphen{row-plot}
  67 \end{itemize}
  68
  69 \section{ifexport}\label{ifexport}\index{ctsimtext,ifexport}%
  70 Export an image file to a standard graphics file.
  71
  72 \usage
  73 \begin{itemize}\itemsep=0pt
  74   \item \doublehyphen{format}
  75   \begin{itemize}\itemsep=0pt
  76     \item \texttt{gm}
  77     \item \texttt{pgmasc}
  78     \item \texttt{png}
  79     \item \texttt{png16}
  80   \end{itemize}
  81   \item \doublehyphen{center}
  82   \begin{itemize}\itemsep=0pt
  83     \item \texttt{median}
  84     \item \texttt{mode}
  85     \item \texttt{mean}
  86   \end{itemize}
  87   \item \doublehyphen{auto}
  88   \begin{itemize}\itemsep=0pt
  89      \item \texttt{full}
  90      \item \texttt{std0.1}
  91      \item \texttt{std0.5}
  92      \item \texttt{std1}
  93      \item \texttt{std2}
  94      \item \texttt{std3}
  95   \end{itemize}
  96   \item \doublehyphen{scale}
  97   \item \doublehyphen{min}
  98   \item \doublehyphen{max}
  99 \end{itemize}
 100
 101 \section{ifinfo}\label{ifinfo}\index{ctsimtext,ifinfo}%
 102
 103 Displays information about an imagefile.
 104
 105 \usage
 106 \begin{itemize}\itemsep=0pt
 107   \item \doublehyphen{labels}
 108   \item \doublehyphen{no-labels}
 109   \item \doublehyphen{stats}
 110   \item \doublehyphen{no-stats}
 111   \item \doublehyphen{help}
 112 \end{itemize}
 113
 114 \section{phm2pj}\label{phm2pj}\index{ctsimtext,phm2pj}%
 115 Simulates collection of X-rays data (projections) around a phantom object.
 116
 117 \usage
 118 \texttt{phm2pj projection-file-name number-of-detectors number-of-views [options...]}
 119
 120 \begin{twocollist}
 121 \twocolitem{\doublehyphen{phantom}}{Select a standard phantom.
 122 \begin{itemize}\itemsep=0pt
 123 \item \texttt{herman}
 124 \item \texttt{shepp-logan}
 125 \item \texttt{unit-pulse}
 126 \end{itemize}
 127 }
 128 \twocolitem{\doublehyphen{phmfile}}{Load a phantom definition definition}
 129
 130 \twocolitem{\doublehyphen{geometry}}{
 131   \begin{itemize}\itemsep=0pt
 132     \item \texttt{parallel}
 133     \item \texttt{equiangular}
 134     \item \texttt{equilinear}
 135   \end{itemize}
 136 }
 137
 138 \twocolitem{\doublehyphen{nray}}{ Number of samples per each detector}
 139
 140 \twocolitem{\doublehyphen{rotangle}}{Sets the rotation amount as a multiple of pi.
 141 For parallel geometries use a rotation angle of \texttt{1} and for equilinear and equiangular
 142 geometries use a rotation angle of \texttt{2}. The default is to use to
 143 appropriate rotation angle based on the geometry.}
 144
 145 \twocolitem{\doublehyphen{view-ratio}}{Sets the field of view as a ratio of the diameter of the phantom.
 146     For normal scanning, a default value of \texttt{1.0} is optimal.}
 147
 148 \twocolitem{\doublehyphen{scan-ratio}}{Sets the length of scanning as a ratio of the view diameter.
 149     For normal scanning, a value of \texttt{1.0} is optimal.}
 150
 151 \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.
 152     For parallel geometries, a value of \texttt{1.0} is optimal. For other
 153     geometries, this should be at least \texttt{2.0} to avoid artifacts.}
 154 \end{twocollist}
 155
 156
 157 \section{phm2if}\label{phm2if}\index{ctsimtext,phm2if}%
 158 Converts a geometric phantom object into an imagefile. The size of the
 159 imagefile in pixels must be specified as well as the number of samples
 160 to average per pixel.
 161
 162 \usage
 163 \begin{twocollist}
 164   \twocolitem{\doublehyphen{nsamples}}{Number of samples in x \& y directions per pixel}
 165   \twocolitem{\doublehyphen{view-ratio}}{Sets the view ration. For normal scanning,
 166   the default value of \texttt{1.0} is optimal.}
 167 \end{twocollist}
 168
 169 \section{pj2if}\label{pj2if}\index{ctsimtext,pj2if}%
 170 Convert a projection file into an imagefile.
 171
 172 \usage
 173 \texttt{pj2if projection-file-name image-file-name x-size ysize [options...]}
 174
 175 \begin{twocollist}
 176 \twocolitem{\doublehyphen{help}}{Print brief online help}
 177 \end{twocollist}
 178
 179 \section{pjinfo}\label{pjinfo}\index{ctsimtext,pjinfo}%
 180 Displays information about a projection file.
 181
 182 \usage
 183 \begin{itemize}\itemsep=0pt
 184   \item \doublehyphen{binaryheader}
 185   \item \doublehyphen{binaryview}
 186   \item \doublehyphen{startview}
 187   \item \doublehyphen{endview}
 188   \item \doublehyphen{dump}
 189 \end{itemize}
 190
 191 \section{pjrec}\label{pjrec}\index{ctsimtext,pjrec}%
 192 Reconstructs the interior of an object from a projection file.
 193
 194 \begin{twocollist}
 195 \twocolitemruled{\textbf{Parameter}}{\textbf{Options}}
 196 \twocolitem{\doublehyphen{filter}}{Selects which filter to apply to
 197 each projection. To properly reconstruct an image, this filter
 198 should be multiplied by the absolute value of distance from zero
 199 frequency.
 200 \begin{itemize}\itemsep=0pt
 201 \item \texttt{abs\_bandlimit}
 202 \item \texttt{abs\_cosine}
 203 \item \texttt{abs\_hamming}
 204 \end{itemize}
 205 } \twocolitem{\doublehyphen{filter-parameter}}{Sets the alpha level
 206 for Hamming window. At setting of \texttt{0.54}, this equals
 207 the Hanning window.}
 208
 209 \twocolitem{\doublehyphen{filter-method}}{Selects the filtering
 210 method. For large numbers of detectors, \texttt{rfftw} is optimal.
 211 For smaller numbers of detectors, \texttt{convolution} might be a
 212 bit faster.
 213 \begin{itemize}\itemsep=0pt
 214 \item \texttt{convolution}
 215 \item \texttt{fourier}
 216 \item \texttt{fourier-table}
 217 \item \texttt{fftw}
 218 \item \texttt{rfftw}
 219 \item fftw
 220 \item rfftw
 221 \end{itemize}
 222 }
 223
 224 \twocolitem{\doublehyphen{filter-generation}}{Selects the filter
 225 generation. With convolution, \texttt{direct} is the proper method
 226 to select. With any of the frequency methods,
 227 \texttt{inverse-fourier} is the best method.
 228 \begin{itemize}\itemsep=0pt
 229 \item direct
 230 \item inverse-fourier
 231 \end{itemize}
 232 }
 233
 234 \twocolitem{\doublehyphen{interpolation}}{Interpolation technique.
 235 \texttt{linear} is optimal.
 236 \begin{itemize}\itemsep=0pt
 237 \item nearest
 238 \item linear
 239 \item cubic
 240 \end{itemize}
 241 }
 242
 243 \twocolitem{\doublehyphen{backprojection}}{Selects the
 244 backprojection technique. A setting of \texttt{idiff} is optimal.
 245 \begin{itemize}\itemsep=0pt
 246 \item trig
 247 \item table
 248 \item diff
 249 \item idiff
 250 \end{itemize}
 251 }
 252
 253 \twocolitem{\doublehyphen{zeropad}}{Zeropad factor. A setting of
 254 \texttt{1} is optimal.}
 255
 256 \end{twocollist}